A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.
Giese, Timothy J; York, Darrin M
2018-03-13
There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg 2+ → Ca 2+ transformations than traditional linear alchemical pathways (with and without soft-core potentials). The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed (e.g., single call to particle-mesh Ewald) leading to better performance. In the case of AMBER, this enables all the performance benefits of GPU-acceleration to be realized, in addition to unlocking the full spectrum of features available within the MD software, such as Hamiltonian replica exchange (HREM). The TI derivative evaluation can be accomplished efficiently in a post-processing step by reanalyzing the statistically independent trajectory frames in parallel for high throughput. We also show how one can evaluate the particle mesh Ewald contribution to the TI derivative evaluation without needing to perform two reciprocal space calculations. We apply the PI-TI method with HREM on GPUs in AMBER to predict p K a values in double stranded RNA molecules and make comparison with experiments. Convergence to under 0.25 units for these systems required 100 ns or more of sampling per window and coupling of windows with HREM. We find that MM charges derived from ab initio QM/MM fragment calculations improve the agreement between calculation and experimental results.
Description of quantum coherence in thermodynamic processes requires constraints beyond free energy
Lostaglio, Matteo; Jennings, David; Rudolph, Terry
2015-03-01
Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.
Description of quantum coherence in thermodynamic processes requires constraints beyond free energy
Lostaglio, Matteo; Jennings, David; Rudolph, Terry
2015-01-01
Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement. PMID:25754774
Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.
Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi
2016-06-01
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While computational methods to delineate the free energy landscape are routinely used to analyze the relative stability of conformational states, to determine phase boundaries, and to compute ligand-receptor binding energies its use in problems involving the cell membrane is limited. Here, we present an overview of four different free energy methods to study morphological transitions in bilayer membranes, induced either by the action of curvature remodeling proteins or due to the application of external forces. Using a triangulated surface as a model for the cell membrane and using the framework of dynamical triangulation Monte Carlo, we have focused on the methods of Widom insertion, thermodynamic integration, Bennett acceptance scheme, and umbrella sampling and weighted histogram analysis. We have demonstrated how these methods can be employed in a variety of problems involving the cell membrane. Specifically, we have shown that the chemical potential, computed using Widom insertion, and the relative free energies, computed using thermodynamic integration and Bennett acceptance method, are excellent measures to study the transition from curvature sensing to curvature inducing behavior of membrane associated proteins. The umbrella sampling and WHAM analysis has been used to study the thermodynamics of tether formation in cell membranes and the quantitative predictions of the computational model are in excellent agreement with experimental measurements. Furthermore, we also present a method based on WHAM and thermodynamic integration to handle problems related to end-point-catastrophe that are common in most free energy methods.
Surface free energy for systems with integrable boundary conditions
International Nuclear Information System (INIS)
Goehmann, Frank; Bortz, Michael; Frahm, Holger
2005-01-01
The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free energy in the thermodynamic limit of systems with integrable boundary conditions as a matrix element of certain projection operators. Specializing to the XXZ spin-1/2 chain we introduce a novel 'finite temperature boundary operator' which characterizes the thermodynamical properties of surfaces related to integrable boundary conditions
Holographic free energy and thermodynamic geometry
Ghorai, Debabrata; Gangopadhyay, Sunandan
2016-12-01
We obtain the free energy and thermodynamic geometry of holographic superconductors in 2+1 dimensions. The gravitational theory in the bulk dual to this 2+1-dimensional strongly coupled theory lives in the 3+1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method.
Holographic free energy and thermodynamic geometry
International Nuclear Information System (INIS)
Ghorai, Debabrata; Gangopadhyay, Sunandan
2016-01-01
We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)
Holographic free energy and thermodynamic geometry
Energy Technology Data Exchange (ETDEWEB)
Ghorai, Debabrata [S.N. Bose National Centre for Basic Sciences, Kolkata (India); Gangopadhyay, Sunandan [Indian Institute of Science Education and Research, Kolkata, Nadia (India); West Bengal State University, Department of Physics, Barasat (India); Inter University Centre for Astronomy and Astrophysics, Pune (India)
2016-12-15
We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)
Calculating zeros: Non-equilibrium free energy calculations
International Nuclear Information System (INIS)
Oostenbrink, Chris; Gunsteren, Wilfred F. van
2006-01-01
Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-10-26
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Berryman, Joshua T; Schilling, Tanja
2013-01-08
Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their absolute free energies is a valuable strategy in certain important cases. We present calculations of absolute free energies of biomolecules, using a combination of the well-known Einstein molecule method (for treating the solute) with a conceptually related method of recent genesis for computing free energies of liquids (to treat the solvent and counterions). The approach is based on thermodynamic integration from a detailed atomistic model to one which is simplified but analytically solvable, thereby giving the absolute free energy as that of the tractable model plus a correction term found numerically. An example calculation giving the free energy with respect to salt concentration for the B- and Z-isomers of all-atom duplex DNA in explicit solvent and counterions is presented. The coexistence salt concentration is found with unprecedented accuracy.
Thermodynamic and energy saving benefits of hydraulic free-piston engines
International Nuclear Information System (INIS)
Zhao, Zhenfeng; Wang, Shan; Zhang, Shuanlu; Zhang, Fujun
2016-01-01
The hydraulic free-piston engine integrates the internal combustion engine with a hydraulic pump. The piston of an HFPE is not connected to the crankshaft and the piston movement is determined by the forces that act upon it. These features optimize combustion and make higher power density and efficiency increase. In this paper, a detailed thermodynamic and energy saving analysis is performed to demonstrate the fundamental efficiency advantage of an HFPE. The thermodynamic results show that the combustion process can be optimized to an ideal engine cycle. The experimental results show that the HFPE combustion process is a nearly constant-volume process; the efficiency is approximately 50%; the piston displacement and velocity curves for a cycle are the same at any frequency, even at a 1.25 Hz. The maximum velocities are of the same value at high or low frequencies. Similarly, pump output flow is not influenced by frequency. The independent cyclic characteristics of HFPE determine that it should work in higher frequencies when the vehicle runs in Japanese 10–15 road conditions. It indicates that a higher working frequency will lead to the starting frequency of HFPE, and a lower frequency will decrease the pressurized pressure of the hydraulic accumulator. - Highlights: • The thermodynamic and energy saving benefits of the HFPEs was investigated. • The approach of combustion optimization was obtained by adjusting the injection timing and compression ratio. • The high efficiency area of HFPE was given as a function of injection timing and compression pressure. • The maximum efficiency of HFPE of 50% was obtained from the prototype. • The method of energy saving with adjusting the piston frequency was examined.
Khavrutskii, Ilja V; Wallqvist, Anders
2010-11-09
This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.
McCarty, J; Clark, A J; Copperman, J; Guenza, M G
2014-05-28
Structural and thermodynamic consistency of coarse-graining models across multiple length scales is essential for the predictive role of multi-scale modeling and molecular dynamic simulations that use mesoscale descriptions. Our approach is a coarse-grained model based on integral equation theory, which can represent polymer chains at variable levels of chemical details. The model is analytical and depends on molecular and thermodynamic parameters of the system under study, as well as on the direct correlation function in the k → 0 limit, c0. A numerical solution to the PRISM integral equations is used to determine c0, by adjusting the value of the effective hard sphere diameter, dHS, to agree with the predicted equation of state. This single quantity parameterizes the coarse-grained potential, which is used to perform mesoscale simulations that are directly compared with atomistic-level simulations of the same system. We test our coarse-graining formalism by comparing structural correlations, isothermal compressibility, equation of state, Helmholtz and Gibbs free energies, and potential energy and entropy using both united atom and coarse-grained descriptions. We find quantitative agreement between the analytical formalism for the thermodynamic properties, and the results of Molecular Dynamics simulations, independent of the chosen level of representation. In the mesoscale description, the potential energy of the soft-particle interaction becomes a free energy in the coarse-grained coordinates which preserves the excess free energy from an ideal gas across all levels of description. The structural consistency between the united-atom and mesoscale descriptions means the relative entropy between descriptions has been minimized without any variational optimization parameters. The approach is general and applicable to any polymeric system in different thermodynamic conditions.
Güssregen, Stefan; Matter, Hans; Hessler, Gerhard; Lionta, Evanthia; Heil, Jochen; Kast, Stefan M
2017-07-24
Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors.
Inquiries into the Nature of Free Energy and Entropy in Respect to Biochemical Thermodynamics
Directory of Open Access Journals (Sweden)
Clinton D. Stoner
2000-08-01
Full Text Available Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to convert spontaneously into thermal energy and for thermal energy to distribute spontaneously and uniformly within the accessible space. The fact that free energy is a Second-Law, expendable energy that makes it possible for thermodynamic work to be done at finite rates is emphasized. Entropy, as originally defined, is pointed out to be the capacity factor for thermal energy that is hidden with respect to temperature; it serves to evaluate the practical quality of thermal energy and to account for changes in the amounts of latent thermal energies in systems maintained at constant temperature. With entropy thus operationally defined, it is possible to see that TDSÃ‚Â° of the Gibbs standard free energy relation DGÃ‚Â°= DHÃ‚Â°-TDSÃ‚Â° serves to account for differences or changes in nonthermal energies that do not contribute to DGÃ‚Â° and that, since DHÃ‚Â° serves to account for differences or changes in total energy, complete enthalpy-entropy (DHÃ‚Â° - TDSÃ‚Â° compensation must invariably occur in isothermal processes for which TDSÃ‚Â° is finite. A major objective was to clarify the means by which free energy is transferred and conserved in sequences of biological reactions coupled by freely diffusible intermediates. In achieving this objective it was found necessary to distinguish between a 'characteristic free energy' possessed by all First-Law energies in amounts equivalent to the amounts of the energies themselves and a 'free energy of concentration' that is intrinsically mechanical and relatively elusive in that it can appear to be free of First-Law energy. The findings in this regard serve to clarify the fact that the transfer of chemical potential energy from one
Schmid, L. A.
1977-01-01
The first and second variations are calculated for the irreducible form of Hamilton's Principle that involves the minimum number of dependent variables necessary to describe the kinetmatics and thermodynamics of inviscid, compressible, baroclinic flow in a specified gravitational field. The form of the second variation shows that, in the neighborhood of a stationary point that corresponds to physically stable flow, the action integral is a complex saddle surface in parameter space. There exists a form of Hamilton's Principle for which a direct solution of a flow problem is possible. This second form is related to the first by a Friedrichs transformation of the thermodynamic variables. This introduces an extra dependent variable, but the first and second variations are shown to have direct physical significance, namely they are equal to the free energy of fluctuations about the equilibrium flow that satisfies the equations of motion. If this equilibrium flow is physically stable, and if a very weak second order integral constraint on the correlation between the fluctuations of otherwise independent variables is satisfied, then the second variation of the action integral for this free energy form of Hamilton's Principle is positive-definite, so the action integral is a minimum, and can serve as the basis for a direct trail and error solution. The second order integral constraint states that the unavailable energy must be maximum at equilibrium, i.e. the fluctuations must be so correlated as to produce a second order decrease in the total unavailable energy.
DEFF Research Database (Denmark)
Pissarra, P.D.; Nielsen, Jens Bredal
1997-01-01
This paper describes the thermodynamic analysis of pathways related to penicillin production in Penicillium chrysogenum. First a thermodynamic feasibility analysis is performed of the L-lysine pathway of which one of the precursors for penicillin biosynthesis (alpha-aminoadipic acid......) is an intermediate. It is found that the L-lysine pathway in P. chrysogenum is thermodynamically feasible and that the calculated standard Gibbs free energy values of the two enzymes controlling the pathway flux indicate that they operate far from equilibrium. It is therefore proposed that the regulation of alpha......-aminoadipate reductase by lysine is important to maintain a high concentration of alpha-aminoadipate in order to direct the carbon flux to penicillin production. Secondly the changes in Gibbs free energy in the penicillin biosynthetic pathway during fed-batch cultivation were studied. The analysis showed that all...
Mechanism of active transport: free energy dissipation and free energy transduction.
Tanford, C
1982-01-01
The thermodynamic pathway for "chemiosmotic" free energy transduction in active transport is discussed with an ATP-driven Ca2+ pump as an illustrative example. Two innovations are made in the analysis. (i) Free energy dissipated as heat is rigorously excluded from overall free energy bookkeeping by focusing on the dynamic equilibrium state of the chemiosmotic process. (ii) Separate chemical potential terms for free energy donor and transported ions are used to keep track of the thermodynamic ...
Analysis of the free-energy surface of proteins from reversible folding simulations.
Directory of Open Access Journals (Sweden)
Lucy R Allen
2009-07-01
Full Text Available Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.
Free energy surfaces in the superconducting mixed state
Finnemore, D. K.; Fang, M. M.; Bansal, N. P.; Farrell, D. E.
1989-01-01
The free energy surface for Tl2Ba2Ca2Cu3O1O has been measured as a function of temperature and magnetic field to determine the fundamental thermodynamic properties of the mixed state. The change in free energy, G(H)-G(O), is found to be linear in temperature over a wide range indicating that the specific heat is independent of field.
Free energy of formation of Mo2C and the thermodynamic properties of carbon in solid molybdenum
Seigle, L. L.; Chang, C. L.; Sharma, T. P.
1979-01-01
As part of a study of the thermodynamical properties of interstitial elements in refractory metals, the free energy of formation of Mo2C is determined, and the thermodynamical properties of C in solution in solid Mo evaluated. The activity of C in the two-phase region Mo + Mo2C is obtained from the C content of iron rods equilibrated with metal + carbide powder mixtures. The free energy of formation of alpha-Mo2C is determined from the activity data. The thermodynamic properties of C in the terminal solid solution are calculated from available data on the solid solubility of C in Mo. Lattice distortion due to misfit of the C atoms in the interstitial sites appears to play a significant role in determining the thermodynamic properties of C in solid Mo.
Ge, Hao; Qian, Hong
2013-06-01
Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further
Mass and free energy of Lovelock black holes
International Nuclear Information System (INIS)
Kastor, David; Traschen, Jennie; Ray, Sourya
2011-01-01
An explicit formula for the ADM mass of an asymptotically AdS black hole in a generic Lovelock gravity theory is presented, identical in form to that in Einstein gravity, but multiplied by a function of the Lovelock coupling constants and the AdS curvature radius. A Gauss' law-type formula relates the mass, which is an integral at infinity, to an expression depending instead on the horizon radius. This and other thermodynamic quantities, such as the free energy, are then analyzed in the limits of small and large horizon radius, yielding results that are independent of the detailed choice of Lovelock couplings. In even dimensions, the temperature diverges in both limits, implying the existence of a minimum temperature for black holes. The negative free energy of sufficiently large black holes implies the existence of a Hawking-Page transition. In odd dimensions, the temperature still diverges for large black holes, which again have negative free energy. However, the temperature vanishes as the horizon radius tends to zero and sufficiently small black holes have positive specific heat.
Eichhorn, Ralf; Aurell, Erik
2014-04-01
'Stochastic thermodynamics as a conceptual framework combines the stochastic energetics approach introduced a decade ago by Sekimoto [1] with the idea that entropy can consistently be assigned to a single fluctuating trajectory [2]'. This quote, taken from Udo Seifert's [3] 2008 review, nicely summarizes the basic ideas behind stochastic thermodynamics: for small systems, driven by external forces and in contact with a heat bath at a well-defined temperature, stochastic energetics [4] defines the exchanged work and heat along a single fluctuating trajectory and connects them to changes in the internal (system) energy by an energy balance analogous to the first law of thermodynamics. Additionally, providing a consistent definition of trajectory-wise entropy production gives rise to second-law-like relations and forms the basis for a 'stochastic thermodynamics' along individual fluctuating trajectories. In order to construct meaningful concepts of work, heat and entropy production for single trajectories, their definitions are based on the stochastic equations of motion modeling the physical system of interest. Because of this, they are valid even for systems that are prevented from equilibrating with the thermal environment by external driving forces (or other sources of non-equilibrium). In that way, the central notions of equilibrium thermodynamics, such as heat, work and entropy, are consistently extended to the non-equilibrium realm. In the (non-equilibrium) ensemble, the trajectory-wise quantities acquire distributions. General statements derived within stochastic thermodynamics typically refer to properties of these distributions, and are valid in the non-equilibrium regime even beyond the linear response. The extension of statistical mechanics and of exact thermodynamic statements to the non-equilibrium realm has been discussed from the early days of statistical mechanics more than 100 years ago. This debate culminated in the development of linear response
The thermodynamic properties of the upper continental crust: Exergy, Gibbs free energy and enthalpy
International Nuclear Information System (INIS)
Valero, Alicia; Valero, Antonio; Vieillard, Philippe
2012-01-01
This paper shows a comprehensive database of the thermodynamic properties of the most abundant minerals of the upper continental crust. For those substances whose thermodynamic properties are not listed in the literature, their enthalpy and Gibbs free energy are calculated with 11 different estimation methods described in this study, with associated errors of up to 10% with respect to values published in the literature. Thanks to this procedure we have been able to make a first estimation of the enthalpy, Gibbs free energy and exergy of the bulk upper continental crust and of each of the nearly 300 most abundant minerals contained in it. Finally, the chemical exergy of the continental crust is compared to the exergy of the concentrated mineral resources. The numbers obtained indicate the huge chemical exergy wealth of the crust: 6 × 10 6 Gtoe. However, this study shows that approximately only 0.01% of that amount can be effectively used by man.
Nonequilibrium thermodynamics and fluctuation relations for small systems
International Nuclear Information System (INIS)
Cao Liang; Ke Pu; Qiao Li-Yan; Zheng Zhi-Gang
2014-01-01
In this review, we give a retrospect of the recent progress in nonequilibrium statistical mechanics and thermodynamics in small dynamical systems. For systems with only a few number of particles, fluctuations and nonlinearity become significant and contribute to the nonequilibrium behaviors of the systems, hence the statistical properties and thermodynamics should be carefully studied. We review recent developments of this topic by starting from the Gallavotti—Cohen fluctuation theorem, and then to the Evans—Searles transient fluctuation theorem, Jarzynski free-energy equality, and the Crooks fluctuation relation. We also investigate the nonequilibrium free energy theorem for trajectories involving changes of the heat bath temperature and propose a generalized free-energy relation. It should be noticed that the non-Markovian property of the heat bath may lead to the violation of the free-energy relation. (topical review - statistical physics and complex systems)
Stochastic Independence as a Resource for Small-Scale Thermodynamics
Lostaglio, Matteo; Mueller, Markus P.; Pastena, Michele
It is well-known in thermodynamics that the creation of correlations costs work. It seems then a truism that if a thermodynamic transformation A --> B is impossible, so will be any transformation that in sending A to B also correlates among them some auxiliary systems C. Surprisingly, we show that this is not the case for non-equilibrium thermodynamics of microscopic systems. On the contrary, the creation of correlations greatly extends the set of accessible states, to the point that we can perform on individual systems and in a single shot any transformation that would otherwise be possible only if the number of systems involved was very large. We also show that one only ever needs to create a vanishingly small amount of correlations (as measured by mutual information) among a small number of auxiliary systems (never more than three). The many, severe constraints of microscopic thermodynamics are reduced to the sole requirement that the non-equilibrium free energy decreases in the transformation. This shows that, in principle, reliable extraction of work equal to the free energy of a system can be performed by microscopic engines.
Stochastic Independence as a Resource in Small-Scale Thermodynamics
Lostaglio, Matteo; Müller, Markus P.; Pastena, Michele
2015-10-01
It is well known in thermodynamics that the creation of correlations costs work. It seems then a truism that if a thermodynamic transformation A →B is impossible, so will be any transformation that in sending A to B also correlates among them some auxiliary systems C . Surprisingly, we show that this is not the case for nonequilibrium thermodynamics of microscopic systems. On the contrary, the creation of correlations greatly extends the set of accessible states, to the point that we can perform on individual systems and in a single shot any transformation that would otherwise be possible only if the number of systems involved was very large. We also show that one only ever needs to create a vanishingly small amount of correlations (as measured by mutual information) among a small number of auxiliary systems (never more than three). The many, severe constraints of microscopic thermodynamics are reduced to the sole requirement that the nonequilibrium free energy decreases in the transformation. This shows that, in principle, reliable extraction of work equal to the free energy of a system can be performed by microscopic engines.
Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M
2017-07-11
Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.
Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris
2016-04-15
The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.
Directory of Open Access Journals (Sweden)
Chellaboina Vijaysekhar
2005-01-01
Full Text Available We develop thermodynamic models for discrete-time large-scale dynamical systems. Specifically, using compartmental dynamical system theory, we develop energy flow models possessing energy conservation, energy equipartition, temperature equipartition, and entropy nonconservation principles for discrete-time, large-scale dynamical systems. Furthermore, we introduce a new and dual notion to entropy; namely, ectropy, as a measure of the tendency of a dynamical system to do useful work and grow more organized, and show that conservation of energy in an isolated thermodynamic system necessarily leads to nonconservation of ectropy and entropy. In addition, using the system ectropy as a Lyapunov function candidate, we show that our discrete-time, large-scale thermodynamic energy flow model has convergent trajectories to Lyapunov stable equilibria determined by the system initial subsystem energies.
Demuynck, Ruben; Rogge, Sven M J; Vanduyfhuys, Louis; Wieme, Jelle; Waroquier, Michel; Van Speybroeck, Veronique
2017-12-12
In order to reliably predict and understand the breathing behavior of highly flexible metal-organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.
2017-01-01
In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials. PMID:29131647
Towards accurate free energy calculations in ligand protein-binding studies.
Steinbrecher, Thomas; Labahn, Andreas
2010-01-01
Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics
Thermodynamic Model and Experimental Study of Oil-free Scroll Compressor
Peng, Bin; Zhao, Shengxian; Li, Yaohong
2017-10-01
In order to study the performance characteristics of oil-free scroll compressor, this paper is based on the basic equation of circle involute profile, and uses the differential geometry theory to calculate the variation law of pressure with volume. Based on the basic law of thermodynamics, the thermodynamic model of the oil-free scroll compressor is established by considering the heat transfer model and the gas leakage model, considering the mass, energy conservation equation and gas state equation. The change of the mass flow rate of the gas in each chamber is obtained by solving the established model by using the improved Euler method. The experiment results show that with the increase of frequency, the temperature, the displacement and the power show a clear upward trend. The thermodynamic model has some guidance and reference for the development and performance analysis of oil-free scroll compressors.
Thermodynamic properties of water solvating biomolecular surfaces
Heyden, Matthias
Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.
Good Practices in Free-energy Calculations
Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher
2013-01-01
As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.
The free-energy cost of interaction between DNA loops.
Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe
2017-10-03
From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.
International Nuclear Information System (INIS)
Levine, R.D.
1979-01-01
The reaction rate constant is expressed as Z exp(-G/sub a//RT). Z is the binary collision frequency. G/sub a/, the free energy of activation, is shown to be the difference between the free energy of the reactive reactants and the free energy of all reactants. The results are derived from both a statistical mechanical and a collision theoretic point of view. While the later is more suitable for an ab-initio computation of the reaction rate, it is the former that lends itself to the search of systematics and of correlations and to compaction of data. Different thermodynamic-like routes to the characterization of G/sub a/ are thus explored. The two most promising ones appear to be the use of thermodynamic type cycles and the changes of dependent variables using the Legendre transform technique. The dependence of G/sub a/ on ΔG 0 , the standard free energy change in the reaction, is examined from the later point of view. It is shown that one can rigorously express this dependence as G/sub a/ = αΔG 0 + G/sub a/ 0 M(α). Here α is the Bronsted slope, α = -par. delta ln k(T)/par. delta(ΔG 0 /RT), G/sub a/ 0 is independent of ΔG 0 and M(α), the Legendre transform of G/sub a/, is a function only of α. For small changes in ΔG 0 , the general result reduces to the familiar ''linear'' free energy relation delta G/sub a/ = α delta ΔG 0 . It is concluded from general considerations that M(α) is a symmetric, convex function of α and hence that α is a monotonically increasing function of ΔG 0 . Experimental data appear to conform well to the form α = 1/[1 + exp(-ΔG 0 /G/sub s/ 0 )]. A simple interpretation of the ΔG 0 dependence of G/sub a/, based on an interpolation of the free energy from that of the reagents to that of the products, is offered. 4 figures, 69 references
Trajectory phase transitions and dynamical Lee-Yang zeros of the Glauber-Ising chain.
Hickey, James M; Flindt, Christian; Garrahan, Juan P
2013-07-01
We examine the generating function of the time-integrated energy for the one-dimensional Glauber-Ising model. At long times, the generating function takes on a large-deviation form and the associated cumulant generating function has singularities corresponding to continuous trajectory (or "space-time") phase transitions between paramagnetic trajectories and ferromagnetically or antiferromagnetically ordered trajectories. In the thermodynamic limit, the singularities make up a whole curve of critical points in the complex plane of the counting field. We evaluate analytically the generating function by mapping the generator of the biased dynamics to a non-Hermitian Hamiltonian of an associated quantum spin chain. We relate the trajectory phase transitions to the high-order cumulants of the time-integrated energy which we use to extract the dynamical Lee-Yang zeros of the generating function. This approach offers the possibility to detect continuous trajectory phase transitions from the finite-time behavior of measurable quantities.
Deng, Nanjie; Zhang, Bin W; Levy, Ronald M
2015-06-09
The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.
Calculation of free-energy differences from computer simulations of initial and final states
International Nuclear Information System (INIS)
Hummer, G.; Szabo, A.
1996-01-01
A class of simple expressions of increasing accuracy for the free-energy difference between two states is derived based on numerical thermodynamic integration. The implementation of these formulas requires simulations of the initial and final (and possibly a few intermediate) states. They involve higher free-energy derivatives at these states which are related to the moments of the probability distribution of the perturbation. Given a specified number of such derivatives, these integration formulas are optimal in the sense that they are exact to the highest possible order of free-energy perturbation theory. The utility of this approach is illustrated for the hydration free energy of water. This problem provides a quite stringent test because the free energy is a highly nonlinear function of the charge so that even fourth order perturbation theory gives a very poor estimate of the free-energy change. Our results should prove most useful for complex, computationally demanding problems where free-energy differences arise primarily from changes in the electrostatic interactions (e.g., electron transfer, charging of ions, protonation of amino acids in proteins). copyright 1996 American Institute of Physics
Finite size effects in the thermodynamics of a free neutral scalar field
Parvan, A. S.
2018-04-01
The exact analytical lattice results for the partition function of the free neutral scalar field in one spatial dimension in both the configuration and the momentum space were obtained in the framework of the path integral method. The symmetric square matrices of the bilinear forms on the vector space of fields in both configuration space and momentum space were found explicitly. The exact lattice results for the partition function were generalized to the three-dimensional spatial momentum space and the main thermodynamic quantities were derived both on the lattice and in the continuum limit. The thermodynamic properties and the finite volume corrections to the thermodynamic quantities of the free real scalar field were studied. We found that on the finite lattice the exact lattice results for the free massive neutral scalar field agree with the continuum limit only in the region of small values of temperature and volume. However, at these temperatures and volumes the continuum physical quantities for both massive and massless scalar field deviate essentially from their thermodynamic limit values and recover them only at high temperatures or/and large volumes in the thermodynamic limit.
Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir
2018-04-10
We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .
Branching trajectory continual integral
International Nuclear Information System (INIS)
Maslov, V.P.; Chebotarev, A.M.
1980-01-01
Heuristic definition of the Feynman continual integral over branching trajectories is suggested which makes it possible to obtain in the closed form the solution of the Cauchy problem for the model Hartree equation. A number of properties of the solution is derived from an integral representation. In particular, the quasiclassical asymptotics, exact solution in the gaussian case and perturbation theory series are described. The existence theorem for the simpliest continual integral over branching trajectories is proved [ru
International Nuclear Information System (INIS)
Zaghloul, Mofreh R.
2009-01-01
Accurate and consistent prediction of thermodynamic properties is of great importance in high-energy density physics and in modeling stellar atmospheres and interiors as well. Modern descriptions of thermodynamic properties of such nonideal plasma systems are sophisticated and/or full of pitfalls that make it difficult, if not impossible, to reproduce. The use of the Saha equation modified at high densities by incorporating simple expressions for depression of ionization potentials is very convenient in that context. However, as it is commonly known, the incorporation of ad hoc or empirical expressions for the depression of ionization potentials in the Saha equation leads to thermodynamic inconsistencies. The problem of thermodynamic consistency of ionization potentials depression in nonideal plasmas is investigated and a criterion is derived, which shows immediately, whether a particular model for the ionization potential depression is self-consistent, that is, whether it can be directly related to a modification of the free-energy function, or not. A backward scheme is introduced which can be utilized to derive nonideality corrections to the free-energy function from formulas of ionization potentials depression derived from plasma microfields or in ad hoc or empirical fashion provided that the aforementioned self-consistency criterion is satisfied. The value and usefulness of such a backward method are pointed out and discussed. The above-mentioned criterion is applied to investigate the thermodynamic consistency of some historic models in the literature and an optional routine is introduced to recover their thermodynamic consistencies while maintaining the same functional dependence on the species densities as in the original models. Sample computational problems showing the effect of the proposed modifications on the computed plasma composition are worked out and presented.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
International Nuclear Information System (INIS)
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-01-01
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields
Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki
2017-06-05
Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Guidelines for the analysis of free energy calculations.
Klimovich, Pavel V; Shirts, Michael R; Mobley, David L
2015-05-01
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.
Path integrals and geometry of trajectories
International Nuclear Information System (INIS)
Blau, M.; Keski-Vakkuri, E.; Niemi, A.J.
1990-01-01
A geometrical interpretation of path integrals is developed in the space of trajectories. This yields a supersymmetric formulation of a generic path integral, with the supersymmetry resembling the BRST supersymmetry of a first class constrained system. If the classical equation of motion is a Killing vector field in the space of trajectories, the supersymmetry localizes the path integral to classical trajectories and the WKB approximation becomes exact. This can be viewed as a path integral generalization of the Duistermaat-Heckman theorem, which states the conditions for the exactness of the WKB approximation for integrals in a compact phase space. (orig.)
Directory of Open Access Journals (Sweden)
Ben Pearre
2012-10-01
Full Text Available Given multiple widespread stationary data sources such as ground-based sensors, an unmanned aircraft can fly over the sensors and gather the data via a wireless link. Performance criteria for such a network may incorporate costs such as trajectory length for the aircraft or the energy required by the sensors for radio transmission. Planning is hampered by the complex vehicle and communication dynamics and by uncertainty in the locations of sensors, so we develop a technique based on model-free learning. We present a stochastic optimisation method that allows the data-ferrying aircraft to optimise data collection trajectories through an unknown environment in situ, obviating the need for system identification. We compare two trajectory representations, one that learns near-optimal trajectories at low data requirements but that fails at high requirements, and one that gives up some performance in exchange for a data collection guarantee. With either encoding the ferry is able to learn significantly improved trajectories compared with alternative heuristics. To demonstrate the versatility of the model-free learning approach, we also learn a policy to minimise the radio transmission energy required by the sensor nodes, allowing prolonged network lifetime.
Direct evaluation of free energy for large system through structure integration approach.
Takeuchi, Kazuhito; Tanaka, Ryohei; Yuge, Koretaka
2015-09-30
We propose a new approach, 'structure integration', enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based simulation, we find that the present method evaluates configurational free energy accurately in disorder states above critical temperature.
Gibbs free energy of formation of lanthanum rhodate by quadrupole mass spectrometer
International Nuclear Information System (INIS)
Prasad, R.; Banerjee, Aparna; Venugopal, V.
2003-01-01
The ternary oxide in the system La-Rh-O is of considerable importance because of its application in catalysis. Phase equilibria in the pseudo-binary system La 2 O 3 -Rh 2 O 3 has been investigated by Shevyakov et. al. Gibbs free energy of LaRhO 3 (s) was determined by Jacob et. al. using a solid state Galvanic cell in the temperature range 890 to 1310 K. No other thermodynamic data were available in the literature. Hence it was decided to determine Gibbs free energy of formation of LaRhO 3 (s) by an independent technique, viz. quadrupole mass spectrometer (QMS) coupled with a Knudsen effusion cell and the results are presented
Calculation of the surface free energy of fcc copper nanoparticles
International Nuclear Information System (INIS)
Jia Ming; Lai Yanqing; Tian Zhongliang; Liu Yexiang
2009-01-01
Using molecular dynamics simulations with the modified analytic embedded-atom method we calculate the Gibbs free energy and surface free energy for fcc Cu bulk, and further obtain the Gibbs free energy of nanoparticles. Based on the Gibbs free energy of nanoparticles, we have investigated the heat capacity of copper nanoparticles. Calculation results indicate that the Gibbs free energy and the heat capacity of nanoparticles can be divided into two parts: bulk quantity and surface quantity. The molar heat capacity of the bulk sample is lower compared with the molar heat capacity of nanoparticles, and this difference increases with the decrease in the particle size. It is also observed that the size effect on the thermodynamic properties of Cu nanoparticles is not really significant until the particle is less than about 20 nm. It is the surface atoms that decide the size effect on the thermodynamic properties of nanoparticles
Tolokh, Igor S.; Vivcharuk, Victor; Tomberli, Bruno; Gray, C. G.
2009-09-01
Molecular dynamics (MD) simulations are used to study the interaction of an anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with a POPG bilayer is employed as a model system for studying the details of membrane adsorption selectivity of cationic antimicrobial peptides. Seventy eight 4 ns MD production run trajectories of the equilibrated system, with six restrained orientations of LFCinB at 13 different separations from the POPG membrane, are generated to determine the free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the profile for this relatively large system, a variant of constrained MD and thermodynamic integration is used. A simplified method for relating the free energy profile to the LFCinB-POPG membrane binding constant is employed to predict a free energy of adsorption of -5.4±1.3kcal/mol and a corresponding maximum adsorption binding force of about 58 pN. We analyze the results using Poisson-Boltzmann theory. We find the peptide-membrane attraction to be dominated by the entropy increase due to the release of counterions and polarized water from the region between the charged membrane and peptide, as the two approach each other. We contrast these results with those found earlier for adsorption of LFCinB on the mammalianlike palmitoyl-oleoyl-phosphatidylcholine membrane.
International Nuclear Information System (INIS)
Naslain, R.; Thebault, J.; Hagenmuller, P.; Bernard, C.
1979-01-01
A thermodynamic approach based on the minimization of the total Gibbs free energy of the system is used to study the chemical vapour deposition (CVD) of boron from BCl 3 -H 2 or BBr 3 -H 2 mixtures on various types of substrates (at 1000 < T< 1900 K and 1 atm). In this approach it is assumed that states close to equilibrium are reached in the boron CVD apparatus. (Auth.)
Kravchenko-Balasha, Nataly; Shin, Young Shik; Sutherland, Alex; Levine, R D; Heath, James R
2016-05-17
Controlling cell migration is important in tissue engineering and medicine. Cell motility depends on factors such as nutrient concentration gradients and soluble factor signaling. In particular, cell-cell signaling can depend on cell-cell separation distance and can influence cellular arrangements in bulk cultures. Here, we seek a physical-based approach, which identifies a potential governed by cell-cell signaling that induces a directed cell-cell motion. A single-cell barcode chip (SCBC) was used to experimentally interrogate secreted proteins in hundreds of isolated glioblastoma brain cancer cell pairs and to monitor their relative motions over time. We used these trajectories to identify a range of cell-cell separation distances where the signaling was most stable. We then used a thermodynamics-motivated analysis of secreted protein levels to characterize free-energy changes for different cell-cell distances. We show that glioblastoma cell-cell movement can be described as Brownian motion biased by cell-cell potential. To demonstrate that the free-energy potential as determined by the signaling is the driver of motion, we inhibited two proteins most involved in maintaining the free-energy gradient. Following inhibition, cell pairs showed an essentially random Brownian motion, similar to the case for untreated, isolated single cells.
Virtual substitution scan via single-step free energy perturbation.
Chiang, Ying-Chih; Wang, Yi
2016-02-05
With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the 'recycling' of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. This article is protected by copyright. All rights reserved. © 2016 Wiley Periodicals, Inc.
An Energy-Aware Trajectory Optimization Layer for sUAS
Silva, William A.
The focus of this work is the implementation of an energy-aware trajectory optimization algorithm that enables small unmanned aircraft systems (sUAS) to operate in unknown, dynamic severe weather environments. The software is designed as a component of an Energy-Aware Dynamic Data Driven Application System (EA-DDDAS) for sUAS. This work addresses the challenges of integrating and executing an online trajectory optimization algorithm during mission operations in the field. Using simplified aircraft kinematics, the energy-aware algorithm enables extraction of kinetic energy from measured winds to optimize thrust use and endurance during flight. The optimization layer, based upon a nonlinear program formulation, extracts energy by exploiting strong wind velocity gradients in the wind field, a process known as dynamic soaring. The trajectory optimization layer extends the energy-aware path planner developed by Wenceslao Shaw-Cortez te{Shaw-cortez2013} to include additional mission configurations, simulations with a 6-DOF model, and validation of the system with flight testing in June 2015 in Lubbock, Texas. The trajectory optimization layer interfaces with several components within the EA-DDDAS to provide an sUAS with optimal flight trajectories in real-time during severe weather. As a result, execution timing, data transfer, and scalability are considered in the design of the software. Severe weather also poses a measure of unpredictability to the system with respect to communication between systems and available data resources during mission operations. A heuristic mission tree with different cost functions and constraints is implemented to provide a level of adaptability to the optimization layer. Simulations and flight experiments are performed to assess the efficacy of the trajectory optimization layer. The results are used to assess the feasibility of flying dynamic soaring trajectories with existing controllers as well as to verify the interconnections between
The thermodynamic solar energy
International Nuclear Information System (INIS)
Rivoire, B.
2002-04-01
The thermodynamic solar energy is the technic in the whole aiming to transform the solar radiation energy in high temperature heat and then in mechanical energy by a thermodynamic cycle. These technic are most often at an experimental scale. This paper describes and analyzes the research programs developed in the advanced countries, since 1980. (A.L.B.)
Introduction to the thermodynamic Bethe ansatz
van Tongeren, Stijn J.
2016-08-01
We give a pedagogical introduction to the thermodynamic Bethe ansatz, a method that allows us to describe the thermodynamics of integrable models whose spectrum is found via the (asymptotic) Bethe ansatz. We set the stage by deriving the Fermi-Dirac distribution and associated free energy of free electrons, and then in a similar though technically more complicated fashion treat the thermodynamics of integrable models, focusing first on the one-dimensional Bose gas with delta function interaction as a clean pedagogical example, secondly the XXX spin chain as an elementary (lattice) model with prototypical complicating features in the form of bound states, and finally the {SU}(2) chiral Gross-Neveu model as a field theory example. Throughout this discussion we emphasize the central role of particle and hole densities, whose relations determine the model under consideration. We then discuss tricks that allow us to use the same methods to describe the exact spectra of integrable field theories on a circle, in particular the chiral Gross-Neveu model. We moreover discuss the simplification of TBA equations to Y systems, including the transition back to integral equations given sufficient analyticity data, in simple examples.
Free energy profiles from single-molecule pulling experiments.
Hummer, Gerhard; Szabo, Attila
2010-12-14
Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.
Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.
Boulougouris, Georgios C
2014-05-15
The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be
Finite-size corrections to the free energies of crystalline solids
Polson, J.M.; Trizac, E.; Pronk, S.; Frenkel, D.
2000-01-01
We analyze the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading (ln N/N) corrections, the remaining free energy is found to depend linearly on 1/N. Extrapolating to the thermodynamic limit (N → ∞), we estimate the free
International Nuclear Information System (INIS)
Escobedo, Fernando A.
2016-01-01
The phase behavior and the homogeneous nucleation of an equimolar mixture of octahedra and cuboctahedra are studied using thermodynamic integration, Gibbs-Duhem integration, and umbrella sampling simulations. The components of this mixture are modeled as polybead objects of equal edge lengths so that they can assemble into a space-filling compound with the CsCl crystal structure. Taking as reference the hard-core system where the compound crystal does not spontaneously nucleate, we quantified the effect of inter-species selective interactions on facilitating the disorder-to-order transition. Facet selective and facet non-selective inter-species attractions were considered, and while the former was expectedly more favorable toward the target tessellating structure, the latter was found to be similarly effective in nucleating the crystal compound. Ranges for the strength of attractions and degree of supersaturation were identified where the nucleation free-energy barrier was small enough to foretell a fast process but large enough to prevent spinodal fluctuations that can trap the system in dense metastable states lacking long-range order. At those favorable conditions, the tendency toward the local orientational order favored by packing entropy is amplified and found to play a key role seeding nuclei with the CsCl structure.
Information-to-free-energy conversion: Utilizing thermal fluctuations.
Toyabe, Shoichi; Muneyuki, Eiro
2013-01-01
Maxwell's demon is a hypothetical creature that can convert information to free energy. A debate that has lasted for more than 100 years has revealed that the demon's operation does not contradict the laws of thermodynamics; hence, the demon can be realized physically. We briefly review the first experimental demonstration of Maxwell's demon of Szilard's engine type that converts information to free energy. We pump heat from an isothermal environment by using the information about the thermal fluctuations of a Brownian particle and increase the particle's free energy.
Nakamura, Tatsuya; Matsumoto, Masakazu; Yagasaki, Takuma; Tanaka, Hideki
2016-03-03
We investigate why no hydrogen-disordered form of ice II has been found in nature despite the fact that most of hydrogen-ordered ices have hydrogen-disordered counterparts. The thermodynamic stability of a set of hydrogen-ordered ice II variants relative to ice II is evaluated theoretically. It is found that ice II is more stable than the disordered variants so generated as to satisfy the simple ice rule due to the lower zero-point energy as well as the pair interaction energy. The residual entropy of the disordered ice II phase gradually compensates the unfavorable free energy with increasing temperature. The crossover, however, occurs at a high temperature well above the melting point of ice III. Consequently, the hydrogen-disordered phase does not exist in nature. The thermodynamic stability of partially hydrogen-disordered ices is also scrutinized by examining the free-energy components of several variants obtained by systematic inversion of OH directions in ice II. The potential energy of one variant is lower than that of the ice II structure, but its Gibbs free energy is slightly higher than that of ice II due to the zero-point energy. The slight difference in the thermodynamic stability leaves the possibility of the partial hydrogen-disorder in real ice II.
International Nuclear Information System (INIS)
Mörtberg, Ulla; Goldenberg, Romain; Kalantari, Zahra; Kordas, Olga; Deal, Brian; Balfors, Berit; Cvetkovic, Vladimir
2017-01-01
Urban development trajectories are changing towards compact, energy-efficient cities and renewable energy sources, and this will strongly affect ecosystem services (ES) that cities are dependent on but tend to disregard. Such ES can be provisioning, regulating and cultural ES, around which competition over land resources will increase with energy system shifts. Much of this can be foreseen to take place within urbanising regions that are simultaneously the living environment of a major part of the human population today. In order to inform critical urban policy decisions, tools for integrated assessment of urban energy and transport options and ecosystem services need to be developed. For this purpose, a case study of the Stockholm region was conducted, analysing three scenarios for the future urbanisation of the region, integrating a transport energy perspective and an ES perspective. The results showed that a dense but polycentric development pattern gives more opportunities for sustainable urban development, while the dense monocentric scenario has apparent drawbacks from an ES perspective. The methodology is compatible with a model integration platform for urban policy support and will thus enable integrated policy assessment of complex urban systems, with the goal of increasing their sustainability. - Highlights: • A diffuse urban pattern leads to low access to jobs and high energy consumption. • A dense monocentric urban pattern implies high energy efficiency and low access to ES. • A dense polycentric urban pattern allows for a combination of urban functions. • ES needs to be integrated into sustainability assessments of urban policy options.
Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead
Directory of Open Access Journals (Sweden)
Fabio Pietrucci
2017-11-01
Full Text Available Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.
Dotov, D G; Kim, S; Frank, T D
2015-02-01
We derive explicit expressions for the non-equilibrium thermodynamical variables of a canonical-dissipative limit cycle oscillator describing rhythmic motion patterns of active systems. These variables are statistical entropy, non-equilibrium internal energy, and non-equilibrium free energy. In particular, the expression for the non-equilibrium free energy is derived as a function of a suitable control parameter. The control parameter determines the Hopf bifurcation point of the deterministic active system and describes the effective pumping of the oscillator. In analogy to the equilibrium free energy of the Landau theory, it is shown that the non-equilibrium free energy decays as a function of the control parameter. In doing so, a similarity between certain equilibrium and non-equilibrium phase transitions is pointed out. Data from an experiment on human rhythmic movements is presented. Estimates for pumping intensity as well as the thermodynamical variables are reported. It is shown that in the experiment the non-equilibrium free energy decayed when pumping intensity was increased, which is consistent with the theory. Moreover, pumping intensities close to zero could be observed at relatively slow intended rhythmic movements. In view of the Hopf bifurcation underlying the limit cycle oscillator model, this observation suggests that the intended limit cycle movements were actually more similar to trajectories of a randomly perturbed stable focus. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
Thermodynamical inequivalence of quantum stress-energy and spin tensors
International Nuclear Information System (INIS)
Becattini, F.; Tinti, L.
2011-01-01
It is shown that different couples of stress-energy and spin tensors of quantum-relativistic fields, which would be otherwise equivalent, are in fact inequivalent if the second law of thermodynamics is taken into account. The proof of the inequivalence is based on the analysis of a macroscopic system at full thermodynamical equilibrium with a macroscopic total angular momentum and a specific instance is given for the free Dirac field, for which we show that the canonical and Belinfante stress-energy tensors are not equivalent. For this particular case, we show that the difference between the predicted angular momentum densities for a rotating system at full thermodynamical equilibrium is a quantum effect, persisting in the nonrelativistic limit, corresponding to a polarization of particles of the order of (ℎ/2π)ω/KT (ω being the angular velocity) and could in principle be measured experimentally. This result implies that specific stress-energy and spin tensors are physically meaningful even in the absence of gravitational coupling and raises the issue of finding the thermodynamically right (or the right class of) tensors. We argue that the maximization of the thermodynamic potential theoretically allows us to discriminate between two different couples, yet for the present we are unable to provide a theoretical method to single out the best couple of tensors in a given quantum field theory. The existence of a nonvanishing spin tensor would have major consequences in hydrodynamics, gravity and cosmology.
Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton
2013-08-15
Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.
Free Energy and Internal Combustion Engine Cycles
Harris, William D.
2012-01-01
The performance of one type (Carnot) of Internal Combustion Engine (ICE) cycle is analyzed within the framework of thermodynamic free energies. ICE performance is different from that of an External Combustion Engine (ECE) which is dictated by Carnot's rule.
Transactive Energy Trajectories of the European and Croatian Energy Policy
International Nuclear Information System (INIS)
Toljan, I.
2014-01-01
The concept of transactive energy requires harmonized operation of all entities involved in the electrical power system on market-oriented bases. Each country creates independently its direction of the development (trajectory) of its power sector, but within the framework of basic trajectories laid down by the acquits communautaire, some of which are mandatory and some of which are only recommended. Transactive energy uses economic signals or incentives for using all available new technologies in the energy sector, from production to consumption, in a way that is definitely more efficient than the previous one. The trajectories are determined by the implementation policy whose principal characteristic is non-acceptance of delay in making decisions. The benchmarking system has been introduced. After setting the goals for 2020, the acquits communautaire additionally set very ambitious goals for 2030, which will also be reflected on the costs of energy generation, and consequently on the input costs of the European economy. The intention is to reduce CO2 emission from the energy sector by 80 percent until 2050. The development of exploitation of gas deposits and the introduction of new technologies places the USA on the global level in a completely different position than before. Coal is being gradually substituted by gas, which has so far been the dominating energy source for generation of electrical energy. The results of analyses indicate that gas supply in the USA will be three times cheaper than in Europe in the next 100 years. Taking into consideration the intended application of the current drilling technology also in Europe, it is to be expected that a significant change in the European energy policy will occur. There are also forecasts in the Republic of Croatia that might significantly change the picture of the Croatian energy industry. It should be kept in mind that finding new energy sources does not imply abandoning the concept of liberalized market
Hofer, Thomas S.; Hünenberger, Philippe H.
2018-06-01
The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained
De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris
2011-07-30
4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.
Nonlinear integral equations for thermodynamics of the sl(r + 1) Uimin-Sutherland model
International Nuclear Information System (INIS)
Tsuboi, Zengo
2003-01-01
We derive traditional thermodynamic Bethe ansatz (TBA) equations for the sl(r+1) Uimin-Sutherland model from the T-system of the quantum transfer matrix. These TBA equations are identical to the those from the string hypothesis. Next we derive a new family of nonlinear integral equations (NLIEs). In particular, a subset of these NLIEs forms a system of NLIEs which contains only a finite number of unknown functions. For r=1, this subset of NLIEs reduces to Takahashi's NLIE for the XXX spin chain. A relation between the traditional TBA equations and our new NLIEs is clarified. Based on our new NLIEs, we also calculate the high-temperature expansion of the free energy
International Nuclear Information System (INIS)
Elsner, Albrecht
2012-01-01
Gibbs's work on the thermodynamic properties of substances presented a complete thermodynamic theory. The formulations of the entropy S and internal energy U as extensive quantities allow the zeros of the real gas to be given: S=0 at absolute zero (Nernst, Planck) and U=0 at the critical point. Consequently, every thermodynamic function is unique and absolutely specified. Interdependences among quantities such as temperature, vapor pressure, chemical potential, volume, entropy, internal energy, and heat capacity are likewise unique and numerically well defined. This is shown for the saturated fluid, water, in the region between absolute zero and the critical point. As a consequence of the calculation of the chemical potential, it follows that the free particle flow in an inhomogeneous system is essentially governed by the difference in chemical potential, and not through the difference in pressure, this effect being of importance for meteorology and oceanography.
Quantum corrections to the stress-energy tensor in thermodynamic equilibrium with acceleration
Becattini, F.; Grossi, E.
2015-08-01
We show that the stress-energy tensor has additional terms with respect to the ideal form in states of global thermodynamic equilibrium in flat spacetime with nonvanishing acceleration and vorticity. These corrections are of quantum origin and their leading terms are second order in the gradients of the thermodynamic fields. Their relevant coefficients can be expressed in terms of correlators of the stress-energy tensor operator and the generators of the Lorentz group. With respect to previous assessments, we find that there are more second-order coefficients and that all thermodynamic functions including energy density receive acceleration and vorticity dependent corrections. Notably, also the relation between ρ and p , that is, the equation of state, is affected by acceleration and vorticity. We have calculated the corrections for a free real scalar field—both massive and massless—and we have found that they increase, particularly for a massive field, at very high acceleration and vorticity and very low temperature. Finally, these nonideal terms depend on the explicit form of the stress-energy operator, implying that different stress-energy tensors of the scalar field—canonical or improved—are thermodynamically inequivalent.
Thermodynamic Aspects and Reprogramming Cellular Energy Metabolism during the Fibrosis Process
Directory of Open Access Journals (Sweden)
Alexandre Vallée
2017-11-01
Full Text Available Fibrosis is characterized by fibroblast proliferation and fibroblast differentiation into myofibroblasts, which generate a relaxation-free contraction mechanism associated with excessive collagen synthesis in the extracellular matrix, which promotes irreversible tissue retraction evolving towards fibrosis. From a thermodynamic point of view, the mechanisms leading to fibrosis are irreversible processes that can occur through changing the entropy production rate. The thermodynamic behaviors of metabolic enzymes involved in fibrosis are modified by the dysregulation of both transforming growth factor β (TGF-β signaling and the canonical WNT/β-catenin pathway, leading to aerobic glycolysis, called the Warburg effect. Molecular signaling pathways leading to fibrosis are considered dissipative structures that exchange energy or matter with their environment far from the thermodynamic equilibrium. The myofibroblastic cells arise from exergonic processes by switching the core metabolism from oxidative phosphorylation to glycolysis, which generates energy and reprograms cellular energy metabolism to induce the process of myofibroblast differentiation. Circadian rhythms are far-from-equilibrium thermodynamic processes. They directly participate in regulating the TGF-β and WNT/β-catenin pathways involved in energetic dysregulation and enabling fibrosis. The present review focusses on the thermodynamic implications of the reprogramming of cellular energy metabolism, leading to fibroblast differentiation into myofibroblasts through the positive interplay between TGF-β and WNT/β-catenin pathways underlying in fibrosis.
Yip, Ngai Yin; Elimelech, Menachem
2012-05-01
The Gibbs free energy of mixing dissipated when fresh river water flows into the sea can be harnessed for sustainable power generation. Pressure retarded osmosis (PRO) is one of the methods proposed to generate power from natural salinity gradients. In this study, we carry out a thermodynamic and energy efficiency analysis of PRO work extraction. First, we present a reversible thermodynamic model for PRO and verify that the theoretical maximum extractable work in a reversible PRO process is identical to the Gibbs free energy of mixing. Work extraction in an irreversible constant-pressure PRO process is then examined. We derive an expression for the maximum extractable work in a constant-pressure PRO process and show that it is less than the ideal work (i.e., Gibbs free energy of mixing) due to inefficiencies intrinsic to the process. These inherent inefficiencies are attributed to (i) frictional losses required to overcome hydraulic resistance and drive water permeation and (ii) unutilized energy due to the discontinuation of water permeation when the osmotic pressure difference becomes equal to the applied hydraulic pressure. The highest extractable work in constant-pressure PRO with a seawater draw solution and river water feed solution is 0.75 kWh/m(3) while the free energy of mixing is 0.81 kWh/m(3)-a thermodynamic extraction efficiency of 91.1%. Our analysis further reveals that the operational objective to achieve high power density in a practical PRO process is inconsistent with the goal of maximum energy extraction. This study demonstrates thermodynamic and energetic approaches for PRO and offers insights on actual energy accessible for utilization in PRO power generation through salinity gradients. © 2012 American Chemical Society
Examining a Thermodynamic Order Parameter of Protein Folding.
Chong, Song-Ho; Ham, Sihyun
2018-05-08
Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding. This is illustrated through the application to the folding-unfolding simulation trajectory of villin headpiece subdomain. We rationalize the suitability of the effective energy as an order parameter by the funneledness of the underlying protein free energy landscape. We also demonstrate that an improved conformational space discretization is achieved by incorporating the effective energy. The most distinctive feature of this thermodynamic order parameter is that it works in pointing to near-native folded structures even when the knowledge of the native structure is lacking, and the use of the effective energy will also find applications in combination with methods of protein structure prediction.
Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid
2017-12-07
Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.
Absolute Hydration Free Energy of Proton from First Principles Electronic Structure Calculations
International Nuclear Information System (INIS)
Zhan, Chang-Guo; Dixon, David A.
2001-01-01
The absolute hydration free energy of the proton, DGhyd298(H+), is one of the fundamental quantities for the thermodynamics of aqueous systems. Its exact value remains unknown despite extensive experimental and computational efforts. We report a first-principles determination of DGhyd298(H+) by using the latest developments in electronic structure theory and massively parallel computers. DGhyd298(H+) is accurately predicted to be -262.4 kcal/mol based on high-level, first-principles solvation-included electronic structure calculations. The absolute hydration free energies of other cations can be obtained by using appropriate available thermodynamic data in combination with this value. The high accuracy of the predicted absolute hydration free energy of proton is confirmed by applying the same protocol to predict DGhyd298(Li+)
Pyroelectric Energy Harvesting: With Thermodynamic-Based Cycles
Saber Mohammadi; Akram Khodayari
2012-01-01
This work deals with energy harvesting from temperature variations using ferroelectric materials as a microgenerator. The previous researches show that direct pyroelectric energy harvesting is not effective, whereas thermodynamic-based cycles give higher energy. Also, at different temperatures some thermodynamic cycles exhibit different behaviours. In this paper pyroelectric energy harvesting using Lenoir and Ericsson thermodynamic cycles has been studied numerically and the two cycles were c...
Free-energy landscape of a hyperstable RNA tetraloop.
Miner, Jacob C; Chen, Alan A; García, Angel E
2016-06-14
We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.
Buoncristiani, A. M.; Smith, B. T.; Byvik, C. E.
1982-01-01
Using general thermodynamic arguments, we analyze the conversion of the energy contained in the radiation from a blackbody to useful work by a quantum system. We show that the energy available for conversion is bounded above by the change in free energy in the incident and reradiated fields and that this free energy change depends upon the temperature of the receiving device. Universal efficiency curves giving the ultimate thermodynamic conversion efficiency of the quantum system are presented in terms of the blackbody temperature and the temperature and threshold energy of the quantum system. Application of these results is made to a variety of systems including biological photosynthetic, photovoltaic, and photoelectrochemical systems.
Evaluation of the accuracy of the free-energy-minimization method
International Nuclear Information System (INIS)
Najafabadi, R.; Srolovitz, D.J.
1995-01-01
We have made a detailed comparison between three competing methods for determining the free energies of solids and their defects: the thermodynamic integration of Monte Carlo (TIMC) data, the quasiharmonic (QH) model, and the free-energy-minimization (FEM) method. The accuracy of these methods decreases from the TIMC to QH to FEM method, while the computational efficiency improves in that order. All three methods yield perfect crystal lattice parameters and free energies at finite temperatures which are in good agreement for three different Cu interatomic potentials [embedded atom method (EAM), Morse and Lennard-Jones]. The FEM error (relative to the TIMC) in the (001) surface free energy and in the vacancy formation energy were found to be much larger for the EAM potential than for the other two potentials. Part of the errors in the FEM determination of the free energies are associated with anharmonicities in the interatomic potentials, with the remainder attributed to decoupling of the atomic vibrations. The anharmonicity of the EAM potential was found to be unphysically large compared with experimental vacancy formation entropy determinations. Based upon these results, we show that the FEM method provides a reasonable compromise between accuracy and computational demands. However, the accuracy of this approach is sensitive to the choice of interatomic potential and the nature of the defect to which it is being applied. The accuracy of the FEM is best in high-symmetry environments (perfect crystal, high-symmetry defects, etc.) and when used to describe materials where the anharmonicity is not too large
Gibbs free energy of formation of liquid lanthanide-bismuth alloys
International Nuclear Information System (INIS)
Sheng Jiawei; Yamana, Hajimu; Moriyama, Hirotake
2001-01-01
The linear free energy relationship developed by Sverjensky and Molling provides a way to predict Gibbs free energies of liquid Ln-Bi alloys formation from the known thermodynamic properties of aqueous trivalent lanthanides (Ln 3(5(6+ ). The Ln-Bi alloys are divided into two isostructural families named as the LnBi 2 (Ln=La, Ce, Pr, Nd and Pm) and LnBi (Ln=Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm and Yb). The calculated Gibbs free energy values are well agreed with experimental data
Procacci, Piero
2016-06-01
In this contribution I critically revise the alchemical reversible approach in the context of the statistical mechanics theory of non-covalent bonding in drug-receptor systems. I show that most of the pitfalls and entanglements for the binding free energy evaluation in computer simulations are rooted in the equilibrium assumption that is implicit in the reversible method. These critical issues can be resolved by using a non-equilibrium variant of the alchemical method in molecular dynamics simulations, relying on the production of many independent trajectories with a continuous dynamical evolution of an externally driven alchemical coordinate, completing the decoupling of the ligand in a matter of a few tens of picoseconds rather than nanoseconds. The absolute binding free energy can be recovered from the annihilation work distributions by applying an unbiased unidirectional free energy estimate, on the assumption that any observed work distribution is given by a mixture of normal distributions, whose components are identical in either direction of the non-equilibrium process, with weights regulated by the Crooks theorem. I finally show that the inherent reliability and accuracy of the unidirectional estimate of the decoupling free energies, based on the production of a few hundreds of non-equilibrium independent sub-nanosecond unrestrained alchemical annihilation processes, is a direct consequence of the funnel-like shape of the free energy surface in molecular recognition. An application of the technique to a real drug-receptor system is presented in the companion paper.
Integration of ecological and thermodynamic concepts in the design of sustainable energy landscapes
Stremke, S.; Koh, J.
2011-01-01
Resource depletion and climate change motivate a transition to sustainable energy systems that make effective use of renewable sources. Whereas nature presents strategies to sustain on the basis of renewables, the Laws of Thermodynamics can help to increase efficiency in energy use. In previous
Wang, Mingming; Luo, Jianjun; Fang, Jing; Yuan, Jianping
2018-03-01
The existence of the path dependent dynamic singularities limits the volume of available workspace of free-floating space robot and induces enormous joint velocities when such singularities are met. In order to overcome this demerit, this paper presents an optimal joint trajectory planning method using forward kinematics equations of free-floating space robot, while joint motion laws are delineated with application of the concept of reaction null-space. Bézier curve, in conjunction with the null-space column vectors, are applied to describe the joint trajectories. Considering the forward kinematics equations of the free-floating space robot, the trajectory planning issue is consequently transferred to an optimization issue while the control points to construct the Bézier curve are the design variables. A constrained differential evolution (DE) scheme with premature handling strategy is implemented to find the optimal solution of the design variables while specific objectives and imposed constraints are satisfied. Differ from traditional methods, we synthesize null-space and specialized curve to provide a novel viewpoint for trajectory planning of free-floating space robot. Simulation results are presented for trajectory planning of 7 degree-of-freedom (DOF) kinematically redundant manipulator mounted on a free-floating spacecraft and demonstrate the feasibility and effectiveness of the proposed method.
Placement by thermodynamic simulated annealing
International Nuclear Information System (INIS)
Vicente, Juan de; Lanchares, Juan; Hermida, Roman
2003-01-01
Combinatorial optimization problems arise in different fields of science and engineering. There exist some general techniques coping with these problems such as simulated annealing (SA). In spite of SA success, it usually requires costly experimental studies in fine tuning the most suitable annealing schedule. In this Letter, the classical integrated circuit placement problem is faced by Thermodynamic Simulated Annealing (TSA). TSA provides a new annealing schedule derived from thermodynamic laws. Unlike SA, temperature in TSA is free to evolve and its value is continuously updated from the variation of state functions as the internal energy and entropy. Thereby, TSA achieves the high quality results of SA while providing interesting adaptive features
International Nuclear Information System (INIS)
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-01-01
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
International Nuclear Information System (INIS)
Yuksel, Yunus Emre; Ozturk, Murat; Dincer, Ibrahim
2016-01-01
Highlights: • Development of a novel solar energy based system for multigenaration applications. • Evaluation of the exergy efficiency and destruction rate in each system component. • Investigation of the varying operating conditions on the system performance. • Evaluation of complete parametric studies and performance analysis of the system. - Abstract: In this paper, a novel solar energy based multigeneration system for producing electricity, hydrogen, hot water, heating and cooling is presented and analyzed thermodynamically for potential applications. The energy and exergy analyses are conducted for entire system and its sub-systems, which are a parabolic trough collector system, a double-stage organic Rankine cycle, a proton exchange membrane electrolyzer, a PEM fuel cycle and a quadruple effect absorption cooling system. The parametric studies are performed in order to indicate the impacts of some key indicators on the integrated system performance. These analyses are simulated by using the Engineering Equation Solver software. The results show that the increase in ambient temperature increases the exergetic coefficient performance of the Quadruple Effect Absorption Cooling System. In addition, the increase in solar intensity, temperature of absorber pipes inner surface and concentration of ammonia in working fluid mixture has the positive effect on produced electricity from the expanders and turbine, and hydrogen from the PEM electrolyzer. According to exergy analyses, the largest exergy destruction rates are obtained in the parabolic trough collector, PEM fuel cell and turbine. Therefore, any improvements in these components would lead to a better efficiency of the integrated system.
Kirmayer, Laurence J.
2018-03-01
In a far-reaching essay, Ramstead and colleagues [1] offer an answer to Schrodinger's question "What is life?" [2] framed in terms of a thermodynamic/information-theoretic free energy principle. In short, "all biological systems instantiate a hierarchical generative model of the world that implicitly minimizes its internal entropy by minimizing free energy" [1]. This model generates dynamic stability-that is, a recurrent set of states that constitute a dynamic attractor. This aspect of their answer has much in common with earlier thermodynamic approaches, like that of Prigogine [3], and with the metabolic self-organization central to Maturana and Varela's notion of autopoiesis [4]. It contrasts with explanations of life that emphasize the mechanics of self-replication [5] or autocatalysis [6,7]. In this approach, there is something gained and something lost. Gained is an explanation and corresponding formalism of great generality. Lost (or at least obscured) is a way to understand the "teleonomics" [8], goal-directedness, purposiveness, or agency of living systems-arguably, precisely what makes us ascribe the quality of "being alive" to an organism. Free energy minimization may be a necessary condition for life, but it is not sufficient to characterize its goals, which vary widely and, at least at the level of individual organisms or populations, clearly can run counter to this principle for long stretches of time.
Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M
2015-09-01
Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.
Rößler, Thomas; Stein, Olaf; Heng, Yi; Baumeister, Paul; Hoffmann, Lars
2018-02-01
The accuracy of trajectory calculations performed by Lagrangian particle dispersion models (LPDMs) depends on various factors. The optimization of numerical integration schemes used to solve the trajectory equation helps to maximize the computational efficiency of large-scale LPDM simulations. We analyzed global truncation errors of six explicit integration schemes of the Runge-Kutta family, which we implemented in the Massive-Parallel Trajectory Calculations (MPTRAC) advection module. The simulations were driven by wind fields from operational analysis and forecasts of the European Centre for Medium-Range Weather Forecasts (ECMWF) at T1279L137 spatial resolution and 3 h temporal sampling. We defined separate test cases for 15 distinct regions of the atmosphere, covering the polar regions, the midlatitudes, and the tropics in the free troposphere, in the upper troposphere and lower stratosphere (UT/LS) region, and in the middle stratosphere. In total, more than 5000 different transport simulations were performed, covering the months of January, April, July, and October for the years 2014 and 2015. We quantified the accuracy of the trajectories by calculating transport deviations with respect to reference simulations using a fourth-order Runge-Kutta integration scheme with a sufficiently fine time step. Transport deviations were assessed with respect to error limits based on turbulent diffusion. Independent of the numerical scheme, the global truncation errors vary significantly between the different regions. Horizontal transport deviations in the stratosphere are typically an order of magnitude smaller compared with the free troposphere. We found that the truncation errors of the six numerical schemes fall into three distinct groups, which mostly depend on the numerical order of the scheme. Schemes of the same order differ little in accuracy, but some methods need less computational time, which gives them an advantage in efficiency. The selection of the integration
Scale-invariant transition probabilities in free word association trajectories
Directory of Open Access Journals (Sweden)
Martin Elias Costa
2009-09-01
Full Text Available Free-word association has been used as a vehicle to understand the organization of human thoughts. The original studies relied mainly on qualitative assertions, yielding the widely intuitive notion that trajectories of word associations are structured, yet considerably more random than organized linguistic text. Here we set to determine a precise characterization of this space, generating a large number of word association trajectories in a web implemented game. We embedded the trajectories in the graph of word co-occurrences from a linguistic corpus. To constrain possible transport models we measured the memory loss and the cycling probability. These two measures could not be reconciled by a bounded diffusive model since the cycling probability was very high (16 % of order-2 cycles implying a majority of short-range associations whereas the memory loss was very rapid (converging to the asymptotic value in ∼ 7 steps which, in turn, forced a high fraction of long-range associations. We show that memory loss and cycling probabilities of free word association trajectories can be simultaneously accounted by a model in which transitions are determined by a scale invariant probability distribution.
Plotnikov, Nikolay V
2014-08-12
Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.
On Integral Invariants for Effective 3-D Motion Trajectory Matching and Recognition.
Shao, Zhanpeng; Li, Youfu
2016-02-01
Motion trajectories tracked from the motions of human, robots, and moving objects can provide an important clue for motion analysis, classification, and recognition. This paper defines some new integral invariants for a 3-D motion trajectory. Based on two typical kernel functions, we design two integral invariants, the distance and area integral invariants. The area integral invariants are estimated based on the blurred segment of noisy discrete curve to avoid the computation of high-order derivatives. Such integral invariants for a motion trajectory enjoy some desirable properties, such as computational locality, uniqueness of representation, and noise insensitivity. Moreover, our formulation allows the analysis of motion trajectories at a range of scales by varying the scale of kernel function. The features of motion trajectories can thus be perceived at multiscale levels in a coarse-to-fine manner. Finally, we define a distance function to measure the trajectory similarity to find similar trajectories. Through the experiments, we examine the robustness and effectiveness of the proposed integral invariants and find that they can capture the motion cues in trajectory matching and sign recognition satisfactorily.
Thermodynamical properties of dark energy
International Nuclear Information System (INIS)
Gong Yungui; Wang Bin; Wang Anzhong
2007-01-01
We have investigated the thermodynamical properties of dark energy. Assuming that the dark energy temperature T∼a -n and considering that the volume of the Universe enveloped by the apparent horizon relates to the temperature, we have derived the dark energy entropy. For dark energy with constant equation of state w>-1 and the generalized Chaplygin gas, the derived entropy can be positive and satisfy the entropy bound. The total entropy, including those of dark energy, the thermal radiation, and the apparent horizon, satisfies the generalized second law of thermodynamics. However, for the phantom with constant equation of state, the positivity of entropy, the entropy bound, and the generalized second law cannot be satisfied simultaneously
Maximally-localized position, Euclidean path-integral, and thermodynamics in GUP quantum mechanics
Bernardo, Reginald Christian S.; Esguerra, Jose Perico H.
2018-04-01
In dealing with quantum mechanics at very high energies, it is essential to adapt to a quasiposition representation using the maximally-localized states because of the generalized uncertainty principle. In this paper, we look at maximally-localized states as eigenstates of the operator ξ = X + iβP that we refer to as the maximally-localized position. We calculate the overlap between maximally-localized states and show that the identity operator can be expressed in terms of the maximally-localized states. Furthermore, we show that the maximally-localized position is diagonal in momentum-space and that the maximally-localized position and its adjoint satisfy commutation and anti-commutation relations reminiscent of the harmonic oscillator commutation and anti-commutation relations. As application, we use the maximally-localized position in developing the Euclidean path-integral and introduce the compact form of the propagator for maximal localization. The free particle momentum-space propagator and the propagator for maximal localization are analytically evaluated up to quadratic-order in β. Finally, we obtain a path-integral expression for the partition function of a thermodynamic system using the maximally-localized states. The partition function of a gas of noninteracting particles is evaluated. At temperatures exceeding the Planck energy, we obtain the gas' maximum internal energy N / 2 β and recover the zero heat capacity of an ideal gas.
Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.
Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu
2013-09-10
Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying
Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.
Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N
2016-06-15
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Martins, Silvia A; Sousa, Sergio F
2013-06-05
The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.
Vehicle Reference Generator for Collision-Free Trajectories in Hazardous Maneuvers
Directory of Open Access Journals (Sweden)
Cuauhtémoc Acosta Lúa
2018-01-01
Full Text Available This paper presents a reference generator for ground vehicles, based on potential fields adapted to the case of vehicular dynamics. The reference generator generates signals to be tracked by the vehicle, corresponding to a trajectory avoiding collisions with obstacles. This generator integrates artificial forces of potential fields of the object surrounding the vehicle. The reference generator is used with a controller to ensure the tracking of the accident-free reference. This approach can be used for vehicle autonomous driving or for active control of manned vehicles. Simulation results, presented for the autonomous driving, consider a scenario inspired by the so-called moose (or elk test, with the presence of other collaborative vehicles.
The free energy principle, negative energy modes, and stability
International Nuclear Information System (INIS)
Morrison, P.J.; Kotschenreuther, M.
1990-01-01
This paper is concerned with instability of equilibria of Hamiltonian, fluid and plasma dynamical systems. Usually the dynamical equilibrium of interest is not the state of thermodynamic equilibrium, and does not correspond to a free energy minimum. The relaxation of this type of equilibrium is conventionally considered to be initiated by linear instability. However, there are many cases where linear instability is not present, but the equilibrium is nonlinearly unstable to arbitrarily small perturbations. This paper is about general free energy expressions for determining the presence of linear or nonlinear instabilities. These expressions are simple and practical, and can be obtained for all equilibria of all ideal fluid and plasma models. By free energy, we mean the energy change upon perturbations of the equilibrium that respect dynamical phase space constraints. This quantity is measured by a self-adjoint quadratic form, called δ 2 F. The free energy can result in instability when δ 2 F is indefinite; i.e. there exist accessible perturbations that lower the free energy of the system. A primary purpose of this paper is to tie together three manifestations of what we will refer to as negative energy modes. The first is the conventional plasma physics notion of negative energy mode that is based on the definition of the energy in a homogeneous dielectric medium. A negative energy mode is a normal mode of the medium (plasma) that possesses negative dielectric energy. The second manifestation occurs in finite degree-of-freedom Hamiltonian normal form theory. The quadratic part of a Hamiltonian in the vicinity of an equilibrium point, which possesses only distinct oscillatory eigenvalues, has an invariant signature. Thus in cases where the quadratic form is indefinite, it is natural to refer to the modes corresponding to the negative signature as negative energy modes
A numerical model on thermodynamic analysis of free piston Stirling engines
Mou, Jian; Hong, Guotong
2017-02-01
In this paper, a new numerical thermodynamic model which bases on the energy conservation law has been used to analyze the free piston Stirling engine. In the model all data was taken from a real free piston Stirling engine which has been built in our laboratory. The energy conservation equations have been applied to expansion space and compression space of the engine. The equation includes internal energy, input power, output power, enthalpy and the heat losses. The heat losses include regenerative heat conduction loss, shuttle heat loss, seal leakage loss and the cavity wall heat conduction loss. The numerical results show that the temperature of expansion space and the temperature of compression space vary with the time. The higher regeneration effectiveness, the higher efficiency and bigger output work. It is also found that under different initial pressures, the heat source temperature, phase angle and engine work frequency pose different effects on the engine’s efficiency and power. As a result, the model is expected to be a useful tool for simulation, design and optimization of Stirling engines.
International Nuclear Information System (INIS)
Morandin, Matteo; Maréchal, François; Mercangöz, Mehmet; Buchter, Florian
2012-01-01
The interest in large scale electricity storage (ES) with discharging time longer than 1 h and nominal power greater than 1 MW, is increasing worldwide as the increasing share of renewable energy, typically solar and wind energy, imposes severe load management issues. Thermo-electrical energy storage (TEES) based on thermodynamic cycles is currently under investigation at ABB corporate research as an alternative solution to pump hydro and compressed air energy storage. TEES is based on the conversion of electricity into thermal energy during charge by means of a heat pump and on the conversion of thermal energy into electricity during discharge by means of a thermal engine. The synthesis and the thermodynamic optimization of a TEES system based on hot water, ice storage and transcritical CO 2 cycles, is discussed in two papers. In this first paper a methodology for the conceptual design of a TEES system based on the analysis of the thermal integration between charging and discharging cycles through Pinch Analysis tools is introduced. According to such methodology, the heat exchanger network and temperatures and volumes of storage tanks are not defined a priori but are determined after the cycle parameters are optimized. For this purpose a heuristic procedure based on the interpretation of the composite curves obtained by optimizing the thermal integration between the cycles was developed. Such heuristic rules were implemented in a code that allows finding automatically the complete system design for given values of the intensive parameters of the charging and discharging cycles only. A base case system configuration is introduced and the results of its thermodynamic optimization are discussed here. A maximum roundtrip efficiency of 60% was obtained for the base case configuration assuming turbomachinery and heat exchanger performances in line with indications from manufacturers. -- Highlights: ► Energy storage based on water, ice, and transcritical CO 2 cycles is
2015-01-01
The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect
The thermodynamic solar energy; Le solaire thermodynamique
Energy Technology Data Exchange (ETDEWEB)
Rivoire, B. [Centre National de la Recherche Scientifique (CNRS-IMP), 66 - Perpignan (France)
2002-04-01
The thermodynamic solar energy is the technic in the whole aiming to transform the solar radiation energy in high temperature heat and then in mechanical energy by a thermodynamic cycle. These technic are most often at an experimental scale. This paper describes and analyzes the research programs developed in the advanced countries, since 1980. (A.L.B.)
Relationship between wave energy and free energy from pickup ions in the Comet Halley environment
Huddleston, D. E.; Johnstone, A. D.
1992-01-01
The free energy available from the implanted heavy ion population at Comet Halley is calculated by assuming that the initial unstable velocity space ring distribution of the ions evolves toward a bispherical shell. Ultimately this free energy adds to the turbulence in the solar wind. Upstream and downstream free energies are obtained separately for the conditions observed along the Giotto spacecraft trajectory. The results indicate that the waves are mostly upstream propagating in the solar wind frame. The total free energy density always exceeds the measured wave energy density because, as expected in the nonlinear process of ion scattering, the available energy is not all immediately released. An estimate of the amount which has been released can be obtained from the measured oxygen ion distributions and again it exceeds that observed. The theoretical analysis is extended to calculate the k spectrum of the cometary-ion-generated turbulence.
Free energy analysis of cell spreading.
McEvoy, Eóin; Deshpande, Vikram S; McGarry, Patrick
2017-10-01
In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading. Simulations suggest that cell spreading can be viewed as a competition between (i) decreasing cytoskeletal free energy due to strain induced assembly of cytoskeletal proteins into contractile SFs, and (ii) increasing elastic free energy due to stretching of the mechanically passive components of the cell. The computed minimum free energy spread area is shown to be lower for a cell on a compliant substrate than on a rigid substrate. Furthermore, a low substrate ligand density is found to limit cell spreading. The predicted dependence of cell spread area on substrate stiffness and ligand density is in agreement with the experiments of Engler et al. (2003). We also simulate the experiments of Théry et al. (2006), whereby initially circular cells deform and adhere to "V-shaped" and "Y-shaped" ligand patches. Analysis of a number of different spread states reveals that deformed configurations with the lowest free energy exhibit a SF distribution that corresponds to experimental observations, i.e. a high concentration of highly aligned SFs occurs along free edges, with lower SF concentrations in the interior of the cell. In summary, the results of this study suggest that cell spreading is driven by free energy minimization based on a competition between decreasing
2015-01-01
Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351
GENERIC Integrators: Structure Preserving Time Integration for Thermodynamic Systems
Öttinger, Hans Christian
2018-04-01
Thermodynamically admissible evolution equations for non-equilibrium systems are known to possess a distinct mathematical structure. Within the GENERIC (general equation for the non-equilibrium reversible-irreversible coupling) framework of non-equilibrium thermodynamics, which is based on continuous time evolution, we investigate the possibility of preserving all the structural elements in time-discretized equations. Our approach, which follows Moser's [1] construction of symplectic integrators for Hamiltonian systems, is illustrated for the damped harmonic oscillator. Alternative approaches are sketched.
Economies Evolve by Energy Dispersal
Directory of Open Access Journals (Sweden)
Stanley Salthe
2009-10-01
Full Text Available Economic activity can be regarded as an evolutionary process governed by the 2nd law of thermodynamics. The universal law, when formulated locally as an equation of motion, reveals that a growing economy develops functional machinery and organizes hierarchically in such a way as to tend to equalize energy density differences within the economy and in respect to the surroundings it is open to. Diverse economic activities result in flows of energy that will preferentially channel along the most steeply descending paths, leveling a non-Euclidean free energy landscape. This principle of 'maximal energy dispersal‘, equivalent to the maximal rate of entropy production, gives rise to economic laws and regularities. The law of diminishing returns follows from the diminishing free energy while the relation between supply and demand displays a quest for a balance among interdependent energy densities. Economic evolution is dissipative motion where the driving forces and energy flows are inseparable from each other. When there are multiple degrees of freedom, economic growth and decline are inherently impossible to forecast in detail. Namely, trajectories of an evolving economy are non-integrable, i.e. unpredictable in detail because a decision by a player will affect also future decisions of other players. We propose that decision making is ultimately about choosing from various actions those that would reduce most effectively subjectively perceived energy gradients.
Thermodynamic modeling of the stacking fault energy of austenitic steels
International Nuclear Information System (INIS)
Curtze, S.; Kuokkala, V.-T.; Oikari, A.; Talonen, J.; Haenninen, H.
2011-01-01
The stacking fault energies (SFE) of 10 austenitic steels were determined in the temperature range 50 ≤ T ≤ 600 K by thermodynamic modeling of the Fe-Cr-Ni-Mn-Al-Si-Cu-C-N system using a modified Olson and Cohen modeling approach (Olson GB, Cohen M. Metall Trans 1976;7A:1897 ). The applied model accounts for each element's contribution to the Gibbs energy, the first-order excess free energies, magnetic contributions and the effect of interstitial nitrogen. Experimental SFE values from X-ray diffraction measurements were used for comparison. The effect of SFE on deformation mechanisms was also studied by electron backscatter diffraction.
Yip, N.Y.; Vermaas, D.A.; Nijmeijer, K.; Elimelech, M.
2014-01-01
Reverse electrodialysis (RED) can harness the Gibbs free energy of mixing when fresh river water flows into the sea for sustainable power generation. In this study, we carry out a thermodynamic and energy efficiency analysis of RED power generation, and assess the membrane power density. First, we
Interaction Free Energies of Eight Sodium Salts and a Phosphatidylcholine Membrane
DEFF Research Database (Denmark)
Wang, C. H.; Ge, Y.; Mortensen, J.
2011-01-01
Many recent reports have discussed specific effects of anions on the properties of lipid membranes and possible roles of such effects within biochemistry. One key parameter in both theoretical and experimental treatments of membrane-salt interactions is the net affinity, that is, the free energy...... salts by dialysis equilibrium measurements. This method provides model free thermodynamic data and allows investigations in the dilute concentration range where solution nonideality and perturbation of membrane structure is limited. The transfer free energy of DMPC from water to salt solutions, Delta mu...
Nikrah, M.; Jafari, S.
2016-06-01
We expand here a theory of a high-gradient laser-excited electron accelerator based on an inverse free-electron laser (inverse-FEL), but with innovations in the structure and design. The electrostatic wiggler used in our scheme, namely termed the Paul wiggler, is generated by segmented cylindrical electrodes with applied oscillatory voltages {{V}\\text{osc}}(t) over {{90}\\circ} segments. The inverse-FEL interaction can be described by the equations that govern the electron motion in the combined fields of both the laser pulse and Paul wiggler field. A numerical study of electron energy and electron trajectories has been made using the fourth-order Runge-Kutta method. The results indicate that the electron attains a considerable energy at short distances in this device. It is found that if the electron has got sufficient suitable wiggler amplitude intensities, it can not only gain higher energy in longer distances, but also can retain it even after the passing of the laser pulse. In addition, the results reveal that the electron energy gains different peaks for different initial axial velocities, so that a suitable small initial axial velocity of e-beam produces substantially high energy gain. With regard to the transverse confinement of the electron beam in a Paul wiggler, there is no applied axial guide magnetic field in this device.
International Nuclear Information System (INIS)
Mansson, B.A.
1990-01-01
Economics, as the social science most concerned with the use and distribution of natural resources, must start to make use of the knowledge at hand in the natural sciences about such resources. In this, thermodynamics is an essential part. In a physicists terminology, human economic activity may be described as a dissipative system which flourishes by transforming and exchanging resources, goods and services. All this involves complex networks of flows of energy and materials. This implies that thermodynamics, the physical theory of energy and materials flows, must have implications for economics. On another level, thermodynamics has been recognized as a physical theory of value, with value concepts similar to those of economic theory. This paper discusses some general aspects of the significance of non-equilibrium thermodynamics for economics. The role of exergy, probably the most important of the physical measures of value, is elucidated. Two examples of integration of thermodynamics with economic theory are reviewed. First, a simple model of a steady-state production system is sued to illustrate the effects of thermodynamic process constraints. Second, the framework of a simple macroeconomic growth model is used to illustrate how some thermodynamic limitations may be integrated in macroeconomic theory
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
International Nuclear Information System (INIS)
Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.
2014-01-01
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases
Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping
Energy Technology Data Exchange (ETDEWEB)
Giovan, Stefan M. [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Scharein, Robert G. [Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada); Hanke, Andreas [Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States); Levene, Stephen D., E-mail: sdlevene@utdallas.edu [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Physics, University of Texas at Dallas, Richardson, Texas 75083 (United States)
2014-11-07
We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.
On thermodynamic and microscopic reversibility
International Nuclear Information System (INIS)
Crooks, Gavin E
2011-01-01
The word 'reversible' has two (apparently) distinct applications in statistical thermodynamics. A thermodynamically reversible process indicates an experimental protocol for which the entropy change is zero, whereas the principle of microscopic reversibility asserts that the probability of any trajectory of a system through phase space equals that of the time reversed trajectory. However, these two terms are actually synonymous: a thermodynamically reversible process is microscopically reversible, and vice versa
Mechanical breakdown in the nuclear multifragmentation phenomena. Thermodynamic analysis
International Nuclear Information System (INIS)
Bulavin, L.A.; Cherevko, K.V.; Sysoev, V.M.
2012-01-01
Based on a similarity of the Van der Waals and nucleon-nucleon interaction the known thermodynamic relations for ordinary liquids are used to analyze the possible decay channels in the proton induced nuclear multifragmentation phenomena. The main features of the different phase trajectories in the P-V plane are compared with the experimental data on multifragmentation. It allowed choosing the phase trajectories with the correct qualitative picture of the phenomena. Based on the thermodynamic analysis of the proton-induced multifragmentation phenomena the most appropriate decay channel corresponding to the realistic phase trajectory is chosen. Macroscopic analysis of the suggested decay channel is done in order to check the possibility of the mechanical breakdown of the heated system. Based on a simple thermodynamic model preliminary quantitative calculations of corresponding macroscopic parameters (energy, pressure) are done and therefore the model verification on macroscopic level is held. It is shown that on macroscopic level the chosen decay channel through the mechanical breakdown meets the necessary conditions for describing the proton-induced multifragmentation phenomena
QM/MM free energy simulations: recent progress and challenges
Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor
2016-01-01
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170
The effect of anisotropy on the thermodynamics of the interacting holographic dark energy model
Hossienkhani, H.; Jafari, A.; Fayaz, V.; Ramezani, A. H.
2018-02-01
By considering a holographic model for the dark energy in an anisotropic universe, the thermodynamics of a scheme of dark matter and dark energy interaction has been investigated. The results suggest that when holographic dark energy and dark matter evolve separately, each of them remains in thermodynamic equilibrium, therefore the interaction between them may be viewed as a stable thermal fluctuation that brings a logarithmic correction to the equilibrium entropy. Also the relation between the interaction term of the dark components and this thermal fluctuation has been obtained. Additionally, for a cosmological interaction as a free function, the anisotropy effects on the generalized second law of thermodynamics have been studied. By using the latest observational data on the holographic dark energy models as the unification of dark matter and dark energy, the observational constraints have been probed. To do this, we focus on observational determinations of the Hubble expansion rate H( z). Finally, we evaluate the anisotropy effects (although low) on various topics, such as the evolution of the statefinder diagnostic, the distance modulus and the spherical collapse from the holographic dark energy model and compare them with the results of the holographic dark energy of the Friedmann-Robertson-Walker and Λ CDM models.
Free energy landscape and molecular pathways of gas hydrate nucleation
Energy Technology Data Exchange (ETDEWEB)
Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Free energy landscape and molecular pathways of gas hydrate nucleation
International Nuclear Information System (INIS)
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-01-01
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
Free energy landscape and molecular pathways of gas hydrate nucleation.
Bi, Yuanfei; Porras, Anna; Li, Tianshu
2016-12-07
Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.
International Nuclear Information System (INIS)
Clausen, Lasse R.
2014-01-01
Integrated and external torrefaction is analyzed and compared via thermodynamic modeling. In this paper, integrated torrefaction is defined as torrefaction integrated with entrained flow gasification. External torrefaction is defined as the decentralized production of torrefied wood pellets and centralized conversion of the pellets by entrained flow gasification. First, the syngas production of the two methods was compared. Second, the two methods were compared by considering complete biorefineries with either integrated torrefaction or external torrefaction. The first part of the analysis showed that the biomass to syngas efficiency can be increased from 63% to 86% (LHV-dry) when switching from external torrefaction to integrated torrefaction. The second part of the analysis showed that the total energy efficiency (biomass to methanol + net electricity) could be increased from 53% to 63% when switching from external torrefaction to integrated torrefaction. The costs of this increase in energy efficiency are as follows: 1) more difficult transport, storage and handling of the biomass feedstock (wood chips vs. torrefied wood pellets); 2) reduced plant size; 3) no net electricity production; and 4) a more complex plant design. - Highlights: • Integrated torrefaction is compared with external torrefaction. • Biomass to syngas energy efficiencies of 63–86% are achieved. • Two thermochemical biorefinery are designed and analysed by thermodynamic modeling. • Biomass to fuel + electricity energy efficiencies of 53–63% are achieved. • The pros and cons of integrated torrefaction are described
Determination of partial molar volumes from free energy perturbation theory†
Vilseck, Jonah Z.; Tirado-Rives, Julian
2016-01-01
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343
Determination of partial molar volumes from free energy perturbation theory.
Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L
2015-04-07
Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.
Pollard, Travis P.; Beck, Thomas L.
2018-06-01
Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of -0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane.
Electrochemical thermodynamic measurement system
Reynier, Yvan [Meylan, FR; Yazami, Rachid [Los Angeles, CA; Fultz, Brent T [Pasadena, CA
2009-09-29
The present invention provides systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and electrochemical energy storage and conversion systems. Systems and methods of the present invention are configured for simultaneously collecting a suite of measurements characterizing a plurality of interconnected electrochemical and thermodynamic parameters relating to the electrode reaction state of advancement, voltage and temperature. Enhanced sensitivity provided by the present methods and systems combined with measurement conditions that reflect thermodynamically stabilized electrode conditions allow very accurate measurement of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and electrochemical systems, such as the energy, power density, current rate and the cycle life of an electrochemical cell.
International Nuclear Information System (INIS)
Wang, Jiangjiang; Wu, Jing; Xu, Zilong; Li, Meng
2017-01-01
Highlights: • Propose a fuel cell trigeneration system integrated with solar-assisted methanol reforming. • Optimize the reaction parameters of methanol steam reforming. • Present the energy and exergy analysis under design and off-design work conditions. • Analyze the contributions of solar energy to the trigeneration system. - Abstract: A solar-assisted trigeneration system for producing electricity, cooling, and heating simultaneously is an alternative scheme to improve energy efficiency and boost renewable energy. This paper proposes a phosphoric acid fuel cell trigeneration system integrated with methanol and steam reforming assisted by solar thermal energy. The trigeneration system consists of a solar heat collection subsystem, methanol steam reforming subsystem, fuel cell power generation subsystem, and recovered heat utilization subsystem. Their respective thermodynamic models are constructed to simulate the system input/output characteristics, and energy and exergy efficiencies are employed to evaluate the system thermodynamic performances. The contribution of solar energy to the system is analyzed using solar energy/exergy share. Through the simulation and analysis of methanol and steam reforming reactions, the optimal reaction pressure, temperature, and methanol to water ratio are obtained to improve the flow rate and content of produced hydrogen. The thermodynamic simulations of the trigeneration system show that the system energy efficiencies at the summer and winter design work conditions are 73.7% and 51.7%, while its exergy efficiencies are 18.8% and 26.1%, respectively. When the solar radiation intensity is different from the design work condition, the total energy and exergy efficiencies in winter decrease approximately by 4.7% and 2.2%, respectively, due to the decrease in solar heat collection efficiency. This proposed novel trigeneration system complemented by solar heat energy and methanol chemical energy is favorable for improving the
Simulated pressure denaturation thermodynamics of ubiquitin.
Ploetz, Elizabeth A; Smith, Paul E
2017-12-01
Simulations of protein thermodynamics are generally difficult to perform and provide limited information. It is desirable to increase the degree of detail provided by simulation and thereby the potential insight into the thermodynamic properties of proteins. In this study, we outline how to analyze simulation trajectories to decompose conformation-specific, parameter free, thermodynamically defined protein volumes into residue-based contributions. The total volumes are obtained using established methods from Fluctuation Solution Theory, while the volume decomposition is new and is performed using a simple proximity method. Native and fully extended ubiquitin are used as the test conformations. Changes in the protein volumes are then followed as a function of pressure, allowing for conformation-specific protein compressibility values to also be obtained. Residue volume and compressibility values indicate significant contributions to protein denaturation thermodynamics from nonpolar and coil residues, together with a general negative compressibility exhibited by acidic residues. Copyright © 2017 Elsevier B.V. All rights reserved.
The thermodynamics of direct air capture of carbon dioxide
International Nuclear Information System (INIS)
Lackner, Klaus S.
2013-01-01
An analysis of thermodynamic constraints shows that the low concentration of carbon dioxide in ambient air does not pose stringent limits on air capture economics. The thermodynamic energy requirement is small even using an irreversible sorbent-based process. A comparison to flue gas scrubbing suggests that the additional energy requirement is small and can be supplied with low-cost energy. In general, the free energy expended in the regeneration of a sorbent will exceed the free energy of mixing, as absorption is usually not reversible. The irreversibility, which grows with the depth of scrubbing, tends to affect flue gas scrubbing more than air capture which can successfully operate while extracting only a small fraction of the carbon dioxide available in air. This is reflected in a significantly lower theoretical thermodynamic efficiency for a single stage flue gas scrubber than for an air capture device, but low carbon dioxide concentration in air still results in a larger energy demand for air capture. The energy required for capturing carbon dioxide from air could be delivered in various ways. I analyze a thermal swing and also a previously described moisture swing which is driven by the evaporation of water. While the total amount of heat supplied for sorbent regeneration in a thermal swing, in accordance with Carnot's principle, exceeds the total free energy requirement, the additional free energy required as one moves from flue gas scrubbing to air capture can be paid with an amount of additional low grade heat that equals the additional free energy requirement. Carnot's principle remains satisfied because the entire heat supplied, not just the additional amount, must be delivered at a slightly higher temperature. Whether the system is driven by water evaporation or by low grade heat, the cost of the thermodynamically-required energy can be as small as $1 to $2 per metric ton of carbon dioxide. Thermodynamics does not pose a practical constraint on the
An asymptotic formula for the free energy density of ideal quantum gases
International Nuclear Information System (INIS)
Mackowiak, J.
1988-01-01
It is shown that the expressions for the free energy density of ideal quantum gases in the canonical and grand canonical ensembles, are identical up to additive terms which vanish in the thermodynamic limit. (orig.)
High Speed Solution of Spacecraft Trajectory Problems Using Taylor Series Integration
Scott, James R.; Martini, Michael C.
2008-01-01
Taylor series integration is implemented in a spacecraft trajectory analysis code-the Spacecraft N-body Analysis Program (SNAP) - and compared with the code s existing eighth-order Runge-Kutta Fehlberg time integration scheme. Nine trajectory problems, including near Earth, lunar, Mars and Europa missions, are analyzed. Head-to-head comparison at five different error tolerances shows that, on average, Taylor series is faster than Runge-Kutta Fehlberg by a factor of 15.8. Results further show that Taylor series has superior convergence properties. Taylor series integration proves that it can provide rapid, highly accurate solutions to spacecraft trajectory problems.
Thermodynamic Performance of Heat Exchangers in a Free Piston Stirling Engine
Directory of Open Access Journals (Sweden)
Ayodeji Sowale
2018-02-01
Full Text Available There is an increasing request in energy recovery systems that are more efficient, environmentally friendly and economical. The free piston Stirling engine has been investigated due to its structural simplicity and high efficiency, coupled with its cogeneration ability. This study presents the numerical investigation of quasi-steady model of a gamma type free piston Stirling engine (FPSE, including the thermodynamic analysis of the heat exchangers. Advanced thermodynamic models are employed to derive the initial set of operational parameters of the FPSE due to the coupling of the piston’s (displacer and piston dynamics and the working process. The proximity effect of the heater and cooler on the regenerator effectiveness in relation to the heat losses, output power, net work and thermal efficiency of the FPSE are also observed and presented in this study. It can be observed that at temperatures of 541.3 °C and 49.8 °C of the heater and cooler, respectively, with heater volume of 0.004 m3, regenerator volume of 0.003 m3 and cooler volume of 0.005 m3, the FPSE produced an output performance of 996.7 W with a thermal efficiency of 23% at a frequency of 30 Hz. This approach can be employed to design effective high performance FPSE due to their complexity and also predict a satisfactory performance.
Continuity of Integrated Density of States - Independent Randomness
Indian Academy of Sciences (India)
In this paper we discuss the continuity properties of the integrated density of states for random models based on that of the single site distribution. Our results are valid for models with independent randomness with arbitrary free parts. In particular in the case of the Anderson type models (with stationary, growing, decaying ...
Moustafa, Sabry Gad Al-Hak Mohammad
-derivative properties exceeds a millionfold for the highest density examined. In addition, the finite-size and long-range cutoff effects of the anharmonic contribution is much smaller than those due to harmonic part. Therefore, we were able to get the thermodynamic limit of thermodynamic properties by extrapolating the harmonic contribution to infinity and fix that with the anharmonic contribution from MS of small systems. Moreover, the anharmonic trajectory shows better features than the conventional one; it equilibrates almost instantaneously and data is less correlated (i.e. good statistics can be obtained with shorter trajectory). As a byproduct of the HMA, the free energy along an isochore is computed using thermodynamic integration (TI) technique of energy. Again, the HMA shows substantial improvement (50--1000 speedup) over the well-known Frenkel-Ladd integration (with Einstein crystal reference) method. Finally, to test the method against a more sophisticated model, we applied it to an embedded-atom-model (EAM) model of iron system. The results show a qualitatively similar behavior as that of LJ model. Finally, the method is applied to tackle one of the long-standing problems of Earth science; namely, the crystal structure of the Earth's inner core (IC). (Abstract shortened by UMI.).
Energy-efficient Trajectory Tracking for Mobile Devices
DEFF Research Database (Denmark)
Kjærgaard, Mikkel Baun; Bhattacharya, Sourav; Blunck, Henrik
2011-01-01
Emergent location-aware applications often require tracking trajectories of mobile devices over a long period of time. To be useful, the tracking has to be energy-efficient to avoid having a major impact on the battery life of the mobile de vice. Furthermore, when trajectory information needs to ...
CaFE: a tool for binding affinity prediction using end-point free energy methods.
Liu, Hui; Hou, Tingjun
2016-07-15
Accurate prediction of binding free energy is of particular importance to computational biology and structure-based drug design. Among those methods for binding affinity predictions, the end-point approaches, such as MM/PBSA and LIE, have been widely used because they can achieve a good balance between prediction accuracy and computational cost. Here we present an easy-to-use pipeline tool named Calculation of Free Energy (CaFE) to conduct MM/PBSA and LIE calculations. Powered by the VMD and NAMD programs, CaFE is able to handle numerous static coordinate and molecular dynamics trajectory file formats generated by different molecular simulation packages and supports various force field parameters. CaFE source code and documentation are freely available under the GNU General Public License via GitHub at https://github.com/huiliucode/cafe_plugin It is a VMD plugin written in Tcl and the usage is platform-independent. tingjunhou@zju.edu.cn. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Chaotic trajectories in the standard map. The concept of anti-integrability
Aubry, Serge; Abramovici, Gilles
1990-07-01
A rigorous proof is given in the standard map (associated with a Frenkel-Kontorowa model) for the existence of chaotic trajectories with unbounded momenta for large enough coupling constant k > k0. These chaotic trajectories (with finite entropy per site) are coded by integer sequences { mi} such that the sequence bi = |m i+1 + m i-1-2m i| be bounded by some integer b. The bound k0 in k depends on b and can be lowered for coding sequences { mi} fulfilling more restrictive conditions. The obtained chaotic trajectories correspond to stationary configurations of the Frenkel-Kontorowa model with a finite (non-zero) photon gap (called gap parameter in dimensionless units). This property implies that the trajectory (or the configuration { ui}) can be uniquely continued as a uniformly continuous function of the model parameter k in some neighborhood of the initial configuration. A non-zero gap parameter implies that the Lyapunov coefficient is strictly positive (when it is defined). In addition, the existence of dilating and contracting manifolds is proven for these chaotic trajectories. “Exotic” trajectories such as ballistic trajectories are also proven to exist as a consequence of these theorems. The concept of anti-integrability emerges from these theorems. In the anti-integrable limit which can be only defined for a discrete time dynamical system, the coordinates of the trajectory at time i do not depend on the coordinates at time i - 1. Thus, at this singular limit, the existence of chaotic trajectories is trivial and the dynamical system reduces to a Bernoulli shift. It is well known that the KAM tori of symplectic dynamical originates by continuity from the invariant tori which exists in the integrible limit (under certain conditions). In a similar way, it appears that the chaotic trajectories of dynamical systems originate by continuity from those which exists at the anti-integrable limits (also under certain conditions).
Thermodynamic basis for effective energy utilization
Energy Technology Data Exchange (ETDEWEB)
Rogers, J. T.
1977-10-15
A major difficulty in a quantitative assessment of effective energy utilization is that energy is always conserved (the First Law of Thermodynamics). However, the Second Law of Thermodynamics shows that, although energy cannot be destroyed, it can be degraded to a state in which it is of no further use for performing tasks. Thus, in considering the present world energy crisis, we are not really concerned with the conservation of energy but with the conservation of its ability to perform useful tasks. A measure of this ability is thermodynamic availability or, a less familiar term, exergy. In a real sense, we are concerned with an entropy-crisis, rather than an energy crisis. Analysis of energy processes on an exergy basis provides significantly different insights into the processes than those obtained from a conventional energy analysis. For example, process steam generation in an industrial boiler may appear quite efficient on the basis of a conventional analysis, but is shown to have very low effective use of energy when analyzed on an exergy basis. Applications of exergy analysis to other systems, such as large fossil and nuclear power stations, are discussed, and the benefits of extraction combined-purpose plants are demonstrated. Other examples of the application of the exergy concept in the industrial and residential energy sectors are also given. The concept is readily adaptable to economic optimization. Examples are given of economic optimization on an availability basis of an industrial heat exchanger and of a combined-purpose nuclear power and heavy-water production plant. Finally, the utility of the concept of exergy in assessing the energy requirements of an industrial society is discussed.
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.
Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
2018-01-01
Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.
Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations
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Federico Fogolari
2018-02-01
Full Text Available Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.
Qi, Xin; Fichthorn, Kristen A
2017-10-19
Though many experimental studies have documented that certain solution-phase additives can play a key role in the shape-selective synthesis of metal nanocrystals, the origins and mechanisms of this shape selectivity are still unclear. One possible role of such molecules is to thermodynamically induce the equilibrium shape of a nanocrystal by altering the interfacial free energies of the facets. Using a multi-scheme thermodynamic integration method that we recently developed [J. Chem. Phys., 2016, 145, 194108], we calculate the solid-liquid interfacial free energies γ sl and investigate the propensity to achieve equilibrium shapes in such syntheses. We first apply this method to Ag(100) and Ag(111) facets in ethylene glycol solution containing polyvinylpyrrolidone (PVP), to mimic the environment in polyol synthesis of Ag nanocrystals. We find that although PVP has a preferred binding to Ag(100), its selectivity is not sufficient to induce a thermodynamic preference for {100}-faceted nanocubes, as has been observed experimentally. This indicates that PVP promotes Ag nanocube formation kinetically rather than thermodynamically. We further quantify the thermodynamic influence of adsorbed solution-phase additives for generic molecules, by building a γ sl ratio/nanocrystal shape map as a function of zero-temperature binding energies. This map can be used to gauge the efficacy of candidate additive molecules for producing targeted thermodynamic nanocrystal shapes. The results indicate that only additives with a strong facet selectivity can impart significant thermodynamic-shape change. Therefore, many of the nanocrystals observed in experiments are likely kinetic products.
Pan, Albert C; Cuello, Luis G; Perozo, Eduardo; Roux, Benoît
2011-12-01
The amount of ionic current flowing through K(+) channels is determined by the interplay between two separate time-dependent processes: activation and inactivation gating. Activation is concerned with the stimulus-dependent opening of the main intracellular gate, whereas inactivation is a spontaneous conformational transition of the selectivity filter toward a nonconductive state occurring on a variety of timescales. A recent analysis of multiple x-ray structures of open and partially open KcsA channels revealed the mechanism by which movements of the inner activation gate, formed by the inner helices from the four subunits of the pore domain, bias the conformational changes at the selectivity filter toward a nonconductive inactivated state. This analysis highlighted the important role of Phe103, a residue located along the inner helix, near the hinge position associated with the opening of the intracellular gate. In the present study, we use free energy perturbation molecular dynamics simulations (FEP/MD) to quantitatively elucidate the thermodynamic basis for the coupling between the intracellular gate and the selectivity filter. The results of the FEP/MD calculations are in good agreement with experiments, and further analysis of the repulsive, van der Waals dispersive, and electrostatic free energy contributions reveals that the energetic basis underlying the absence of inactivation in the F103A mutation in KcsA is the absence of the unfavorable steric interaction occurring with the large Ile100 side chain in a neighboring subunit when the intracellular gate is open and the selectivity filter is in a conductive conformation. Macroscopic current analysis shows that the I100A mutant indeed relieves inactivation in KcsA, but to a lesser extent than the F103A mutant.
Integrating Computational Chemistry into a Course in Classical Thermodynamics
Martini, Sheridan R.; Hartzell, Cynthia J.
2015-01-01
Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…
A novel constraint for thermodynamically designing DNA sequences.
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Qiang Zhang
Full Text Available Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap.
RNA Thermodynamic Structural Entropy.
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Juan Antonio Garcia-Martin
Full Text Available Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs. However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http
RNA Thermodynamic Structural Entropy.
Garcia-Martin, Juan Antonio; Clote, Peter
2015-01-01
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http
Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom
2018-01-09
We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.
Free energy of mixing of acetone and methanol: a computer simulation investigation.
Idrissi, Abdenacer; Polok, Kamil; Barj, Mohammed; Marekha, Bogdan; Kiselev, Mikhail; Jedlovszky, Pál
2013-12-19
The change of the Helmholtz free energy, internal energy, and entropy accompanying the mixing of acetone and methanol is calculated in the entire composition range by the method of thermodynamic integration using three different potential model combinations of the two compounds. In the first system, both molecules are described by the OPLS, and in the second system, both molecules are described by the original TraPPE force field, whereas in the third system a modified version of the TraPPE potential is used for acetone in combination with the original TraPPE model of methanol. The results reveal that, in contrast with the acetone-water system, all of these three model combinations are able to reproduce the full miscibility of acetone and methanol, although the thermodynamic driving force of this mixing is very small. It is also seen, in accordance with the finding of former structural analyses, that the mixing of the two components is driven by the entropy term corresponding to the ideal mixing, which is large enough to overcompensate the effect of the energy increase and entropy loss due to the interaction of the unlike components in the mixtures. Among the three model combinations, the use of the original TraPPE model of methanol and modified TraPPE model of acetone turns out to be clearly the best in this respect, as it is able to reproduce the experimental free energy, internal energy, and entropy of mixing values within 0.15 kJ/mol, 0.2 kJ/mol, and 1 J/(mol K), respectively, in the entire composition range. The success of this model combination originates from the fact that the use of the modified TraPPE model of acetone instead of the original one in these mixtures improves the reproduction of the entropy of mixing, while it retains the ability of the original model of excellently reproducing the internal energy of mixing.
International Nuclear Information System (INIS)
Araoz, Joseph A.; Salomon, Marianne; Alejo, Lucio; Fransson, Torsten H.
2014-01-01
The reliability of modelling and simulation of energy systems strongly depends on the prediction accuracy of each system component. This is the case of Stirling engine-based systems, where an accurate modelling of the engine performance is very important to understand the overall system behaviour. In this sense, many Stirling engine analyses with different approaches have been already developed. However, there is a lack of Stirling engine models suitable for the integration into overall system simulations. In this context, this paper aims to develop a rigorous Stirling engine model that could be easily integrated into combined heat and power schemes for the overall techno-economic analysis of these systems. The model developed considers a Stirling engine with adiabatic working spaces, isothermal heat exchangers, dead volumes, and imperfect regeneration. Additionally, it considers mechanical pumping losses due to friction, limited heat transfer and thermal losses on the heat exchangers. The model is suitable for different engine configurations (alpha beta and gamma engines). It was developed using Aspen Custom Modeller ® (ACM®) as modelling software. The set of equations were solved using ACM ® equation solver for steady-state operation. However, due to the dynamic behaviour of the cycle, a C++ code was integrated to solve iteratively a set of differential equations. This resulted in a cyclic steady-state model that calculates the power output and thermal requirements of the system. The predicted efficiency and power output were compared with the numerical model and the experimental work reported by the NASA Lewis Research Centre for the GPU-3 Stirling engine. This showed average absolute errors around ±4% for the brake power, and ±5% for the brake efficiency at different frequencies. However, the model also showed large errors (±15%) for these calculations at higher frequencies and low pressures. Additional results include the calculation of the cyclic
Thermodynamics of 2D string theory
International Nuclear Information System (INIS)
Alexandrov, Sergei Yu.; V.A. Fock Department of Theoretical Physics, St. Petersburg University
2003-01-01
We calculate the free energy, energy and entropy in the matrix quantum mechanical formulation of 2D string theory in a background strongly perturbed by tachyons with the imaginary minkowskian momentum ±i/R ('Sine-Liouville' theory). The system shows a thermodynamical behaviour corresponding to the temperature T={1/(2π R)}. We show that the microscopically calculated energy of the system satisfies the usual thermodynamical relations and leads to a non-zero entropy. (author)
Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide
Cohen, Samuel I. A.; Cukalevski, Risto; Michaels, Thomas C. T.; Šarić, Andela; Törnquist, Mattias; Vendruscolo, Michele; Dobson, Christopher M.; Buell, Alexander K.; Knowles, Tuomas P. J.; Linse, Sara
2018-05-01
Mapping free-energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in a range of disorders. Here, we generalize the strategy used to probe free-energy landscapes in protein folding to determine the activation energies and entropies that characterize each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer's disease. Our results reveal that interactions between monomeric Aβ42 and amyloid fibrils during fibril-dependent secondary nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reaction trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilization of adsorbing peptides in conformations amenable to nucleation, resulting in a dramatic lowering of the activation energy for nucleation.
Thermodynamics of adaptive molecular resolution.
Delgado-Buscalioni, R
2016-11-13
A relatively general thermodynamic formalism for adaptive molecular resolution (AMR) is presented. The description is based on the approximation of local thermodynamic equilibrium and considers the alchemic parameter λ as the conjugate variable of the potential energy difference between the atomistic and coarse-grained model Φ=U (1) -U (0) The thermodynamic formalism recovers the relations obtained from statistical mechanics of H-AdResS (Español et al, J. Chem. Phys. 142, 064115, 2015 (doi:10.1063/1.4907006)) and provides relations between the free energy compensation and thermodynamic potentials. Inspired by this thermodynamic analogy, several generalizations of AMR are proposed, such as the exploration of new Maxwell relations and how to treat λ and Φ as 'real' thermodynamic variablesThis article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).
Bryce, Richard A
2011-04-01
The ability to accurately predict the interaction of a ligand with its receptor is a key limitation in computer-aided drug design approaches such as virtual screening and de novo design. In this article, we examine current strategies for a physics-based approach to scoring of protein-ligand affinity, as well as outlining recent developments in force fields and quantum chemical techniques. We also consider advances in the development and application of simulation-based free energy methods to study protein-ligand interactions. Fuelled by recent advances in computational algorithms and hardware, there is the opportunity for increased integration of physics-based scoring approaches at earlier stages in computationally guided drug discovery. Specifically, we envisage increased use of implicit solvent models and simulation-based scoring methods as tools for computing the affinities of large virtual ligand libraries. Approaches based on end point simulations and reference potentials allow the application of more advanced potential energy functions to prediction of protein-ligand binding affinities. Comprehensive evaluation of polarizable force fields and quantum mechanical (QM)/molecular mechanical and QM methods in scoring of protein-ligand interactions is required, particularly in their ability to address challenging targets such as metalloproteins and other proteins that make highly polar interactions. Finally, we anticipate increasingly quantitative free energy perturbation and thermodynamic integration methods that are practical for optimization of hits obtained from screened ligand libraries.
Martyushev, Leonid M.
2018-03-01
The paper [1] is certainly very useful and important for understanding living systems (e.g. brain) as adaptive, self-organizing patterns. There is no need to enumerate all advantages of the paper, they are obvious. The purpose of my brief comment is to discuss one issue which, as I see it, was not thought out by the authors well enough. As a consequence, their ideas do not find as wide distribution as they otherwise could have found. This issue is related to the name selected for the principle forming the basis of their approach: free-energy principle (FEP). According to the sec. 2.1 [1]: "It asserts that all biological systems maintain their integrity by actively reducing the disorder or dispersion (i.e., entropy) of their sensory and physiological states by minimizing their variational free energy." Let us note that the authors suggested different names for the principle in their earlier works (an objective function, a function of the ensemble density encoded by the organism's configuration and the sensory data to which it is exposed, etc.), and explicitly and correctly mentioned that the free energy and entropy considered by them had nothing in common with the quantities employed in physics [2,3]. It is also obvious that a purely information-theoretic approach used by the authors with regard to the problems under study allows many other wordings and interpretations. However, in spite of this fact, in their last papers as well as in the present paper, the authors choose specifically FEP. Apparently, it may be explained by the intent to additionally base their approach on the foundation of statistical thermodynamics and therefore to demonstrate the universality of the described method. However, this is exactly what might cause misunderstandings specifically among physicists and consequently in their rejection and ignoring of FEP. The physical analogy employed by the authors has the following fundamental inconsistencies: In physics, free energy is used to describe
Post-flight trajectory reconstruction of suborbital free-flyers using GPS raw data
Ivchenko, N.; Yuan, Y.; Linden, E.
2017-08-01
This paper describes the reconstruction of postflight trajectories of suborbital free flying units by using logged GPS raw data. We took the reconstruction as a global least squares optimization problem, using both the pseudo-range and Doppler observables, and solved it by using the trust-region-reflective algorithm, which enabled navigational solutions of high accuracy. The code tracking was implemented with a large number of correlators and least squares curve fitting, in order to improve the precision of the code start times, while a more conventional phased lock loop was used for Doppler tracking. We proposed a weighting scheme to account for fast signal strength variation due to free-flier fast rotation, and a penalty for jerk to achieve a smooth solution. We applied these methods to flight data of two suborbital free flying units launched on REXUS 12 sounding rocket, reconstructing the trajectory, receiver clock error and wind up rates. The trajectory exhibits a parabola with the apogee around 80 km, and the velocity profile shows the details of payloadwobbling. The wind up rates obtained match the measurements from onboard angular rate sensors.
Post-flight trajectory reconstruction of suborbital free-flyers using GPS raw data
Directory of Open Access Journals (Sweden)
Ivchenko N.
2017-08-01
Full Text Available This paper describes the reconstruction of postflight trajectories of suborbital free flying units by using logged GPS raw data. We took the reconstruction as a global least squares optimization problem, using both the pseudo-range and Doppler observables, and solved it by using the trust-region-reflective algorithm, which enabled navigational solutions of high accuracy. The code tracking was implemented with a large number of correlators and least squares curve fitting, in order to improve the precision of the code start times, while a more conventional phased lock loop was used for Doppler tracking. We proposed a weighting scheme to account for fast signal strength variation due to free-flier fast rotation, and a penalty for jerk to achieve a smooth solution. We applied these methods to flight data of two suborbital free flying units launched on REXUS 12 sounding rocket, reconstructing the trajectory, receiver clock error and wind up rates. The trajectory exhibits a parabola with the apogee around 80 km, and the velocity profile shows the details of payloadwobbling. The wind up rates obtained match the measurements from onboard angular rate sensors.
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
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Klipp Edda
2006-12-01
Full Text Available Abstract Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases.
International Nuclear Information System (INIS)
Schwenke, G.K.
2001-01-01
The thermodynamics of the quaternary hydrogen-carbon oxygen-tungsten system and its binary and ternary sub-systems are reviewed. Published thermodynamic data are evaluated, and expression for free energies of formation are chosen. These expressions are integrated with and equilibrium-calculating algorithm, producing a powerful tool for understanding and improving the manufacture of tungsten and tungsten carbide. Three examples are presented: reduction/carburization of tungstic oxide with hydrogen, carbon, and methane. (author)
Uncertainty Quantification in Alchemical Free Energy Methods.
Bhati, Agastya P; Wan, Shunzhou; Hu, Yuan; Sherborne, Brad; Coveney, Peter V
2018-05-02
Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.
Thermodynamic assessment of integrated biogas-based micro-power generation system
International Nuclear Information System (INIS)
Hosseini, Seyed Ehsan; Barzegaravval, Hasan; Wahid, Mazlan Abdul; Ganjehkaviri, Abdolsaeid; Sies, Mohsin Mohd
2016-01-01
Highlights: • A thermodynamic modelling of an integrated biogas-based micro-power generation system is reported. • The impact of design parameters on the thermodynamic performance of the system is evaluated. • High turbine inlet temperatures lead the system to the higher energy and exergy efficiency and higher power generation. • Enhancement of GT isentropic efficiency incurs negative effects on the performance of air preheater and heat exchanger. • The rate of power generation increases by the enhancement of steam turbine pressure in ORC. - Abstract: In this paper, a thermodynamic modelling of an integrated biogas (60%CH_4 + 40%CO_2) micro-power generation system for electricity generation is reported. This system involves a gas turbine cycle and organic Rankine cycle (ORC) where the wasted heat of gas turbine cycle is recovered by closed ORC. The net output power of the micro-power generation system is fixed at 1.4 MW includes 1 MW power generated by GT and 0.4 MW by ORC. Energy and exergy assessments and related parametric studies are carried out, and parameters that influence on energy and exergy efficiency are evaluated. The performance of the system with respect to variation of design parameters such as combustion air inlet temperature, turbine inlet temperature, compressor pressure ratio, gas turbine isentropic efficiency and compressor isentropic efficiency (from the top cycle) and steam turbine inlet pressure, and condenser pressure (from bottoming cycle) is evaluated. The results reveal that by the increase of gas turbine isentropic efficiency, the outlet temperature of gas turbine decreases which incurs negative impacts on the performance of air preheater and heat exchanger, however the energy and exergy efficiency increases in the whole system. By the increase of air compressor pressure ratio, the energy and exergy of the combined cycle decreases. The exergy efficiency of ORC alters by the variation of gas turbine parameters which can be
Thermodynamics of Inozemtsev's elliptic spin chain
International Nuclear Information System (INIS)
Klabbers, Rob
2016-01-01
We study the thermodynamic behaviour of Inozemtsev's long-range elliptic spin chain using the Bethe ansatz equations describing the spectrum of the model in the infinite-length limit. We classify all solutions of these equations in that limit and argue which of these solutions determine the spectrum in the thermodynamic limit. Interestingly, some of the solutions are not selfconjugate, which puts the model in sharp contrast to one of the model's limiting cases, the Heisenberg XXX spin chain. Invoking the string hypothesis we derive the thermodynamic Bethe ansatz equations (TBA-equations) from which we determine the Helmholtz free energy in thermodynamic equilibrium and derive the associated Y-system. We corroborate our results by comparing numerical solutions of the TBA-equations to a direct computation of the free energy for the finite-length hamiltonian. In addition we confirm numerically the interesting conjecture put forward by Finkel and González-López that the original and supersymmetric versions of Inozemtsev's elliptic spin chain are equivalent in the thermodynamic limit.
Thermodynamical motivation of the Polish energy policy
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Ziębik Andrzej
2013-02-01
Full Text Available Basing on the first and second law of thermodynamics the fundamental trends in the Polish energy policy are analysed, including the aspects of environmental protection. The thermodynamical improvement of real processes (reduction of exergy losses is the main way leading to an improvement of the effectivity of energy consumption. If the exergy loss is economically not justified, we have to do with an error from the viewpoint of the second law analysis. The paper contains a thermodynamical analysis of the ratio of final and primary energy, as well as the analysis of the thermo-ecological cost and index of sustainable development concerning primary energy. Analyses of thermo-ecological costs concerning electricity and centralized heat production have been also carried out. The effect of increasing the share of high-efficiency cogeneration has been analyzed, too. Attention has been paid to an improved efficiency of the transmission and distribution of electricity, which is of special importance from the viewpoint of the second law analysis. The improvement of the energy effectivity in industry was analyzed on the example of physical recuperation, being of special importance from the point of view of exergy analysis.
Niu, Gang; Capellini, Giovanni; Schubert, Markus Andreas; Niermann, Tore; Zaumseil, Peter; Katzer, Jens; Krause, Hans-Michael; Skibitzki, Oliver; Lehmann, Michael; Xie, Ya-Hong; von Känel, Hans; Schroeder, Thomas
2016-03-04
The integration of dislocation-free Ge nano-islands was realized via selective molecular beam epitaxy on Si nano-tip patterned substrates. The Si-tip wafers feature a rectangular array of nanometer sized Si tips with (001) facet exposed among a SiO2 matrix. These wafers were fabricated by complementary metal-oxide-semiconductor (CMOS) compatible nanotechnology. Calculations based on nucleation theory predict that the selective growth occurs close to thermodynamic equilibrium, where condensation of Ge adatoms on SiO2 is disfavored due to the extremely short re-evaporation time and diffusion length. The growth selectivity is ensured by the desorption-limited growth regime leading to the observed pattern independence, i.e. the absence of loading effect commonly encountered in chemical vapor deposition. The growth condition of high temperature and low deposition rate is responsible for the observed high crystalline quality of the Ge islands which is also associated with negligible Si-Ge intermixing owing to geometric hindrance by the Si nano-tip approach. Single island as well as area-averaged characterization methods demonstrate that Ge islands are dislocation-free and heteroepitaxial strain is fully relaxed. Such well-ordered high quality Ge islands present a step towards the achievement of materials suitable for optical applications.
Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.
Iida, Shinji; Nakamura, Haruki; Higo, Junichi
2016-06-15
We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).
Linking landscape structure and rainfall runoff behaviour in a thermodynamic optimality context
Zehe, Erwin; Ehret, Uwe; Blume, Theresa; Kleidon, Axel; Scherer, Ulrike; Westhoff, Martijn
2015-04-01
gradients, and thus a faster relaxation back towards local thermodynamic equilibrium. Thermodynamic optimality principles allow for a priory optimization of the resistance field at a given gradient, not in the sense how they exactly look like but in the sense how they function with respect to export and dissipation of free energy associated with rainfall runoff processes. Based on this framework we explored the possibility of independent predictions of rainfall runoff, in the sense that the a-priory optimum model structures should match independent observations. We found that spatially organized patterns of soils and macropores observed in two distinctly different landscapes are in close accordance with thermodynamic optima expressed either by minimized relaxation times towards local thermodynamic equilibrium in cohesive soils or as steady state in the potential energy of soil water in non-cohesive soils. Predicted rainfall runoff based on the two optimized model structures was in both catchments in acceptable accordance with independent discharge observations. However, the nature of these optima suggests there might be two distinctly different thermodynamically optimal regimes of rainfall runoff behaviour. In the capillary- or c--regime, free energy dynamics of soil water is dominated by changes in its capillary binding energy, which is the case for cohesive soils. Soil wetting during rainfall in the c-regime implies pushing the system back towards LTE, especially after long dry spells. Dead ended macropores (roots, worm burrows which end in the soil matrix) act as dissipative wetting structures by enlarging water flows against steep gradients in soil water potential after long dry spells. This implies accelerated depletion of these gradients and faster relaxation back towards LTE during rainfall runoff. In the c-regime several optimum macropore densities with respect to maximization of net reduction of free energy exist. This is because the governing equation is a second
Coupled thermodynamic-dynamic semi-analytical model of free piston Stirling engines
Energy Technology Data Exchange (ETDEWEB)
Formosa, F., E-mail: fabien.formosa@univ-savoie.f [Laboratoire SYMME, Universite de Savoie, BP 80439, 74944 Annecy le Vieux Cedex (France)
2011-05-15
Research highlights: {yields} The free piston Stirling behaviour relies on its thermal and dynamic features. {yields} A global semi-analytical model for preliminary design is developed. {yields} The model compared with NASA-RE1000 experimental data shows good correlations. -- Abstract: The study of free piston Stirling engine (FPSE) requires both accurate thermodynamic and dynamic modelling to predict its performances. The steady state behaviour of the engine partly relies on non linear dissipative phenomena such as pressure drop loss within heat exchangers which is dependant on the temperature within the associated components. An analytical thermodynamic model which encompasses the effectiveness and the flaws of the heat exchangers and the regenerator has been previously developed and validated. A semi-analytical dynamic model of FPSE is developed and presented in this paper. The thermodynamic model is used to define the thermal variables that are used in the dynamic model which evaluates the kinematic results. Thus, a coupled iterative strategy has been used to perform a global simulation. The global modelling approach has been validated using the experimental data available from the NASA RE-1000 Stirling engine prototype. The resulting coupled thermodynamic-dynamic model using a standardized description of the engine allows efficient and realistic preliminary design of FPSE.
Coupled thermodynamic-dynamic semi-analytical model of free piston Stirling engines
International Nuclear Information System (INIS)
Formosa, F.
2011-01-01
Research highlights: → The free piston Stirling behaviour relies on its thermal and dynamic features. → A global semi-analytical model for preliminary design is developed. → The model compared with NASA-RE1000 experimental data shows good correlations. -- Abstract: The study of free piston Stirling engine (FPSE) requires both accurate thermodynamic and dynamic modelling to predict its performances. The steady state behaviour of the engine partly relies on non linear dissipative phenomena such as pressure drop loss within heat exchangers which is dependant on the temperature within the associated components. An analytical thermodynamic model which encompasses the effectiveness and the flaws of the heat exchangers and the regenerator has been previously developed and validated. A semi-analytical dynamic model of FPSE is developed and presented in this paper. The thermodynamic model is used to define the thermal variables that are used in the dynamic model which evaluates the kinematic results. Thus, a coupled iterative strategy has been used to perform a global simulation. The global modelling approach has been validated using the experimental data available from the NASA RE-1000 Stirling engine prototype. The resulting coupled thermodynamic-dynamic model using a standardized description of the engine allows efficient and realistic preliminary design of FPSE.
Sidler, Dominik; Schwaninger, Arthur; Riniker, Sereina
2016-10-21
In molecular dynamics (MD) simulations, free-energy differences are often calculated using free energy perturbation or thermodynamic integration (TI) methods. However, both techniques are only suited to calculate free-energy differences between two end states. Enveloping distribution sampling (EDS) presents an attractive alternative that allows to calculate multiple free-energy differences in a single simulation. In EDS, a reference state is simulated which "envelopes" the end states. The challenge of this methodology is the determination of optimal reference-state parameters to ensure equal sampling of all end states. Currently, the automatic determination of the reference-state parameters for multiple end states is an unsolved issue that limits the application of the methodology. To resolve this, we have generalised the replica-exchange EDS (RE-EDS) approach, introduced by Lee et al. [J. Chem. Theory Comput. 10, 2738 (2014)] for constant-pH MD simulations. By exchanging configurations between replicas with different reference-state parameters, the complexity of the parameter-choice problem can be substantially reduced. A new robust scheme to estimate the reference-state parameters from a short initial RE-EDS simulation with default parameters was developed, which allowed the calculation of 36 free-energy differences between nine small-molecule inhibitors of phenylethanolamine N-methyltransferase from a single simulation. The resulting free-energy differences were in excellent agreement with values obtained previously by TI and two-state EDS simulations.
Application of a linear free energy relationship to crystalline solids of MO2 and M(OH)4
International Nuclear Information System (INIS)
Xu Huifang; Barton, L.L.
1999-01-01
In this letter, a linear free energy relationship developed by Sverjensky and Molling is used to predict the Gibbs free energies of formation of crystalline phases of M 4+ O 2 and M 4+ (OH) 4 from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The modified Sverjensky and Molling equation for tetravalent cations is expressed as ΔG 0 f,M v X = a M v X ΔG 0 n,M 4+ + b M v X + β M v X r M 4+ , where the coefficients a M v X , b M v X and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG 0 f,M v X is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 4+ is the standard non-solvation energy of cation M 4+ . By fitting the equation to the existing thermodynamic data, the coefficients in the equation for the MO 2 family minerals are estimated to be: a M v X = 0.670, β M v X = 32 (kcal/mol A), and b = -430.02 (kcal/mol). The constrained relationship can be used to predict the standard Gibbs free energies of formation of crystalline phases and fictive phases (i.e., phases which are thermodynamically unstable and do not occur at standard conditions) within the isostructural families of M 4+ O 2 and M 4+ (OH) 4 if the standard Gibbs free energies of formation of the tetravalent cations are known. (orig.)
OPTIMAL AIRCRAFT TRAJECTORIES FOR SPECIFIED RANGE
Lee, H.
1994-01-01
For an aircraft operating over a fixed range, the operating costs are basically a sum of fuel cost and time cost. While minimum fuel and minimum time trajectories are relatively easy to calculate, the determination of a minimum cost trajectory can be a complex undertaking. This computer program was developed to optimize trajectories with respect to a cost function based on a weighted sum of fuel cost and time cost. As a research tool, the program could be used to study various characteristics of optimum trajectories and their comparison to standard trajectories. It might also be used to generate a model for the development of an airborne trajectory optimization system. The program could be incorporated into an airline flight planning system, with optimum flight plans determined at takeoff time for the prevailing flight conditions. The use of trajectory optimization could significantly reduce the cost for a given aircraft mission. The algorithm incorporated in the program assumes that a trajectory consists of climb, cruise, and descent segments. The optimization of each segment is not done independently, as in classical procedures, but is performed in a manner which accounts for interaction between the segments. This is accomplished by the application of optimal control theory. The climb and descent profiles are generated by integrating a set of kinematic and dynamic equations, where the total energy of the aircraft is the independent variable. At each energy level of the climb and descent profiles, the air speed and power setting necessary for an optimal trajectory are determined. The variational Hamiltonian of the problem consists of the rate of change of cost with respect to total energy and a term dependent on the adjoint variable, which is identical to the optimum cruise cost at a specified altitude. This variable uniquely specifies the optimal cruise energy, cruise altitude, cruise Mach number, and, indirectly, the climb and descent profiles. If the optimum
Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge
Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.
2016-01-01
Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749
Mass-independent area (or entropy) and thermodynamic volume products in conformal gravity
Pradhan, Parthapratim
2017-06-01
In this work, we investigate the thermodynamic properties of conformal gravity in four dimensions. We compute the area (or entropy) functional relation for this black hole (BH). We consider both de Sitter (dS) and anti-de Sitter (AdS) cases. We derive the Cosmic-Censorship-Inequality which is an important relation in general relativity that relates the total mass of a spacetime to the area of all the BH horizons. Local thermodynamic stability is studied by computing the specific heat. The second-order phase transition occurs at a certain condition. Various types of second-order phase structure have been given for various values of a and the cosmological constant Λ in the Appendix. When a = 0, one obtains the result of Schwarzschild-dS and Schwarzschild-AdS cases. In the limit aM ≪ 1, one obtains the result of Grumiller spacetime, where a is nontrivial Rindler parameter or Rindler acceleration and M is the mass parameter. The thermodynamic volume functional relation is derived in the extended phase space, where the cosmological constant is treated as a thermodynamic pressure and its conjugate variable as a thermodynamic volume. The mass-independent area (or entropy) functional relation and thermodynamic volume functional relation that we have derived could turn out to be a universal quantity.
Partitioning a macroscopic system into independent subsystems
Delle Site, Luigi; Ciccotti, Giovanni; Hartmann, Carsten
2017-08-01
We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several fields of theoretical and applied physics. The thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e. particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.
Thermodynamically self-consistent integral equations and the structure of liquid metals
International Nuclear Information System (INIS)
Pastore, G.; Kahl, G.
1987-01-01
We discuss the application of the new thermodynamically self-consistent integral equations for the determination of the structural properties of liquid metals. We present a detailed comparison of the structure (S(q) and g(r)) for models of liquid alkali metals as obtained from two thermodynamically self-consistent integral equations and some published exact computer simulation results; the range of states extends from the triple point to the expanded metal. The theories which only impose thermodynamic self-consistency without any fitting of external data show an excellent agreement with the simulation results, thus demonstrating that this new type of integral equation is definitely superior to the conventional ones (hypernetted chain, Percus-Yevick, mean spherical approximation, etc). (author)
Stochastic thermodynamics, fluctuation theorems and molecular machines
International Nuclear Information System (INIS)
Seifert, Udo
2012-01-01
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (review article)
Thermodynamic activity measurements of U-Zr alloys by Knudsen effusion mass spectrometry
International Nuclear Information System (INIS)
Kanno, Masayoshi; Yamawaki, Michio; Koyama, Tadafumi; Morioka, Nobuo
1988-01-01
Vaporization of a series of U-Zr alloys, a fundamental subsystem of the promising metallic fuel U-Pu-Zr, was studied by using a tantalum Knudsen cell coupled with a mass spectrometer in the temperature range 1700-2060 K. Thermodynamic activities partial molar Gibbs free energies and integral molar Gibbs free energies of mixing were calculated from the partial vapor pressures of uranium over these alloys. The activities of uranium exhibit negative deviations from ideality, especially in the uranium-rich composition region. Both the solidus and liquidus lines for this system estimated from the activities show negative deviations from the tentative phase diagram previously reported. (orig.)
Thermodynamic analysis of a pulse tube engine
International Nuclear Information System (INIS)
Moldenhauer, Stefan; Thess, André; Holtmann, Christoph; Fernández-Aballí, Carlos
2013-01-01
Highlights: ► Numerical model of the pulse tube engine process. ► Proof that the heat transfer in the pulse tube is out of phase with the gas velocity. ► Proof that a free piston operation is possible. ► Clarifying the thermodynamic working principle of the pulse tube engine. ► Studying the influence of design parameters on the engine performance. - Abstract: The pulse tube engine is an innovative simple heat engine based on the pulse tube process used in cryogenic cooling applications. The working principle involves the conversion of applied heat energy into mechanical power, thereby enabling it to be used for electrical power generation. Furthermore, this device offers an opportunity for its wide use in energy harvesting and waste heat recovery. A numerical model has been developed to study the thermodynamic cycle and thereby help to design an experimental engine. Using the object-oriented modeling language Modelica, the engine was divided into components on which the conservation equations for mass, momentum and energy were applied. These components were linked via exchanged mass and enthalpy. The resulting differential equations for the thermodynamic properties were integrated numerically. The model was validated using the measured performance of a pulse tube engine. The transient behavior of the pulse tube engine’s underlying thermodynamic properties could be evaluated and studied under different operating conditions. The model was used to explore the pulse tube engine process and investigate the influence of design parameters.
Life, hierarchy, and the thermodynamic machinery of planet Earth.
Kleidon, Axel
2010-12-01
Throughout Earth's history, life has increased greatly in abundance, complexity, and diversity. At the same time, it has substantially altered the Earth's environment, evolving some of its variables to states further and further away from thermodynamic equilibrium. For instance, concentrations in atmospheric oxygen have increased throughout Earth's history, resulting in an increased chemical disequilibrium in the atmosphere as well as an increased redox gradient between the atmosphere and the Earth's reducing crust. These trends seem to contradict the second law of thermodynamics, which states for isolated systems that gradients and free energy are dissipated over time, resulting in a state of thermodynamic equilibrium. This seeming contradiction is resolved by considering planet Earth as a coupled, hierarchical and evolving non-equilibrium thermodynamic system that has been substantially altered by the input of free energy generated by photosynthetic life. Here, I present this hierarchical thermodynamic theory of the Earth system. I first present simple considerations to show that thermodynamic variables are driven away from a state of thermodynamic equilibrium by the transfer of power from some other process and that the resulting state of disequilibrium reflects the past net work done on the variable. This is applied to the processes of planet Earth to characterize the generation and transfer of free energy and its dissipation, from radiative gradients to temperature and chemical potential gradients that result in chemical, kinetic, and potential free energy and associated dynamics of the climate system and geochemical cycles. The maximization of power transfer among the processes within this hierarchy yields thermodynamic efficiencies much lower than the Carnot efficiency of equilibrium thermodynamics and is closely related to the proposed principle of Maximum Entropy Production (MEP). The role of life is then discussed as a photochemical process that generates
Thermodynamic performance assessment of wind energy systems: An application
International Nuclear Information System (INIS)
Redha, Adel Mohammed; Dincer, Ibrahim; Gadalla, Mohamed
2011-01-01
In this paper, the performance of wind energy system is assessed thermodynamically, from resource and technology perspectives. The thermodynamic characteristics of wind through energy and exergy analyses are considered and both energetic and exergetic efficiencies are studied. Wind speed is affected by air temperature and pressure and has a subsequent effect on wind turbine performance based on wind reference temperature and Bernoulli's equation. VESTAS V52 wind turbine is selected for (Sharjah/UAE). Energy and exergy efficiency equations for wind energy systems are further developed for practical applications. The results show that there are noticeable differences between energy and exergy efficiencies and that exergetic efficiency reflects the right/actual performance. Finally, exergy analysis has been proven to be the right tool used in design, simulation, and performance evaluation of all renewable energy systems. -- Highlights: → In this research the performance of wind energy system is assessed thermodynamically, from resource and technology perspectives. → Energy and exergy equations for wind energy systems are further developed for practical applications. → Thermodynamic characteristics of wind turbine systems through energetic and exergetic efficiencies are evaluated from January till March 2010. → Exergy efficiency describes the system irreversibility and the minimum irreversibility exists when the wind speed reaches 11 m/s. → The power production during March was about 17% higher than the month of February and 66% higher than January.
Thermodynamical properties of liquid lanthanides-A variational approach
Energy Technology Data Exchange (ETDEWEB)
Patel, H. P. [Department of Physics, Veer Narmad South Gujarat University, Surat 395 007, Gujarat (India); Department of Applied Physics, S. V. National Institute of Technology, Surat 395 007, Gujarat (India); Thakor, P. B., E-mail: pbthakor@rediffmail.com [Department of Physics, Veer Narmad South Gujarat University, Surat 395 007, Gujarat (India); Sonvane, Y. A. [Department of Applied Physics, S. V. National Institute of Technology, Surat 395 007, Gujarat (India)
2015-06-24
Thermodynamical properties like Entropy (S), Internal energy (E) and Helmholtz free energy (F) of liquid lanthanides using a variation principle based on the Gibbs-Bogoliubuv (GB) inequality with Percus Yevick hard sphere reference system have been reported in the present investigation. To describe electron-ion interaction we have used our newly constructed parameter free model potential along with Sarkar et al. local field correction function. Lastly, we conclude that our newly constructed model potential is capable to explain the thermodynamical properties of liquid lanthanides.
International Nuclear Information System (INIS)
El-Emam, Rami Salah; Dincer, Ibrahim
2014-01-01
This paper investigates the performance of a RO (reverse osmosis) desalination plant at different seawater salinity values. An energy recovery Pelton turbine is integrated with the desalination plant. Thermodynamic analysis, based on the first and second laws of thermodynamics, as well as a thermo-based economic analysis is performed for the proposed system. The effects of the system components irreversibilities on the economics and cost of product water are parametrically studied through the thermoeconomic analysis. The exergy analysis shows that large irreversibilities occur in the high pressure pump and in the RO module. Both thermodynamic and thermoeconomic performances of the overall system are investigated under different operating parameters. For the base case; the system achieves an exergy efficiency of 5.82%. The product cost is estimated to be 2.451 $/m 3 and 54.2 $/MJ when source water with salinity of 35,000 ppm is fed to the system. - Highlights: • Thermodynamic and exergoeconomic analyses are performed for SWRO with energy recovery. • Parametric studies are done to study effects of operating conditions on performance. • Different seawater sources with different salinity values are tested. • At base case, plant exergy efficiency is 5.82% and product cost is 2.451 $/m 3
International Nuclear Information System (INIS)
Xu, H.; Wang, Y.
1999-01-01
In this letter, a linear free energy relationship is used to predict the Gibbs free energies of formation of crystalline phases of pyrochlore and zirconolite families with stoichiometry of MCaTi 2 O 7 (or, CaMTi 2 O 7 ,) from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The linear free energy relationship for tetravalent cations is expressed as ΔG f,M v X 0 =a M v X ΔG n,M 4+ 0 +b M v X +β M v X r M 4+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG n,M 4+ 0 is the standard non-solvation energy of cation M 4+ . The coefficients for the structural family of zirconolite with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4284.67 (kJ/mol), and β M v X =27.2 (kJ/mol nm). The coefficients for the structural family of pyrochlore with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4174.25 (kJ/mol), and β M v X =13.4 (kJ/mol nm). Using the linear free energy relationship, the Gibbs free energies of formation of various zirconolite and pyrochlore phases are calculated. (orig.)
The thermodynamic database COST MP0602 for materials for high-temperature lead-free soldering
Czech Academy of Sciences Publication Activity Database
Kroupa, Aleš; Dinsdale, A.; Watson, A.; Vřešťál, J.; Zemanová, Adéla; Brož, P.
2012-01-01
Roč. 48, č. 3 (2012), s. 339-346 ISSN 1450-5339 R&D Projects: GA MŠk LD11024 Institutional support: RVO:68081723 Keywords : CALPHAD method * lead-free solders * thermodynamic database Subject RIV: BJ - Thermodynamics Impact factor: 1.435, year: 2012
Tang, Hui-Yi; Wang, Jian-Hui; Ma, Yong-Li
2014-06-01
For a small system at a low temperature, thermal fluctuation and quantum effect play important roles in quantum thermodynamics. Starting from micro-canonical ensemble, we generalize the Boltzmann-Gibbs statistical factor from infinite to finite systems, no matter the interactions between particles are considered or not. This generalized factor, similar to Tsallis's q-form as a power-law distribution, has the restriction of finite energy spectrum and includes the nonextensivities of the small systems. We derive the exact expression for distribution of average particle numbers in the interacting classical and quantum nonextensive systems within a generalized canonical ensemble. This expression in the almost independent or elementary excitation quantum finite systems is similar to the corresponding ones obtained from the conventional grand-canonical ensemble. In the reconstruction for the statistical theory of the small systems, we present the entropy of the equilibrium systems and equation of total thermal energy. When we investigate the thermodynamics for the interacting nonextensive systems, we obtain the system-bath heat exchange and "uncompensated heat" which are in the thermodynamical level and independent on the detail of the system-bath coupling. For ideal finite systems, with different traps and boundary conditions, we calculate some thermodynamic quantities, such as the specific heat, entropy, and equation of state, etc. Particularly at low temperatures for the small systems, we predict some novel behaviors in the quantum thermodynamics, including internal entropy production, heat exchanges between the system and its surroundings and finite-size effects on the free energy.
The calculation of thermodynamic properties of molecules
DEFF Research Database (Denmark)
van Speybroeck, Veronique; Gani, Rafiqul; Meier, Robert Johan
2010-01-01
Thermodynamic data are key in the understanding and design of chemical processes. Next to the experimental evaluation of such data, computational methods are valuable and sometimes indispensable tools in obtaining heats of formation and Gibbs free energies. The major toolboxes to obtain such quan......Thermodynamic data are key in the understanding and design of chemical processes. Next to the experimental evaluation of such data, computational methods are valuable and sometimes indispensable tools in obtaining heats of formation and Gibbs free energies. The major toolboxes to obtain...... molecules the combination of group contribution methods with group additive values that are determined with the best available computational ab initio methods seems to be a viable alternative to obtain thermodynamic properties near chemical accuracy. New developments and full use of existing tools may lead...
International Nuclear Information System (INIS)
Vakalis, S.; Patuzzi, F.; Baratieri, M.
2017-01-01
Highlights: • Analysis of plants for electricity, heat and materials production. • Thermodynamic analysis by using exergy, entransy and statistical entropy. • Extrapolation of a single efficiency index by combining the thermodynamic parameters. • Application of methodology for two monitored small scale gasifiers. - Abstract: Modern gasification plants, should be treated as poly-generation facilities because, alongside the production of electricity and heat, valuable or waste materials streams are generated. Thus, integrated methods should be introduced in order to account for the full range and the nature of the products. Application of conventional hybrid indicators that convert the output into monetary units or CO_2 equivalents are a source of bias because of the inconsistency of the conversion factors and unreliability of the available data. Therefore, this study introduces a novel thermodynamic-based method for assessing gasification plants performance by means of exergy, entransy and statistical entropy. A monitoring campaign has been implemented on two small scale gasifiers and the results have been applied on the proposed method. The energy plants are compared in respect to their individual thermodynamic parameters for energy production and materials distribution. In addition, the method returns one single value which is a resultant of all the investigated parameters and is a characteristic value of the overall performance of an energy plant.
Trajectory Control of Scale-Free Dynamical Networks with Exogenous Disturbances
International Nuclear Information System (INIS)
Yang Hongyong; Zhang Shun; Zong Guangdeng
2011-01-01
In this paper, the trajectory control of multi-agent dynamical systems with exogenous disturbances is studied. Suppose multiple agents composing of a scale-free network topology, the performance of rejecting disturbances for the low degree node and high degree node is analyzed. Firstly, the consensus of multi-agent systems without disturbances is studied by designing a pinning control strategy on a part of agents, where this pinning control can bring multiple agents' states to an expected consensus track. Then, the influence of the disturbances is considered by developing disturbance observers, and disturbance observers based control (DOBC) are developed for disturbances generated by an exogenous system to estimate the disturbances. Asymptotical consensus of the multi-agent systems with disturbances under the composite controller can be achieved for scale-free network topology. Finally, by analyzing examples of multi-agent systems with scale-free network topology and exogenous disturbances, the verities of the results are proved. Under the DOBC with the designed parameters, the trajectory convergence of multi-agent systems is researched by pinning two class of the nodes. We have found that it has more stronger robustness to exogenous disturbances for the high degree node pinned than that of the low degree node pinned. (interdisciplinary physics and related areas of science and technology)
Thermodynamic modeling of the Al-U and Co-U systems
International Nuclear Information System (INIS)
Wang, J.; Liu, X.J.; Wang, C.P.
2008-01-01
The thermodynamic assessments of the Al-U and Co-U systems have been carried out by using the CALPHAD (Calculation of Phase Diagrams) method on the basis of the experimental data including thermodynamic properties and phase equilibria. Gibbs free energies of the solution phases were described by the subregular solution models with the Redlich-Kister equation, and those of the intermetallic compounds described by the sublattice models. A consistent set of thermodynamic parameters has been derived for describing the Gibbs free energies of each solution phase and intermetallic compounds in the Al-U and Co-U binary systems. The calculated phase diagrams and thermodynamic properties in the Al-U and Co-U systems are in good agreement with experimental data
On the character of consciousness
Directory of Open Access Journals (Sweden)
Arto eAnnila
2016-03-01
Full Text Available The human brain is a particularly demanding system to infer its nature from observations. Thus, there is on one hand plenty of room for theorizing and on the other hand a pressing need for a rigorous theory. We apply statistical mechanics of open systems to describe the brain as a hierarchical system in consuming free energy in least time. This holistic tenet accounts for cellular metabolism, neuronal signaling, cognitive processes all together or any other process by a formal equation of motion that extends down to the ultimate precision of one quantum of action. According to this general thermodynamic theory cognitive processes are no different by their operational and organizational principle from other natural processes. Cognition too will emerge and evolve along path-dependent and non-determinate trajectories by consuming free energy in least time to attain thermodynamic balance within the nervous system itself and with its surrounding systems. Specifically, consciousness can be ascribed to a natural process that integrates various neural networks for coherent consumption of free energy, i.e., for meaningful deeds. The whole hierarchy of integrated systems can be formally summed up to thermodynamic entropy. The holistic tenet provides insight to the character of consciousness also by acknowledging awareness in other systems at other levels of nature’s hierarchy.
2014-01-01
Background Binding free energy and binding hot spots at protein-protein interfaces are two important research areas for understanding protein interactions. Computational methods have been developed previously for accurate prediction of binding free energy change upon mutation for interfacial residues. However, a large number of interrupted and unimportant atomic contacts are used in the training phase which caused accuracy loss. Results This work proposes a new method, βACV ASA , to predict the change of binding free energy after alanine mutations. βACV ASA integrates accessible surface area (ASA) and our newly defined β contacts together into an atomic contact vector (ACV). A β contact between two atoms is a direct contact without being interrupted by any other atom between them. A β contact’s potential contribution to protein binding is also supposed to be inversely proportional to its ASA to follow the water exclusion hypothesis of binding hot spots. Tested on a dataset of 396 alanine mutations, our method is found to be superior in classification performance to many other methods, including Robetta, FoldX, HotPOINT, an ACV method of β contacts without ASA integration, and ACV ASA methods (similar to βACV ASA but based on distance-cutoff contacts). Based on our data analysis and results, we can draw conclusions that: (i) our method is powerful in the prediction of binding free energy change after alanine mutation; (ii) β contacts are better than distance-cutoff contacts for modeling the well-organized protein-binding interfaces; (iii) β contacts usually are only a small fraction number of the distance-based contacts; and (iv) water exclusion is a necessary condition for a residue to become a binding hot spot. Conclusions βACV ASA is designed using the advantages of both β contacts and water exclusion. It is an excellent tool to predict binding free energy changes and binding hot spots after alanine mutation. PMID:24568581
Modeling the basic superconductor thermodynamical-statistical characteristics
International Nuclear Information System (INIS)
Palenskis, V.; Maknys, K.
1999-01-01
In accordance with the Landau second-order phase transition and other thermodynamical-statistical relations for superconductors, and using the energy gap as an order parameter in the electron free energy presentation, the fundamental characteristics of electrons, such as the free energy, the total energy, the energy gap, the entropy, and the heat capacity dependences on temperature were obtained. The obtained modeling results, in principle, well reflect the basic low- and high-temperature superconductor characteristics
Tanaka, Shigenori
2016-03-07
A computational scheme to describe the temporal evolution of thermodynamic functions in stochastic nonequilibrium processes of isothermal classical systems is proposed on the basis of overdamped Langevin equation under given potential and temperature. In this scheme the associated Fokker-Planck-Smoluchowski equation for the probability density function is transformed into the imaginary-time Schrödinger equation with an effective Hamiltonian. The propagator for the time-dependent wave function is expressed in the framework of the path integral formalism, which can thus represent the dynamical behaviors of nonequilibrium molecular systems such as those conformational changes observed in protein folding and ligand docking. The present study then employs the diffusion Monte Carlo method to efficiently simulate the relaxation dynamics of wave function in terms of random walker distribution, which in the long-time limit reduces to the ground-state eigenfunction corresponding to the equilibrium Boltzmann distribution. Utilizing this classical-quantum correspondence, we can describe the relaxation processes of thermodynamic functions as an approach to the equilibrium state with the lowest free energy. Performing illustrative calculations for some prototypical model potentials, the temporal evolutions of enthalpy, entropy, and free energy of the classical systems are explicitly demonstrated. When the walkers initially start from a localized configuration in one- or two-dimensional harmonic or double well potential, the increase of entropy usually dominates the relaxation dynamics toward the equilibrium state. However, when they start from a broadened initial distribution or go into a steep valley of potential, the dynamics are driven by the decrease of enthalpy, thus causing the decrease of entropy associated with the spatial localization. In the cases of one- and two-dimensional asymmetric double well potentials with two minimal points and an energy barrier between them
Solid/liquid interfacial free energies in binary systems
Nason, D.; Tiller, W. A.
1973-01-01
Description of a semiquantitative technique for predicting the segregation characteristics of smooth interfaces between binary solid and liquid solutions in terms of readily available thermodynamic parameters of the bulk solutions. A lattice-liquid interfacial model and a pair-bonded regular solution model are employed in the treatment with an accommodation for liquid interfacial entropy. The method is used to calculate the interfacial segregation and the free energy of segregation for solid-liquid interfaces between binary solutions for the (111) boundary of fcc crystals. The zone of compositional transition across the interface is shown to be on the order of a few atomic layers in width, being moderately narrower for ideal solutions. The free energy of the segregated interface depends primarily upon the solid composition and the heats of fusion of the component atoms, the composition difference of the solutions, and the difference of the heats of mixing of the solutions.
Thermodynamics and statistical mechanics an integrated approach
Shell, M Scott
2015-01-01
Learn classical thermodynamics alongside statistical mechanics with this fresh approach to the subjects. Molecular and macroscopic principles are explained in an integrated, side-by-side manner to give students a deep, intuitive understanding of thermodynamics and equip them to tackle future research topics that focus on the nanoscale. Entropy is introduced from the get-go, providing a clear explanation of how the classical laws connect to the molecular principles, and closing the gap between the atomic world and thermodynamics. Notation is streamlined throughout, with a focus on general concepts and simple models, for building basic physical intuition and gaining confidence in problem analysis and model development. Well over 400 guided end-of-chapter problems are included, addressing conceptual, fundamental, and applied skill sets. Numerous worked examples are also provided together with handy shaded boxes to emphasize key concepts, making this the complete teaching package for students in chemical engineer...
Applied Thermodynamics: Grain Boundary Segregation
Directory of Open Access Journals (Sweden)
Pavel Lejček
2014-03-01
Full Text Available Chemical composition of interfaces—free surfaces and grain boundaries—is generally described by the Langmuir–McLean segregation isotherm controlled by Gibbs energy of segregation. Various components of the Gibbs energy of segregation, the standard and the excess ones as well as other thermodynamic state functions—enthalpy, entropy and volume—of interfacial segregation are derived and their physical meaning is elucidated. The importance of the thermodynamic state functions of grain boundary segregation, their dependence on volume solid solubility, mutual solute–solute interaction and pressure effect in ferrous alloys is demonstrated.
International Nuclear Information System (INIS)
Polettini, Matteo; Esposito, Massimiliano
2014-01-01
In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks “in a box”, whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s Y between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s Y . We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction
Polettini, Matteo; Esposito, Massimiliano
2014-07-14
In this paper and Paper II, we outline a general framework for the thermodynamic description of open chemical reaction networks, with special regard to metabolic networks regulating cellular physiology and biochemical functions. We first introduce closed networks "in a box", whose thermodynamics is subjected to strict physical constraints: the mass-action law, elementarity of processes, and detailed balance. We further digress on the role of solvents and on the seemingly unacknowledged property of network independence of free energy landscapes. We then open the system by assuming that the concentrations of certain substrate species (the chemostats) are fixed, whether because promptly regulated by the environment via contact with reservoirs, or because nearly constant in a time window. As a result, the system is driven out of equilibrium. A rich algebraic and topological structure ensues in the network of internal species: Emergent irreversible cycles are associated with nonvanishing affinities, whose symmetries are dictated by the breakage of conservation laws. These central results are resumed in the relation a + b = s(Y) between the number of fundamental affinities a, that of broken conservation laws b and the number of chemostats s(Y). We decompose the steady state entropy production rate in terms of fundamental fluxes and affinities in the spirit of Schnakenberg's theory of network thermodynamics, paving the way for the forthcoming treatment of the linear regime, of efficiency and tight coupling, of free energy transduction, and of thermodynamic constraints for network reconstruction.
Piaggi, Paolo; Thearle, Marie S; Krakoff, Jonathan; Votruba, Susanne B
2015-08-01
Body fat-free mass (FFM), energy expenditure (EE), and respiratory quotient (RQ) are known predictors of daily food intake. Because FFM largely determines EE, it is unclear whether body composition per se or the underlying metabolism drives dietary intake. The objective of the study was to test whether 24-hour measures of EE and RQ and their components influence ad libitum food intake independently of FFM. One hundred seven healthy individuals (62 males/45 females, 84 Native Americans/23 whites; age 33 ± 8 y; body mass index 33 ± 8 kg/m(2); body fat 31% ± 8%) had 24-hour measures of EE in a whole-room indirect calorimeter during energy balance, followed by 3 days of ad libitum food intake using computerized vending machine systems. Body composition was estimated by dual-energy x-ray absorptiometry. FFM, 24-hour EE, RQ, spontaneous physical activity, sleeping EE (sleeping metabolic rate), awake and fed thermogenesis, and ad libitum food intake (INTAKE) were measured. Higher 24-hour RQ (P FFM (P = .65), were independent predictors of INTAKE. Mediation analysis demonstrated that 24-hour EE is responsible for 80% of the FFM effect on INTAKE (44.5 ± 16.9 kcal ingested per kilogram of FFM, P= .01), whereas the unique effect due to solely FFM was negligible (10.6 ± 23.2, P = .65). Spontaneous physical activity (r = 0.33, P = .001), but not sleeping metabolic rate (P = .71), positively predicted INTAKE, whereas higher awake and fed thermogenesis determined greater INTAKE only in subjects with a body mass index of 29 kg/m(2) or less (r = 0.44, P = .01). EE and RQ, rather than FFM, independently determine INTAKE, suggesting that competitive energy-sensing mechanisms driven by the preferential macronutrient oxidation and total energy demands may regulate food intake.
Debbasch, F.
2011-01-01
The logical structure of classical thermodynamics is presented in a modern, geometrical manner. The first and second law receive clear, operatively oriented statements and the Gibbs free energy extremum principle is fully discussed. Applications relevant to chemistry, such as phase transitions, dilute solutions theory and, in particular, the law…
Entropy and energy quantization: Planck thermodynamic calculation
International Nuclear Information System (INIS)
Mota e Albuquerque, Ivone Freire da.
1988-01-01
This dissertation analyses the origins and development of the concept of entropy and its meaning of the second Law of thermodynamics, as well as the thermodynamics derivation of the energy quantization. The probabilistic interpretation of that law and its implication in physics theory are evidenciated. Based on Clausius work (which follows Carnot's work), we analyse and expose in a original way the entropy concept. Research upon Boltzmann's work and his probabilistic interpretation of the second Law of thermodynamics is made. The discuss between the atomistic and the energeticist points of view, which were actual at that time are also commented. (author). 38 refs., 3 figs
New Perspectives on Spontaneous Brain Activity: Dynamic Networks and Energy Matter.
Tozzi, Arturo; Zare, Marzieh; Benasich, April A
2016-01-01
Spontaneous brain activity has received increasing attention as demonstrated by the exponential rise in the number of published article on this topic over the last 30 years. Such "intrinsic" brain activity, generated in the absence of an explicit task, is frequently associated with resting-state or default-mode networks (DMN)s. The focus on characterizing spontaneous brain activity promises to shed new light on questions concerning the structural and functional architecture of the brain and how they are related to "mind". However, many critical questions have yet to be addressed. In this review, we focus on a scarcely explored area, specifically the energetic requirements and constraints of spontaneous activity, taking into account both thermodynamical and informational perspectives. We argue that the "classical" definitions of spontaneous activity do not take into account an important feature, that is, the critical thermodynamic energetic differences between spontaneous and evoked brain activity. Spontaneous brain activity is associated with slower oscillations compared with evoked, task-related activity, hence it exhibits lower levels of enthalpy and "free-energy" (i.e., the energy that can be converted to do work), thus supporting noteworthy thermodynamic energetic differences between spontaneous and evoked brain activity. Increased spike frequency during evoked activity has a significant metabolic cost, consequently, brain functions traditionally associated with spontaneous activity, such as mind wandering, require less energy that other nervous activities. We also review recent empirical observations in neuroscience, in order to capture how spontaneous brain dynamics and mental function can be embedded in a non-linear dynamical framework, which considers nervous activity in terms of phase spaces, particle trajectories, random walks, attractors and/or paths at the edge of the chaos. This takes us from the thermodynamic free-energy, to the realm of "variational
Thermodynamics of Inozemtsev's elliptic spin chain
Energy Technology Data Exchange (ETDEWEB)
Klabbers, Rob, E-mail: rob.klabbers@desy.de
2016-06-15
We study the thermodynamic behaviour of Inozemtsev's long-range elliptic spin chain using the Bethe ansatz equations describing the spectrum of the model in the infinite-length limit. We classify all solutions of these equations in that limit and argue which of these solutions determine the spectrum in the thermodynamic limit. Interestingly, some of the solutions are not selfconjugate, which puts the model in sharp contrast to one of the model's limiting cases, the Heisenberg XXX spin chain. Invoking the string hypothesis we derive the thermodynamic Bethe ansatz equations (TBA-equations) from which we determine the Helmholtz free energy in thermodynamic equilibrium and derive the associated Y-system. We corroborate our results by comparing numerical solutions of the TBA-equations to a direct computation of the free energy for the finite-length hamiltonian. In addition we confirm numerically the interesting conjecture put forward by Finkel and González-López that the original and supersymmetric versions of Inozemtsev's elliptic spin chain are equivalent in the thermodynamic limit.
Free field theories of spin-mass trajectories and quantum electrodynamics in the null plane
Energy Technology Data Exchange (ETDEWEB)
Bart, G.R.; Fenster, S.
1976-06-01
The ten generators of the Poincare algebra for quantum electrodynamics and other gauge theories are given in the null plane. The explicit correspondence of their field-theoretic form to the Bacry-Chang group-theoretic form in the free case is pointed out. It is then noticed that the forms are independent of the spin and allow inclusion of charge quantum numbers at will, which indicates that they represent an advantageous free-particle starting point for a hadron theory with positive spin-mass trajectories (SMT) and with interaction. The internal oscillator content is extracted for both gauge theories and dual resonance models. Interactions are cubic and quartic in the fields. In the dual model they encompass the SMT, whereas no straightforward extension to SMT is possible for the manifestly covariant theories. The requirements of a field-theoretic SMT interaction are spelled out in an algebraic form which guarantees Poincare invariance; however no such interaction is yet known. The approach indicates how a realistic spectrum might be achieved without composite hadrons and incorporating full Poincare invariance.
Free field theories of spin-mass trajectories and quantum electrodynamics in the null plane
International Nuclear Information System (INIS)
Bart, G.R.; Fenster, S.
1976-06-01
The ten generators of the Poincare algebra for quantum electrodynamics and other gauge theories are given in the null plane. The explicit correspondence of their field-theoretic form to the Bacry-Chang group-theoretic form in the free case is pointed out. It is then noticed that the forms are independent of the spin and allow inclusion of charge quantum numbers at will, which indicates that they represent an advantageous free-particle starting point for a hadron theory with positive spin-mass trajectories (SMT) and with interaction. The internal oscillator content is extracted for both gauge theories and dual resonance models. Interactions are cubic and quartic in the fields. In the dual model they encompass the SMT, whereas no straightforward extension to SMT is possible for the manifestly covariant theories. The requirements of a field-theoretic SMT interaction are spelled out in an algebraic form which guarantees Poincare invariance; however no such interaction is yet known. The approach indicates how a realistic spectrum might be achieved without composite hadrons and incorporating full Poincare invariance
Buchkremer, S.; Klocke, F.
2017-01-01
Performance and operational safety of many metal parts in engineering depend on their surface integrity. During metal cutting, large thermomechanical loads and high gradients of the loads concerning time and location act on the surfaces and may yield significant structural material modifications, which alter the surface integrity. In this work, the derivation and validation of a model of nanostructural surface modifications in metal cutting are presented. For the first time in process modeling, initiation and kinetics of these modifications are predicted using a thermodynamic potential, which considers the interdependent developments of plastic work, dissipation, heat conduction and interface energy as well as the associated productions and flows of entropy. The potential is expressed based on the free Helmholtz energy. The irreversible thermodynamic state changes in the workpiece surface are homogenized over the volume in order to bridge the gap between discrete phenomena involved with the initiation and kinetics of dynamic recrystallization and its macroscopic implications for surface integrity. The formulation of the thermodynamic potential is implemented into a finite element model of orthogonal cutting of steel AISI 4140. Close agreement is achieved between predicted nanostructures and those obtained in transmission electron microscopical investigations of specimen produced in cutting experiments.
Thermodynamic analysis of a liquid air energy storage system
International Nuclear Information System (INIS)
Guizzi, Giuseppe Leo; Manno, Michele; Tolomei, Ludovica Maria; Vitali, Ruggero Maria
2015-01-01
The rapid increase in the share of electricity generation from renewable energy sources is having a profound impact on the power sector; one of the most relevant effects of this trend is the increased importance of energy storage systems, which can be used to smooth out peaks and troughs of production from renewable energy sources. Besides their role in balancing the electric grid, energy storage systems may provide also several other useful services, such as price arbitrage, stabilizing conventional generation, etc.; therefore, it is not surprising that many research projects are under way in order to explore the potentials of new technologies for electric energy storage. This paper presents a thermodynamic analysis of a cryogenic energy storage system, based on air liquefaction and storage in an insulated vessel. This technology is attractive thanks to its independence from geographical constraints and because it can be scaled up easily to grid-scale ratings, but it is affected by a low round-trip efficiency due to the energy intensive process of air liquefaction. The present work aims to assess the efficiency of such a system and to identify if and how it can achieve an acceptable round-trip efficiency (in the order of 50–60%).
Rapid Calculation of Spacecraft Trajectories Using Efficient Taylor Series Integration
Scott, James R.; Martini, Michael C.
2011-01-01
A variable-order, variable-step Taylor series integration algorithm was implemented in NASA Glenn's SNAP (Spacecraft N-body Analysis Program) code. SNAP is a high-fidelity trajectory propagation program that can propagate the trajectory of a spacecraft about virtually any body in the solar system. The Taylor series algorithm's very high order accuracy and excellent stability properties lead to large reductions in computer time relative to the code's existing 8th order Runge-Kutta scheme. Head-to-head comparison on near-Earth, lunar, Mars, and Europa missions showed that Taylor series integration is 15.8 times faster than Runge- Kutta on average, and is more accurate. These speedups were obtained for calculations involving central body, other body, thrust, and drag forces. Similar speedups have been obtained for calculations that include J2 spherical harmonic for central body gravitation. The algorithm includes a step size selection method that directly calculates the step size and never requires a repeat step. High-order Taylor series integration algorithms have been shown to provide major reductions in computer time over conventional integration methods in numerous scientific applications. The objective here was to directly implement Taylor series integration in an existing trajectory analysis code and demonstrate that large reductions in computer time (order of magnitude) could be achieved while simultaneously maintaining high accuracy. This software greatly accelerates the calculation of spacecraft trajectories. At each time level, the spacecraft position, velocity, and mass are expanded in a high-order Taylor series whose coefficients are obtained through efficient differentiation arithmetic. This makes it possible to take very large time steps at minimal cost, resulting in large savings in computer time. The Taylor series algorithm is implemented primarily through three subroutines: (1) a driver routine that automatically introduces auxiliary variables and
Diffusion in multicomponent systems: a free energy approach
International Nuclear Information System (INIS)
Emmanuel, Simon; Cortis, Andrea; Berkowitz, Brian
2004-01-01
This work examines diffusion in ternary non-ideal systems and derives coupled non-linear equations based on a non-equilibrium thermodynamic approach in which an explicit expression for the free energy is substituted into standard diffusion equations. For ideal solutions, the equations employ four mobility parameters (M aa , M ab , M ba , and M bb ), and uphill diffusion is predicted for certain initial conditions and combinations of mobilities. For the more complex case of ternary Simple Mixtures, two non-ideality parameters (χ ac and χ bc ) that are directly related to the excess free energy of mixing are introduced. The solution of the equations is carried out by means of two different numerical schemes: (1) spectral collocation and (2) finite element. An error minimization technique is coupled with the spectral collocation method and applied to diffusional profiles to extract the M and χ parameters. The model satisfactorily reproduces diffusional profiles from published data for silicate melts. Further improvements in numerical and experimental techniques are then suggested
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P
2010-06-07
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis. Copyright (c) 2010 Elsevier Ltd. All rights reserved.
Interfacial thermodynamics of water and six other liquid solvents.
Pascal, Tod A; Goddard, William A
2014-06-05
We examine the thermodynamics of the liquid-vapor interface by direct calculation of the surface entropy, enthalpy, and free energy from extensive molecular dynamics simulations using the two-phase thermodynamics (2PT) method. Results for water, acetonitrile, cyclohexane, dimethyl sulfoxide, hexanol, N-methyl acetamide, and toluene are presented. We validate our approach by predicting the interfacial surface tensions (IFT--excess surface free energy per unit area) in excellent agreement with the mechanical calculations using Kirkwood-Buff theory. Additionally, we evaluate the temperature dependence of the IFT of water as described by the TIP4P/2005, SPC/Ew, TIP3P, and mW classical water models. We find that the TIP4P/2005 and SPC/Ew water models do a reasonable job of describing the interfacial thermodynamics; however, the TIP3P and mW are quite poor. We find that the underprediction of the experimental IFT at 298 K by these water models results from understructured surface molecules whose binding energies are too weak. Finally, we performed depth profiles of the interfacial thermodynamics which revealed long tails that extend far into what would be considered bulk from standard Gibbs theory. In fact, we find a nonmonotonic interfacial free energy profile for water, a unique feature that could have important consequences for the absorption of ions and other small molecules.
Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse
Wan, Yuan; Moessner, Roderich
2017-10-01
Thermal fluctuations can lift the degeneracy of a ground state manifold, producing a free-energy landscape without accidentally degenerate minima. In a process known as order by disorder, a subset of states incorporating symmetry breaking may be selected. Here, we show that such a free-energy landscape can be controlled in a nonequilibrium setting as the slow motion within the ground state manifold is governed by the fast modes out of it. For the paradigmatic case of the classical pyrochlore X Y antiferromagnet, we show that a uniform magnetic field pulse can excite these fast modes to generate a tunable effective free-energy landscape with minima at thermodynamically unstable portions of the ground state manifold.
The free energy landscape of small molecule unbinding.
Directory of Open Access Journals (Sweden)
Danzhi Huang
2011-02-01
Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.
Elements of sub-quantum thermodynamics: quantum motion as ballistic diffusion
International Nuclear Information System (INIS)
Groessing, G; Fussy, S; Pascasio, J Mesa; Schwabl, H
2011-01-01
By modelling quantum systems as emerging from a (classical) sub-quantum thermodynamics, the quantum mechanical 'decay of the wave packet' is shown to simply result from sub-quantum diffusion with a specific diffusion coefficient varying in time due to a particle's changing thermal environment. It is thereby proven that free quantum motion strictly equals ballistic diffusion. The exact quantum mechanical trajectory distributions and the velocity field of the Gaussian wave packet are thus derived solely from classical physics. Moreover, also quantum motion in a linear (e.g., gravitational) potential is shown to equal said ballistic diffusion. Quantitative statements on the trajectories' characteristic behaviours are obtained which provide a detailed 'micro-causal' explanation in full accordance with momentum conservation.
Tracing back resonances to families of Regge trajectories. New finite energy sum rules
International Nuclear Information System (INIS)
Mandelbrojt, Jacques.
1975-04-01
An amplitude is supposed to be expressed for large enough energies as a sum of contributions of Regge poles. Calling family of trajectories the set of trajectories which differ by integers from one of them, a correspondance, such that the energy and width of a given resonance depend on only family of trajectories, is established between resonances of the amplitude and families of trajectories. The contribution to the amplitude of each family of trajectories is shown to satisfy the same finite energy sum rules as does the amplitude itself. In these sum rules the resonance approximation can be made where the only resonances that will appear are those which are in correspondence with the family [fr
Functional approach without path integrals to finite temperature free fermions
International Nuclear Information System (INIS)
Souza, S.M. de; Santos, O. Rojas; Thomaz, M.T.
1999-01-01
Charret et al applied the properties of Grassmann generators to develop a new method to calculate the coefficients of the high temperature expansion of the grand canonical partition function of self-interacting fermionic models on d-dimensions (d ≥1). The methodology explores the anti-commuting nature of fermionic fields and avoids the calculation of the fermionic path integral. we apply this new method to the relativistic free Dirac fermions and recover the known results in the literature without the β-independent and μindependent infinities that plague the continuum path integral formulation. (author)
Thermodynamic stabilization of colloids
Stol, R.J.; Bruyn, P.L. de
An analysis is given of the conditions necessary for obtaining a thermodynamically stable dispersion (TSD) of solid particles in a continuous aqueous solution phase. The role of the adsorption of potential-determining ions at the planar interface in lowering the interfacial free energy (γ) to
Free energies of stable and metastable pores in lipid membranes under tension.
den Otter, Wouter K
2009-11-28
The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation. The change of genus upon pore formation is exploited to estimate the saddle-splay modulus or Gaussian curvature modulus of the membrane leaflets. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.
Thermodynamic analysis of elastic-plastic deformation
International Nuclear Information System (INIS)
Lubarda, V.
1981-01-01
The complete set of constitutive equations which fully describes the behaviour of material in elastic-plastic deformation is derived on the basis of thermodynamic analysis of the deformation process. The analysis is done after the matrix decomposition of the deformation gradient is introduced into the structure of thermodynamics with internal state variables. The free energy function, is decomposed. Derive the expressions for the stress response, entropy and heat flux, and establish the evolution equation. Finally, we establish the thermodynamic restrictions of the deformation process. (Author) [pt
Thermodynamic modeling of the Ce-Zn and Pr-Zn systems
International Nuclear Information System (INIS)
Wang, C.P.; Chen, X.; Liu, X.J.; Pan, F.S.; Ishida, K.
2008-01-01
In order to develop the thermodynamic database of phase equilibria in the Mg-Zn-Re (Re: rare earth element) base alloys, the thermodynamic assessments of the Ce-Zn and Pr-Zn systems were carried out by using the calculation of phase diagrams (CALPHAD) method on the basis of the experimental data including thermodynamic properties and phase equilibria. Based on the available experimental data, Gibbs free energies of the solution phases (liquid, bcc, fcc, hcp and dhcp) were modeled by the subregular solution model with the Redlich-Kister formula, and those of the intermetallic compounds were described by the sublattice model. A consistent set of thermodynamic parameters has been derived for describing the Gibbs free energies of each solution phase and intermetallic compound in the Ce-Zn and Pr-Zn binary systems. An agreement between the present calculated results and experimental data is obtained
Energy Technology Data Exchange (ETDEWEB)
Mi, Bin-Zhou, E-mail: mbzfjerry2008@126.com [Department of Basic Curriculum, North China Institute of Science and Technology, Beijing 101601 (China); Department of Physics, School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083 (China); Zhai, Liang-Jun [The School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001 (China); Hua, Ling-Ling [Department of Basic Curriculum, North China Institute of Science and Technology, Beijing 101601 (China)
2016-01-15
The effect of magnetic spin correlation on the thermodynamic properties of Heisenberg ferromagnetic single-walled nanotubes are comprehensively investigated by use of the double-time Green's function method. The influence of temperature, spin quantum number, diameter of the tube, anisotropy strength and external magnetic field to internal energy, free energy, and magnon specific heat are carefully calculated. Compared to the mean field approximation, the consideration of the magnetic correlation effect significantly improves the internal energy values at finite temperature, while it does not so near zero temperature, and this effect is related to the diameter of the tube, anisotropy strength, and spin quantum number. The magnetic correlation effect lowers the internal energy at finite temperature. As a natural consequence of the reduction of the internal energy, the specific heat is reduced, and the free energy is elevated. - Highlights: • Magnon specific heat and free energy of Heisenberg ferromagnetic single-walled nanotubes (HFM-SWNTs) are investigated. • The magnetic correlations effect has a considerable contribution to the thermodynamics properties of HFM-SWNTs. • Magnetic correlation effects are always to lower the internal energy at finite temperature. • At Curie point, magnetic correlation energy is much less than zero. • The peak values of magnon specific heat curves rise and shift right towards higher temperatures with the diameter of tubes, the anisotropy strength, and the spin quantum number rising.
International Nuclear Information System (INIS)
Zhou, Zhihua; Wu, Shengwei; Du, Tao; Chen, Guanyi; Zhang, Zhiming; Zuo, Jian; He, Qing
2016-01-01
Highlights: • Investigate the suitable application scope of free cooling system. • Simulate and predict its COP and carbon reduction. • Compare the temperature changes of underground soil between free cooling mode and conventional cooling mode. • Suggest the use of free cooling. - Abstract: Ground coupled heat pump (GCHP) systems have been widely implemented due to its potential benefits of energy savings. However, very few studies attempted to examine the operational performance of GCHP system integrated with borehole free cooling (i.e. using the circulating water in ground heat exchanger for the cooling purpose). A typical office building in Tianjin was chosen for a detailed case study. Both experiments and numerical simulation are employed to examine the efficiency of proposed GCHP system by means of comparing the normal running mode (NRM) and the energy-saving running mode (ESRM) in terms of the energy consumption and soil temperature variation. The results showed that the energy efficiency ratio (EER_s_y_s_t_e_m) of the system increased every year in winter but decreased gradually in summer during 10 years of operation. In winter, the EER_s_y_s_t_e_m of NRM was 3.4% higher than that of ESRM. In summer, the EER_s_y_s_t_e_m of NRM was 0.5% lower than that of ESRM under the same normal cooling mode (NM_c). The EER_s_y_s_t_e_m of free cooling mode (FM_c) could reach as high as 23.35, which was 5.2 times higher than that of NM_c. In summer, the EER_s_y_s_t_e_m of ESRM was 13.58 on average, which was 2.6 times higher than that of NRM. The soil temperature gained minor rise under both modes during 10 years’ operation. This study revealed that there are significant energy savings benefits if the GCHP system is integrated with FM_c. Meanwhile, the requirements related to temperature and humidity can be satisfied when the indoor thermal and moisture load are not too high. Therefore, the integration of FM_c with GCHP system could be considered for the operation
Singularity-free interpretation of the thermodynamics of supercooled water
International Nuclear Information System (INIS)
Sastry, S.; Debenedetti, P.G.; Sciortino, F.; Stanley, H.E.
1996-01-01
The pronounced increases in isothermal compressibility, isobaric heat capacity, and in the magnitude of the thermal expansion coefficient of liquid water upon supercooling have been interpreted either in terms of a continuous, retracing spinodal curve bounding the superheated, stretched, and supercooled states of liquid water, or in terms of a metastable, low-temperature critical point. Common to these two scenarios is the existence of singularities associated with diverging density fluctuations at low temperature. We show that the increase in compressibility upon lowering the temperature of a liquid that expands on cooling, like water, is not contingent on any singular behavior, but rather is a thermodynamic necessity. We perform a thermodynamic analysis for an anomalous liquid (i.e., one that expands when cooled) in the absence of a retracing spinodal and show that one may in general expect a locus of compressibility extrema in the anomalous regime. Our analysis suggests that the simplest interpretation of the behavior of supercooled water consistent with experimental observations is free of singularities. We then develop a waterlike lattice model that exhibits no singular behavior, while capturing qualitative aspects of the thermodynamics of water. copyright 1996 The American Physical Society
WATEQ3 geochemical model: thermodynamic data for several additional solids
International Nuclear Information System (INIS)
Krupka, K.M.; Jenne, E.A.
1982-09-01
Geochemical models such as WATEQ3 can be used to model the concentrations of water-soluble pollutants that may result from the disposal of nuclear waste and retorted oil shale. However, for a model to competently deal with these water-soluble pollutants, an adequate thermodynamic data base must be provided that includes elements identified as important in modeling these pollutants. To this end, several minerals and related solid phases were identified that were absent from the thermodynamic data base of WATEQ3. In this study, the thermodynamic data for the identified solids were compiled and selected from several published tabulations of thermodynamic data. For these solids, an accepted Gibbs free energy of formation, ΔG 0 /sub f,298/, was selected for each solid phase based on the recentness of the tabulated data and on considerations of internal consistency with respect to both the published tabulations and the existing data in WATEQ3. For those solids not included in these published tabulations, Gibbs free energies of formation were calculated from published solubility data (e.g., lepidocrocite), or were estimated (e.g., nontronite) using a free-energy summation method described by Mattigod and Sposito (1978). The accepted or estimated free energies were then combined with internally consistent, ancillary thermodynamic data to calculate equilibrium constants for the hydrolysis reactions of these minerals and related solid phases. Including these values in the WATEQ3 data base increased the competency of this geochemical model in applications associated with the disposal of nuclear waste and retorted oil shale. Additional minerals and related solid phases that need to be added to the solubility submodel will be identified as modeling applications continue in these two programs
Lee, Tae Geol; Kim, Myung Soo; Park, Seung C.
1996-04-01
Dynamics of the four-centered elimination reaction CH2OH+→CHO++H2 has been investigated over the internal energy range 4.6-5.9 eV using the classical trajectory method. A realistic semiempirical potential reported previously [J. Chem. Phys. (in press, 1996)] has been used for the calculation. It has been found that the disposal of the nonfixed excess energy at the transition state and of the reverse critical energy can be considered independently as manifest in the sum rule analysis. The former is determined statistically while the latter dynamically. Based on the above idea, a method to determine the kinetic energy release distribution originating only from the reverse critical energy has been developed.
Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel
2014-06-05
Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.
Grams, G.; Giraud, S.; Fantina, A. F.; Gulminelli, F.
2018-03-01
The aim of the present study is to calculate the nuclear distribution associated at finite temperature to any given equation of state of stellar matter based on the Wigner-Seitz approximation, for direct applications in core-collapse simulations. The Gibbs free energy of the different configurations is explicitly calculated, with special care devoted to the calculation of rearrangement terms, ensuring thermodynamic consistency. The formalism is illustrated with two different applications. First, we work out the nuclear statistical equilibrium cluster distribution for the Lattimer and Swesty equation of state, widely employed in supernova simulations. Secondly, we explore the effect of including shell structure, and consider realistic nuclear mass tables from the Brussels-Montreal Hartree-Fock-Bogoliubov model (specifically, HFB-24). We show that the whole collapse trajectory is dominated by magic nuclei, with extremely spread and even bimodal distributions of the cluster probability around magic numbers, demonstrating the importance of cluster distributions with realistic mass models in core-collapse simulations. Simple analytical expressions are given, allowing further applications of the method to any relativistic or nonrelativistic subsaturation equation of state.
Directory of Open Access Journals (Sweden)
Dra Nurjanah
2017-12-01
Full Text Available The research was aimed at developing learning resources for mathematics logic using the hypothetical learning trajectory designed through reflection on the history of Indonesian independence struggle. The study was carried out at the Department of Mathematics Education of the Faculty of Teacher Training and Educational Sciences Nusantara Islamic University (Uninus. The study used design research consisted of three stages: preparing the experiments, design the experiments, and retrospective analysis. Preparing the experiments stage has been completed and design the experiments stage is currently under preparation. The main activities accomplished in preparing the experiments stage consisted of: studies of Indonesian independence struggle, curriculum analysis, literature review, and early prototype design. Design the experiments phase has enabled the development of the research instruments. The learning trajectory which has been designed in the first stage involved: reflections on the history of Indonesian independence struggle; implication and bi-implication; implication, bi-implication and their truth in the context of the history of the Indonesian independence struggle; and implication, bi-implication and their truth in the context of mathematics. Based on the results of discussions with colleagues, the students’ ability in mathematical thinking can be developed by using the history of Indonesian independence struggle as the context of learning in a mathematics logics course.
A Robot Trajectory Optimization Approach for Thermal Barrier Coatings Used for Free-Form Components
Cai, Zhenhua; Qi, Beichun; Tao, Chongyuan; Luo, Jie; Chen, Yuepeng; Xie, Changjun
2017-10-01
This paper is concerned with a robot trajectory optimization approach for thermal barrier coatings. As the requirements of high reproducibility of complex workpieces increase, an optimal thermal spraying trajectory should not only guarantee an accurate control of spray parameters defined by users (e.g., scanning speed, spray distance, scanning step, etc.) to achieve coating thickness homogeneity but also help to homogenize the heat transfer distribution on the coating surface. A mesh-based trajectory generation approach is introduced in this work to generate path curves on a free-form component. Then, two types of meander trajectories are generated by performing a different connection method. Additionally, this paper presents a research approach for introducing the heat transfer analysis into the trajectory planning process. Combining heat transfer analysis with trajectory planning overcomes the defects of traditional trajectory planning methods (e.g., local over-heating), which helps form the uniform temperature field by optimizing the time sequence of path curves. The influence of two different robot trajectories on the process of heat transfer is estimated by coupled FEM models which demonstrates the effectiveness of the presented optimization approach.
Thermodynamic calculation of phase equilibria of the U-Ga and U-W systems
International Nuclear Information System (INIS)
Wang, J.; Liu, X.J.; Wang, C.P.
2008-01-01
The thermodynamic assessments of the U-Ga and U-W systems have been carried out by using the CALPHAD (calculation of phase diagrams) method using experimental data including thermodynamic properties and phase equilibria. Gibbs free energies of the solution phases were described by the subregular solution models with the Redlich-Kister equation, and those of the intermetallic compounds were described by the sublattice models. A consistent set of thermodynamic parameters has been derived for the Gibbs free energy of each phase in the U-Ga and U-W binary systems, respectively. The calculated phase diagrams and thermodynamic properties in the U-Ga and U-W systems are in good agreement with experimental data
Quantum Coherence, Time-Translation Symmetry, and Thermodynamics
Directory of Open Access Journals (Sweden)
Matteo Lostaglio
2015-04-01
Full Text Available The first law of thermodynamics imposes not just a constraint on the energy content of systems in extreme quantum regimes but also symmetry constraints related to the thermodynamic processing of quantum coherence. We show that this thermodynamic symmetry decomposes any quantum state into mode operators that quantify the coherence present in the state. We then establish general upper and lower bounds for the evolution of quantum coherence under arbitrary thermal operations, valid for any temperature. We identify primitive coherence manipulations and show that the transfer of coherence between energy levels manifests irreversibility not captured by free energy. Moreover, the recently developed thermomajorization relations on block-diagonal quantum states are observed to be special cases of this symmetry analysis.
A Thermodynamic Point of View on Dark Energy Models
Directory of Open Access Journals (Sweden)
Vincenzo F. Cardone
2017-07-01
Full Text Available We present a conjugate analysis of two different dark energy models, namely the Barboza–Alcaniz parameterization and the phenomenologically-motivated Hobbit model, investigating both their agreement with observational data and their thermodynamical properties. We successfully fit a wide dataset including the Hubble diagram of Type Ia Supernovae, the Hubble rate expansion parameter as measured from cosmic chronometers, the baryon acoustic oscillations (BAO standard ruler data and the Planck distance priors. This analysis allows us to constrain the model parameters, thus pointing at the region of the wide parameters space, which is worth focusing on. As a novel step, we exploit the strong connection between gravity and thermodynamics to further check models’ viability by investigating their thermodynamical quantities. In particular, we study whether the cosmological scenario fulfills the generalized second law of thermodynamics, and moreover, we contrast the two models, asking whether the evolution of the total entropy is in agreement with the expectation for a closed system. As a general result, we discuss whether thermodynamic constraints can be a valid complementary way to both constrain dark energy models and differentiate among rival scenarios.
Calculation of absolute protein-ligand binding free energy using distributed replica sampling.
Rodinger, Tomas; Howell, P Lynne; Pomès, Régis
2008-10-21
Distributed replica sampling [T. Rodinger et al., J. Chem. Theory Comput. 2, 725 (2006)] is a simple and general scheme for Boltzmann sampling of conformational space by computer simulation in which multiple replicas of the system undergo a random walk in reaction coordinate or temperature space. Individual replicas are linked through a generalized Hamiltonian containing an extra potential energy term or bias which depends on the distribution of all replicas, thus enforcing the desired sampling distribution along the coordinate or parameter of interest regardless of free energy barriers. In contrast to replica exchange methods, efficient implementation of the algorithm does not require synchronicity of the individual simulations. The algorithm is inherently suited for large-scale simulations using shared or heterogeneous computing platforms such as a distributed network. In this work, we build on our original algorithm by introducing Boltzmann-weighted jumping, which allows moves of a larger magnitude and thus enhances sampling efficiency along the reaction coordinate. The approach is demonstrated using a realistic and biologically relevant application; we calculate the standard binding free energy of benzene to the L99A mutant of T4 lysozyme. Distributed replica sampling is used in conjunction with thermodynamic integration to compute the potential of mean force for extracting the ligand from protein and solvent along a nonphysical spatial coordinate. Dynamic treatment of the reaction coordinate leads to faster statistical convergence of the potential of mean force than a conventional static coordinate, which suffers from slow transitions on a rugged potential energy surface.
Thermodynamic properties of organic compounds estimation methods, principles and practice
Janz, George J
1967-01-01
Thermodynamic Properties of Organic Compounds: Estimation Methods, Principles and Practice, Revised Edition focuses on the progression of practical methods in computing the thermodynamic characteristics of organic compounds. Divided into two parts with eight chapters, the book concentrates first on the methods of estimation. Topics presented are statistical and combined thermodynamic functions; free energy change and equilibrium conversions; and estimation of thermodynamic properties. The next discussions focus on the thermodynamic properties of simple polyatomic systems by statistical the
Energy Technology Data Exchange (ETDEWEB)
Yang, Y. Isaac [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)
2016-03-07
In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.
Zhou, S.; Solana, J. R.
2018-03-01
Monte Carlo NVT simulations have been performed to obtain the thermodynamic and structural properties and perturbation coefficients up to third order in the inverse temperature expansion of the Helmholtz free energy of fluids with potential models proposed in the literature for diamond and wurtzite lattices. These data are used to analyze performance of a coupling parameter series expansion (CPSE). The main findings are summarized as follows, (1) The CPSE provides accurate predictions of the first three coefficient in the inverse temperature expansion of Helmholtz free energy for the potential models considered and the thermodynamic properties of these fluids are predicted more accurately when the CPSE is truncated at second or third order. (2) The Barker-Henderson (BH) recipe is appropriate for determining the effective hard sphere diameter for strongly repulsive potential cores, but its performance worsens with increasing the softness of the potential core. (3) For some thermodynamic properties the first-order CPSE works better for the diamond potential, whose tail is dominated by repulsive interactions, than for the potential, whose tail is dominated by attractive interactions. However, the first-order CPSE provides unsatisfactory results for the excess internal energy and constant-volume excess heat capacity for the two potential models.
Hentz, A; Parkinson, G S; Quinn, P D; Muñoz-Márquez, M A; Woodruff, D P; Grande, P L; Schiwietz, G; Bailey, P; Noakes, T C Q
2009-03-06
The energy spectrum associated with scattering of 100 keV H+ ions from the outermost few atomic layers of Cu(111) in different scattering geometries provides direct evidence of trajectory-dependent electronic energy loss. Theoretical simulations, combining standard Monte Carlo calculations of the elastic scattering trajectories with coupled-channel calculations to describe inner-shell ionization and excitation as a function of impact parameter, reproduce the effects well and provide a means for far more complete analysis of medium-energy ion scattering data.
Thermodynamics of spinning branes and their dual field theories
DEFF Research Database (Denmark)
Harmark, Troels; Obers, N. A.
2000-01-01
We discuss general spinning p-branes of string and M-theory and use their thermodynamics along with the correspondence between near-horizon brane solutions and field theories with 16 supercharges to describe the thermodynamic behavior of these theories in the presence of voltages under the R......-symmetry. The thermodynamics is used to provide two pieces of evidence in favor of a smooth interpolation function between the free energy at weak and strong coupling of the field theory. (i) A computation of the boundaries of stability shows that for the D2, D3, D4, M2 and M5-branes the critical values of Omega/T in the two...... limits are remarkably close and (ii) The tree-level R^4 corrections to the spinning D3-brane generate a decrease in the free energy at strong coupling towards the weak coupling result. We also comment on the generalization to spinning brane bound states and their thermodynamics, which are relevant...
DEFF Research Database (Denmark)
Clausen, Lasse Røngaard
2014-01-01
Integrated and external torrefaction is analyzed and compared via thermodynamic modeling. In this paper, integrated torrefaction is defined as torrefaction integrated with entrained flow gasification. External torrefaction is defined as the decentralized production of torrefied wood pellets...... and centralized conversion of the pellets by entrained flow gasification. First, the syngas production of the two methods was compared. Second, the two methods were compared by considering complete biorefineries with either integrated torrefaction or external torrefaction. The first part of the analysis showed...... from external torrefaction to integrated torrefaction. The costs of this increase in energy efficiency are as follows: 1) more difficult transport, storage and handling of the biomass feedstock (wood chips vs. torrefied wood pellets); 2) reduced plant size; 3) no net electricity production; and 4...
Is applicable thermodynamics of negative temperature for living organisms?
Atanasov, Atanas Todorov
2017-11-01
During organismal development the moment of sexual maturity can be characterizes by nearly maximum basal metabolic rate and body mass. Once the living organism reaches extreme values of the mass and the basal metabolic rate, it reaches near equilibrium thermodynamic steady state physiological level with maximum organismal complexity. Such thermodynamic systems that reach equilibrium steady state level at maximum mass-energy characteristics can be regarded from the prospective of thermodynamics of negative temperature. In these systems the increase of the internal and free energy is accompanied with decrease of the entropy. In our study we show the possibility the living organisms to regard as thermodynamic system with negative temperature
Fluctuation theorems and atypical trajectories
International Nuclear Information System (INIS)
Sahoo, M; Lahiri, S; Jayannavar, A M
2011-01-01
In this work, we have studied simple models that can be solved analytically to illustrate various fluctuation theorems. These fluctuation theorems provide symmetries individually to the distributions of physical quantities such as the classical work (W c ), thermodynamic work (W), total entropy (Δs tot ) and dissipated heat (Q), when the system is driven arbitrarily out of equilibrium. All these quantities can be defined for individual trajectories. We have studied the number of trajectories which exhibit behaviour unexpected at the macroscopic level. As the time of observation increases, the fraction of such atypical trajectories decreases, as expected at the macroscale. The distributions for the thermodynamic work and entropy production in nonlinear models may exhibit a peak (most probable value) in the atypical regime without violating the expected average behaviour. However, dissipated heat and classical work exhibit a peak in the regime of typical behaviour only.
Free Energy Rate Density and Self-organization in Complex Systems
Georgiev, Georgi Yordanov; Gombos, Erin; Bates, Timothy; Henry, Kaitlin; Casey, Alexander; Daly, Michael
2015-01-01
One of the most important tasks in science is to understand the self-organization's arrow of time. To attempt this we utilize the connection between self-organization and non-equilibrium thermodynamics. Eric Chaisson calculated an exponential increase of Free Energy Rate Density (FERD) in Cosmic Evolution, from the Big Bang until now, paralleling the increase of system's structure. We term these studies "Devology". We connect FERD to the principle of least action for complex systems, driving ...
Partition thermodynamics of ionic surfactants between phosphatidylcholine vesicle and water phases
Chu, Shin-Chi; Hung, Chia-Hui; Wang, Shun-Cheng; Tsao, Heng-Kwong
2003-08-01
The partition of ionic surfactants (sodium alkyl sulfate and alkyl trimethyl ammonium bromide) between phosphatidylcholine vesicles and aqueous phase is investigated by simple conductometry under different temperatures. The experimental results can be well represented by the proposed regular solution theory and the thermodynamic parameters satisfy the thermodynamic consistency. The deviation from ideal partition is manifested through the effective interaction energy between lipid and surfactant wb, which is O(kT) large. It is found that wb rises as the alkyl chain is decreased for a specified head group. This is attributed to significant mismatch of chain lengths between surfactant and lipid molecules. The partition coefficient K declines with increasing temperature. The energy barrier from bilayer to aqueous phase, Δμ/kT∝ln K, is in the range of 16-26 kJ/mol. As the alkyl chain length is decreased for a given head group, Δμ is lowered by 1.3-1.5 kJ/mol per methylene group. Two independent analyses are employed to confirm this result. Using the thermodynamic parameters determined from experiments, the internal energy, entropy, and free energy of the partition process can be derived. Partition is essentially driven by the internal energy gain. The solubilizing ability, which is represented by the maximum surfactant-lipid ratio in the bilayer, Reb also decreases in accord with the K parameter. It is because the change in temperature influences the surfactant incorporation into the bilayer more than the formation of micelles.
Real-time terminal area trajectory planning for runway independent aircraft
Xue, Min
The increasing demand for commercial air transportation results in delays due to traffic queues that form bottlenecks along final approach and departure corridors. In urban areas, it is often infeasible to build new runways, and regardless of automation upgrades traffic must remain separated to avoid the wakes of previous aircraft. Vertical or short takeoff and landing aircraft as Runway Independent Aircraft (RIA) can increase passenger throughput at major urban airports via the use of vertiports or stub runways. The concept of simultaneous non-interfering (SNI) operations has been proposed to reduce traffic delays by creating approach and departure corridors that do not intersect existing fixed-wing routes. However, SNI trajectories open new routes that may overfly noise-sensitive areas, and RIA may generate more noise than traditional jet aircraft, particularly on approach. In this dissertation, we develop efficient SNI noise abatement procedures applicable to RIA. First, we introduce a methodology based on modified approximated cell-decomposition and Dijkstra's search algorithm to optimize longitudinal plane (2-D) RIA trajectories over a cost function that minimizes noise, time, and fuel use. Then, we extend the trajectory optimization model to 3-D with a k-ary tree as the discrete search space. We incorporate geography information system (GIS) data, specifically population, into our objective function, and focus on a practical case study: the design of SNI RIA approach procedures to Baltimore-Washington International airport. Because solutions were represented as trim state sequences, we incorporated smooth transition between segments to enable more realistic cost estimates. Due to the significant computational complexity, we investigated alternative more efficient optimization techniques applicable to our nonlinear, non-convex, heavily constrained, and discontinuous objective function. Comparing genetic algorithm (GA) and adaptive simulated annealing (ASA
Phonon spectra, electronic, and thermodynamic properties of WS2 nanotubes.
Evarestov, Robert A; Bandura, Andrei V; Porsev, Vitaly V; Kovalenko, Alexey V
2017-11-15
Hybrid density functional theory calculations are performed for the first time on the phonon dispersion and thermodynamic properties of WS 2 -based single-wall nanotubes. Symmetry analysis is presented for phonon modes in nanotubes using the standard (crystallographic) factorization for line groups. Symmetry and the number of infra-red and Raman active modes in achiral WS 2 nanotubes are given for armchair and zigzag chiralities. It is demonstrated that a number of infrared and Raman active modes is independent on the nanotube diameter. The zone-folding approach is applied to find out an impact of curvature on electron and phonon band structure of nanotubes rolled up from the monolayer. Phonon frequencies obtained both for layers and nanotubes are used to compute the thermal contributions to their thermodynamic functions. The temperature dependences of energy, entropy, and heat capacity of nanotubes are estimated with respect to those of the monolayer. The role of phonons in the stability estimation of nanotubes is discussed based on Helmholtz free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Latella, Ivan; Pérez-Madrid, Agustín
2013-10-01
The local thermodynamics of a system with long-range interactions in d dimensions is studied using the mean-field approximation. Long-range interactions are introduced through pair interaction potentials that decay as a power law in the interparticle distance. We compute the local entropy, Helmholtz free energy, and grand potential per particle in the microcanonical, canonical, and grand canonical ensembles, respectively. From the local entropy per particle we obtain the local equation of state of the system by using the condition of local thermodynamic equilibrium. This local equation of state has the form of the ideal gas equation of state, but with the density depending on the potential characterizing long-range interactions. By volume integration of the relation between the different thermodynamic potentials at the local level, we find the corresponding equation satisfied by the potentials at the global level. It is shown that the potential energy enters as a thermodynamic variable that modifies the global thermodynamic potentials. As a result, we find a generalized Gibbs-Duhem equation that relates the potential energy to the temperature, pressure, and chemical potential. For the marginal case where the power of the decaying interaction potential is equal to the dimension of the space, the usual Gibbs-Duhem equation is recovered. As examples of the application of this equation, we consider spatially uniform interaction potentials and the self-gravitating gas. We also point out a close relationship with the thermodynamics of small systems.
Surface dependency in thermodynamics of ideal gases
International Nuclear Information System (INIS)
Sisman, Altug
2004-01-01
The Casimir-like size effect rises in ideal gases confined in a finite domain due to the wave character of atoms. By considering this effect, thermodynamic properties of an ideal gas confined in spherical and cylindrical geometries are derived and compared with those in rectangular geometry. It is seen that an ideal gas exhibits an unavoidable quantum surface free energy and surface over volume ratio becomes a control variable on thermodynamic state functions in microscale. Thermodynamics turns into non-extensive thermodynamics and geometry difference becomes a driving force since the surface over volume ratio depends on the geometry
Thermodynamics of nanoadsorption from solution: Theoretical and experimental research
International Nuclear Information System (INIS)
Wen, Yan-Zhen; Xue, Yong-Qiang; Cui, Zi-Xiang; Wang, Yan
2015-01-01
Highlights: • The thermodynamic theory of nanoadsorption was proposed. • The thermodynamic relations of nanoadsorption were derived. • The results of the experiments are accord with the theory. - Abstract: In this study, the effect of nanoparticle size on adsorption thermodynamics was investigated. The results of theoretical and experimental studies show that particle size significantly affects the equilibrium constant and thermodynamic properties of nanoadsorption. Relationships between the equilibrium constant, thermodynamic properties and particle size were derived using the thermodynamic theory of nanoadsorption. The equilibrium constant and thermodynamic properties were obtained by investigating the adsorption of Cu 2+ onto different sizes of nano-ZnO and the adsorption of Ag + onto different sizes of nano-TiO 2 . Good agreement was achieved between results obtained by experiments and predicted by theoretical analyses. The equilibrium constant and the molar Gibbs free energy of nanoadsorption were found to increase with smaller nanoparticle size. However, the effects of particle size on the molar enthalpy and the molar entropy are uncertain. In addition, the molar Gibbs free energy, the molar enthalpy, the molar entropy and the logarithm of the equilibrium constant are linearly related to the reciprocal of the diameter of the nanoparticle. The thermodynamic properties revealed in this study may provide important guidelines for research and application in the field of nanoadsorption
Directory of Open Access Journals (Sweden)
Miyo Takahiro
2004-11-01
Full Text Available Abstract Background Seasonal fluctuations in susceptibility to organophosphate insecticides were observed in the Katsunuma population of Drosophila melanogaster for two consecutive years; susceptibility to three organophosphates tended to increase in the fall. To examine the hypothesis that variation in fitness among resistant and susceptible genotypes could trigger the change of genetic constitution within the fall population, we investigated density-independent population projection trajectories starting from single adult females with characteristics of chromosome-substituted lines resistant and susceptible to the three organophosphates. Results Density-independent population projection trajectories, expressed as the ratios of the number of each chromosome-substituted line to that of line SSS, for which all chromosomes were derived from the susceptible line, showed significant declines in numbers with time for all the resistant chromosome-substituted lines. Conclusion The declining tendency in the density-independent population projection trajectories of the resistant chromosome-substituted lines could explain the simultaneous decline in the levels of resistance to the three organophosphates, observed in the Katsunuma population in the fall.
Jarzynski equality: connections to thermodynamics and the second law.
Palmieri, Benoit; Ronis, David
2007-01-01
The one-dimensional expanding ideal gas model is used to compute the exact nonequilibrium distribution function. The state of the system during the expansion is defined in terms of local thermodynamics quantities. The final equilibrium free energy, obtained a long time after the expansion, is compared against the free energy that appears in the Jarzynski equality. Within this model, where the Jarzynski equality holds rigorously, the free energy change that appears in the equality does not equal the actual free energy change of the system at any time of the process. More generally, the work bound that is obtained from the Jarzynski equality is an upper bound to the upper bound that is obtained from the first and second laws of thermodynamics. The cancellation of the dissipative (nonequilibrium) terms that result in the Jarzynski equality is shown in the framework of response theory. This is used to show that the intuitive assumption that the Jarzynski work bound becomes equal to the average work done when the system evolves quasistatically is incorrect under some conditions.
Designing train-speed trajectory with energy efficiency and service quality
Jia, Jiannan; Yang, Kai; Yang, Lixing; Gao, Yuan; Li, Shukai
2018-05-01
With the development of automatic train operations, optimal trajectory design is significant to the performance of train operations in railway transportation systems. Considering energy efficiency and service quality, this article formulates a bi-objective train-speed trajectory optimization model to minimize simultaneously the energy consumption and travel time in an inter-station section. This article is distinct from previous studies in that more sophisticated train driving strategies characterized by the acceleration/deceleration gear, the cruising speed, and the speed-shift site are specifically considered. For obtaining an optimal train-speed trajectory which has equal satisfactory degree on both objectives, a fuzzy linear programming approach is applied to reformulate the objectives. In addition, a genetic algorithm is developed to solve the proposed train-speed trajectory optimization problem. Finally, a series of numerical experiments based on a real-world instance of Beijing-Tianjin Intercity Railway are implemented to illustrate the practicability of the proposed model as well as the effectiveness of the solution methodology.
Thermodynamics of nuclear track chemical etching
Rana, Mukhtar Ahmed
2018-05-01
This is a brief paper with new and useful scientific information on nuclear track chemical etching. Nuclear track etching is described here by using basic concepts of thermodynamics. Enthalpy, entropy and free energy parameters are considered for the nuclear track etching. The free energy of etching is determined using etching experiments of fission fragment tracks in CR-39. Relationship between the free energy and the etching temperature is explored and is found to be approximately linear. The above relationship is discussed. A simple enthalpy-entropy model of chemical etching is presented. Experimental and computational results presented here are of fundamental interest in nuclear track detection methodology.
New methods of thermodynamics; Nouvelles methodes en thermodynamique
Energy Technology Data Exchange (ETDEWEB)
NONE
2001-07-01
This day, organized by the SFT French Society of Thermology, took stock on the new methods in the domain of the thermodynamics. Eight papers have been presented during this day: new developments of the thermodynamics in finite time; the optimal efficiency of energy converters; a version of non-equilibrium thermodynamics with entropy and information as positive and negative thermal change; the role of thermodynamics in process integration; application of the thermodynamics to critical nuclear accidents; the entropic analysis help in the case of charge and discharge state of an energy storage process; fluid flow threw a stable state in the urban hydraulic; a computer code for phase diagram prediction. (A.L.B.)
Thermodynamic calculations in ternary titanium–aluminium–manganese system
Directory of Open Access Journals (Sweden)
ANA I. KOSTOV
2008-04-01
Full Text Available Thermodynamic calculations in the ternary Ti–Al–Mn system are shown in this paper. The thermodynamic calculations were performed using the FactSage thermochemical software and database, with the aim of determining thermodynamic properties, such as activities, coefficient of activities, partial and integral values of the enthalpies and Gibbs energies of mixing and excess energies at two different temperatures: 2000 and 2100 K. Bearing in mind that no experimental data for the Ti–Al–Mn ternary system have been obtained or reported. The obtained results represent a good base for further thermodynamic analysis and may be useful as a comparison with some future critical experimental results and thermodynamic optimization of this system.
International Nuclear Information System (INIS)
Ziębik, Andrzej; Malik, Tomasz; Liszka, Marcin
2015-01-01
Integration of a CHP steam plant with an installation of coal gasification and gas turbine leads to an IGCC-CHP (integrated gasification combined cycle-combined heat and power). Two installations of coal gasification have been analyzed, i.e. pressurized entrained flow gasifier – case 1 and pressurized fluidized bed gasifier with CO_2 recirculation – case 2. Basing on the results of mathematical modelling of an IGCC-CHP plant, the algorithms of calculating typical energy indices have been derived. The following energy indices are considered, i.e. coefficient of heat performance and relative savings of chemical energy of fuels. The results of coefficients of heat performance are contained between 1.87 and 2.37. Values exceeding 1 are thermodynamically justified because the idea of cogeneration of heat and electricity based on combining cycles of the heat engine and heat pump the efficiency of which exceeds 1. Higher values concerning waste heat replace more thermodynamically effective sources of heat in CHP plants. Relative savings of the chemical energy of fuels are similar in both cases of IGCC-CHP plants and are contained between the lower value of the CHP (combined heat and power) plants fuelled with coal and higher value of CHP plants fired with natural gas. - Highlights: • Energy savings of fuel is an adequate measure of cogeneration. • Relative energy savings of IGCC-CHP is near the result of a gas and steam CHP. • COHP (coefficient of heat performance) can help to divide fuel between heat fluxes. • Higher values of COHP in the case of waste heat recovery result from the lower thermal parameters.
Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.
Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R
2014-10-14
The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a
SNG from coal: thermodynamic and kinetic constraints; use of nuclear energy
International Nuclear Information System (INIS)
Shapira, D.
1983-01-01
Part I contains an analysis of the thermodynamic constraints of converting coal to SNG. It is shown that the thermodynamic constraints that limit the thermal efficiency are not inherent, but are the result of design decisions, based on available technology, as well as on the kinetic properties of available catalysts. The latter, limits the yield of methane to that obtainable at global equilibrium over carbon in the presence of CO, H 2 , CO 2 and H 2 O. The equilibrium composition is shown to be independent of the thermodynamic properties of the char or coal fed. These limitations give the nonisothermal two-stage processes significant thermodynamic advantages. The analysis in part I results in suggesting directions for modifying present processes in order to obtain higher thermal efficiences. It also presents two-stage process schemes which may have significant advantages over present technology. As the methodology used for the thermodynamic analysis contains some novel elements, it should be of interest to the reaction engineer in general, and should be applicable to a wide range of catalytic and noncatalytic processes. Part II focuses on the use of nuclear energy in the production of synthetic fuel. Two processes for the production of hydrogen (which is used in coal-to-SNG processes) are analyzed and compared. The two processes are: 1) hydrogen from electrolysis of water using nuclear heat. 2) Hydrogen from steam reforming of methane using nuclear heat. The method used is differential economic analysis which focuses on evaluating the inherent advantages and disadvantages of the proposed technologies. Part II shows that the use of high temperature heat in production of hydrogen from coal is less attractive than the use of the same heat to generate electricity and split water into H 2 and O 2
Thermodynamic analysis of (Ni, Fe)3Al formation by mechanical alloying
International Nuclear Information System (INIS)
Adabavazeh, Z.; Karimzadeh, F.; Enayati, M.H.
2012-01-01
Highlights: ► (Ni, Fe) 3 Al intermetallic compound was synthesized by mechanical alloying. ► We use a thermodynamic analysis to predict the more stable phase. ► We calculate the Gibbs free-energy changes by using extended Miedema model. ► The results of MA compared with thermodynamic analysis and showed a good agreement with it. - Abstract: (Ni, Fe) 3 Al intermetallic compound was synthesized by mechanical alloying (MA) of Ni, Fe and Al elemental powder mixtures of composition Ni 50 Fe 25 Al 25 . Phase transformation and microstructure characteristics of the alloy powders were investigated by X-ray diffraction (XRD). The results show that mechanical alloying resulted in a Ni (Al, Fe) solid solution. By continued milling, this structure transformed to the disordered (Ni, Fe) 3 Al intermetallic compound. A thermodynamic model developed on the basis of extended theory of Miedema is used to calculate the Gibbs free-energy changes. Final product of MA is a phase having minimal Gibbs free energy compared with other competing phases in Ni–Fe–Al system. However in Ni–Fe–Al system, the most stable phase at all compositions is intermetallic compound (not amorphous phase or solid solution). The results of MA were compared with thermodynamic analysis and revealed the leading role of thermodynamic on the formation of MA product prediction.
International Nuclear Information System (INIS)
Oró, Eduard; Depoorter, Victor; Pflugradt, Noah; Salom, Jaume
2015-01-01
In the last years the total energy demand of data centres has experienced a dramatic increase which is expected to continue. This is why data centres industry and researchers are working on implementing energy efficiency measures and integrating renewable energy to overcome energy dependence and to reduce operational costs and CO 2 emissions. The cooling system of these unique infrastructures can account for 40% of the total energy consumption. To reduce the energy consumption, free cooling strategies are used more and more, but so far there has been little research about the potential of thermal energy storage (TES) solutions to match energy demand and energy availability. Hence, this work intends to provide an overview of the potential of the integration of direct air free cooling strategy and TES systems into data centres located at different European locations. For each location, the benefit of using direct air free cooling is evaluated energetically and economically for a data centre of 1250 kW. The use of direct air free cooling is shown to be feasible. This does not apply the TES systems by itself. But when using TES in combination with an off-peak electricity tariff the operational cooling cost can be drastically reduced. - Highlights: • The total annual hours for direct air free cooling in data centres are calculated. • The potential of TES integration in data centres is evaluated. • The implementation of TES to store the ambient air cold is not recommended. • TES is feasible if combined with redundant chillers and off-peak electricity price. • The cooling electricity cost is being reduced up to 51%, depending on the location
Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations
Directory of Open Access Journals (Sweden)
Cedrix J. Dongmo Foumthuim
2018-01-01
Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.
MCB. A continuous energy Monte Carlo burnup simulation code
International Nuclear Information System (INIS)
Cetnar, J.; Wallenius, J.; Gudowski, W.
1999-01-01
A code for integrated simulation of neutrinos and burnup based upon continuous energy Monte Carlo techniques and transmutation trajectory analysis has been developed. Being especially well suited for studies of nuclear waste transmutation systems, the code is an extension of the well validated MCNP transport program of Los Alamos National Laboratory. Among the advantages of the code (named MCB) is a fully integrated data treatment combined with a time-stepping routine that automatically corrects for burnup dependent changes in reaction rates, neutron multiplication, material composition and self-shielding. Fission product yields are treated as continuous functions of incident neutron energy, using a non-equilibrium thermodynamical model of the fission process. In the present paper a brief description of the code and applied methods are given. (author)
Thermodynamics of Weakly Measured Quantum Systems.
Alonso, Jose Joaquin; Lutz, Eric; Romito, Alessandro
2016-02-26
We consider continuously monitored quantum systems and introduce definitions of work and heat along individual quantum trajectories that are valid for coherent superposition of energy eigenstates. We use these quantities to extend the first and second laws of stochastic thermodynamics to the quantum domain. We illustrate our results with the case of a weakly measured driven two-level system and show how to distinguish between quantum work and heat contributions. We finally employ quantum feedback control to suppress detector backaction and determine the work statistics.
Liu, Jianbo; Song, Kihyung; Hase, William L; Anderson, Scott L
2005-12-22
Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.
Thermodynamic description of Hofmeister effects on the LCST of thermosensitive polymers.
Heyda, Jan; Dzubiella, Joachim
2014-09-18
Cosolvent effects on protein or polymer collapse transitions are typically discussed in terms of a two-state free energy change that is strictly linear in cosolute concentration. Here we investigate in detail the nonlinear thermodynamic changes of the collapse transition occurring at the lower critical solution temperature (LCST) of the role-model polymer poly(N-isopropylacrylamide) [PNIPAM] induced by Hofmeister salts. First, we establish an equation, based on the second-order expansion of the two-state free energy in concentration and temperature space, which excellently fits the experimental LCST curves and enables us to directly extract the corresponding thermodynamic parameters. Linear free energy changes, grounded on generic excluded-volume mechanisms, are indeed found for strongly hydrated kosmotropes. In contrast, for weakly hydrated chaotropes, we find significant nonlinear changes related to higher order thermodynamic derivatives of the preferential interaction parameter between salts and polymer. The observed non-monotonic behavior of the LCST can then be understood from a not yet recognized sign change of the preferential interaction parameter with salt concentration. Finally, we find that solute partitioning models can possibly predict the linear free energy changes for the kosmotropes, but fail for chaotropes. Our findings cast strong doubt on their general applicability to protein unfolding transitions induced by chaotropes.
Application of thermodynamics to silicate crystalline solutions
Saxena, S. K.
1972-01-01
A review of thermodynamic relations is presented, describing Guggenheim's regular solution models, the simple mixture, the zeroth approximation, and the quasi-chemical model. The possibilities of retrieving useful thermodynamic quantities from phase equilibrium studies are discussed. Such quantities include the activity-composition relations and the free energy of mixing in crystalline solutions. Theory and results of the study of partitioning of elements in coexisting minerals are briefly reviewed. A thermodynamic study of the intercrystalline and intracrystalline ion exchange relations gives useful information on the thermodynamic behavior of the crystalline solutions involved. Such information is necessary for the solution of most petrogenic problems and for geothermometry. Thermodynamic quantities for tungstates (CaWO4-SrWO4) are calculated.
Bueno, Marta; Camacho, Carlos J; Sancho, Javier
2007-09-01
The bioinformatics revolution of the last decade has been instrumental in the development of empirical potentials to quantitatively estimate protein interactions for modeling and design. Although computationally efficient, these potentials hide most of the relevant thermodynamics in 5-to-40 parameters that are fitted against a large experimental database. Here, we revisit this longstanding problem and show that a careful consideration of the change in hydrophobicity, electrostatics, and configurational entropy between the folded and unfolded state of aliphatic point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. This significant improvement is achieved with essentially no free parameters, validating past theoretical and experimental efforts to understand the thermodynamics of protein folding. Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost completely compensated by similar interactions operating in the unfolded ensemble. Not surprisingly, the problem of properly accounting for the solvent contribution to the free energy of polar and charged group mutations, as well as of mutations that disrupt the protein backbone remains open. 2007 Wiley-Liss, Inc.
Local thermodynamic equilibrium in rapidly heated high energy density plasmas
International Nuclear Information System (INIS)
Aslanyan, V.; Tallents, G. J.
2014-01-01
Emission spectra and the dynamics of high energy density plasmas created by optical and Free Electron Lasers (FELs) depend on the populations of atomic levels. Calculations of plasma emission and ionization may be simplified by assuming Local Thermodynamic Equilibrium (LTE), where populations are given by the Saha-Boltzmann equation. LTE can be achieved at high densities when collisional processes are much more significant than radiative processes, but may not be valid if plasma conditions change rapidly. A collisional-radiative model has been used to calculate the times taken by carbon and iron plasmas to reach LTE at varying densities and heating rates. The effect of different energy deposition methods, as well as Ionization Potential Depression are explored. This work shows regimes in rapidly changing plasmas, such as those created by optical lasers and FELs, where the use of LTE is justified, because timescales for plasma changes are significantly longer than the times needed to achieve an LTE ionization balance
Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)
Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei
2014-01-01
NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.
Lee, M.W.; Meuwly, M.
2013-01-01
The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.
Energy Optimal Trajectories in Human Arm Motion Aiming for Assistive Robots
Directory of Open Access Journals (Sweden)
Lelai Zhou
2017-01-01
Full Text Available The energy expenditure in human arm has been of great interests for seeking optimal human arm trajectories. This paper presents a new way for calculating metabolic energy consumption of human arm motions. The purpose is to reveal the relationship between the energy consumption and the trajectory of arm motion, and further, the acceleration and arm orientation contributions. Human arm motion in horizontal plane is investigated by virtue of Qualisys motion capture system. The motion data is post-processed by a biomechanical model to obtain the metabolic expenditure. Results on the arm motion kinematics, dynamics and metabolic energy consumption, are included.
Quantum Rényi relative entropies affirm universality of thermodynamics.
Misra, Avijit; Singh, Uttam; Bera, Manabendra Nath; Rajagopal, A K
2015-10-01
We formulate a complete theory of quantum thermodynamics in the Rényi entropic formalism exploiting the Rényi relative entropies, starting from the maximum entropy principle. In establishing the first and second laws of quantum thermodynamics, we have correctly identified accessible work and heat exchange in both equilibrium and nonequilibrium cases. The free energy (internal energy minus temperature times entropy) remains unaltered, when all the entities entering this relation are suitably defined. Exploiting Rényi relative entropies we have shown that this "form invariance" holds even beyond equilibrium and has profound operational significance in isothermal process. These results reduce to the Gibbs-von Neumann results when the Rényi entropic parameter α approaches 1. Moreover, it is shown that the universality of the Carnot statement of the second law is the consequence of the form invariance of the free energy, which is in turn the consequence of maximum entropy principle. Further, the Clausius inequality, which is the precursor to the Carnot statement, is also shown to hold based on the data processing inequalities for the traditional and sandwiched Rényi relative entropies. Thus, we find that the thermodynamics of nonequilibrium state and its deviation from equilibrium together determine the thermodynamic laws. This is another important manifestation of the concepts of information theory in thermodynamics when they are extended to the quantum realm. Our work is a substantial step towards formulating a complete theory of quantum thermodynamics and corresponding resource theory.
Triangle-free graphs whose independence number equals the degree
DEFF Research Database (Denmark)
Brandt, Stephan
2010-01-01
In a triangle-free graph, the neighbourhood of every vertex is an independent set. We investigate the class S of triangle-free graphs where the neighbourhoods of vertices are maximum independent sets. Such a graph G must be regular of degree d = α (G) and the fractional chromatic number must sati...
Thermodynamical Aspects of Modified Holographic Dark Energy Model
International Nuclear Information System (INIS)
Li Hui; Zhang Yi
2014-01-01
We investigate the unified first law and the generalized second law in a modified holographic dark energy model. The thermodynamical analysis on the apparent horizon can work and the corresponding entropy formula is extracted from the systematic algorithm. The entropy correction term depends on the extra-dimension number of the brane as expected, but the interplay between the correction term and the extra dimensions is more complicated. With the unified first law of thermodynamics well-founded, the generalized second law of thermodynamics is discussed and it is found that the second law can be violated in certain circumstances. Particularly, if the number of the extra dimensions is larger than one, the generalized law of thermodynamics is always satisfied; otherwise, the validity of the second law can only be guaranteed with the Hubble radius greatly smaller than the crossover scale r c of the 5-dimensional DGP model. (geophysics, astronomy, and astrophysics)
International Nuclear Information System (INIS)
Toghyani, Somayeh; Baniasadi, Ehsan; Afshari, Ebrahim
2016-01-01
Highlights: • The performance of an integrated nano-fluid based solar Rankine cycle is studied. • The effect of solar intensity, ambient temperature, and volume fraction is evaluated. • The concept of Finite Time Thermodynamics is applied. • It is shown that CuO/oil nano-fluid has the best performance from exergy perspective. - Abstract: In this paper, the performance of an integrated Rankine power cycle with parabolic trough solar system and a thermal storage system is simulated based on four different nano-fluids in the solar collector system, namely CuO, SiO_2, TiO_2 and Al_2O_3. The effects of solar intensity, dead state temperature, and volume fraction of different nano-particles on the performance of the integrated cycle are studied using second law of thermodynamics. Also, the genetic algorithm is applied to optimize the net output power of the solar Rankine cycle. The solar thermal energy is stored in a two-tank system to improve the overall performance of the system when sunlight is not available. The concept of Finite Time Thermodynamics is applied for analyzing the performance of the solar collector and thermal energy storage system. This study reveals that by increasing the volume fraction of nano-particles, the exergy efficiency of the system increases. At higher dead state temperatures, the overall exergy efficiency is increased, and higher solar irradiation leads to considerable increase of the output power of the system. It is shown that among the selected nano-fluids, CuO/oil has the best performance from exergy perspective.
International Nuclear Information System (INIS)
Xu, H.
1999-01-01
In this letter, the Sverjensky-Molling equation derived from a linear free energy relationship is used to calculate the Gibbs free energies of formation of zirconolite crystalline phases (MZrTi 2 O 7 and MHfTi 2 O 7 ) from the known thermodynamic properties of the corresponding aqueous divalent cations (M 2+ ). Sverjensky-Molling equation is expressed as ΔG 0 f,M v X =a M v X ΔG 0 n,M 2+ +b M v X +β M v X r M 2+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 2+ is the ionic radius of M 2+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 2+ is the standard non-solvation energy of cation M 2+ . This relationship can be used to predict the Gibbs free energies of formation of various fictive phases (such as BaZrTi 2 O 7 , SrZrTi 2 O 7 , PbZrTi 2 O 7 , etc.) that may form solid solution with CaZrTi 2 O 7 in actual Synroc-based nuclear waste forms. Based on obtained linear free energy relationships, it is predicted that large cations (e.g., Ba and Ra) prefer to be in perovskite structure, and small cations (e.g., Ca, Zn, and Cd) prefer to be in zirconolite structure. (orig.)
Quantum trajectories in complex space: One-dimensional stationary scattering problems
International Nuclear Information System (INIS)
Chou, C.-C.; Wyatt, Robert E.
2008-01-01
One-dimensional time-independent scattering problems are investigated in the framework of the quantum Hamilton-Jacobi formalism. The equation for the local approximate quantum trajectories near the stagnation point of the quantum momentum function is derived, and the first derivative of the quantum momentum function is related to the local structure of quantum trajectories. Exact complex quantum trajectories are determined for two examples by numerically integrating the equations of motion. For the soft potential step, some particles penetrate into the nonclassical region, and then turn back to the reflection region. For the barrier scattering problem, quantum trajectories may spiral into the attractors or from the repellers in the barrier region. Although the classical potentials extended to complex space show different pole structures for each problem, the quantum potentials present the same second-order pole structure in the reflection region. This paper not only analyzes complex quantum trajectories and the total potentials for these examples but also demonstrates general properties and similar structures of the complex quantum trajectories and the quantum potentials for one-dimensional time-independent scattering problems
Shenoy, Vivek B; Wang, Hailong; Wang, Xiao
2016-02-06
We propose a chemo-mechanical model based on stress-dependent recruitment of myosin motors to describe how the contractility, polarization and strain in cells vary with the stiffness of their surroundings and their shape. A contractility tensor, which depends on the distribution of myosin motors, is introduced to describe the chemical free energy of the cell due to myosin recruitment. We explicitly include the contributions to the free energy that arise from mechanosensitive signalling pathways (such as the SFX, Rho-Rock and MLCK pathways) through chemo-mechanical coupling parameters. Taking the variations of the total free energy, which consists of the chemical and mechanical components, in accordance with the second law of thermodynamics provides equations for the temporal evolution of the active stress and the contractility tensor. Following this approach, we are able to recover the well-known Hill relation for active stresses, based on the fundamental principles of irreversible thermodynamics rather than phenomenology. We have numerically implemented our free energy-based approach to model spatial distribution of strain and contractility in (i) cells supported by flexible microposts, (ii) cells on two-dimensional substrates, and (iii) cells in three-dimensional matrices. We demonstrate how the polarization of the cells and the orientation of stress fibres can be deduced from the eigenvalues and eigenvectors of the contractility tensor. Our calculations suggest that the chemical free energy of the cell decreases with the stiffness of the extracellular environment as the cytoskeleton polarizes in response to stress-dependent recruitment of molecular motors. The mechanical energy, which includes the strain energy and motor potential energy, however, increases with stiffness, but the overall energy is lower for cells in stiffer environments. This provides a thermodynamic basis for durotaxis, whereby cells preferentially migrate towards stiffer regions of the
Ben-Naim, Arieh
1987-01-01
This book deals with a subject that has been studied since the beginning of physical chemistry. Despite the thousands of articles and scores of books devoted to solvation thermodynamics, I feel that some fundamen tal and well-established concepts underlying the traditional approach to this subject are not satisfactory and need revision. The main reason for this need is that solvation thermodynamics has traditionally been treated in the context of classical (macroscopic) ther modynamics alone. However, solvation is inherently a molecular pro cess, dependent upon local rather than macroscopic properties of the system. Therefore, the starting point should be based on statistical mechanical methods. For many years it has been believed that certain thermodynamic quantities, such as the standard free energy (or enthalpy or entropy) of solution, may be used as measures of the corresponding functions of solvation of a given solute in a given solvent. I first challenged this notion in a paper published in 1978 b...
Kleidon, Axel
2012-01-01
The Earth's chemical composition far from chemical equilibrium is unique in our Solar System, and this uniqueness has been attributed to the presence of widespread life on the planet. Here, I show how this notion can be quantified using non-equilibrium thermodynamics. Generating and maintaining disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. With this approach and associated limits, I show that the ability of abiotic processes to generate geochemical free energy that can be used to transform the surface–atmosphere environment is strongly limited to less than 1 TW. Photosynthetic life generates more than 200 TW by performing photochemistry, thereby substantiating the notion that a geochemical composition far from equilibrium can be a sign for strong biotic activity. Present-day free energy consumption by human activity in the form of industrial activity and human appropriated net primary productivity is of the order of 50 TW and therefore constitutes a considerable term in the free energy budget of the planet. When aiming to predict the future of the planet, we first note that since global changes are closely related to this consumption of free energy, and the demands for free energy by human activity are anticipated to increase substantially in the future, the central question in the context of predicting future global change is then how human free energy demands can increase sustainably without negatively impacting the ability of the Earth system to generate free energy. This question could be evaluated with climate models, and the potential deficiencies in these models to adequately represent the thermodynamics of the Earth system are discussed. Then, I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would
Kleidon, Axel
2012-03-13
The Earth's chemical composition far from chemical equilibrium is unique in our Solar System, and this uniqueness has been attributed to the presence of widespread life on the planet. Here, I show how this notion can be quantified using non-equilibrium thermodynamics. Generating and maintaining disequilibrium in a thermodynamic variable requires the extraction of power from another thermodynamic gradient, and the second law of thermodynamics imposes fundamental limits on how much power can be extracted. With this approach and associated limits, I show that the ability of abiotic processes to generate geochemical free energy that can be used to transform the surface-atmosphere environment is strongly limited to less than 1 TW. Photosynthetic life generates more than 200 TW by performing photochemistry, thereby substantiating the notion that a geochemical composition far from equilibrium can be a sign for strong biotic activity. Present-day free energy consumption by human activity in the form of industrial activity and human appropriated net primary productivity is of the order of 50 TW and therefore constitutes a considerable term in the free energy budget of the planet. When aiming to predict the future of the planet, we first note that since global changes are closely related to this consumption of free energy, and the demands for free energy by human activity are anticipated to increase substantially in the future, the central question in the context of predicting future global change is then how human free energy demands can increase sustainably without negatively impacting the ability of the Earth system to generate free energy. This question could be evaluated with climate models, and the potential deficiencies in these models to adequately represent the thermodynamics of the Earth system are discussed. Then, I illustrate the implications of this thermodynamic perspective by discussing the forms of renewable energy and planetary engineering that would
A simulation assessment of the thermodynamics of dense ion-dipole mixtures with polarization
International Nuclear Information System (INIS)
Bastea, Sorin
2014-01-01
Molecular dynamics (MD) simulations are employed to ascertain the relative importance of various electrostatic interaction contributions, including induction interactions, to the thermodynamics of dense, hot ion-dipole mixtures. In the absence of polarization, we find that an MD-constrained free energy term accounting for the ion-dipole interactions, combined with well tested ionic and dipolar contributions, yields a simple, fairly accurate free energy form that may be a better option for describing the thermodynamics of such mixtures than the mean spherical approximation (MSA). Polarization contributions induced by the presence of permanent dipoles and ions are found to be additive to a good approximation, simplifying the thermodynamic modeling. We suggest simple free energy corrections that account for these two effects, based in part on standard perturbative treatments and partly on comparisons with MD simulation. Even though the proposed approximations likely need further study, they provide a first quantitative assessment of polarization contributions at high densities and temperatures and may serve as a guide for future modeling efforts
Antenna entropy in plant photosystems does not reduce the free energy for primary charge separation.
Jennings, Robert C; Zucchelli, Giuseppe
2014-12-01
We have investigated the concept of the so-called "antenna entropy" of higher plant photosystems. Several interesting points emerge: 1. In the case of a photosystemwhich harbours an excited state, the “antenna entropy” is equivalent to the configurational (mixing) entropy of a thermodynamic canonical ensemble. The energy associated with this parameter has been calculated for a hypothetical isoenergetic photosystem, photosystem I and photosystem II, and comes out in the range of 3.5 - 8% of the photon energy considering 680 nm. 2. The “antenna entropy” seems to be a rather unique thermodynamic phenomenon, in as much as it does not modify the free energy available for primary photochemistry, as has been previously suggested. 3. It is underlined that this configurational (mixing) entropy, unlike heat dispersal in a thermal system, does not involve energy dilution. This points out an important difference between thermal and electronic energy dispersal. Copyright © 2014 Elsevier B.V. All rights reserved.
Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions.
Li, Isaac T S; Walker, Gilbert C
2010-05-12
The hydrophobic interaction is significantly responsible for driving protein folding and self-assembly. To understand it, the thermodynamics, the role of water structure, the dewetting process surrounding hydrophobes, and related aspects have undergone extensive investigations. Here, we examine the hypothesis that polymer-solvent interfacial free energy is adequate to describe the energetics of the collapse of a hydrophobic homopolymer chain at fixed temperature, which serves as a much simplified model for studying the hydrophobic collapse of a protein. This implies that changes in polymer-solvent interfacial free energy should be directly proportional to the force to extend a collapsed polymer into a bad solvent. To test this hypothesis, we undertook single-molecule force spectroscopy on a collapsed, single, polystyrene chain in water-ethanol and water-salt mixtures where we measured the monomer solvation free energy from an ensemble average conformations. Different proportions within the binary mixture were used to create solvents with different interfacial free energies with polystyrene. In these mixed solvents, we observed a linear correlation between the interfacial free energy and the force required to extend the chain into solution, which is a direct measure of the solvation free energy per monomer on a single chain at room temperature. A simple analytical model compares favorably with the experimental results. This knowledge supports a common assumption that explicit water solvent may not be necessary for cases whose primary concerns are hydrophobic interactions and hydrophobic hydration.
High-Speed Solution of Spacecraft Trajectory Problems Using Taylor Series Integration
Scott, James R.; Martini, Michael C.
2010-01-01
It has been known for some time that Taylor series (TS) integration is among the most efficient and accurate numerical methods in solving differential equations. However, the full benefit of the method has yet to be realized in calculating spacecraft trajectories, for two main reasons. First, most applications of Taylor series to trajectory propagation have focused on relatively simple problems of orbital motion or on specific problems and have not provided general applicability. Second, applications that have been more general have required use of a preprocessor, which inevitably imposes constraints on computational efficiency. The latter approach includes the work of Berryman et al., who solved the planetary n-body problem with relativistic effects. Their work specifically noted the computational inefficiencies arising from use of a preprocessor and pointed out the potential benefit of manually coding derivative routines. In this Engineering Note, we report on a systematic effort to directly implement Taylor series integration in an operational trajectory propagation code: the Spacecraft N-Body Analysis Program (SNAP). The present Taylor series implementation is unique in that it applies to spacecraft virtually anywhere in the solar system and can be used interchangeably with another integration method. SNAP is a high-fidelity trajectory propagator that includes force models for central body gravitation with N X N harmonics, other body gravitation with N X N harmonics, solar radiation pressure, atmospheric drag (for Earth orbits), and spacecraft thrusting (including shadowing). The governing equations are solved using an eighth-order Runge-Kutta Fehlberg (RKF) single-step method with variable step size control. In the present effort, TS is implemented by way of highly integrated subroutines that can be used interchangeably with RKF. This makes it possible to turn TS on or off during various phases of a mission. Current TS force models include central body
Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures
International Nuclear Information System (INIS)
Procacci, Piero
2015-01-01
In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems
Communication: Theoretical prediction of free-energy landscapes for complex self-assembly
Energy Technology Data Exchange (ETDEWEB)
Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)
2015-01-14
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.
Thermodynamics and stability of hyperbolic charged black holes
International Nuclear Information System (INIS)
Cai Ronggen; Wang Anzhong
2004-01-01
In AdS space the black hole horizon can be a hypersurface with a positive, zero, or negative constant curvature, resulting in different horizon topology. Thermodynamics and stability of black holes in AdS spaces are quite different for different horizon curvatures. In this paper we study thermodynamics and stability of hyperbolic charged black holes with negative constant curvature horizon in the grand canonical ensemble and canonical ensemble, respectively. They include hyperbolic Reissner-Nordstroem black holes in arbitrary dimensions and hyperbolic black holes in the D=5,4,7 gauged supergravities. It is found that associated Gibbs free energies are always negative, which implies that these black hole solutions are globally stable and the black hole phase is dominant in the grand canonical ensemble, but there is a region in the phase space where the black hole is not locally thermodynamically stable with a negative heat capacity for a given gauge potential. In the canonical ensemble, the Helmholtz free energies are not always negative and heat capacities with fixed electric charge are not always positive, which indicates that the Hawking-Page phase transition may happen and black holes are not always locally thermodynamically stable
Microbial diversity arising from thermodynamic constraints
Großkopf, Tobias; Soyer, Orkun S
2016-01-01
The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705
Microbial diversity arising from thermodynamic constraints.
Großkopf, Tobias; Soyer, Orkun S
2016-11-01
The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.
Understanding the edge effect in wetting: a thermodynamic approach.
Fang, Guoping; Amirfazli, A
2012-06-26
Edge effect is known to hinder spreading of a sessile drop. However, the underlying thermodynamic mechanisms responsible for the edge effect still is not well-understood. In this study, a free energy model has been developed to investigate the energetic state of drops on a single pillar (from upright frustum to inverted frustum geometries). An analysis of drop free energy levels before and after crossing the edge allows us to understand the thermodynamic origin of the edge effect. In particular, four wetting cases for a drop on a single pillar with different edge angles have been determined by understanding the characteristics of FE plots. A wetting map describing the four wetting cases is given in terms of edge angle and intrinsic contact angle. The results show that the free energy barrier observed near the edge plays an important role in determining the drop states, i.e., (1) stable or metastable drop states at the pillar's edge, and (2) drop collapse by liquid spilling over the edge completely or staying at an intermediate sidewall position of the pillar. This thermodynamic model presents an energetic framework to describe the functioning of the so-called "re-entrant" structures. Results show good consistency with the literature and expand the current understanding of Gibbs' inequality condition.
Dolenc, Jožica; Oostenbrink, Chris; Koller, Jože; van Gunsteren, Wilfred F.
2005-01-01
Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG)·d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand–solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand–DNA binding. PMID:15687382
Dolenc, Jozica; Oostenbrink, Chris; Koller, Joze; van Gunsteren, Wilfred F
2005-01-01
Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of the ligands free in solution and when bound to DNA, the mobility and the hydrogen-bonding patterns of the ligands were studied, as well as their hydration. It is shown that even though distamycin is less hydrated than netropsin, the loss of ligand-solvent interactions is very similar for both ligands. The relative mobilities of the ligands in their bound and free forms indicate a larger entropic penalty for distamycin when binding to the minor groove compared with netropsin, partially explaining the lower binding affinity of the distamycin molecule. The detailed structural and energetic insights obtained from the molecular dynamics simulations allow for a better understanding of the factors determining ligand-DNA binding.
Methods for thermodynamic evaluation of battery state of health
Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T
2013-05-21
Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.
Zero-point energy constraint in quasi-classical trajectory calculations.
Xie, Zhen; Bowman, Joel M
2006-04-27
A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.
Reconfiguring Independent Sets in Claw-Free Graphs
Bonsma, P.S.; Kamiński, Marcin; Wrochna, Marcin; Ravi, R.; Gørtz, Inge Li
We present a polynomial-time algorithm that, given two independent sets in a claw-free graph G, decides whether one can be transformed into the other by a sequence of elementary steps. Each elementary step is to remove a vertex v from the current independent set S and to add a new vertex w (not in
Directory of Open Access Journals (Sweden)
Wassim M. Haddad
2012-02-01
Full Text Available In this paper, we combine the two universalisms of thermodynamics and dynamical systems theory to develop a dynamical system formalism for classical thermodynamics. Specifically, using a compartmental dynamical system energy flow model we develop a state-space dynamical system model that captures the key aspects of thermodynamics, including its fundamental laws. In addition, we establish the existence of a unique, continuously differentiable global entropy function for our dynamical system model, and using Lyapunov stability theory we show that the proposed thermodynamic model has finite-time convergent trajectories to Lyapunov stable equilibria determined by the system initial energies. Finally, using the system entropy, we establish the absence of Poincaré recurrence for our thermodynamic model and develop clear and rigorous connections between irreversibility, the second law of thermodynamics, and the entropic arrow of time.
Huang, Jinfeng; Zhu, Yali; Sun, Bin; Yao, Yuan; Liu, Junjun
2016-03-01
The protonation state of the Asp dyad is important as it can reveal enzymatic mechanisms, and the information this provides can be used in the development of drugs for proteins such as memapsin 2 (BACE-1), HIV-1 protease, and rennin. Conventional molecular dynamics (MD) simulations have been successfully used to determine the preferred protonation state of the Asp dyad. In the present work, we demonstrate that the results obtained from conventional MD simulations can be greatly influenced by the particular force field applied or the values used for control parameters. In principle, free-energy changes between possible protonation states can be used to determine the protonation state. We show that protonation state prediction by the thermodynamic integration (TI) method is insensitive to force field version or to the cutoff for calculating nonbonded interactions (a control parameter). In the present study, the protonation state of the Asp dyad predicted by TI calculations was the same regardless of the force field and cutoff value applied. Contrary to the intuition that conventional MD is more efficient, our results clearly show that the TI method is actually more efficient and more reliable for determining the protonation state of the Asp dyad.
Thermodynamics in f(G,T Gravity
Directory of Open Access Journals (Sweden)
M. Sharif
2018-01-01
Full Text Available This paper explores the nonequilibrium behavior of thermodynamics at the apparent horizon of isotropic and homogeneous universe model in f(G,T gravity (G and T represent the Gauss-Bonnet invariant and trace of the energy-momentum tensor, resp.. We construct the corresponding field equations and analyze the first as well as generalized second law of thermodynamics in this scenario. It is found that an auxiliary term corresponding to entropy production appears due to the nonequilibrium picture of thermodynamics in first law. The universal condition for the validity of generalized second law of thermodynamics is also obtained. Finally, we check the validity of generalized second law of thermodynamics for the reconstructed f(G,T models (de Sitter and power-law solutions. We conclude that this law holds for suitable choices of free parameters.
Florea, R. M.
2017-06-01
Basic material concept, technology and some results of studies on aluminum matrix composite with dispersive aluminum nitride reinforcement was shown. Studied composites were manufactured by „in situ” technique. Aluminum nitride (AlN) has attracted large interest recently, because of its high thermal conductivity, good dielectric properties, high flexural strength, thermal expansion coefficient matches that of Si and its non-toxic nature, as a suitable material for hybrid integrated circuit substrates. AlMg alloys are the best matrix for AlN obtaining. Al2O3-AlMg, AlN-Al2O3, and AlN-AlMg binary diagrams were thermodynamically modelled. The obtained Gibbs free energies of components, solution parameters and stoichiometric phases were used to build a thermodynamic database of AlN- Al2O3-AlMg system. Obtaining of AlN with Liquid-phase of AlMg as matrix has been studied and compared with the thermodynamic results. The secondary phase microstructure has a significant effect on the final thermal conductivity of the obtained AlN. Thermodynamic modelling of AlN-Al2O3-AlMg system provided an important basis for understanding the obtaining behavior and interpreting the experimental results.
Directory of Open Access Journals (Sweden)
Devin W McBride
Full Text Available The activity coefficient is largely considered an empirical parameter that was traditionally introduced to correct the non-ideality observed in thermodynamic systems such as osmotic pressure. Here, the activity coefficient of free-solvent is related to physically realistic parameters and a mathematical expression is developed to directly predict the activity coefficients of free-solvent, for aqueous protein solutions up to near-saturation concentrations. The model is based on the free-solvent model, which has previously been shown to provide excellent prediction of the osmotic pressure of concentrated and crowded globular proteins in aqueous solutions up to near-saturation concentrations. Thus, this model uses only the independently determined, physically realizable quantities: mole fraction, solvent accessible surface area, and ion binding, in its prediction. Predictions are presented for the activity coefficients of free-solvent for near-saturated protein solutions containing either bovine serum albumin or hemoglobin. As a verification step, the predictability of the model for the activity coefficient of sucrose solutions was evaluated. The predicted activity coefficients of free-solvent are compared to the calculated activity coefficients of free-solvent based on osmotic pressure data. It is observed that the predicted activity coefficients are increasingly dependent on the solute-solvent parameters as the protein concentration increases to near-saturation concentrations.
Exploring the free energy landscape: from dynamics to networks and back.
Directory of Open Access Journals (Sweden)
Diego Prada-Gracia
2009-06-01
Full Text Available Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.
International Nuclear Information System (INIS)
Oluleye, Gbemi; Smith, Robin
2016-01-01
Highlights: • MILP model developed for integration of waste heat recovery technologies in process sites. • Five thermodynamic cycles considered for exploitation of industrial waste heat. • Temperature and quantity of multiple waste heat sources considered. • Interactions with the site utility system considered. • Industrial case study presented to illustrate application of the proposed methodology. - Abstract: Thermodynamic cycles such as organic Rankine cycles, absorption chillers, absorption heat pumps, absorption heat transformers, and mechanical heat pumps are able to utilize wasted thermal energy in process sites for the generation of electrical power, chilling and heat at a higher temperature. In this work, a novel systematic framework is presented for optimal integration of these technologies in process sites. The framework is also used to assess the best design approach for integrating waste heat recovery technologies in process sites, i.e. stand-alone integration or a systems-oriented integration. The developed framework allows for: (1) selection of one or more waste heat sources (taking into account the temperatures and thermal energy content), (2) selection of one or more technology options and working fluids, (3) selection of end-uses of recovered energy, (4) exploitation of interactions with the existing site utility system and (5) the potential for heat recovery via heat exchange is also explored. The methodology is applied to an industrial case study. Results indicate a systems-oriented design approach reduces waste heat by 24%; fuel consumption by 54% and CO_2 emissions by 53% with a 2 year payback, and stand-alone design approach reduces waste heat by 12%; fuel consumption by 29% and CO_2 emissions by 20.5% with a 4 year payback. Therefore, benefits from waste heat utilization increase when interactions between the existing site utility system and the waste heat recovery technologies are explored simultaneously. The case study also shows
Directory of Open Access Journals (Sweden)
Caselle Michele
2007-09-01
Full Text Available Abstract Background Specific binding of proteins to DNA is one of the most common ways gene expression is controlled. Although general rules for the DNA-protein recognition can be derived, the ambiguous and complex nature of this mechanism precludes a simple recognition code, therefore the prediction of DNA target sequences is not straightforward. DNA-protein interactions can be studied using computational methods which can complement the current experimental methods and offer some advantages. In the present work we use physical effective potentials to evaluate the DNA-protein binding affinities for the λ repressor-DNA complex for which structural and thermodynamic experimental data are available. Results The binding free energy of two molecules can be expressed as the sum of an intermolecular energy (evaluated using a molecular mechanics forcefield, a solvation free energy term and an entropic term. Different solvation models are used including distance dependent dielectric constants, solvent accessible surface tension models and the Generalized Born model. The effect of conformational sampling by Molecular Dynamics simulations on the computed binding energy is assessed; results show that this effect is in general negative and the reproducibility of the experimental values decreases with the increase of simulation time considered. The free energy of binding for non-specific complexes, estimated using the best energetic model, agrees with earlier theoretical suggestions. As a results of these analyses, we propose a protocol for the prediction of DNA-binding target sequences. The possibility of searching regulatory elements within the bacteriophage λ genome using this protocol is explored. Our analysis shows good prediction capabilities, even in absence of any thermodynamic data and information on the naturally recognized sequence. Conclusion This study supports the conclusion that physics-based methods can offer a completely complementary
Anderson, Emma L; Tilling, Kate; Fraser, Abigail; Macdonald-Wallis, Corrie; Emmett, Pauline; Cribb, Victoria; Northstone, Kate; Lawlor, Debbie A; Howe, Laura D
2013-07-01
Methods for the assessment of changes in dietary intake across the life course are underdeveloped. We demonstrate the use of linear-spline multilevel models to summarize energy-intake trajectories through childhood and adolescence and their application as exposures, outcomes, or mediators. The Avon Longitudinal Study of Parents and Children assessed children's dietary intake several times between ages 3 and 13 years, using both food frequency questionnaires (FFQs) and 3-day food diaries. We estimated energy-intake trajectories for 12,032 children using linear-spline multilevel models. We then assessed the associations of these trajectories with maternal body mass index (BMI), and later offspring BMI, and also their role in mediating the relation between maternal and offspring BMIs. Models estimated average and individual energy intake at 3 years, and linear changes in energy intake from age 3 to 7 years and from age 7 to 13 years. By including the exposure (in this example, maternal BMI) in the multilevel model, we were able to estimate the average energy-intake trajectories across levels of the exposure. When energy-intake trajectories are the exposure for a later outcome (in this case offspring BMI) or a mediator (between maternal and offspring BMI), results were similar, whether using a two-step process (exporting individual-level intercepts and slopes from multilevel models and using these in linear regression/path analysis), or a single-step process (multivariate multilevel models). Trajectories were similar when FFQs and food diaries were assessed either separately, or when combined into one model. Linear-spline multilevel models provide useful summaries of trajectories of dietary intake that can be used as an exposure, outcome, or mediator.
The second laws of quantum thermodynamics.
Brandão, Fernando; Horodecki, Michał; Ng, Nelly; Oppenheim, Jonathan; Wehner, Stephanie
2015-03-17
The second law of thermodynamics places constraints on state transformations. It applies to systems composed of many particles, however, we are seeing that one can formulate laws of thermodynamics when only a small number of particles are interacting with a heat bath. Is there a second law of thermodynamics in this regime? Here, we find that for processes which are approximately cyclic, the second law for microscopic systems takes on a different form compared to the macroscopic scale, imposing not just one constraint on state transformations, but an entire family of constraints. We find a family of free energies which generalize the traditional one, and show that they can never increase. The ordinary second law relates to one of these, with the remainder imposing additional constraints on thermodynamic transitions. We find three regimes which determine which family of second laws govern state transitions, depending on how cyclic the process is. In one regime one can cause an apparent violation of the usual second law, through a process of embezzling work from a large system which remains arbitrarily close to its original state. These second laws are relevant for small systems, and also apply to individual macroscopic systems interacting via long-range interactions. By making precise the definition of thermal operations, the laws of thermodynamics are unified in this framework, with the first law defining the class of operations, the zeroth law emerging as an equivalence relation between thermal states, and the remaining laws being monotonicity of our generalized free energies.
Thermodynamic analysis of environmental problems of energy
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Kaganovich Boris M.
2017-01-01
Full Text Available The paper discusses the problems of the ecological analysis of physicochemical processes in power units and the impact of energy systems on the nature in large territorial regions. The model of extreme intermediate states developed at the Energy Systems Institute based on the principles of classical equilibrium thermodynamics was chosen to devise specific computational methods. The results of the conducted studies are presented and directions for further work are outlined.
Integrated Free-Piston Generators: An Overview
Energy Technology Data Exchange (ETDEWEB)
Arshad, Waqas M.; Thelin, Peter; Sadarangani, Chandur [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Electrical Machines and Power Electronics; Baeckstroem, Thomas [ABB Group Services-Corporate Research, Vaesteraas (Sweden)
2002-08-01
The free-piston generator is an energy conversion device that integrates a combustion engine and an electrical generator into a single unit. Thereby the intermediary crankshaft stage present in conventional hybrid topologies is eliminated. This has benefits in efficiency, weight reduction, robustness, variable compression operation and multi-fuel possibilities. This paper presents the free-piston generator concepts, along with the expected benefits and drawbacks. A literature survey is provided. Results from a simplified combustion modeling process are presented in terms of piston motion profiles. These have implications upon the dimensioning and selection of an appropriate electrical machine. Specifications for the electrical machine are outlined. Some distinct electrical machine solutions are presented and discussed. An application of the free-piston generator in a series hybrid vehicle is also proposed.
Ando, Tadashi; Yu, Isseki; Feig, Michael; Sugita, Yuji
2016-11-23
The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell. Here, we evaluate the free energy changes upon macromolecular association in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calculations using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromolecules represented by spheres with different radii mimics the physiological concentrations of macromolecules in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromolecular association evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affects both specific and nonspecific molecular associations, suggesting that not only the volume fraction but also the size distribution of macromolecules are important factors for evaluating in vivo crowding effects. This study relates in vitro experiments on macromolecular crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.
Modeling free energy availability from Hadean hydrothermal systems to the first metabolism.
Simoncini, E; Russell, M J; Kleidon, A
2011-12-01
Off-axis Hydrothermal Systems (HSs) are seen as the possible setting for the emergence of life. As the availability of free energy is a general requirement to drive any form of metabolism, we ask here under which conditions free energy generation by geologic processes is greatest and relate these to the conditions found at off-axis HSs. To do so, we present a conceptual model in which we explicitly capture the energetics of fluid motion and its interaction with exothermic reactions to maintain a state of chemical disequilibrium. Central to the interaction is the temperature at which the exothermic reactions take place. This temperature not only sets the equilibrium constant of the chemical reactions and thereby the distance of the actual state to chemical equilibrium, but these reactions also shape the temperature gradient that drives convection and thereby the advection of reactants to the reaction sites and the removal of the products that relate to geochemical free energy generation. What this conceptual model shows is that the positive feedback between convection and the chemical kinetics that is found at HSs favors a greater rate of free energy generation than in the absence of convection. Because of the lower temperatures and because the temperature of reactions is determined more strongly by these dynamics rather than an external heat flux, the conditions found at off-axis HSs should result in the greatest rates of geochemical free energy generation. Hence, we hypothesize from these thermodynamic considerations that off-axis HSs seem most conducive for the emergence of protometabolic pathways as these provide the greatest, abiotic generation rates of chemical free energy.
New perspectives in thermodynamics
International Nuclear Information System (INIS)
Serrin, J.
1986-01-01
The last decade has seen a unity of method and approach in the foundations of thermodynamics and continuum mechanics, in which rigorous laws of thermodynamics have been combined with invariance notions of mechanics to produce new and deep understanding. Real progress has been made in finding a set of appropriate concepts for classical thermodynamics, by which energy conservation and the Clausius inequality can be given well-defined meanings for arbitrary processes and which allow an approach to the entropy concept which is free of traditional ambiguities. There has been, moreover, a careful scrutiny of long established but nevertheless not sharply defined concepts such as the Maxwell equal-area rule, the famous Gibbs phase rule, and the equivalence of work and heat. The thirteen papers in this volume accordingly gather together for the first time the many ideas and concepts which have raised classical thermodynamics from a heuristic and intuitive science to the level of precision presently demanded of other branches of mathematical physics
Energy field of thermodynamic syste'ms
International Nuclear Information System (INIS)
Volchenkova, R.A.
1984-01-01
To reveal the qualitative and quantitative rules, regulating the properties of macro- and microsystems consideration is being given to the dependence of system enthalpy on environmental conditions. It was concluded that the dependence of material system enthalpy on temperature represents the energy field, containing the energy boundaries of phase states, described by exponential functions, in which the elements are arranged monotonically in the sequence of change of interatomic bonds, correlated with their physicomechanical properties; energy boundaries of phase states at that emanate from a single point, which is a reference a single point, which a reference one for the whole material system and determining its energy state in initial position. The presented energy field of thermodynamic systems enables to consider the change of their physicomechanical properties and energy state in dynamic process, depending on environmental parameters. Energy characteristics of single-component systems (W, Re, Hf, Nb, Mo etc) are given
Non-hard sphere thermodynamic perturbation theory.
Zhou, Shiqi
2011-08-21
A non-hard sphere (HS) perturbation scheme, recently advanced by the present author, is elaborated for several technical matters, which are key mathematical details for implementation of the non-HS perturbation scheme in a coupling parameter expansion (CPE) thermodynamic perturbation framework. NVT-Monte Carlo simulation is carried out for a generalized Lennard-Jones (LJ) 2n-n potential to obtain routine thermodynamic quantities such as excess internal energy, pressure, excess chemical potential, excess Helmholtz free energy, and excess constant volume heat capacity. Then, these new simulation data, and available simulation data in literatures about a hard core attractive Yukawa fluid and a Sutherland fluid, are used to test the non-HS CPE 3rd-order thermodynamic perturbation theory (TPT) and give a comparison between the non-HS CPE 3rd-order TPT and other theoretical approaches. It is indicated that the non-HS CPE 3rd-order TPT is superior to other traditional TPT such as van der Waals/HS (vdW/HS), perturbation theory 2 (PT2)/HS, and vdW/Yukawa (vdW/Y) theory or analytical equation of state such as mean spherical approximation (MSA)-equation of state and is at least comparable to several currently the most accurate Ornstein-Zernike integral equation theories. It is discovered that three technical issues, i.e., opening up new bridge function approximation for the reference potential, choosing proper reference potential, and/or using proper thermodynamic route for calculation of f(ex-ref), chiefly decide the quality of the non-HS CPE TPT. Considering that the non-HS perturbation scheme applies for a wide variety of model fluids, and its implementation in the CPE thermodynamic perturbation framework is amenable to high-order truncation, the non-HS CPE 3rd-order or higher order TPT will be more promising once the above-mentioned three technological advances are established. © 2011 American Institute of Physics
Thermodynamics a complete undergraduate course
Steane, Andrew M
2016-01-01
This is an undergraduate textbook in thermodynamics—the science of heat, work, temperature, and entropy. The text presents thermodynamics in and of itself, as an elegant and powerful set of ideas and methods. These methods open the way to understanding a very wide range of phenomena in physics, chemistry, engineering, and biology. Starting out from an introduction of concepts at first year undergraduate level, the roles of temperature, internal energy, and entropy are explained via the laws of thermodynamics. The text employs a combination of examples, exercises, and careful discussion, with a view to conveying the feel of the subject as well as avoiding common misunderstandings. The Feynman–Smuluchowski ratchet, Szilard’s engine, and Maxwell’s daemon are used to elucidate entropy and the second law. Free energy and thermodynamic potentials are discussed at length, with applications to solids as well as fluids and flow processes. Thermal radiation is discussed, and the main ideas significant to global...
Thermodynamic properties of potassium chloride aqueous solutions
Zezin, Denis; Driesner, Thomas
2017-04-01
Potassium chloride is a ubiquitous salt in natural fluids, being the second most abundant dissolved salt in many geological aqueous solutions after sodium chloride. It is a simple solute and strong electrolyte easily dissociating in water, however the thermodynamic properties of KCl aqueous solutions were never correlated with sufficient accuracy for a wide range of physicochemical conditions. In this communication we propose a set of parameters for a Pitzer-type model which allows calculation of all necessary thermodynamic properties of KCl solution, namely excess Gibbs free energy and derived activity coefficient, apparent molar enthalpy, heat capacity and volume, as well as osmotic coefficient and activity of water in solutions. The system KCl-water is one of the best studied aqueous systems containing electrolytes. Although extensive experimental data were collected for thermodynamic properties of these solutions over the years, the accurate volumetric data became available only recently, thus making possible a complete thermodynamic formulation including a pressure dependence of excess Gibbs free energy and derived properties of the KCl-water liquids. Our proposed model is intended for calculation of major thermodynamic properties of KCl aqueous solutions at temperatures ranging from freezing point of a solution to 623 K, pressures ranging from saturated water vapor up to 150 MPa, and concentrations up to the salt saturation. This parameterized model will be further implemented in geochemical software packages and can facilitate the calculation of aqueous equilibrium for reactive transport codes.
Serrano, Arnaldo L; Lomont, Justin P; Tu, Ling-Hsien; Raleigh, Daniel P; Zanni, Martin T
2017-11-22
Transiently populated oligomers formed en route to amyloid fibrils may constitute the most toxic aggregates associated with many amyloid-associated diseases. Most nucleation theories used to describe amyloid aggregation predict low oligomer concentrations and do not take into account free energy costs that may be associated with structural rearrangements between the oligomer and fiber states. We have used isotope labeling and two-dimensional infrared spectroscopy to spectrally resolve an oligomeric intermediate during the aggregation of the human islet amyloid protein (hIAPP or amylin), the protein associated with type II diabetes. A structural rearrangement includes the F 23 G 24 A 25 I 26 L 27 region of hIAPP, which starts from a random coil structure, evolves into ordered β-sheet oligomers containing at least 5 strands, and then partially disorders in the fibril structure. The supercritical concentration is measured to be between 150 and 250 μM, which is the thermodynamic parameter that sets the free energy of the oligomers. A 3-state kinetic model fits the experimental data, but only if it includes a concentration independent free energy barrier >3 kcal/mol that represents the free energy cost of refolding the oligomeric intermediate into the structure of the amyloid fibril; i.e., "oligomer activation" is required. The barrier creates a transition state in the free energy landscape that slows fibril formation and creates a stable population of oligomers during the lag phase, even at concentrations below the supercritical concentration. Largely missing in current kinetic models is a link between structure and kinetics. Our experiments and modeling provide evidence that protein structural rearrangements during aggregation impact the populations and kinetics of toxic oligomeric species.
Thermodynamic properties of amphiphilic antidepressant drug citalopram HBr
International Nuclear Information System (INIS)
Usman, M.; Khan, A.
2010-01-01
Association characteristics of antidepressant during Citalopram hydrobromide in water Have been examined and its thermodynamic parameters have been calculated using tensiometery and conductometry. The critical micelle concentration (cmc) was determined by surface tension measurement at 30 deg. C and Surface activity was studied by measuring surface parameters i.e. surface pressure, JI, surface excess concentration, area per molecule of drug and standard Gibbs free energy of adsorption, delta G. The electrical conductivity was measured as a function of concentration at various temperatures and cmc was calculated in the temperature range 20-50 deg. C. Thermodynamic parameters i.e. standard free energy of micellization, delta G standard enthalpy of micellization, delta H/sub m/ and standard entropy of micellization, delta S/sub m/ were calculated from cmc value using closed association model. (author)
Stochastic and Macroscopic Thermodynamics of Strongly Coupled Systems
Directory of Open Access Journals (Sweden)
Christopher Jarzynski
2017-01-01
Full Text Available We develop a thermodynamic framework that describes a classical system of interest S that is strongly coupled to its thermal environment E. Within this framework, seven key thermodynamic quantities—internal energy, entropy, volume, enthalpy, Gibbs free energy, heat, and work—are defined microscopically. These quantities obey thermodynamic relations including both the first and second law, and they satisfy nonequilibrium fluctuation theorems. We additionally impose a macroscopic consistency condition: When S is large, the quantities defined within our framework scale up to their macroscopic counterparts. By satisfying this condition, we demonstrate that a unifying framework can be developed, which encompasses both stochastic thermodynamics at one end, and macroscopic thermodynamics at the other. A central element in our approach is a thermodynamic definition of the volume of the system of interest, which converges to the usual geometric definition when S is large. We also sketch an alternative framework that satisfies the same consistency conditions. The dynamics of the system and environment are modeled using Hamilton’s equations in the full phase space.
Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
2016-08-09
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass
Zhang, Baofeng; D'Erasmo, Michael P; Murelli, Ryan P; Gallicchio, Emilio
2016-09-30
We report the results of a binding free energy-based virtual screening campaign of a library of 77 α-hydroxytropolone derivatives against the challenging RNase H active site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus-1. Multiple protonation states, rotamer states, and binding modalities of each compound were individually evaluated. The work involved more than 300 individual absolute alchemical binding free energy parallel molecular dynamics calculations and over 1 million CPU hours on national computing clusters and a local campus computational grid. The thermodynamic and structural measures obtained in this work rationalize a series of characteristics of this system useful for guiding future synthetic and biochemical efforts. The free energy model identified key ligand-dependent entropic and conformational reorganization processes difficult to capture using standard docking and scoring approaches. Binding free energy-based optimization of the lead compounds emerging from the virtual screen has yielded four compounds with very favorable binding properties, which will be the subject of further experimental investigations. This work is one of the few reported applications of advanced-binding free energy models to large-scale virtual screening and optimization projects. It further demonstrates that, with suitable algorithms and automation, advanced-binding free energy models can have a useful role in early-stage drug-discovery programs.
Thermodynamics and energy conversion
Struchtrup, Henning
2014-01-01
This textbook gives a thorough treatment of engineering thermodynamics with applications to classical and modern energy conversion devices. Some emphasis lies on the description of irreversible processes, such as friction, heat transfer and mixing, and the evaluation of the related work losses. Better use of resources requires high efficiencies, therefore the reduction of irreversible losses should be seen as one of the main goals of a thermal engineer. This book provides the necessary tools. Topics include: car and aircraft engines, including Otto, Diesel and Atkinson cycles, by-pass turbofan engines, ramjet and scramjet; steam and gas power plants, including advanced regenerative systems, solar tower, and compressed air energy storage; mixing and separation, including reverse osmosis, osmotic powerplants, and carbon sequestration; phase equilibrium and chemical equilibrium, distillation, chemical reactors, combustion processes, and fuel cells; the microscopic definition of entropy. The book i...
Thermodynamic Product Relations for Generalized Regular Black Hole
International Nuclear Information System (INIS)
Pradhan, Parthapratim
2016-01-01
We derive thermodynamic product relations for four-parametric regular black hole (BH) solutions of the Einstein equations coupled with a nonlinear electrodynamics source. The four parameters can be described by the mass (m), charge (q), dipole moment (α), and quadrupole moment (β), respectively. We study its complete thermodynamics. We compute different thermodynamic products, that is, area product, BH temperature product, specific heat product, and Komar energy product, respectively. Furthermore, we show some complicated function of horizon areas that is indeed mass-independent and could turn out to be universal.
A Tractable Disequilbrium Framework for Integrating Computational Thermodynamics and Geodynamics
Spiegelman, M. W.; Tweed, L. E. L.; Evans, O.; Kelemen, P. B.; Wilson, C. R.
2017-12-01
The consistent integration of computational thermodynamics and geodynamics is essential for exploring and understanding a wide range of processes from high-PT magma dynamics in the convecting mantle to low-PT reactive alteration of the brittle crust. Nevertheless, considerable challenges remain for coupling thermodynamics and fluid-solid mechanics within computationally tractable and insightful models. Here we report on a new effort, part of the ENKI project, that provides a roadmap for developing flexible geodynamic models of varying complexity that are thermodynamically consistent with established thermodynamic models. The basic theory is derived from the disequilibrium thermodynamics of De Groot and Mazur (1984), similar to Rudge et. al (2011, GJI), but extends that theory to include more general rheologies, multiple solid (and liquid) phases and explicit chemical reactions to describe interphase exchange. Specifying stoichiometric reactions clearly defines the compositions of reactants and products and allows the affinity of each reaction (A = -Δ/Gr) to be used as a scalar measure of disequilibrium. This approach only requires thermodynamic models to return chemical potentials of all components and phases (as well as thermodynamic quantities for each phase e.g. densities, heat capacity, entropies), but is not constrained to be in thermodynamic equilibrium. Allowing meta-stable phases mitigates some of the computational issues involved with the introduction and exhaustion of phases. Nevertheless, for closed systems, these problems are guaranteed to evolve to the same equilibria predicted by equilibrium thermodynamics. Here we illustrate the behavior of this theory for a range of simple problems (constructed with our open-source model builder TerraFERMA) that model poro-viscous behavior in the well understood Fo-Fa binary phase loop. Other contributions in this session will explore a range of models with more petrologically interesting phase diagrams as well as
Matta, Chérif F; Massa, Lou
2015-09-01
Half a century ago, Johnson and Knudsen resolved the puzzle of the apparent low efficiency of the kidney (∼ 0.5%) compared to most other bodily organs (∼ 40%) by taking into account the entropic cost of ion sorting, the principal function of this organ. Similarly, it is shown that the efficiency of energy transduction of the chemiosmotic proton-motive force by ATP synthase is closer to 90% instead of the oft-quoted textbook value of only 60% when information theoretic considerations are applied to the mitochondrion. This high efficiency is consistent with the mechanical energy transduction of ATP synthase known to be close to the 100% thermodynamic limit. It would have been wasteful for evolution to maximize the mechanical energy transduction to 100% while wasting 40% of the chemiosmotic free energy in the conversion of the proton-motive force into mechanical work before being captured as chemical energy in adenosine 5'-triphosphate.
Trigenerative micro compressed air energy storage: Concept and thermodynamic assessment
International Nuclear Information System (INIS)
Facci, Andrea L.; Sánchez, David; Jannelli, Elio; Ubertini, Stefano
2015-01-01
Highlights: • The trigenerative-CAES concept is introduced. • The thermodynamic feasibility of the trigenerative-CAES is assessed. • The effects of the relevant parameter on the system performances are dissected. • Technological issues on the trigenerative-CAES are highlighted. - Abstract: Energy storage is a cutting edge front for renewable and sustainable energy research. In fact, a massive exploitation of intermittent renewable sources, such as wind and sun, requires the introduction of effective mechanical energy storage systems. In this paper we introduce the concept of a trigenerative energy storage based on a compressed air system. The plant in study is a simplified design of the adiabatic compressed air energy storage and accumulates mechanical and thermal (both hot and cold) energy at the same time. We envisage the possibility to realize a relatively small size trigenerative compressed air energy storage to be placed close to the energy demand, according to the distributed generation paradigm. Here, we describe the plant concept and we identify all the relevant parameters influencing its thermodynamic behavior. Their effects are dissected through an accurate thermodynamic model. The most relevant technological issues, such as the guidelines for a proper choice of the compressor, expander and heat exchangers are also addressed. Our results show that T-CAES may have an interesting potential as a distributed system that combines electricity storage with heat and cooling energy production. We also show that the performances are significantly influenced by some operating and design parameters, whose feasibility in real applications must be considered.
Ellison, Donald H.; Englander, Jacob A.; Conway, Bruce A.
2017-01-01
The multiple gravity assist low-thrust (MGALT) trajectory model combines the medium-fidelity Sims-Flanagan bounded-impulse transcription with a patched-conics flyby model and is an important tool for preliminary trajectory design. While this model features fast state propagation via Keplers equation and provides a pleasingly accurate estimation of the total mass budget for the eventual flight suitable integrated trajectory it does suffer from one major drawback, namely its temporal spacing of the control nodes. We introduce a variant of the MGALT transcription that utilizes the generalized anomaly from the universal formulation of Keplers equation as a decision variable in addition to the trajectory phase propagation time. This results in two improvements over the traditional model. The first is that the maneuver locations are equally spaced in generalized anomaly about the orbit rather than time. The second is that the Kepler propagator now has the generalized anomaly as its independent variable instead of time and thus becomes an iteration-free propagation method. The new algorithm is outlined, including the impact that this has on the computation of Jacobian entries for numerical optimization, and a motivating application problem is presented that illustrates the improvements that this model has over the traditional MGALT transcription.
Thermodynamic calculation of a district energy cycle
International Nuclear Information System (INIS)
Hoehlein, B.; Bauer, A.; Kraut, G.; Scherberich, F.D.
1975-08-01
This paper presents a calculation model for a nuclear district energy circuit. Such a circuit means the combination of a steam reforming plant with heat supply from a high-temperature nuclear reactor and a methanation plant with heat production for district heating or electricity production. The model comprises thermodynamic calculations for the endothermic methane reforming reaction as well as the exothermic CO-hydrogenation in adiabatic reactors and allows the optimization of the district energy circuit under consideration. (orig.) [de
Minimum energy consumption process synthesis for energy saving
Energy Technology Data Exchange (ETDEWEB)
Xiao-Ping, Jia [Institute for Petroleum and Chemical Industry, Qingdao University of Science and Technology, Qingdao 266042, Shandong (China); Department of Environmental Science and Engineering, Tsinghua University, Beijing 100084 (China); Fang, Wang; Shu-Guang, Xiang; Xin-Sun, Tan; Fang-Yu, Han [Institute for Petroleum and Chemical Industry, Qingdao University of Science and Technology, Qingdao 266042, Shandong (China)
2008-05-15
The paper presents a synthesis strategy for the chemical processes with energy saving. The concept of minimum energy consumption process (MECP) is proposed. Three characteristics of MECP are introduced, including thermodynamic minimum energy demand, energy consumption efficiency and integration degree. These characteristics are evaluated according to quantitative thermodynamic analysis and qualitative knowledge rules. The procedure of synthesis strategy is proposed to support the generation of MECP alternatives, which combine flowsheet integration and heat integration. The cases studies will focus on how integration degrees of a process affect the energy-saving results. The separation sequences of the hydrodealkylation of toluene (HDA) process and ethanol distillation process as case studies are used to illustrate. (author)
Thermoeconomic analysis of a solar enhanced energy storage concept based on thermodynamic cycles
International Nuclear Information System (INIS)
Henchoz, Samuel; Buchter, Florian; Favrat, Daniel; Morandin, Matteo; Mercangöz, Mehmet
2012-01-01
Large scale energy storage may play an increasingly important role in the power generation and distribution sector, especially when large shares of renewable energies will have to be integrated into the electrical grid. Pumped-hydro is the only large scale storage technology that has been widely used. However the spread of this technology is limited by geographic constraints. In the present work, a particular implementation of a storage concept based on thermodynamic cycles, invented by ABB Switzerland ltd. Corporate Research, has been analysed thermoeconomically. A variant using solar thermal collectors is presented. It benefits from the synergy between daily variations in solar irradiance and in electricity demand. This results in an effective increase of the electric energy storage efficiency. A steady state multi-objective optimization of a 50 MW plant was done; minimizing the investment costs and maximizing the energy storage efficiency. Several types of cold storage substances have been implemented in the formulation and two different types of solar collector were investigated. A storage efficiency of 57% at a cost of 1200 USD/kW was calculated for an optimized plant using solar energy. Finally, a computation of the behaviour of the plant along the year showed a yearly availability of 84.4%. -- Highlights: ► A variant of electric energy storage based on thermodynamic cycles is presented. ► It uses solar collectors to improve the energy storage efficiency. ► An optimization minimizing capital cost and maximizing energy storage efficiency, was carried out. ► Capital costs lie between 982 and 3192 USD/kW and efficiency between 43.8% and 84.4%.
Directory of Open Access Journals (Sweden)
Qingxuan Jia
2014-01-01
Full Text Available The aim of this paper is to analyze load-carrying capacity of redundant free-floating space manipulators (FFSM in trajectory tracking task. Combined with the analysis of influential factors in load-carrying process, evaluation of maximum load-carrying capacity (MLCC is described as multiconstrained nonlinear programming problem. An efficient algorithm based on repeated line search within discontinuous feasible region is presented to determine MLCC for a given trajectory of the end-effector and corresponding joint path. Then, considering the influence of MLCC caused by different initial configurations for the starting point of given trajectory, a kind of maximum payload initial configuration planning method is proposed by using PSO algorithm. Simulations are performed for a particular trajectory tracking task of the 7-DOF space manipulator, of which MLCC is evaluated quantitatively. By in-depth research of the simulation results, significant gap between the values of MLCC when using different initial configurations is analyzed, and the discontinuity of allowable load-carrying capacity is illustrated. The proposed analytical method can be taken as theoretical foundation of feasibility analysis, trajectory optimization, and optimal control of trajectory tracking task in on-orbit load-carrying operations.
Bishop, Kevin P; Roy, Pierre-Nicholas
2018-03-14
Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.
Thermodynamics of pairing phase transition in nuclei
International Nuclear Information System (INIS)
Karim, Afaque; Ahmad, Shakeb
2014-01-01
The pairing gaps, pairing energy, heat capacity and entropy are calculated within BCS (Bardeen- Cooper-Schrieffer) based quasi particle approach, including thermal fluctuations on pairing field within pairing model for all nuclei (light, medium, heavy and super heavy nuclei). Quasi particles approach in BCS theory was introduced and reformulated to study various properties. For thermodynamic behavior of nuclei at finite temperatures, the anomalous averages of creation and annihilation operators are introduced. It is solved self consistently at finite temperatures to obtain BCS Hamiltonian. After doing unitary transformation, we obtained the Hamiltonian in the diagonal form. Thus, one gets temperature dependence gap parameter and pairing energy for nuclei. Moreover, the energy at finite temperatures is the sum of the condensation energy and the thermal energy of fermionic quasi particles. With the help of BCS Hamiltonian, specific heat, entropy and free energy are calculated for different nuclei. In this paper the gap parameter occupation number and pairing energy as a function of temperature which is important for all the light, medium, heavy and super heavy nuclei is calculated. Moreover, the various thermo dynamical quantities like specific heat, entropy and free energy is also obtained for different nuclei. Thus, the thermodynamics of pairing phase transition in nuclei is studied
Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.
2008-03-01
Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.
International Nuclear Information System (INIS)
Lim, Gyeong Hui
2008-03-01
This book consists of 15 chapters, which are basic conception and meaning of statistical thermodynamics, Maxwell-Boltzmann's statistics, ensemble, thermodynamics function and fluctuation, statistical dynamics with independent particle system, ideal molecular system, chemical equilibrium and chemical reaction rate in ideal gas mixture, classical statistical thermodynamics, ideal lattice model, lattice statistics and nonideal lattice model, imperfect gas theory on liquid, theory on solution, statistical thermodynamics of interface, statistical thermodynamics of a high molecule system and quantum statistics
Some problems on the thermodynamic state of the metallogenetic systems
International Nuclear Information System (INIS)
Mingarro, E.
1965-01-01
In order to get a classification of the uranium deposits, the geological processes have been ordered in thermodynamic systems according to the independent parameters that define their equilibrium state. Also, to apply the phase rule, we suppose that the ore forming elements are always ideally mobile components; that is, in the geological systems, these components are defined by their chemical potentials. In this paper, we show that in random conditions, i. e.; for any possible value of the factors of equilibrium or state the stable mineralizations are formed only in metasomatic regimes; so that the mineralogical sequence is a function both of the Helmholtz's free energy and the crystallisation pressure of the minerals. (Author) 7 refs
Development of a Stirling System Dynamic Model with Enhanced Thermodynamics
Regan, Timothy F.; Lewandowski, Edward J.
2005-02-01
The Stirling Convertor System Dynamic Model developed at NASA Glenn Research Center is a software model developed from first principles that includes the mechanical and mounting dynamics, the thermodynamics, the linear alternator, and the controller of a free-piston Stirling power convertor, along with the end user load. As such it represents the first detailed modeling tool for fully integrated Stirling convertor-based power systems. The thermodynamics of the model were originally a form of the isothermal Stirling cycle. In some situations it may be desirable to improve the accuracy of the Stirling cycle portion of the model. An option under consideration is to enhance the SDM thermodynamics by coupling the model with Gedeon Associates' Sage simulation code. The result will be a model that gives a more accurate prediction of the performance and dynamics of the free-piston Stirling convertor. A method of integrating the Sage simulation code with the System Dynamic Model is described. Results of SDM and Sage simulation are compared to test data. Model parameter estimation and model validation are discussed.
Simulating metabolism with statistical thermodynamics.
Cannon, William R
2014-01-01
New methods are needed for large scale modeling of metabolism that predict metabolite levels and characterize the thermodynamics of individual reactions and pathways. Current approaches use either kinetic simulations, which are difficult to extend to large networks of reactions because of the need for rate constants, or flux-based methods, which have a large number of feasible solutions because they are unconstrained by the law of mass action. This report presents an alternative modeling approach based on statistical thermodynamics. The principles of this approach are demonstrated using a simple set of coupled reactions, and then the system is characterized with respect to the changes in energy, entropy, free energy, and entropy production. Finally, the physical and biochemical insights that this approach can provide for metabolism are demonstrated by application to the tricarboxylic acid (TCA) cycle of Escherichia coli. The reaction and pathway thermodynamics are evaluated and predictions are made regarding changes in concentration of TCA cycle intermediates due to 10- and 100-fold changes in the ratio of NAD+:NADH concentrations. Finally, the assumptions and caveats regarding the use of statistical thermodynamics to model non-equilibrium reactions are discussed.
Energy Technology Data Exchange (ETDEWEB)
Takahashi, R; Kamima, T [Cancer Institute Hospital of Japanese Foundation for Cancer Research, Koto, Tokyo (Japan); Tachibana, H [National Cancer Center, Kashiwa, Chiba (Japan)
2016-06-15
Purpose: To investigate the effect of the trajectory files from linear accelerator for Clarkson-based independent dose verification in IMRT and VMAT plans. Methods: A CT-based independent dose verification software (Simple MU Analysis: SMU, Triangle Products, Japan) with a Clarksonbased algorithm was modified to calculate dose using the trajectory log files. Eclipse with the three techniques of step and shoot (SS), sliding window (SW) and Rapid Arc (RA) was used as treatment planning system (TPS). In this study, clinically approved IMRT and VMAT plans for prostate and head and neck (HN) at two institutions were retrospectively analyzed to assess the dose deviation between DICOM-RT plan (PL) and trajectory log file (TJ). An additional analysis was performed to evaluate MLC error detection capability of SMU when the trajectory log files was modified by adding systematic errors (0.2, 0.5, 1.0 mm) and random errors (5, 10, 30 mm) to actual MLC position. Results: The dose deviations for prostate and HN in the two sites were 0.0% and 0.0% in SS, 0.1±0.0%, 0.1±0.1% in SW and 0.6±0.5%, 0.7±0.9% in RA, respectively. The MLC error detection capability shows the plans for HN IMRT were the most sensitive and 0.2 mm of systematic error affected 0.7% dose deviation on average. Effect of the MLC random error did not affect dose error. Conclusion: The use of trajectory log files including actual information of MLC location, gantry angle, etc should be more effective for an independent verification. The tolerance level for the secondary check using the trajectory file may be similar to that of the verification using DICOM-RT plan file. From the view of the resolution of MLC positional error detection, the secondary check could detect the MLC position error corresponding to the treatment sites and techniques. This research is partially supported by Japan Agency for Medical Research and Development (AMED)
Thermodynamic and Spectrophotometric Studies of Electron Donor ...
African Journals Online (AJOL)
Some features of the formed complex, such as molar ratio of the reaction and effect of time ... Thermodynamic parameters were determined as well, the method was ... enthalpy change (ÄH) was steady at -0.254 kcal.mol-1 while the free energy ...
Keshavarzi, Ezat; Kamalvand, Mohammad
2009-04-23
The structure and properties of fluids confined in nanopores may show a dramatic departure from macroscopic bulk fluids. The main reason for this difference lies in the influence of system walls. In addition to the entropic wall effect, system walls can significantly change the energy of the confined fluid compared to macroscopic bulk fluids. The energy effect of the walls on a nanoconfined fluid appears in two forms. The first effect is the cutting off of the intermolecular interactions by the walls, which appears for example in the integrals for calculation of the thermodynamic properties. The second wall effect involves the wall-molecule interactions. In such confined fluids, the introduction of wall forces and the competition between fluid-wall and fluid-fluid forces could lead to interesting thermodynamic properties, including new kinds of phase transitions not observed in the macroscopic fluid systems. In this article, we use the perturbative fundamental measure density functional theory to study energy effects on the structure and properties of a hard core two-Yukawa fluid confined in a nanoslit. Our results show the changes undergone by the structure and phase transition of the nanoconfined fluids as a result of energy effects.
Quantum and Information Thermodynamics: A Unifying Framework Based on Repeated Interactions
Strasberg, Philipp; Schaller, Gernot; Brandes, Tobias; Esposito, Massimiliano
2017-04-01
We expand the standard thermodynamic framework of a system coupled to a thermal reservoir by considering a stream of independently prepared units repeatedly put into contact with the system. These units can be in any nonequilibrium state and interact with the system with an arbitrary strength and duration. We show that this stream constitutes an effective resource of nonequilibrium free energy, and we identify the conditions under which it behaves as a heat, work, or information reservoir. We also show that this setup provides a natural framework to analyze information erasure ("Landauer's principle") and feedback-controlled systems ("Maxwell's demon"). In the limit of a short system-unit interaction time, we further demonstrate that this setup can be used to provide a thermodynamically sound interpretation to many effective master equations. We discuss how nonautonomously driven systems, micromasers, lasing without inversion and the electronic Maxwell demon can be thermodynamically analyzed within our framework. While the present framework accounts for quantum features (e.g., squeezing, entanglement, coherence), we also show that quantum resources do not offer any advantage compared to classical ones in terms of the maximum extractable work.
Thermodynamics of Phantom Energy Accreting onto a Black Hole in Einstein—Power—Maxwell Gravity
International Nuclear Information System (INIS)
Abbas, G.; Ramzan, R. M.
2013-01-01
We investigate the phantom energy accretion onto a 3D black hole formulated in the Einstein—Power—Maxwell theory, and present the conditions for critical accretion of phantom energy onto the black hole. Further, we discuss the thermodynamics of phantom energy accreting onto the black hole and find that the first law of thermodynamics is easily satisfied while the second law and the generalized second law of thermodynamics remain invalid and conditionally valid, respectively. The results for the Banados—Teitelboim—Zanelli black hole can be recovered by taking Maxwellian contribution equal to zero
Future Trajectories of Renewable Energy Consumption in the European Union
Directory of Open Access Journals (Sweden)
Federica Cucchiella
2018-02-01
Full Text Available Renewable energy sources (RESs are able to reduce the European Union (EU’s dependence on foreign energy imports, also meeting sustainable objectives to tackle climate change and to enhance economic opportunities. Energy management requires a quantitative analysis and the European Commission follows the performance of each Member State (MS in order to define the corrective measures towards 2020 targets. Starting from historical data reported in the Eurostat database and through a mathematical model, this work proposes future trajectories towards 2020 of the share of energy from renewables (REs in terms of gross final energy consumption (GFEC. Furthermore, a quantitative analysis based on two indices—(i the share of REs in GFEC, and (ii gross final renewable energy consumption (GFREC per capita—permits a comparison among 28 MSs. The share of REs in GFEC in EU 28 varies from 19.4% to 21.8% in future trajectories towards 2020. Sweden and Finland occupy the top part of the ranking, while six MSs (Belgium, France, Ireland, Luxembourg, The Netherlands, and the United Kingdom are not able to reach the 2020 targets.
Analysis of free text in electronic health records for identification of cancer patient trajectories
DEFF Research Database (Denmark)
Jensen, Kasper; Soguero-Ruiz, Cristina; Mikalsen, Karl Oyvind
2017-01-01
With an aging patient population and increasing complexity in patient disease trajectories, physicians are often met with complex patient histories from which clinical decisions must be made. Due to the increasing rate of adverse events and hospitals facing financial penalties for readmission......, there has never been a greater need to enforce evidence-led medical decision-making using available health care data. In the present work, we studied a cohort of 7,741 patients, of whom 4,080 were diagnosed with cancer, surgically treated at a University Hospital in the years 2004-2012. We have developed...... a methodology that allows disease trajectories of the cancer patients to be estimated from free text in electronic health records (EHRs). By using these disease trajectories, we predict 80% of patient events ahead in time. By control of confounders from 8326 quantified events, we identified 557 events...
International Nuclear Information System (INIS)
Mrugalla, Florian; Kast, Stefan M
2016-01-01
Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)
Bounded energy exchange as an alternative to the third law of thermodynamics
Energy Technology Data Exchange (ETDEWEB)
Heidrich, Matthias, E-mail: Heidrich_Matthias@web.de
2016-10-15
This paper introduces a postulate explicitly forbidding the extraction of an infinite amount of energy from a thermodynamic system. It also introduces the assumption that no measuring equipment is capable of detecting arbitrarily small energy exchanges. The Kelvin formulation of the second law is reinterpreted accordingly. Then statements related to both the unattainability version and the entropic version of the third law are derived. The value of any common thermodynamic potential of a one-component system at absolute zero of temperature is ascertained if some assumptions with regard to the state space can be made. The point of view is the phenomenological, macroscopic and non-statistical one of classical thermodynamics.
Bounded energy exchange as an alternative to the third law of thermodynamics
International Nuclear Information System (INIS)
Heidrich, Matthias
2016-01-01
This paper introduces a postulate explicitly forbidding the extraction of an infinite amount of energy from a thermodynamic system. It also introduces the assumption that no measuring equipment is capable of detecting arbitrarily small energy exchanges. The Kelvin formulation of the second law is reinterpreted accordingly. Then statements related to both the unattainability version and the entropic version of the third law are derived. The value of any common thermodynamic potential of a one-component system at absolute zero of temperature is ascertained if some assumptions with regard to the state space can be made. The point of view is the phenomenological, macroscopic and non-statistical one of classical thermodynamics.
Thermodynamic properties of pressurized PH3 superconductor
Koka, S.; Rao, G. Venugopal
2018-05-01
The paper presents the superconducting thermodynamic functions determined for pressurized phosphorus trihydride (PH3). In particular, free energy difference ΔF, thermodynamic critical field Hc, specific heat etc. have been calculated using analytical expressions. The calculations were performed in the frame work of the strong-coupling formalism. The obtained dimensionless parameters: RΔ ≡ 2Δ(0)/kBTc, RC ≡ ΔC(Tc)/CN(Tc) and RH≡TcCN(Tc)/Hc2(0) are 4.05, 1.96 and 0.156 respectively, which significantly differ from the values arising from the BCS theory of superconductivity. The thermodynamic properties strongly depend on the depairing electron correlations and retardation effects.
Gibbs Free Energy of Formation for Selected Platinum Group Minerals (PGM
Directory of Open Access Journals (Sweden)
Spiros Olivotos
2016-01-01
Full Text Available Thermodynamic data for platinum group (Os, Ir, Ru, Rh, Pd and Pt minerals are very limited. The present study is focused on the calculation of the Gibbs free energy of formation (ΔfG° for selected PGM occurring in layered intrusions and ophiolite complexes worldwide, applying available experimental data on their constituent elements at their standard state (ΔG = G(species − ΔG(elements, using the computer program HSC Chemistry software 6.0. The evaluation of the accuracy of the calculation method was made by the calculation of (ΔGf of rhodium sulfide phases. The calculated values were found to be ingood agreement with those measured in the binary system (Rh + S as a function of temperature by previous authors (Jacob and Gupta (2014. The calculated Gibbs free energy (ΔfG° followed the order RuS2 < (Ir,OsS2 < (Pt, PdS < (Pd, PtTe2, increasing from compatible to incompatible noble metals and from sulfides to tellurides.
Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.
König, Gerhard; Brooks, Bernard R
2015-05-01
Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics/quantum mechanics simulations. This article is part of a Special Issue
Thermodynamics and structure of liquid alkali metals from the charged-hard-sphere reference fluid
International Nuclear Information System (INIS)
Lai, S.K.; Akinlade, O.; Tosi, M.P.
1989-12-01
The evaluation of thermodynamic properties of liquid alkali metals is re-examined in the approach based on the Gibbs-Bogoliubov inequality and using the fluid of charged hard spheres in the mean spherical approximation as reference system, with a view to achieving consistency with the liquid structure factor. The perturbative variational calculation of the Helmholtz free energy is based on an ab initio and highly reliable nonlocal pseudopotential. Only limited improvement is found in the calculated thermodynamic functions, even when full advantage is taken of the two variational parameters inherent in this approach. The role of thermodynamic self-consistency between the equations of state of the reference fluid derived from the routes of the internal energy and of the virial theorem is then discussed, using previous results by Hoye and Stell. An approximate evaluation of the corresponding contribution to the free energy of liquid alkali metals yields appreciable improvements in both the thermodynamic functions and the liquid structure factor. It thus appears that an accurate treatment of thermodynamic self-consistency in the charged-hard-sphere system may help to resolve some of the difficulties that are commonly met in the evaluation of thermodynamic and structural properties of liquid metals. (author). 55 refs, 4 figs, 4 tabs
Kou, Jisheng
2017-12-09
A general diffuse interface model with a realistic equation of state (e.g. Peng-Robinson equation of state) is proposed to describe the multi-component two-phase fluid flow based on the principles of the NVT-based framework which is an attractive alternative recently over the NPT-based framework to model the realistic fluids. The proposed model uses the Helmholtz free energy rather than Gibbs free energy in the NPT-based framework. Different from the classical routines, we combine the first law of thermodynamics and related thermodynamical relations to derive the entropy balance equation, and then we derive a transport equation of the Helmholtz free energy density. Furthermore, by using the second law of thermodynamics, we derive a set of unified equations for both interfaces and bulk phases that can describe the partial miscibility of multiple fluids. A relation between the pressure gradient and chemical potential gradients is established, and this relation leads to a new formulation of the momentum balance equation, which demonstrates that chemical potential gradients become the primary driving force of fluid motion. Moreover, we prove that the proposed model satisfies the total (free) energy dissipation with time. For numerical simulation of the proposed model, the key difficulties result from the strong nonlinearity of Helmholtz free energy density and tight coupling relations between molar densities and velocity. To resolve these problems, we propose a novel convex-concave splitting of Helmholtz free energy density and deal well with the coupling relations between molar densities and velocity through very careful physical observations with a mathematical rigor. We prove that the proposed numerical scheme can preserve the discrete (free) energy dissipation. Numerical tests are carried out to verify the effectiveness of the proposed method.
Quantum corrections to thermodynamics of quasitopological black holes
Directory of Open Access Journals (Sweden)
Sudhaker Upadhyay
2017-12-01
Full Text Available Based on the modification to area-law due to thermal fluctuation at small horizon radius, we investigate the thermodynamics of charged quasitopological and charged rotating quasitopological black holes. In particular, we derive the leading-order corrections to the Gibbs free energy, charge and total mass densities. In order to analyze the behavior of the thermal fluctuations on the thermodynamics of small black holes, we draw a comparative analysis between the first-order corrected and original thermodynamical quantities. We also examine the stability and bound points of such black holes under effect of leading-order corrections.
Thermodynamic analysis of a milk pasteurization process assisted by geothermal energy
International Nuclear Information System (INIS)
Yildirim, Nurdan; Genc, Seda
2015-01-01
Renewable energy system is an important concern for sustainable development of the World. Thermodynamic analysis, especially exergy analysis is an intense tool to assess sustainability of the systems. Food processing industry is one of the energy intensive sectors where dairy industry consumes substantial amount of energy among other food industry segments. Therefore, in this study, thermodynamic analysis of a milk pasteurization process assisted by geothermal energy was studied. In the system, a water–ammonia VAC (vapor absorption cycle), a cooling section, a pasteurizer and a regenerator were used for milk pasteurization. Exergetic efficiencies of each component and the whole system were separately calculated. A parametric study was undertaken. In this regard, firstly the effect of the geothermal resource temperature on (i) the total exergy destruction of the absorption cycle and the whole system, (ii) the efficiency of the VAC, the whole system and COP (coefficient of performance) of the VAC, (iii) the flow rate of the pasteurized milk were investigated. Then, the effect of the geothermal resource flow rate on the pasteurization load was analyzed. The exergetic efficiency of the whole system was calculated as 56.81% with total exergy destruction rate of 13.66 kW. The exergetic results were also illustrated through the Grassmann diagram. - Highlights: • Geothermal energy assisted milk pasteurization system was studied thermodynamically. • The first study on exergetic analysis of a milk pasteurization process with VAC. • The thermodynamic properties of water–ammonia mixture were calculated by using EES. • Energetic and exergetic efficiency calculated as 71.05 and 56.81%, respectively.
A thermodynamic study for the optimization of stable operation of free piston Stirling engines
Energy Technology Data Exchange (ETDEWEB)
Rogdakis, E.D.; Bormpilas, N.A.; Koniakos, I.K. [National Technical Univerisity, Athens (Greece). Dept. of Mechanical Engineering
2004-03-01
One of the most novel applications of the Stirling cycle is in the free piston configuration that was initially designed by W. Beale. In free piston Stirling engines (FPSEs), there are no mechanical linkages coupling the pistons or displacers, the motions of the reciprocating components follow the working gas pressure variations. Fillipo de Monte and G. Benvenuto have recently proposed a linearization technique of the dynamic balance equations. The aim of this paper is to predict the thermodynamic conditions for stable operation of FPSEs and their modeling. The equations of the angular velocity are solved analytically in terms of the working gas mass and the displacer-piston phase angle of the machine. Using the criterion of stable engine cyclic steady operation, a mathematically rigorous form is obtained for the main parameters of the engine. Furthermore, for simplicity reasons, thermodynamic magnitudes are obtained using the Schmidt analysis (isothermal model). (author)
A thermodynamic study for the optimization of stable operation of free piston Stirling engines
International Nuclear Information System (INIS)
Rogdakis, E.D.; Bormpilas, N.A.; Koniakos, I.K.
2004-01-01
One of the most novel applications of the Stirling cycle is in the free piston configuration that was initially designed by W. Beale. In free piston Stirling engines (FPSEs), there are no mechanical linkages coupling the pistons or displacers, the motions of the reciprocating components follow the working gas pressure variations. Fillipo de Monte and G. Benvenuto have recently proposed a linearization technique of the dynamic balance equations. The aim of this paper is to predict the thermodynamic conditions for stable operation of FPSEs and their modeling. The equations of the angular velocity are solved analytically in terms of the working gas mass and the displacer-piston phase angle of the machine. Using the criterion of stable engine cyclic steady operation, a mathematically rigorous form is obtained for the main parameters of the engine. Furthermore, for simplicity reasons, thermodynamic magnitudes are obtained using the Schmidt analysis (isothermal model)
Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B.; Martens, Christopher S.; DeVincenzi, Don (Technical Monitor)
2000-01-01
Among the most fundamental constraints governing the distribution of microorganisms in the environment is the availability of chemical energy at biologically useful levels. To assess the minimum free energy yield that can support microbial metabolism in situ, we examined the thermodynamics of H2-consuming processes in anoxic sediments from Cape Lookout Bight, NC, USA. Depth distributions of H2 partial pressure, along with a suite of relevant concentration data, were determined in sediment cores collected in November (at 14.5 C) and August (at 27 C) and used to calculate free energy yields for methanogenesis and sulfate reduction. At both times of year, and for both processes, free energy yields gradually decreased (became less negative) with depth before reaching an apparent asymptote. Sulfate reducing bacteria exhibited an asymptote of -19.1 +/- 1.7 kj(mol SO4(2-)(sup -1) while methanogenic archaea were apparently supported by energy yields as small as -10.6 +/- 0.7 kj(mol CH4)(sup -1).
Thermodynamics of spin chains of Haldane–Shastry type and one-dimensional vertex models
International Nuclear Information System (INIS)
Enciso, Alberto; Finkel, Federico; González-López, Artemio
2012-01-01
We study the thermodynamic properties of spin chains of Haldane–Shastry type associated with the A N−1 root system in the presence of a uniform external magnetic field. To this end, we exactly compute the partition function of these models for an arbitrary finite number of spins. We then show that these chains are equivalent to a suitable inhomogeneous classical Ising model in a spatially dependent magnetic field, generalizing the results of Basu-Mallick et al. for the zero magnetic field case. Using the standard transfer matrix approach, we are able to compute in closed form the free energy per site in the thermodynamic limit. We perform a detailed analysis of the chains’ thermodynamics in a unified way, with special emphasis on the zero field and zero temperature limits. Finally, we provide a novel interpretation of the thermodynamic quantities of spin chains of Haldane–Shastry type as weighted averages of the analogous quantities over an ensemble of classical Ising models. - Highlights: ► Partition function of spin chains of Haldane–Shastry type in magnetic field. ► Equivalence to classical inhomogeneous Ising models. ► Free energy per site, other thermodynamic quantities in thermodynamic limit. ► Zero field, zero temperature limits. ► Thermodynamic equivalence with ensemble of classical Ising models.
Thermodynamic and economic analysis on geothermal integrated combined-cycle power plants
International Nuclear Information System (INIS)
Bettocchi, R.; Cantore, G.; Negri di Montenegro, G.; Gadda, E.
1992-01-01
This paper considers geothermal integrated power plants obtained matching a geothermal plant with, a two pressure level combined plant. The purpose of the paper is the evaluation of thermodynamic and economic aspects on geothermal integrated combined-cycle power plant and a comparison with conventional solutions. The results show that the integrated combined plant power is greater than the sum of combined cycle and geothermal plant powers considered separately and that the integrated plant can offer economic benefits reaching the 16% of the total capital required
On the Correct Formulation of the First Law of Thermodynamics
Kalanov, Temur Z.
2006-04-01
The critical analysis of the generally accepted formulation of the first law of thermodynamics is proposed. The purpose of the analysis is to prove that the standard formulation contains a mathematical error and to offer the correct formulation. The correct formulation is based on the concepts of function and differential of function. Really, if internal energy Uof a system is a function of two independent variables Q=Q(t) (describing of the thermal form of energy) and R=R(t) (describing non-thermal form of energy), then the correct formulation of the first law of thermodynamics is: dU(Q,R)dt=( UQ )RdQdt+( UR )QdRdt, where t and -( UR )Q / ( UR )Q ( UQ ) . - ( UQ )R are time and measure of mutual transformation of forms of energy, correspondingly. General conclusion: standard thermodynamics is incorrect.
Thermodynamic parameters of elasticity and electrical conductivity ...
African Journals Online (AJOL)
The thermodynamic parameters (change in free energy of elasticity, DGe; change in enthalpy of elasticity, DHe; and change in entropy of elasticity, DSe) and the electrical conductivity of natural rubber composites reinforced separately with some agricultural wastes have been determined. Results show that the reinforced ...
Development of an Integrated Intelligent Multi -Objective Framework for UAV Trajectory Generation
Wilburn, Jennifer Nicole
This thesis explores a variety of path planning and trajectory generation schemes intended for small, fixed-wing Unmanned Aerial Vehicles. Throughout this analysis, discrete and pose-based methods are investigated. Pose-based methods are the focus of this research due to their increased flexibility and typically lower computational overhead. Path planning in 3 dimensions is also performed. The 3D Dubins methodology presented is an extension of a previously suggested approach and addresses both the mathematical formulation of the methodology, as well as an assessment of numerical issues encountered and the solutions implemented for these. The main contribution of this thesis is a 3-dimensional clothoid trajectory generation algorithm, which produces flyable paths of continuous curvature to ensure a more followable commanded path. This methodology is an extension of the 3D Dubins method and the 2D clothoid method, which have been implemented herein. To ensure flyability of trajectories produced by 3D pose-based trajectory generation methodologies, a set of criteria are specified to limit the possible solutions to only those flyable by the aircraft. Additionally, several assumptions are made concerning the motion of the aircraft in order to simplify the path generation problem. The 2D and 3D clothoid and Dubins trajectory planners are demonstrated through a trajectory tracking performance comparison between first the 2D Dubins and 2D clothoid methods using a position proportional-integral-derivative controller, then the 3D Dubins and 3D clothoid methods using both a position proportional-integral-derivative controller and an outer-loop non-linear dynamic inversion controller, within the WVU UAV Simulation Environment. These comparisons are demonstrated for both nominal and off-nominal conditions, and show that for both 2D and 3D implementations, the clothoid path planners yields paths with better trajectory tracking performance as compared to the Dubins path planners
Emigration trajectories of former Portuguese emigrants: the construction of family integrity
Directory of Open Access Journals (Sweden)
Filipa Daniela Marques
2012-06-01
Full Text Available Constructing family integrity is a normative developmental challenge for older people, which is influenced by the family and social systems. This exploratory study examines the emigration trajectories of former Portuguese emigrants, now in old age, who returned to their home country (Portugal. And aims to contribute to a better understand of the influence of emigration experiences in the construction of family integrity versus disconnection and alienation.
International Nuclear Information System (INIS)
Fuss, M.C.; Sanz, A.G.; Blanco, F.; Limao-Vieira, P.; Brunger, M.J.; Garcia, G.
2014-01-01
Tetrahydrofuran (THF, C 4 H 8 O) has a molecular structure that is similar to the ribose in the DNA backbone and is used as a surrogate of ribose to get electron scattering cross sections. Total, integral inelastic and integral and differential elastic cross sections have been calculated with the screening-corrected additivity rule (SCAR) method based on the independent atom model (IAM) for electron scattering from THF. Since the permanent dipole moment of THF enhances rotational excitation particularly at low energies and for small angles, an estimate of the rotational excitation cross section was also computed by assuming the interaction with a free electric dipole as an independent, additional process. Our theoretical results compare very favourably to the existing experimental data. Finally, a self-consistent set of integral and differential interaction cross-sections for the incident energy range 1 eV - 10 keV is established for use in our low energy particle track simulation (LEPTS). All cross section data are supplied numerically in tabulated form. (authors)
THERMODYNAMIC PARAMETERS OF LEAD SULFIDE CRYSTALS IN THE CUBIC PHASE
Directory of Open Access Journals (Sweden)
T. O. Parashchuk
2016-07-01
Full Text Available Geometric and thermodynamic parameters of cubic PbS crystals were obtained using the computer calculations of the thermodynamic parameters within density functional theory method DFT. Cluster models for the calculation based on the analysis of the crystal and electronic structure. Temperature dependence of energy ΔE and enthalpy ΔH, Gibbs free energy ΔG, heat capacity at constant pressure CP and constant volume CV, entropy ΔS were determined on the basis of ab initio calculations of the crystal structure of molecular clusters. Analytical expressions of temperature dependences of thermodynamic parameters which were approximated with quantum-chemical calculation points have been presented. Experimental results compared with theoretically calculated data.
Matoz-Fernandez, D A; Linares, D H; Ramirez-Pastor, A J
2012-09-04
The statistical thermodynamics of straight rigid rods of length k on triangular lattices was developed on a generalization in the spirit of the lattice-gas model and the classical Guggenheim-DiMarzio approximation. In this scheme, the Helmholtz free energy and its derivatives were written in terms of the order parameter, δ, which characterizes the nematic phase occurring in the system at intermediate densities. Then, using the principle of minimum free energy with δ as a parameter, the main adsorption properties were calculated. Comparisons with Monte Carlo simulations and experimental data were performed in order to evaluate the outcome and limitations of the theoretical model.
Methods and systems for thermodynamic evaluation of battery state of health
Yazami, Rachid; McMenamin, Joseph; Reynier, Yvan; Fultz, Brent T
2014-12-02
Described are systems and methods for accurately characterizing thermodynamic and materials properties of electrodes and battery systems and for characterizing the state of health of electrodes and battery systems. Measurement of physical attributes of electrodes and batteries corresponding to thermodynamically stabilized electrode conditions permit determination of thermodynamic parameters, including state functions such as the Gibbs free energy, enthalpy and entropy of electrode/electrochemical cell reactions, that enable prediction of important performance attributes of electrode materials and battery systems, such as energy, power density, current rate, cycle life and state of health. Also provided are systems and methods for charging a battery according to its state of health.
Beyond heat baths II: framework for generalized thermodynamic resource theories
Yunger Halpern, Nicole
2018-03-01
Thermodynamics, which describes vast systems, has been reconciled with small scales, relevant to single-molecule experiments, in resource theories. Resource theories have been used to model exchanges of energy and information. Recently, particle exchanges were modeled; and an umbrella family of thermodynamic resource theories was proposed to model diverse baths, interactions, and free energies. This paper motivates and details the family’s structure and prospective applications. How to model electrochemical, gravitational, magnetic, and other thermodynamic systems is explained. Szilárd’s engine and Landauer’s Principle are generalized, as resourcefulness is shown to be convertible not only between information and gravitational energy, but also among diverse degrees of freedom. Extensive variables are associated with quantum operators that might fail to commute, introducing extra nonclassicality into thermodynamic resource theories. An early version of this paper partially motivated the later development of noncommutative thermalization. This generalization expands the theories’ potential for modeling realistic systems with which small-scale statistical mechanics might be tested experimentally.
pycalphad: CALPHAD-based Computational Thermodynamics in Python
Directory of Open Access Journals (Sweden)
Richard Otis
2017-01-01
Full Text Available The pycalphad software package is a free and open-source Python library for designing thermodynamic models, calculating phase diagrams and investigating phase equilibria using the CALPHAD method. It provides routines for reading thermodynamic databases and solving the multi-component, multi-phase Gibbs energy minimization problem. The pycalphad software project advances the state of thermodynamic modeling by providing a flexible yet powerful interface for manipulating CALPHAD data and models. The key feature of the software is that the thermodynamic models of individual phases and their associated databases can be programmatically manipulated and overridden at run-time without modifying any internal solver or calculation code. Because the models are internally decoupled from the equilibrium solver and the models themselves are represented symbolically, pycalphad is an ideal tool for CALPHAD database development and model prototyping.
Lagrangian formulation of irreversible thermodynamics and the second law of thermodynamics.
Glavatskiy, K S
2015-05-28
We show that the equations which describe irreversible evolution of a system can be derived from a variational principle. We suggest a Lagrangian, which depends on the properties of the normal and the so-called "mirror-image" system. The Lagrangian is symmetric in time and therefore compatible with microscopic reversibility. The evolution equations in the normal and mirror-imaged systems are decoupled and describe therefore independent irreversible evolution of each of the systems. The second law of thermodynamics follows from a symmetry of the Lagrangian. Entropy increase in the normal system is balanced by the entropy decrease in the mirror-image system, such that there exists an "integral of evolution" which is a constant. The derivation relies on the property of local equilibrium, which states that the local relations between the thermodynamic quantities in non-equilibrium are the same as in equilibrium.
Yip, Ngai Yin; Vermaas, David A; Nijmeijer, Kitty; Elimelech, Menachem
2014-05-06
Reverse electrodialysis (RED) can harness the Gibbs free energy of mixing when fresh river water flows into the sea for sustainable power generation. In this study, we carry out a thermodynamic and energy efficiency analysis of RED power generation, and assess the membrane power density. First, we present a reversible thermodynamic model for RED and verify that the theoretical maximum extractable work in a reversible RED process is identical to the Gibbs free energy of mixing. Work extraction in an irreversible process with maximized power density using a constant-resistance load is then examined to assess the energy conversion efficiency and power density. With equal volumes of seawater and river water, energy conversion efficiency of ∼ 33-44% can be obtained in RED, while the rest is lost through dissipation in the internal resistance of the ion-exchange membrane stack. We show that imperfections in the selectivity of typical ion exchange membranes (namely, co-ion transport, osmosis, and electro-osmosis) can detrimentally lower efficiency by up to 26%, with co-ion leakage being the dominant effect. Further inspection of the power density profile during RED revealed inherent ineffectiveness toward the end of the process. By judicious early discontinuation of the controlled mixing process, the overall power density performance can be considerably enhanced by up to 7-fold, without significant compromise to the energy efficiency. Additionally, membrane resistance was found to be an important factor in determining the power densities attainable. Lastly, the performance of an RED stack was examined for different membrane conductivities and intermembrane distances simulating high performance membranes and stack design. By thoughtful selection of the operating parameters, an efficiency of ∼ 37% and an overall gross power density of 3.5 W/m(2) represent the maximum performance that can potentially be achieved in a seawater-river water RED system with low
Energy Systems Integration Laboratory | Energy Systems Integration Facility
| NREL Integration Laboratory Energy Systems Integration Laboratory Research in the Energy Systems Integration Laboratory is advancing engineering knowledge and market deployment of hydrogen technologies. Applications include microgrids, energy storage for renewables integration, and home- and station
International Nuclear Information System (INIS)
Zhang, De-Long; Zhang, Qun; Zhang, Pei; Kang, Jian; Wong, Wing-Han; Yu, Dao-Yin
2016-01-01
Graphical abstract: Diffusion growth of Ga"3"+-doped LiTaO_3(LT) thin film was studied thermodynamically. Some Ga"3"+-doped LT thin films were grown on LT surface by in-diffusion of homogeneously coated Ga_2O_3 film at the temperature range of (1273 to 1473) K. The Ga"3"+ profile in the grown thin film was analyzed by secondary ion mass spectrometry. Form the measured Ga"3"+ profiles, some thermodynamic parameters were obtained. These include diffusivity, diffusion constant, chemical activation energy, solubility, solubility constant and enthalpy of solution. These parameters are crucial to design and growth of a Ga"3"+-doped LT thin film with desired Ga"3"+ profile for integrated optics application. A thermodynamic model is suggested for the growth and verified experimentally. - Highlights: • Diffusion growth of Ga"3"+-doped LiTaO_3 thin film were studied thermodynamically. • Diffusion constant is 1.41 · 10"−"6 m"2/s and activation energy is 237.2 kJ/mol. • Solubility constant is 22.9 · 10"2"6 ions/m"3 and enthalpy of solution is 28.9 kJ/mol. • Ga"3"+ dopant has small effect on LiTaO_3 refractive index. • Ga"3"+ growth can be described by a Fick-type equation with a constant diffusivity. - Abstract: A thermodynamic study was performed on diffusion growth of Ga"3"+-doped LiTaO_3(LT) thin film for integrated optics. Some Ga"3"+-doped LT thin films were grown on LT surface by in-diffusion of homogeneously coated Ga_2O_3 film at the temperature range of (1273 to 1473) K. After growth, the refractive indices at Ga"3"+-doped and un-doped surface parts were measured by prism coupling technique and Li composition there was evaluated from the measured refractive indices. The results show that Ga"3"+ dopant has small effect on the LT index. Li_2O out-diffusion is not measurable. The Ga"3"+ profile in the grown thin film was analysed by secondary ion mass spectrometry. It is found that the grown Ga"3"+ ions follow a complementary error function profile. A
Muhammed, Zahed; Arai, Satoshi; Saijo, Shinya; Yamato, Ichiro; Murata, Takeshi; Suenaga, Atsushi
2012-07-01
Vacuolar ATPase (V-ATPase) of Enterococcus hirae is composed of a soluble catalytic domain (V₁; NtpA₃-B₃-D-G) and an integral membrane domain (V₀; NtpI-K₁₀) connected by a central and two peripheral stalks (NtpC, NtpD-G and NtpE-F). Recently nucleotide binding of catalytic NtpA monomer has been reported (Arai et al.). In the present study, we calculated the nucleotide binding affinity of NtpA by molecular dynamics (MD) simulation/free energy calculation using MM-GBSA approach based on homology modeled structure of NtpA monomer docked with ATP analogue, adenosine 5'-[β, γ-imido] triphosphate (AMP-PNP). The calculated binding free energies showed qualitatively good agreement with experimental data. The calculation was cross-validated further by the rigorous method, thermodynamic integration (TI) simulation. Finally, the interaction between NtpA and nucleotides at the atomic level was investigated by the analyses of components of free energy and the optimized model structures obtained from MD simulations, suggesting that electrostatic contribution is responsible for the difference in nucleotide binding to NtpA monomer. This is the first observation and suggestion to explain the difference of nucleotide binding properties in V-ATPase NtpA subunit, and our method can be a valuable primary step to predict nucleotide binding affinity to other subunits (NtpAB, NtpA₃B₃) and to explore subunit interactions and eventually may help to understand energy transduction mechanism of E. hirae V-ATPase. Copyright © 2012 Elsevier Inc. All rights reserved.
What Is Energy Systems Integration? | Energy Systems Integration Facility |
NREL What Is Energy Systems Integration? What Is Energy Systems Integration? Energy systems integration (ESI) is an approach to solving big energy challenges that explores ways for energy systems to Research Community NREL is a founding member of the International Institute for Energy Systems Integration
Irreversible thermodynamic analysis and application for molecular heat engines
Lucia, Umberto; Açıkkalp, Emin
2017-09-01
Is there a link between the macroscopic approach to irreversibility and microscopic behaviour of the systems? Consumption of free energy keeps the system away from a stable equilibrium. Entropy generation results from the redistribution of energy, momentum, mass and charge. This concept represents the essence of the thermodynamic approach to irreversibility. Irreversibility is the result of the interaction between systems and their environment. The aim of this paper is to determine lost works in a molecular engine and compare results with macro (classical) heat engines. Firstly, irreversible thermodynamics are reviewed for macro and molecular cycles. Secondly, irreversible thermodynamics approaches are applied for a quantum heat engine with -1/2 spin system. Finally, lost works are determined for considered system and results show that macro and molecular heat engines obey same limitations. Moreover, a quantum thermodynamic approach is suggested in order to explain the results previously obtained from an atomic viewpoint.
Stability of black holes based on horizon thermodynamics
Directory of Open Access Journals (Sweden)
Meng-Sen Ma
2015-12-01
Full Text Available On the basis of horizon thermodynamics we study the thermodynamic stability of black holes constructed in general relativity and Gauss–Bonnet gravity. In the framework of horizon thermodynamics there are only five thermodynamic variables E, P, V, T, S. It is not necessary to consider concrete matter fields, which may contribute to the pressure of black hole thermodynamic system. In non-vacuum cases, we can derive the equation of state, P=P(V,T. According to the requirements of stable equilibrium in conventional thermodynamics, we start from these thermodynamic variables to calculate the heat capacity at constant pressure and Gibbs free energy and analyze the local and global thermodynamic stability of black holes. It is shown that P>0 is the necessary condition for black holes in general relativity to be thermodynamically stable, however this condition cannot be satisfied by many black holes in general relativity. For black hole in Gauss–Bonnet gravity negative pressure can be feasible, but only local stable black hole exists in this case.
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Facility | NREL Energy Systems Integration Facility Videos Energy Systems Integration Facility Integration Facility NREL + SolarCity: Maximizing Solar Power on Electrical Grids Redefining What's Possible for Renewable Energy: Grid Integration Robot-Powered Reliability Testing at NREL's ESIF Microgrid
Kou, Jisheng
2016-11-25
A general diffuse interface model with a realistic equation of state (e.g. Peng-Robinson equation of state) is proposed to describe the multi-component two-phase fluid flow based on the principles of the NVT-based framework which is a latest alternative over the NPT-based framework to model the realistic fluids. The proposed model uses the Helmholtz free energy rather than Gibbs free energy in the NPT-based framework. Different from the classical routines, we combine the first law of thermodynamics and related thermodynamical relations to derive the entropy balance equation, and then we derive a transport equation of the Helmholtz free energy density. Furthermore, by using the second law of thermodynamics, we derive a set of unified equations for both interfaces and bulk phases that can describe the partial miscibility of two fluids. A relation between the pressure gradient and chemical potential gradients is established, and this relation leads to a new formulation of the momentum balance equation, which demonstrates that chemical potential gradients become the primary driving force of fluid motion. Moreover, we prove that the proposed model satisfies the total (free) energy dissipation with time. For numerical simulation of the proposed model, the key difficulties result from the strong nonlinearity of Helmholtz free energy density and tight coupling relations between molar densities and velocity. To resolve these problems, we propose a novel convex-concave splitting of Helmholtz free energy density and deal well with the coupling relations between molar densities and velocity through very careful physical observations with a mathematical rigor. We prove that the proposed numerical scheme can preserve the discrete (free) energy dissipation. Numerical tests are carried out to verify the effectiveness of the proposed method.
A thermodynamic description of quarks at the subquark level
International Nuclear Information System (INIS)
Fitzpatrick, G.L.
1985-01-01
A thermodynamic basis for the description of quarks at the subquark level is proposed. It is suggested that subquarks are ultrarelativistic objects confined to the quark radius R. Thus they experience accelerations of the order a≅c/sup 2//R. But this means that information excluding horizons (iota) comparable to quark radii R, namely iota≅c/sup 2//a≅R, are present. Such horizons force us to describe quarks, at the subquark level, via thermodynamics. This thermodynamic description must involve unconventional negative energy Rindler vacua, rather than the conventional zero energy Minkowski vacuum. In an average thermodynamic sense, these Rindler vacua cancel excess kinetic energy of the subquarks, thereby removing an objection to theories involving subquarks. In any such theory it is necessary to assign an Unruh temperature T, where kT≅(h/2πc)a≅(hc/2πR), to the subquark matter. The author argues that T must be the temperature of the early universe phase transition (probably first order) at which quarks condensed into hadrons. Thus quarks have a temperature T independent of hadron mass. He shows how quark properties may be derived in the foregoing thermodynamic context
Smith, J. A.; Froyd, K. D.; Toon, O. B.
2012-12-01
We construct tables of reaction enthalpies and entropies for the association reactions involving sulfuric acid vapor, water vapor, and the bisulfate ion. These tables are created from experimental measurements and quantum chemical calculations for molecular clusters and a classical thermodynamic model for larger clusters. These initial tables are not thermodynamically consistent. For example, the Gibbs free energy of associating a cluster consisting of one acid molecule and two water molecules depends on the order in which the cluster was assembled: add two waters and then the acid or add an acid and a water and then the second water. We adjust the values within the tables using the method of Lagrange multipliers to minimize the adjustments and produce self-consistent Gibbs free energy surfaces for the neutral clusters and the charged clusters. With the self-consistent Gibbs free energy surfaces, we calculate size distributions of neutral and charged clusters for a variety of atmospheric conditions. Depending on the conditions, nucleation can be dominated by growth along the neutral channel or growth along the ion channel followed by ion-ion recombination.
General equilibrium second-order hydrodynamic coefficients for free quantum fields
Buzzegoli, M.; Grossi, E.; Becattini, F.
2017-10-01
We present a systematic calculation of the corrections of the stress-energy tensor and currents of the free boson and Dirac fields up to second order in thermal vorticity, which is relevant for relativistic hydrodynamics. These corrections are non-dissipative because they survive at general thermodynamic equilibrium with non vanishing mean values of the conserved generators of the Lorentz group, i.e. angular momenta and boosts. Their equilibrium nature makes it possible to express the relevant coefficients by means of correlators of the angular-momentum and boost operators with stress-energy tensor and current, thus making simpler to determine their so-called "Kubo formulae". We show that, at least for free fields, the corrections are of quantum origin and we study several limiting cases and compare our results with previous calculations. We find that the axial current of the free Dirac field receives corrections proportional to the vorticity independently of the anomalous term.
Teaching elementary thermodynamics and energy conversion: Opinions
International Nuclear Information System (INIS)
Gaggioli, Richard A.
2010-01-01
This presentation deals with innovation in teaching and understanding of thermodynamic principles. Key features of the approach being advocated are: (a) postulation of the existence of entropy, (b) explicitly associating energy transfers with other transports, (c) stating the 2nd Law in terms of Gibbs' available-energy, (d) systematic use of software such as EES. The paper outlines and elaborates upon an introductory course. Major headings in the course are: basic concepts: properties, additive properties and balances, primitive properties, energy, 1st Law. entropy, elementary academic applications of balances, available-energy, second law, exergy, thermostatic property relations, EES. Applications to processes, fluid flow, Heat transfer, thermochemical. Applications to devices, single-process, compound-process, systems (consisting of devices and processes functioning together).
Thermodynamics of solvation and solvophobic effect in formamide
International Nuclear Information System (INIS)
Sedov, I.A.; Stolov, M.A.; Solomonov, B.N.
2013-01-01
Highlights: • Enthalpies of solution of apolar organic compounds in formamide were measured. • Gibbs free energies of solution were experimentally determined. • Influence of the solvophobic effect on solvation thermodynamics was studied. • Thermodynamic features of solutions in formamide resemble those of aqueous solutions. -- Abstract: Using semi-adiabatic calorimetry, we measured the enthalpies of solution for various low-polar compounds including alkanes, aromatic hydrocarbons and their halogenated derivatives in formamide at temperature of 298 K. For the same compounds, the values of limiting activity coefficients in formamide were determined using GC headspace analysis at 298 K, and Gibbs free energies of solution and solvation were calculated. Based on these data and the available literature values of the Gibbs free energy of solvation in formamide for a number of other low-polar solutes, a study of the solvophobic effect in this solvent is performed, and its resemblance to the hydrophobic effect in aqueous solutions is demonstrated. It is shown that the contribution of the solvophobic effect into the solvation Gibbs free energy in formamide is much higher than that in aliphatic alcohols, but lower than that in water. Like in water, the magnitude of this contribution for different solutes linearly increases with the solute molecular volume. Solvophobic effect also significantly affects the enthalpies of dissolution in formamide, causing them to be more negative in the case of alkanes and more positive in the case of arenes
International Nuclear Information System (INIS)
Hubbard, W.B.; Dewitt, H.E.
1985-01-01
A model free energy is presented which accurately represents results from 45 high-precision Monte Carlo calculations of the thermodynamics of hydrogen-helium mixtures at pressures of astrophysical and planetophysical interest. The free energy is calculated using free-electron perturbation theory (dielectric function theory), and is an extension of the expression given in an earlier paper in this series. However, it fits the Monte Carlo results more accurately, and is valid for the full range of compositions from pure hydrogen to pure helium. Using the new free energy, the phase diagram of mixtures of liquid metallic hydrogen and helium is calculated and compared with earlier results. Sample results for mixing volumes are also presented, and the new free energy expression is used to compute a theoretical Jovian adiabat and compare the adiabat with results from three-dimensional Thomas-Fermi-Dirac theory. The present theory gives slightly higher densities at pressures of about 10 megabars. 20 references
Hubbard, W. B.; Dewitt, H. E.
1985-01-01
A model free energy is presented which accurately represents results from 45 high-precision Monte Carlo calculations of the thermodynamics of hydrogen-helium mixtures at pressures of astrophysical and planetophysical interest. The free energy is calculated using free-electron perturbation theory (dielectric function theory), and is an extension of the expression given in an earlier paper in this series. However, it fits the Monte Carlo results more accurately, and is valid for the full range of compositions from pure hydrogen to pure helium. Using the new free energy, the phase diagram of mixtures of liquid metallic hydrogen and helium is calculated and compared with earlier results. Sample results for mixing volumes are also presented, and the new free energy expression is used to compute a theoretical Jovian adiabat and compare the adiabat with results from three-dimensional Thomas-Fermi-Dirac theory. The present theory gives slightly higher densities at pressures of about 10 megabars.
Heavy quark free energy in QCD and in gauge theories with gravity duals
Noronha, Jorge
2010-09-01
Recent lattice results in pure glue SU(3) theory at high temperatures have shown that the expectation value of the renormalized Polyakov loop approaches its asymptotic limit at high temperatures from above. We show that this implies that the “heavy quark free energy” obtained from the renormalized loop computed on the lattice does not behave like a true thermodynamic free energy. While this should be expected to occur in asymptotically free gauge theories such as QCD, we use the gauge/string duality to show that in a large class of strongly coupled gauge theories with nontrivial UV fixed points the Polyakov loop reaches its asymptotic value from above only if the dimension of the relevant operator used to deform the conformal field theory is greater than or equal to 3.
Directory of Open Access Journals (Sweden)
David Sedmidubsky
2017-07-01
Full Text Available Nonstoichiometric oxides form a new chapter in tailored materials. Founding and construction of thermodynamic functions related to solid (geologic materials is traced showing interactions between Czech Professor F. Wald and Russians R.S. Kurnakov and D.S. Korzhinskiy in the early definition of phases and characterization of partly open systems. Development of thermodynamic concepts regarding solid-state description is reviewed. For the associated definition of a mobile component the hyperfree energy was invented and recently applied on several systems. A novel term plutability is put forward as a measure of material susceptibility towards free component uptake as a result of varying predictors such as temperature, pressure and activity. Ehrenfest-like equations involving the changes of plutabilities were derived.
Granet, Irving
2014-01-01
Fundamental ConceptsIntroductionThermodynamic SystemsTemperatureForce and MassElementary Kinetic Theory of GasesPressureReviewKey TermsEquations Developed in This ChapterQuestionsProblemsWork, Energy, and HeatIntroductionWorkEnergyInternal EnergyPotential EnergyKinetic EnergyHeatFlow WorkNonflow WorkReviewKey TermsEquations Developed in This ChapterQuestionsProblemsFirst Law of ThermodynamicsIntroductionFirst Law of ThermodynamicsNonflow SystemSteady-Flow SystemApplications of First Law of ThermodynamicsReviewKey TermsEquations Developed in This ChapterQuestionsProblemsThe Second Law of ThermodynamicsIntroductionReversibility-Second Law of ThermodynamicsThe Carnot CycleEntropyReviewKey TermsEquations Developed in This ChapterQuestionsProblemsProperties of Liquids and GasesIntroductionLiquids and VaporsThermodynamic Properties of SteamComputerized PropertiesThermodynamic DiagramsProcessesReviewKey TermsEquations Developed in This ChapterQuestionsProblemsThe Ideal GasIntroductionBasic ConsiderationsSpecific Hea...
The Thermodynamic Machinery of Life
Kurzynski, Michal
2006-01-01
Living organisms are open thermodynamic systems whose functional structure has developed and been kinetically frozen during the historical process of biological evolution. A thermodynamics of both nonequilibrium and complex systems is needed for their description. In this book, the foundations of such a thermodynamics are presented. Biological processes at the cellular level are considered as coupled chemical reactions and transport processes across internal and the cytoplasmic membrane. All these processes are catalyzed by specific enzymes hence the kinetics of enzymatic catalysis and its control are described here in detail. The coupling of several processes through a common enzyme is considered in the context of free energy or signal transduction. Special attention is paid to evidence for a rich stochastic internal dynamics of native proteins and its possible role in the control of enzyme activity and in the action of biological molecular machines.
Thermodynamic assessment of the Sn-Co lead-free solder system
Liu, Libin; Andersson, Cristina; Liu, Johan
2004-09-01
The Sn-Co-Cu eutectic alloy can be a less expensive alternative for the Sn-Ag-Cu alloy. In order to find the eutectic solder composition of the Sn-Co-Cu system, the Sn-Co binary system has been thoroughly assessed with the calculation of phase diagram (CALPHAD) method. The liquid phase, the FCC and HCP Co-rich solid solution, and the BCT Sn-rich solid solution have been described by the Redlich-Kister model. The Hillert-Jarl-Inden model has been used to describe the magnetic contributions to Gibbs energy in FCC and HCP. The CoSn2, CoSn, Co3Sn2_β, and Co3Sn2_α phases have been treated as stoichiometric phases. A series of thermodynamic parameters have been obtained. The calculated phase diagram and thermodynamic properties are in good agreement with the experimental data. The obtained thermodynamic data was used to extrapolate the ternary Sn-Co-Cu phase diagram. The composition of the Sn-rich eutectic point of the Sn-Co-Cu system was found to be 224°C, 0.4% Co, and 0.7% Cu.
Integration of the North American energy market; Integration du marche Nord-Americain de l'energie
Energy Technology Data Exchange (ETDEWEB)
Lapointe, A
2002-07-01
The US energy policy of President Bush administration proposes to develop a North American energy framework with a greater energy integration between Canada, the USA and Mexico in the respect of the sovereignty of each country. This article tries to evaluate the integration status of the energy sector in Northern America with respect to the North American free-exchange agreement and to the deregulation process observed in the natural gas and electric power sectors. The commercial energy fluxes between Canada, Mexico and the US show that the integration is a reality and that it is in constant progress. This integration is particularly important in the case of Canada and the USA while major constraints remain in Mexico where the property and exploitation of natural resources is a government monopoly. For this reason, Mexico could never exploit the full potentialities of its resources and suffers from a chronical under-investment in its energy infrastructures which limits the energy trade. Despite this, there is a strong will from the Mexican authorities to ensure the modernization of its energy sector and to contribute more to the integration process of the north American energy market. A series of reforms, and in particular the fiscal reform started by the government should reduce the excessive dependence of the government incomes with the dividends from the energy sector. This should allow the different government companies to reinvest more its benefits in order to improve the existing infrastructures and to increase the capacities (in particular in the gas and electricity sectors). Finally, the recent will of the government to open the gas sector should allow the development of this energy source. (J.S.)
Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics
Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.
2015-12-01
Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.
Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)
2015-12-28
Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.
Sheng, Tian; Sun, Shi-Gang
2017-11-01
Experiments have found that the porphyrin-like FeN4 site in Fe-N-C materials is highly efficient for the electrochemical reduction of CO2 into CO. In this work, we investigated the reduction mechanisms on FeN4 embedded graphene layer catalyst with some explicit water molecules by combining the constrained ab initio molecular dynamics simulations and thermodynamic integrations. The reaction free energy and electron transfer in each elementary step were identified. The initial CO2 activation was identified to go through the first electron transfer to form adsorbed CO2- anion and the CO desorption was the rate limiting step in the overall catalytic cycle.
Shimazaki, Eriko; Tashiro, Akiko; Kumagai, Hitomi; Kumagai, Hitoshi
2017-04-01
Relation between the thermodynamic parameters obtained from water sorption isotherms and the degree of reduction in the glass transition temperature (T g ), accompanied by water sorption, was quantitatively studied. Two well-known glassy food materials namely, wheat gluten and maltodextrin were used as samples. The difference between the chemical potential of water in a solution and that of pure water ([Formula: see text]), the difference between the chemical potential of solid in a solution and that of a pure solid ([Formula: see text]), and the change in the integral Gibbs free energy ([Formula: see text]) were obtained by analyzing the water sorption isotherms using solution thermodynamics. The parameter [Formula: see text] correlated well with ΔT g (≡T g - T g0 ; where T g0 is the glass transition temperature of dry material), which had been taken to be an index of plasticizing effect. This indicates that plasticizing effect of water on foods can be evaluated through the parameter [Formula: see text].
Ross, David S; Thurston, George M; Lutzer, Carl V
2008-08-14
In this paper we present a method for determining the free energies of ternary mixtures from light scattering data. We use an approximation that is appropriate for liquid mixtures, which we formulate as a second-order nonlinear partial differential equation. This partial differential equation (PDE) relates the Hessian of the intensive free energy to the efficiency of light scattering in the forward direction. This basic equation applies in regions of the phase diagram in which the mixtures are thermodynamically stable. In regions in which the mixtures are unstable or metastable, the appropriate PDE is the nonlinear equation for the convex hull. We formulate this equation along with continuity conditions for the transition between the two equations at cloud point loci. We show how to discretize this problem to obtain a finite-difference approximation to it, and we present an iterative method for solving the discretized problem. We present the results of calculations that were done with a computer program that implements our method. These calculations show that our method is capable of reconstructing test free energy functions from simulated light scattering data. If the cloud point loci are known, the method also finds the tie lines and tie triangles that describe thermodynamic equilibrium between two or among three liquid phases. A robust method for solving this PDE problem, such as the one presented here, can be a basis for optical, noninvasive means of characterizing the thermodynamics of multicomponent mixtures.
Heating without heat: Thermodynamics of passive energy filters between finite systems.
Muñoz-Tapia, R; Brito, R; Parrondo, J M R
2017-09-01
Passive filters allowing the exchange of particles in a narrow band of energy are currently used in microrefrigerators and energy transducers. In this Rapid Communication, we analyze their thermal properties using linear irreversible thermodynamics and kinetic theory, and discuss a striking phenomenon: the possibility of simultaneously increasing or decreasing the temperatures of two systems without any supply of energy. This occurs when the filter induces a flow of particles whose energy is between the average energies of the two systems. Here we show that this selective transfer of particles does not need the action of any sort of Maxwell demon and can be carried out by passive filters without compromising the second law of thermodynamics. This phenomenon allows us to design cycles between two reservoirs at temperatures T_{1}
Nonlocal kinetic energy functionals by functional integration
Mi, Wenhui; Genova, Alessandro; Pavanello, Michele
2018-05-01
Since the seminal studies of Thomas and Fermi, researchers in the Density-Functional Theory (DFT) community are searching for accurate electron density functionals. Arguably, the toughest functional to approximate is the noninteracting kinetic energy, Ts[ρ], the subject of this work. The typical paradigm is to first approximate the energy functional and then take its functional derivative, δ/Ts[ρ ] δ ρ (r ) , yielding a potential that can be used in orbital-free DFT or subsystem DFT simulations. Here, this paradigm is challenged by constructing the potential from the second-functional derivative via functional integration. A new nonlocal functional for Ts[ρ] is prescribed [which we dub Mi-Genova-Pavanello (MGP)] having a density independent kernel. MGP is constructed to satisfy three exact conditions: (1) a nonzero "Kinetic electron" arising from a nonzero exchange hole; (2) the second functional derivative must reduce to the inverse Lindhard function in the limit of homogenous densities; (3) the potential is derived from functional integration of the second functional derivative. Pilot calculations show that MGP is capable of reproducing accurate equilibrium volumes, bulk moduli, total energy, and electron densities for metallic (body-centered cubic, face-centered cubic) and semiconducting (crystal diamond) phases of silicon as well as of III-V semiconductors. The MGP functional is found to be numerically stable typically reaching self-consistency within 12 iterations of a truncated Newton minimization algorithm. MGP's computational cost and memory requirements are low and comparable to the Wang-Teter nonlocal functional or any generalized gradient approximation functional.
International Nuclear Information System (INIS)
Wang, Jiangjiang; Lu, Yanchao; Yang, Ying; Mao, Tianzhi
2016-01-01
This study aims to present a thermodynamic performance analysis and to optimize the configurations of a hybrid combined cooling, heating and power (CCHP) system incorporating solar energy and natural gas. A basic natural gas CCHP system containing a power generation unit, a heat recovery system, an absorption cooling system and a storage tank is integrated with solar photovoltaic (PV) panels and/or a heat collector. Based on thermodynamic modeling, the thermodynamic performance, including energy and exergy efficiencies, under variable work conditions, such as electric load factor, solar irradiance and installation ratio, of the solar PV panels and heat collector is investigated and analyzed. The results of the energy supply side analysis indicate that the integration of solar PV into the CCHP system more efficiently improves the exergy efficiency, whereas the integration of a solar heat collector improves the energy efficiency. To match the building loads, the optimization method combined with the operation strategy is employed to optimize the system configurations to maximize the integrated benefits of energy and economic costs. The optimization results of demand–supply matching demonstrate that the integration of a solar heat collector achieves a better integrated performance than the solar PV integration in the specific case study. - Highlights: • Design a CCHP system integrated with solar PV and heat collector. • Present the energy and exergy analyses under variable work conditions. • Propose an optimization method of CCHP system for demand-supply matching.
The Nanoconfined Free Radical Polymerization: Reaction Kinetics and Thermodynamics
Zhao, Haoyu; Simon, Sindee
The reaction kinetics and thermodynamics of nanoconfined free radical polymerizations are investigated for methyl methacrylate (MMA) and ethyl methacrylate (EMA) monomers using differential scanning calorimetry. Controlled pore glass is used as the confinement medium with pore diameters as small as 7.5 nm; the influence of both hydrophobic (silanized such that trimethylsilyl groups cover the surface) and hydrophilic (native silanol) surfaces is investigated. Propagation rates increase when monomers are reacted in the hydrophilic pores presumably due to the specific interactions between the carbonyl and silanol groups; however, the more flexible EMA monomer shows weaker effects. On the other hand, initial rates of polymerization in hydrophobic pores are unchanged from the bulk. In both pores, the onset of autoacceleration occurs earlier due to the reduced diffusivity of confined chains, which may be compensated at high temperatures. In addition to changes in kinetics, the reaction thermodynamics can be affected under nanoconfinement. Specifically, the ceiling temperature (Tc) is shifted to lower temperatures in nanopores, with pore surface chemistry showing no significant effects; the equilibrium conversion is also reduced at high temperatures below Tc. These observations are attributed to a larger negative change in entropy on propagation for the confined system, with the MMA system again showing greater effects. Funding from ACS PRF is gratefully acknowledged.
International Nuclear Information System (INIS)
Ragavan, Anpalaki J.
2006-01-01
Linear free energy relationships for trivalent cations with crystalline M 2 O 3 and, M(OH) 3 phases of lanthanides and actinides were developed from known thermodynamic properties of the aqueous trivalent cations, modifying the Sverjensky and Molling equation. The linear free energy relationship for trivalent cations is as ΔG f,MvX 0 =a MvX ΔG n,M 3+ 0 +b MvX +β MvX r M 3+ , where the coefficients a MvX , b MvX , and β MvX characterize a particular structural family of MvX, r M 3+ is the ionic radius of M 3+ cation, ΔG f,MvX 0 is the standard Gibbs free energy of formation of MvX and ΔG n,M 3+ 0 is the standard non-solvation free energy of the cation. The coefficients for the oxide family are: a MvX =0.2705, b MvX =-1984.75 (kJ/mol), and β MvX =197.24 (kJ/molnm). The coefficients for the hydroxide family are: a MvX =0.1587, b MvX =-1474.09 (kJ/mol), and β MvX =791.70 (kJ/molnm).
Thermodynamic data for uranium fluorides
International Nuclear Information System (INIS)
Leitnaker, J.M.
1983-03-01
Self-consistent thermodynamic data have been tabulated for uranium fluorides between UF 4 and UF 6 , including UF 4 (solid and gas), U 4 F 17 (solid), U 2 F 9 (solid), UF 5 (solid and gas), U 2 F 10 (gas), and UF 6 (solid, liquid, and gas). Included are thermal function - the heat capacity, enthalpy, and free energy function, heats of formation, and vaporization behavior
International Nuclear Information System (INIS)
Taheri, M.H.; Mosaffa, A.H.; Farshi, L. Garousi
2017-01-01
In this work, a novel integrated biomass based multigeneration energy system is presented and investigated for power, cooling and hydrogen production. The proposed system consists of a combination of biomass integrated gasifier-gas turbine cycle, a Rankine cycle, a cascade organic Rankine cycle, an absorption refrigeration system and a PEM to produce hydrogen. This system uses cold energy of LNG as a thermal sink. Comprehensive thermodynamic and economic analyses as well as an optimization are performed. The effects of operating parameters on thermodynamic performance and total cost rate are investigated for overall system and subsystems. The results show that the fuel mass flow rate is the dominant factor affecting the variation of energy efficiency and total cost rate. An increase in fuel mass flow rate from 4 kg s"−"1 to 10 kg s"−"1 leads to a decrease of 8.5% and an increase of 122.8% overall energy efficiency and total cost rate, respectively. Also, the largest increase in exergy efficiency occurs when gas turbine inlet temperature increases. The results of optimization showed that the highest net power output, mass flow rate of natural gas delivered to city and the flue gas temperature discharged to the environment are obtained for the exergy efficiency optimal design. - Highlights: • A novel multigeneration system is investigated and optimized thermodynamically and economically. • This system is proposed for power, cooling and hydrogen production. • Proposed system uses LNG cold energy thermal sink that can generate power after vaporization. • The effects of operating parameters on energy and exergy efficiencies and total cost rate are investigated. • An optimization is applied based on the energy, exergy and economic viewpoints.
Nonequilibrium thermodynamics and energy efficiency in weight loss diets
Directory of Open Access Journals (Sweden)
Fine Eugene J
2007-07-01
Full Text Available Abstract Carbohydrate restriction as a strategy for control of obesity is based on two effects: a behavioral effect, spontaneous reduction in caloric intake and a metabolic effect, an apparent reduction in energy efficiency, greater weight loss per calorie consumed. Variable energy efficiency is established in many contexts (hormonal imbalance, weight regain and knock-out experiments in animal models, but in the area of the effect of macronutrient composition on weight loss, controversy remains. Resistance to the idea comes from a perception that variable weight loss on isocaloric diets would somehow violate the laws of thermodynamics, that is, only caloric intake is important ("a calorie is a calorie". Previous explanations of how the phenomenon occurs, based on equilibrium thermodynamics, emphasized the inefficiencies introduced by substrate cycling and requirements for increased gluconeogenesis. Living systems, however, are maintained far from equilibrium, and metabolism is controlled by the regulation of the rates of enzymatic reactions. The principles of nonequilibrium thermodynamics which emphasize kinetic fluxes as well as thermodynamic forces should therefore also be considered. Here we review the principles of nonequilibrium thermodynamics and provide an approach to the problem of maintenance and change in body mass by recasting the problem of TAG accumulation and breakdown in the adipocyte in the language of nonequilibrium thermodynamics. We describe adipocyte physiology in terms of cycling between an efficient storage mode and a dissipative mode. Experimentally, this is measured in the rate of fatty acid flux and fatty acid oxidation. Hormonal levels controlled by changes in dietary carbohydrate regulate the relative contributions of the efficient and dissipative parts of the cycle. While no experiment exists that measures all relevant variables, the model is supported by evidence in the literature that 1 dietary carbohydrate, via its
Thermodynamic DFT analysis of natural gas.
Neto, Abel F G; Huda, Muhammad N; Marques, Francisco C; Borges, Rosivaldo S; Neto, Antonio M J C
2017-08-01
Density functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6-311++G(d,p), B3LYP/6-31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6-311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstract Investigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory.
Free energy barriers to evaporation of water in hydrophobic confinement.
Sharma, Sumit; Debenedetti, Pablo G
2012-11-08
We use umbrella sampling Monte Carlo and forward and reverse forward flux sampling (FFS) simulation techniques to compute the free energy barriers to evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of the gap width, at 1 bar and 298 K. The evaporation mechanism for small (1 × 1 nm(2)) surfaces is found to be fundamentally different from that for large (3 × 3 nm(2)) surfaces. In the latter case, the evaporation proceeds via the formation of a gap-spanning tubular cavity. The 1 × 1 nm(2) surfaces, in contrast, are too small to accommodate a stable vapor cavity. Accordingly, the associated free energy barriers correspond to the formation of a critical-sized cavity for sufficiently large confining surfaces, and to complete emptying of the gap region for small confining surfaces. The free energy barriers to evaporation were found to be of O(20kT) for 14 Å gaps, and to increase by approximately ~5kT with every 1 Å increase in the gap width. The entropy contribution to the free energy of evaporation was found to be independent of the gap width.
Thermodynamic characteristics of a novel supercritical compressed air energy storage system
International Nuclear Information System (INIS)
Guo, Huan; Xu, Yujie; Chen, Haisheng; Zhou, Xuezhi
2016-01-01
Highlights: • A novel supercritical compressed air energy storage system is proposed. • The energy density of SC-CAES is approximately 18 times larger than that of conventional CAES. • The characteristic of thermodynamics and exergy destruction is comprehensively analysed. • The corresponding optimum relationship between charging and discharging pressure is illustrated. • A turning point of efficiency is indicated because of the heat transfer of crossing the critical point. - Abstract: A novel supercritical compressed air energy storage (SC-CAES) system is proposed by our team to solve the problems of conventional CAES. The system eliminates the dependence on fossil fuel and large gas-storage cavern, as well as possesses the advantages of high efficiency by employing the special properties of supercritical air, which is significant for the development of electrical energy storage. The thermodynamic model of the SC-CAES system is built, and the thermodynamic characters are revealed. Through the exergy analysis of the system, the processes of the larger exergy destruction include compression, expansion, cold storage/heat exchange and throttle. Furthermore, sensitivity analysis shows that there is an optimal energy releasing pressure to make the system achieve the highest efficiency when energy storage pressure is constant. The efficiency of SC-CAES is expected to reach about 67.41% when energy storage pressure and energy releasing pressure are 120 bar and 95.01 bar, respectively. At the same time, the energy density is 18 times larger than that of conventional CAES. Sensitivity analysis also shows the change laws of system efficiency varying with other basic system parameters. The study provides support for the design and engineering of SC-CAES.
Thermodynamic properties of open noncritical string in external electromagnetic field
International Nuclear Information System (INIS)
Lichtzier, I.M.; Odintsov, S.D.; Bytsenko, A.A.
1991-01-01
We investigate the thermodynamics of open noncritical string (charged and neutral) in an external constant magnetic field. The free energy and Hagedorn temperature are calculated. It is shown that Hagedorn temperature is the same as in the absence of constant magnetic field. We present also the expressions for the free energy and Hagedorn temperature of the neutral open noncritical string in an external constant electromagnetic field. In this case Hagedorn temperature depends on the external electric field. (author)
The use of a path independent integral in non-linear fracture mechanics
International Nuclear Information System (INIS)
Hellen, T.K.
1977-01-01
The use of the Rice J-intergral to assess conditions at a crack tip in an elastic or non-linear elastic body is well known. The integral equals the energy release rate and is path independent for any contour surrounding the crack tip provided no other singularities are encompassed. The path independence propertiy breaks down, however, in more general situations such as in three dimensional stress systems, plasticity unloading, thermal or creep states. Hence the required crack tip characteristics represented by the value of the integral round a contour whose radius about the tip tends to zero, is not reproduced along contours away from the tip. Consequently, an alternative integral, designated J*, has been proposed which equals J for elastic cases and in the other cases cited above remains path independent. A computer program for calculating the J and J* integrals has been developed as an extension to the BERSAFE finite element system. A full analysis of the cracked structure including plasticity, creep and thermal strains is conducted and the results are stored on a permanent data set. The integral values may then be calculated using the post-processor program for any number of contours and load or time steps, without recourse to further expensive computations. (Auth. )
Multivariable extrapolation of grand canonical free energy landscapes
Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.
2017-12-01
We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.
Introduction to integrable many-body systems II
International Nuclear Information System (INIS)
Samaj, L.
2010-01-01
This is the second part of a three-volume introductory course about integrable systems of interacting bodies. The models of interest are quantum spin chains with nearest-neighbor interactions between spin operators, in particular Heisenberg spin- 2 models. The Ising model in a transverse field, expressible as a quadratic fermion form by using the Jordan-Wigner transformation, is the subject of Sect. 12. The derivation of the coordinate Bethe ansatz for the XXZ Heisenberg chain and the determination of its absolute ground state in various regions of the anisotropy parameter are presented in Sect. 13. The magnetic properties of the ground state are explained in Sect. 14. Sect. 15 concerns excited states and the zero-temperature thermodynamics of the XXZ model. The thermodynamics of the XXZ Heisenberg chain is derived on the basis of the string hypothesis in Sect. 16; the thermodynamic Bethe ansatz equations are analyzed in high-temperature and low-temperature limits. An alternative derivation of the thermodynamics without using strings, leading to a non-linear integral equation determining the free energy, is the subject of Sect. 17. A nontrivial application of the Quantum Inverse Scattering method to the fully anisotropic XYZ Heisenberg chain is described in Section 18. Section 19 deals with integrable cases of isotropic spin chains with an arbitrary spin. (Author)
Theoretical investigation of the thermodynamic properties of metallic thin films
International Nuclear Information System (INIS)
Hung, Vu Van; Phuong, Duong Dai; Hoa, Nguyen Thi; Hieu, Ho Khac
2015-01-01
The thermodynamic properties of metallic thin films with face-centered cubic structure at ambient conditions were investigated using the statistical moment method including the anharmonicity effects of thermal lattice vibrations. The analytical expressions of Helmholtz free energy, lattice parameter, linear thermal expansion coefficient, specific heats at the constant volume and constant pressure were derived in terms of the power moments of the atomic displacements. Numerical calculations of thermodynamic properties have been performed for Au and Al thin films and compared with those of bulk metals. This research proposes that thermodynamic quantities of thin films approach the values of bulk when the thickness of thin film is about 70 nm. - Highlights: • Thermodynamic properties of thin films were investigated using the moment method. • Expressions of Helmholtz energy, expansion coefficient, specific heats were derived. • Calculations for Au, Al thin films were performed and compared with those of bulks
Theoretical investigation of the thermodynamic properties of metallic thin films
Energy Technology Data Exchange (ETDEWEB)
Hung, Vu Van [Vietnam Education Publishing House, 81 Tran Hung Dao, Hanoi (Viet Nam); Phuong, Duong Dai [Hanoi National University of Education, 136 Xuan Thuy, Hanoi (Viet Nam); Hoa, Nguyen Thi [University of Transport and Communications, Lang Thuong, Dong Da, Hanoi (Viet Nam); Hieu, Ho Khac, E-mail: hieuhk@duytan.edu.vn [Institute of Research and Development, Duy Tan University, K7/25 Quang Trung, Danang (Viet Nam)
2015-05-29
The thermodynamic properties of metallic thin films with face-centered cubic structure at ambient conditions were investigated using the statistical moment method including the anharmonicity effects of thermal lattice vibrations. The analytical expressions of Helmholtz free energy, lattice parameter, linear thermal expansion coefficient, specific heats at the constant volume and constant pressure were derived in terms of the power moments of the atomic displacements. Numerical calculations of thermodynamic properties have been performed for Au and Al thin films and compared with those of bulk metals. This research proposes that thermodynamic quantities of thin films approach the values of bulk when the thickness of thin film is about 70 nm. - Highlights: • Thermodynamic properties of thin films were investigated using the moment method. • Expressions of Helmholtz energy, expansion coefficient, specific heats were derived. • Calculations for Au, Al thin films were performed and compared with those of bulks.
Chong, Song-Ho; Ham, Sihyun
2015-04-21
Protein aggregation in aqueous cellular environments is linked to diverse human diseases. Protein aggregation proceeds through a multistep process initiated by conformational transitions, called protein misfolding, of monomer species toward aggregation-prone structures. Various forms of aggregate species are generated through the association of misfolded monomers including soluble oligomers and amyloid fibrils. Elucidating the molecular mechanisms and driving forces involved in the misfolding and subsequent association has been a central issue for understanding and preventing protein aggregation diseases such as Alzheimer's, Parkinson's, and type II diabetes. In this Account, we provide a thermodynamic perspective of the misfolding and aggregation of the amyloid-beta (Aβ) protein implicated in Alzheimer's disease through the application of fluctuating thermodynamics. This approach "dissects" the conventional thermodynamic characterization of the end states into the one of the fluctuating processes connecting them, and enables one to analyze variations in the thermodynamic functions that occur during the course of protein conformational changes. The central quantity in this approach is the solvent-averaged effective energy, f = Eu + Gsolv, comprising the protein potential energy (Eu) and the solvation free energy (Gsolv), whose time variation reflects the protein dynamics on the free energy landscape. Protein configurational entropy is quantified by the magnitude of fluctuations in f. We find that misfolding of the Aβ monomer when released from a membrane environment to an aqueous phase is driven by favorable changes in protein potential energy and configurational entropy, but it is also accompanied by an unfavorable increase in solvation free energy. The subsequent dimerization of the misfolded Aβ monomers occurs in two steps. The first step, where two widely separated monomers come into contact distance, is driven by water-mediated attraction, that is, by a
Thermodynamics aspects of noise-induced phase synchronization.
Pinto, Pedro D; Oliveira, Fernando A; Penna, André L A
2016-05-01
In this article, we present an approach for the thermodynamics of phase oscillators induced by an internal multiplicative noise. We analytically derive the free energy, entropy, internal energy, and specific heat. In this framework, the formulation of the first law of thermodynamics requires the definition of a synchronization field acting on the phase oscillators. By introducing the synchronization field, we have consistently obtained the susceptibility and analyzed its behavior. This allows us to characterize distinct phases in the system, which we have denoted as synchronized and parasynchronized phases, in analogy with magnetism. The system also shows a rich complex behavior, exhibiting ideal gas characteristics for low temperatures and susceptibility anomalies that are similar to those present in complex fluids such as water.
Thermodynamics aspects of noise-induced phase synchronization
Pinto, Pedro D.; Oliveira, Fernando A.; Penna, André L. A.
2016-05-01
In this article, we present an approach for the thermodynamics of phase oscillators induced by an internal multiplicative noise. We analytically derive the free energy, entropy, internal energy, and specific heat. In this framework, the formulation of the first law of thermodynamics requires the definition of a synchronization field acting on the phase oscillators. By introducing the synchronization field, we have consistently obtained the susceptibility and analyzed its behavior. This allows us to characterize distinct phases in the system, which we have denoted as synchronized and parasynchronized phases, in analogy with magnetism. The system also shows a rich complex behavior, exhibiting ideal gas characteristics for low temperatures and susceptibility anomalies that are similar to those present in complex fluids such as water.
Tomba, J. Pablo
2017-01-01
The use of free energy plots to understand the concept of thermodynamic equilibrium has been shown to be of great pedagogical value in materials science. Although chemical equilibrium is also amenable to this kind of analysis, it is not part of the agenda of materials science textbooks. Something similar is found in chemistry branches, where free…
Casimir-Foucault interaction: Free energy and entropy at low temperature
Intravaia, Francesco; Ellingsen, Simen Å.; Henkel, Carsten
2010-09-01
It was recently found that thermodynamic anomalies which arise in the Casimir effect between metals described by the Drude model can be attributed to the interaction of fluctuating Foucault (or eddy) currents [F. Intravaia and C. Henkel, Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.103.130405 103, 130405 (2009).] We focus on the transverse electric (TE) polarization, where the anomalies occur, and show explicitly that the two leading terms of the low-temperature correction to the Casimir free energy of interaction between two plates are identical to those pertaining to the Foucault current interaction alone, up to a correction which is very small for good metals. Moreover, a mode density along real frequencies is introduced, showing that the TE contribution to the Casimir free energy, as given by the Lifshitz theory, separates in a natural manner into contributions from eddy currents and propagating cavity modes, respectively. The latter have long been known to be of little importance to the low-temperature Casimir anomalies. This convincingly demonstrates that eddy current modes are responsible for the large temperature correction to the Casimir effect between Drude metals, predicted by the Lifshitz theory, but not observed in experiments.
Casimir-Foucault interaction: Free energy and entropy at low temperature
International Nuclear Information System (INIS)
Intravaia, Francesco; Ellingsen, Simen A.; Henkel, Carsten
2010-01-01
It was recently found that thermodynamic anomalies which arise in the Casimir effect between metals described by the Drude model can be attributed to the interaction of fluctuating Foucault (or eddy) currents [F. Intravaia and C. Henkel, Phys. Rev. Lett. 103, 130405 (2009).] We focus on the transverse electric (TE) polarization, where the anomalies occur, and show explicitly that the two leading terms of the low-temperature correction to the Casimir free energy of interaction between two plates are identical to those pertaining to the Foucault current interaction alone, up to a correction which is very small for good metals. Moreover, a mode density along real frequencies is introduced, showing that the TE contribution to the Casimir free energy, as given by the Lifshitz theory, separates in a natural manner into contributions from eddy currents and propagating cavity modes, respectively. The latter have long been known to be of little importance to the low-temperature Casimir anomalies. This convincingly demonstrates that eddy current modes are responsible for the large temperature correction to the Casimir effect between Drude metals, predicted by the Lifshitz theory, but not observed in experiments.
Energy Systems Integration Facility News | Energy Systems Integration
Facility | NREL Energy Systems Integration Facility News Energy Systems Integration Facility Energy Dataset A massive amount of wind data was recently made accessible online, greatly expanding the Energy's National Renewable Energy Laboratory (NREL) has completed technology validation testing for Go
Thermodynamic analysis of fatty acid esterification for fatty acid alkyl esters production
International Nuclear Information System (INIS)
Voll, Fernando A.P.; Silva, Camila da; Rossi, Carla C.R.S.; Guirardello, Reginaldo; Castilhos, Fernanda de; Oliveira, J. Vladimir; Cardozo-Filho, Lucio
2011-01-01
The development of renewable energy source alternatives has become a planet need because of the unavoidable fossil fuel scarcity and for that reason biodiesel production has attracted growing interest over the last decade. The reaction yield for obtaining fatty acid alkyl esters varies significantly according to the operating conditions such as temperature and the feed reactants ratio and thus investigation of the thermodynamics involved in such reactional systems may afford important knowledge on the effects of process variables on biodiesel production. The present work reports a thermodynamic analysis of fatty acid esterification reaction at low pressure. For this purpose, Gibbs free energy minimization was employed with UNIFAC and modified Wilson thermodynamic models through a nonlinear programming model implementation. The methodology employed is shown to reproduce the most relevant investigations involving experimental studies and thermodynamic analysis.
Analysis of retarding field energy analyzer transmission by simulation of ion trajectories
van de Ven, T. H. M.; de Meijere, C. A.; van der Horst, R. M.; van Kampen, M.; Banine, V. Y.; Beckers, J.
2018-04-01
Retarding field energy analyzers (RFEAs) are used routinely for the measurement of ion energy distribution functions. By contrast, their ability to measure ion flux densities has been considered unreliable because of lack of knowledge about the effective transmission of the RFEA grids. In this work, we simulate the ion trajectories through a three-gridded RFEA using the simulation software SIMION. Using idealized test cases, it is shown that at high ion energy (i.e., >100 eV) the transmission is equal to the optical transmission rather than the product of the individual grid transparencies. Below 20 eV, ion trajectories are strongly influenced by the electric fields in between the grids. In this region, grid alignment and ion focusing effects contribute to fluctuations in transmission with ion energy. Subsequently the model has been used to simulate the transmission and energy resolution of an experimental RFEA probe. Grid misalignments reduce the transmission fluctuations at low energy. The model predicts the minimum energy resolution, which has been confirmed experimentally by irradiating the probe with a beam of ions with a small energy bandwidth.
Thermodynamic Integration Methods, Infinite Swapping and the Calculation of Generalized Averages
Doll, J. D.; Dupuis, P.; Nyquist, P.
2016-01-01
In the present paper we examine the risk-sensitive and sampling issues associated with the problem of calculating generalized averages. By combining thermodynamic integration and Stationary Phase Monte Carlo techniques, we develop an approach for such problems and explore its utility for a prototypical class of applications.
Energy Systems Integration News | Energy Systems Integration Facility |
the Energy Systems Integration Facility as part of NREL's work with SolarCity and the Hawaiian Electric Companies. Photo by Amy Glickson, NREL Welcome to Energy Systems Integration News, NREL's monthly date on the latest energy systems integration (ESI) developments at NREL and worldwide. Have an item
Nonequilibrium Thermodynamics of Hydrate Growth on a Gas-Liquid Interface
Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben
2018-04-01
We develop a continuum-scale phase-field model to study gas-liquid-hydrate systems far from thermodynamic equilibrium. We design a Gibbs free energy functional for methane-water mixtures that recovers the isobaric temperature-composition phase diagram under thermodynamic equilibrium conditions. The proposed free energy is incorporated into a phase-field model to study the dynamics of hydrate formation on a gas-liquid interface. We elucidate the role of initial aqueous concentration in determining the direction of hydrate growth at the interface, in agreement with experimental observations. Our model also reveals two stages of hydrate growth at an interface—controlled by a crossover in how methane is supplied from the gas and liquid phases—which could explain the persistence of gas conduits in hydrate-bearing sediments and other nonequilibrium phenomena commonly observed in natural methane hydrate systems.
Coupling-parameter expansion in thermodynamic perturbation theory.
Ramana, A Sai Venkata; Menon, S V G
2013-02-01
An approach to the coupling-parameter expansion in the liquid state theory of simple fluids is presented by combining the ideas of thermodynamic perturbation theory and integral equation theories. This hybrid scheme avoids the problems of the latter in the two phase region. A method to compute the perturbation series to any arbitrary order is developed and applied to square well fluids. Apart from the Helmholtz free energy, the method also gives the radial distribution function and the direct correlation function of the perturbed system. The theory is applied for square well fluids of variable ranges and compared with simulation data. While the convergence of perturbation series and the overall performance of the theory is good, improvements are needed for potentials with shorter ranges. Possible directions for further developments in the coupling-parameter expansion are indicated.
Thermodynamics of Bioreactions.
Held, Christoph; Sadowski, Gabriele
2016-06-07
Thermodynamic principles have been applied to enzyme-catalyzed reactions since the beginning of the 1930s in an attempt to understand metabolic pathways. Currently, thermodynamics is also applied to the design and analysis of biotechnological processes. The key thermodynamic quantity is the Gibbs energy of reaction, which must be negative for a reaction to occur spontaneously. However, the application of thermodynamic feasibility studies sometimes yields positive Gibbs energies of reaction even for reactions that are known to occur spontaneously, such as glycolysis. This article reviews the application of thermodynamics in enzyme-catalyzed reactions. It summarizes the basic thermodynamic relationships used for describing the Gibbs energy of reaction and also refers to the nonuniform application of these relationships in the literature. The review summarizes state-of-the-art approaches that describe the influence of temperature, pH, electrolytes, solvents, and concentrations of reacting agents on the Gibbs energy of reaction and, therefore, on the feasibility and yield of biological reactions.
Is there a link between selectivity and binding thermodynamics profiles?
Tarcsay, Ákos; Keserű, György M
2015-01-01
Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding. Copyright © 2014 Elsevier Ltd. All rights reserved.
Energy Technology Data Exchange (ETDEWEB)
Weber, Jochem W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Laird, Daniel [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Costello, Ronan [Wave Venture; Roberts, Jesse [Sandia National Laboratories; Bull, Diana [Sandia National Laboratories; Babarit, Aurelien [Ecole Centrale de Nantes; Nielsen, Kim [Ramboll; Ferreira, Claudio Bittencourt [DNV-GL; Kennedy, Ben [Wave Venture
2017-09-14
This paper presents a comparative assessment of three fundamentally different wave energy converter technology development trajectories. The three technology development trajectories are expressed and visualised as a function of technology readiness levels and technology performance levels. The assessment shows that development trajectories that initially prioritize technology readiness over technology performance are likely to require twice the development time, consume a threefold of the development cost, and are prone to a risk of technical or commercial failure of one order of magnitude higher than those development trajectories that initially prioritize technology performance over technology readiness.
International Nuclear Information System (INIS)
Usman, Muhammad; Rashid, Muhammad Abid; Mansha, Asim; Siddiq, Mohammad
2013-01-01
Graphical abstract: - Highlights: • Free energy of adsorption is more negative than free energy of micellization. • Micellization becomes more spontaneous at high temperature. • There is strong interaction between PFM and SDS. - Abstract: This manuscript reports the physicochemical behavior of antibiotic amphiphilic drug pefloxacin mesylate (PFM) and its interaction with anionic surfactant, sodium dodecyl sulfate (SDS). The data of surface tension and electrical conductivity are helpful to detect the CMC as well as to calculate surface parameters, i.e. surface pressure, π, surface excess concentration, Γ, area per molecule of drug and standard Gibbs free energy of adsorption, ΔG ads and thermodynamic parameters like standard free energy of micellization, ΔG m , standard enthalpy of micellization, ΔH m and standard entropy of micellization, ΔS m . The interaction of this drug with anionic surfactant, sodium dodecyl sulfate (SDS) was studied by electrical conductivity and UV/visible spectroscopy. This enabled us to compute the values of partition coefficient (K x ), free energy of partition, ΔG p , binding constant, K b , free energy of binding, ΔG b , number of drug molecules per micelle, n, and thermodynamic parameters of drug–surfactant interaction
International Nuclear Information System (INIS)
Cakici, Duygu Melek; Erdogan, Anil; Colpan, Can Ozgur
2017-01-01
In this study, the thermodynamic performance of an integrated geothermal powered supercritical regenerative organic Rankine cycle (ORC) and parabolic trough solar collectors (PTSC) is assessed. A thermal model based on the principles of thermodynamics (mass, energy, and exergy balances) and heat transfer is first developed for the components of this integrated system. This model gives the performance assessment parameters of the system such as the electrical and exergetic efficiencies, total exergy destruction and loss, productivity lack, fuel depletion ratio, and improvement potential rate. To validate this model, the data of an existing geothermal power plant based on a supercritical ORC and literature data for the PTSC are used. After validation, parametric studies are conducted to assess the effect of some of the important design and operating parameters on the performance of the system. As a result of these studies, it is found that the integration of ORC and PTSC systems increases the net power output but decreases the electrical and exergetic efficiencies of the integrated system. It is also shown that R134a is the most suitable working fluid type for this system; and the PTSCs and air cooled condenser are the main sources of the exergy destructions. - Highlights: • A geothermal power plant integrated with PTSC is investigated. • Different approaches for defining the exergetic efficiency are used. • The PTSCs and ACC are the main sources of the exergy destructions. • R134a gives the highest performance for any number of collectors studied.
Thermodynamic forces in coarse-grained simulations
Noid, William
Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.
International Nuclear Information System (INIS)
Evans, R.; Kumaravadivel, R.
1976-01-01
A simple scheme for determining the ion density profile and the surface tension of a liquid metal is described. Assuming that the interaction between metallic pseudo-ions is of the form introduced by Evans, an approximate expression for the excess free energy of the system is derived using the thermodynamic perturbation theory of Weeks, Chandler and Anderson. This excess free energy is then minimized with respect to a parameter which specifies the ion density profile, and the surface tension is given directly. From a consideration of the dependence of the interionic forces on the electron density it is predicted that the ions should take up a very steep density profile at the liquid metal surface. This behaviour is contrasted with that to be expected for rare-gas fluids in which the interatomic forces are density-independent. The values of the surface tension calculated for liquid Na, K and Al from a simplified version of the theory are in reasonable agreement with experiment. (author)
Lin, Jiefeng; Babbitt, Callie W; Trabold, Thomas A
2013-01-01
A methodology that integrates life cycle assessment (LCA) with thermodynamic analysis is developed and applied to evaluate the environmental impacts of producing biofuels from waste biomass, including biodiesel from waste cooking oil, ethanol from corn stover, and compressed natural gas from municipal solid wastes. Solid oxide fuel cell-based auxiliary power units using bio-fuel as the hydrogen precursor enable generation of auxiliary electricity for idling heavy-duty trucks. Thermodynamic analysis is applied to evaluate the fuel conversion efficiency and determine the amount of fuel feedstock needed to generate a unit of electrical power. These inputs feed into an LCA that compares energy consumption and greenhouse gas emissions of different fuel pathways. Results show that compressed natural gas from municipal solid wastes is an optimal bio-fuel option for SOFC-APU applications in New York State. However, this methodology can be regionalized within the U.S. or internationally to account for different fuel feedstock options. Copyright © 2012 Elsevier Ltd. All rights reserved.
The energy balance of a plasma in partial local thermodynamic equilibrium
Kroesen, G.M.W.; Schram, D.C.; Timmermans, C.J.; de Haas, J.C.M.
1990-01-01
The energy balance for electrons and heavy particles constituting a plasma in partial local thermodynamic equilibrium is derived. The formulation of the energy balance used allows for evaluation of the source terms without knowledge of the particle and radiation transport situation, since most of
Free breathing whole-heart 3D CINE MRI with self-gated Cartesian trajectory.
Usman, M; Ruijsink, B; Nazir, M S; Cruz, G; Prieto, C
2017-05-01
To present a method that uses a novel free-running self-gated acquisition to achieve isotropic resolution in whole heart 3D Cartesian cardiac CINE MRI. 3D cardiac CINE MRI using navigator gating results in long acquisition times. Recently, several frameworks based on self-gated non-Cartesian trajectories have been proposed to accelerate this acquisition. However, non-Cartesian reconstructions are computationally expensive due to gridding, particularly in 3D. In this work, we propose a novel highly efficient self-gated Cartesian approach for 3D cardiac CINE MRI. Acquisition is performed using CArtesian trajectory with Spiral PRofile ordering and Tiny golden angle step for eddy current reduction (so called here CASPR-Tiger). Data is acquired continuously under free breathing (retrospective ECG gating, no preparation pulses interruption) for 4-5min and 4D whole-heart volumes (3D+cardiac phases) with isotropic spatial resolution are reconstructed from all available data using a soft gating technique combined with temporal total variation (TV) constrained iterative SENSE reconstruction. For data acquired on eight healthy subjects and three patients, the reconstructed images using the proposed method had good contrast and spatio-temporal variations, correctly recovering diastolic and systolic cardiac phases. Non-significant differences (P>0.05) were observed in cardiac functional measurements obtained with proposed 3D approach and gold standard 2D multi-slice breath-hold acquisition. The proposed approach enables isotropic 3D whole heart Cartesian cardiac CINE MRI in 4 to 5min free breathing acquisition. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.
Trajectory phases of a quantum dot model
International Nuclear Information System (INIS)
Genway, Sam; Hickey, James M; Garrahan, Juan P; Armour, Andrew D
2014-01-01
We present a thermodynamic formalism to study the trajectories of charge transport through a quantum dot coupled to two leads in the resonant-level model. We show that a close analogue of equilibrium phase transitions exists for the statistics of transferred charge; by tuning an appropriate ‘counting field’, crossovers to different trajectory phases are possible. Our description reveals a mapping between the statistics of a given device and current measurements over a range of devices with different dot–lead coupling strengths. Furthermore insight into features of the trajectory phases are found by studying the occupation of the dot conditioned on the transported charge between the leads; this is calculated from first principles using a trajectory biased two-point projective measurement scheme. (paper)
Merrill, Raymond Gabriel; Qu, Min; Vavrina, Matthew A.; Englander, Jacob A.; Jones, Christopher A.
2014-01-01
This paper presents mission performance analysis methods and results for the Asteroid Robotic Redirect Mission (ARRM) option to capture a free standing boulder on the surface of a 100 m or larger NEA. It details the optimization and design of heliocentric low-thrust trajectories to asteroid targets for the ARRM solar electric propulsion spacecraft. Extensive searches were conducted to determine asteroid targets with large pick-up mass potential and potential observation opportunities. Interplanetary trajectory approximations were developed in method based tools for Itokawa, Bennu, 1999 JU3, and 2008 EV5 and were validated by end-to-end integrated trajectories.
On nonlinear statistical thermodynamics of boundary plasma with postactions
International Nuclear Information System (INIS)
Temko, S.W.; Temko, K.W.; Kuz'min, S.K.
1992-01-01
The authors use the statistical thermodynamics of small systems proposed before their publications for boundary weakly ionized plasma with postaction. Boundary properties of the plasma is taken into account by two ways: (1) suppose that only small number of very quick particles are able to leave the cloud having done entrance into outer medium work; (2) take into account the interaction between particles and inner surface of the cloud. Interactions in the boundary plasma are described by corresponding potential functions. The potential functions are mathematical models of real interactions in boundary plasma. Choosing of potential functions, their numerical parameters, geometrical form and dimensions of the cloud is made by using the methods of optimal experiment planning, maximum likelihood and computer experiment. Free energy of the cloud is a likelihood function. State of boundary plasma with admixtures is described by vector-density of particles distribution. Term ''distribution'' is used here in Sobolev-Schwartc sense. The authors obtain the vector-density of particles distribution in cloud which gives the condition minimum of free energy for every time moment under quasistatistical equilibrium. The system of conditions for free energy conditional minimizing for every time moment includes integral equilibrium equations, ''non-hard normalization'' and additional conditions taken as a result of analyzing physical and physical-chemical nature of boundary plasma. To obtain conditional minimum of free energy it is necessary to solve the system of conditions. First of all they solve equilibrium problem by the authors method. They obtain vector-density of particles distribution in the cloud. Then using method of random walk with postaction between sets of random walk process they build distribution function of random vector-density
Evans, Cherice; Findley, Gary L.
The quasi-free electron energy V0 (ρ) is important in understanding electron transport through a fluid, as well as for modeling electron attachment reactions in fluids. Our group has developed an isotropic local Wigner-Seitz model that allows one to successfully calculate the quasi-free electron energy for a variety of atomic and molecular fluids from low density to the density of the triple point liquid with only a single adjustable parameter. This model, when coupled with the quasi-free electron energy data and the thermodynamic data for the fluids, also can yield optimized intermolecular potential parameters and the zero kinetic energy electron scattering length. In this poster, we give a review of the isotropic local Wigner-Seitz model in comparison to previous theoretical models for the quasi-free electron energy. All measurements were performed at the University of Wisconsin Synchrotron Radiation Center. This work was supported by a Grants from the National Science Foundation (NSF CHE-0956719), the Petroleum Research Fund (45728-B6 and 5-24880), the Louisiana Board of Regents Support Fund (LEQSF(2006-09)-RD-A33), and the Professional Staff Congress City University of New York.
Towards a thermodynamics of active matter.
Takatori, S C; Brady, J F
2015-03-01
Self-propulsion allows living systems to display self-organization and unusual phase behavior. Unlike passive systems in thermal equilibrium, active matter systems are not constrained by conventional thermodynamic laws. A question arises, however, as to what extent, if any, can concepts from classical thermodynamics be applied to nonequilibrium systems like active matter. Here we use the new swim pressure perspective to develop a simple theory for predicting phase separation in active matter. Using purely mechanical arguments we generate a phase diagram with a spinodal and critical point, and define a nonequilibrium chemical potential to interpret the "binodal." We provide a generalization of thermodynamic concepts like the free energy and temperature for nonequilibrium active systems. Our theory agrees with existing simulation data both qualitatively and quantitatively and may provide a framework for understanding and predicting the behavior of nonequilibrium active systems.
International Nuclear Information System (INIS)
Henke, Paul S.; Mak, Chi H.
2014-01-01
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg 2+ that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure
Energy Technology Data Exchange (ETDEWEB)
Henke, Paul S. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Mak, Chi H., E-mail: cmak@usc.edu [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States); Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089 (United States)
2014-08-14
The thermodynamic stability of a folded RNA is intricately tied to the counterions and the free energy of this interaction must be accounted for in any realistic RNA simulations. Extending a tight-binding model published previously, in this paper we investigate the fundamental structure of charges arising from the interaction between small functional RNA molecules and divalent ions such as Mg{sup 2+} that are especially conducive to stabilizing folded conformations. The characteristic nature of these charges is utilized to construct a discretely connected energy landscape that is then traversed via a novel application of a deterministic graph search technique. This search method can be incorporated into larger simulations of small RNA molecules and provides a fast and accurate way to calculate the free energy arising from the interactions between an RNA and divalent counterions. The utility of this algorithm is demonstrated within a fully atomistic Monte Carlo simulation of the P4-P6 domain of the Tetrahymena group I intron, in which it is shown that the counterion-mediated free energy conclusively directs folding into a compact structure.
Relativistic thermodynamics of Fluids. l
International Nuclear Information System (INIS)
Havas, P.; Swenson, R.J.
1979-01-01
In 1953, Stueckelberg and Wanders derived the basic laws of relativistic linear nonequilibrium thermodynamics for chemically reacting fluids from the relativistic local conservation laws for energy-momentum and the local laws of production of substances and of nonnegative entropy production by the requirement that the corresponding currents (assumed to depend linearly on the derivatives of the state variables) should not be independent. Generalizing their method, we determine the most general allowed form of the energy-momentum tensor T/sup alphabeta/ and of the corresponding rate of entropy production under the same restriction on the currents. The problem of expressing this rate in terms of thermodynamic forces and fluxes is discussed in detail; it is shown that the number of independent forces is not uniquely determined by the theory, and seven possibilities are explored. A number of possible new cross effects are found, all of which persist in the Newtonian (low-velocity) limit. The treatment of chemical reactions is incorporated into the formalism in a consistent manner, resulting in a derivation of the law for rate of production, and in relating this law to transport processes differently than suggested previously. The Newtonian limit is discussed in detail to establish the physical interpretation of the various terms of T/sup alphabeta/. In this limit, the interpretation hinges on that of the velocity field characterizing the fluid. If it is identified with the average matter velocity following from a consideration of the number densities, the usual local conservation laws of Newtonian nonequilibrium thermodynamics are obtained, including that of mass. However, a slightly different identification allows conversion of mass into energy even in this limit, and thus a macroscopic treatment of nuclear or elementary particle reactions. The relation of our results to previous work is discussed in some detail
van Gunsteren, WF; Daura, [No Value; Mark, AE
2002-01-01
Many quantities that are standardly used to characterize a chemical system are related to free-energy differences between particular states of the system. By statistical mechanics, free-energy differences may be expressed in terms of averages over ensembles of atomic configurations for the molecular
Paula Leite, Rodolfo; Freitas, Rodrigo; Azevedo, Rodolfo; de Koning, Maurice
2016-11-01
The Uhlenbeck-Ford (UF) model was originally proposed for the theoretical study of imperfect gases, given that all its virial coefficients can be evaluated exactly, in principle. Here, in addition to computing the previously unknown coefficients B11 through B13, we assess its applicability as a reference system in fluid-phase free-energy calculations using molecular simulation techniques. Our results demonstrate that, although the UF model itself is too soft, appropriately scaled Uhlenbeck-Ford (sUF) models provide robust reference systems that allow accurate fluid-phase free-energy calculations without the need for an intermediate reference model. Indeed, in addition to the accuracy with which their free energies are known and their convenient scaling properties, the fluid is the only thermodynamically stable phase for a wide range of sUF models. This set of favorable properties may potentially put the sUF fluid-phase reference systems on par with the standard role that harmonic and Einstein solids play as reference systems for solid-phase free-energy calculations.
Hudson, Phillip S; Woodcock, H Lee; Boresch, Stefan
2015-12-03
Carrying out free energy simulations (FES) using quantum mechanical (QM) Hamiltonians remains an attractive, albeit elusive goal. Renewed efforts in this area have focused on using "indirect" thermodynamic cycles to connect "low level" simulation results to "high level" free energies. The main obstacle to computing converged free energy results between molecular mechanical (MM) and QM (ΔA(MM→QM)), as recently demonstrated by us and others, is differences in the so-called "stiff" degrees of freedom (e.g., bond stretching) between the respective energy surfaces. Herein, we demonstrate that this problem can be efficiently circumvented using nonequilibrium work (NEW) techniques, i.e., Jarzynski's and Crooks' equations. Initial applications of computing ΔA(NEW)(MM→QM), for blocked amino acids alanine and serine as well as to generate butane's potentials of mean force via the indirect QM/MM FES method, showed marked improvement over traditional FES approaches.
Relation of the second law of thermodynamics to the power conversion of energy fluctuations
International Nuclear Information System (INIS)
Yater, J.C.
1979-01-01
The relation of the second law of thermodynamics to the power conversion of fluctuation energy is analyzed using the master equation of the model for the conversion circuit. The performance equation for independent particles shows that the power-conversion performance is given by the second law both for classical and quantum-effect diodes. The relation of the second law to power-conversion models based on the theoretical and experimental results for diode performance for interacting particles exhibiting many-body, multiparticle, or other anomalous and excess-current effects is examined. The performance equations are derived from the master equation for models for interacting particles to determine the conditions required by the second law for power conversion. These conditions are given in terms of the distribution throughout the power-conversion circuit for all the parameters that determine the particle and multiparticle barrier-crossing probability such as the effective mass and spectral density functions. Circuits for spectroscopic measurements for power-conversion circuits with interacting particles are noted. Using selected experimental values for the diode nonlinearity factors in these circuits, open circuit voltages are computed that are not predicted by the second law of thermodynamics
On the integration scheme along a trajectory for the characteristics method
International Nuclear Information System (INIS)
Le Tellier, Romain; Hebert, Alain
2006-01-01
The issue of the integration scheme along a trajectory which appears for all tracking-based transport methods is discussed from the point of view of the method of characteristics. The analogy with the discrete ordinates method in slab geometry is highlighted along with the practical limitation in transposing high-order S N schemes to a trajectory-based method. We derived an example of such a transposition starting from the linear characteristic scheme. This new scheme is compared with the standard flat-source approximation of the step characteristic scheme and with the diamond differencing scheme. The numerical study covers a 1D analytical case, 2D one-group critical and fixed-source benchmarks and finally a realistic multigroup calculation on a BWR-MOX assembly
Thermodynamic modeling of the U–Zr system – A revisit
International Nuclear Information System (INIS)
Xiong, Wei; Xie, Wei; Shen, Chao; Morgan, Dane
2013-01-01
Graphical abstract: Display Omitted -- Abstract: A new thermodynamic description of the U–Zr system is developed using the CALPHAD (CALculation of PHAse Diagrams) method with the aid of ab initio calculations. Thermodynamic properties, such as heat capacity, activities, and enthalpy of mixing, are well predicted using the improved thermodynamic description in this work. The model-predicted enthalpies of formation for the bcc and δ phases are in good agreement with the results from DFT + U ab initio calculations. The calculations in this work show better agreements with experimental data comparing with the previous assessments. Using the integrated method of ab initio and CALPHAD modeling, an unexpected relation between the enthalpy of formation of the δ phase and energy of Zr with hexagonal structure is revealed and the model improved by fitting these energies together. The present work has demonstrated that ab initio calculations can help support a successful thermodynamic assessment of actinide systems, for which the thermodynamic properties are often difficult to measure
Zhu, Na
This thesis presents an overview of the previous research work on dynamic characteristics and energy performance of buildings due to the integration of PCMs. The research work on dynamic characteristics and energy performance of buildings using PCMs both with and without air-conditioning is reviewed. Since the particular interest in using PCMs for free cooling and peak load shifting, specific research efforts on both subjects are reviewed separately. A simplified physical dynamic model of building structures integrated with SSPCM (shaped-stabilized phase change material) is developed and validated in this study. The simplified physical model represents the wall by 3 resistances and 2 capacitances and the PCM layer by 4 resistances and 2 capacitances respectively while the key issue is the parameter identification of the model. This thesis also presents the studies on the thermodynamic characteristics of buildings enhanced by PCM and on the investigation of the impacts of PCM on the building cooling load and peak cooling demand at different climates and seasons as well as the optimal operation and control strategies to reduce the energy consumption and energy cost by reducing the air-conditioning energy consumption and peak load. An office building floor with typical variable air volume (VAV) air-conditioning system is used and simulated as the reference building in the comparison study. The envelopes of the studied building are further enhanced by integrating the PCM layers. The building system is tested in two selected cities of typical climates in China including Hong Kong and Beijing. The cold charge and discharge processes, the operation and control strategies of night ventilation and the air temperature set-point reset strategy for minimizing the energy consumption and electricity cost are studied. This thesis presents the simulation test platform, the test results on the cold storage and discharge processes, the air-conditioning energy consumption and demand
Thermodynamic free-energy minimization for unsupervised fusion of dual-color infrared breast images
Szu, Harold; Miao, Lidan; Qi, Hairong
2006-04-01
function [A] may vary from the point tumor to its neighborhood, we could not rely on neighborhood statistics as did in a popular unsupervised independent component analysis (ICA) mathematical statistical method, we instead impose the physics equilibrium condition of the minimum of Helmholtz free-energy, H = E - T °S. In case of the point breast cancer, we can assume the constant ground state energy E ° to be normalized by those benign neighborhood tissue, and then the excited state can be computed by means of Taylor series expansion in terms of the pixel I/O data. We can augment the X-ray mammogram technique with passive IR imaging to reduce the unwanted X-rays during the chemotherapy recovery. When the sequence is animated into a movie, and the recovery dynamics is played backward in time, the movie simulates the cameras' potential for early detection without suffering the PD=0.1 search uncertainty. In summary, we applied two satellite-grade dual-color IR imaging cameras and advanced military (automatic target recognition) ATR spectrum fusion algorithm at the middle wavelength IR (3 - 5μm) and long wavelength IR (8 - 12μm), which are capable to screen malignant tumors proved by the time-reverse fashion of the animated movie experiments. On the contrary, the traditional thermal breast scanning/imaging, known as thermograms over decades, was IR spectrum-blind, and limited to a single night-vision camera and the necessary waiting for the cool down period for taking a second look for change detection suffers too many environmental and personnel variabilities.
Hybridization thermodynamics of DNA bound to gold nanoparticles
International Nuclear Information System (INIS)
Lang, Brian
2010-01-01
Isothermal Titration Calorimetry (ITC) was used to study the thermodynamics of hybridization on DNA-functionalized colloidal gold nanoparticles. When compared to the thermodynamics of hybridization of DNA that is free in solution, the differences in the values of the Gibbs free energy of reaction, Δ r G o , the enthalpy, Δ r H o , and entropy, Δ r S o , were small. The change in Δ r G o between the free and bound states was always positive but with statistical significance outside the 95% confidence interval, implying the free DNA is slightly more stable than when in the bound state. Additionally, ITC was also able to reveal information about the binding stoichiometry of the hybridization reactions on the DNA-functionalized gold nanoparticles, and indicates that there is a significant fraction of the DNA on gold nanoparticle surface that is unavailable for DNA hybridization. Furthermore, the fraction of available DNA is dependent on the spacer group on the DNA that is used to span the gold surface from that to the probe DNA.
Thermodynamics properties of lanthanide series near melting point-A pseudopotential approach
Suthar, P. H.; Gajjar, P. N.
2018-04-01
The present paper deals with computational study of thermodynamics properties for fifteen elements of lanthanide series. The Helmholtz free energy (F), Internal energy (E) and Entropy (S)have been computed using variational method based on the Gibbs-Bogoliubov (GB) along with Percus-Yevick hard sphere reference system and Gajjar's model potential. The local field correction function proposed by Taylor is applied to introduce the exchange and correlation effects in the study of thermodynamics of these metals. The present results in comparison with available theoretical and experimental are found to be in good agreement and confirm the ability of the model potential.
A new model for thermodynamic analysis on wetting behavior of superhydrophobic surfaces
International Nuclear Information System (INIS)
Zhang Hongyun; Li Wen; Fang Guoping
2012-01-01
Superhydrophobic surfaces have shown inspiring applications in microfluidics, and self-cleaning coatings owing to water-repellent and low-friction properties. However, thermodynamic mechanism responsible for contact angle hysteresis (CAH) and free energy barrier (FEB) have not been understood completely yet. In this work, we propose an intuitional 3-dimension (3D) droplet model along with a reasonable thermodynamic approach to gain a thorough insight into the physical nature of CAH. Based on this model, the relationships between radius of three-phase contact line, change in surface free energy (CFE), average or local FEB and contact angle (CA) are established. Moreover, a thorough theoretical consideration is given to explain the experimental phenomena related to the superhydrophobic behavior. The present study can therefore provide some guidances for the practical fabrications of the superhydrophobic surfaces.
Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.
Liang, Huiyun; Bourdon, Allen K; Chen, Liao Y; Phelix, Clyde F; Perry, George
2018-06-11
Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K M and high V MAX , specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free energy for β-d-glucose to be -4.6 kcal/mol in agreement with the experimental value of -4.4 kcal/mol ( K M = 1.4 mM). We also compute the hydration energy of β-d-glucose, -18.0 kcal/mol vs the experimental data, -17.8 kcal/mol. In this, we establish a dynamics-based connection from GLUT3's crystal structure to its cellular thermodynamics with quantitative accuracy. We predict equal Arrhenius barriers for glucose uptake and efflux through GLUT3 to be tested in future experiments.
Work extraction and thermodynamics for individual quantum systems
Skrzypczyk, Paul; Short, Anthony J.; Popescu, Sandu
2014-06-01
Thermodynamics is traditionally concerned with systems comprised of a large number of particles. Here we present a framework for extending thermodynamics to individual quantum systems, including explicitly a thermal bath and work-storage device (essentially a ‘weight’ that can be raised or lowered). We prove that the second law of thermodynamics holds in our framework, and gives a simple protocol to extract the optimal amount of work from the system, equal to its change in free energy. Our results apply to any quantum system in an arbitrary initial state, in particular including non-equilibrium situations. The optimal protocol is essentially reversible, similar to classical Carnot cycles, and indeed, we show that it can be used to construct a quantum Carnot engine.
Directory of Open Access Journals (Sweden)
Ashley R Long
Full Text Available The ADP/ATP Carrier (AAC is the most abundant transporter of the mitochondrial inner membrane. The central role that this transporter plays in cellular energy production highlights the importance of understanding its structure, function, and the basis of its pathologies. As a means of preparing proteoliposomes for the study of membrane proteins, several groups have explored the use of cell-free translation systems to facilitate membrane protein integration directly into preformed unilamellar vesicles without the use of surfactants. Using AAC as a model, we report for the first time the detergent-free reconstitution of a mitochondrial inner membrane protein into liposomes using a wheat germ-based in vitro translation system. Using a host of independent approaches, we demonstrate the efficient integration of AAC into vesicles with an inner membrane-mimetic lipid composition and, more importantly, that the integrated AAC is functionally active in transport. By adding liposomes at different stages of the translation reaction, we show that this direct integration is obligatorily cotranslational, and by synthesizing stable ribosome-bound nascent chain intermediates, we show that the nascent AAC polypeptide interacts with lipid vesicles while ribosome-bound. Finally, we show that the presence of the phospholipid cardiolipin in the liposomes specifically enhances AAC translation rate as well as the efficiency of vesicle association and integration. In light of these results, the possible mechanisms of liposome-assisted membrane protein integration during cell-free translation are discussed with respect to the mode of integration and the role of specific lipids.
Gravitational entropy and thermodynamics away from the horizon
Energy Technology Data Exchange (ETDEWEB)
Brustein, Ram, E-mail: ramyb@bgu.ac.il [Department of Physics, Ben-Gurion University, Beer-Sheva 84105 (Israel); CAS, Ludwig-Maximilians-Universitaet Muenchen, 80333 Muenchen (Germany); Medved, A.J.M., E-mail: j.medved@ru.ac.za [Department of Physics and Electronics, Rhodes University, Grahamstown 6140 (South Africa)
2012-08-29
We define, by an integral of geometric quantities over a spherical shell of arbitrary radius, an invariant gravitational entropy. This definition relies on defining a gravitational energy and pressure, and it reduces at the horizon of both black branes and black holes to Wald's Noether charge entropy. We support the thermodynamic interpretation of the proposed entropy by showing that, for some cases, the field theory duals of the entropy, energy and pressure are the same as the corresponding quantities in the field theory. In this context, the Einstein equations are equivalent to the field theory thermodynamic relation TdS=dE+PdV supplemented by an equation of state.
Incremental binding free energies of aluminum (III) vs. magnesium (II) complexes
International Nuclear Information System (INIS)
Mercero, Jose M.; Mujika, Jon I.; Matxain, Jon M.; Lopez, Xabier; Ugalde, Jesus M.
2003-01-01
A sequential ligand addition to the aluminum (III) cation has been studied using the B3LYP functional and a combined all-electron/pseudopotentials basis set. The aluminum complexes are compared with analogous magnesium (II) complexes. Different thermodynamical data, such as incremental binding energies, enthalpies, entropies and free energies, are presented for these addition reactions. While the magnesium (II) cation can only accommodate three negatively charged ligands, aluminum (III) accommodates four even after including bulk solvent effects. The main differences between both cations complexing with the neutral ligands, is that aluminum (III) is not able to form complexes with methanol until the number of methanol ligands is equal to 3. Magnesium (II) prefers to bind methanol and formamide when the number of ligands is small, while aluminum prefers formamide. For the largest complexes both cations prefer to bind water
Low temperature heat capacities and thermodynamic functions described by Debye-Einstein integrals.
Gamsjäger, Ernst; Wiessner, Manfred
2018-01-01
Thermodynamic data of various crystalline solids are assessed from low temperature heat capacity measurements, i.e., from almost absolute zero to 300 K by means of semi-empirical models. Previous studies frequently present fit functions with a large amount of coefficients resulting in almost perfect agreement with experimental data. It is, however, pointed out in this work that special care is required to avoid overfitting. Apart from anomalies like phase transformations, it is likely that data from calorimetric measurements can be fitted by a relatively simple Debye-Einstein integral with sufficient precision. Thereby, reliable values for the heat capacities, standard enthalpies, and standard entropies at T = 298.15 K are obtained. Standard thermodynamic functions of various compounds strongly differing in the number of atoms in the formula unit can be derived from this fitting procedure and are compared to the results of previous fitting procedures. The residuals are of course larger when the Debye-Einstein integral is applied instead of using a high number of fit coefficients or connected splines, but the semi-empiric fit coefficients keep their meaning with respect to physics. It is suggested to use the Debye-Einstein integral fit as a standard method to describe heat capacities in the range between 0 and 300 K so that the derived thermodynamic functions are obtained on the same theory-related semi-empiric basis. Additional fitting is recommended when a precise description for data at ultra-low temperatures (0-20 K) is requested.
Yang, Sam
The dissertation presents the mathematical formulation, experimental validation, and application of a volume el