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Daniel Borgis - One of the best experts on this subject based on the ideXlab platform.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
arXiv: Soft Condensed Matter, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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 ap- proximation for the free-energy functional, the so-called homogeneous reference uid approximation, we show that the hydration free-energies computed for a dataset of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by two to three orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canoni- cal 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 justifcation to empirical partial molar volume corrections that have been proposed recently.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
Volodymyr P Sergiievskyi - One of the best experts on this subject based on the ideXlab platform.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
arXiv: Soft Condensed Matter, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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 ap- proximation for the free-energy functional, the so-called homogeneous reference uid approximation, we show that the hydration free-energies computed for a dataset of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by two to three orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canoni- cal 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 justifcation to empirical partial molar volume corrections that have been proposed recently.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
Michael R Von Spakovsky - One of the best experts on this subject based on the ideXlab platform.
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low temperature atomistic spin relaxation and non equilibrium intensive properties using steepest entropy ascent quantum inspired Thermodynamics modeling
Journal of Physics: Condensed Matter, 2019Co-Authors: Ryo Yamada, Michael R Von Spakovsky, W T ReynoldsAbstract:The magnetization of body-centered cubic iron at low temperatures is calculated with the steepest-entropy-ascent quantum Thermodynamics (SEAQT) framework. This framework assumes that a Thermodynamic property in an isolated system traces the path through state space with the greatest entropy production. Magnetization is calculated from the expected value of a Thermodynamic Ensemble of quantized spin waves based on the Heisenberg spin model applied to an Ensemble of coupled harmonic oscillators. A realistic energy landscape is obtained from a magnon dispersion relation calculated using spin-density-functional-theory. The equilibrium magnetization as well as the evolution of magnetization from a non-equilibrium state to equilibrium are calculated from the path of steepest entropy ascent determined from the SEAQT equation of motion in state space. The framework makes it possible to model the temperature and time-dependence of magnetization without a detailed description of magnetic damping. The approach is also used to define intensive properties (temperature and magnetic field strength) that are fundamentally, i.e. canonically or grand canonically, valid for any non-equilibrium state. Given the assumed magnon dispersion relation, the SEAQT framework is used to calculate the equilibrium magnetization at different temperatures and external magnetic fields and the results are shown to closely agree with experiment for temperatures less than 500 K. The time-dependent evolution of magnetization from different initial states and interactions with a reservoir is also predicted.
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CH4 Adsorption Probability on GaN(0001) and (000−1) during Metalorganic Vapor Phase Epitaxy and Its Relationship to Carbon Contamination in the Films
MDPI AG, 2019Co-Authors: Akira Kusaba, Michael R Von Spakovsky, Pawel Kempisty, Yoshihiro KangawaAbstract:Suppression of carbon contamination in GaN films grown using metalorganic vapor phase epitaxy (MOVPE) is a crucial issue in its application to high power and high frequency electronic devices. To know how to reduce the C concentration in the films, a sequential analysis based on first principles calculations is performed. Thus, surface reconstruction and the adsorption of the CH4 produced by the decomposition of the Ga source, Ga(CH3)3, and its incorporation into the GaN sub-surface layers are investigated. In this sequential analysis, the dataset of the adsorption probability of CH4 on reconstructed surfaces is indispensable, as is the energy of the C impurity in the GaN sub-surface layers. The C adsorption probability is obtained based on steepest-entropy-ascent quantum Thermodynamics (SEAQT). SEAQT is a Thermodynamic Ensemble-based, non-phenomenological framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium. This framework is suitable especially when one studies the adsorption behavior of an impurity molecule because the conventional approach, the chemical potential control method, cannot be applied to a quantitative analysis for such a system. The proposed sequential model successfully explains the influence of the growth orientation, GaN(0001) and (000−1), on the incorporation of C into the film. This model can contribute to the suppression of the C contamination in GaN MOVPE
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steepest entropy ascent model of mesoscopic quantum systems far from equilibrium along with generalized Thermodynamic definitions of measurement and reservoir
Physical Review E, 2018Co-Authors: Michael R Von SpakovskyAbstract:This paper presents a nonequilibrium, first-principles, Thermodynamic-Ensemble based model for the relaxation process of interacting non-equilibrium systems. This model is formulated using steepest-entropy-ascent quantum Thermodynamics (SEAQT) and its equation of motion for a grand canonical Ensemble and is applied to a many particle system of classical or indistinguishable particles. Two kinds of interactions are discussed, including pure heat diffusion and heat and mass diffusion together. Since no local equilibrium assumption is made, the conjugate fluxes and forces are intrinsic to the subspaces of the state space of one system and/or of the state space of the two interacting systems. They are derived via the concepts of hypoequilibrium state and nonequilibrium intensive properties, which describe the nonmutual equilibrium status between subspaces of the Thermodynamic state space of a single system and/or of the state space of the two interacting systems. The Onsager relations are shown to be Thermodynamic kinematic features of the system and are found without knowledge of the detailed mechanics of the dynamic process. A fundamental Thermodynamic explanation for the measurement of each intensive property of a system in a nonequilibrium state is given. The fundamental Thermodynamic definition of reservoir is also discussed. Finally, the equation of motion for a system undergoing multiple interactions is provided, which permits the modeling of a network of local systems in nonequilibrium at any spatial and temporal scale.
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modeling the nonequilibrium effects in a nonquasi equilibrium Thermodynamic cycle based on steepest entropy ascent and an isothermal isobaric Ensemble
Energy, 2016Co-Authors: Michael R Von SpakovskyAbstract:Conventional first principle approaches for studying nonequilibrium or far-from-equilibrium processes depend on the mechanics of individual particles or quantum states. They also require many details of the mechanical features of a system to arrive at a macroscopic property. In contrast, Thermodynamics provides an approach for determining macroscopic property values without going into these details, because the overall effect of particle dynamics results, for example, at stable equilibrium in an invariant pattern of the “Maxwellian distribution”, which in turn leads to macroscopic properties. However, such an approach is not generally applicable to a nonequilibrium process except in the near-equilibrium realm. To adequately address these drawbacks, steepest-entropy-ascent quantum Thermodynamics (SEAQT) provides a first principle, Thermodynamic-Ensemble approach applicable to the entire nonequilibrium realm. Based on prior developments by the authors, this paper applies the SEAQT framework to modeling the nonquasi-equilibrium cycle, which a system with variable volume undergoes. Using the concept of hypoequilibrium state and nonequilibrium intensive properties, this framework provides a complete description of the nonequilibrium evolution in state of the system. Results presented here reveal how nonequilibrium effects influence the performance of the cycle.
Guanchen Li - One of the best experts on this subject based on the ideXlab platform.
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Modeling the Non-Equilibrium Process of the Chemical Adsorption of Ammonia on GaN(0001) Reconstructed Surfaces Based on Steepest-Entropy-Ascent Quantum Thermodynamics.
Materials, 2017Co-Authors: Akira Kusaba, Guanchen Li, Michael R. Von Spakovsky, Yoshihiro Kangawa, Koichi KakimotoAbstract:Clearly understanding elementary growth processes that depend on surface reconstruction is essential to controlling vapor-phase epitaxy more precisely. In this study, ammonia chemical adsorption on GaN(0001) reconstructed surfaces under metalorganic vapor phase epitaxy (MOVPE) conditions (3Ga-H and Nad-H + Ga-H on a 2 × 2 unit cell) is investigated using steepest-entropy-ascent quantum Thermodynamics (SEAQT). SEAQT is a Thermodynamic-Ensemble based, first-principles framework that can predict the behavior of non-equilibrium processes, even those far from equilibrium where the state evolution is a combination of reversible and irreversible dynamics. SEAQT is an ideal choice to handle this problem on a first-principles basis since the chemical adsorption process starts from a highly non-equilibrium state. A result of the analysis shows that the probability of adsorption on 3Ga-H is significantly higher than that on Nad-H + Ga-H. Additionally, the growth temperature dependence of these adsorption probabilities and the temperature increase due to the heat of reaction is determined. The non-equilibrium Thermodynamic modeling applied can lead to better control of the MOVPE process through the selection of preferable reconstructed surfaces. The modeling also demonstrates the efficacy of DFT-SEAQT coupling for determining detailed non-equilibrium process characteristics with a much smaller computational burden than would be entailed with mechanics-based, microscopic-mesoscopic approaches.
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steepest entropy ascent quantum Thermodynamic modeling of the relaxation process of isolated chemically reactive systems using density of states and the concept of hypoequilibrium state
Physical Review E, 2016Co-Authors: Guanchen Li, Von Spakovsky MrAbstract:This paper presents a study of the nonequilibrium relaxation process of chemically reactive systems using steepest-entropy-ascent quantum Thermodynamics (SEAQT). The trajectory of the chemical reaction, i.e., the accessible intermediate states, is predicted and discussed. The prediction is made using a Thermodynamic-Ensemble approach, which does not require detailed information about the particle mechanics involved (e.g., the collision of particles). Instead, modeling the kinetics and dynamics of the relaxation process is based on the principle of steepest-entropy ascent (SEA) or maximum-entropy production, which suggests a constrained gradient dynamics in state space. The SEAQT framework is based on general definitions for energy and entropy and at least theoretically enables the prediction of the nonequilibrium relaxation of system state at all temporal and spatial scales. However, to make this not just theoretically but computationally possible, the concept of density of states is introduced to simplify the application of the relaxation model, which in effect extends the application of the SEAQT framework even to infinite energy eigenlevel systems. The energy eigenstructure of the reactive system considered here consists of an extremely large number of such levels (on the order of 10^{130}) and yields to the quasicontinuous assumption. The principle of SEA results in a unique trajectory of system Thermodynamic state evolution in Hilbert space in the nonequilibrium realm, even far from equilibrium. To describe this trajectory, the concepts of subsystem hypoequilibrium state and temperature are introduced and used to characterize each system-level, nonequilibrium state. This definition of temperature is fundamental rather than phenomenological and is a generalization of the temperature defined at stable equilibrium. In addition, to deal with the large number of energy eigenlevels, the equation of motion is formulated on the basis of the density of states and a set of associated degeneracies. Their significance for the nonequilibrium evolution of system state is discussed. For the application presented, the numerical method used is described and is based on the density of states, which is specifically developed to solve the SEAQT equation of motion. Results for different kinds of initial nonequilibrium conditions, i.e., those for gamma and Maxwellian distributions, are studied. The advantage of the concept of hypoequilibrium state in studying nonequilibrium trajectories is discussed.
Guillaume Jeanmairet - One of the best experts on this subject based on the ideXlab platform.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
arXiv: Soft Condensed Matter, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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 ap- proximation for the free-energy functional, the so-called homogeneous reference uid approximation, we show that the hydration free-energies computed for a dataset of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by two to three orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canoni- cal 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 justifcation to empirical partial molar volume corrections that have been proposed recently.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
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fast computation of solvation free energies with molecular density functional theory Thermodynamic Ensemble partial molar volume corrections
Journal of Physical Chemistry Letters, 2014Co-Authors: Volodymyr P Sergiievskyi, Guillaume Jeanmairet, Maximilien Levesque, Daniel BorgisAbstract: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.
