Jean-Marc Simon - Academia.edu (original) (raw)
Papers by Jean-Marc Simon
The Journal of Chemical Physics
The Kirkwood–Buff theory is a cornerstone of the statistical mechanics of liquids and solutions. ... more The Kirkwood–Buff theory is a cornerstone of the statistical mechanics of liquids and solutions. It relates volume integrals over the radial distribution function, so-called Kirkwood–Buff integrals (KBIs), to particle number fluctuations and thereby to various macroscopic thermodynamic quantities such as the isothermal compressibility and partial molar volumes. Recently, the field has seen a strong revival with breakthroughs in the numerical computation of KBIs and applications to complex systems such as bio-molecules. One of the main emergent results is the possibility to use the finite volume KBIs as a tool to access finite volume thermodynamic quantities. The purpose of this Perspective is to shed new light on the latest developments and discuss future avenues.
Molecular Simulation, 2017
The modelling of thermodynamic properties of liquids from local density fluctuations is relevant ... more The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood-Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the inverse of the size of these subvolumes, estimates for KB integrals in the thermodynamic limit are obtained. Two system size effects are observed in MD simulations: (1) effects due to the size of the simulation box and the size of the finite subvolume embedded in the simulation box, and (2) effects due to computing radial distribution functions (RDF) from a closed and finite system. In this study, we investigate the two effects in detail by computing KB integrals using the following methods: (1) Monte Carlo simulations of finite subvolumes of a liquid with an analytic RDF and (2) MD simulations of a WCA mixture for various simulation box sizes, but at the same thermodynamic state. We investigate the effect of the size of the simulation box and quantify the differences compared to KB integrals computed in the thermodynamic limit. We demonstrate that calculations of KB integrals should not be extended beyond half the size of the simulation box. For finite-size effects related to the RDF, we find that the Van der Vegt correction (J Chem Theory Comput. 2013;9:1347) yields the most accurate results.
Fluid Phase Equilibria, 2018
The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties o... more The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure [1, 2]. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of Radial Distribution Functions (RDF) over volume but can also be obtained from density fluctuations in the grandcanonical ensemble [3]. Various methods have been proposed to estimate KB integrals from molecular simulation. In this presentation, based on reference [4], I will review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention will be paid to finite-size effects [4, 5]. I will also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.
Physchem
Kirkwood–Buff Integral (KBI) theory is an important method for the analysis of the structural and... more Kirkwood–Buff Integral (KBI) theory is an important method for the analysis of the structural and thermodynamic properties of liquid solutions. For solids, the calculation of KBIs has become possible only recently through the finite-volume generalisation of KBI theory, but it has so far only been applied to monoatomic crystals. Here, we show that KBI theory can be applied to solid mixtures and compute the KBIs of a ArxXe1−x solid solution, for 0
The Journal of Physical Chemistry B, 2004
We show using non-equilibrium molecular dynamics that there is local equilibrium in the surface w... more We show using non-equilibrium molecular dynamics that there is local equilibrium in the surface when a two-phase fluid of n-octane is exposed to a large temperature gradient (10 8 K/m). The surface is defined according to Gibbs, and the transport across the surface is described with non-equilibrium thermodynamics. The structure of the surface in the presence of the gradient is the same as if the interface was in equilibrium, as measured by the variation across the surface of the pressure component that is parallel to the surface. The surface is in local equilibrium by this criterion and because the equation of state for the surface was unaltered by a large heat flux. The surface has a small entropy and is thus more structured than a surface of argon particles. The excess thermal resistance coefficient and the coupling coefficient for transport of heat and mass were calculated and found to be smaller than corresponding coefficients from kinetic theory and for argon-like particles, probably because molecular vibrations contribute to heat transfer. Away from the triple point, the heat of transfer was more than 30% of the value of the enthalpy of evaporation, which means that the surface has a large impact on the heat flux across it. This will be of practical importance in non-equilibrium models for phase transitions. The results support the basic assumptions in non-equilibrium thermodynamics and enable us to give linear flux force relations of transport with surface tension dependent transfer coefficients.
The Journal of Physical Chemistry B, 2011
We show how density and energy fluctuations of small nonperiodic systems embedded in a reservoir ... more We show how density and energy fluctuations of small nonperiodic systems embedded in a reservoir can be used to determine macroscopic thermodynamic properties like the enthalpy density and the thermodynamic correction factor. For mixtures, the same formalism leads to a very convenient method to obtain so-called total correlation function integrals, also often referred to as KirkwoodÀBuff integrals. Using finite size scaling, the properties obtained for small systems can be extrapolated to the macroscopic system limit provided that the system is sufficiently far from the critical point. As derived in our previous work (Chem. Phys. Lett. 2011, 504, 199À201), the finite size scaling is significant and depends on 1/L, where L is the length of the small system in one dimension. By considering a reservoir with an ensemble of embedded small systems, we can use the scaling arising from surface effects to determine properties for macroscopic systems by extrapolation. We demonstrate this method for the WCA and LJ fluids, as well a for a heterogeneous system, i.e., argon adsorbed in silicalite-1 zeolite.
Molecular Physics, 2012
This article may be used for research, teaching, and private study purposes. Any substantial or s... more This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae, and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand, or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
Physical Review E, 2007
Surface transfer coefficients are determined by nonequilibrium molecular dynamics simulations for... more Surface transfer coefficients are determined by nonequilibrium molecular dynamics simulations for a Lennard-Jones fluid with a long-range spline potential. In earlier work ͓A.
The Journal of Physical Chemistry B
Chemical Communications
Adsorption isotherms of H2 and D2 in pure silica chabazite at 47 K show an unexpected step associ... more Adsorption isotherms of H2 and D2 in pure silica chabazite at 47 K show an unexpected step associated with an increase of the D2/H2 adsorption selectivity due to molecular rearrangement.
The Journal of Physical Chemistry C
In this paper we report the use of Grand Canonical Monte Carlo (GCMC) simulations to characterize... more In this paper we report the use of Grand Canonical Monte Carlo (GCMC) simulations to characterize the competitive trapping of CO and N2 molecules into clathrates, for various gas compositions in the temperature range from 50 to 150 K. The simulations evidence a preferential trapping of CO with respect to N2. This leads to the formation of clathrates that are preferentially filled with CO at equilibrium, irrespective of the composition of the gas phase, the fugacity, and the temperature. Moreover, the results of the simulations show that the small cages of the clathrate structure are always filled first, independent of either the guest structure or the temperature. This issue has been associated with the rather significant differences in the calculated heats of encapsulation (∼2–3 kJ/mol) between the smallest and the largest cages. In addition, calculations with the simplified ideal adsorbed solution theory (IAST) are developed to allow a comparison with the results arising from the GCMC simulations. Inter...
Physical chemistry chemical physics : PCCP, Jan 29, 2017
Small systems are known to deviate from the classical thermodynamic description, among other thin... more Small systems are known to deviate from the classical thermodynamic description, among other things due to their large surface area to volume ratio compared to corresponding big systems. As a consequence, extensive thermodynamic properties are no longer proportional to the volume, but are instead higher order functions of size and shape. We investigate such functions for second moments of probability distributions of fluctuating properties in the grand-canonical ensemble, focusing specifically on the volume and surface terms of Hadwiger's theorem, explained in Klain, Mathematika, 1995, 42, 329-339. We resolve the shape dependence of the surface term and show, using Hill's nanothermodynamics [Hill, J. Chem. Phys., 1962, 36, 3182], that the surface satisfies the thermodynamics of a flat surface as described by Gibbs [Gibbs, The Scientific Papers of J. Willard Gibbs, Volume 1, Thermodynamics, Ox Bow Press, Woodbridge, Connecticut, 1993]. The Small System Method (SSM), first der...
Journal of agricultural and food chemistry, Jan 26, 2016
The transfer of oxygen through a corked bottleneck was investigated using a manometric technique.... more The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effec...
Journal of Agricultural and Food Chemistry, 2016
Chemical Physics Letters, 2014
We find by examination of density profiles that carbon dioxide adsorbs on graphite in two distinc... more We find by examination of density profiles that carbon dioxide adsorbs on graphite in two distinct layers. We report the activity coefficient, entropy and enthalpy for CO 2 in each layer using a convenient computational method, the Small System Method, thereby extending this method to surfaces. This opens up the possibility to study thermodynamic properties for a wide range of surface phenomena.
A study of the influence of density on the thermodynamic characteristics and dynamical behavior o... more A study of the influence of density on the thermodynamic characteristics and dynamical behavior of ethene molecules in liquid phase at 123 K is performed by molecular dynamic simulation technique. The simulations were carried out using an all atom model of ethene molecule and for the density of the system in the range from 600 to 900 kg.m −3 and at 1.26 kg.m −3 in the gas phase. The calculated change of the Gibbs free energy with pressure does not reveal any phase transition of the system under the external conditions used in the calculations. The analysis of the infrared spectra shows strong modifications upon the increasing of the density, in agreement with experimental results. Firstly, going from gas to liquid phase, the change in rotational motion of the molecules modifies the shape of the infrared bands and secondly, the frequencies of the bands shift upwards while the pressure increases. The data obtained are discussed in relation to studies of molecules adsorbed in microporous materials.
The Journal of Chemical Physics
The Kirkwood–Buff theory is a cornerstone of the statistical mechanics of liquids and solutions. ... more The Kirkwood–Buff theory is a cornerstone of the statistical mechanics of liquids and solutions. It relates volume integrals over the radial distribution function, so-called Kirkwood–Buff integrals (KBIs), to particle number fluctuations and thereby to various macroscopic thermodynamic quantities such as the isothermal compressibility and partial molar volumes. Recently, the field has seen a strong revival with breakthroughs in the numerical computation of KBIs and applications to complex systems such as bio-molecules. One of the main emergent results is the possibility to use the finite volume KBIs as a tool to access finite volume thermodynamic quantities. The purpose of this Perspective is to shed new light on the latest developments and discuss future avenues.
Molecular Simulation, 2017
The modelling of thermodynamic properties of liquids from local density fluctuations is relevant ... more The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood-Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the inverse of the size of these subvolumes, estimates for KB integrals in the thermodynamic limit are obtained. Two system size effects are observed in MD simulations: (1) effects due to the size of the simulation box and the size of the finite subvolume embedded in the simulation box, and (2) effects due to computing radial distribution functions (RDF) from a closed and finite system. In this study, we investigate the two effects in detail by computing KB integrals using the following methods: (1) Monte Carlo simulations of finite subvolumes of a liquid with an analytic RDF and (2) MD simulations of a WCA mixture for various simulation box sizes, but at the same thermodynamic state. We investigate the effect of the size of the simulation box and quantify the differences compared to KB integrals computed in the thermodynamic limit. We demonstrate that calculations of KB integrals should not be extended beyond half the size of the simulation box. For finite-size effects related to the RDF, we find that the Van der Vegt correction (J Chem Theory Comput. 2013;9:1347) yields the most accurate results.
Fluid Phase Equilibria, 2018
The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties o... more The Kirkwood-Buff (KB) theory provides a rigorous framework to predict thermodynamic properties of isotropic liquids from the microscopic structure [1, 2]. Several thermodynamic quantities relate to KB integrals, such as partial molar volumes. KB integrals are expressed as integrals of Radial Distribution Functions (RDF) over volume but can also be obtained from density fluctuations in the grandcanonical ensemble [3]. Various methods have been proposed to estimate KB integrals from molecular simulation. In this presentation, based on reference [4], I will review the available methods to compute KB integrals from molecular simulations of finite systems, and particular attention will be paid to finite-size effects [4, 5]. I will also review various applications of KB integrals computed from simulations. These applications demonstrate the importance of computing KB integrals for relating findings of molecular simulation to macroscopic thermodynamic properties of isotropic liquids.
Physchem
Kirkwood–Buff Integral (KBI) theory is an important method for the analysis of the structural and... more Kirkwood–Buff Integral (KBI) theory is an important method for the analysis of the structural and thermodynamic properties of liquid solutions. For solids, the calculation of KBIs has become possible only recently through the finite-volume generalisation of KBI theory, but it has so far only been applied to monoatomic crystals. Here, we show that KBI theory can be applied to solid mixtures and compute the KBIs of a ArxXe1−x solid solution, for 0
The Journal of Physical Chemistry B, 2004
We show using non-equilibrium molecular dynamics that there is local equilibrium in the surface w... more We show using non-equilibrium molecular dynamics that there is local equilibrium in the surface when a two-phase fluid of n-octane is exposed to a large temperature gradient (10 8 K/m). The surface is defined according to Gibbs, and the transport across the surface is described with non-equilibrium thermodynamics. The structure of the surface in the presence of the gradient is the same as if the interface was in equilibrium, as measured by the variation across the surface of the pressure component that is parallel to the surface. The surface is in local equilibrium by this criterion and because the equation of state for the surface was unaltered by a large heat flux. The surface has a small entropy and is thus more structured than a surface of argon particles. The excess thermal resistance coefficient and the coupling coefficient for transport of heat and mass were calculated and found to be smaller than corresponding coefficients from kinetic theory and for argon-like particles, probably because molecular vibrations contribute to heat transfer. Away from the triple point, the heat of transfer was more than 30% of the value of the enthalpy of evaporation, which means that the surface has a large impact on the heat flux across it. This will be of practical importance in non-equilibrium models for phase transitions. The results support the basic assumptions in non-equilibrium thermodynamics and enable us to give linear flux force relations of transport with surface tension dependent transfer coefficients.
The Journal of Physical Chemistry B, 2011
We show how density and energy fluctuations of small nonperiodic systems embedded in a reservoir ... more We show how density and energy fluctuations of small nonperiodic systems embedded in a reservoir can be used to determine macroscopic thermodynamic properties like the enthalpy density and the thermodynamic correction factor. For mixtures, the same formalism leads to a very convenient method to obtain so-called total correlation function integrals, also often referred to as KirkwoodÀBuff integrals. Using finite size scaling, the properties obtained for small systems can be extrapolated to the macroscopic system limit provided that the system is sufficiently far from the critical point. As derived in our previous work (Chem. Phys. Lett. 2011, 504, 199À201), the finite size scaling is significant and depends on 1/L, where L is the length of the small system in one dimension. By considering a reservoir with an ensemble of embedded small systems, we can use the scaling arising from surface effects to determine properties for macroscopic systems by extrapolation. We demonstrate this method for the WCA and LJ fluids, as well a for a heterogeneous system, i.e., argon adsorbed in silicalite-1 zeolite.
Molecular Physics, 2012
This article may be used for research, teaching, and private study purposes. Any substantial or s... more This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae, and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand, or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
Physical Review E, 2007
Surface transfer coefficients are determined by nonequilibrium molecular dynamics simulations for... more Surface transfer coefficients are determined by nonequilibrium molecular dynamics simulations for a Lennard-Jones fluid with a long-range spline potential. In earlier work ͓A.
The Journal of Physical Chemistry B
Chemical Communications
Adsorption isotherms of H2 and D2 in pure silica chabazite at 47 K show an unexpected step associ... more Adsorption isotherms of H2 and D2 in pure silica chabazite at 47 K show an unexpected step associated with an increase of the D2/H2 adsorption selectivity due to molecular rearrangement.
The Journal of Physical Chemistry C
In this paper we report the use of Grand Canonical Monte Carlo (GCMC) simulations to characterize... more In this paper we report the use of Grand Canonical Monte Carlo (GCMC) simulations to characterize the competitive trapping of CO and N2 molecules into clathrates, for various gas compositions in the temperature range from 50 to 150 K. The simulations evidence a preferential trapping of CO with respect to N2. This leads to the formation of clathrates that are preferentially filled with CO at equilibrium, irrespective of the composition of the gas phase, the fugacity, and the temperature. Moreover, the results of the simulations show that the small cages of the clathrate structure are always filled first, independent of either the guest structure or the temperature. This issue has been associated with the rather significant differences in the calculated heats of encapsulation (∼2–3 kJ/mol) between the smallest and the largest cages. In addition, calculations with the simplified ideal adsorbed solution theory (IAST) are developed to allow a comparison with the results arising from the GCMC simulations. Inter...
Physical chemistry chemical physics : PCCP, Jan 29, 2017
Small systems are known to deviate from the classical thermodynamic description, among other thin... more Small systems are known to deviate from the classical thermodynamic description, among other things due to their large surface area to volume ratio compared to corresponding big systems. As a consequence, extensive thermodynamic properties are no longer proportional to the volume, but are instead higher order functions of size and shape. We investigate such functions for second moments of probability distributions of fluctuating properties in the grand-canonical ensemble, focusing specifically on the volume and surface terms of Hadwiger's theorem, explained in Klain, Mathematika, 1995, 42, 329-339. We resolve the shape dependence of the surface term and show, using Hill's nanothermodynamics [Hill, J. Chem. Phys., 1962, 36, 3182], that the surface satisfies the thermodynamics of a flat surface as described by Gibbs [Gibbs, The Scientific Papers of J. Willard Gibbs, Volume 1, Thermodynamics, Ox Bow Press, Woodbridge, Connecticut, 1993]. The Small System Method (SSM), first der...
Journal of agricultural and food chemistry, Jan 26, 2016
The transfer of oxygen through a corked bottleneck was investigated using a manometric technique.... more The transfer of oxygen through a corked bottleneck was investigated using a manometric technique. First, the effect of cork compression on oxygen transfer was evaluated without considering the glass/cork interface. No significant effect of cork compression (at 23% strain, corresponding to the compression level of cork in a bottleneck for still wines) was noticeable on the effective diffusion coefficient of oxygen. The mean value of the effective diffusion coefficient is equal to 10(-8) m(2) s(-1), with a statistical distribution ranging from 10(-10) to 10(-7) m(2) s(-1), which is of the same order of magnitude as for the non-compressed cork. Then, oxygen transfer through cork compressed in a glass bottleneck was determined to assess the effect of the glass/cork interface. In the particular case of a gradient-imposed diffusion of oxygen through our model corked bottleneck system (dry cork without surface treatment; 200 and ∼0 hPa of oxygen on both sides of the sample), the mean effec...
Journal of Agricultural and Food Chemistry, 2016
Chemical Physics Letters, 2014
We find by examination of density profiles that carbon dioxide adsorbs on graphite in two distinc... more We find by examination of density profiles that carbon dioxide adsorbs on graphite in two distinct layers. We report the activity coefficient, entropy and enthalpy for CO 2 in each layer using a convenient computational method, the Small System Method, thereby extending this method to surfaces. This opens up the possibility to study thermodynamic properties for a wide range of surface phenomena.
A study of the influence of density on the thermodynamic characteristics and dynamical behavior o... more A study of the influence of density on the thermodynamic characteristics and dynamical behavior of ethene molecules in liquid phase at 123 K is performed by molecular dynamic simulation technique. The simulations were carried out using an all atom model of ethene molecule and for the density of the system in the range from 600 to 900 kg.m −3 and at 1.26 kg.m −3 in the gas phase. The calculated change of the Gibbs free energy with pressure does not reveal any phase transition of the system under the external conditions used in the calculations. The analysis of the infrared spectra shows strong modifications upon the increasing of the density, in agreement with experimental results. Firstly, going from gas to liquid phase, the change in rotational motion of the molecules modifies the shape of the infrared bands and secondly, the frequencies of the bands shift upwards while the pressure increases. The data obtained are discussed in relation to studies of molecules adsorbed in microporous materials.