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Laboratoire Interdisciplinaire Carnot de Bourgogne

SIMON Jean-Marc

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 Bureau: C311
 Département IRM (ASP)


Dr Jean-Marc SIMON (1967),

PhD (Université Paris XI Orsay, 1997) speciality Physical chemistry; Habilitation (HDR) University of Burgundy 2011

- Associate Professor (Maître de Conférences) at the chemistry department since 1998 at the Université de Bourgogne (31th section, physical chemistry).
- Assistant Professor (ATER) Université Paris XI Orsay, 1998;
- Guest Professor 2005-2006, at the Physical Chemistry department  of NTNU, University of Trondheim  (Norvège), 2007-2008 at the center of advanced studies in Oslo.

Research topics: Adsorption phenomena in porous solids and surfaces
Non-equilibrium thermodynamics, nanothermodynamics, application of statistical mechanics tools to molecular simulations (molecular dynamics and Monte Carlo)

H-index: 20 (2018), 66 articles (64 impact factors >1) 2 book chapters

Research gate :

publications see Google scholar

Current granted projects: 1- Simulation of trapping and separation of hydrogen isotopes (CEA), 1 post doc. (2016-2020)

2- Simulation of the diffusion of He in PdT (CEA) (2016-2018)

3- ANR MI2C (2015-2019) Multiscale Investigations of the impact of Mineral Impurities on gas trapping within Clathrate Hydrates, 1 PhD.

4- Labbex Action: Novel materials for efficient biomarker preconcentration in the presence of water in human breath analysis by micro-sensor

Research experience

Research experience:

Adsorption and transport at surfaces: simulation as a support for experiments.  

Keywords: Molecular dynamics simulations, non-equilibrium molecular dynamics, heterogeneous systems, surface and interface, membrane, vibrational spectroscopy, microporous system, zeolite, irreversible thermodynamics, parallel computing, statistical thermodynamics, experiments, nanothermodynamics

Adsorption kinetics and equilibrium of organic and water molecules in a microporous structure
The main objective of my research group (Adsorption on Porous Solids) is to understand, from a fundamental point of view, the mechanism of adsorption of different types of molecules on microporous organic or inorganic materials. We have a long experience (more than 40 years) in the study of the adsorption in siliceous microporous materials called zeolites. In order to have a fully understanding of what’s occuring at the surface we have a multi approach combining Monte-Carlo simulation (MC) using “GIBBS” code, quantum density functional theory (DFT) using VASP and mainly molecular dynamics for the simulation parts and experiments (thermogravimetry, BET, calorimetry, DRX, infrared experiments, …). Monte Carlo methods are very efficient and considered as the standard for computing adsorption equilibrium in zeolites or in structured solids. DFT gives an intimate view of the interaction of molecules with surfaces, in particular it informs on the possibility of the molecule to react chemically and then study chemisorption, which is not directly accessible for classical MC and MD. In adsorption science, MD simulations are mostly used to calculate diffusion coefficients under equilibrium conditions.
The idea was first to mimic the adsorption processes under “realistic” conditions  as it is studied experimentally in our group. For that purpose, a molecular dynamics code was developped that can simulate both the kinetics of adsorption (transient non-equilibrium molecular dynamics) and the adsorption properties under equilibrium of fluids in contact with a solid surface (porous or not). This kind of simulations gives the possibility to directly investigate the adsorption kinetics because it gives access to the phenomena occurring at surfaces and then we could estimate their influences on the global transfer of mass and energy. Mainly, we were motivated by the fact that the values of diffusion coefficients measured by various techniques show huge differences. In general, methods based on equilibrium states (pulse field NMR or Quasi Elastic Neutron Scattering, equilibrium MD) lead to values several orders of magnitude higher than those obtained from uptake methods (gravimetry, Zero Length Column, etc). By computing the kinetics of adsorption and the equilibrium state in the same simulation runs we were able to investigate these inconsistent results under “consistent” conditions. Like in experiments we obtained different diffusion coefficient values both under equilibrium and from the kinetics of adsorption. The simulations highlighted the important role played by the external surface as a resistance to mass transfer. This is an explanation for the large distribution of the experimental results although the ratio surface/volume of the zeolite crystals, of micrometer sizes, are much lower than in simulation. Since the beginning of our project, it has been evidenced experimentally that a part of these inconsistencies is accordingly attributed to surface effects and also to internal crystal defects.

          a-Transport across surfaces.
In addition to experimenting [A9, A15], we simulated kinetics of adsorption with different gases  [A11, A21, A22] n-butane, n-hexane, 2-methylpentane and mixtures on aggregates or membranes of the zeolite silicalite. We pointed out that the limiting step of the adsorption kinetics might be, depending on the experimental conditions: the intracrystalline diffusion, as expected; the transport across the external surface (including defects); the release of the heat of adsorption; or even the transport in the gas phase between the particules of zeolite. In collaboration with Signe Kjelstrup and Dick Bedeaux from NTNU (Trondheim, Norway), we studied the transfer of heat and mass and their coupling at the external surface of a membrane of zeolite silicalite in contact with a gas of n-butane. The results confirmed that large energetic effects take place during the kinetics of adsorption and lead to non-isothermal adsorption processes [A21, A22, A31, Ch2]. Although this non-isothermal adsorption process had been witnessed in experiments and attributed to high resistances to heat transfer at the external surface of the zeolites, it has never been investigated using molecular dynamics simulations. Similarly to the liquid-vapor interfaces (see below), we verified that the non-equilibrium thermodynamics theory is valid to describe the transfer of mass and heat both across the external surface and inside the crystal [A29, A31, Ch2]. Based on mass and thermal resistances computed across the surface we concluded that the heat resistance and the coupling term play a major role in non-isothermal kinetics, they slow down  (by a factor 10 in our simulations) the adsorption kinetics. As shown by experiments, this particular behavior is only important for small molecules with a high diffusion coefficient inside the pores and it can be neglected otherwise.

         b-Surface under equilibrium - Adsorption equilibrium.
We also investigated the adsorption equilibrium state. Thermodynamic properties (isotherm, energy of adsorption) [A11, A29, A30, A32], dynamical properties at the external surface  [A14, A48] and in the adsorbed phase and infrared spectra were computed on these confined systems and compared well with experiments when available [A12, A16]. The infrared spectra are easy to obtain experimentally; they are particularly helpful for a better understanding of the state of confined molecules. Comparing the vibrational spectra of confined molecules with that of the gas phase, one observes shifts of the main vibrational bands and a partial destruction of the rovibrational structures. These shifts can be the consequence of condensation effects [A8], they can also be the signature of specific adsorption sites inside the porous matrix. Interpreting the modifications of the experimental spectra is often very complex and we performed atomic simulations to have a better interpretation of the spectra: quantum simulations  [A30, A56] and MD simulations [A8, A12, A16, A17]. For the system ethylene/silicalite  at ambient temperature we observed in experiments a splitting of the ν12 band (scissoring HCH vibration type) after a loading of 4 molecules per unit cell. Using MD simulations we showed that ethylene molecules are very mobile inside the pore structure and we could clearly attribute this splitting to a condensation of ethylene molecules inside the pores and not to the presence of the molecules on specific adsorption sites as it was supposed before.
For the n-butane – silicalite system, equilibrium adsorption isotherms were computed at different temperatures both for molecules located inside the pores [A29] and on the external surfaces of the zeolite [A30]. The adsorption isotherms of the external surface strongly depend of the state of the surface, roughness, different adsorption sites, etc. By simulating the transfer of n-butane molecules through surfaces with different shapes and roughness, we obtained different mass resistances and adsorption kinetics. These results indicated that the presence of defects at external surfaces has a lot of influences on the mass transfer. Analyses of adsorption/desorption rates were also performed  on the same system [A14]. We calculated sticking coefficients and obtained values approaching one, it means that the molecules located in the gas phase were systematically adsorbed when they hit the zeolite surface. We also got very small values of the desorption coefficient, lower than 0.1, meaning that adsorbed molecules hardly escaped to the gas phase. These results were important for people measuring diffusion coefficient with pulse field NMR methods, because it is a prerequisite for the interpretation of the experimental results [A14]. The results also reinforce the vision of the role of mass resistance played by the external surface in agreement with the non-equilibrium thermodynamics. A systematic study of the rates of adsorption/desorption for different hydrocarbon molecules was presented in a recent article [A48].  Depending on the type of molecules, on the adsorption enthalpy, on the coverage, on the intra-zeolite diffusion coefficients, the sticking coefficients could differ significantly from the value one.
In an attempt to better understand the isotherm step of n-heptane in silicalite, neutron scattering experiments and MD simulations were performed [A25, A32]. Comparing both sets of data we could locate very accurately the adsorption sites in the porous structure. As expected, the positions of the molecules shifted a bit at the step of the isotherm. This phenomenon was known from the literature and we could relate it to a dynamical locking effect of the molecules inside the sinusoidal channels and not to a commensurate freezing as it was generally admitted. A direct consequence of this locking effect was a large increase of the diffusion coefficient in the straight channel and the presence of single file diffusion regime.
Since a few years we are studying the interaction of water with solids materials like gypsum (for the cement industry LAFARGE), metal organic frameworks (MOF) or gas hydrates. Using DFT calculations, we simulated the hydration of anhydrous gypsum and we saw that the first water molecules are chemisorbed on the external surface of the material that explains a step visible at small pressure on the experimental isotherm. We recently made a comparison of the infrared spectra of metal organic framework (MOF) MIL53-Al including water molecules obtained from experiments and DFT [A56]. The main result was to identify the vibrational signatures of water molecules adsorbed on different adsorption sites. Concerning gas hydrates we obtained an ANR grant (MI2C) to study the effect of solid impurities on the stabilisation of clathrates.
We also started to work with O. Mousis from the astrophysics lab. (LAM) in Marseilles to apply the adsorption properties in the context of astrophysics. We were able to propose a scenario of formation of the comet ‘TCHOURI’ [A57], based on the adsorption properties of mixed gas hydrates of N2 and CO. We are also working on a new scenarios of methane sequestration in the martian zeolites [A58].

Transport properties of liquid-vapour surfaces by molecular dynamics simulation
Although a few studies have been dedicated to the extension of irreversible thermodynamics theory to heterogeneous systems over the last 50 years, little direct evidence of the validity of this theory and its limits are available. The MD simulations give the possibility to directly “see” what is happening locally at the scale of the heterogeneities, on surfaces, under equilibrium and out of equilibrium. In collaboration with the group of Prof. Signe Kjelstrup and Dick Bedeaux (NTNU, Trondheim) we used MD simulations as “experiments” to validate and improve the theory so that it becomes an efficient tool both to analyze and quantify the transport phenomena across surfaces and membranes and to give quantitative criteria to improve the efficiency of processes happening on surfaces.
We studied, using direct non-equilibrium molecular dynamics simulations, the heat and mass fluxes and their coupling across a liquid-vapour interface of atomic and molecular species for pure compounds [A10, A18, A23, A24]. The results show that the main assumptions of the heterogeneous irreversible thermodynamics, that is to say the local equilibrium hypothesis and the linear relations flux-thermodynamics forces are valid across surfaces for these systems. As a consequence, we could calculate the surface resistances and examined the role played by the surfaces in the kinetics processes. In general the absolute values of the resistances to mass and heat transfer and their coupling increase with the surface tension (they are obviously null at the critical point). This study is now extended to more complex systems, for zeolite (MFI) membrane in contact with a gas of adsorptive compounds (n-butane) [A11, A21, A22, A26, A29, A31, Ch2] see below, and for binary systems [A36, A38]. In all cases we obtained a large excess of resistance to mass and heat transfer at the surface compared with the adjacent bulk phases. Considering that the surface has a thickness of a few angstroms (it is infinite at the critical point), we showed that the main resistance to the heat transfer is located at the gas side of the surface and at the denser side of the surface for the mass flux. The heat of transfer, which describes the coupling between heat and mass, is large of the same amplitude that the heat of evaporation/adsorption.
This study on transport coefficients across interfaces is the complement to other studies on bulk systems that I have done during my thesis and later, on the Soret effect in n-alkanes liquid mixtures [A3, A4, A5, A6] and in reactive systems F2=2F [A19, A20] and  H2=2H [A49, A52]. For the fluorine systems we showed that the use of non-equilibrium thermodynamics is valid even for systems submitted to extreme temperature gradients (1011K/m) of the order of magnitude of what is present in flames.
A summary and compilation of our results on the validity of the irreversible thermodynamics at surfaces is available in one paper [A27]. A large part of these results were used as an “experimental” proof to validate the non-equilibrium theory and are included in a textbook dedicated to the “Non-equilibrium thermodynamics of heterogeneous systems” from my coworkers S. Kjelstrup and D. Bedeaux in 2008 (World Scientific).

H2 in PEM fuel cell, for storage in zeolite faujasite or reacting at high temperatures
         a- PEM fuel cell: equilibrium and diffusion of H2 on graphite
This project was done in order to better understand the working conditions of the PEM fuel cell at the anode side. From previous experimental work it was shown that the H2 molecules could not reach the catalytic site directly from the gas phase, it was assumed that it should diffuse towards it on the graphite surface. In collaboration with Signe Kjelstrup from NTNU, we studied the adsorption and diffusion properties of H2 on the surface of graphite. We measured surface diffusion coefficients doing Quasi Elastic Neutron Scattering experiments and we simulated graphite membrane in contact with a gas of H2 molecules by molecular dynamics.
The simulated results showed a good agreement with experiments [A26, A34, A35] for both the surface diffusion coefficients and the adsorption isotherm at low temperatures (<90K). The use of molecular dynamics gave new insights in the dynamics of the molecules adsorbed at the surface. Although the adsorbed amount of hydrogen was negligible at the ambient temperature, we clearly showed that the molecules moved on the surface on large distances, about 80 Å, before being desorbed. This surprising result clearly indicated that hydrogen molecules could reach catalytic sites diffusing on the graphite support, as it was assumed.
The analysis of the rates of adsorption and desorption gave additional insights in the “dynamics” of equilibrium at the surface. Because hydrogen molecules were very mobile when adsorbed, the rates did not obey the classical statistical theories of kinetics of adsorption and desorption: Langmuir kinetics, adsorption rate theory or statistical rate theory. From the simulation results, we proposed new expressions where rates were simply proportional to the activity coefficients of the departure phases: gas phase for adsorption and adsorbed phase for desorption. It was interesting to notice that although the kinetics didn’t follow the Langmuir kinetics, our expressions gave however the classical Langmuir isotherm.  

         b- Storage of H2 and D2 on faujasite at low temperature (<100 K)
In collaboration with the CEA (Valduc) we studied the isotope separation of hydrogen for storage applications on zeolite faujasite (Na-X) comparing experiments and simulations (MD, MC, DFT).  From MD simulations using the quantum Feynman Hibbs (FH) correction method, we could see a different mechanism of adsorption for H2, D2, T2 below 100K that could explain separation, the heavy isotopes being favourably stored [A63]. The project also includes the study of the transport of hydrogen into the faujasite and across membranes made of faujasite using MD simulations. While the heavier isotopes diffuse more slowly than H2 in the gas phase the tendency is inversed inside the zeolite crystal, this is due to quantum effects, and this is in agreement with QENS measurements.

         c- Reaction H2=2H at high temperatures
In that study we focused on the homogeneous dissociation of the dihydrogen at different temperatures (150 to 20 000 K) using liquid or gas densities. The equilibrium constants could be computed at different temperatures and the reaction enthalpy using the small system method (see below), the results agree with experiments when available [A49, A50]. These results were obtained using classical MD simulations with a three body interaction potential that mimic the reaction H2=2H. This type of simulation helps to better understand the interaction of reactive molecules with their environment at a larger scale than what is generally done using quantum calculation.

Statistical thermodynamics and original simulation solutions
As a user of molecular simulations, a large part of my work is dedicated to the creation of computer codes. I mainly wrote molecular dynamics (MD) codes to simulate specific physical conditions (equilibrium and non-equilibrium) and statistical thermodynamics tools to analyse the data. Concerning the physics of the codes, a large majority of the problems we faced have ever been treated in the literature and in particular in books dedicated to molecular simulations. However because we studied original complex systems and computed new properties, we had to develop new algorithms in the codes or/and to propose new statistical thermodynamics solutions.  I mentioned some of them in the previous paragraphs, like the transient non-equilibrium molecular dynamics simulation to study the kinetics of adsorption or the analysis of the rates of adsorption/desorption for H2 on graphite. In the following I will shortly present two additional cases.
An aspect of my work was dedicated to the investigation of the thermodynamic limits of the simulated systems, or part of them, under equilibrium and out of equilibrium. In a reactive system F2=2F submitted to huge temperature gradients [A19], up to 1012 K/m, we studied the velocity distribution functions of the two species. We observed shifts from the Maxwell-Boltzmann distribution that were linearly proportional to the temperature gradients and identical for both species. Despite the extreme conditions, those properties gave a statistical basis for the use of non-equilibrium thermodynamics in reacting systems. For liquid vapour systems, we could show that the equation of state of the surface was unaltered by large heat and mass fluxes in agreement with the local equilibrium hypothesis [A10, A18, A24]. We also investigated the definition of the temperature of adsorbed molecules (here argon on zeolite MFI) [A37]. Taken a temperature definition based on the equipartition of kinetic energy or based on the interaction potential we obtained different local values of the temperature, however they were identical for volumes of the size of unit crystalline cell and multiple of them. This clearly shows a thermodynamic limit (the size of a unit cell) for the temperature. This specific behaviour, the difference between the two temperatures, is not observed in fluid systems. An obvious but important consequence of the presence of spatial limits for a consistent thermodynamic description is that it fixes a lower limit for the studied systems. Sometimes the system being heterogeneous by nature this limit does not exist or the system is small enough that the classical thermodynamics cannot be simply applied (like in very small aggregates) or local heterogeneities appear in a homogenous system (like nucleation). The necessity to describe such systems however had imposed to develop new thermodynamic approaches. This is for example the case when we treated transport in heterogeneous systems using the irreversible thermodynamics, in the following is presented a new approach of smallness and its application to molecular simulation.  

In collaboration with colleagues from NTNU (Signe Kjelstrup, Dick Bedeaux, Sondre Schnell), Thijs Vlugt from TU-Delft  and Peter Kruger from Chiba University (Japan) we have recently developed a new method to calculate thermodynamic properties of macroscopic systems by extrapolating properties of systems of molecular dimensions [A39, Pr9, A40, A41, A42, A44, A45, A46, A47, A50, A51, A52, A53, A54, A55, A61, A62, A64, A65]  the small system method (SSM). Appropriate scaling laws for small systems were derived using the thermodynamics of small systems from T. H. Hill (from the sixties), also called nanothermodynamics when applied to nanosize objects. For different thermodynamic variables (partial enthalpy, partial volume, partial chemical potential, …) we  showed and demonstrated that their values vary linearly with the inverse of the system size in the grand canonical ensemble. This trend is a surface over volume property and until very small sizes it is independent on the shape of the volume investigated [A62, A65]. This defines "a shape thermodynamic limit" [A65] which is in agreement with the Gibbs surface excess description [A62]. Additionally, we could show that the Kirkwood Buff expression that is used to link structure and thermodynamic properties is not properly used in general and we gave exact expressions [A45, A46, A47, A64, A65]. Beyond the verification of the above equations and the validation of the thermodynamics of small systems by molecular simulations, these new developments gave us new tools to analyse molecular simulations. We could for example calculate Fick’s diffusion coefficients for multicomponents systems [A41, A44, A46], partial molar volumes of Na+ and Cl- of salt water [A47] or partial molar enthalpies in reacting systems that was hardly possible using standard methods [A52, A54].  In an attempt to better characterize phase transitions this method was also applied to macroscopic grain dynamics with Marcos Salazar  [A61] and to charged latex particles in water with Christophe Labbez both from my group in Dijon. The success of the new procedure has interesting implications: the procedure helps to define smallness, and precise thermodynamic relations on the nano-meter and higher scales, it also helps to define local equilibrium or verify the validity of thermodynamic relations.


Lire ses publications


Phd Thesis, Orsay, France April 3rd 1997: Etude de la thermodiffusion dans des mélanges fluides de n-alcanes par simulation numérique de la dynamique moléculaire, thesis directors: Bernard Rousseau, Alain Fuchs (Study of Thermaldiffusion of fluid alkane mixtures using molecular dynamics), written in French

Habilitation thesis (HDR), Dijon, France, Decembre 7th 2011: Adsorption and transport at surfaces. A molecular dynamics approach. (Written in English)

Book Chapters

Ch1- Chapter title:  Diffusion: a Molecular Description de l’ouvrage Confluence. Interdisciplinary Communications, J.M. Simon,  ed.: Centre for Advanced Study, Oslo,  (2009).

Ch2- Chapter Title:  Non-equilibrium Thermodynamics Applied to Adsorption de l’ouvrage IUPAC Experimental Thermodynamics Volume X : Non-equilibrium Thermodynamics with Applications, 178-203 (2015) Roy. Soc. Chem., Cambridge, Eds D. Bedeaux, S. Kjelstrup, J. Sengers DOI:10.1039/9781782622543-00178.

Published Articles in International Journals

A1- Molecular dynamics study of the phase transitions in sulfur hexafluoride clusters of various sizes, F.M. Bénière, A. Boutin, J. M. Simon, A. H. Fuchs, M. F. de Feraudy, G. Torchet, J. Chem. Phys, 97, 10472 (1993)

A2- The phase transitions of sulphur hexafluoride by molecular dynamics simulation, A. Boutin, J. M. Simon, A. H. Fuchs, Molecular Physics, 81, 1165 (1994)

A3-  Détermination du facteur de thermodiffusion par simulation numérique de la dynamique moléculaire, B. Rousseau, A. H. Fuchs, Simon J. M., Entropie, 184-185, 62-67 (1994)

A4- Propriétés de transport en phase liquide : une approche par simulation numérique de la dynamique moléculaire, J.M. Simon, A.H. Fuchs, B. Rousseau, Revue de l'Institut Francais Du Pétrole, 51, 97-104 (1996)

A5- Thermal diffusion in alkane binary mixtures. A molecular dynamics approach, J.M. Simon, D.K. Dysthe, A.H. Fuchs,  B. Rousseau, Fluid Phase Equilibria, 150-151, 151-159 (1998)

A6- Thermal diffusion in methane n-decane mixtures by molecular dynamics using spherical and flexible multicenter models., J.M. Simon , B. Rousseau, D.K. Dysthe, B. Hafskjold, Entropie, 217, 29-35 (1999)

A7- Flux expressions and NEMD perturbations for models of semi-flexible molecules, A. Perronace, J.M. Simon, B. Rousseau, G. Ciccoti, Mol. Phys., 99,  1139 (2001)

A8-  Effect of the density on the infrared spectra of liquid ethene by molecular dynamics simulations, J.M. Simon, A. Decrette, K.S. Smirnov, J.P. Bellat, S. Marcati, Entropie, 239/240, 103-106 (2002)

A9- Adsorption and diffusion of linear and branched C6 paraffins in a ZSM-5 zeolite, E. Lemaire, A. Decrette, J.P. Bellat, J.M. Simon, A. Méthivier, E. Jolimaitre, Studies in Surface Science and Catalysis, 142B, 1571-1578 (2002)

A10- Thermal Flux Through a Surface of n-octane. A Non-Equilibrium Molecular Dynamics Study, J.M. Simon, S. Kjelstrup, D. Bedeaux, B. Hafskjold, J. Phys. Chem. B, 108, 7186 (2004).

A11- Kinetics of Adsorption of n-butane on an Aggregate of Silicalite by Transient Non-equilibrium Molecular Dynamics, J.M. Simon, A. Decrette, J.B. Bellat, J.M. Salazar, Mol. Sim., 30, 621 (2004), papier invité.

A12-  Experimental and simulated infrared spectroscopic studies of the interaction of ethylene on a MFI zeolite, V. Bernardet, A. Decrette, J.M. Simon, O. Bertrand, G. Weber, J.B. Bellat, Mol. Phys., 102, 1859 (2004).

A13- Monte Carlo versus molecular dynamics simulations in heterogeneous systems: An application to the n-pentane liquid-vapor interface, F. Goujon, P. Malfreyt, J.M. Simon, A. Boutin, B. Rousseau, A. H. Fuchs, J. Chem. Phys., 121, 12559 (2004).

A14- Sticking probability on zeolites, J.M. Simon, J.B. Bellat, S. Vasenkov, J. Kärger, J. Phys. Chem B, 109, 13523 (2005).

A15-  Adsorption and Coadsorption of 2-methylpentane and 2,2-dimethylbutane in a ZSM-5 Zeolite, J.P. Bellat, E. Lemaire, J.M. Simon, G. Weber, A.C. Dubeuil, Adsorption, 11, 109-114 (2005)
A16- Infrared spectroscopic study of ethylene adsorbed on silicalite : Experiments and Molecular Dynamics simulation, V. Bernardet, A. Decrette, J. M. Simon, O. Bertrand,  G. Weber, J. P. Bellat, Adsorption, 11, 383-389 (2005)

A17- Gravimetric and FTIR study of the interaction of tetramethylethylene on a MFI zeolite, V. Bernardet, A. Decrette, J. M. Simon, O. Bertrand,  G. Weber, J. P. Bellat, Stud. Surf. Sci. Catal. 158, 1145-1152 (2005)

A18- Interface film resistivities for heat and mass transfer integral relations verified by non-equilibrium molecular dynamics, J.M. Simon, D. Bedeaux, S. Kjelstrup, J. Xu, E. Johannessen, J. Phys. Chem. B 110, 18528 (2006)

A19- Transport properties of 2F  F2 in a temperature gradient as studied by molecular dynamics simulations, J. Xu, S. Kjelstrup, D. Bedeaux, J.M. Simon, Phys. Chem. Chem. Phys. 9, 969 (2007)

A20- The heat of transfer in a chemical reaction at equilibrium, J. Xu, S. Kjelstrup, D. Bedeaux, J.M. Simon, J. Non-Equil. Thermod. 32, issue 3 (2007)

A21- Numerical evidence for a thermal driving force during adsorption of butane in silicalite. J. M. Simon, I. Inzoli, D. Bedeaux, S. Kjelstrup, Mol. Sim. 33, 839 (2007), (papier invité).

A22- Thermal effects during adsorption of n-butane on a slilicalite-1 membrane. A non-equilibrium molecular dynamics study. I. Inzoli , J.-M. Simon, S. Kjelstrup, D. Bedeaux. Journal of Colloid and Interface Science 313, 563 (2007)

A23- Transfer coefficients for evaporation of a system with a Lennard-Jones long-range spline potential. Jialin Ge, S. Kjelstrup, D. Bedeaux, J.M. Simon, B. Rousseau. Phys. Rev. E.75, 61604 (2007)

A24- Integral relations, a simplified method to find interfacial resistivities for heat and mass transfer, J. Ge, D. Bedeaux, J.M. Simon, S. Kjelstrup, Physica A 385, 421 (2007)

A25- Heptane adsorption in silicalite-I: Neutron scattering Investigation, N. Floquet, J.-P. Coulomb, J.-M. Simon , J.-P. Bellat, G. Weber, G. Andre, J. Phys. Chem. C 111, 18182 (2007)

A26- A quasi-elastic neutron scattering investigation of the hydrogen surface self diffusion on polymer electrolyte membrane fuel cell catalyst support. O.-E. Haas, J. M. Simon, S. Kjelstrup, A. L. Ramstad, P. Fouquet, J. Phys. Chem. C 112, 3121 (2008)

A27- Criteria for validity of thermodynamic equations from non-equilibrium molecular dynamics simulations, S. Kjelstrup; D. Bedeaux, I. Inzoli, J.M. Simon, Energy 33, 1185 (2008), (papier invité).

A28- Is the Ca2+-ATPase from sarcoplasmic reticulum also a heat pump?, S. Kjelstrup; L. de Meis, D. Bedeaux, J.M. Simon, European Biophysics Journal 38 , 59 (2008).

A29- Thermal Diffusion and Partial Molar Enthalpy Variations of n-Butane in Silicalite-1, I. Inzoli; J.M. Simon, D. Bedeaux, S. Kjelstrup, J. Phys. Chem. B 112, 14937 (2008).

A30- Surface Adsorption Isotherms and Surface Excess Densities of n-Butane in Silicalite-1, I. Inzoli; J.M. Simon, S. Kjelstrup, Langmuir 25, 1518 (2009).

A31- Transport coefficients of n-butane into and through the surface of silicalite-1 from non-equilibrium molecular dynamics study., I. Inzoli, S. Kjelstrup, D. Bedeaux, J.-M. Simon, Micro. Meso. Mat., 125, 112 (2009), (papier invité).

A32- Heptane adsorption in silicalite-I: molecular  dynamics simulation, N. Floquet, J.M. Simon, J.P. Coulomb, J.P. Bellat, G. Weber, G. Andre, Micro. Meso. Mat. 122, 61 (2009)

A33-  Experimental IR study and ab initio modelling of ethylene adsorption in a MFI - type host zeolite N. Zvereva-Loëte , A. Ballandras, G. Weber, M. Rotger  , V. Boudon, J.-M. Simon, Mol. Phys. 107, 2081 (2009).

A34- Investigation of surface self-diffusion of hydrogen on PEM fuel cell catalyst support. O.-E. Haas, J.-M. Simon, S. Kjelstrup,  J. Phys Chem C.  113,  20281 (2009)

A35- Adsorption and Desorption of H2 on Graphite by Molecular Dynamics Simulations, J.-M. Simon, O.-E. Haas, S. Kjelstrup, J. Phys Chem C.  114,  10212 (2010)

A36- Thermodynamics properties of a liquid-vapor interface in a two-component system, I. Inzoli, , S. Kjelstrup, D. Bedeaux, J.-M. Simon, Chemical Engineering Science 65, 4105 (2010)

A37- Temperature at small scales: A lower limit for a thermodynamic description, J;-M. Simon, J. M. Rubi, J. Phys. Chem. B 115, 1422 (2011)

A38- Transfer coefficients for the liquid-vapor interface of a two component mixture, I. Inzoli, S. Kjelstrup, D. Bedeaux, J.-M. Simon, Chemical Engineering Science 66, 4533 (2011)

A39-  Thermodynamics of a small system in a μT reservoir, S. K. Schnell, T. J. H. Vlugt, J.-M. Simon, D. Bedeaux, S. Kjelstrup, Chem. Phys. Let. 504, 199 (2011)

A40- Calculating thermodynamic properties from fluctuations at small scales, S. K. Schnell, X. Liu, J.-M. Simon, A. Bardow, D. Bedeaux, T. J. H. Vlugt, S. Kjelstrup, J. Phys. Chem. B, 115, 10911 (2011)

A41- Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics, X. Liu, S. K. Schnell, J.-M. Simon, D. Bedeaux, S. Kjelstrup, A. Bardow, T. J. H. Vlugt, J. Phys. Chem. B, 115, 12921 (2011) + Correction J. Phys. Chem. B, 116, 6070 (2012)

A42- Thermodynamics of small systems embedded in a reservoir: a detailed analysis of finite size effects S. K. Schnell, T. J. H. Vlugt, J.-M. Simon, D. Bedeaux, S. Kjelstrup, Mol. Phys. 110, 1069 (2012)  (papier invité). S. Schnell a obtenu le prix du Journal Molecular Physics « early career researcher prize » pour cet article.

A43- Diffusion of oxygen in cork S. Lequin, D. Chassagne, T. Karbowiak, J.-M. Simon, C. Paulin, J.-P. Bellat, Journal of Agricultural and Food Chemistry 60, 3348 (2012)

A44-  Fick diffusion coefficients in ternary liquid systems from equilibrium molecular dynamics simulations, X. Liu, A. Martin-Calvo, E. McGarrity, S. K. Schnell, S. Calero, J.-M. Simon, D. Bedeaux, S. Kjelstrup, A. Bardow, T. J. H. Vlugt, Ind. Eng. Chem. Res. , 51, 10247 (2012)

A45- Kirkwood-Buff Integrals for Finite Volumes, P. Kruger, S. K. Schnell, D. Bedeaux, S. Kjelstrup, T. J. H. Vlugt, J.-M. Simon, J. Phys. Chem. Lett., 4, 235 (2013)

A46- Diffusion Coefficients from molecular dynamics in binary and ternary mixtures,  X. Liu, S. K. Schnell, J. M. Simon, P. Kruger, D. Bedeaux, S. Kjelstrup, A. Bardow, T. J. H. Vlugt, Int. J. of Thermophys, 34, 1169 (2013). (review paper)

A47- How to apply Kirkwood-buff theory of individual species in salt solutions, S. K. Schnell, P. Englebienne, J.-M. Simon, P. Kruger, S. P. Balayi, S. Kjelstrup, D. Bedeaux, A. Bardow, T. J. H. Vlugt, Chemical Physics Letters 582, 154 (2013).

A48- Adsorption and desorption surface dynamics of gaseous adsorbate on silicalite-1 by molecular dynamics simulation, J.-M. Simon, J.-P. Bellat, J. M. Salazar, invited paper in Molecular Simulation 40, 52 (2014).

A49- Equilibrium properties of the reaction H2=2H by classical molecular dynamics simulations, R. Skorpa, J.-M. Simon, D. Bedeaux, S. Kjelstrup, PCCP 16, 1227 (2014).

A50- Bridging scales with thermodynamics: From nano to macro, S. Kjelstrup, S. K. Schnell, T. J. H. Vlugt, J.-M. Simon, A. Bardow, D. Bedeaux, T.Trinh, Journal Advances in Natural Sciences: Nanoscience and Nanotechnology 5, 023002 (2014). (invited paper).

A51- Thermodynamic characterization of two layers of CO2 on a graphite surface, T.Trinh, D. Bedeaux, J.-M. Simon, S. Kjelstrup, Chem. Phys. Let.  612, 214 (2014)

A52- The reaction enthalpy of hydrogen dissociation calculated with the small system method from simulation of molecular fluctuations, R. Skorpa, J.-M. Simon, D. Bedeaux, S. Kjelstrup, PCCP 16, 19681 (2014).

A53- Diffusion of oxygen through cork stopper: is it a knudsen or a fickian mechanism? A. Lagorce-Tachon, T. Karboviak, J.-M. Simon, R. Gougeon, J.-P. Bellat, J. Agric. Food, 62, 9180 (2014)

A54- Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics
Simulation, S. K. Schnell, R. Skorpa, D. Bedeaux, S. Kjelstrup, T. J. H. Vlugt, J.-M. Simon, J. Chem. Phys. 141, 144501 (2014)

A55- Calculation of chemical potential and activity coefficient on two layers of CO2 adsorbed on a graphite surface, T.Trinh, D. Bedeaux, J.-M. Simon, S. Kjelstrup,  PCCP, 17, 1226 (2015).

A56- Characterization of adsorbed water in MIL-53(Al) by FTIR spectroscopy and ab-initio calculations, J.M. Salazar, G. Weber, J.-M. Simon, I. Berzerkhyy, J.-P. Bellat, JCP 2015, Vol 142 DOI: 10.1063/1.4914903

A57- A 32-70 K formation temperature range for the ice grains agglomerated by comet 67P/Churyumov-Gerasimenko. S. Lectez, J.-M. Simon, O. Mousis, S. Picaud, K. Altwegg, M. Rubin, J.M. Salazar, The Astrophysical Journal letters Vol 805/L1 (2015)

A58- Martian zeolites as a source of atmospheric methane, O. Mousis, J.-M. Simon, J.-P. Bellat, F. Schmidt, S. Bouley, E. Chassefière, V. Sautter, Y. Quesnel, S. Picaud, S. Lectez, Icarus 2016, DOI : 10.1016/j.icarus.2016.05.035

A59- Rebuttal to « Permeation of cork revisited », A. Lagorce-Tachon, T. Karboviak, J.-M. Simon, R. Gougeon, J.-P. Bellat, J. Agric. Food, 64, 4185 (2016)

A60- About the Role of the Bottleneck/Cork Interface on Oxygen Transfer, A. Lagorce-Tachon, T. Karboviak, C. Paulin, J.-M. Simon, R. Gougeon, J.-P. Bellat, J. Agric. Food, 64, 6672 (2016)

A61- Dynamic Self-assembly of Non-Brownian Spheres,  M. Salazar, J.-M. Simon, J. C. Ruiz-Suárez, F. Peñuñuri, O. Carvente,  EPJ web of Conferences, 140, 4001 (2017) .

A62- Size and shape effects on thermodynamic properties of nanoscale volumes of water, B. Strøm, J.-M. Simon, S. K. Schnell, S. Kjelstrup, J. He, D. Bedeaux, PCCP, 19, 9016 (2017).

A63- Adsorption of hydrogen isotopes in the zeolite NaX: Experiments and simulations, JM Salazar, S Lectez, C Gauvin, M Macaud, JP Bellat, G Weber, I Bezverkhyy, JM Simon, Int. J. Hydrogen Energy, 42,  13099 (2017)

A64- Finite-size effects of Kirkwood–Buff integrals from molecular simulations, N Dawass, P Krüger, SK Schnell, D Bedeaux, S Kjelstrup, JM Simon, TJH Vlugt, Mol. Sim. in press. (2017) DOI: 10.1080/08927022.2017.1416114

A65- Kirkwood–Buff integrals of finite systems: shape effects, N. Dawass, P. Krüger, J.M. Simon, T. JH Vlugt, Mol.phys. in press (2018)  DOI:10.1080/00268976.2018.1434908

A66- Contribution of image processing for analyzing the cellular structure of cork, A. Lagorce‐Tachon, F. Mairesse, T. Karbowiak, R. D Gougeon, J.P. Bellat, T. Sliwa, J.-M. Simon, J. Chemometrics in press (2018) DOI: 10.1002/cem.2988


  • Chimie générale, physico chimie, thermodynamique (L1-L3, M1), simulation moléculaire (M2)


  • Depuis 2012 : responsable pédagogique du MASTER-2 QESIS  (plus de 30 élèves chaque année en contrat de professionalisation).
  • Depuis 2012: Membre élu du Conseil National des Universités (31ème section).  
  • Depuis 2014: Membre élu du conseil scientifique du laboratoire LICB


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Université de Bourgogne