DOI

1

Carbon membranes for efficient water-ethanol separation - Gravelle, Simon and Yoshida, Hiroaki and Joly, Laurent and Ybert, Christophe and Bocquet, Lyderic

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : We demonstrate, on the basis of molecular dynamics simulations, the possibility of an efficient water-ethanol separation using nanoporous carbon membranes, namely, carbon nanotube membranes, nanoporous graphene sheets, and multilayer graphene membranes. While these carbon membranes are in general permeable to both pure liquids, they exhibit a counter-intuitive ``self-semi-permeability'' to water in the presence of water-ethanol mixtures. This originates in a preferred ethanol adsorption in nanoconfinement that prevents water molecules from entering the carbon nanopores. An osmotic pressure is accordingly expressed across the carbon membranes for the water-ethanol mixture, which agrees with the classic van't Hoff type expression. This suggests a robust and versatile membrane-based separation, built on a pressure-driven reverse-osmosis process across these carbon-based membranes. In particular, the recent development of large-scale ``graphene-oxide'' like membranes then opens an avenue for a versatile and efficient ethanol dehydration using this separation process, with possible application for bio-ethanol fabrication. Published by AIP Publishing.

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : We demonstrate, on the basis of molecular dynamics simulations, the possibility of an efficient water-ethanol separation using nanoporous carbon membranes, namely, carbon nanotube membranes, nanoporous graphene sheets, and multilayer graphene membranes. While these carbon membranes are in general permeable to both pure liquids, they exhibit a counter-intuitive ``self-semi-permeability'' to water in the presence of water-ethanol mixtures. This originates in a preferred ethanol adsorption in nanoconfinement that prevents water molecules from entering the carbon nanopores. An osmotic pressure is accordingly expressed across the carbon membranes for the water-ethanol mixture, which agrees with the classic van't Hoff type expression. This suggests a robust and versatile membrane-based separation, built on a pressure-driven reverse-osmosis process across these carbon-based membranes. In particular, the recent development of large-scale ``graphene-oxide'' like membranes then opens an avenue for a versatile and efficient ethanol dehydration using this separation process, with possible application for bio-ethanol fabrication. Published by AIP Publishing.

DOI

2

Miming the cancer-immune system competition by kinetic Monte Carlo simulations - Bianca, Carlo and Lemarchand, Annie

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance. Published by AIP Publishing.

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : In order to mimic the interactions between cancer and the immune system at cell scale, we propose a minimal model of cell interactions that is similar to a chemical mechanism including autocatalytic steps. The cells are supposed to bear a quantity called activity that may increase during the interactions. The fluctuations of cell activity are controlled by a so-called thermostat. We develop a kinetic Monte Carlo algorithm to simulate the cell interactions and thermalization of cell activity. The model is able to reproduce the well-known behavior of tumors treated by immunotherapy: the first apparent elimination of the tumor by the immune system is followed by a long equilibrium period and the final escape of cancer from immunosurveillance. Published by AIP Publishing.

DOI

3

Direct coevolutionary couplings reflect biophysical residue interactions in proteins - Coucke, Alice and Uguzzoni, Guido and Oteri, Francesco and Cocco, Simona and Monasson, Remi and Weigt, Martin

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.

JOURNAL OF CHEMICAL PHYSICS 145, (2016)

Abstract : Coevolution of residues in contact imposes strong statistical constraints on the sequence variability between homologous proteins. Direct-Coupling Analysis (DCA), a global statistical inference method, successfully models this variability across homologous protein families to infer structural information about proteins. For each residue pair, DCA infers 21 x 21 matrices describing the coevolutionary coupling for each pair of amino acids (or gaps). To achieve the residue-residue contact prediction, these matrices are mapped onto simple scalar parameters; the full information they contain gets lost. Here, we perform a detailed spectral analysis of the coupling matrices resulting from 70 protein families, to show that they contain quantitative information about the physico-chemical properties of amino-acid interactions. Results for protein families are corroborated by the analysis of synthetic data from lattice-protein models, which emphasizes the critical effect of sampling quality and regularization on the biochemical features of the statistical coupling matrices. Published by AIP Publishing.

DOI

4

Hard-sphere melting and crystallization with event-chain Monte Carlo - Isobe, Masaharu and Krauth, Werner

JOURNAL OF CHEMICAL PHYSICS 143, (2015)

Abstract : We simulate crystallization and melting with local Monte Carlo (LMC), with event-chain Monte Carlo (ECMC), and with event-driven molecular dynamics (EDMD) in systems with up to one million three-dimensional hard spheres. We illustrate that our implementations of the three algorithms rigorously coincide in their equilibrium properties. We then study nucleation in the NVE ensemble from the fcc crystal into the homogeneous liquid phase and from the liquid into the homogeneous crystal. ECMC and EDMD both approach equilibrium orders of magnitude faster than LMC. ECMC is also notably faster than EDMD, especially for the equilibration into a crystal from a disordered initial condition at high density. ECMC can be trivially implemented for hard-sphere and for soft-sphere potentials, and we suggest possible applications of this algorithm for studying jamming and the physics of glasses, as well as disordered systems. (C) 2015 AIP Publishing LLC.

JOURNAL OF CHEMICAL PHYSICS 143, (2015)

Abstract : We simulate crystallization and melting with local Monte Carlo (LMC), with event-chain Monte Carlo (ECMC), and with event-driven molecular dynamics (EDMD) in systems with up to one million three-dimensional hard spheres. We illustrate that our implementations of the three algorithms rigorously coincide in their equilibrium properties. We then study nucleation in the NVE ensemble from the fcc crystal into the homogeneous liquid phase and from the liquid into the homogeneous crystal. ECMC and EDMD both approach equilibrium orders of magnitude faster than LMC. ECMC is also notably faster than EDMD, especially for the equilibration into a crystal from a disordered initial condition at high density. ECMC can be trivially implemented for hard-sphere and for soft-sphere potentials, and we suggest possible applications of this algorithm for studying jamming and the physics of glasses, as well as disordered systems. (C) 2015 AIP Publishing LLC.

DOI

5

Generalized event-chain Monte Carlo: Constructing rejection-free global-balance algorithms from infinitesimal steps - Michel, Manon and Kapfer, Sebastian C. and Krauth, Werner

JOURNAL OF CHEMICAL PHYSICS 140, (2014)

Abstract : In this article, we present an event-driven algorithm that generalizes the recent hard-sphere event-chain Monte Carlo method without introducing discretizations in time or in space. A factorization of the Metropolis filter and the concept of infinitesimal Monte Carlo moves are used to design a rejection-free Markov-chain Monte Carlo algorithm for particle systems with arbitrary pairwise interactions. The algorithm breaks detailed balance, but satisfies maximal global balance and performs better than the classic, local Metropolis algorithm in large systems. The new algorithm generates a continuum of samples of the stationary probability density. This allows us to compute the pressure and stress tensor as a byproduct of the simulation without any additional computations. (C) 2014 AIP Publishing LLC.

JOURNAL OF CHEMICAL PHYSICS 140, (2014)

Abstract : In this article, we present an event-driven algorithm that generalizes the recent hard-sphere event-chain Monte Carlo method without introducing discretizations in time or in space. A factorization of the Metropolis filter and the concept of infinitesimal Monte Carlo moves are used to design a rejection-free Markov-chain Monte Carlo algorithm for particle systems with arbitrary pairwise interactions. The algorithm breaks detailed balance, but satisfies maximal global balance and performs better than the classic, local Metropolis algorithm in large systems. The new algorithm generates a continuum of samples of the stationary probability density. This allows us to compute the pressure and stress tensor as a byproduct of the simulation without any additional computations. (C) 2014 AIP Publishing LLC.

DOI

6

Equation of state of water under negative pressure - Davitt, Kristina and Rolley, Etienne and Caupin, Frederic and Arvengas, Arnaud and Balibar, Sebastien

JOURNAL OF CHEMICAL PHYSICS 133, (2010)

Abstract : We report on the simultaneous measurements of the speed of sound and the density in liquid water under negative pressure. Application of a focused acoustic wave to the bulk liquid is able to generate negative pressures before nucleation of the vapor phase occurs. A method for time-resolved Brillouin scattering is developed to measure the speed of sound during the passage of a 1 MHz ultrasonic wave. This is coupled with a fiber optic probe hydrophone which allows the determination of the density. Together, these methods give an ambient temperature equation of state of metastable liquid water down to the acoustic cavitation threshold. Empirical equations of state of water are based on experimental data at positive pressure; the validity of their extrapolation to negative pressures had been tested only indirectly or with very weakly metastable liquid. We provide thermodynamic data that prove the fidelity of recent equations of state down to -26 MPa. However, this raises questions regarding the nature of the cavitation threshold observed in acoustic experiments, which is far less negative than expected. (C) 2010 American Institute of Physics. [doi:10.1063/1.3495971]

JOURNAL OF CHEMICAL PHYSICS 133, (2010)

Abstract : We report on the simultaneous measurements of the speed of sound and the density in liquid water under negative pressure. Application of a focused acoustic wave to the bulk liquid is able to generate negative pressures before nucleation of the vapor phase occurs. A method for time-resolved Brillouin scattering is developed to measure the speed of sound during the passage of a 1 MHz ultrasonic wave. This is coupled with a fiber optic probe hydrophone which allows the determination of the density. Together, these methods give an ambient temperature equation of state of metastable liquid water down to the acoustic cavitation threshold. Empirical equations of state of water are based on experimental data at positive pressure; the validity of their extrapolation to negative pressures had been tested only indirectly or with very weakly metastable liquid. We provide thermodynamic data that prove the fidelity of recent equations of state down to -26 MPa. However, this raises questions regarding the nature of the cavitation threshold observed in acoustic experiments, which is far less negative than expected. (C) 2010 American Institute of Physics. [doi:10.1063/1.3495971]

DOI

7

Force spectroscopy of a single artificial biomolecule bond: The Kramers' high-barrier limit holds close to the critical force - Husson, J. and Dogterom, M. and Pincet, F.

JOURNAL OF CHEMICAL PHYSICS 130, (2009)

Abstract : We use a minimal system with a single micron-size bead trapped with optical tweezers to investigate the kinetics of escape under force. Surprisingly, the exponential decay of the off rate with the barrier energy is still valid close to the critical force. Hence, the high viscosity approximation derived by Kramers in the case of a high energy barrier holds even for an energy barrier close to the thermal energy. Several recent models describe a single biomolecule bond by a smooth single-barrier energy profile. When this approach is accurate enough, our result justifies the use of Kramers' approximation in the high-force regime, close to the critical force of the system, as done in recent single biomolecule bond studies.

JOURNAL OF CHEMICAL PHYSICS 130, (2009)

Abstract : We use a minimal system with a single micron-size bead trapped with optical tweezers to investigate the kinetics of escape under force. Surprisingly, the exponential decay of the off rate with the barrier energy is still valid close to the critical force. Hence, the high viscosity approximation derived by Kramers in the case of a high energy barrier holds even for an energy barrier close to the thermal energy. Several recent models describe a single biomolecule bond by a smooth single-barrier energy profile. When this approach is accurate enough, our result justifies the use of Kramers' approximation in the high-force regime, close to the critical force of the system, as done in recent single biomolecule bond studies.

DOI

8

Solution of the Percus-Yevick equation for hard disks - Adda-Bedia, M. and Katzav, E. and Vella, D.

JOURNAL OF CHEMICAL PHYSICS 128, (2008)

Abstract : The authors solve the Percus-Yevick equation in two dimensions by reducing it to a set of simple integral equations. They numerically obtain both the pair correlation function and the equation of state for a hard disk fluid and find good agreement with available Monte Carlo results. The present method of resolution may be generalized to any even dimension. (C) 2008 American Institute of Physics.

JOURNAL OF CHEMICAL PHYSICS 128, (2008)

Abstract : The authors solve the Percus-Yevick equation in two dimensions by reducing it to a set of simple integral equations. They numerically obtain both the pair correlation function and the equation of state for a hard disk fluid and find good agreement with available Monte Carlo results. The present method of resolution may be generalized to any even dimension. (C) 2008 American Institute of Physics.

DOI

9

Solution of the Percus-Yevick equation for hard disks (vol 128, art no 184508, 2008) - Adda-Bedia, M. and Katzav, E. and Vella, D.

JOURNAL OF CHEMICAL PHYSICS 129, (2008)

JOURNAL OF CHEMICAL PHYSICS 129, (2008)

DOI

10

Solution of the Percus-Yevick equation for hard hyperspheres in even dimensions - Adda-Bedia, M. and Katzav, E. and Vella, D.

JOURNAL OF CHEMICAL PHYSICS 129, (2008)

Abstract : We solve the Percus-Yevick equation in even dimensions by reducing it to a set of simple integrodifferential equations. This work generalizes an approach we developed previously for hard disks. We numerically obtain both the pair correlation function and the virial coefficients for a fluid of hyperspheres in dimensions d = 4, 6, and 8, and find good agreement with the available exact results and Monte Carlo simulations. This paper confirms the alternating character of the virial series for d >= 6 and provides the first evidence for an alternating character for d = 4. Moreover, we show that this sign alternation is due to the existence of a branch point on the negative real axis. It is this branch point that determines the radius of convergence of the virial series, whose value we determine explicitly for d = 4, 6, 8. Our results complement, and are consistent with, a recent study in odd dimensions [R. D. Rohrmann et al., J. Chem. Phys. 129, 014510 (2008)]. (C) 2008 American Institute of Physics.

JOURNAL OF CHEMICAL PHYSICS 129, (2008)

Abstract : We solve the Percus-Yevick equation in even dimensions by reducing it to a set of simple integrodifferential equations. This work generalizes an approach we developed previously for hard disks. We numerically obtain both the pair correlation function and the virial coefficients for a fluid of hyperspheres in dimensions d = 4, 6, and 8, and find good agreement with the available exact results and Monte Carlo simulations. This paper confirms the alternating character of the virial series for d >= 6 and provides the first evidence for an alternating character for d = 4. Moreover, we show that this sign alternation is due to the existence of a branch point on the negative real axis. It is this branch point that determines the radius of convergence of the virial series, whose value we determine explicitly for d = 4, 6, 8. Our results complement, and are consistent with, a recent study in odd dimensions [R. D. Rohrmann et al., J. Chem. Phys. 129, 014510 (2008)]. (C) 2008 American Institute of Physics.