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129 results on '"Borgis, D."'

1. Solvation in atomic liquids: connection between Gaussian field theory and density functional theory

Author

Sergiievskyi, V., Levesque, M., Rotenberg, B., and Borgis, D.

Subjects
Physics - Chemical Physics, Condensed Matter - Statistical Mechanics
Abstract

For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core --- indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional., Comment: 14 pages, 4 figures

Published
2017
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4. Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments

Author

Marinica, D.C., Gregoire, G., Desfrancois, C., Schermann, J.P., Borgis, D., and Gaigeot, M.P.

Subjects
Alanine -- Chemical properties, Molecular dynamics -- Analysis, Dissociation -- Analysis, Chemicals, plastics and rubber industries
Abstract

Density functional theory-based Car-Parrinello molecular dynamics is presented at 300 K of the gas-phased ionized Ala-Ala-[H.sup.+] peptide in trans and cis form in accordance with the IR-MPD experimental studies conducted. The experimental IR-MPD spectrum was found to be in excellent agreement in terms of band positions, band shapes and bandwidth.

Published
2006

5. Computing thermal Wigner densities with the phase integration method.

Author

Beutier, J., Borgis, D., Vuilleumier, R., and Bonella, S.

Subjects
*THERMAL analysis, *WIGNER distribution, *PHASE transitions, *MATHEMATICAL models, *MONTE Carlo method, *ALGORITHMS, *PATH integrals
Abstract

We discuss how the Phase Integration Method (PIM), recently developed to compute symmetrized time correlation functions [M. Monteferrante, S. Bonella, and G. Ciccotti, Mol. Phys. 109, 3015 (2011)], can be adapted to sampling/generating the thermal Wigner density, a key ingredient, for example, in many approximate schemes for simulating quantum time dependent properties. PIM combines a path integral representation of the density with a cumulant expansion to represent the Wigner function in a form calculable via existing Monte Carlo algorithms for sampling noisy probability densities. The method is able to capture highly non-classical effects such as correlation among the momenta and coordinates parts of the density, or correlations among the momenta themselves. By using alternatives to cumulants, it can also indicate the presence of negative parts of the Wigner density. Both properties are demonstrated by comparing PIM results to those of reference quantum calculations on a set of model problems. [ABSTRACT FROM AUTHOR]

Published
2014
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8. Extracting effective normal modes from equilibrium dynamics at finite temperature.

Author

Martinez, M., Gaigeot, M.-P., Borgis, D., and Vuilleumier, R.

Subjects
THERMODYNAMIC equilibrium, URACIL, DENSITY functionals, FOURIER transforms, MOLECULAR dynamics, THERMODYNAMICS
Abstract

A general method for obtaining effective normal modes of a molecular system from molecular dynamics simulations is presented. The method is based on a localization criterion for the Fourier transformed velocity time-correlation functions of the effective modes. For a given choice of the localization function used, the method becomes equivalent to the principal mode analysis (PMA) based on covariance matrix diagonalization. On the other hand, a proper choice of the localization function leads to a novel method with a strong analogy with the usual normal mode analysis of equilibrium structures, where the Hessian system at the minimum energy structure is replaced by the thermal averaged Hessian, although the Hessian itself is never actually calculated. This method does not introduce any extra numerical cost during the simulation and bears the same simplicity as PMA itself. It can thus be readily applied to ab initio molecular dynamics simulations. Three such examples are provided here. First we recover effective normal modes of an isolated formaldehyde molecule computed at 20 K in very good agreement with the results of a normal mode analysis performed at its equilibrium structure. We then illustrate the applicability of the method for liquid phase studies. The effective normal modes of a water molecule in liquid water and of a uracil molecule in aqueous solution can be extracted from ab initio molecular dynamics simulations of these two systems at 300 K. [ABSTRACT FROM AUTHOR]

Published
2006
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12. A quantum molecular-dynamics study of proton-transfer reactions along asymmetrical H bonds in solution.

Author

Azzouz, H. and Borgis, D.

Subjects
*QUANTUM theory, *PROTON transfer reactions, *CHEMICAL bonds, *ANALYTICAL mechanics
Abstract

A molecular-dynamics study of a model for AH-B⇌A--H+B reactions in liquid chloromethane is presented. The parameters of the model are fitted to those of typical OH–N proton-transfer complexes. The rate constant is computed at a quantum level for complexes of various H-bond strength and A-B equilibrium distance. The influence of the properties of the complex on the proton-transfer mechanism is outlined. Also the static and dynamical role of the solvent, the tunneling contribution to the rate, and the associated kinetic isotope effect are discussed. The rate calculations are based on two independent methods. First a curve-crossing, transition-state rate formula which, although related to standard charge-transfer theories, presents some original features and allows the determination of the rate at very low computational cost is developed. The curve-crossing results are compared to those of a path-integral, quantum transition-state calculation. The overall agreement between the two methods is satisfactory, although there is a discrepancy in the adiabatic reaction regime; a rigorous estimation of the transmission coefficients would be needed then. Finally, it is shown that zero-point energy and parabolic barrier tunneling factors added to the classical transition-state-theory rate constant are unable to describe properly the quantum effects in the present case. [ABSTRACT FROM AUTHOR]

Published
1993
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13. An adiabatic dynamical simulation study of the Zundel polarization of strongly H-bonded complexes in solution.

Author

Borgis, D., Tarjus, G., and Azzouz, H.

Subjects
*CHEMICAL bonds, *QUANTUM theory, *HYDROGEN, *SOLUTION (Chemistry)
Abstract

We study, by an adiabatic dynamical simulation technique, a mixed classical-quantum model for strongly H-bonded complexes in polar solvents. The solvent influence on the adiabatic proton dynamics is interpreted in terms of a protonic polarization effect, usually referred to as the Zundel polarization. The relation to the solvent-induced proton transfer and the consequences on the broadening of the infrared absorption spectrum are discussed. We show that for increasing solvent-complex coupling, the system passes from an ‘‘oscillatory’’ to a ‘‘reactive’’ behavior, whereas the Zundel polarization passes from a familiar electronic-like regime to a saturated regime. In the latter case, a large band broadening, comparable to experimental observations, is obtained in the calculated infrared spectrum. [ABSTRACT FROM AUTHOR]

Published
1992
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14. Raman spectroscopy of fast pre-reactive, reactive, and post-reactive molecular motions in liquids.

Author

Viot, P., Tarjus, G., Borgis, D., and Bratos, S.

Subjects
RAMAN spectroscopy, LIQUIDS
Abstract

A theory is presented to study the effect on the isotropic Raman spectra of pre-reactive, reactive, and post-reactive molecular motions in the case of fast conformational changes. The reaction dynamics is pictured as a diffusion along the reaction coordinate and is supposed to obey a one-dimensional Smoluchowski equation. The resulting correlation functions exhibit several modes, some of which are generated by pre-reactive and post-reactive processes. Their spectral manifestation is studied in detail. [ABSTRACT FROM AUTHOR]

Published
1989
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17. Physicochimie : molécules, milieux

Author

Hapiot, Philippe, Abdelmoula, Mustapha, Assfeld, Xavier, Aupiais, Jean, Baaden, Marc, Bergamini, Jean-Francois, Bertani, Philippe, Borgis, D., Combellas, Catherine, Cotte, Marine, Eisenstein, Odile, Guillaume, François, Legube, Bernard, Lojou, Elisabeth, Markovitsi, Dimitra, Marquette, Arnaud, Maurel, François, Nakatani, Keitaro, Pereira-Ramos, Jean Pierre, Walcarius, Alain, Wortham, Henri, and Baaden, Marc

Subjects
chimie pour l'environnement, radiochimie, photochimie, électrochimie, [CHIM] Chemical Sciences, spectroscopies, chimie analytique, résonances magnétiques, chimie théorique, spectroscopie de masse
Abstract

Comme indiqué dans son intitulé, le domaine d’expertise de la section 13 est celui de la physico-chimie, discipline frontière par excellence. Il ressort que les thématiques abordées dans ce rapport de conjoncture couvrent de larges domaines disciplinaires. Nous nous promènerons donc de la chimie théorique, aux spectroscopies, à l’électrochimie et la photo-chimie, jusqu’aux sciences analytiques et leurs applications vers l’environnement ou le patrimoine. On retrouve au centre de ces activités, la modélisation (un des piliers de la section 13) et le besoin constant de développer de nouvelles méthodologies en rapport avec les avancées récentes. Cette diversité thématique explique la longueur un peu hors norme de ce document.

Published
2010

18. Physicochimie : molécules, milieux: Rapport 2010 de conjoncture du Comité National de la Recherche Scientifique

Author

Philippe Hapiot, Mustapha Abdelmoula, Xavier Assfeld, Jean Aupiais, Marc Baaden, Jean-Francois Bergamini, Philippe Bertani, Borgis, D., Catherine Combellas, Marine Cotte, Odile Eisenstein, François Guillaume, Bernard Legube, Elisabeth Lojou, Dimitra Markovitsi, Arnaud Marquette, François Maurel, Keitaro Nakatani, Jean Pierre Pereira-Ramos, Alain Walcarius, Henri Wortham, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université Henri Poincaré - Nancy 1 (UHP), Laboratoire de Physique et Chimie Théoriques (LPCT), Institut de Chimie du CNRS (INC)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), DAM Île-de-France (DAM/DIF), Direction des Applications Militaires (DAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de biochimie théorique [Paris] (LBT (UPR_9080)), Institut de biologie physico-chimique (IBPC (FR_550)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Strasbourg (UNISTRA), Analyse et environnement (LAE), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Interfaces, Traitements, Organisation et Dynamique des Systèmes (ITODYS (UMR_7086)), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Université Paris Cité (UPCité), European Synchrotron Radiation Facility (ESRF), Laboratoire d'Archéologie Moléculaire et Structurale (LAMS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut Charles Gerhardt Montpellier - Institut de Chimie Moléculaire et des Matériaux de Montpellier (ICGM), Ecole Nationale Supérieure de Chimie de Montpellier (ENSCM)-Institut de Chimie du CNRS (INC)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Moléculaires (ISM), Université Montesquieu - Bordeaux 4-Université Sciences et Technologies - Bordeaux 1 (UB)-École Nationale Supérieure de Chimie et de Physique de Bordeaux (ENSCPB)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Chimie de l'eau et traitement de l'eau, Institut de Chimie des Milieux et Matériaux de Poitiers (IC2MP), Université de Poitiers-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université de Poitiers-Institut national des sciences de l'Univers (INSU - CNRS)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Francis PERRIN (LFP - URA 2453), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Service des Photons, Atomes et Molécules (SPAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Photophysique et Photochimie Supramoléculaires et Macromoléculaires (PPSM), École normale supérieure - Cachan (ENS Cachan)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie et des Matériaux Paris-Est (ICMPE), Institut de Chimie du CNRS (INC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie Physique et Microbiologie pour l'Environnement (LCPME), Laboratoire Chimie de l'environnement (LCE), and Aix Marseille Université (AMU)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
chimie pour l'environnement, radiochimie, photochimie, électrochimie, spectroscopies, [CHIM]Chemical Sciences, chimie analytique, résonances magnétiques, chimie théorique, spectroscopie de masse
Abstract

International audience; Comme indiqué dans son intitulé, le domaine d’expertise de la section 13 est celui de la physico-chimie, discipline frontière par excellence. Il ressort que les thématiques abordées dans ce rapport de conjoncture couvrent de larges domaines disciplinaires. Nous nous promènerons donc de la chimie théorique, aux spectroscopies, à l’électrochimie et la photo-chimie, jusqu’aux sciences analytiques et leurs applications vers l’environnement ou le patrimoine. On retrouve au centre de ces activités, la modélisation (un des piliers de la section 13) et le besoin constant de développer de nouvelles méthodologies en rapport avec les avancées récentes. Cette diversité thématique explique la longueur un peu hors norme de ce document.

Published
2010

20. Coarse grained models of solvent and proteins

Author

Borgis, D., Analyse et environnement (LAE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

Conférence du 4 au 6 Décembre 2005. Communication par affiche.

Published
2005

21. De la phase gazeuse à la phase liquide

Author

Borgis, D., Analyse et environnement (LAE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

Conférence du 28 Août au 2 Septembre 2005. Communication par affiche.

Published
2005

22. Dynamique moléculaire: explorer un ensemble thermodynamique avec des trajectoires

Author

Borgis, D., Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (LAMBE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

Conférence du 6 au 10 Juin 2005. Communication par affiche.

Published
2005

23. Quantized time correlation function approach to nonadiabatic decay rates in condensed phase: Application to solvated electrons in water and in methanol

Author

Borgis, D., Analyse et environnement (LAE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

Conférence du 18 au 20 Mai 2005. Communication par affiche.

Published
2005

24. Quantized time correlation function approach to nonadiabatic decay rates in condensed phase

Author

Borgis, D., Analyse et environnement (LAE), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph]
Abstract

Conférence du 14 au 16 mars 2005. Communication par affiche.

Published
2005

37. Wavefunction quantization of the proton motion in a H5O2+dimer solvated in liquid water

Author

Vuilleumier, R. and Borgis, D.

Abstract

The infrared spectroscopy of the transient H5O2+species in liquid water is studied. The potential energy surface of the system is modeled by a two-state Empirical Valence Bond (EVB) model. The quantization of the central proton of the dimer H5O2+is described by a three-dimensional time-dependent gaussian wavefunction within an adiabatic molecular dynamics simulation, or by using an effective parameterization of the EVB model, using a preliminary path-integral calculation. It is shown that the H5O2+complex in solution displays a strong absorption between 1000 and 2000cm−1. We demonstrate that the contribution of the asymmetric O–H+stretch cannot be unambiguously assigned, due to its close coupling to the other modes of the dimer. The oxygen–oxygen stretching mode of the dimer strongly modulates the infrared spectrum of the central proton while the effect of the solvent is mainly to induce an asymmetry of the central O–H–O+bond of H5O2+leading, partly, to absorption at higher frequencies.

Published
2000
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38. Quantum Dynamics of an Excess Proton in Water Using an Extended Empirical Valence-Bond Hamiltonian

Author

Vuilleumier, R. and Borgis, D.

Abstract

The classical and quantum dynamics of an excess proton in water is studied by molecular dynamics simulations. The electronic structure of the system is described by an extended multistate valence-bond Hamiltonian that allows for the breaking and formation of O−H+ bonds. The proton quantum character is treated by means of an effective (path-integral) proton-transfer surface. Whereas classical simulations predict that the hydrated proton appears in a mixture of %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% and %@mt;sys@%H%@sb@%9%@sbx@%O%@sx@%4%@be@%+%@sxx@%%@mx@% structures, inclusion of proton quantization leads to the prevalence of %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% . The proton-transfer mechanism can be described mostly as the translocation of a transient %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% structure across the water hydrogen-bond network. The computed lifetime of a particular %@mt;sys@%H%@sb@%5%@sbx@%O%@sx@%2%@be@%+%@sxx@%%@mx@% is close to 2 ps, a value compatible with experimental estimates.

Published
1998

49. Properties and characterization of materials

Author

Salanne, M., Celino, M., Borgis, D., Jeanmairet, G., Walker, A., Aeberhard, U., Giusepponi, S., and Gusso, M.

Subjects
surface systems / generation, geothermal energy
Abstract

Development of characterization methods and tools to address structural, electronic and optical properties of materials from the atomic-scale models. Characterization procedures to assess the reliability of the numerical models. Application of MDFT code to supercapacitor materials screening. Coupling of codes to increase accurateness of the computed properties. Modeling of materials at different lenght scales. Description of applications via continuous models. Model settings to design large scale simulations to address accurately macroscopic properties., H2020

Published
2018
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50. Optimization Of Methods

Author

Deutsch, T., Celino, M., Duchemin, I., Salanne, Borgis, D., Walker, U., Aeberhard, U., Giusepponi, S., and Gusso, M.

Subjects
geothermal energy, non technical
Abstract

Optimization of all numerical codes ported in the infrastructure and used for supercapacitors, PV and batteries. The scope of deliverable D3.2 is to report the new advances in the field of materials for energy that comes from the search of new methodologies and models that could be more efficient on the new generation of computer hardware for exascale. In this respect, deliverable D3.2 is a transversal deliverable that report the new advances related to activities described in task T3.2, T3.3 and T3.4., H2020

Published
2017
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