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1

A simple polarizable model of water based on classical Drude oscillators

Lamoureux, Guillaume, MacKerell, Alexander D., Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 581 KB

english, 2003

2

Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions

Luo, Yun, Roux, Benoît

Journal:

The Journal of Physical Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 2.49 MB

english, 2010

3

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

Deng, Yuqing, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 380 KB

english, 2008

4

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

Yu, Haibo, Whitfield, Troy W., Harder, Edward, Lamoureux, Guillaume, Vorobyov, Igor, Anisimov, Victor M., MacKerell, Alexander D., Roux, Benoît

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 1.07 MB

english, 2010

5

Rate constants in quantum mechanical systems: A rigorous and practical path-integral formulation for computer simulations

Nilmadhab Chakrabarti, Tucker Carrington Jr, Benoı̂t Roux

Journal:

Chemical Physics Letters

Year:

1998

Language:

english

File:

PDF, 167 KB

english, 1998

6

Extension to the weighted histogram analysis method: combining umbrella sampling with free energy calculations

Marc Souaille, Benoı̂t Roux

Journal:

Computer Physics Communications

Year:

2001

Language:

english

File:

PDF, 198 KB

english, 2001

7

Optimized atomic radii for protein continuum electrostatics solvation forces

Mafalda Nina, Wonpil Im, Benoı̂t Roux

Journal:

Biophysical Chemistry

Year:

1999

Language:

english

File:

PDF, 113 KB

english, 1999

8

Implicit solvent models

Benoı̂t Roux, Thomas Simonson

Journal:

Biophysical Chemistry

Year:

1999

Language:

english

File:

PDF, 211 KB

english, 1999

9

Computations of Standard Binding Free Energies with Molecular Dynamics Simulations

Deng, Yuqing, Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 512 KB

english, 2009

10

Solvation of complex molecules in a polar liquid: An integral equation theory

Beglov, Dmitrii, Roux, Benoi^t

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 535 KB

english, 1996

11

Molecular Basis of Proton Blockage in Aquaporins

Nilmadhab Chakrabarti, Emad Tajkhorshid, Benoı̂t Roux, Régis Pomès

Journal:

Year:

2004

Language:

english

File:

PDF, 353 KB

english, 2004

12

Theoretical and computational models of ion channels

Journal:

Current Opinion in Structural Biology

Year:

2002

Language:

english

File:

PDF, 94 KB

english, 2002

13

On the origin of the electrostatic potential difference at a liquid-vacuum interface

Harder, Edward, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 219 KB

english, 2008

14

Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics

Jiang, Wei, Hodoscek, Milan, Roux, Benoît

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 256 KB

english, 2009

15

Electrostatics of Ion Stabilization in a ClC Chloride Channel Homologue from Escherichia coli

José D. Faraldo-Gómez, Benoı̂t Roux

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 3.13 MB

english, 2004

16

Critical assessment of a proposed model of Shaker

Muriel Lainé, Diane M Papazian, Benoı̂t Roux

Journal:

Year:

2004

Language:

english

File:

PDF, 529 KB

english, 2004

17

Ions and Counterions in a Biological Channel: A Molecular Dynamics Simulation of OmpF Porin from Escherichia coli in an Explicit Membrane with 1 M KCl Aqueous Salt Solution

Wonpil Im, Benoı̂t Roux

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.49 MB

english, 2002

18

Ion Permeation and Selectivity of OmpF Porin: A Theoretical Study Based on Molecular Dynamics, Brownian Dynamics, and Continuum Electrodiffusion Theory

Wonpil Im, Benoı̂t Roux

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 2.49 MB

english, 2002

19

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations

Jiang, Wei, Roux, Benoît

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 2.59 MB

english, 2010

20

CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application

Jo, Sunhwan, Jiang, Wei, Lee, Hui Sun, Roux, Benoı̂t, Im, Wonpil

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 883 KB

english, 2013

21

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

Jiang, Wei, Hardy, David J., Phillips, James C., MacKerell, Alexander D., Schulten, Klaus, Roux, Benoît

Journal:

The Journal of Physical Chemistry Letters

Year:

2011

Language:

english

File:

PDF, 737 KB

english, 2011

22

The Solvation Structure of Na + and K + in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations

Rowley, Christopher N., Roux, Benoı̂t

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 356 KB

english, 2012

23

Six-site polarizable model of water based on the classical Drude oscillator

Yu, Wenbo, Lopes, Pedro E. M., Roux, Benoı̂t, MacKerell, Alexander D.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 960 KB

english, 2013

24

On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method

Roux, Benoı̂t, Weare, Jonathan

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 501 KB

english, 2013

25

Molecular Dynamics Study of a Polymeric Reverse Osmosis Membrane

Harder, Edward, Walters, D. Eric, Bodnar, Yaroslav D., Faibish, Ron S., Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 2.55 MB

english, 2009

26

Self-Learning Adaptive Umbrella Sampling Method for the Determination of Free Energy Landscapes in Multiple Dimensions

Wojtas-Niziurski, Wojciech, Meng, Yilin, Roux, Benoı̂t, Bernèche, Simon

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.10 MB

english, 2013

27

Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm

Lamoureux, Guillaume, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 481 KB

english, 2003

28

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

Lin, Bin, Lopes, Pedro E. M., Roux, Benoı̂t, MacKerell, Alexander D.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.27 MB

english, 2013

29

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

Baker, Christopher M., Lopes, Pedro E. M., Zhu, Xiao, Roux, Benoît, MacKerell, Alexander D.

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 326 KB

english, 2010

30

Generalized solvent boundary potential for computer simulations

Im, Wonpil, Bernèche, Simon, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 564 KB

english, 2001

31

Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations

Beglov, Dmitrii, Roux, Benoi^t

Journal:

The Journal of Chemical Physics

Year:

1994

Language:

english

File:

PDF, 1.28 MB

english, 1994

32

Ion Selectivity of α-Hemolysin with a β-Cyclodextrin Adapter. I. Single Ion Potential of Mean Force and Diffusion Coefficient

Luo, Yun, Egwolf, Bernhard, Walters, D. Eric, Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 4.38 MB

english, 2010

33

Energetics of Double-Ion Occupancy in the Gramicidin A Channel

Li, Yuhui, Andersen, Olaf S., Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 1.32 MB

english, 2010

34

Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations

Egwolf, Bernhard, Luo, Yun, Walters, D. Eric, Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 3.75 MB

english, 2010

35

Gramicidin A Backbone and Side Chain Dynamics Evaluated by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Experiments. II: Nuclear Magnetic Resonance Experiments

Vostrikov, Vitaly V., Gu, Hong, Ingólfsson, Helgi I., Hinton, James F., Andersen, Olaf S., Roux, Benoît, Koeppe, Roger E.

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

36

Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials

Maragliano, Luca, Vanden-Eijnden, Eric, Roux, Benoît

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 2.11 MB

english, 2009

37

Integrated Continuum Dielectric Approaches To Treat Molecular Polarizability and the Condensed Phase: Refractive Index and Implicit Solvation

Truchon, Jean-François, Nicholls, Anthony, Roux, Benoît, Iftimie, Radu I., Bayly, Christopher I.

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 3.04 MB

english, 2009

38

Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome

Ge, Xiaoxia, Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 4.45 MB

english, 2010

39

RNA Structure Determination Using SAXS Data

Yang, Sichun, Parisien, Marc, Major, François, Roux, Benoît

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 3.99 MB

english, 2010

40

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

Shivakumar, Devleena, Deng, Yuqing, Roux, Benoît

Journal:

Journal of Chemical Theory and Computation

Year:

2009

Language:

english

File:

PDF, 855 KB

english, 2009

41

Potential of mean force and reaction rates for proton transfer in acetylacetone

Hinsen, Konrad, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

1997

Language:

english

File:

PDF, 445 KB

english, 1997

42

Electrostatic free energy calculations using the generalized solvent boundary potential method

Banavali, Nilesh K., Im, Wonpil, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2002

Language:

english

File:

PDF, 315 KB

english, 2002

43

Grand canonical Monte Carlo simulations of water in protein environments

Woo, Hyung-June, Dinner, Aaron R., Roux, Benoît

Journal:

The Journal of Chemical Physics

Year:

2004

Language:

english

File:

PDF, 810 KB

english, 2004

44

Numerical solution of the hypernetted chain equation for a solute of arbitrary geometry in three dimensions

Beglov, Dmitrii, Roux, Benoi^t

Journal:

The Journal of Chemical Physics

Year:

1995

Language:

english

File:

PDF, 577 KB

english, 1995

45

Hyperspectral optical near-field imaging: Looking graded photonic crystals and photonic metamaterials in color

Dellinger, Jean, Van Do, K., Le Roux, Xavier, de Fornel, Frédérique, Cassan, Eric, Cluzel, Benoı̂t

Journal:

Applied Physics Letters

Year:

2012

Language:

english

File:

PDF, 1.92 MB

english, 2012

46

Calculating excess chemical potentials using dynamic simulations in the fourth dimension

Pomès, Régis, Eisenmesser, Elan, Post, Carol B., Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 340 KB

english, 1999

47

Brownian dynamics simulations of ions channels: A general treatment of electrostatic reaction fields for molecular pores of arbitrary geometry

Im, Wonpil, Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 769 KB

english, 2001

48

Spatial dependence of time-dependent friction for pair diffusion in a simple fluid

Straub, John E., Berne, Bruce J., Roux, Benoi^t

Journal:

The Journal of Chemical Physics

Year:

1990

Language:

english

File:

PDF, 914 KB

english, 1990

49

Building Markov state models along pathways to determine free energies and rates of transitions

Pan, Albert C., Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 1.42 MB

english, 2008

50

Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories

Sezer, Deniz, Freed, Jack H., Roux, Benoı̂t

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 253 KB

english, 2008