Berne, Bruce J. - Department of Chemistry, Columbia University

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Berne, Bruce J. - Department of Chemistry, Columbia University

Hydrogen-Bond Kinetics in the Solvation Shell of a Polypeptide Huafeng Xu and B. J. Berne*
Comment on "Can a Continuum Solvent Model Reproduce the Free Energy Landscape of a
Solvation and reorganization energies in polarizable molecular and continuum solvents
Multiple ``time step'' Monte Carlo simulations: Application to charged systems with Ewald summation
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Ground state of the quantum anisotropic planar rotor model: A finite size scaling study of the orientational orderdisorder phase transition
Multicanonical jump walk annealing: An efficient method for geometric optimization
Calculating the hopping rate for diffusion in molecular liquids: CS2 J. Daniel Gezelter, Eran Rabani, and B. J. Bernea)
Volumr 93. number 3 CtIEhlICAL PHYSICS LETTERS 26 Novcmbcr 1982 REACTION DYNAMICS IN AN ERGODICSYSTEM:THE SIAMESESTADIUM BILLIARD *
Massively parallel molecular dynamics simulations of
318 Berne Accounts of Chemical Research ecule XY as compared to those of the free molecule,
Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy
VoIume 117, number 3 CHEMICAL PHYSICS LEl-l-ERS 14 June 1985 PATH-IN"JXGR.AL SIlMuLA TION OF PURE WATER *
Drying and Hydrophobic Collapse of Paraffin Plates Xuhui Huang, Ruhong Zhou,, and Bruce J. Berne*,,
Transport properties of normal liquid helium: Comparison of various methodologies
Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems: Application to Liquid Argon
Path-integral diffusion Monte Carlo: Calculation of observables of many-body systems in the ground state
Reply to Comment on: Reversible multiple time scale molecular dynamics M. Tuckerman and B. J. Berne
J. Phys. Chem. 1988, 92, 3711-3725 3711 loss associated with the transition between states is offset by a
Journal of Statistical Physics, Vol. 43, Nos. 5/6, 1986 Path Integral Monte Carlo Methods
Hydrogen-Bond Dynamics in the Air-Water Interface Pu Liu, Edward Harder, and B. J. Berne*
Theory and simulation of polar and nonpolar polarizable fluids Jianshu Caoa) and B. J. Berne
A New Semiempirical Approach to Study Ground and Excited States of Metal Complexes in Biological Systems
Reply to Comment on "Electrostatic Potentials and Free Energies of Solvation of Polar and
Effect of pressure on hydrogen bonding in glycerol: A molecular dynamics investigation
NUMBER FLUCTUATION SPECTROSCOPY OF MOTILE MICROORGANISMS
Effects of Polarizability on the Hydration of the Chloride Ion Steven J. Stuart and B. J. Berne*
Hydrophobic Interactions and Dewetting between Plates with Hydrophobic and Hydrophilic Lan Hua, Ronen Zangi,
Global Optimization: Quantum Thermal Annealing with Path Integral Monte Carlo Yong-Han Lee and B. J. Berne*
some. Similar to nucleic acidtemplated pro-tein libraries, DNA-templated synthetic
J. Phys. Chem. 1995, 99, 2885-2892 2885 Molecular Dynamics Study of the Dependence of Water Solvation Free Energy on Solute
Computer simulation of solid CGOusing multiple time-step algorithms Piero Procaccia) and B. J. Berne
The energy-dependent transmission coefficient and the energy distribution of classical particles escaping from a metastable well
Polarizable molecules in the vibrational spectroscopy of water
Replica Exchange with Solute Tempering: Efficiency in Large Scale Systems Xuhui Huang,, Morten Hagen, Byungchan Kim, Richard A. Friesner, Ruhong Zhou,, and
J. Phys. Chem. 1987, 91, 4995-4998 Calculation of Dynamic Friction on Intramolecular Degrees of Freedom
Urea's Action on Hydrophobic Interactions Ronen Zangi,,
Solvent Effects on the Self-Assembly of 1-Bromoeicosane on Graphite. Part I. Scanning Tunneling Microscopy
Volume 107. number 2 CHEMICAL PHYSICS LETTERS 1.5 !day 1983 REACTION RATE FOR ISOMERIZATION IN A MOLECULAR BEAM
Quantum and classical relaxation rates from classical simulations Joel S. Bader and B. J. Berne
Can Water Polarizability Be Ignored in Hydrogen Bond Kinetics? Huafeng Xu, Harry A. Stern, and B. J. Berne*
The simulation of electronic absorption spectrum of a chromophore coupled to a condensed phase environment: Maximum entropy versus
INELASTIC LIGHT SCATTERING BY LARGE STRUCTURED PARTICLES
Volume 116, number 6 CHEMICAL PHYSICS LETTERS 24 May 1985 PATH INTEGRAL METHODS FOR SIMULATING ELECTRONIC SPECTRA ~
Corrections BIOPHYSICS, CHEMISTRY. For the article ``Destruction of long-range
Dynamics of Water Confined in the Interdomain Region of a Multidomain Protein Lan Hua, Xuhui Huang, Ruhong Zhou,, and B. J. Berne*,,
Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
NUCLEATION IN FINITE SYSTEMS: THEORY AND COMPUTER SIMULATION*t
proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Dewetting transitions in protein cavities
Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM)
The absorption spectrum of the solvated electron in fluid helium by maximum entropy inversion of imaginary time correlation functions
Integrated Modeling Program, Applied Chemical Theory JAY L. BANKS,1
Urea denaturation by stronger dispersion interactions with proteins than water implies a 2-stage unfolding
Development of an Accurate and Robust Polarizable Molecular Mechanics Force Field from ab Initio Quantum Chemistry
Electronic properties of CdSe nanocrystals in the absence and presence of a dielectric medium
Molecular dynamics algorithm for multiple time scales: Systems with long range forces
Autobiography of Bruce J. Berne "You can take the boy out of Brooklyn but you cannot take
Single homopolypeptide chains collapse into mechanically rigid conformations
Molecular dynamics with multiple time scales: The selection of efficient reference system propagators
Hydrophobic hydration around a pair of apolar species in C. Pangali,b) M. Rao, and B. J. Berne
MOLECULARPHYSICS,1973, VOL. 26, No. 2, 281-290 Interference effects in sequential decay
First passage time distribution in stochastic processes with moving and static absorbing boundaries with application to biological rupture
Elastic Bag Model for Molecular Dynamics Simulations of Solvated Systems: Application to Liquid Water and Solvated Peptides
Quantum path minimization: An efficient method for global optimization Pu Liu and B. J. Berne
J. Phys. Chem. 1988, 92, 1721-1730 1721 In view of the theoretical prediction for configuration A, the
Dewetting-induced collapse of hydrophobic particles X. Huang, C. J. Margulis, and B. J. Berne*
VOLUME 85, NUMBER 2 P H Y S I C A L R E V I E W L E T T E R S 10 JULY 2000 Rabani, Gezelter, and Berne Reply: In our recent Letter
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Do Molecules as Small as Neopentane Induce a Hydrophobic Response Similar to That of Large Hydrophobic Surfaces?
J. Phys. Chem. 1993,97, 13841-13851 13841 Effective Potentials for Liquid Water Using Polarizable and Nonpolarizable Models
Self-Assembly of Small Polycyclic Aromatic Hydrocarbons on Graphite: A Combined Scanning Tunneling Microscopy and Theoretical Approach
Free Energy of the Hydrophobic Interaction from Molecular Dynamics Simulations: The Effects of Solute and Solvent Polarizability
Molecular dynamics for nonequilibrium systems in which there are a small number of very hot particles in a cold bath
A new quantum propagator for hard sphere and cavity systems J. Caoa) and B J Berne. .
An Experimental and Theoretical Study of the Formation of Nanostructures of Self-Assembled Cyanuric Acid through Hydrogen Bond Networks on Graphite
Effect of Ions on the Hydrophobic Interaction between Ronen Zangi, Morten Hagen, and B. J. Berne*
Thermodynamic Properties of Liquid Water: An Application of a Nonparametric Approach to Computing
2166 J. Phys. Chem. 1982, 86, 2166-2177 Isomerizatlon Dynamics and the Transition to Chaos
3994 J. Phys. Chem. 1985,89, 3994-3998 The divergence as L -m in the first term on the right-hand side
Serial Replica Exchange Morten Hagen, Byungchan Kim, Pu Liu, Richard A. Friesner, and B. J. Berne*
Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo
Solvent Effects on the Self-Assembly of 1-Bromoeicosane on Graphite. Part II. Theory Boaz Ilan,,,
Response to ``Comment on a critique of the instantaneous normal mode ,,INM... approach to diffusion'' J. Chem. Phys. 109, 4693 ,,1998...
Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations
Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?
Volume 77, number 1 CHEMICAL PHYSICS LETTERS 1 Janwiry 1981 A MONTE CARLO PROCEDURE FOR THE STUDY OF SOLVENT EFFECTS
Subscriber access provided by Columbia Univ Libraries Journal of the American Chemical Society is published by the American Chemical
Volume 75, number 1 CHEMICAL PHYSICS LETTERS 1 October 1980 ISOMERIZATION DYNAMICS lN LiQUlDS BY MOLECULAR DYNAMlCS*
On the force bias Monte Carlo simulation of simple M. Rao and B. J. Berne
Activated rate processes: The reactive flux method for one-dimensional surface diffusion
Solvation energies and electronic spectra in polar, polarizable media: Simulation tests of dielectric continuum theory
On the Bayesian approach to calculating time correlation functions in quantum systems; reaction dynamics
Stochastic molecular dynamics in systems with multiple time scales and memory friction
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6720 J. Phys. Chem. 1984, 88, 6120-6721 model to the trajectory data for N(T)is compared with those of
Motifs for molecular recognition exploiting hydrophobic enclosure in proteinligand binding
Ultra-high vacuum scanning tunneling microscopy and theoretical studies of 1-halohexane monolayers
A comparison of exact quantum mechanical and various semiclassical treatments for the vibronic absorption spectrum: The case of fast
Efficient molecular dynamics and hybrid Monte Carlo algorithms for path integrals
VOLUME 82, NUMBER 18 P H Y S I C A L R E V I E W L E T T E R S 3 MAY 1999 Direct Observation of Stretched-Exponential Relaxation in Low-Temperature
Subscriber access provided by Columbia Univ Libraries The Journal of Physical Chemistry B is published by the American Chemical
Volume 93. number 3 CHCMICAL PHYSICS LClTERS 26 Nuvcmbcr 1982 REACTION DYNAMICS IN A NON-ERCODIC SYSTEM: THE SIAMESE STADIUM BILLIARD *
Large scale simulation of macromolecules in solution: Combining the periodic fast multipole method with multiple time step integrators
Destruction of long-range interactions by a single mutation in lysozyme
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Energy Dissipation in Nonlinear Systems Coupled to a Bath: On the Use of Perturbative Eran Rabani and B. J. Berne*
Volume 55. number 3 CffEIMICALPHYSICS LETTERS I May 1978 ON A NOVEL MONTE CARLO SCHEME FDR SLMULATING WATER AND AQUEOUS SOLUTiONS*
Abstract. This paper provides a perspective on the use of the reactive ux formalism for calculating rate constants
BIOPOLYMERS VOL. 12, 1161-1169 (1973) Electrophoretic Light Scattering as a Probe of
Copyright1974.Allrightsreseroed LASER LIGHT SCATTERING
ASSEMBLY OF MICROTUBULES 755 Oosawa, F., Asakura, S.. Hotta. K., Imai, N. & Ooi, J. (1959). J. Polymer Sci. 37, 323-
BIOPOLYMERS Irreversible ThermodynamicAnalysis of
MOLECULARPHYSICS, 1976, VOL. 32, No. 2, 363-378 The coupling between translational and rotational motions
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Downloaded 30 Dec 2003 to 128.59.114.15. Redistribution subject to AIP license or copyright, see http://ojps.aip.org/jcpo/jcpcr.jsp Downloaded 30 Dec 2003 to 128.59.114.15. Redistribution subject to AIP license or copyright, see http://ojps.aip.org/jcpo/j
1498 J. Phys. Chem. 1981, 85, 1498-1505 Molecular Dynamic Simulation of the Structure of Water in the Vicinity of a Solvated
5188 J.Phys. Chem. 1985, 89, 5188-5191 On Determining Reaction Kinetics by Molecular Dynamics Using Absorbing Barriers
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Molecullar dynamics algorithm for multiple time scales: Systems with disparate IYMSSeS
Comparison of rate theories for generalized Langevin dynamics Susan C. Tucker,") Mark E. Tuckerman, and Bruce J. Berne
Computer Physics Conununications 63 (1991) 415--426 415 North-Holland
Density dependence of excess electronic ground-state energies in simple atomic fluids
Reversible multiple time scale molecular dynamics M. Tuckermar?) and B. J. Berne
Diffusion-limited reactions in spherical cavities Amy L. R. Bug, Elizabeth L. Grossman, and Dane D. Morgan III
Many-body dispersion forces of polarizable clusters and liquids J Caoa) and B J Berne
Vibrational relaxation in simple fluids: Comparison of theory and simulation
Theory of polarizable liquid crystals: Optical birefringence Jianshu Caoa)and B. J. Berne
A Born-Oppenheimer approximation for path integrals with an application to electron solvation in polarizable fluids
Method for accelerating chain folding and mixing Zhihua Liu and B. J. Berne
Electron solvation in methane and ethane Zhihua Liu and Bruce J. Berne
J. Phys. Chem. 1994,98, 68856892 6885 A Multiple-Time-StepMolecular Dynamics Algorithm for Macromolecules
Dynamical fluctuating charge force fields: Application to liquid water Steven W. Rick, Steven J. Stuart, and B. J. Berne
A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins
7172 J. Am. Chem. SOC.1995,117, 7172-7179 Molecular Dynamics Calculation of the Effect of Solvent
10674 J. Phys. Chem. 1995, 99, 10674-10685 Simulated Annealing of a Protein in a Continuum Solvent by Multiple-Time-StepMolecular
A scaling and mapping theory for excess electrons in simple fluids Jianshu Cao
Hydrodynamic calculation of the frequency dependent friction on the bond of a diatomic molecule
J. Phys. Chem. 1995, 99, 2893-2899 2893 Computer Simulation of Hydrophobic Hydration Forces on Stacked Plates at Short Range
The energy relaxation of a nonlinear oscillator coupled to a linear bath Joel S. Badera)
On the calculation of dynamical properties of solvated electrons by maximum entropy analytic continuation of path integral
VOLUME 77, NUMBER 13 P H Y S I C A L R E V I E W L E T T E R S 23 SEPTEMBER 1996 Path-Integral Monte Carlo Scheme for Rigid Tops: Application to the Quantum Rotator
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 88008803, August 1996
Circumventing the pathological behavior of path-integral Monte Carlo for systems with Coulomb potentials
Vibronic spectra in condensed matter: A comparison of exact quantum mechanical and various semiclassical treatments for harmonic baths
Constructing ab initio force fields for molecular dynamics simulations Yi-Ping Liu, Kyungsun Kim, B. J. Berne, Richard A. Friesner, and Steven W. Ricka)
Volume 145,number I CHEMICAL PHYSICS LETTERS 18March 1988 HYDROPHOBIC INTERACTION BETWEEN A METHANE MOLECULE
On the application of numerical analytic continuation methods to the study of quantum mechanical vibrational relaxation processes
Classical theories of reaction dynamics: Transition state theory, spatial diusion controlled reactions, and the energy diusion limit
The dependence of the rate constant for isomerization on the competition between intramolecular vibrational relaxation and energy transfer
Nonradiative relaxation processes in condensed phases: Quantum versus classical baths
Multicanonical jump walking: A method for efficiently sampling rough energy landscapes
Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Initio Quantum Chemistry
Real time quantum correlation functions. I. Centroid molecular dynamics of anharmonic systems
Real time quantum correlation functions. II. Maximum entropy numerical analytic continuation of path integral Monte Carlo and centroid
VOLUME 83, NUMBER 22 P H Y S I C A L R E V I E W L E T T E R S 29 NOVEMBER 1999 Second-Order Reentrant Phase Transition in the Quantum Anisotropic Planar Rotor Model
Surface Curvature Effects in the Aqueous Ionic Solvation of the Chloride Ion Steven J. Stuart*
FEATURE ARTICLE On the Adequacy of Mixed Quantum-Classical Dynamics in Condensed Phase Systems
Classical Approximation to Nonradiative Electronic Relaxation in Condensed Phase Systems Eran Rabani, S. A. Egorov,, and B. J. Berne*
Quantum mechanical canonical rate theory: A new approach based on the reactive flux and numerical analytic continuation methods
Ann. Phys. (Leipzig) 9 (2000) 910, 668 678 A renormalization approach to quantum thermal
Quantum Thermal Annealing with Renormalization: Application to a Frustrated Model Yong-Han Lee and B. J. Berne*
Quantum time correlation functions from complex time Monte Carlo simulations: A maximum entropy approach
Quantum Rate Constants from Short-Time Dynamics: An Analytic Continuation Eunji Sim, Goran Krilov, and B. J. Berne*
Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems
Quantum effects in liquid water: Path-integral simulations of a flexible and polarizable ab initio model
The free energy landscape for hairpin folding in explicit water
The calculation of transport properties in quantum liquids using the maximum entropy numerical
Can a continuum solvent model reproduce the free energy landscape of a -hairpin folding in water?
Helix Unfolding and Intramolecular Hydrogen Bond Dynamics in Small r-Helices in Explicit Solvent
Multiple ``time step'' Monte Carlo Balazs Hetenyia)
Computer Simulation of a "Green Chemistry" Room-Temperature Ionic Solvent C. J. Margulis, H. A. Stern, and B. J. Berne*
On the Calculation of Diffusion Coefficients in Confined Fluids and Interfaces with an Application to the Liquid-Vapor Interface of Water
Reply to the Comment on "Do Molecules as Small as Neopentane Induce a Hydrophobic
Efficient Simulation Method for Polarizable Protein Force Fields: Application to the Simulation of BPTI in Liquid
Observation of a dewetting transition in the collapse of the melittin tetramer
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
Why Is the Partial Molar Volume of CO2 So Small When Dissolved in a Room Temperature Ionic Liquid? Structure and
Hydrophobic Aided Replica Exchange: an Efficient Algorithm for Protein Folding in Explicit Solvent
Aggregation and Dispersion of Small Hydrophobic Particles in Aqueous Electrolyte Ronen Zangi and B. J. Berne*
Frustrated Ostwald Ripening in Self-Assembled Monolayers of Cruciform -Systems
Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy
Nanoscale Dewetting Transition in Protein Complex Folding Lan Hua, Xuhui Huang,*,, Pu Liu,,| Ruhong Zhou,, and Bruce J. Berne*,,
Probing the chemistry of thioredoxin catalysis Arun P. Wiita1,2
Subscriber access provided by Columbia Univ Libraries Journal of the American Chemical Society is published by the American Chemical
Subscriber access provided by Columbia Univ Libraries Journal of the American Chemical Society is published by the American Chemical
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A Systematic Comparison of Pairwise and Many-Body Silica Potentials
Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy
Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls
Competition of Electrostatic and Hydrophobic Interactions between Small Hydrophobes and Model Enclosures
Thermal and Structural Stability of Adsorbed Proteins Sumit Sharma,
ADDITIONS AND CORRECTIONS 2008, Volume 112B
A Displaced-Solvent Functional Analysis of Model Hydrophobic Enclosures
Water's role in the force-induced unfolding of ubiquitin
THE JOURNAL OF CHEMICAL PHYSICS 134, 014103 (2011) Efficient multiple time scale molecular dynamics: Using colored noise
PUBLISHED ONLINE: 9 JANUARY 2011 | DOI: 10.1038/NPHYS1865 Quantum fluctuations can promote or inhibit
Ligand binding to protein-binding pockets with wet and dry regions
Published: January 19, 2011 r 2011 American Chemical Society 1323 dx.doi.org/10.1021/jp105160a |J. Phys. Chem. B 2011, 115, 13231326
Subscriber access provided by Columbia Univ Libraries Nano Letters is published by the American Chemical Society. 1155 Sixteenth
Molecular dynamics in systems with multiple time scales: Systems with stiff and soft degrees of freedom and with short and long range forces
Structure and Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water: A Comparative Study of the Effects of Solvent and Protein Polarizability
Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function
Vibrational energy relaxation in the condensed phases: Quantum vs classical bath for multiphonon processes
Electrostatic Potentials and Free Energies of Solvation of Polar and Charged Molecules Gerhard Hummer,* Lawrence R. Pratt, and Angel E. Garcia
ON THE CALCULATION OF TIME CORRELATIONFUNCTIONS
Dynamical Fluctuating Charge Force Fields: The Aqueous Solvation of Amides
Smart walking: A new method for Boltzmann sampling of protein conformations
Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model
Erratum: Theory and simulation of polar and nonpolar polarizable [J. Chem. Phys. 99, 6998 (1993)]
Chemical theory and computation ighlighting this issue of PNAS
Published: June 29, 2011 r 2011 American Chemical Society 9431 dx.doi.org/10.1021/jp204407d |J. Phys. Chem. B 2011, 115, 94319438
Published: December 05, 2011 r 2011 American Chemical Society 378 dx.doi.org/10.1021/jp209568n |J. Phys. Chem. B 2012, 116, 378389