Bruce J. Berne

Bruce J. Berne


My research is concerned with structural and dynamic processes in condensed phase systems and biomacromolecular systems.

Our key concerns are in several broad areas: the properties of water and aqueous solutions of peptides and proteins, and the development of new fluctuating charge force fields to treat electrostatic polarization effects in these systems. Using these force fields, we have been studying the statics and dynamics of solvation, especially in photophysical properties. We have also embarked on a quest to understand the strengths and weaknesses of continuum dielectric theories of solvation and have been actively working on the theory of chemical reactions and vibrational relaxation in molecules dissolved in condensed matter. Finally, we are studying the development of Monte Carlo and molecular dynamic path integral techniques for evaluating the structure and dynamics of quantum degrees of freedom in condensed systems, including electron solvation and electron transfer reactions.

Because we often study the more complex many-body systems, it is necessary to utilize powerful analytical methods of statistical mechanics as well as state-of-the-art methods of computer simulation involving molecular dynamics and Monte Carlo techniques. We have been successful in inventing powerful new methods for treating the multiple time scale problem in molecular dynamics. Our new Reference System Propagator Algorithm (RESPA) is being adopted throughout the world. Recently we have extended it to large-protein solutions and have achieved remarkable speedups on serial and parallel computers. We are also deeply involved in developing methods for simulating the structure and dynamics in quantum many-body systems using image enhancement technology such as the Maximum Entropy algorithms.

We are heavily involved in devising new computational methods and force fields for simulating protein folding kinetics. We have extensive collaborations with the Blue Gene Team at IBM. The Blue Gene project aims to construct a massively parallel petaflop computer for protein folding.

Lingle Wang and B. J. Berne, “Efficient Sampling of Puckering States of Monosaccharides Through Replica Excahnage with Solute Tempering and Bond Softening”,  J. Chem. Phys. 149, 07306 (2018)

Robert Abel, Lingle Wang, Ed Harder, B. J. Berne, and Richard A. Friesner, “Advancing Drug Discovery through Enhanced Free Energy Calculations”, Accts Chem. Res., 3, e17000, 1-8 (2017)

Pratyush Tiwary,  Jagannath Mondal, and B. J. Berne, “How and when does an anti-cancer drug leave its binding site?”, Science Advances, 3, e17000, 1-8 (2017)

Tiwary, B.J. Berne, “Predicting reaction coordinates in energy landscapes with diffusion anisotropy”, J. Chem. Phys., 147, 152701 (2017)

Pratyush Tiwary and B. J. Berne, “How wet should be the reaction coordinate in ligand unbinding”, J. Chem. Phys. 145, 054113 (2016)

Jagannath Mondal, Pratyush Tiwary, and B. J. Berne, “How a kinase inhibitor withstands gatekeeper residue mutations”, J. Amer. Chem. Soc., 138, 4608-4615  (2016)

Pratyush Tiwary and B. J. Berne, “How wet should be the reaction coordinate in ligand unbinding”, J. Chem. Phys. 145, 054113 (2016)

Pratyush Tiwary and B. J. Berne, “Spectral gap optimization of order parameters for sampling complex molecular systems”, Proc. Nat. Acad. Sci. USA, 113, 2839-2844 (2016)

Jagannath Mondal; Joseph Morrone and B. J. Berne, “How hydrophobic drying forces impact the kinetics of molecular recognition”, Proc. Nat. Acad. Sci. USA , 110, 13277-13282 (2013)

Joseph Morrone, Jingyuan Li and B. J. Berne, “Interplay between Hydrodynamics and the Free Energy Surface in the Assembly of Nanoscale Hydrophobes”, J. Phys. Chem. B, 116, 378-389 (2012)

Lingle Wang, Richard A. Friesner, and B. J. Berne, “On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities”, Proc. Nat. Acad. Sci.,USA, 109, 6, 1937-1942 (2012)

Lingle Wang, B. J. Berne, and R. A. Friesner, “Protein-Ligand binding: Contributions from wet and dry regions of the binding pocket”, Proc. Nat. Acad. Sci. (USA), 108, 1326-1330 (2011).

Ruhong Zhou, Jingyuan Li, Lan Hua, Zaixing Yang, and B. J. Berne, Comment on “Urea-Mediated Protein Denaturation: A Consensus View,” J. Phys. Chem. B, 115, 1323-1326 (2011)

Joseph Morrone, Thomas Markland, and B. J. Berne, “A new method for sampling resonances in multiple time scale molecular dynamics using a high frequency colored noise thermostat”, J. Chem. Phys.,134, 14103 (2011)

Thomas E. Markland, Joseph A. Morrone, B. J. Berne, Kunimasa Miyazaki, Eran Rabani, and David R. Reichman, “Quantum fluctuations can promote or inhibit glass formation”, Nature Physics, 107, 134-137 (2011).

Zhonghan Hu, Liwen Cheng and B. J. Berne, “First passage time distribution in stochastic processes with absorbing boundaries and its application to biological rupture experiments”, J. Chem. Phys., 133, 034105 (2010).

Lingle Wang, Richard A. Friesner and B. J. Berne, “Hydrophobic Interactions in Model Enclosures from Small to Large Length Scales: Nonadditivity in Explicit and Implicit Solvent Models”, J. Faraday Discussions, 2010, DOI: 10.1039/B925521B.

Joseph Morrone, Ruhong Zhou and B. J. Berne, Molecular dynamics with multiple time scales: “How to avoid pitfalls, J. Theoretical and Computational Chemistry”, 6, 1798-1804, (2010).

Tom Young, Lan Hua, Xuhui Huang,Robert Abel, Richard A. Friesner and Bruce J. Berne, “Dewetting in the active sites of proteins, Proteins Structure, Function and Bioinformatics 78”, 1856-1869, (2010).

Robert Abel, Lingle Wang, Richard A. Friesner and B. J. Berne, “A displaced-solvent functional analysis of model hydrophobic enclosures”, J. Comp. Theor. Chem., 6, 2924-2934 (2010).
Lingle Wang, Richard A. Friesner and B. J. Berne, “Competition of Electrostatic and Hydrophobic Interactions Between Small Hydrophobes and Model Enclosures”, J. Phys. Chem. B., 114, 7294-7309, (2010).

Tzu-Ling Kuoa, Sergi Garcia-Manyesb, Jingyuan Li, Itay Bareld, Hui Lue, Bruce J. Berne, Michael Urbakhd, Joseph Klafter and Julio M. Fernხndez, “Probing static disorder in Arrhenius kinetics by single- molecule force spectroscopy”, Proc. Nat. Acad. Sci., USA., 107, 11336-40, (2010)

Sumit Sharma, B. J. Berne and Sanat K. Kumar, “Thermal and Structural Stability of Adsorbed Proteins”, Biophysical Journal, 99, 1157-1165, (2010)

Jingyuan Li, Julio Fernandez, and B. J. Berne, “Water’s role in the force induced unfolding of ubiquitin”, Proc. Nat. Acad. Sci. (USA), 107, 19284-19289 (2010)

Tom Young, Robert Abel, Byung Chan Kim, Richard A. Friesner, and B. J. Berne, “Solvent Chemical Potential Mapping of Complex Surfaces”, In Preparation (2010).

Lorna Dougan, Jingyuan Li, Carmen L. Badillaa, B. J. Berne, and Julio M. Fernandez, “Single homopolypeptide chains collapse into mechanically rigid conformations”, Proc. Nat. Acad. Sci. USA 106,12605-12610, (2009).

Rual Perez-Jimenez, Jingyuan Li, Pallav Kosuri, Inmaculada Sanchez-Romero, Arun P. Wiita, David Rodriguez-Larrea, Ana Chueca, Arne Holmgren, Antonio Miranda-Vizuete, Katja Becker, Seung-Hyun Cho, Jon Beckwith, Eric Gelhaye, Jean Pierre Jacquot, Eric Gaucher, Jose M. Sanchez-Ruiz, Bruce Berne, and Julio M. Fernandez, “Diversity of Chemical Mechanisms in Thioredoxin Catalysis, Nature, Structure and Molecular Biology”. 16, 890-896, (2009)

Bruce J. Berne, John D. Weeks, and Ruhong Zhou, “Dewetting and Hydrophobic Interaction in Physical and Biological Systems”, Annu. Rev. Phys. Chem. 60, 85-103 (2009).

Lingle Wang, Robert Able, Richard A. Friesner, and Bruce J. Berne, “Thermodynamic Properties of Liquid Water: An Application of a Nonparametric Approach to Computing the Entropy of a Neat Fluid”, J. Chem. Theo. Comput. 5, 1462-1473, (2009)

Lan Hua, Ronen Zangi, and Bruce J. Berne, “Hydrophobic interactions and dewetting between plates with hydrophobic and hydrophilic domains”, J. Phys. Chem. C 113, 5244-5253, (2009).

Ronen Zangi, Ruhong Zhou, and Bruce J. Berne, “Urea’s Action on Hydrophobic Interactions”, J. Am. Chem. Soc., 131,1535-1541 (2009)

Lan Hua, Ronen Zangi, and Bruce J. Berne, “Hydrophobic Interactions and Dewetting between Plates with Hydrophobic and Hydrophilic Domains”, J. Phys. Chem. C (2008) In Press

Gina M. Florio, Boaz Ilan, Thomas Mueller, Tova L. Werblowsky, Bruce J. Berne and George W. Flynn, “Chain-Length Effects on the Self-Assembly of Short 1-Bromoalkanes Monolayers on Graphite”, J. Phys. Chem. C, 112, 18067-18075 (2008)

Lan Hua, Ruhong Zhou, David Thirumalai, and Bruce J. Berne, “Urea Denaturation by Stronger Dispersion Interactions with Proteins than Water Implies a Two Stage Unfolding”, Proc. Nat. Acad. Sci. USA, 105, 16928-16933 (2008)

Boaz Ilan, Gina Florio, Mark Hybersten, Bruce J. Berne, and George W. Flynn, “Scanning Tunneling Microscopy Images of Alkane Derivatives on Graphite: Role of Electronic Effects”, Nano Lett., 8, 3160-3165 (2008)

Frauke Graeter, Pascal Heider, Ronen Zangi, and Bruce J. Berne, “Dissecting Entropic Coiling and Poor Solvent Effects in Protein Collapse”, J. A. Chem. Soc., 130, 11578-11579 (2008)

Mary Griffin Krone, Lan Hua, Patricia Soto, Ruhong Zhou, Bruce J. Berne, and Joan-Emma Shea, “Role of Water in Mediating the Assembly of Alzheimer Amyloid-Beta ab16-22 Protofilaments”, J. Am. Chem. Soc., 130, 11066-11072 (2008)

Ronen Zangi and Bruce J. Berne, “Temperature Dependence of Dimerization and Dewetting Large Scale Hydrophpobes: A Molecular Dynamics Study”, J. Phys. Chem. B, 112, 8634-8644 (2008)

Robert Abel, Tom Young, Ramy Farid, B. J. Berne, and Richard A. Friesner, “The Role of the Active Site Solvent in Thermodynamics of Factor Xa-Ligand Binding”, J. Am. Chem. Soc., 130, 2817-2831 (2008)

Ruhong Zhou, Maria Eleftheriou, C. C. Hon, R. S. Germain, Ajay K. Royyuru, and Bruce J. Berne, “Massively Parallel Molecular Dynamics Simulations of Lysozome Unfolding”, IBM J. Res. and Dev., 52, 19-30 (2008)