Department of Chemistry, Columbia University
3000 Broadway, mail code 3103
New York, NY 10027

work:+1 212-854-2186

fax:+1 212-932-1289

bb8@columbia.edu

Research Summary

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.

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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)

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