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Chemistry & Chemical Biology / New Brunswick |
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Ronald M. Levy Board of Governors Professor of Chemistry B. A. 1970, Reed College Ph.D. 1976, Harvard University |
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Research
Summary
We use a combination of computer simulations, statistical mechanics and modeling, to study the structure, function, folding, and dynamics of proteins in solution. Current research projects include problems in the statistical mechanics of solutions, protein folding and ligand binding, and protein dynamics on longer time scales. We are interested in the interplay between computational models and experiments at different levels of spatial and temporal resolution from atomic to mesoscopic, and from femtoseconds to seconds. Together with a group of investigators with complementary expertise in molecular biology, statistical physics, control theory, and computer science, we are working to develop computational models for complex biological systems involved in the regulation of gene expression.Awards & Honors
National Institutes of Health Research Career Development Award (1982-86)
National Institutes of Health Fogarty Fellow (1986)
John Simon Guggenheim Foundation Fellow (1995-96)
Rutgers University Board of Trustees Award for Excellence in Research (1996)
Japan Society for the Promotion of Science Fellowship (1996)
AAAS, Fellow (1998)
Board of Governors Professor of Chemistry (2002)
Representative Publications
Banks, J.L., H.S. Beard, Y. Cao, A.E. Cho, W. Damm, R. Farid, A.K. Felts, T.A. Halgren, D.T. Mainz, J.R. Maple, R. Murphy, D.M. Philipp, M.P. Repasky, L.Y. Zhang, B.J. Berne, R.A. Friesner, E. Gallicchio, and R.M. Levy. Integrated Modeling Program, Applied Chemical Theory (IMPACT). J. Comp. Chem., in press.
Knight, J.L.,V. Mekler, J.Mukhopadhyay, R.H. Ebright and R.M. Levy. Distance-Restrained Docking of Rifampicin and Rifamycin SV to RNA Polymerase Using Systematic FRET Measurements: Developing Benchmarks of Model Quality and Reliability. Biophys. J., 88, 925-938 (2005).
Andrec, M., A.K. Felts, E. Gallicchio, and R.M. Levy. Protein Folding Pathways from Replica Exchange Simulations and a Kinetic Network Model. Proceedings Natl. Acad. Sci. USA, 102, 6801-6806 (2005).
Gallicchio, E., M. Andrec, A.K. Felts, and R.M. Levy. Temperature Weighted Histogram Analysis Method, Replica Exchange, and Transition Paths. J. Phys. Chem. B, 109, 6722-6731 (2005).
Chekmarev, D., T. Ishida, and R.M. Levy. Long time conformational transitions of alanine dipeptide in aqueous solution: continuous and discrete state kinetic models. J. Phys. Chem. B, 108, 19487-19495 (2004).
Andrec, M., B.N. Kholodenko, R.M. Levy, and E. Sontag. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: Structure and accuracy. J. Theoret. Biol., 232, 427-441 (2005).
Mukhopadhyay, J., E. Sineva, J. Knight, R.M. Levy, and R.H. Ebright. Antibacterial peptide microcin J25 inhibits transcription by binding within, and obstructing, the RNA polymerase secondary channel. Molecular Cell. 14, 739-751 (2004).
Felts, A.K., Y. Harano, E. Gallicchio, R.M. Levy. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGNP implicit solvent model. PROTEINS: Structure, Function, and Bioinformatics, 56, 310-321 (2004).
Gallicchio E., and R.M. Levy. AGBNP, an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J. Comp. Chem., 25, 479-499 (2004).