Bernard Brooks, Ph.D.

Senior Investigator

Laboratory of Computational Biophysics


Building 12, Room 3053B
12 South Drive
Bethesda, MD 20814


Research Topics

Dr. Brooks' research group have been involved in CHARMM development and oversight for more than 30 years. His research efforts have involved the development of new methods to assist the interpretation of experiment, for integrating multiple computational models into a single (multiscale) computation, the development of methods for normal mode analysis of large bio-macromolecules, new enhanced sampling methods, new restraint methods, and techniques for finding reaction pathways in complex systems. All of these developments are integrated into CHARMM, a complete tool for complementing and enhancing experimental research.


Bernard Brooks earned an S.B. in chemistry from Massachussets Institute of Technology in 1975 and a Ph.D. in chemistry from University of California, Berkeley in 1979. He did his postdoctoral at Harvard University under the supervision of the Dr. Martin Karplus and he joined the NIH in 1990 as a staff fellow in the Division of Computer Research and Technology at the National Institutes of Health. In 1998 we become the Chief of Molecular Graphics and Simulation Section of the Laboratory of Structural Biology and in 1998 he occupied the position of Chief of the Computational Biophysics Section of the Laboratory of Biophysical Chemistry of the National Heart, Lung and Blood Institute. Since 2005 he is the Chief of the Laboratory of Computational Biology at the NHLBI. In 2008 he receive the NHLBI Oustanding Mentor Award and in 2010 he got the NIH Merit Award in recognition of defining the needs of supercomputing power to meet contemporary scientific needs at NIH.

Selected Publications

  1. Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30(10):1545-614.
  2. Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nat Commun. 2017;8:15443.
  3. Simmonett AC, Pickard FC 4th, Ponder JW, Brooks BR. An empirical extrapolation scheme for efficient treatment of induced dipoles. J Chem Phys. 2016;145(16):164101.
  4. Damjanovic A, Miller BT, Okur A, Brooks BR. Reservoir pH replica exchange. J Chem Phys. 2018;149(7):072321.

Related Scientific Focus Areas

This page was last updated on Tuesday, February 1, 2022