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		Search Text: Home/< Back ToThe Science/Computational Biophysics
  Computational Biophysics
    The Laboratory of Computational Biophysics is a group of researchers, led by Dr. Bernard Brooks, who use high-performance computing and macromolecular simulation to investigate problems in biophysics and chemistry.
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  Bernard Brooks, Ph.D.
          Senior Investigator
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      Meet the Team
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  Senior Investigator Research Interests
            
  Research Interests
              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.
  Projects

            Molecular Dynamics Simulations of Biological Macromolecules Molecular dynamics simulations are used to predict or explain function or structures of peptides and proteins and their substrates.
	Development of Theoretical Methods for Studying Biological Macromolecules New theoretical techniques are developed and characterized. These efforts are usually coupled with software development, and involve the systematic testing and evaluation of new ideas.
	Three-dimensional Structures of Biological Macromolecule We use computational techniques with experimental data to determine the three-dimensional structures of biological macromolecules and molecular assemblies. Experimental techniques include electron microscopy, electron tomography, NMR spectroscopy, and CD spectroscopy.
	Development of Advance Computer Hardware and Software We develop and refine parallel computing techniques for macromolecular simulation and build suitable hardware required to efficiently execute it.

          
Software

            CHARMM
	CHARMM Tutorial
	ProBiS Server
	Open MM
	CPPTRAJ

          
High Performance Computing Section

            The High Performance Computing Section of the Laboratory of Computational Biology is part of the Biochemistry and Biophysics Center Division of Intramural Research National Heart, Lung, and Blood Institute of the National Institutes of Health. This Section is a group of researchers who support and maintain the LoBoS cluster that allows scientists in the laboratory to use high-performance computing to investigate biological systems by using molecular dynamics. This Section is lead by John Legato.
      
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    Lab Group


        
            The Laboratory of Computational Biophysics is a group of researchers who use high-performance computing to investigate molecular dynamics.
      CBS
Featured Publications
                A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.
            Authors:Roe DR, Brooks BR.
                                                                                                                        
            The Journal of Chemical Physics
      
                2020 Aug 07;153(5):
        Read Publication
                      A double exponential potential for van der Waals interaction.
            Authors:Wu X, Brooks BR.
                                                                                                                        
            AIP Advances
      
                2020 Jun 07;9(6):
        Read Publication
                      Psi4 1.4: Open-source software for high-throughput quantum chemistry.
            Authors:Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O'Brien JS, Waldrop JM, Brooks BR
                                                                                                                        
            Journal of Chemical Physics
      
                2020 May 14;152(18):
        Read Publication
                      A deep learning approach for the blind logP prediction in SAMPL6 challenge.
            Authors:Prasad S, Brooks BR.
                                                                                                                        
            Journal of Computer-Aided Molecular Design
      
                2020 May 01;34(5):535-542
        Read Publication
                      Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge.
            Authors:Jones MR, Brooks BR.
                                                                                                                        
            Journal of Computer-Aided Molecular Design
      
                2020 May 01;34(5):
        Read Publication
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  Meet the Team

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            Bernard Brooks, Ph.D.
                Senior Investigator
                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.
    
          Contact the lab
    12 South DrBethesda, MD 20814United States
        Phone:
                    301-496-0148
                Fax:
            301-480-6153
  Félix  Aviat, Ph.D.
        

    Visiting Postdoctoral Fellow

        felix.aviat@nih.gov
            Ada Chen headshot
    
            Ada Chen
        

    Predoc Visiting Fellow

        ada@jhu.edu
            Ana Damjanovic
    
            Ana Damjanović, Ph.D.
        

    PSC

        adamjan1@jhu.edu
        
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                    Ana's Profile
            Phillip Hudson, Ph.D.
        

    Postdoctoral Fellow

        phillip.hudson@nih.gov
            Mahdi Ghorbani
        

    Visiting Predoctoral Fellow

        mahdi.ghorbani@nih.gov
        
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                    Mahdi's Profile
            Jiyeon
    
            Jiyeon Min
        

    Visiting Predoctoral Fellow

        jiyeon.min@nih.gov
            Samarjeet Prasad headshot
    
            Samarjeet Prasad
        

    Predoctoral IRTA Fellow

        samar.samarjeet@nih.gov
        
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                    Samarjeet's Profile
            Andrew Simmonett headshot
    
            Andy Simmonett, Ph.D.
        

    Staff Scientist

        andrew.simmonett@nih.gov
        
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                    Andy's Profile
            Xiongwu Wu headshot
    
            Xiongwu Wu, Ph.D.
        

    Staff Scientist

        wuxw@nhlbi.nih.gov
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