Thesis: Theoretical Studies on the Interaction and Binding Energies in Protein-DNA Complexes.
Advisor: Prof. B. Jayaram, Department of Chemistry, Indian Institute of Technology (IIT), New Delhi.
Indian Institute of Technology (IIT), New Delhi, India. M.S. Chemistry 1993-1995Thesis: Energetic Aspects of the Role of the Helix-turn-Helix motif in DNA Recognition.
St. Xaviers College, Ahmedabad, India B.S. Chemistry 1990-1993|
Coordinator, Computational Biophysics |
Jan 2005-Present |
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Senior Research Associate |
April 2002-Present |
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Research Associate |
April 2001-April 2002 |
Working with Prof. D. L. Beveridge, Wesleyan University (Grant: NIH, HHMI)
Research and develop methods to study binding energy components in protein-ligand complexes, entropic effects, solvent models, cooperativity in biomolecular systems using Molecular Simulation techniques.
Design and develop data mining tools and techniques for research on large molecular simulation databases.
Research structural bioinformatics of DNA: predict sequence-structure relationships.
Consult and support the use of modeling and simulation tools for molecular biophysics research in the chemistry, molecular biology and biochemistry departments.
Taught “Molecular Modeling, Dynamics and Design”. Wesleyan University, Spring 2004, 2006.
Taught sections of “Bioinformatics”. Wesleyan University, Fall 2002.
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Post-Doctoral Fellow |
October1999- February 2001 |
Worked with Dr. C. Chipot, LCTN Nancy. (Grant: Aventis Pharma, Paris)
Designed and implemented Free Energy calculation methods for alchemical transformations (Free Energy Perturbation and Thermodynamic Integration) in a massively parallel, state-of-the-art molecular dynamics simulation environment (NAMD).
Developed a SQL DB to store and retrieve sequence directed structural information of DNA from a library of MD Simulation data. It has a browser based graphical interface – used Transact SQL and Java Technology (J2EE, JDBC, JSP, Servlets). (http://humphry.chem.wesleyan.edu:8080/MDDNA)
Alchemical Transformations in NAMD Simulations. Implemented the Dual topology scheme for molecular transformation. Programming Concepts: Object Oriented Design, Data Drive Parallelism, C++. (http://www.ks.uiuc.edu/Research/namd/tutorial/AlchemicalFEP.pdf)
Designed and developed tools in C, Perl and FORTRAN for the analysis of structural and energetic aspects of DNA and protein-DNA complexes.
Developed a quasi-harmonic approach in C for the estimation of configurational entropy in biomolecular complexes based on all atom molecular dynamics trajectory data.
Implemented the distance dependent sigmoidal dielectric function in the molecular simulation package AMBER for the treatment of solvent electrostatic effects.
Maintenance and Administration of Workstations and Desktop Machines.
Built and managed PC cluster with 16 nodes running Linux Operating System.
SGI, Linux Servers and Windows desktop machines.
Maintain and operate websites and web-servers.
Programming Languages: C++, C, FORTRAN, Perl, SQL, Java (JDBC, Servlets, JSP), Prolog.
Math/Stat Tools: R, SPSS, Matlab.
Comput Chem Tools: AMBER, NAMD, CHARMM, Insight (Accelrys), Delphi (FDPB), MOE, Gaussian.
Bioinformatics Tools: Deep View, BLAST, CLUSTAL.
Mentored 4 undergraduate honors student projects.
Teaching Assistant at Undergraduate Laboratory Course in Chemistry, 1996-1998.
Peer Review articles for the Biophysical Journal, Journal of Biomolecular Structure and Dynamics and Nucleic Acids Research.
Participate in grant proposal writing.
Seminar: “Informatics of DNA Simulation trajectories: Tools and Techniques”. International Society for Quantum Biology and Pharmacology Presidents Meet at Como, Italy, June 2004.
Seminar: “Analysis of molecular dynamics simulations of DNA: Using relational database and web based tools”. ChemInfo Division, Annual ACS Meeting, NY, USA, Sept 2003.
Seminar: “Dynamic morphology of protein-DNA complexes”. XIII Conversation on Biomolecular Stereodynamics, SUNY at Albany, USA, June 21-25, 2003.
Poster: “Free energy simulation in a massively parallel environment: a test case study”. Computational Biophysics 2000 From Macromolecules to Drugs, Nice, France, June 2000.
Visiting scientist IBPC, Paris (Lab of Prof. Richard Lavery) (Sept 1999). Development of methods for the estimation of deformation energy associated with DNA conformational changes during protein-DNA complexation. PI: Prof. B. Jayaram, IIT, New Delhi (Grant: IFCPAR)
Dept of Science and Tech (DST) and Council for Scientific and Industrial Research (CSIR), Govt of India, Travel Grant. XI Conv Biomol Stereodyn at SUNY at Albany, USA. June 1999.
Best poster “Energetics of protein-DNA recognition: Interaction of DNA with proteins containing the helix-turn-helix motif’, XII International Conference on Computers in Chemistry Research and Education, University of Pune, India, Jan 1998.
Best poster “Computer Aided Design of λ Repressor and Cro fragments with altered operator specificities”, Symposium on Structural Biology / 24th Annual Meeting of Indian Biophysical Society, Indian Institute of Science, Bangalore, India, December 9-12, 1996.
Graduate Aptitude Test in Engineering Fellowship, Indian Institutes of Technology (IIT). 1995-1999.
Dr. T .V. Venkatraman Scholarship (1991-92) Developed “Orientation Expert” an expert system in Turbo Prolog for predicting functional group substitution patterns in aromatic ring compounds.