Suman Chakrabarty

Contact information University of Southern California Department of Chemistry 3620 McClintock Avenue, SGM 418 Los Angeles, CA 90089-1062, USA Voice: +1-607-342-4366 Fax: +1-213-740-2701 E-mail: sumancha@usc.edu chakrabarty.suman@gmail.com Homepage: www.namusite.com

Career Interest Academia: Research and teaching Current Research Interests

Proton transfer pathways and rate processes in Cytochrome c Oxidase: Trying to develop a microscopic understanding through structure-function correlation, accurate description of protein electrostatics and available experimental data on specic mutant enzymes Structure based pKa calculation and ionization state prediction of deeply buried protein residues Prediction of water content in protein cavities and ligand binding sites Temperature dependent kinetic isotope eects in enzymatic reactions Development of physically motivated coarse grained (CG) models to bridge the wide range of length/timescales relevant to biological and chemical systems

Education Post-doctoral Research (September 2009 - to date) : University of Southern California, USA Advisor: Arieh Warshel Broad area of research: Computational molecular biophysics Current project: Proton transfer pathways and rate processes in Cytochrome c Oxidase Ph.D. (Thesis defense: July 2010) : Indian Institute of Science, Bangalore, India Advisor: Biman Bagchi Broad area of research: Phase transition in soft condensed matter systems Thesis title: Computer simulation studies of dynamics of phase transition in soft-condensed matter: isotropic-nematic, gas-liquid, and polymer collapse M.S. (by research) : 2002 - 2005 : part of integrated PhD program in Indian Institute of Science, Bangalore, India Project thesis title: Theoretical Studies into Model Liquid Crystalline System and Preferential Solvation in Binary Mixture CGPA (Cumulative Grate Point Average): 7.0/8.0 Rank: 1 Relevant courses: advanced statistical mechanics, mathematical methods for physics, computers in chemistry etc. B.Sc. (Honours) : 1999 - 2002 : Presidency College, Kolkata under University of Calcutta Major in Chemistry, with Physics and Mathematics as auxiliary subjects 1 of 4

 First division; 75% marks in Chemistry University rank: 5 Publications in refereed journals

1. Coarse grained model for exploring voltage dependent ion channels, A. Dryga,S. Chakrabarty, S. Vicatos and A. Warshel, Biochim. Biophys. Acta (2011) (In press). doi:10.1016/j.bbamem.2011.07.043. 2. Proton-transport Mechanisms in Cytochrome c Oxidase Revealed by Studies of Kinetic Isotope Eects, A. Johansson, S. Chakrabarty, C. B. Siberg, M. Hgbom, o o A. Warshel and P. Brzezinski, Biochim. Biophys. Acta, 1807, 1083 (2011). 3. Exploration of the Cytochrome c Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Eects, S. Chakrabarty, I. Namslauer, P. Brzezinski and A. Warshel Biochim. Biophys. Acta, 1807, 413 (2011). 4. Anomalous Behavior of Linear Hydrocarbon Chains in Water-DMSO Binary Mixture at Low DMSO Concentration, R. Ghosh, S. Banerjee, S. Chakrabarty and B. Bagchi J. Phys. Chem. B, 115, 7612 (2011). 5. Temperature dependent free energy surface of polymer folding from equilibrium and quench studies, S. Chakrabarty and B. Bagchi, J. Chem. Phys., 133, 214901 (2010). 6. Self-Organization of n-Alkane Chains in Water: Length Dependent Crossover from Helix and Toroid to Molten Globule, S. Chakrabarty and B. Bagchi, J. Phys. Chem. B 113, 8446 (2009). 7. Gas-liquid nucleation in two dimensional system, M. Santra, S. Chakrabarty and B. Bagchi, J. Chem. Phys. 129, 234704 (2008). 8. Reply to comment on Elucidating the mechanism of nucleation near the gas-liquid spinodal, S. Chakrabarty, M. Santra and B. Bagchi, Phys. Rev. Lett. 101, 019602 (2008). 9. Elucidating the mechanism of nucleation near the gas-liquid spinodal, P. Bhimalapuram, S. Chakrabarty, and B. Bagchi, Phys. Rev. Lett. 98, 206104 (2007). 10. Power law relaxation and glassy dynamics in Lebwohl-Lasher model near isotropicnematic phase transition, S. Chakrabarty, D. Chakrabarti, and B. Bagchi, Phys. Rev. E 73, 061706 (2006). 11. Universal power law in the orientational relaxation in thermotropic liquid crystals, D. Chakrabarti, P. P. Jose, S. Chakrabarty and B. Bagchi, Phys. Rev. Lett. 95, 197801 (2005).

Awards and Distinctions

Burg Postdoctoal Teaching Award (Spring 2011) by the Department of Chemistry, University of Southern California, USA Nominated and sponsored (by Siemens AG) for attending the 59th Meeting of Nobel Laureates in Lindau - dedicated to Chemistry - from 28 June to 3 July 2009 Poster prize at WATOC 2008 (Eighth Triennial Congress of the World Association of Theoretical and Computational Chemists) (September, 2008) 2 of 4

 Research Fellowship awarded by Council for Scientic and Industrial Research (CSIR), India (2005 - 2009) Best student of the year award on humanitarian grounds from Presidency College, Kolkata (2002)

Academic Experience

Strong background in general/physical chemistry Experience in equilibrium and non-equilibrium statistical mechanics and their applications on dierent model systems Various advanced computer simulation and modelling techniques (with experience of writing the relevant computer programs from scratch): Molecular dynamics (in NVE, NVT and NPT ensembles) Monte Carlo (in NVT, NPT and VT ensembles) Non-Boltzmann sampling methods to access rare events and estimate free energy barriers: umbrella sampling, transition matrix Monte Carlo (TMMC), WHAM, metadynamics etc. QM/MM calculations using Empirical Valence Bond (EVB) approach to quantitatively calculate free energy barrier of chemical reactions in solution and proteins (enzymes) Protein electrostatics: Quantitative estimation of solvation free energy, binding free energy and pKa of key residues in enzymes using microscopic and semi-microscopic methods like PDLD, PDLD-S/LRA etc. Langevin/Brownian dynamics simulation of polymeric systems Expertise in the following simulation packages: GROMACS, Molaris (actively participating in development)

Technical Skills Programming and other languages: Fortran (77, 90), C, Python, Bash shell, A sed, awk, L TEX, HTML Operating systems: Dierent Linux distributions (mainly Ubuntu, Fedora, Gentoo), Microsoft Windows (XP and 7) Utilities: Mathematica, Matlab, VMD, Pymol, Visual Python, gnuplot, xmgrace etc. Experience of Linux system administration and cluster maintenance for the current and previous research groups of about 10 users An ardent follower of GNU and FOSS (Free and Open Source Software) movement; Strong interest in recent technological/scientic advances across the world; Highly interested to learn and adopt new ideas and techniques for own research

Conferences 1. Protein Electrostatics, Telluride Science Research Center, July 2011.

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2. Frontiers in the simulation of Macromolecules (symposium in honour of Prof. Arieh Warshel), November 2010, USA: Poster title: Exploration of the Cytochrome c Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Eects. 3. WATOC 2008 (triennial congress of The World Association of Theoretical and Computational Chemists), September 2008, Sydney, Australia: Poster prize was awarded for the poster titled Understanding nucleation near the spinodal (in 2and 3-dimensions). 4. Gordon Research Conference titled Liquids, Chemistry & Physics Of at Holderness School, Plymouth, NH, USA, July-August 2007. Poster title: Elucidating the mechanism of nucleation and growth near gas-liquid spinodal. 5. Conference on Nucleation, Aggregation and Growth, January 2007, at Jawaharlal Nehru Centre for Advanced Scientic Research, Bangalore, India. 6. Theoretical Chemistry Symposium (TCS - 2006), December 2006, School of Chemistry, Bharathidasan University, Tiruchirappalli - 620 024, India. Poster title: Power law relaxation and glassy dynamics near isotropic-nematic transition. 7. DAE-BRNS Symposium on Theoretical Chemistry (TCS - 2004), December 2004, Bhabha Atomic Research Centre, Trombay, Mumbai - 400 085, India. Poster title: Theoretical Studies into Preferential Solvation in Binary Mixture. 8. 22nd International Conference on Statistical Physics, July 2004, Department of Physics, Indian Institute of Science, Bangalore - 560012, India. 9. International Symposium on Spectroscopy, Structure and Dynamics, December 2002, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India.

Workshops

School on Understanding molecular simulation conducted by D. Frenkel and B. Smit at Jawaharlal Nehru Centre for Advanced Scientic Research, Bangalore, India on January, 2007.

Teaching experience

1. Mentored teaching under Burg Postdoctoral Teaching Award (Spring 2011): Advanced graduate course CHEM 599 titled Modeling Biophysical Systems and Processes. Primary course instructor: Arieh Warshel 2. Teaching assistant of the graduate level course IP-SS 201 (AUG, 2001) titled Thermodynamics and Statistical Mechanics, at Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore for 3 semesters. Course instructor: Biman Bagchi

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