Curriculum vitae of Suman Chakrabarty: Download (in pdf format)

Broad area of research

Theoretical physical chemistry

Computational molecular biophysics

Education

• Ph.D. (Thesis submission: September 2009): Indian Institute of Science, Bangalore, India
  • Advisor: Prof. Biman Bagchi
  • Broad area of research: Theoretical physical chemistry
  • Thesis title: Computer simulation studies of dynamics of phase transition in soft-condensed matter: isotropic-nematic, gas-liquid, and polymer collapse
  • Date of thesis defense: July 2010
• M.S. (by research): 2002 - 2005: part of integrated PhD program in Indian Institute of Science, Bangalore, India
  • Advisor: Prof. Biman Bagchi
  • Project thesis title: Theoretical studies into model liquid crystalline system and preferential solvation in binary mixture
  • CGPA: 7.0/8.0 (First division with distinction)
  • 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
  • Subjects: Major in Chemistry, with Physics and Mathematics as auxiliary subjects
  • Marks: 75% in Chemistry (First class)
  • University rank: 5

Work experience

• Post-doctoral Research (September 2009 - to date): University of Southern California, USA
  • Advisor: Prof. Arieh Warshel
  • Broad area of research: Computational molecular biophysics
  • Current research project: Proton transfer pathways and rate processes in Cytochrome c Oxidase

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)
• Research Fellowship awarded by Council for Scientific and Industrial Research (CSIR), India (2005 - 2009)
• Summer research fellowship (2 months) awarded by Indian Academy of Sciences, Bangalore, India (2002)
• Best student of the year award on humanitarian grounds from Presidency College, Kolkata (2002)

Research Experience

• Computer simulation studies on model systems: Simplified model systems often help to identify the key factors behind certain physical phenomena. I have experience in studying isotropic-nematic transition in a model liquid crystalline system (Lebwohl-Lasher model) and phase transition in Ising-like models.
• Nucleation and growth in gas-liquid transition: I have worked on nucleation and growth of liquid phase in a highly supersaturated gas phase very close to the spinodal curve. This work gave me exposure to studying rare events and calculation of high free energy barriers using non-Boltzmann sampling methods. I have used both conventional umbrella sampling method and more advanced Transition Matrix Monte Carlo (TMMC) to force the system cross and sample high barrier regions of the underlying free energy surface.
• Folding and crystallization of polymers in solution: I have studied length dependent crossover of polymer stability and structure in solution. During this project I have used the Metadynamics method to explore the large conformational space of a polymer chain and compute the underlying free energy surfaces. Also, I had experience in running Langevin/Brownian dynamics simulations to study crystallization of very long (500-mer and more) polymer chains.
• Proton transfer in Cytochrome c Oxidase: During my postdoctoral work I have used both QM/MM calculations using Empirical Valence Bond (EVB) approach and semi-macroscopic solvation models (e.g. PDLD) to quantitatively calculate free energy barrier of the proton transfer processes. I have also learned to compute the pKa of key protein residues using both semi-macroscopic and microscopic methods. It was extremely challenging to reproduce the experimentally observed barriers for various mutant enzymes and explain their molecular origin.
• Coarse grained (CG) model for voltage dependent ion channels: I have been part of development of a CG model for voltage dependent ion channels. This model includes a complete microscopic representation of the electrodes, electrolyte, membrane and protein system. I have been involved in validation of the electrode representation, electrolyte charge distribution and reproducing capacittance of the membrane systems.

Academic Skills

• Strong background in general/physical chemistry
• Experience in equilibrium and non-equilibrium statistical mechanics and their applications on different 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 μVT 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, sed, awk, LATEX, HTML
• Operating systems: Different 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/scientific advances across the world; Highly interested to learn and adopt new ideas and techniques for own research

Conferences

1. Young Investigator Meeting, Boston, October 2011: Poster title: “Biology and Chemistry in silico: A molecular perspective”.
2. Protein Electrostatics, Telluride Science Research Center, July 2011.
3. 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 Effects”.
4. 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 2- and 3-dimensions)”.
5. 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”.
6. Conference on “Nucleation, Aggregation and Growth”, January 2007, at Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.
7. 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”.
8. 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”.
9. 22nd International Conference on Statistical Physics, July 2004, Department of Physics, Indian Institute of Science, Bangalore - 560012, India.
10. 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 Prof. Dan Frenkel and Prof. Berend Smit at Jawaharlal Nehru Centre for Advanced Scientific 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: Prof. Arieh Warshel
2. Teaching assistant of the graduate level course IP-SS 201 titled Thermodynamics and Statistical Mechanics, at Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore for 3 semesters. Course instructor: Prof. Biman Bagchi