Sanjib Senapati Department of Biotechnology Areas of interest: Computational Biophysics and Green Chemistry.

Sanjib Senapati is currently a Professor in the Department of Biotechnology, IIT Madras. Before his tenure at IITM, he was a research scientist in the Dept. of Chemistry and Biochemistry, University of California, San Diego (2003-2005) and prior to that he was a Post Doctoral fellow at University of North Carolina Chapel Hill, USA (2000-2003). He obtained his Ph.D. in theoretical chemistry from IIT Kanpur in 2001. His area of research includes Computational Biophysics and Green Chemistry.

How does your group keep HPCE cluster busy?

Our Computational Biophysics Group at IIT Madras focusses on understanding the relationship between protein structure, function and dynamics. We use HPCE cluster to perform Molecular dynamic / Monte Carlo / Brownian dynamic simulations of protein-ligand and protein-protein complexes. We try to address the changes involved in protein structure and dynamics upon binding the drugs / inhibitors / substrates and with mutation. Subsequently, we determine binding strength and specificity. We also elucidate the specific interactions between DNA / proteins and solvents to understand the long-term stability of various biomolecules in ionic liquids.

How do you see HPCE landscape in the domain of your research area change over the years?

Recent advancements in both the hardware technology and freely available software have made it possible to study the large biological systems in tractable timeline. HPCE at IIT Madras has helped our research immensely. While some years ago we used to simulate systems of 10,000 atoms for months to get reasonable amount of data, now we dare to simulate whole virus particles of ~1.5 million atoms. Thanks to CPU–GPU combinations that have accelerated these calculations. I foresee even a bigger upslope in years to come with upcoming technology and algorithms!

What would you suggest to new faculty members and new students in your research area?

Resources are plenty, just go ahead and execute your ideas! Students, be brave and choose your problem, but, please do sufficient homework before submitting the jobs to make sure the proper utilization of the facility!