About Us


The research interests in our group are a combination of topics in biochemistry, molecular biophysics and high performance computing. We develop and use theoretical methods along with computational simulations to investigate biomolecules. We are particularly interested in biomolecules that have implications for clean energy, environment and human health. We closely work with experimental collaborators for development and validation of our computational models.

In the area of biochemistry and molecular biophysics, we are interested in the interrelation between protein structure, folding, dynamics and function. The group has investigated a number of enzyme systems including the cyclophilin A, plasmid encoded dihydrofolate reductase, and the proteins ubiquitin and rubredoxin for investigating the connection between internal motions and their function. In collaboration with another computational group (for higher-order statistics based analysis), we are developing new methodologies for identification of conformational sub-states that are relevant for protein function. We are also collaborating with enzymologist and neutron scattering experts to develop a joint computational-experimental strategy to explore the structure-dynamics-function of proteins.

On the other side, in the area of computational science and engineering we are actively involved in designing new computational algorithms and software performance optimization on emerging hardware architectures (including heterogeneous architectures with FPGAs and GPUs), and open source software development. We have recently optimized and ported molecular dynamics code (LAMMPS) on GPUs with 20 fold speed-up compared to the CPU-only code. The insights gained are being applied to optimize popular MD codes and methods on the current and future heterogeneous architectures. We are also investigating fault-tolerance and performance auto-tuning strategies for improved end-user productivity on the future computing platforms. Other software developed in the group include VigyaanCD, an open source software workbench for bio/chemical modeling.

Highlights



Cover Feature: IEEE Computer (2007), 40.

Journal Cover: J. Phys. Chem. B (2009), 113 (52).

Journal Cover: J. Phys. Chem. B (2011), 115 (28).

Cover Feature: PLoS Biology (2011), 9 (11).


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