Researcher: Pradip Biswas, Ph.D.
Dr. Pradip Biswas, Assistant Professor of Physics, has established a computational biophysics and bioengineering group to perform biomolecular modeling, development of force-field, classical and multiscale molecular dynamic simulation, and docking. The objective is to investigate the reaction mechanisms and transition states of proteins and a molecular level understanding of protein adsorption of polymer surfaces.
Currently ongoing projects are:
- Multiscale Quantum-Mechanical-Molecular-Mechanical (QMMM) study of iNOS to elucidate the roles of the tetrahydrobiopterin and L-Arginine in the reaction mechanism of nitric oxide (NO) synthesis. The uncoupling of the NOS system has been implicated in the development of hypertension. Elucidation of this mechanism would be beneficial to understanding the disease state versus the normotensive NOS system. This project is in collaboration with Dr. Valentin Gogonea of Cleveland State University, Ohio.
- Development of a multiphase simulation protocol in CHARMM (Chemistry at Harvard Molecular Mechanics) for simultaneous use of dedicated force fields for the solid phase polymers and liquid phase proteins and to perform simulations to understand the conformational and functional changes on the adsorbed proteins. This project is in collaboration with Dr. Robert Latour of Clemson University, South Carolina.
- Study of the role of calcium binding proteins (CaBP) in impairing the binding of estrogen-estrogen receptor (ER)-CaM complex to DNA and therefore preventing ER-alpha-dependent transcription as it applies to breast cancer. This project is in collaboration with Dr. Rajnarayanan.
- Development of an ab-initio type classical force field so as to get rid of the suitability of parameters (making them topology independent) and concerns about polarization.
For simulations, Dr. Biswas has established a small cluster with four quad core rack servers and one master server and is in the process of buying another sixquad core rack servers, summer, 2009 with more to be added in fall, 2009. These servers will be housed in the Information Technology sector.
Undergraduate students working in the project currently share the space in the physics lab. A dedicated computer cluster room for proper maintenance of the cluster and dedicated undergraduate working space with a proper computer facility will help the planned and ongoing research of the Biswas group. Two recent undergraduates trained in physics research have been accepted into graduate school.