Dr. Subhendu Roy

Research

We have openings for PhD students! We study the fundamental biological processes of life that are carried out by proteins using the principles of physics and chemistry through computer simulations. We try to understand the structure, function and dynamics of these fascinating molecular machines using various levels of computational and theoretical methods like Molecular Dynamics (MD) simulations, Quantum Mechanics (QM), QM/MM and Coarse-Grained methods with an ultimate target to formulate a rational protein design protocol. Our work aims specifically at designing artificial enzymes to address some of the burning issues in health, energy and environmental sectors. We also plan to express and charaterize the computationaly desgined enzymes experimentally. We are currently interested in the following research topics. (1) Understanding and Design of Artificial Enzymes (4) Simulation studies of drug-target proteins to understand the mechanism and design suitable inhibitor/drug (2) Computer simulations of proton transport, elctron transport and ion transport in Photosystem II, Nitrogenase,        Respiratory complexes, Rhodopsins, Ion channels (3) Coarse-Grained (CG) simulations of molecular motors (e.g., ATP Synthase) and other complex biological systems    We strive not only to explain structure-function correlation of complex biological systems, but also on making experimentally testable predictions. The research has fundamental and practical implications in drug design, enzyme design, antibiotic resistance, bioenergetics and optogenetics system design.