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Research
My research involves the theoretical and computational studies of the physical properties of bio-molecules. The general goal is to develop physical models and theoretical techniques for the simulation, statistical analysis, and design of the structure and dynamics of biological macromolecules and their complexes. The current effort is focused around proteins.
Proteins are natural nanomachines consisting of heteropolymeric chains of amino acids (polypeptides), with the amazing property of being able to self-assemble (fold) into unique 3-D structures. These structures allow them to perform their biological function. The process of folding is a relatively slow and complex process and presents a formidable theoretical challenge.
One of my projects involves the development of more accurate and efficient coarse grain models of proteins. In order to carry out long time simulations of complex systems, the resolution of the protein models is simplified to capture the relevant features. This requires the re-derivation of effective potentials and the design of efficient simulation techniques. These models can then be used to study the physical properties of proteins, including the determination of their native structure.
Another project involves the design of protein sequences to yield a desired 3-D structure ( de novo protein sequence design). The objective is to find a sequence of amino acids that self assemble into a target structure, with optimal stability, kinetic, and functional properties, under given solvent or physical conditions such as temperature. This problem has important applications in the development of novel nano-machines and drug design.
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