STUDENT SEMINAR
Speaker: Mr. Subhajit Acharya
Research Supervisor: Prof. Biman Bagchi
Topic: Use of collective coordinates in physical and biological systems
Date & Time: Thursday, 10th November 2022 at 4:00 PM
Venue: AG02/03, Chemical Sciences Building
Abstract:
The order-disorder phenomenon is important in many branches of science because the transformation is accompanied by changes in many physical properties. In the last few decades, several mathematical models of collective variables have been proposed that could better describe the phenomenon. Some physiochemical processes such as gas-liquid nucleation, paramagnetic to ferromagnetic transition, the isotropic-nematic transition of liquid crystal, conformational changes of biomolecules, protein folding, etc., are activated processes that involve rare transitions between stable states in the free energy surface. Understanding the underlying mechanism and computing rates associated with such processes is a central feature of many applications. In this talk, I shall mainly focus on protein folding, which is a vital cellular process in living cells. Protein must be correctly folded into its unique three-dimensional structure in order to function properly. Otherwise, unfolded or misfolded proteins contribute to the pathology of many diseases. In the talk, I shall briefly discuss the folding puzzle known as the Leventhal paradox and how the folding funnel concept removes the conflict between kinetic control and thermodynamic control for sufficiently stable protein structures.
The apparent complexity of folded protein structure and the extraordinary diversity of conformational states of unfolded proteins make challenging even the description of protein folding in atomistic terms. I shall survey the difference between the kinetics of complex chemical processes, such as protein folding, and the kinetics of simple chemical processes, whose understanding forms the basis of the most commonly used reaction rate theories. I shall discuss the possible scenarios that could arise while studying the kinetics of this complex process. I shall briefly discuss the formalism developed by Bryngelson and Wolynesto understand protein folding as a configurational space diffusion on a rugged free energy landscape. Next, I shall address the scaling relation between the protein folding timescale and the size of the protein. I shall conclude my talk by discussing the use of orientational order parameters to study different liquid crystal phases.
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