TCB Seminar

All-atom Simulations of the Hierarchical Dynamics of Proteins on Timescale of Seconds and the Experimental Verifications

Professor Yang Zhang
Department of Nuclear, Plasma, and Radiological Engineering
University of Illinois
Unknown Location

Monday, April 10, 2017
3:00 pm
3269 Beckman Institute

Abstract

Energy landscape, the high-dimensional hypersurface in the configuration space, has been a valuable concept in qualitatively describing non-equilibrium matter and the associated complex processes that occur over a very long timescale, such as the viscous flow of supercooled liquids, the folding of polypeptide chains into structured proteins, and the self-assembly of micro-units into functional objects. Despite extensive studies, the enduring challenge is still how to quantify the energy landscape. To address this challenge, we developed a Relaxation-Excitation Mode Analysis (REMA) framework, which incorporates the kinetic theory and the energy landscape theory by treating the many-body collisions explicitly. Using REMA, important statistics of the activation barriers (“mountains”) and metabasins (“valleys”) of the energy landscape become accessible from experimentally measurable two-point correlation functions, e.g. using quasi-elastic and inelastic scattering experiments. On the computational side, we developed an improved history-dependent metadynamics method which allows the direct sampling of the above-mentioned statistics of the potential energy landscape. In this talk, I will present our all-atom simulations of the energy landscape and the hierarchical dynamics of proteins on the timescale of seconds and the experimental verifications.