Hong Kong University of Science and Technology

“Investigating Conformational Changesof Biological Macromolecules UsingKinetic Network Models“

Abstract:

Simulating biologically relevant timescales at atomic resolution is a challenging task since typical atomistic simulations are at least two orders of magnitude shorter.  Markov State Models (MSMs), a kinetic network model, built from molecular dynamics (MD) simulations provide one means of overcoming this gap without sacrificing atomic resolution by extracting long time dynamics from short MD simulations through the coarse graining on the phase space and time. In this talk, I will demonstrate the power of kinetic network models by applying it to simulate the complex conformational changes, that occurs at tens to hundreds of microsecond timescales for a large RNA Polymerase II complex containing nearly half million atoms.  Furthermore, I will introduce a new efficient dynamic clustering algorithm for the automatic construction of MSMs for multi-body systems.  We have successfully applied this new algorithm to model the protein-ligand recognition and self-assembly of co-polymers.  Finally, I will introduce a new algorithm using the projection operator approach to identify optimal kinetic lumping and recover slowest conformational dynamics of complex systems.

Short biography:

Xuhui Huang is an Associate Professor of Chemistry at the Hong Kong University of Science and Technology. He obtained his Ph.D. degree from Columbia University in 2006 with Prof. Bruce Berne. He did his postdoc research at Stanford University with Profs. Michael Levitt (Nobel Laureate in Chemistry) and Vijay Pande, He joined HKUST as an assistant professor in 2010, and received an early promotion to the tenured Associated Professor in Jan 2015. His research is focused on developing and applying statistical mechanics based algorithms to model functional conformational changes of complex biological systems. He has published over 60 papers in top journals including Science, Nature, PNAS, and JACS.  He has also received a series of awards including the OpenEye Outstanding Junior Faculty Award in American Chemical Society Division of Computers in Chemistry (2014); School Research Award, HKUST School of Science (2013), and Hong Kong Research Grant Council Early Career Award (2013); and American Chemical Society CCG Excellence Award (2006).

Salle de réunion ISIS – Rez-de-Chaussée

ISIS – 8, allée Gaspard Monge, Campus Esplanade

Contact : mcecchini@unistra.fr