Topic: Simulating Conformational Changes of Biological Macromolecules

Speaker: Xuhui Huang, Hong Kong University of Science and Technology, China

Time: 2:30 p.m., May 11, 2016

Venue: Conference Room 410, Building B12, SCUT South Campus

Abstract:

Simulating biologically relevant timescales at atomic resolution using Molecular Dynamics (MD) simulations 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 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 MSMs by applying it to simulate complex conformational changes includingprotein misfolding and functional conformational changes of a large RNA transcription complex (close to half million atoms). In addition, 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 kinetics of protein-ligand binding, and self-assembly of polymers.