09/19/19 - 9:45 AM to 11:00 AM
Department Seminar: Professor Wei Yang
Free Energy Sampling of Long-Timescale Biomolecular Dynamics: the Energy Flow Viewpoint
Biomolecules aimlessly fluctuate in their functional environments and occasionally undergo characteristic activated transitions; these rare conformational events usually play pivotal roles in biological functions. In the past decade, understanding rare activated events at the atomistic level, especially mapping the corresponding free energy landscapes via molecular dynamics (MD) simulation, has been an immense focus in the fields of theoretical chemistry and computational biophysics. Although a large number of reports have been published to claim success, it has been increasingly clear that such attempts seem to be still far reaching to the existing strategies. As is widely known, a major general challenge lies in the fact that a majority of biologically important conformational transitions occur at timescales above the ranges of hundreds of microseconds to milliseconds. In contrast, currently commonly accessible timescales for GPU-based MD simulations are around tens of nanoseconds to microseconds depending on system size. To overcome this challenge, a physics-based enhanced sampling strategy, the orthogonal space sampling scheme, was introduced and enriched in the past decade by the group of the speaker. Such scheme allows physically essential energy flows related to target events to be specifically accelerated and thereby lead to practically robust and efficient sampling. Recent mathematical and algorithmic developments and applications will be discussed in this talk.
Professor Yang's research interest targets the development and application of state-of-art multi-spectrum atomistic simulation techniques including QM/MM calculation, free energy simulation, conformation path simulation, motion analysis etc., to understand the hidden nature of complex biological phenomena. Specifically, his research program includes three directions:
- first principle based protein and ligand design;
- simulation study of multi-timescale biochemical & biophysical events such as DNA repair, motion- coupled biomolecular recognition, and enzymatic reactions; and
- development of simulation techniques to describe complex systems and enhance efficiency of biomolecular simulations.
Professor Yang is a professor in the Department of Chemistry & Biochemisty and the Institute of Molecular Biophysics. He earned his Bachelor of Science in chemistry from Tsinghua University in Beijing, and his doctorate in computational chemistry from the State University of New York at Stony Brook. He was a post-doctoral researcher in biophysics at Harvard University.
Event DetailsLocation: 331 Smith HallHost: Professor Jiali Gao