College of Liberal Arts & Sciences

Free Energy Sampling of Long-Timescale Biomolecular Dynamics: the Energy Flow Viewpoint”

Tuesday, October 1, 2019

Title:           Free Energy Sampling of Long-Timescale Biomolecular Dynamics: the Energy Flow Viewpoint
Time:           11:00 a.m.
Location:    Room 202 MRB
Presenter:  Wei Yang (Professor of Chemistry and Biochemistry, Institute of Molecular Biophysics Florida State University Tallahassee, Florida)

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.



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