TCB Seminar

Weighted Ensemble Simulation: Tackling the Challenges of Long-timescale Kinetics

PROFESSOR Lillian Chong
Chemistry
University of Pittsburgh
Pittsburgh, PA

Monday, December 14, 2020
3:00 pm
Zoom webinar link

Abstract

The weighted ensemble (WE) path sampling strategy exploits intermittent communication among quasi-independent simulations with rigorous statistical resampling that introduces no bias in the generated pathways, thereby enabling the calculation of rate constants for rare events (e.g. protein folding or binding). WE simulations have yielded unbiased ensembles of continuous pathways and rate constants of biological processes with up to orders of magnitude less overall computing time than would be required by standard simulations, enabling the generation of complete, atomically detailed pathways for protein binding/unbinding and protein folding processes. The WE strategy can be applied at any scale with any type of stochastic dynamics engine from ab initio molecular dynamics simulations to particle-based cell-scale simulations and beyond. I will present our recent applications of the WE strategy as well as challenges that remain in tackling long-timescale kinetics.