PROFESSOR Daniel Zuckerman
Physics of Biophysics
Oregon Health & Science University
Portland, Oregon

Monday, October 26, 2020
3:00 pm (CT)
Zoom webinar recording

Abstract

How do molecular machines really work? And how can molecular simulations be accelerated to yield reliable insights into such machines? To address the first question, we will explore standard chemical kinetics models of machine function, but with a twist - seeking to find a range of models that can perform a given function. The results point to possible functional and mechanistic heterogeneity of machines beyond what is typically presented in literature cartoons. For the second question, we examine a simple extension to Markov state models that incorporates history information intrinsic to molecular dynamics trajectories. The history-augmented extension is shown to be a powerful tool for analyzing mechanisms and can be further exploited for reliable analysis of non-equilibrium data resulting from weighted ensemble simulations. Bio: https://www.ohsu.edu/school-of-medicine/zuckerman-lab/biography Lab: https://www.ohsu.edu/school-of-medicine/zuckerman-lab