Coarse-Graining Markov State Models

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• Dr Edina Rosta, UCL
• Wednesday 03 November 2021, 14:30-15:30
• Dept of Chemistry, Wolfson Lecture Theatre and Zoom: Meeting ID: 977 4633 0653 Passcode: 379093.

If you have a question about this talk, please contact Lisa Masters.

Markov state models (MSMs) provide a useful framework for understanding the kinetics of highly complex systems. Accordingly, MSM -based methods are increasingly popular to analyse and drive molecular dynamics simulations, including biasing and unbiasing simulations to enhance sampling. However, the dimensionality of these models is still very large when we consider a space of selected discretised collective variables. We developed kinetics-based coarse graining methods to identify metastable and transition states using variational objective functions: the second eigenvalue corresponding to the slowest relaxation time, and the Kemeny constant, corresponding to the sum of all relaxation times of the system. We show that these objective functions are closely related to mean first passage times that may be easier available in various applications of complex networks beyond molecular simulations.

This talk is part of the Theory - Chemistry Research Interest Group series.

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