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Center for Nonlinear Studies |
Conformational change within proteins is central to function, yet difficult to sample. Molecular dynamics, run without any modifications, will sample within wells, but poorly on transition events. This talk will discuss our recent advances in dynamic importance sampling and its application to adenylate kinase, potassium channels, Ca-ATPase, and several other model systems. Our approach biases with correction and enables an ability to sample on transition events by creating an ensemble set of independent trajectories. With sufficient sampling, these transition ensembles can be related to relative free energy, pathways, and kinetics.
Host: Anurag Sethi, T-6