College of Liberal Arts & Sciences

The generalized-ensemble simulations and its application to the protein folding problem

November 9, Mon 2009
1:00 pm, MRB 200 Conference Room

Dr. Yuji Sugita

Theoretical Biochemistry Laboratory, RIKEN

Due to the multiple-minima problem (or quasi-ergodicity problem) in biomolecular simulations, the conventional molecular dynamics or Monte Carlo methods can not sample wide conformational spaces of proteins in solution. By contrast, the simulations based on the generalized-ensemble algorithms overcome this difficulty by performing a random walk in potential energy space and other parameter space. From one simulation run, we can obtain canonical ensemble averages of physical quantities as functions of temperature by the single/multiple histogram reweighting techniques. In the seminar, we introduce several generalized-ensemble methods that have been developed by us. We also show our recent folding simulations of villin headpiece subdomain in explicit water by using multicanonical replica-exchange method.


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