TCBG Seminar

“Simulating complex biochemical processes by the combined use of metadynamics and replica exchange”

Prof. Alessandro Laio
Statistical and Biological Phsyics
International School for Advanced Studies
Trieste, Italy

Monday, April 1, 2013
3:00 pm (CT)
3269 Beckman Institute


We will present a method1 that combines replica exchange2 with metadynamics3 and allows, with a moderate computational effort, the simultaneous reconstruction of the free energy as a function of a large number of variables. This allows simulating very complex reactions, like protein folding, in which the reaction coordinate is totally unknown. We will discuss applications of the methodology to protein folding, to amyloid aggregation, and to the study of drug-protein interaction. [1] S. Piana and A. Laio, J. Phys. Chem. B 111, 4553 (2007). [2] Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999). [3] A. Laio and M. Parrinello, Proc. Natl. Acad. Sci. USA 99,12562 (2002).

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