Peter Kramer
Rensselaer Polytechnic Institute

Stochastic Mode Reduction with Metastability in Biomolecular Modeling

One approach to accelerating biomolecular simulations is to simulate explicitly only certain slow degrees of freedom of interest, incorporating the effects of the remaining ``fast'' variables through effective stochastic models.  We illustrate a systematic multi-scale stochastic mode reduction procedure on a simple model problem with metastability -- a high potential energy barrier separating different conformational states.  Metastability is a prevalent feature in biomolecular systems.  We show in particular how the metastability can lead to various effective stochastic equations for the slow degrees of freedom depending on the relations between the physical parameters and properties of the potential energy landscape.  This work is in collaboration with Jessika Walter, Christof Schuette, Carsten Hartmann, and Wilhelm Huisinga at the Free University of Berlin.