TY - GEN A1 - Sarich, Marco A1 - Banisch, Ralf A1 - Hartmann, Carsten A1 - Schütte, Christof T1 - Markov State Models for Rare Events in Molecular Dynamics N2 - Rare but important transition events between long lived states are a key feature of many molecular systems. In many cases the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible even on the most powerful computers because of the immensely long simulation timescales needed. Recently a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls. T3 - ZIB-Report - 13-52 KW - rare events KW - Markov state models KW - long timescales KW - optimal control Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42420 SN - 1438-0064 ER -