Rare switching events in non-stationary systems

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DOI http://dx.doi.org/10.1063/1.4704812
Reference N.B. Becker and P.R. ten Wolde, Rare switching events in non-stationary systems, J. Chem. Phys. 136, (Article number: 174119), 1-15 (2012)
Group Biochemical Networks

Physical systems with many degrees of freedom can often be understood in terms of transitions between a small number of metastable states. For time-homogeneous systems with short-term memory these transitions are fully characterized by a set of rate constants. We consider the question how to
extend such a coarse-grained description to non-stationary systems and to systems with finite memory. We identify the physical regimes in which time-dependent rates are meaningful, and state microscopic expressions that can be used to measure both externally time-dependent and history-dependent rates in microscopic simulations. Our description can be used to generalize Markov state models to time-dependent Markovian or non-Markovian systems.