Numerical analysis of first-passage processes in finite Markov chains exhibiting metastability

We describe state-reduction algorithms for the analysis of first-passage processes in discrete- and continuous-time finite Markov chains. We present a formulation of the graph transformation algorithm that allows for the evaluation of exact mean first-passage times, stationary probabilities, and committor probabilities for all nonabsorbing nodes of a Markov chain in a single computation. Calculation of the committor probabilities within the state-reduction formalism is readily generalizable to the first hitting problem for any number of alternative target states. We then show that a state-reduction algorithm can be formulated to compute the expected number of times that each node is visited along a first-passage path. Hence, all properties required to analyze the first-passage path ensemble (FPPE) at both a microscopic and macroscopic level of detail, including the mean and variance of the first-passage time distribution, can be computed using state-reduction methods. In particular, we derive expressions for the probability that a node is visited along a direct transition path, which proceeds without returning to the initial state, considering both the nonequilibrium and equilibrium (steady-state) FPPEs. The reactive visitation probability provides a rigorous metric to quantify the dynamical importance of a node for the productive transition between two endpoint states and thus allows the local states that facilitate the dominant transition mechanisms to be readily identified. The state-reduction procedures remain numerically stable even for Markov chains exhibiting metastability, which can be severely ill-conditioned. The rare event regime is frequently encountered in realistic models of dynamical processes, and our methodology therefore provides valuable tools for the analysis of Markov chains in practical applications. We illustrate our approach with numerical results for a kinetic network representing a structural transition in an atomic cluster.