Transition rate theory, spectral analysis, and reactive paths.

Abstract

The kinetics of a dynamical system dominated by two metastable states is examined from the perspective of the activated-dynamics reactive flux formalism, Markov state eigenvalue spectral decomposition, and committor-based transition path theory. Analysis shows that the different theoretical formulations are consistent, clarifying the significance of the inherent microscopic lag-times that are implicated, and that the most meaningful one-dimensional reaction coordinate in the region of the transition state is along the gradient of the committor in the multidimensional subspace of collective variables. It is shown that the familiar reactive flux activated dynamics formalism provides an effective route to calculate the transition rate in the case of a narrow sharp barrier but much less so in the case of a broad flat barrier. In this case, the standard reactive flux correlation function decays very slowly to the plateau value that corresponds to the transmission coefficient. Treating the committor function as a reaction coordinate does not alleviate all issues caused by the slow relaxation of the reactive flux correlation function. A more efficient activated dynamics simulation algorithm may be achieved from a modified reactive flux weighted by the committor. Simulation results on simple systems are used to illustrate the various conceptual points.