Identification of slow molecular order parameters for Markov model construction

A goal in the kinetic characterization of a macromolecular system is the description of its slow relaxation processes, involving (i) identification of the structural changes involved in these pro-cesses, and (ii) estimation of the rates or timescales at which these slow processes occur. Most of the approaches to this task, including Markov models, Master-equation models, and kinetic network models, start by discretizing the high-dimensional state space and then characterize re-laxation processes in terms of the eigenvectors and eigenvalues of a discrete transition matrix. The practical success of such an approach depends very much on the ability to finely discretize the slow order parameters. How can this task…