Calculating mean first passage times from Markov models of proteins

Abstract

Assuming that the dynamics of peptides and proteins can be described by Markov transitions between different configurational states, we present a method which can calculate the mean first passage time (MFPT) between sets of initial and final states. The method is described in detail and differences between this and a method commonly employed [1] are explained. It is shown that the proposed method is (i) more general in allowing sets of final states, (ii) significantly faster, (iii) more accurate since it does not involve the calculation of infinite summations. Particular attention is given to the biologically important case of multiple final states.