Maximum Flux Transition Paths of Conformational Change
Abstract
Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space. The computational task becomes that of computing the "center" of such a cluster. A good way to define the center employs the concept of a committor, whose value at a point in collective variable space is the probability that a trajectory at that point will reach B before A. The committor "foliates" the transition region into a collection of isocommittors. The maximum flux transition path is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories. (This path is different from that of the MaxFlux method of Huo and Straub.) To make the calculation tractable, three approximations are introduced. It is shown that a maximum flux transition path is at least qualitatively superior to a minimum free energy path, in particular when a minimum free energy path has cusps. These qualities aid in the construction of simple and robust algorithms. Such an algorithm and its performance is discussed.Keywords
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