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Unbiased computation of transition times by pathway recombination

By J. Kuipers and G.T. Barkema

Abstract

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance, nucleation, protein folding, and chemical reactions. For these systems, direct simulation of phase space trajectories does not efficiently determine most physical quantities of interest. The past decade has seen the advent of methods circumventing brute force simulation. For most dynamical quantities, these methods all share the drawback of systematical errors. We present a novel method for generating ensembles of phase space trajectories. By sampling small pieces of these trajectories in different phase space domains and piecing them together in a smart way using equilibrium properties, we obtain physical quantities such as transition times. This method does not have any systematical error and is very efficient; the computational effort to calculate the first passage time across a free energy barrier does not increase with the height of the barrier. The strength of the method is shown in the Ising model. Accurate measurements of nucleation times span almost ten orders of magnitude and reveal corrections to classical nucleation theory

Year: 2008
OAI identifier: oai:dspace.library.uu.nl:1874/32740
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