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Abstract
A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation
of protein-association reactions and other events whose frequencies of outcomes are
constricted by free energy barriers. The method features a weighted ensemble of trajectories
in configuration space with energy levels dictating the proper correspondence between
"particles" and probability. Instead of waiting a very long time for an unlikely event
to occur, the probability packets are split, and small packets of probability are
allowed to diffuse almost immediately into regions of configuration space that are
less likely to be sampled. The method has been applied to the Northrup and Erickson
(1992) model of docking-type diffusion-limited reactions and yields reaction rate
constants in agreement with those obtained by direct Brownian simulation, but at a
fraction of the CPU time (10(-4) to 10(-3), depending on the model). Because the method
is essentially a variant of standard Brownian dynamics algorithms, it is anticipated
that weighted-ensemble Brownian dynamics, in conjunction with biophysical force models,
can be applied to a large class of association reactions of interest to the biophysics
community.