Literature DB >> 11304388

Efficient dynamic importance sampling of rare events in one dimension.

D M Zuckerman1, T B Woolf.   

Abstract

Exploiting stochastic path-integral theory, we obtain by simulation substantial gains in efficiency for the computation of reaction rates in one-dimensional, bistable, overdamped stochastic systems. Using a well-defined measure of efficiency, we compare implementations of "dynamic importance sampling" (DIMS) methods to unbiased simulation. The best DIMS algorithms are shown to increase efficiency by factors of approximately 20 for a 5k(B)T barrier height and 300 for 9k(B)T, compared to unbiased simulation. The gains result from close emulation of natural (unbiased), instantonlike crossing events with artificially decreased waiting times between events that are corrected for in rate calculations. The artificial crossing events are generated using the closed-form solution to the most probable crossing event described by the Onsager-Machlup action. While the best biasing methods require the second derivative of the potential (resulting from the "Jacobian" term in the action, which is discussed at length), algorithms employing solely the first derivative do nearly as well. We discuss the importance of one-dimensional models to larger systems, and suggest extensions to higher-dimensional systems.

Mesh:

Year:  2000        PMID: 11304388     DOI: 10.1103/PhysRevE.63.016702

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  13 in total

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Review 7.  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

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10.  Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

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Journal:  J Chem Theory Comput       Date:  2014-06-03       Impact factor: 6.006

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