منابع مشابه
Nonequilibrium Rare-Event Sampling
This paper by Berryman and Schilling [1] has been in the literature for a year now, and is a valuable addition to the battery of techniques available to study nonequilibrium processes by molecular simulation; but it seems not to have attracted much attention. In the challenging field of " rare events " , there are three broad target areas, of increasing degree of difficulty: (a) systems in equi...
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We discuss uniform sampling algorithms that are based on stochastic growth methods, using sampling of extreme configurations of polymers in simple lattice models as a motivation. We shall show how a series of clever enhancements to a fifty-odd year old algorithm, the Rosenbluth method, led to a cutting-edge algorithm capable of uniform sampling of equilibrium statistical mechanical systems of p...
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Rare events are ubiquitous in many different fields, yet they are notoriously difficult to simulate because few, if any, events are observed in a conventional simulation run. Over the past several decades, specialized simulation methods have been developed to overcome this problem. We review one recently developed class of such methods, known as forward flux sampling. Forward flux sampling uses...
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SFI Working Papers contain accounts of scienti5ic work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in peer-reviewed journals or proceedings volumes, but not papers that have already appeared in print. Except for papers by our external faculty, papers must be based on work done at SFI, inspired by an invited vis...
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Stochastic simulation has been a powerful tool for studying the dynamics of gene regulatory networks, particularly in terms of understanding how cell-phenotype stability and fate-transitions are impacted by noisy gene expression. However, gene networks often have dynamics characterized by multiple attractors. Stochastic simulation is often inefficient for such systems, because most of the simul...
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ژورنال
عنوان ژورنال: Chaos: An Interdisciplinary Journal of Nonlinear Science
سال: 2019
ISSN: 1054-1500,1089-7682
DOI: 10.1063/1.5120509