title: Simulating rare events using a weighted ensemble-based string method.
abstract: We introduce an extension to the weighted ensemble (WE) path sampling method to restrict sampling to a one-dimensional path through a high dimensional phase space. Our method, which is based on the finite-temperature string method, permits efficient sampling of both equilibrium and non-equilibrium systems. Sampling obtained from the WE method guides the adaptive refinement of a Voronoi tessellation of order parameter space, whose generating points, upon convergence, coincide with the principle reaction pathway. We demonstrate the application of this method to several simple, two-dimensional models of driven Brownian motion and to the conformational change of the nitrogen regulatory protein C receiver domain using an elastic network model. The simplicity of the two-dimensional models allows us to directly compare the efficiency of the WE method to conventional brute force simulations and other path sampling algorithms, while the example of protein conformational change demonstrates how the method can be used to efficiently study transitions in the space of many collective variables.
authors: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA. jla65@pitt.edu
authors: Joshua L
authors: JL
authors: Adelman
authors: Michael
authors: M
authors: Grabe
mesh_terms: D000465:Algorithms; D056004:Molecular Dynamics Simulation; D051922:PII Nitrogen Regulatory Proteins / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D051922:PII Nitrogen Regulatory Proteins
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