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Title: The time dependent propensity function for acceleration of spatial stochastic simulation of reaction–diffusion systems

The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy.
Authors:
 [1] ;  [1] ;  [2] ;  [1]
  1. Department of Computer Science, University of California, Santa Barbara (United States)
  2. Teradata Inc., El Segundo, California (United States)
Publication Date:
OSTI Identifier:
22382120
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of Computational Physics; Journal Volume: 274; Other Information: Copyright (c) 2014 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; ACCELERATION; ACCURACY; ALGORITHMS; COMPUTERIZED SIMULATION; DIFFUSION; EFFICIENCY; GAIN; RESOLUTION; STOCHASTIC PROCESSES