Stiffness detection and reduction in discrete stochastic simulation of biochemical systems
Authors: 
Yang Pu, Layne T. Watson, Yang CaoAuthors Info & Claims
Yang Pu, Layne T. Watson, Yang CaoAuthors Info & ClaimsArticle No.: 88, Pages 1 - 8
Abstract
Typical multiscale biochemical models contain fast-scale and slow-scale reactions, where "fast" reactions fire much more frequently than "slow" ones. This feature often causes stiffness in discrete stochastic simulation methods such as Gillespie's algorithm and tau-leaping methods leading to inefficient simulation. This paper proposes a new strategy to automatically detect stiffness and identify species that cause stiffness. Stiffness reduction methods are also discussed. Numerical results on a heat shock protein regulation model demonstrate the efficiency and accuracy of the proposed method for multiscale biochemical systems.
References
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- Stiffness detection and reduction in discrete stochastic simulation of biochemical systems
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Published In
April 2010
1726 pages
ISBN:9781450300698
- General Chairs:
- Robert McGraw,
- Eric Imsand,
- Program Chair:
- Michael J. Chinni
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- SCS: Society for Modeling and Simulation International
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Society for Computer Simulation International
San Diego, CA, United States
Publication History
Published: 11 April 2010
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- University of California Santa Barbara
- National Institutes of Health
- Division of Computing and Communication Foundations
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SpringSim '10
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- SCS
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