Journal
JOURNAL OF COMPUTATIONAL PHYSICS
Volume 227, Issue 19, Pages 8672-8684Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.jcp.2008.06.010
Keywords
stochastic chemical kinetic systems; stochastic processes; transition paths and transition rates; large deviation theory; numerical methods; constraint optimization
Funding
- NSF [DMS-0609315]
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We present a new framework for finding the optimal transition paths of metastable stochastic chemical kinetic systems with large system size. The optimal transition paths are identified to be the most probable paths according to the Large Deviation Theory of stochastic processes. Dynamical equations for the optimal transition paths are derived using the variational principle. A modified Minimum Action Method (MAM) is proposed as a numerical scheme to solve the optimal transition paths. Applications to Gene Regulatory Networks such as the toggle switch model and the Lactose Operon Model in Escherichia coli are presented as numerical examples. (C) 2008 Elsevier Inc. All rights reserved.
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