Journal article
Asynchronous tau-leaping
The Journal of chemical physics, Vol.144(12), pp.125104-125104
03/28/2016
DOI: 10.1063/1.4944575
PMCID: PMC4818278
PMID: 27036481
Abstract
Stochastic simulation of cell signaling pathways and genetic regulatory networks has contributed to the understanding of cell function; however, investigation of larger, more complicated systems requires computationally efficient algorithms. tau-leaping methods, which improve efficiency when some molecules have high copy numbers, either use a fixed leap size, which does not adapt to changing state, or recalculate leap size at a heavy computational cost. We present a hybrid simulation method for reaction-diffusion systems which combines exact stochastic simulation and tau-leaping in a dynamic way. Putative times of events are stored in a priority queue, which reduces the cost of each step of the simulation. For every reaction and diffusion channel at each step of the simulation the more efficient of an exact stochastic event or a tau-leap is chosen. This new approach removes the inherent trade-off between speed and accuracy in stiff systems which was present in all tau-leaping methods by allowing each reaction channel to proceed at its own pace. Both directions of reversible reactions and diffusion are combined in a single event, allowing bigger leaps to be taken. This improves efficiency for systems near equilibrium where forward and backward events are approximately equally frequent. Comparison with existing algorithms and behaviour for five test cases of varying complexity shows that the new method is almost as accurate as exact stochastic simulation, scales well for large systems, and for various problems can be significantly faster than tau-leaping. (C) 2016 AIP Publishing LLC.
Details
- Title: Subtitle
- Asynchronous tau-leaping
- Creators
- Zbigniew Jedrzejewski-Szmek - George Mason UniversityKim T. Blackwell - George Mason University
- Resource Type
- Journal article
- Publication Details
- The Journal of chemical physics, Vol.144(12), pp.125104-125104
- DOI
- 10.1063/1.4944575
- PMID
- 27036481
- PMCID
- PMC4818278
- NLM abbreviation
- J Chem Phys
- ISSN
- 0021-9606
- eISSN
- 1089-7690
- Publisher
- Amer Inst Physics
- Number of pages
- 18
- Grant note
- R01 AA16022 / NIH-NSF program on Collaborative Research in Computational Neuroscience through NIH
- Language
- English
- Date published
- 03/28/2016
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Iowa Neuroscience Institute
- Record Identifier
- 9984446267902771
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