Journal article
Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations
The Journal of chemical physics, Vol.137(15), pp.154111-154111
10/21/2012
DOI: 10.1063/1.4758459
PMCID: PMC3487926
PMID: 23083152
Abstract
The spatial direct method with gradient-based diffusion is an accelerated stochastic reaction-diffusion simulation algorithm that treats diffusive transfers between neighboring subvolumes based on concentration gradients. This recent method achieved a marked improvement in simulation speed and reduction in the number of time-steps required to complete a simulation run, compared with the exact algorithm, by sampling only the net diffusion events, instead of sampling all diffusion events. Although the spatial direct method with gradient-based diffusion gives accurate means of simulation ensembles, its gradient-based diffusion strategy results in reduced fluctuations in populations of diffusive species. In this paper, we present a new improved algorithm that is able to anticipate all possible microscopic fluctuations due to diffusive transfers in the system and incorporate this information to retain the same degree of fluctuations in populations of diffusing species as the exact algorithm. The new algorithm also provides a capability to set the desired level of fluctuation per diffusing species, which facilitates adjusting the balance between the degree of exactness in simulation results and the simulation speed. We present numerical results that illustrate the recovery of fluctuations together with the accuracy and efficiency of the new algorithm. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4758459]
Details
- Title: Subtitle
- Improved spatial direct method with gradient-based diffusion to retain full diffusive fluctuations
- Creators
- Wonryull Koh - George Mason UniversityKim T. Blackwell - George Mason University
- Resource Type
- Journal article
- Publication Details
- The Journal of chemical physics, Vol.137(15), pp.154111-154111
- DOI
- 10.1063/1.4758459
- PMID
- 23083152
- PMCID
- PMC3487926
- NLM abbreviation
- J Chem Phys
- ISSN
- 0021-9606
- eISSN
- 1089-7690
- Publisher
- Amer Inst Physics
- Number of pages
- 14
- Grant note
- RO1 AA18066; AA16022 / CRCNS program (NSF) through NIH R44AA018066 / NATIONAL INSTITUTE ON ALCOHOL ABUSE AND ALCOHOLISM; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute on Alcohol Abuse & Alcoholism (NIAAA) RO1 AA18066; AA16022 / CRCNS program (NIH)
- Language
- English
- Date published
- 10/21/2012
- Academic Unit
- Roy J. Carver Department of Biomedical Engineering; Iowa Neuroscience Institute
- Record Identifier
- 9984446278502771
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