A framework for discrete stochastic simulation on 3D moving boundary domains [electronic resource].
- Washington, D.C. : United States. Dept. of Energy. Office of Science, 2016. and Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy
- Physical Description:
- Article numbers 184,113 : digital, PDF file
- Additional Creators:
- United States. Department of Energy. Office of Science, National Institutes of Health (U.S.), United States. Army Research Office, National Science Foundation (U.S.), and United States. Department of Energy. Office of Scientific and Technical Information
- Restrictions on Access:
- Free-to-read Unrestricted online access
- We have developed a method for modeling spatial stochastic biochemical reactions in complex, three-dimensional, and time-dependent domains using the reaction-diffusion master equation formalism. In particular, we look to address the fully coupled problems that arise in systems biology where the shape and mechanical properties of a cell are determined by the state of the biochemistry and vice versa. To validate our method and characterize the error involved, we compare our results for a carefully constructed test problem to those of a microscale implementation. Finally, we demonstrate the effectiveness of our method by simulating a model of polarization and shmoo formation during the mating of yeast. The method is generally applicable to problems in systems biology where biochemistry and mechanics are coupled, and spatial stochastic effects are critical.
- Published through SciTech Connect., 11/14/2016., Journal of Chemical Physics 145 18 ISSN 0021-9606 AM, Brian Drawert; Stefan Hellander; Michael Trogdon; Tau-Mu Yi; Linda Petzold., and Univ. of California Santa Barbara, Santa Barbara, CA (United States)
- Funding Information:
- SC0008975, R01-GM113241, R01-EB014877, W911NF-09-0001, and DMS-1001012
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