A framework for discrete stochastic simulation on 3D moving boundary domains

Drawert, Brian; Hellander, Stefan; Trogdon, Michael; Yi, Tau-Mu; Petzold, Linda

doi:10.1063/1.4967338

Title: A framework for discrete stochastic simulation on 3D moving boundary domains

Journal Article · Mon Nov 14 00:00:00 EST 2016 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4967338· OSTI ID:1332016

^[1]; Hellander, Stefan ^[1];

^[2]; Yi, Tau-Mu ^[3]; Petzold, Linda ^[4]

Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Computer Science
Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Mechanical Engineering
Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Molecular, Cellular, and Developmental Biology
Univ. of California Santa Barbara, Santa Barbara, CA (United States). Dept. of Computer Science and Dept. of Mechanical Engineering

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.

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Research Organization:: Univ. of California Santa Barbara, Santa Barbara, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); US Army Research Office (ARO); National Science Foundation (NSF)

Grant/Contract Number:: sc0008975; R01-GM113241; R01-EB014877; W911NF-09-0001; DMS-1001012

OSTI ID:: 1332016

Alternate ID(s):: OSTI ID: 1420730; OSTI ID: 1423940

Journal Information:: Journal of Chemical Physics, Journal Name: Journal of Chemical Physics Vol. 145 Journal Issue: 18; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 11 works

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Cited By (2)

Simulating biological processes: stochastic physics from whole cells to colonies Earnest, Tyler M.; Cole, John A.; Luthey-Schulten, Zaida Reports on Progress in Physics, Vol. 81, Issue 5 https://doi.org/10.1088/1361-6633/aaae2c	journal	April 2018
The effect of cell geometry on polarization in budding yeast Trogdon, Michael; Drawert, Brian; Gomez, Carlos PLOS Computational Biology, Vol. 14, Issue 6 https://doi.org/10.1371/journal.pcbi.1006241	journal	June 2018

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Title: A framework for discrete stochastic simulation on 3D moving boundary domains

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