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

Content Provider	Europe PMC
Author	Drawert, Brian Hellander, Stefan Trogdon, Michael Yi, Tau-Mu Petzold, Linda
Copyright Year	2016
Abstract	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. 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.
Related Links	https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5116030&blobtype=pdf
Page Count	12
ISSN	00219606
Volume Number	145
DOI	10.1063/1.4967338
PubMed Central reference number	PMC5116030
Issue Number	18
PubMed reference number	27846706
Journal	The Journal of Chemical Physics [J Chem Phys]
e-ISSN	10897690
Language	English
Publisher	AIP Publishing LLC
Publisher Date	2016-11-01
Access Restriction	Open
Rights License	0021-9606/2016/145(18)/184113/12/$0.00 © 2016 Author(s).
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Medicine Physical and Theoretical Chemistry