title: A framework for discrete stochastic simulation on 3D moving boundary domains.
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.
authors.affiliation: Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Drawert
authors.affiliation: Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Hellander
authors.affiliation: Department of Mechanical Engineering, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Trogdon
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
authors.forename: Tau-Mu
authors.initials: TM
authors.lastname: Yi
authors.affiliation: Department of Computer Science, University of California-Santa Barbara, Santa Barbara, California 93106, USA.
authors.forename: Linda
authors.initials: L
authors.lastname: Petzold
mesh_terms: D001696:Biomechanical Phenomena; D004058:Diffusion; D007700:Kinetics; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000502:physiology; D013269:Stochastic Processes; D049490:Systems Biology