title: Stochastic reaction-diffusion processes with embedded lower-dimensional structures.
abstract: Small copy numbers of many molecular species in biological cells require stochastic models of the chemical reactions between the molecules and their motion. Important reactions often take place on one-dimensional structures embedded in three dimensions with molecules migrating between the dimensions. Examples of polymer structures in cells are DNA, microtubules, and actin filaments. An algorithm for simulation of such systems is developed at a mesoscopic level of approximation. An arbitrarily shaped polymer is coupled to a background Cartesian mesh in three dimensions. The realization of the system is made with a stochastic simulation algorithm in the spirit of Gillespie. The method is applied to model problems for verification and two more detailed models of transcription factor interaction with the DNA.
authors.affiliation: Division of Scientific Computing, Department of Information Technology, Uppsala University, P.O. Box 337, 75105, Uppsala, Sweden, siyang.wang@it.uu.se.
authors.forename: Siyang
authors.initials: S
authors.lastname: Wang
authors.forename: Johan
authors.initials: J
authors.lastname: Elf
authors.forename: Stefan
authors.initials: S
authors.lastname: Hellander
authors.forename: Per
authors.initials: P
authors.lastname: Lötstedt
mesh_terms: D001704:Biopolymers / Q000502:physiology*; D008954:Models, Biological; D015233:Models, Statistical
chemical_list: D001704:Biopolymers