title: Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface.
abstract: Smoldyn is a spatial and stochastic biochemical simulator. It treats each molecule of interest as an individual particle in continuous space, simulating molecular diffusion, molecule-membrane interactions and chemical reactions, all with good accuracy. This article presents several new features.
  
  
  
  Smoldyn now supports two types of rule-based modeling. These are a wildcard method, which is very convenient, and the BioNetGen package with extensions for spatial simulation, which is better for complicated models. Smoldyn also includes new algorithms for simulating the diffusion of surface-bound molecules and molecules with excluded volume. Both are exact in the limit of short time steps and reasonably good with longer steps. In addition, Smoldyn supports single-molecule tracking simulations. Finally, the Smoldyn source code can be accessed through a C/C ++ language library interface.
  
  
  
  Smoldyn software, documentation, code, and examples are at http://www.smoldyn.org .
  
  
  
  steven.s.andrews@gmail.com.
authors.affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.|Isaac Newton Institute for Mathematical Sciences, Cambridge CB3 0EH, UK.
authors.forename: Steven S
authors.initials: SS
authors.lastname: Andrews
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D046609:Libraries, Digital; D008956:Models, Chemical; D008958:Models, Molecular; D012984:Software