title: Multiscale reaction-diffusion simulations with Smoldyn.
abstract: Smoldyn is a software package for stochastic modelling of spatial biochemical networks and intracellular systems. It was originally developed with an accurate off-lattice particle-based model at its core. This has recently been enhanced with the addition of a computationally efficient on-lattice model, which can be run stand-alone or coupled together for multiscale simulations using both models in regions where they are most required, increasing the applicability of Smoldyn to larger molecule numbers and spatial domains. Simulations can switch between models with only small additions to their configuration file, enabling users with existing Smoldyn configuration files to run the new on-lattice model with any reaction, species or surface descriptions they might already have.
  
  
  METHODS
  Source code and binaries freely available for download at www.smoldyn.org, implemented in C/C++ and supported on Linux, Mac OSX and MS Windows.
authors: Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and.
authors: Martin
authors: M
authors: Robinson
authors: Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, United States.
authors: Steven S
authors: SS
authors: Andrews
authors: Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, United Kingdom and.
authors: Radek
authors: R
authors: Erban
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D004058:Diffusion; D008954:Models, Biological; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D015398:Signal Transduction; D012984:Software