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What Smoldyn is

Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.

Smoldyn is easy to use and easy to install. It is more accurate and faster than other particle-based simulators. Smoldyn's unique features include: a "virtual experimenter" who can manipulate or measure the simulated system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.

News

Smoldyn 2.44 released June 27, 2016

  • Supports rule-based modeling with both wildcards and BioNetGen.
  • Allows variables and arithmetic in input files.
  • Improved Windows installation.
  • Improved Libsmoldyn compiling and linking.
  • Improved excluded volume interactions.
  • New tutorial section in User's Manual.

Research Highlight

Crowding

Excluded volume effects in on- and off-lattice reaction-diffusion models

Meinecke, L. and M. Eriksson, ArXiv 2016

Simulations with off-lattice Brownian dynamics (e.g. Smoldyn) are computationally expensive in crowded environments. This paper investigates the extent to which on-lattice simulations can simulate reactions and diffusion in the presence of crowders. The authors show that diffusion is slowed down in the off-lattice model since randomly distributed obstacles effectively exclude more volume than those ordered on an artificial grid. Crowded reaction rates can be both increased and decreased by the grid structure. Grid artifacts increase with increasing crowder density. The authors conclude that the computationally more efficient on-lattice simulations are accurate only for low crowder densities.

Smoldyn is written and maintained by Steve Andrews. Development has been supported by the National Institutes of Health, the U.S. Department of Energy, the National Science Foundation, and the MITRE Corporation, albeit never by funding that was dedicated specifically for this purpose.

NIH DOE NSF MITRE