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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 2.54 released August 27, 2017

  • Partial support for moving surfaces
    • Compartments can translate or diffuse.
  • Rule-based modeling with wildcards or BioNetGen.
    • On-the-fly reaction network generation.
    • Rules for molecular properties
    • Properties for rule-based reactions
  • Improved arithmetic in input files.
  • Minor bug fixes.

Research Highlight

Particle track

Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling

Changjiang You, Tatiana T. Marquez-Lago, Christian Paolo Richter, Stephan Wilmes, Ignacio Moraga, K. Christopher Garcia, André Leier, Jacob Piehler, Science Advances 2:e1600452, 2016

Recent results have suggested that cell plasma membranes may be compartmentalized into small corrals or microcompartments by the underlying membrane cytoskeleton. This paper combined experimental and simulation approaches to investigate the consequences of those microcompartments on receptor dimerization. The authors showed that it stabilized receptor dimers and caused dissociated receptors to reassociate rapidly, thus helping maintain signaling complexes.

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