smoldyn_banner

Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution. It treats other molecules implicity, which enables it to simulate tens 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 chemical system.

Smoldyn's algorithms are exceptionally accurate. In particular, algorithms for molecular diffusion, chemical reactions, and molecule-surface interactions are essentially exact. This permits the use of relatively long time steps, which makes simulations run quickly.

Smoldyn is easy to use and easy to install. It also offers several unique features, such as 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 2.09 released Jan. 6, 2010

  • Installs on Mac, Linux, or Windows systems
  • Vastly improved graphics quality
  • Quantitative molecule-surface interactions: adsorption, desorption, and partial transmission
  • New system boundaries for simulating unbounded systems accurately and efficiently
  • Libmoleculizer module automatically generates the reaction network for protein-protein binding and protein modifications
  • Spatially variable diffusion coefficients can be simulated

Research Highlight

ecoli		 A Smoldyn E. coli signaling model that Lipkow and Odde developed. The red and black molecules depict a spatial gradient of phosphorylated and unphosphorylated messenger proteins. This research predicts stable gradients for several total protein concentrations. They arise from spatially separate kinases and phosphatases, activity-dependent protein associations, and slower diffusion coefficients for larger molecules.

Smoldyn is written and maintained by Steve Andrews. Development has been supported by the National Institutes of Health, the U.S. Department of Energy, and the National Science Foundation.

NIHDOENSF