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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 features include: simulations in 1, 2, or 3 dimensions, a "virtual experimenter" who can manipulate or measure the simulated system, molecules with excluded volume, rule-based modeling, and Python bindings.

News

Smoldyn 2.67 released November 2, 2021

  • Improved Python interface
    • Supports all core Smoldyn functionality
    • Installs from regular download
    • Many Python example files
  • Long range force simulation
    • New command for long-range intermolecular forces
    • User-definable force equation
  • Preliminary filament support

Research Highlight

Yeast polarization

Ratiometric GPCR signaling enables directional sensing in yeast

Henderson, N.T., M. Pablo, D. Ghose, M.R. Clark-Cotton, T.R. Zyla, J. Nolen, T.C. Elston, D.J. Lew PLoS Biol. 17:e3000484, 2019

Yeast cells sense extracellular concentration gradients of pheromone molecules by determining which side of the cell binds more pheromone molecules. This is challenging because yeast cells are small, there are few enough receptors to create stochastic effects, and the receptors are not distributed evenly over the cell surface, but yeast nevertheless accomplish it reliably. By combining experiments, such as shown in the figure, with spatial simulations, the authors found that yeast cells detect the fraction of occupied receptors rather than absolute numbers.

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