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.


Smoldyn 2.72 released August 17, 2023

  • Support for diffusion coefficient changes (e.g. lipid rafts)
  • Improved command line options
  • Added a command line input for logging diagnostics
  • Fixed a bug that affected excluded volume reactions
  • Allows longer input strings

Research Highlight


Colloidal Physics Modeling Reveals How Per-Ribosome Productivity Increases with Growth Rate in Escherichia coli

Maheshwari, A.J., A.M. Sunol, E. Gonzalez, D. Endy, R.N. Zia mBio 14:e02865-22, 2023

As cells are fed more nutrients so that they grow faster, they clearly need to produce proteins at a faster rate. However, it has been shown that they don't have a corresponding increase in the number of ribosomes, which implies that each ribosome must produce proteins faster. These authors explored how this works using particle-based simulations with "Colloidal Smoldyn", which is their extension of the Smoldyn software. In agreement with prior results, they found that faster growth rates lead to greater macromolecular crowding within cells and that this affects reaction rates in two opposing ways: rates increase due to higher effective reactant concentrations, and decrease due to inhibited diffusion. They showed that the former effect dominates in this case, thereby answering the question of how individual ribosomes are able to produce proteins faster with higher cell growth rates.

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.