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.


Smoldyn 2.36 released June 9, 2015

  • Fixed a bug that affected bounce reactions in very rare cases.
  • Changed default graphic display rate, resulting in much faster simulations.

Added web support for data calibration

  • Completely unrelated to Smoldyn, but may be useful for researchers who calibrate quantitative data.

Surface diffusion errors

  • Surface diffusion turns out to be less accurate than anticipated when using small panels. This will be fixed in the next release.

Research Highlight

chromosome domains

Nucleolar tethering mediates pairing between the IgH and Myc loci

Daniel E. Strongin, Mark Groudine, Joan C. Ritland Politz, Nucleus 5:474-481, 2014

The genome is spatially organized within the eukaryotic nucleus. One aspect of this is that gene loci on different chromosomes can preferentially colocalize. Using mouse strains that have different gene arragements on their chromosomes, these authors investigated the driving force behind the colocalization of the IgH and Myc loci. They found that it arose when both loci were on chromosomes that had nucleolar organizer regions (NORs). These are sites of ribosomal DNA repeat sequences, which nucleate nucleoli. Together with simulations, these results implied that chromosome tethering to nucleoli can help colocalize genes. The figure shows one chromosome in yellow, another in blue, and nucleoli in red, in a strain where colocalization occurs.

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.