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 2.38 released October 22, 2015

  • Fixed a substantial bug in surface diffusion. In the process, made surface diffusion run faster.
  • Added support for single molecule tracking simulations including reaction logging and serial number control.
  • Added inter-surface reactions, growing simulation volumes, and several commands.
  • Fixed several minor bugs.

Added web support for data calibration

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

Research Highlight

Bax model

Bax monomers form dimer units in the membrane that further self-assemble into multiple oligomeric species

Subburaj, Y., K. Cosentino, M. Axmann, E. Pedrueza-Villalmanzo, E. Hermann, S. Bleicken, J. Spatz, and A.J. García-Sáez, Nature Comm. 6:8042, 2015

Bax is a key regulator of apoptosis, mediating cytochrome c release to the cytosol via oligomerization in the outer mitochondrial membrane. These authors investigated the molecular mechanism of Bax assembly and regulation by other Bcl-2 members. They found that Bax binds to the membrane in a monomeric state and then rapidly self-assembles. They also show that other proteins, cBid and Bcl-xL, help drive Bax activity. Based on these experimental results, they developed a theoretical model, using Smoldyn, which presents a new mechanism for the molecular pathway of Bax assembly to form the apoptotic pore.

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.