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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, so it can 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 biological system. Smoldyn is easy to use and easy to install. It is also both 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. |
NewsSmoldyn 2.15 released July 20, 2010
Forum reopenedSmoldyn described in PLoS Comp. Biol. |
Research Highlight |
The figure shows a model of mating partner selection by yeast cells, from our recent PLoS Comp. Biol. paper. The mesh sphere on the outside is an "unbounded-emitter" type surface that makes the system behave like it is unbounded, while also limiting the number of molecules that Smoldyn has to simulate. The central sphere is a "receiver" cell that detects pheromone molecules (black dots) that are secreted by the surrounding cells. It determines the direction to the "target" cell, which is shown at the right and secretes pheromone faster than the other cells, through the gradient of pheromone-bound receptors (red dots) and unbound receptors (blue dots). This work showed that mating partner selection is vastly improved when the receiver cell secretes a pheromone-degrading protein called Bar1 (green dots). |
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.
