What Smoldyn isSmoldyn 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, enabling it can 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 relatively 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. |
NewsSmoldyn 2.25 released Sept. 26, 2011
Fast GPU Smoldyn implementations
Smoldyn in Virtual Cell
Upcoming talks about Smoldyn
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Research Highlight
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Computational investigation of the changing patterns of subtype specific NMDA receptor activation during physiological glutametergic neurotransmissionSingh, P., A.J. Hockenberry, V. Tiruvadi, and D.F. Meaney, PLoS Comput. Biol. 7:e1002106, 2011Neural NMDA receptors mediate many physiological functions, including the molecular basis for learning and memory. These receptors exist in various subtypes, which enables them to discriminate between different types of signals. Using Smoldyn models, the authors found that different receptors have different dynamic ranges, that specific subtypes dominate in long-term depression and long-term potentiation situations, and that the content of a specific subtype enhances response magnitude and fidelity during long-term potentiation. The yellow and red portions of the figure show pre- and post-synaptic regions, while dots represent receptors. |
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.
