What Smoldyn isSmoldyn 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 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 2.26 released March 2, 2012
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Research Highlight
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Spatiotemporal maps of CaMKII in dendritic spinesKhan, S., T.S. Reese, N. Rajpoot, and A. Shabbir, J. Comput. Neurosci. In press, 2012The authors investigated the sequestration of calcium calmodulin dependent kinase (CaMKII) in neural dendritic spines, which is a key cellular mechanism for the formation and storage of memories. The figure shows confocal microscopy data of GFP-CamKII localization shortly the GFP was photo-activated at the asterisk; bright green regions, such as at the spine tip, indicate CamKII sequestration, while red regions indicate low CamKII concentrations. Smoldyn simulations showed that a major cause of sequestion is the high number of cytoskeletal binding sites at spine tips, rather than high binding affinities. |
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.
