Smoldyn on Graphics Processing Units: Massively Parallel Brownian Dynamics Simulations
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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As we obtain better abilities to observe cellular biochemistry at the single cell / molecular levels, such as through fluorescent correlation spectroscopy and single particle tracking, evidences are accumulating that the cells may be taking advantage of intracellular spatial features to realize and optimize their functions. Computer simulation is a useful means to bridge the gap between the microscopic, physico-chemical picture of how macro-molecules diffuse and react, and the scales of time and space where biochemistry and physiology take place.