Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs

Denis V. Gladkov, Samuel Alberts, Roshan M. D’Souza, Steven Andrews
Department of Mechanical Engineering, UW-Milwaukee, 3200 N Cramer Street, Milwaukee, WI, 53211
19th High Performance Computing Symposium (SpringSim), 2011


   title={Accelerating the Smoldyn Spatial Stochastic Biochemical Reaction Network Simulator Using GPUs},

   author={Gladkov, D. and Albters, S. and D’Souza, R. and Andrews, S.},



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Smoldyn is a spatio-temporal biochemical reaction network simulator. It belongs to a class of methods called particle-based methods and is capable of handling effects such as molecular crowding. Individual molecules are modelled as point objects that can diffuse and react in a control volume. Since each molecule has to be simulated individually, the computational complexity of the simulator is quite high. Efficiently executing high fidelity models (> 10^6 molecules) is not feasible with traditional serial computing on central processing units (CPUs). In this paper we present novel dataparallel algorithms designed to execute on graphics processing units (GPUs) to handle the computational complexity. Our preliminary implementation can handle diffusion, zeroorder, uni-molecular, and bi-molecular reactions. Our preliminary results show performance gain of over 200x over the original implementation without loss of accuracy.
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