Study on an Optimistic Reaction-Diusion Simulator based on Gillespie SSA

The parallel simulation of biochemical reactions is a very interesting problem: biochemical systems are inherently parallel, yet the majority of the algorithms to simulate them, including the well-known and widespread Gillespie SSA, are strictly sequential. Here we investigate, in a general way, how to characterize the simulation of biochemical systems in terms of Discrete Event Simulation. We dissect their inherent parallelism in order both to exploit the work done in this area and to speed-up their simulation. We study the peculiar characteristics of discrete biological simulations in order to select the parallelization technique which provides the greater benefits, as well as to touch its limits. We then focus on reaction-diffusion systems: we design and implement an efficient parallel algorithm for simulating such systems that include both reactions between entities and movements throughout the space. This is the preliminary version of a paper that was published in Proceedings of the sixth international conference on Computational Methods in Systems Biology (CMSB2008), LNBI 5307, pp. 191 – 210. The original publication is available at http://www.springerlink.com/content/w341771l12012560