A fully pipelined FPGA architecture for stochastic simulation of chemical systems

Simulation of chemical systems allows bio-chemists to understand how the interactions of individual molecules can lead to cellular and organism level behaviour. When the concentration of moleculesis very small, it is necessary to model every single chemical interaction in a Monte-Carlo simulation, presenting a huge computational burden. This paper presents a new fully pipelined architecture for chemical simulation, which avoids the traditional approach of optimising for minimum operation count, and instead optimises for throughput and parallelism. We show that even though this leads to a higher asymptotic operation count per simulation step, it allows for a much greater degree of spatial and pipeline parallelism, and the increased area is offset by much greater throughput. The new architecture is implemented in a Virtex-6 SX475T and can sustain a rate of over 1 billion reactions per second for problems with less than 64 reactions. Compared against existing chemical simulators on small to medium size chemical models, the new architecture is 30-100 times faster than a commercial software simulator running on an 8-core 3.4GHz Core i7, and 12-30 times faster than the best existing FPGA simulators.