Efficient Simulation of Reaction Systems on Graphics Processing Units

Abstract

Reaction systems represent a theoretical framework based on the regulation mechanisms of facilitation and inhibition of biochemical reactions. The dynamic process defined by a reaction system is typically derived by hand, starting from the set of reactions and a given context sequence. However, this procedure may be error-prone and time-consuming, especially when the size of the reaction system increases. Here we present HERESY, a simulator of reaction systems accelerated on Graphics Processing Units (GPUs). HERESY is based on a fine-grained parallelization strategy, whereby all reactions are simultaneously executed on the GPU, therefore reducing the overall running time of the simulation. HERESY is particularly advantageous for the simulation of large-scale reaction systems, consisting of hundreds or thousands of reactions. By considering as test case some reaction systems with an increasing number of reactions and entities, as well as an increasing number of entities per reaction, we show that HERESY allows up to 29A— speed-up with respect to a CPU-based simulator of reaction systems. Finally, we provide some directions for the optimization of HERESY, considering minimal reaction systems in normal form.