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The Many Roads to the Simulation of Reaction Systems

Ferretti Claudio, Leporati Alberto, Manzoni Luca, Porreca Antonio E.

Fundamenta Informaticae

2020

Vol. 171, nr 1-4

175--188

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool for biochemical systems, but in order to be able to employ them effectively in the field the presence of efficient and widely available simulators is essential. Here we explore three different algorithms and implementations of the simulation, comparing them to the current state of the art. We also show that we can obtain performances comparable to GPU-based simulations on real-world systems by using a carefully tuned CPU-based simulator.