The Many Roads to the Simulation of Reaction Systems

Issue title: Interdisciplinary Nature of Information Processing Special Issue Dedicated to Giancarlo Mauri on the Occasion of His 70th Birthday

Guest editors: Alberto Dennunzio, Gheorghe Păun, Grzegorz Rozenberg and Claudio Zandron

Article type: Research Article

Authors: Ferretti, Claudio^{a; *} | Leporati, Alberto^a | Manzoni, Luca^a | Porreca, Antonio E.^b

Affiliations: [a] Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milan, Italy. ferretti@disco.unimib.it, leporati@disco.unimib.it, luca.manzoni@disco.unimib.it | [b] Aix Marseille Université, Université de Toulon, CNRS, LIS, Marseille, France. antonio.porreca@lis-lab.fr

Correspondence: [*] Address for correspondence: Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano-Bicocca, Viale Sarca 336, 20126 Milan, Italy

Abstract: 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.

Keywords: Reaction Systems, Simulation of Biochemical Systems

DOI: 10.3233/FI-2020-1878

Journal: Fundamenta Informaticae, vol. 171, no. 1-4, pp. 175-188, 2020