The many roads to the simulation of reaction systems

DOI10.3233/FI-2020-1878MaRDI QIDQ5114214zbMATHFDO

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

Publication date 21 June 2020

Published in Fundamenta Informaticae (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1904.07445

zbMATH Keywords

reaction systemssimulation of biochemical systems

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biologically inspired models of computation (DNA computing, membrane computing, etc.) (68Q07)

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.

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(11)

• Reaction-based models of biochemical networks
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• WEBRSIM: a web-based reaction systems simulator
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• Simulating reversible computation with reaction systems
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• Efficient simulation of reaction systems on graphics processing units
• A simple membrane computing method for simulating bio-chemical reactions
• Biochemical reaction rules with constraints
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• Simple reaction systems and their classification

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