The many roads to the simulation of reaction systems

DOI10.3233/FI-2020-1878zbMATH Open1435.68094arXiv1904.07445MaRDI QIDQ5114214FDOQ5114214

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

Publication date: 21 June 2020

Published in: Fundamenta Informaticae (Search for Journal in Brave)

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.

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

Recommendations

• Efficient simulation of reaction systems on graphics processing units
• Reaction systems
• Simple reaction systems and their classification
• WEBRSIM: a web-based reaction systems simulator
• Reaction systems made simple. A normal form and a classification theorem

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)

Cited In (4)

• Title not available (Why is that?)
• A logical and graphical framework for reaction systems
• Title not available (Why is that?)
• Title not available (Why is that?)

This page was built for publication: The many roads to the simulation of reaction systems

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5114214)