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Artificial Chemistries$
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Wolfgang Banzhaf and Lidia Yamamoto

Print publication date: 2015

Print ISBN-13: 9780262029438

Published to MIT Press Scholarship Online: September 2016

DOI: 10.7551/mitpress/9780262029438.001.0001

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Computing Chemical Reactions

Computing Chemical Reactions

(p.63) Chapter 4 Computing Chemical Reactions
Artificial Chemistries

Wolfgang Banzhaf

Lidia Yamamoto

The MIT Press

This chapter examines various reactor algorithms that are frequently used in artificial chemistries. We contrast macroscopic, deterministic reaction algorithms and microscopic, stochastic reaction algorithms. The Chemical Master Equation is introduced, followed by well-known simulation algorithms such as Gillespie’s direct method and tau-leaping. An overview of algorithms that simulate spatial and multicompartmental chemistries then follows, from numerical integration to stochastic reaction-diffusion algorithms based on subvolumes.

Keywords:   Chemical master equation, Kinetic Monte Carlo method, Next reaction method, Next subvolume method, Reaction diffusion, Stochastic simulation algorithm, Tau leaping

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