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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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Modeling Biological Systems

Modeling Biological Systems

(p.373) Chapter 18 Modeling Biological Systems
Artificial Chemistries

Wolfgang Banzhaf

Lidia Yamamoto

The MIT Press

This chapter is devoted to one of the main applications of artificial chemistries, the modeling of biological systems. The chapter starts at the molecular level, with algorithms that model RNA and protein folding. An introduction to models of enzymatic reactions and the binding of proteins to genes then follows. Models of the dynamics of biochemical pathways are discussed next, with focus on metabolic networks. An overview of algorithms to simulate the large-scale reaction networks common in biology is presented afterwards. Genetic regulatory networks (GRNs) are examples of such large-scale reaction networks, and are discussed next. A treatment of cell differentiation, multicellularity and morphogenesis concludes the chapter.

Keywords:   Biochemical pathway, Cell differentiation, Enzyme kinetics, Genetic regulatory network, Hill kinetics, Metabolic network, Morphogenesis, Multicellularity, Protein folding, RNA folding

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