- Title Pages
- Epigraph
- Preface
-
Chapter 1 Introduction -
Chapter 2 Basic Concepts of Artificial Chemistries -
Chapter 3 The Matrix Chemistry as an Example -
Chapter 4 Computing Chemical Reactions -
Chapter 5 The Chemistry of Life -
Chapter 6 The Essence of Life -
Chapter 7 Evolution -
Chapter 8 Complexity and Open-Ended Evolution -
Chapter 9 Rewriting Systems -
Chapter 10 Automata and Machines -
Chapter 11 Bio-inspired Artificial Chemistries -
Chapter 12 The Structure of Organizations -
Chapter 13 The Dynamics of Organizations -
Chapter 14 Self-Organization and Emergent Phenomena -
Chapter 15 Constructive Dynamical Systems -
Chapter 16 Applications of Artificial Chemistries -
Chapter 17 Computing with Artificial Chemistries -
Chapter 18 Modeling Biological Systems -
Chapter 19 Wet Artificial Chemistries -
Chapter 20 Beyond Chemistry and Biology -
Chapter 21 Summary and Perspectives - Further Reading
-
Appendix: Setting up Your Own Artificial Chemistry System - Bibliography
- Author Index
- Subject Index
Modeling Biological Systems
Modeling Biological Systems
- Chapter:
- (p.373) Chapter 18 Modeling Biological Systems
- Source:
- Artificial Chemistries
- Author(s):
Wolfgang Banzhaf
Lidia Yamamoto
- Publisher:
- 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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- Title Pages
- Epigraph
- Preface
-
Chapter 1 Introduction -
Chapter 2 Basic Concepts of Artificial Chemistries -
Chapter 3 The Matrix Chemistry as an Example -
Chapter 4 Computing Chemical Reactions -
Chapter 5 The Chemistry of Life -
Chapter 6 The Essence of Life -
Chapter 7 Evolution -
Chapter 8 Complexity and Open-Ended Evolution -
Chapter 9 Rewriting Systems -
Chapter 10 Automata and Machines -
Chapter 11 Bio-inspired Artificial Chemistries -
Chapter 12 The Structure of Organizations -
Chapter 13 The Dynamics of Organizations -
Chapter 14 Self-Organization and Emergent Phenomena -
Chapter 15 Constructive Dynamical Systems -
Chapter 16 Applications of Artificial Chemistries -
Chapter 17 Computing with Artificial Chemistries -
Chapter 18 Modeling Biological Systems -
Chapter 19 Wet Artificial Chemistries -
Chapter 20 Beyond Chemistry and Biology -
Chapter 21 Summary and Perspectives - Further Reading
-
Appendix: Setting up Your Own Artificial Chemistry System - Bibliography
- Author Index
- Subject Index
