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E-grāmata: Artificial Chemistries

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, (Memorial University of Newfoundland)
  • Formāts: 576 pages
  • Sērija : The MIT Press
  • Izdošanas datums: 17-Jul-2015
  • Izdevniecība: MIT Press
  • Valoda: eng
  • ISBN-13: 9780262329460
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  • Formāts: 576 pages
  • Sērija : The MIT Press
  • Izdošanas datums: 17-Jul-2015
  • Izdevniecība: MIT Press
  • Valoda: eng
  • ISBN-13: 9780262329460
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The field of Artificial Life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of Artificial Chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from primitive, prebiotic forms of self-organization, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In Artificial Chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found both in the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. This book offers an introduction to the fundamental concepts of ACs, covering both theory and practical applications.

After a general overview of the field and its methodology, the book reviews important aspects of biology, including basic mechanisms of evolution; discusses examples of ACs drawn from the literature; considers fundamental questions of how order can emerge, emphasizing the concept of chemical organization (a closed and self-maintaining set of chemicals); and surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs.

Preface xi
I Foundations
1(74)
1 Introduction
3(8)
2 Basic Concepts of Artificial Chemistries
11(34)
2.1 Modeling and Simulation
11(4)
2.2 Chemistry Concepts
15(10)
2.3 General Structure of an Artificial Chemistry
25(6)
2.4 A Few Important Distinctions
31(2)
2.5 Two Examples
33(5)
2.6 Frequently Used Techniques in ACs
38(5)
2.7 Summary
43(2)
3 The Matrix Chemistry as an Example
45(18)
3.1 The Basic Matrix Chemistry
46(4)
3.2 The Simplest System, N = 4
50(5)
3.3 The System N = 9
55(4)
3.4 Systems with Larger N
59(2)
3.5 Summary
61(2)
4 Computing Chemical Reactions
63(12)
4.1 From Macroscopic to Microscopic Chemical Dynamics
63(2)
4.2 Stochastic Reaction Algorithms
65(6)
4.3 Spatial and Multicompartmental Algorithms
71(2)
4.4 Summary
73(2)
II Life and Evolution
75(104)
5 The Chemistry of Life
77(34)
5.1 What Is Life?
79(1)
5.2 The Building Blocks of Life
80(13)
5.3 The Organization of Modern Cells
93(7)
5.4 Multicellular Organisms
100(9)
5.5 Summary
109(2)
6 The Essence of Life
111(28)
6.1 A Minimal Cell
111(8)
6.2 Origin of Life
119(11)
6.3 Artificial Chemistry Contributions to Origin of Life Research
130(6)
6.4 Summary
136(3)
7 Evolution
139(20)
7.1 Evolution: Taming Combinatorics to Improve Life
140(1)
7.2 Evolutionary Dynamics from an AC Perspective
141(13)
7.3 Artificial Chemistries for Evolution
154(3)
7.4 Summary and Open Issues
157(2)
8 Complexity and Open-Ended Evolution
159(20)
8.1 Evolution: Steering Self-Organization and Promoting Innovation
159(2)
8.2 Coevolutionary Dynamics in Ecologies
161(4)
8.3 Robustness and Evolvability
165(4)
8.4 Complexity Growth
169(6)
8.5 Toward Open-Ended Artificial Evolution
175(2)
8.6 Summary
177(2)
III Approaches to Artificial Chemistries
179(76)
9 Rewriting Systems
181(14)
9.1 Lambda Calculus
182(2)
9.2 Gamma
184(2)
9.3 The Chemical Abstract Machine
186(1)
9.4 Chemical Rewriting System on Multisets
187(1)
9.5 P systems
188(3)
9.6 MGS
191(2)
9.7 Other Formal Calculi Inspired by a Chemical Metaphor
193(1)
9.8 L-Systems and Other Rewriting Systems
193(1)
9.9 Summary
194(1)
10 Automata and Machines
195(30)
10.1 Finite State Automata
196(1)
10.2 Turing Machines
197(1)
10.3 Von Neumann Machines
198(2)
10.4 Cellular Automata
200(2)
10.5 Examples of Artificial Chemistries Based on Turing Machines
202(5)
10.6 Artificial Chemistries Based on von Neumann Machines
207(8)
10.7 Artificial Chemistries Based on Cellular Automata
215(7)
10.8 Summary
222(3)
11 Bio-inspired Artificial Chemistries
225(30)
11.1 String-Based Artificial Chemistries
225(9)
11.2 Lock-and-Key Artificial Chemistries
234(6)
11.3 Networks
240(8)
11.4 Spatial Structuring and Movement in Artificial Chemistries
248(6)
11.5 Summary
254(1)
IV Order Construction
255(66)
12 The Structure of Organizations
257(18)
12.1 Basic Definitions
259(3)
12.2 Generators
262(1)
12.3 Bringing Order into Organizations
263(2)
12.4 Novelty and Innovation
265(1)
12.5 Examples of the Statics of Organizations
266(4)
12.6 How to Calculate Closed and Self-Maintaining Sets
270(3)
12.7 Summary
273(2)
13 The Dynamics of Organizations
275(12)
13.1 Flows, Stoichiometry and Kinetic Constants
275(2)
13.2 Examples of the Dynamics of Organization
277(5)
13.3 Observing Organizations
282(1)
13.4 Probabilistic Notions of Closure and Self-Maintenance
283(2)
13.5 Summary
285(2)
14 Self-Organization and Emergent Phenomena
287(20)
14.1 Examples of Self-Organizing Systems
288(1)
14.2 Explanatory Concepts of Self-Organization
289(6)
14.3 The Emergence of Phenomena
295(3)
14.4 Explanatory Concepts of Emergence
298(6)
14.5 Emergence and Top-Down Causation
304(2)
14.6 Summary
306(1)
15 Constructive Dynamical Systems
307(14)
15.1 Novelty, Innovation, Emergence
307(2)
15.2 Birth Processes at the Same Level
309(8)
15.3 The Emergence of Entities on a Higher Level
317(2)
15.4 Summary
319(2)
V Applications
321(128)
16 Applications of Artificial Chemistries
323(22)
16.1 Robots Controlled by Artificial Chemistries
324(6)
16.2 ACs for Networking
330(4)
16.3 Language Dynamics and Evolution
334(4)
16.4 Music Composition Using Algorithmic Chemistries
338(1)
16.5 Proof Systems
339(1)
16.6 Artificial Chemistry and Genetic Programming
340(4)
16.7 Summary
344(1)
17 Computing with Artificial Chemistries
345(28)
17.1 Principles of implementation
346(9)
17.2 Search and Optimization Algorithms Inspired by Chemistry
355(3)
17.3 Distributed Algorithms Using Chemical Computing
358(8)
17.4 In Silico Simulation of Wet Chemical Computing
366(6)
17.5 Summary
372(1)
18 Modeling Biological Systems
373(32)
18.1 Folding Algorithms
374(5)
18.2 Basic Kinetics of Biomolecular Interactions
379(4)
18.3 Biochemical Pathways
383(8)
18.4 Modeling Genetic Regulatory Networks
391(5)
18.5 Cell Differentiation and Multicellularity
396(2)
18.6 Morphogenesis
398(5)
18.7 Summary
403(2)
19 Wet Artificial Chemistries
405(34)
19.1 Artificial Building Blocks of Life
405(6)
19.2 Synthetic Life and Protocells
411(6)
19.3 Chemical and Biochemical Computation
417(14)
19.4 In Vivo Computing with Bacteria and Other Living Organisms
431(4)
19.5 Ethical Issues
435(2)
19.6 Summary
437(2)
20 Beyond Chemistry and Biology
439(10)
20.1 Mechanical Self-Assembly
439(3)
20.2 Nuclear and Particle Physics
442(2)
20.3 Economic Systems
444(2)
20.4 Social Systems
446(2)
20.5 Summary
448(1)
VI Conclusions
449(12)
21 Summary and Perspectives
451(10)
21.1 Some Common Criticisms of the Artificial Chemistry Approach
451(2)
21.2 Delimiting the Borders of the Field
453(3)
21.3 Main Features of Artificial Chemistries
456(3)
21.4 Conclusion
459(2)
Further Reading
461(4)
Appendix: Setting up Your Own Artificial Chemistry System
465(16)
The PyCellChemistry Package
465(3)
Writing Your Own Artificial Chemistry in Python
468(10)
Further Resources
478(3)
Bibliography 481(50)
Author Index 531(14)
Subject Index 545