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ОбложкаBanzhaf W. Artificial chemistries / W.Banzhaf, L.Yamamoto. - Cambridge; London: MIT press, 2015. - xv, 555 p.: ill., tab. - Bibliogr.: p.481-530. - Auth. ind.: p.531-543. – Sub. ind.: p.545-555. - ISBN 978-0-262-02943-8
Шифр: (И/Е0-B22) 02
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
Preface ........................................................ xi

I  Foundations .................................................. 1
1  Introduction ................................................. 3
2  Basic Concepts of Artificial Chemistries .................... 11
   2.1  Modeling and Simulation ................................ 11
   2.2  Chemistry Concepts ..................................... 15
   2.3  General Structure of an Artificial Chemistry ........... 25
   2.4  A Few Important Distinctions ........................... 31
   2.5  Two Examples ........................................... 33
   2.6  Frequently Used Techniques in ACs ...................... 38
   2.7  Summary ................................................ 43
3  The Matrix Chemistry as an Example .......................... 45
   3.1  The Basic Matrix Chemistry ............................. 46
   3.2  The Simplest System, N = 4 ............................. 50
   3.3  The System N = 9 ....................................... 55
   3.4  Systems with Larger N .................................. 59
   3.5  Summary ................................................ 61
4  Computing Chemical Reactions ................................ 63
   4.1  From Macroscopic to Microscopic Chemical Dynamics ...... 63
   4.2  Stochastic Reaction Algorithms ......................... 65
   4.3  Spatial and Multicompartmental Algorithms .............. 71
   4.4  Summary ................................................ 73

II. Life and Evolution ......................................... 75
5  The Chemistry of Life ....................................... 77
   5.1  What Is Life? .......................................... 79
   5.2  The Building Blocks of Life ............................ 80
   5.3  The Organization of Modern Cells ....................... 93
   5.4  Multicellular Organisms ............................... 100
   5.5  Summary ............................................... 109
6  The Essence of Life ........................................ 111
   6.1  A Minimal Cell ........................................ 111
   6.2  Origin of Life ........................................ 119
   6.3  Artificial Chemistry Contributions to Origin of Life
        Research .............................................. 130
   6.4  Summary ............................................... 136
7  Evolution .................................................. 139
   7.1  Evolution: Taming Combinatorics to Improve Life ....... 140
   7.2  Evolutionary Dynamics from an AC Perspective .......... 141
   7.3  Artificial Chemistries for Evolution .................. 154
   7.4  Summary and Open Issues ............................... 157
8  Complexity and Open-Ended Evolution ........................ 159
   8.1  Evolution: Steering Self-Organization and Promoting
        Innovation ............................................ 159
   8.2  Coevolutionary Dynamics in Ecologies .................. 161
   8.3  Robustness and Evolvability ........................... 165
   8.4  Complexity Growth ..................................... 169
   8.5  Toward Open-Ended Artificial Evolution ................ 175
   8.6  Summary ............................................... 177

III. Approaches to Artificial Chemistries ..................... 179
9  Rewriting Systems .......................................... 181
   9.1  Lambda Calculus ....................................... 182
   9.2  Gamma ................................................. 184
   9.3  The Chemical Abstract Machine ......................... 186
   9.4  Chemical Rewriting System on Multisets ................ 187
   9.5  P systems ............................................. 188
   9.6  MGS ................................................... 191
   9.7  Other Formal Calculi Inspired by a Chemical Metaphor .. 193
   9.8  L-Systems and Other Rewriting Systems ................. 193
   9.9  Summary ............................................... 194
10 Automata and Machines ...................................... 195
   10.1 Finite State Automata ................................. 196
   10.2 Turing Machines ....................................... 197
   10.3 Von Neumann Machines .................................. 198
   10.4 Cellular Automata ..................................... 200
   10.5 Examples of Artificial Chemistries Based on Turing
        Machines .............................................. 202
   10.6 Artificial Chemistries Based on von Neumann Machines .. 207
   10.7 Artificial Chemistries Based on Cellular Automata ..... 215
   10.8 Summary ............................................... 222
11 Bio-inspired Artificial Chemistries ........................ 225
   11.1 String-Based Artificial Chemistries ................... 225
   11.2 Lock-and-Key Artificial Chemistries ................... 234
   11.3 Networks .............................................. 240
   11.4 Spatial Structuring and Movement in Artificial
        Chemistries ........................................... 248
   11.5 Summary ............................................... 254

IV. Order Construction ........................................ 255
12 The Structure of Organizations ............................. 257
   12.1 Basic Definitions ..................................... 259
   12.2 Generators ............................................ 262
   12.3 Bringing Order into Organizations ..................... 263
   12.4 Novelty and Innovation ................................ 265
   12.5 Examples of the Statics of Organizations .............. 266
   12.6 How to Calculate Closed and Self-Maintaining Sets ..... 270
   12.7 Summary ............................................... 273
13 The Dynamics of Organizations .............................. 275
   13.1 Flows, Stoichiometry and Kinetic Constants ............ 275
   13.2 Examples of the Dynamics of Organization .............. 277
   13.3 Observing Organizations ............................... 282
   13.4 Probabilistic Notions of Closure and Self-
        Maintenance ........................................... 283
   13.5 Summary ............................................... 285
14 Self-Organization and Emergent Phenomena ................... 287
   14.1 Examples of Self-Organizing Systems ................... 288
   14.2 Explanatory Concepts of Self-Organization ............. 289
   14.3 The Emergence of Phenomena ............................ 295
   14.4 Explanatory Concepts of Emergence ..................... 298
   14.5 Emergence and Top-Down Causation ...................... 304
   14.6 Summary ............................................... 306
15 Constructive Dynamical Systems ............................. 307
   15.1 Novelty, Innovation, Emergence ........................ 307
   15.2 Birth Processes at the Same Level ..................... 309
   15.3 The Emergence of Entities on a Higher Level ........... 317
   15.4 Summary ............................................... 319

V. Applications ............................................... 321
16 Applications of Artificial Chemistries ..................... 323
   16.1 Robots Controlled by Artificial Chemistries ........... 324
   16.2 ACs for Networking .................................... 330
   16.3 Language Dynamics and Evolution ....................... 334
   16.4 Music Composition Using Algorithmic Chemistries ....... 338
   16.5 Proof Systems ......................................... 339
   16.6 Artificial Chemistry and Genetic Programming .......... 340
   16.7 Summary ............................................... 344
17 Computing with Artificial Chemistries ...................... 345
   17.1 Principles of implementation .......................... 346
   17.2 Search and Optimization Algorithms Inspired by
        Chemistry ............................................. 355
   17.3 Distributed Algorithms Using Chemical Computing ....... 358
   17.4 InSilico Simulation of Wet Chemical Computing ......... 366
   17.5 Summary ............................................... 372
18 Modeling Biological Systems ................................ 373
   18.1 Folding Algorithms .................................... 374
   18.2 Basic Kinetics of Bio molecular Interactions .......... 379
   18.3 Biochemical Pathways .................................. 383
   18.4 Modeling Genetic Regulatory Networks .................. 391
   18.5 Cell Differentiation and Multicellularity ............. 396
   18.6 Morphogenesis ......................................... 398
   18.7 Summary ............................................... 403
19 Wet Artificial Chemistries ................................. 405
   19.1 Artificial Building Blocks of Life .................... 405
   19.2 Synthetic Life and Protocells ......................... 411
   19.3 Chemical and Biochemical Computation .................. 417
   19.4 In Vivo Computing with Bacteria and Other Living
        Organisms ............................................. 431
   19.5 Ethical Issues ........................................ 435
   19.6 Summary ............................................... 437
20 Beyond Chemistry and Biology ............................... 439
   20.1 Mechanical Self-Assembly .............................. 439
   20.2 Nuclear and Particle Physics .......................... 442
   20.3 Economic Systems ...................................... 444
   20.4 Social Systems ........................................ 446
   20.5 Summary ............................................... 448

VI. Conclusions ............................................... 449
21 Summary and Perspectives ................................... 451
   21.1 Some Common Criticisms of the Artificial Chemistry
        Approach .............................................. 451
   21.2 Delimiting the Borders of the Field ................... 453
   21.3 Main Features of Artificial Chemistries ............... 456
   21.4 Conclusion ............................................ 459

Further Reading ............................................... 461
Appendix: Setting up Your Own Artificial Chemistry System ..... 465
The PyCellChemistry Package ................................... 465
Writing Your Own Artificial Chemistry in Python ............... 468
Further Resources ............................................. 478
Bibliography .................................................. 481
Author Index .................................................. 531
Subject Index ................................................. 545

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