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