Enjoying Natural Computing. Essays dedicated to Mario de Jesús Pérez-Jiménez

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Foreword......Page 3 Contents......Page 5 1 Introduction......Page 7 2.1 Insertion, Deletion, and Substitution......Page 12 2.2 Register Machines......Page 13 2.4 Input-Driven Register Machines and Counter Automata......Page 14 3 Tissue P Automata as Multiset Pushdown Automata......Page 15 3.1 Accepting Strings......Page 18 3.2 Input-Driven Tissue P Automata......Page 19 3.3 One-Membrane Antiport P Automata......Page 20 4 Examples and Results......Page 21 References......Page 24 1 Introduction......Page 27 2 Membrane Systems......Page 28 3 The Efficiency of Membrane Systems......Page 30 4 A New Solution to N-Queens Problem......Page 31 References......Page 37 1 Introduction......Page 39 2 Basic Concepts......Page 40 2.1 Modifications of the System Used in the Model Definition......Page 41 3 Description of a Scenario......Page 43 4 Experiments and Results......Page 46 5 Conclusions......Page 48 References......Page 49 1 Introduction......Page 51 2 Preliminaries......Page 52 3 A Small SNPSP System for Computing Functions......Page 54 4 A Small SNPSP System for Generating Numbers......Page 58 5 Discussions and Final Remarks......Page 61 References......Page 62 1 Introduction......Page 63 2 Basic Definitions and Results......Page 64 3 Generation of Hilbert Words......Page 65 4 Approximating Polygons for the Hilbert Curve......Page 66 5 Lebesgue's Space-Filling Curve and Approximating Polygons......Page 69 References......Page 70 1 Introduction......Page 72 2 Preliminaries and Basic Notions......Page 73 2.1 P Colonies......Page 74 3 Logical Representation of P Colonies......Page 76 References......Page 81 1 Introduction......Page 83 2 Preliminaries......Page 84 3 The Fair Proportion Is a Shapley Value......Page 85 4 The Unrooted Subnet Shapley Value on a Rooted Phylogenetic Network......Page 89 5 Conclusions......Page 92 References......Page 93 1 Introduction......Page 94 2 Preliminaries and Definitions......Page 96 3 P Colony Automata and the LL(k) Condition......Page 101 References......Page 103 ACORD - Ant Colony Optimization & BNF Grammar Rule Derivation......Page 105 1 Introduction......Page 106 2 Ant Colony Optimization Overview......Page 108 3 ACORD Algorithm......Page 111 4 Conclusion......Page 116 References......Page 117 1 Introduction......Page 120 2 Historical Overview of Modelling Works in MC......Page 121 2.2 The Dawn of Brainstorming Era......Page 122 2.3 Reaching Maturity......Page 123 3 At the Crossroads of Cell Biology and Computation......Page 125 3.2 Multienvironment P Systems and Multi-compartmental Gillespie Algorithm......Page 126 4.1 Probabilistic Systems......Page 128 5 Ongoing and Upcoming Modelling Works......Page 131 References......Page 132 1 Introduction......Page 136 2.1 Kernel P System Basic Definitions......Page 137 2.2 Kernel P System Rules......Page 138 2.3 Kernel P System Execution Strategies......Page 139 3 Identifiable Transitions in kP Systems......Page 141 References......Page 146 1 Introduction......Page 148 2.2 Searching......Page 149 2.3 Machine Learning......Page 150 3 Other Areas of Computer Science......Page 152 4 Graphics......Page 153 5 Other Buds......Page 154 References......Page 155 1 Introduction......Page 161 2 JENA Software Source Code Design......Page 165 3 Example: Gel Electrophoresis on DNA......Page 170 References......Page 174 1 Introduction......Page 176 2 Preliminaries......Page 178 2.1 Running Example......Page 179 3.2 Mass Conservation Analysis......Page 181 3.3 Overview of the Implementation......Page 182 3.4 Example of Usage......Page 183 4 The Web-Service......Page 184 5 Discussion......Page 185 References......Page 186 2 Confluence vs Determinism......Page 188 2.1 Simulation of Priorities......Page 189 3.1 Building and Filling the Membrane Structure at Runtime......Page 191 4 Membrane Division vs Internal Evolution......Page 192 4.1 Putting a Turing Machine Inside a Membrane......Page 193 5 Deep vs Shallow Membrane Structures......Page 194 References......Page 195 1 Shannon's Entropy and Thermodynamic Entropy......Page 198 2 Entropy and Computation......Page 202 References......Page 207 1 Introduction......Page 210 2 P Systems with Compound Terms......Page 212 3 cP Terms Grammar and Unification......Page 213 4 cP Rules Grammar......Page 215 5 cP Numbers......Page 218 6 cP Lists......Page 220 7 cP Associative arrays......Page 221 8.1 Distributed Echo Algorithm – Synchronous vs. Asynchrnous......Page 222 8.2 Fairness and Unbounded Non-determinism......Page 224 9.1 Efficient Summary Statistics......Page 225 10 cP -recursion......Page 227 11 Evaluations and Conclusions......Page 230 References......Page 232 1 Introduction......Page 234 2.1 SNQ P Systems......Page 235 2.2 Register Machines......Page 236 3.1 SNQ P Systems with Two Spikes......Page 237 3.2 SNQ P Systems with only One Type of Spikes......Page 239 4 Further Improvements Ideas on SNQ P Systems......Page 240 References......Page 241 1 Introduction......Page 243 2 Design Patterns for Membrane Computing......Page 245 2.1 The Exponential Space Pattern......Page 246 2.2 The All Present Pattern......Page 248 2.3 The No If Not Yes Pattern......Page 250 3 Practical Examples......Page 252 3.1 Solution to SAT Using Polarizations and Membrane Division......Page 253 3.2 Solution to SAT Using Dissolution and Membrane Creation......Page 255 3.3 Solution to SAT Using Polarizations and Membrane Separation......Page 256 3.4 Solution to SAT Using Minimal Cooperation (with Minimal Production) and Membrane Division......Page 258 References......Page 260 1 Introduction......Page 262 2 Spiking Neural P Systems and Variants......Page 263 3 Theoretical Results of Spiking Neural P Systems......Page 266 4 Applications of Spiking Neural P Systems......Page 269 5 Concluding Remarks and Future Research Lines......Page 270 References......Page 271 1 Introduction......Page 275 1.1 Preliminaries......Page 277 2 Aggregating Multiset Rewriting Systems......Page 278 References......Page 284 1 Introduction......Page 285 2.1 Circular Post Machines......Page 287 2.2 Insertion-Deletion Systems......Page 288 3 Computational Completeness......Page 289 4 Conclusions and Discussions......Page 294 References......Page 295 1 Introduction......Page 297 2 Simulation Software for P Systems......Page 298 2.1 The Visual Environment MeCoSim......Page 299 2.3 PMCGPU for Accelerated Simulations......Page 300 3.1 Model Personalization with MeCoSim......Page 304 3.2 Simulation with PMCGPU Through P-Lingua......Page 305 4 Conclusions and Perspectives......Page 307 References......Page 308 1 Introduction......Page 310 2 Virus Machine......Page 311 3.1 A Virus Machine for Addition......Page 313 3.2 A Virus Machine for Subtraction......Page 314 3.3 A Virus Machine for Multiplication......Page 316 3.4 A Virus Machine for Division......Page 318 4 Conclusions and Future Work......Page 321 References......Page 322 1 Introduction......Page 324 2.1 Kernel Clustering Problems......Page 325 2.2 Basic Idea......Page 326 2.3 Algorithm Implementation......Page 327 3.1 Data Sets......Page 328 3.4 Performance Measures......Page 329 3.5 Experimental Results......Page 330 References......Page 333