Systems Self-Assembly (eBook)

Cover 1
Series Dedication 6
Table of Contents 8
Preface 12
Chapter 1. Self-Organised Nanoparticle Assemblies: A Panoply of Patterns 18
1. Introduction 18
2. Pattern Formation: Spanning the Nanoscopic to the Macroscopic 20
3. Quantifying Morphology and Topology 25
4. Evolving to Equilibrium 30
5. Conclusions 34
Acknowledgements 35
References 35
Chapter 2. Biomimetic Design of Dynamic Self-Assembling Systems 38
1. Introduction 38
2. Definitions 39
3. Advantages 42
4. Biological Examples-Molecular to Macroscopic 44
5. Heuristics of Rational DySA Design 48
6. DySA Design in Practice: Magnetohydrodynamic Systems 50
7. Examples of Bioinspired DySA 55
8. Conclusion 59
References 59
Chapter 3. Computing by Self-Assembly:DNA Molecules, Polyominoes, Cells 66
1. Introduction 66
2. Language-Theory Prerequisites 68
3. Sticker Systems 70
4. Computing with Shapes 73
5. Self-Assembly P Systems 76
6. Universality of a Restricted Class of Self-Assembly P Systems 81
7. One Further Universality Result 91
8. Final Remarks 93
Acknowledgement 93
References 93
Chapter 4. Evolutionary Design of a Model of Self-Assembling Chemical Structures 96
1. Design of Self-Assembling Chemical Systems 96
2. Dynamic-Bonding Dissipative Particle Dynamics (dbDPD) 98
3. Genetic Algorithm for Chemical Structures 100
4. Results 101
5. Discussion 113
6. Conclusion 114
Acknowledgements 115
References 115
Chapter 5. Self-Assembly as an Engineering Concept across Size Scales 118
1. Introduction 118
2. Two-Dimensional Templated Self-Assembly 122
3. 2-D Self-Assembly without a Template 129
4. Conclusions 135
References 137
Chapter 6. Probabilistic Analysis of Self-Assembled Molecular Networks 140
1. Introduction 140
2. Resource Redundancy Based Fault-Tolerance 143
3. Background 146
4. Over-all Probabilistic Design Methodology and Framework 150
5. Experimental Results and Analysis 156
6. Conclusion 166
References 166
Chapter 7. The "Programming Language'' of Dynamic Self-Assembly 170
1. Introduction 170
2. The RAM Computing Model 173
3. Proteins as Elements of a RAM Computer 175
4. Hierarchical RAM Computing 180
5. RAM Programs in Living Systems 182
6. Programmed Dynamic Self-Assembly 188
7. Conclusion 193
Acknowledgements 195
References 195
Chapter 8. Self-Assembled Computer Architectures 198
1. Introduction 198
2. Technology for Self-Assembled Computers 199
3. Challenges 202
4. Architecture Case Studies 206
5. Conclusions 213
References 213
Chapter 9. Simulation of Self-Assembly Processes Using Abstract Reduction Systems 216
1. Introduction 216
2. A Short MGS Presentation 219
3. Aggregation Processes in MGS 221
4. Accretive Growth of Sierpinski Triangles 223
5. Handling Arbitrary Shapes 227
6. Self-Assembled Polymers 231
7. Carving Sierpinski Triangles 233
8. Conclusions 238
Acknowledgements 239
References 240
Chapter 10. Computer Aided Search for Optimal Self-Assembly Systems 242
1. Introduction 242
2. Definitions 243
3. Counting to n at tau=2 246
4. Finding Optimal Reduced-Size Tile Systems 250
5. Conclusions 258
Acknowledgements 260
References 260
Chapter 11. Programmable Self-Assembly-Theoretical Aspects and DNA-Linked Nanoparticles 262
1. Introduction 262
2. Fundamental Aspects of Programmable Self-Assembly 263
3. Sticky Graphs 267
4. Programmable Self-Assembly Using DNA-Linked Nanoparticles 270
5. Conclusions 274
References 274
Chapter 12. From Microscopic Rules to Emergent Cooperativity in Large-Scale Patterns 276
1. Introduction 276
2. Emergence of Complex Geometries 279
3. Dynamic Response of Complex Spin Networks 285
4. Conclusions 292
Acknowledgements 295
References 295
Chapter 13. Automated Self-Assembling Programming 298
1. Self-Assembly, Self-Organisation and Natural Computation 298
2. Evolutionary Algorithms for Parameter and Structural Learning in Self-Assembly Model Systems 300
3. Self-Assembly Models for Unconventional Computing 313
4. Conclusions 320
Acknowledgements 320
References 320
Index 326
Colour Plate Section 328