| | Contents | |
| | | |
| |
| | Preface | V |
| | List of contributors | XIV |
| 1 | Mathematical results on scale-free random graphs (Béla Bollobás and Oliver M. Riordan) | 1 |
| 1 | Introduction | 1 |
| 1.2 | Classical models of random graphs | 2 |
| 1.3 | Results for classical random graphs | 4 |
| 1.4 | The Watts-Strogatz `small-world' model | 5 |
| 1.5 | Scale-free models | 6 |
| 1.6 | The Barabási-Albert model | 7 |
| 1.7 | The LCD model and G(n)m | 9 |
| 1.8 | The Buckley-Osthus model | 11 |
| 1.9 | The copying model | 12 |
| 1.10 | The Cooper-Frieze model | 13 |
| 1.11 | Directed scale-free graphs | 15 |
| 1.12 | Clustering coefficient and small subgraphs | 17 |
| 1.13 | Pairings on [0, 1]and the diameter of the LCD model | 22 |
| 1.14 | Robustness and vulnerability | 24 |
| 1.15 | The case [0, 1]: plane-oriented recursive trees | 27 |
| 1.16 | Conclusion | 32 |
| | References | 32 |
| 2 | Random graphs as models of networks (Mark E. J. Newman) | 35 |
| 2.1 | Introduction | 35 |
| 2.2 | Random graphs with specified degree distributions | 40 |
| 2.3 | Probability generating functions | 45 |
| 2.3.1 | Properties of generating functions | 46 |
| 2.3.2 | Examples | 46 |
| 2.4 | Properties of undirected graphs | 47 |
| 2.4.1 | Distribution of component sizes | 47 |
| 2.4.2 | Mean component size | 50 |
| 2.4.3 | Above the phase transition | 51 |
| 2.5 | Properties of directed graphs | 53 |
| 2.5.1 | Generating functions | 54 |
| 2.5.2 | Results | 54 |
| 2.6 | Networks with clustering | 56 |
| 2.7 | Models defined on random graphs | 58 |
| 2.7.1 | Network resilience | 58 |
| 2.7.2 | Epidemiology | 61 |
| 2.7.3 | The SIR model | 62 |
| 2.7.4 | Solution of the SIR model | 63 |
| 2.8 | Summary | 65 |
| | References | 65 |
| 3 | Emergence of scaling in complex networks (Albert-László Barabási) | 69 |
| 3.1 | Introduction | 69 |
| 3.2 | Network models | 70 |
| 3.2.1 | Random networks | 70 |
| 3.2.2 | Scale-free networks | 70 |
| 3.2.3 | Scale-free model | 73 |
| 3.3 | Fitness model and Bose-Einstein condensation | 75 |
| 3.4 | The Achilles' Heel of complex networks | 76 |
| 3.5 | A deterministic scale-free model | 79 |
| 3.6 | Outlook | 81 |
| 3.7 | Acknowledgments | 82 |
| | References | 82 |
| 4 | Structural properties of scale-free networks (Reuven Cohen, Shlomo Havlin, and Daniel ben-Avraham) | 85 |
| 4.1 | Introduction | 85 |
| 4.1.1 | Random graphs | 85 |
| 4.1.2 | Scale-free networks | 86 |
| 4.2 | Small and Ultra-small worlds | 87 |
| 4.2.1 | Diameter of scale-free networks | 88 |
| 4.2.2 | Minimal graphs and lower bound | 88 |
| 4.2.3 | The general case of random scale-free networks | 89 |
| 4.3 | Percolation | 92 |
| 4.3.1 | Random breakdown | 92 |
| 4.3.2 | Percolation critical threshold | 93 |
| 4.3.3 | Generating functions | 95 |
| 4.3.4 | Intentional attack | 96 |
| 4.3.5 | Critical exponents | 97 |
| 4.3.6 | Fractal dimension | 100 |
| 4.4 | Percolation in directed networks | 101 |
| 4.4.1 | Threshold | 102 |
| 4.4.2 | Critical exponents | 103 |
| 4.5 | Efficient immunization strategies | 104 |
| 4.5.1 | Acquaintance immunization | 105 |
| 4.6 | Summary and outlook | 106 |
| | References | 107 |
| 5 | Epidemics and immunization in scale-free networks (Romualdo Pastor-Satorras and Alessandro Vespignani) | 111 |
| 5.1 | Introduction | 111 |
| 5.2 | Computers and epidemiology | 112 |
| 5.3 | Epidemic spreading in homogeneous networks | 114 |
| 5.4 | Real data analysis | 116 |
| 5.5 | Epidemic spreading in scale-free networks | 118 |
| 5.5.1 | Analytic solution for the Barabási-Albert network | 119 |
| 5.5.2 | Finite size scale-free networks | 122 |
| 5.6 | Immunization of scale-free networks | 123 |
| 5.6.1 | Uniform immunization | 124 |
| 5.6.2 | Targeted immunization | 125 |
| 5.7 | Conclusions | 127 |
| | References | 128 |
| 6 | Cells and genes as networks in nematode development and evolution (Ralf J. Sommer) | 131 |
| 6.1 | Introduction | 131 |
| 6.2 | Nematode developmental biology: studying processes at a cellular level | 132 |
| 6.3 | Nematode Vulva formation as a case study | 132 |
| 6.4 | Nematode collections | 136 |
| 6.5 | Cellular networks: how cells change their function | 136 |
| 6.5.1 | Evolution of vulva position | 136 |
| 6.5.2 | Evolution of vulval cell fate specification | 136 |
| 6.6 | Genetic networks: how genes change their function | 139 |
| 6.6.1 | Evolution of lin-39 function | 139 |
| 6.6.2 | Evolution of mab-5 function | 141 |
| 6.7 | Conclusion | 142 |
| | References | 142 |
| 7 | Complex networks in genomics and proteomics (Ricard V. Solé and Romualdo Pastor-Satorras) | 145 |
| 7.1 | Introduction | 145 |
| 7.2 | Cellular networks | 148 |
| 7.2.1 | Two-gene networks | 149 |
| 7.2.2 | Random networks | 150 |
| 7.3 | Three interconnected levels of cellular nets | 153 |
| 7.4 | Small world graphs and scale-free nets | 154 |
| 7.5 | Scale-free proteomes: gene duplication models | 157 |
| 7.5.1 | Mean-field rate equation for the average connectivity | 157 |
| 7.5.2 | Rate equation for the node distribution nk | 159 |
| 7.5.3 | Numerical simulations | 162 |
| 7.6 | Discussion | 164 |
| | References | 164 |
| 8 | Correlation profiles and motifs in complex networks (Sergei Maslov, Kim Sneppen, and Uri Alon) | 168 |
| 8.1 | Introduction | 168 |
| 8.2 | Randomization algorithm: Constructing the proper null model | 172 |
| 8.3 | Correlation profiles: Yeast molecular networks and the Internet | 177 |
| 8.4 | Network motifs: Transcriptional regulation in E. coli | 189 |
| 8.5 | Discussion: What it may all mean? | 194 |
| | References | 196 |
| 9 | Theory of interacting neural networks (Wolfgang Kinzel) | 199 |
| 9.1 | Introduction | 199 |
| 9.2 | On-line training | 200 |
| 9.3 | Generalisation | 201 |
| 9.4 | Time series prediction and generation | 203 |
| 9.5 | Self-interaction | 206 |
| 9.6 | Agents competing in a closed market | 207 |
| 9.7 | Synchronisation by mutual learning | 208 |
| 9.8 | Cryptography | 210 |
| 9.9 | Conclusions | 213 |
| | References | 216 |
| 10 | Modelling food webs (Barbara Drossel and Alan J. McKane) | 218 |
| 10.1 | Introduction | 218 |
| 10.2 | Basic properties of food webs | 221 |
| 10.3 | Static models | 226 |
| 10.4 | Dynamic models | 227 |
| 10.4.1 | Two-species models | 228 |
| 10.4.2 | Generalized dynamical equations | 230 |
| 10.4.3 | The complexity-stability debate | 232 |
| 10.5 | Assembly models and evolutionary models | 235 |
| 10.5.1 | Toy models | 235 |
| 10.5.2 | Species assembly models | 236 |
| 10.5.3 | Evolutionary models | 238 |
| 10.6 | Conclusions | 241 |
| | References | 242 |
| 11 | Traffic networks (Kai Nagel) | 248 |
| 11.1 | Introduction | 248 |
| 11.2 | Dynamics on networks | 250 |
| 11.2.1 | The four step process and static assignment | 250 |
| 11.2.2 | Simple link dynamics and the queue model | 252 |
| 11.2.3 | Virtual reality micro-simulations | 253 |
| 11.2.4 | CA implementations of virtual reality micro-simulations | 255 |
| 11.2.5 | Traffic in networks | 258 |
| 11.3 | Particles are intelligent | 260 |
| 11.3.1 | Route generation | 260 |
| 11.3.2 | Activity generation | 261 |
| 11.3.3 | Housing, land use, freight, life style, et al | 261 |
| 11.3.4 | Day-to-day learning, feedback, and relaxation | 261 |
| 11.3.5 | Within-day re-planning | 262 |
| 11.3.6 | Individualization of knowledge | 263 |
| 11.3.7 | State of the art | 263 |
| 11.4 | Distributed computing and the network of interactions | 264 |
| 11.4.1 | Distributed computing of the traffic micro-simulation | 265 |
| 11.4.2 | Distributed computing of plans generation | 267 |
| 11.5 | Outlook: Dynamics of networks | 268 |
| 11.6 | Conclusion | 268 |
| | References | 269 |
| 12 | Economic networks (Alan Kirman) | 273 |
| 12.1 | Introduction | 273 |
| 12.2 | Economics and sociology | 274 |
| 12.3 | The economic consequences of networks | 275 |
| 12.4 | Fixed network: stochastic interaction | 278 |
| 12.5 | Random graphs and networks | 280 |
| 12.6 | Emerging networks | 281 |
| 12.7 | The strategic formation of networks | 282 |
| 12.8 | Emerging random graphs | 283 |
| 12.9 | The identification problem | 291 |
| 12.10 | Conclusion | 292 |
| | References | 293 |
| 13 | Local search in unstructured networks (Lada A. Adamic, Rajan M. Lukose, Bernardo A. Huberman) | 295 |
| 13.1 | Introduction | 295 |
| 13.2 | Search in power-law random graphs | 297 |
| 13.2.1 | Intuition | 297 |
| 13.2.2 | Random walk search | 298 |
| 13.2.3 | Search utilizing high degree nodes | 301 |
| 13.3 | Simulation | 303 |
| 13.4 | Comparison with Poisson distributed graphs | 306 |
| 13.5 | Gnutella | 308 |
| 13.6 | Path finding | 310 |
| 13.7 | Shortening the shortest path | 312 |
| 13.7.1 | Iterative deepening | 313 |
| 13.8 | Adaptive search | 314 |
| 13.9 | Conclusion | 315 |
| | References | 316 |
| 14 | Accelerated growth of networks (Sergei N. Dorogovtsev and Jose F. F. Mendes) | 318 |
| 14.1 | Acceleration | 318 |
| 14.2 | Reasons for acceleration | 321 |
| 14.3 | Degree distributions of networks | 321 |
| 14.3.1 | Types of degree distribution | 321 |
| 14.3.2 | Power-law degree distribution | 324 |
| 14.4 | General relations for accelerated growth | 326 |
| 14.5 | Scaling relations for accelerated growth | 328 |
| 14.6 | Degree distributions produced by acceleration | 329 |
| 14.6.1 | Model for < 2 | 329 |
| 14.6.2 | Model for > 2 | 330 |
| 14.6.3 | Dynamically induced accelerated growth | 330 |
| 14.6.4 | Partial copying of edges and multifractality | 330 |
| 14.7 | Evolution of the Word Web | 331 |
| 14.8 | Wealth distribution in evolving societies | 336 |
| 14.8.1 | Stable (stagnating) societies | 337 |
| 14.8.2 | Developing and degrading societies | 337 |
| | References | 339 |
| 15 | Social percolators and self organized criticality (Gérard Weisbuch and Sorin Solomon) | 342 |
| 15.1 | Introduction | 342 |
| 15.2 | Social percolation | 343 |
| 15.2.1 | Simple models | 343 |
| 15.3 | Adjustment meta-dynamics | 346 |
| 15.3.1 | Slow adjustment | 346 |
| 15.3.2 | Fast adjustment | 347 |
| 15.4 | Conclusions | 351 |
| | References | 353 |
| 16 | Graph theory and the evolution of autocatalytic networks (Sanjay Jain and Sandeep Krishna) | 355 |
| 16.1 | Introduction | 355 |
| 16.2 | Graph theory and autocatalytic sets . | 357 |
| 16.2.1 | Directed graphs and their adjacency matrices | 357 |
| 16.2.2 | Autocatalytic sets | 363 |
| 16.3 | A dynamical system on a fixed graph | 366 |
| 16.3.1 | Attractors of equation (16.1) | 368 |
| 16.4 | Graph dynamics | 375 |
| 16.5 | Self Organization | 377 |
| 16.5.1 | The random phase | 378 |
| 16.5.2 | The growth phase | 381 |
| 16.5.3 | The organized phase | 384 |
| 16.6 | Catastrophes and recoveries in the organized phase | 384 |
| 16.6.1 | Catastrophes, core-shifts and a classification of proximate causes | 389 |
| 16.6.2 | Recoveries | 391 |
| 16.6.3 | Correlation between graph theoretic nature of perturbation and its short and long term impact | 392 |
| 16.7 | Concluding remarks | 392 |
| | References | 394 |
| | Index | 396 |