Dynamics On and Of Complex Networks (eBook)

Preface 6
Contents 10
List of Contributors 12
Biological Sciences 16
From Network Structure to Dynamics and Back Again: Relating Dynamical Stability and Connection Topology in Biological Complex Systems 17
1 Introduction 17
2 Biological Networks: Some Examples Across Length Scales 19
3 From Structure to Dynamics 24
4 From Dynamics to Structure 26
5 Evolution of Robust Networks 28
References 30
Regulation of Apoptosis via the NFkB Pathway: Modeling and Analysis 32
1 Introduction 32
2 The Model 33
3 Analysis of Boolean Models 36
4 Results and Discussion 40
5 Conclusion 44
References 45
Network-Based Models in Molecular Biology 47
1 Introduction 47
2 Molecular Biological Networks 50
3 Identifying Molecular Biological Networks 51
4 Dynamics of Molecular Biological Networks 54
5 Dynamics on Molecular Biological Networks 56
Acknowledgments 60
Appendix 1: Large-Scale Detection of Interaction Networks 60
Appendix 2: Some Important Definitions 62
References 64
Ecological Networks: Structure, Interaction Strength, and Stability 69
1 Introduction 69
2 Food Web Structure, Interaction Strength, and Stability 75
3 Results 77
4 Discussion and Conclusion 79
References 80
Signaling and Feedback in Biological Networks 85
1 Introduction 85
2 Signaling 86
3 Feedback 91
4 Combining Multiple Feedback Loops 98
5 Concluding Remarks 102
Acknowledgments 103
References 103
Social Sciences 106
Topographic Spreading Analysis of an Empirical Sex Workers’ Network 107
1 Introduction 107
2 Uniform Transmission Model 109
3 Links Weighted with Transmission Probabilities 113
4 Spreading on the Gonorrhea Graph 120
5 Summary and Discussion 123
Acknowledgments 126
References 126
Spectral Characterization of Network Structures and Dynamics 127
1 Introduction 127
2 Growing Networks 128
3 Graph Operators and their Spectral Properties 129
4 Functional and Dynamical Aspects Determined by the First Eigenvalue 134
5 Spectral Plots and What They May Tell Us 135
References 140
Dynamics of Social Complex Networks: Some Insights into Recent Research 143
1 Introduction: Social Networks as Complex Networks 143
2 Approaching the Dynamics on and of Social Networks Separately 144
3 Coevolution: Social Networks and Phenomena 146
4 Conclusions 150
References 151
The Structure and Dynamics of Linguistic Networks 154
1 Introduction 154
2 Lexical Networks 155
3 Word Co-Occurrence Networks 159
4 Phonological Networks 162
5 Applications in NLP and IR 164
6 Conclusion 169
References 171
Networks Generated from Natural Language Text 176
1 Introduction 176
2 Power Laws in Rank-Frequency Distribution 177
3 Scale-Free Small Worlds in Language Data 182
References 192
Information Sciences 195
Efficiency of Navigation in Indexed Networks 196
1 Introduction 196
2 Indexing and Search Schemes 197
3 Network Models 200
4 Numerical Results 201
5 Discussion 204
References 204
Evolution of Apache Open Source Software 206
1 Software: A General Paradigm for Network Systems? 206
2 The Apache Call Graphs 208
3 Evolution of Apache: Global Measures 208
4 Evolution of Apache: Models of Network Structure 215
5 Discussion and Conclusions 220
Acknowledgments 221
References 221
Some New Applications of Network Growth Models 223
1 Introduction 223
2 The Model 226
3 Generating Networks with Desired Properties 229
4 Preserving Network Structure from Disruptions 235
5 Conclusion 240
Acknowledgments 241
References 241
The Big Friendly Giant: The Giant Component in Clustered Random Graphs 243
1 Introduction 243
2 Generating Functions 245
3 The Critical Point 248
4 The Size of the GC and Its Robustness 252
5 Simulations and Real Data 254
6 Discussion 255
Acknowledgments 256
References 256
Technological Networks 259
1 Introduction 259
2 The Internet 260
3 Peer-to-Peer Networks 268
4 Conclusion 277
References 278
Advances in the Theory of Complex Networks 281
1 Introduction 281
2 The ABC of Complex Networks 281
3 Two Current Hot Problems in Complex Networks 289
4 Concluding Remarks 297
References 297
Glossary of Essential Terms 300
Index 306