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Biomolecular Feedback Systems
Domitilla Del Vecchio & Richard M. Murray

Book Description | Reviews
Preface [in PDF format] | Chapter 1 [in PDF format]

TABLE OF CONTENTS:

Preface vii
1 Introductory Concepts 1
1.1 Systems biology: Modeling, analysis and role of feedback 1
1.2 The cell as a system 8
1.3 Control and dynamical systems tools 11
1.4 Input/output modeling 18
1.5 From systems to synthetic biology 22
1.6 Further reading 28
2 Dynamic Modeling of Core Processes 29
2.1 Modeling chemical reactions 29
2.2 Transcription and translation 44
2.3 Transcriptional regulation 55
2.4 Post-transcriptional regulation 70
2.5 Cellular subsystems 81
Exercises 86
3 Analysis of Dynamic Behavior 89
3.1 Analysis near equilibria 89
3.2 Robustness 103
3.3 Oscillatory behavior 113
3.4 Bifurcations 124
3.5 Model reduction techniques 127
Exercises 133
4 Stochastic Modeling and Analysis 139
4.1 Stochastic modeling of biochemical systems 139
4.2 Simulation of stochastic systems 154
4.3 Input/output linear stochastic systems 157
Exercises 164
5 Biological Circuit Components 169
5.1 Introduction to biological circuit design 169
5.2 Negative autoregulation 171
5.3 The toggle switch 177
5.4 The repressilator 180
5.5 Activator-repressor clock 184
5.6 An incoherent feedforward loop (IFFL) 189
5.7 Bacterial chemotaxis 191
Exercises 203
6 Interconnecting Components 205
6.1 Input/output modeling and the modularity assumption 205
6.2 Introduction to retroactivity 206
6.3 Retroactivity in gene circuits 209
6.4 Retroactivity in signaling systems 214
6.5 Insulation devices: Retroactivity attenuation 219
6.6 A case study on the use of insulation devices 236
Exercises 239
7 Design Tradeoffs 243
7.1 Competition for shared cellular resources 243
7.2 Stochastic effects: Design tradeoffs in systems with large gains 253
Exercises 257
Bibliography 259
Index 267

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File created: 4/21/2017

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