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Biomolecular feedback systems

Author: Domitilla Del Vecchio; Richard M Murray
Publisher: Princeton : Princeton University Press, ©2015.
Edition/Format:   Print book : EnglishView all editions and formats
Summary:

Provides an introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. This book begins with modeling tools such as reaction-rate equations,  Read more...

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Document Type: Book
All Authors / Contributors: Domitilla Del Vecchio; Richard M Murray
ISBN: 9780691161532 0691161534
OCLC Number: 913110005
Description: vi, 275 p. : il. ; 27 cm
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
Responsibility: Domitilla Del Vecchio, Richard M. Murray.

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"The authors did superbly in combining the biophysical processes and corresponding mathematics... This book serves both as a primer and a reference for constructing synthetic biological circuits with Read more...

 
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