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Biomolecular Feedback Systems
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Main description:

This book provides an accessible introduction to the principles and tools for modeling, analyzing, and synthesizing biomolecular systems. It begins with modeling tools such as reaction-rate equations, reduced-order models, stochastic models, and specific models of important core processes. It then describes in detail the control and dynamical systems tools used to analyze these models. These include tools for analyzing stability of equilibria, limit cycles, robustness, and parameter uncertainty. Modeling and analysis techniques are then applied to design examples from both natural systems and synthetic biomolecular circuits. In addition, this comprehensive book addresses the problem of modular composition of synthetic circuits, the tools for analyzing the extent of modularity, and the design techniques for ensuring modular behavior. It also looks at design trade-offs, focusing on perturbations due to noise and competition for shared cellular resources.Featuring numerous exercises and illustrations throughout, Biomolecular Feedback Systems is the ideal textbook for advanced undergraduates and graduate students. For researchers, it can also serve as a self-contained reference on the feedback control techniques that can be applied to biomolecular systems.Provides a user-friendly introduction to essential concepts, tools, and applicationsCovers the most commonly used modeling methodsAddresses the modular design problem for biomolecular systemsUses design examples from both natural systems and synthetic circuitsSolutions manual (available only to professors at press.princeton.edu)An online illustration package is available to professors at press.princeton.edu


Preface vii1 Introductory Concepts 11.1 Systems biology: Modeling, analysis and role of feedback 11.2 The cell as a system 81.3 Control and dynamical systems tools 111.4 Input/output modeling 181.5 From systems to synthetic biology 221.6 Further reading 282 Dynamic Modeling of Core Processes 292.1 Modeling chemical reactions 292.2 Transcription and translation 442.3 Transcriptional regulation 552.4 Post-transcriptional regulation 702.5 Cellular subsystems 81Exercises 863 Analysis of Dynamic Behavior 893.1 Analysis near equilibria 893.2 Robustness 1033.3 Oscillatory behavior 1133.4 Bifurcations 1243.5 Model reduction techniques 127Exercises 1334 Stochastic Modeling and Analysis 1394.1 Stochastic modeling of biochemical systems 1394.2 Simulation of stochastic systems 1544.3 Input/output linear stochastic systems 157Exercises 1645 Biological Circuit Components 1695.1 Introduction to biological circuit design 1695.2 Negative autoregulation 1715.3 The toggle switch 1775.4 The repressilator 1805.5 Activator-repressor clock 1845.6 An incoherent feedforward loop (IFFL) 1895.7 Bacterial chemotaxis 191Exercises 2036 Interconnecting Components 2056.1 Input/output modeling and the modularity assumption 2056.2 Introduction to retroactivity 2066.3 Retroactivity in gene circuits 2096.4 Retroactivity in signaling systems 2146.5 Insulation devices: Retroactivity attenuation 2196.6 A case study on the use of insulation devices 236Exercises 2397 Design Tradeoffs 2437.1 Competition for shared cellular resources 2437.2 Stochastic effects: Design tradeoffs in systems with large gains 253Exercises 257Bibliography 259Index 267


ISBN-13: 9781400850501
Publisher: Princeton University Press
Publication date: December, 2014
Pages: 392

Subcategories: Biochemistry