Biomolecular Feedback Systems

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Domitilla Del Vecchio and Richard M. Murray

This page contains information on the text Biomolecular Feedback Systems by Domitilla Del Vecchio and Richard M. Murray.

Copyright in this book is held by Princeton University Press, who have kindly agreed to allow us to keep the book available on the web.

This textbook is intended for researchers interested in the application of feedback and control to biomolecular systems. The material has been designed so that it can be used in parallel with Feedback Systems as part of a course on biomolecular feedback and control systems, or as a standalone reference for readers who have had a basic course in feedback and control theory.

Contents

Preface and Contents (PDF) Chapter 1: Introductory Concepts (PDF) Systems Biology: Modeling, Analysis and the Role of Feedback The Cell as a System Control and Dynamical Systems Tools Input/Output Modeling From Systems to Synthetic Biology Chapter 2: Core Processes (PDF) Modeling Chemical Reactions Transcription and Translation Transcriptional Regulation Post-Transcriptional Regulation Cellular Subsystems Chapter 3: Dynamic Behavior (PDF) Analysis Near Equilibria Robustness Oscillatory Behavior Bifurcations Model Reduction Techniques Chapter 4: Stochastic Modeling and Analysis (PDF) Stochastic Modeling of Biochemical Systems Simulation of Stochastic Systems Input/Output Linear Stochastic Systems

Chapter 5: Biological Circuit Components (PDF) Introduction to Biological Circuit Design Negative Autoregulation The Toggle Switch The Repressilator Activator-repressor Clock An Incoherent Feedforward Loop (IFFL) Bacterial Chemotaxis Chapter 6: Interconnecting Components (PDF) Input/Output Modeling and the Modularity Assumption Introduction to Retroactivity Retroactivity in Gene Circuits Retroactivity in Signaling Systems Insulation Devices: Retroactivity Attentuation A Case Study on the Use of Insulation Devices Chapter 7: Design Tradeoffs (PDF) Competition for Shared Cellular Resources Stochastic Effects: Design Tradeoffs in Systems with Large Gains Chapter 8: Resource Competition (PDF) Resource competition in bacterial genetic circuits Resource competition in mammalian genetic circuits Feedforward control to mitigate the effects of resource sharing Feedback control to mitigate the effects of resource sharing Bibliography and Index (PDF)

Resources

• List of errata