Supplement: Biomolecular Feedback Systems

Domitilla Del Vecchio (MIT) and Richard M. Murray (Caltech)

WARNING: This page is out of date. See http://www.cds.caltech.edu/~murray/BFSwiki for the latest version

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. This book is being written by Domitilla Del Vecchio and Richard Murray based on a variety of presentations, lectures and notes.

Note: These notes are in draft form and may contain errors. Permission is granted to download and print a copy for individual use, but this material may not be reproduced, in whole or in part, without written consent from the author.

News (archive)

• 14 Sep 2014: The contents of this page have been moved to http://www.cds.caltech.edu/~murray/BFSwiki.
• 19 Jan 2014: Updated chapters on circuits, modules and tradeoffs (Ch 5-7) + bibliography. A complete manuscript (PDF) is also available.
• 6 Jan 2014: Updated chapter on stochastic modeling and analysis (Ch 4)
• 11 Dec 2013: Updated chapter on dynamic behavior (Ch 3)
• 7 Dec 2013: Updated chapter on core processes (Ch 2)
• 5 Dec 2013: Updated contents, preface, introduction (Ch 1) and references
• 12 Jul 2012: Updated outline; new PDFs posted. A complete manuscript (PDF) is also available.

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 Techniques 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 Appendix A: A Primer on Control Theory Bibliography and Index (PDF)