Supplement: Biomolecular Feedback Systems

From FBSwiki

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

This supplement 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. The supplement 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)

• 16 Jan 2012: Updated outline; new PDFs for all chapters and appendices (coming later today)
• 23 Jan 2011: Updated Ch 3: split out robustness analysis section and added intro material for oscillations section
• 16 Jan 2011: Posted updated copy of Ch 3 and fixed link to Ch 4
  • Ch 3: notation changed to match Ch 2 + lots of little fixes
• 27 Dec 2010: Updated outline, with updated links to Ch 1, 2 and 4
  • Ch 1: previous cell biology tutorial has been moved to Appendix A; replaced with general intro
  • Ch 2: moved cell dynamics and control to Ch 1; added new examples
  • Ch 4: moved overview of random processes to Appendix C; chapter still very incomplete
• 30 Mar 2010: Posted circuits and modularity chapters

Contents

Preface and Contents (PDF) Chapter 1: Introductory Concepts (PDF) Systems Biology: Modeling, Analysis and the Role of Feedback Dynamics and Control in the Cell Control and Dynamical Systems Tools 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) Input/Output Modeling Analysis Near Equilibria Robustness Analysis of Reaction Rate Equations Oscillatory Behavior Bifurcations Model Reduction Techniques Chapter 4: Stochastic Behavior (PDF) Stochastic Modeling of Biochemical Systems Simulation of Stochastic Systems Linearized Modeling and Analysis Chapter 5: Feedback Examples The lac Operon (PDF) (Heat shock) (Phage λ) Bacterial chemotaxis (PDF) (Signaling pathways in yeast)

Chapter 6: Biological Circuit Components (PDF) Biological Circuit Design Introduction Self-repressed Gene The Toggle Switch The Repressilator Activator-repressor Clock Chapter 7: Interconnecting Components (PDF) Input/Output Modeling and the Modularity Assumption Introduction to Retroactivity Retroactivity in Gene Transcriptional Circuits Retroactivity in Signaling Systems Insulation Devices to Enforce Modularity Retroactivity and noise Chapter 8: Design Tradeoffs and Examples Appendix A: Cell Biology Primer (from NCBI) What is a Cell What is a Genome Molecular Genetics: Piecing It Together NHGRI Talking Glossary Appendix B: A Primer on Control Theory (PDF) System modeling, Dynamic behavior Linear systems, Reachability Transfer functions, Frequency response PID control Limits of performance, Robust performance Appendix C: Random Processes (PDF) Random Variables Continuous-State Random Processes Discrete-State Random Processes Bibliography and Index (PDF)

Additional Information

• ASCC 2009 Workshop - Analysis and Design of Biomolecular Feedback Systems
• Engineering Principles in Biological Systems: 10-12 December 2008, Cold Spring Harbor Laboratory
• Design Principles in Biological Systems: 24-28 April 2008, Institute for Mathematics and Its Applications (IMA)
• Engineering Principles in Biological Systems: 6-8 December 2006, Cold Spring Harbor Laboratory