Supplement: Biomolecular Feedback Systems

From AMwiki

Domitilla Del Vecchio (U. Michigan/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)

• 31 Jan 2010: Updated copy of Chapter 3 posted
• 09 Jan 2010: Updated copies of Chapter 2 + frontmatter/backmatter posted
• 23 Dec 2009: updated supplement main page to a new format

Contents

Preface and Contents (PDF) Chapter 1: Cell Biology Primer (from NCBI) What is a Cell What is a Genome Molecular Genetics: Piecing It Together NHGRI Talking Glossary Chapter 2: Core Processes (PDF) The Cell as a Dynamical System Modeling Techniques Transcription and Translation Transcriptional Regulation Post-Transcriptional and Post-Translational Regulation Cellular Subsystems Chapter 3: Dynamic Behavior (PDF) Analysis Near Equilibria Analysis of Reaction Rate Equations Limit Cycle Behavior Analysis Using Describing Functions Bifurcations Model Reduction Techniques

Chapter 4: Stochastic Behavior Stochastic Systems Stochastic Modeling of Biochemical Systems Analysis of Stochastic Systems Linearized Modeling and Analysis Markov Chain Modeling and Analysis System Identification Techniques Chapter 5: Feedback Examples Lac Operon Bacterial chemotaxis Phage λ Signaling pathways in yeast Chapter 6: Biological Circuit Components Chapter 7: Interconnecting Components Chapter 8: Design Tradeoffs Chapter 9: Design Examples 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