Difference between revisions of "Supplement: Biomolecular Feedback Systems"

Revision as of 15:44, 20 July 2013

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)

20 Jul 2013: Updated outline and new PDFs are being posted over the next month.
12 Jul 2012: Updated outline; new PDFs posted. A complete manuscript (PDF) is also available.
16 Jan 2012: Updated outline; new PDFs for all chapters and appendices (coming later today)

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)
- 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
- Input/Output Linear Stochastic Systems
Chapter 5: Feedback Examples (PDF)
- The lac Operon
- Bacterial chemotaxis|bfs-chemotaxis

Chapter 6: Biological Circuit Components (PDF)
- Introduction to Biological Circuit Design
- Negative Autoregulation
- The Toggle Switch
- The Repressilator
- Activator-repressor Clock
- An Incoherent Feedforward Loop (IFFL)
Chapter 7: 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
Chapter 8: Design Tradeoffs (PDF)
- Metabolic Burden
- Stochastic Effects: Design Tradeoffs between Retroactivity and Noise
Appendix A: Cell Biology Primer (from NCBI)
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

@@ Line 22: / Line 22: @@
 * Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|20Jul13}}
 ** Systems Biology: Modeling, Analysis and the Role of Feedback
-** Dynamics and Control in the Cell
+** The Cell as a System
 ** Control and Dynamical Systems Tools
 ** Input/Output Modeling

Difference between revisions of "Supplement: Biomolecular Feedback Systems"

Revision as of 15:44, 20 July 2013

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