Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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** Linearized Modeling and Analysis
** Linearized Modeling and Analysis
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
** {{BFS pdf|The lac Operon|bfs-lacoperon|16Jan12}}
** The lac Operon
** (Heat shock)
** (Heat shock)
** (Phage <math>\lambda</math>)
** (Phage <math>\lambda</math>)
** {{BFS pdf|Bacterial chemotaxis|bfs-chemotaxis|11Mar10}}
** Bacterial chemotaxis|bfs-chemotaxis
** (Signaling pathways in yeast)
** (Signaling pathways in yeast)
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Revision as of 18:05, 12 July 2012

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)
  • 12 Jul 2012: Updated outline; new PDFs posted.
  • 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


  • 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 (PDF)
    • The lac Operon
    • (Heat shock)
    • (Phage )
    • Bacterial chemotaxis|bfs-chemotaxis
    • (Signaling pathways in yeast)

Additional Information