Supplement: Biomolecular Feedback Systems

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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)
  • 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

Additional Information