Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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* {{BFS pdf|Preface and Contents|bfs-frontmatter|20Jul13}}
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* {{BFS pdf|Preface and Contents|bfs-frontmatter|05Dec13}}
* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|20Jul13}}
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* Chapter 1: {{BFS pdf|Introductory Concepts|bfs-intro|05Dec13}}
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
 
** Systems Biology: Modeling, Analysis and the Role of Feedback
 
** The Cell as a System
 
** The Cell as a System
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** Simulation of Stochastic Systems
 
** Simulation of Stochastic Systems
 
** Input/Output Linear Stochastic Systems
 
** Input/Output Linear Stochastic Systems
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* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
 
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
 
** The ''lac'' Operon
 
** The ''lac'' Operon
 
** Bacterial chemotaxis|bfs-chemotaxis
 
** Bacterial chemotaxis|bfs-chemotaxis
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* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
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* Chapter 5: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
 
** Introduction to Biological Circuit Design
 
** Introduction to Biological Circuit Design
 
** Negative Autoregulation
 
** Negative Autoregulation
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** Activator-repressor Clock
 
** Activator-repressor Clock
 
** An Incoherent Feedforward Loop (IFFL)
 
** An Incoherent Feedforward Loop (IFFL)
* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|11Jul12}}
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* Chapter 6: {{BFS pdf|Interconnecting Components|bfs-modules|11Jul12}}
 
** Input/Output Modeling and the Modularity Assumption
 
** Input/Output Modeling and the Modularity Assumption
 
** Introduction to Retroactivity
 
** Introduction to Retroactivity
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** Retroactivity in Signaling Systems
 
** Retroactivity in Signaling Systems
 
** Insulation Devices: Retroactivity Attentuation  
 
** Insulation Devices: Retroactivity Attentuation  
* Chapter 8: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|11Jul12}}
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* Chapter 7: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|11Jul12}}
 
** Metabolic Burden
 
** Metabolic Burden
 
** Stochastic Effects: Design Tradeoffs between Retroactivity and Noise
 
** Stochastic Effects: Design Tradeoffs between Retroactivity and Noise
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* Appendix A: Control Systems Primer
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* Appendix A: Cell Biology Primer (from NCBI)
 
* Appendix A: Cell Biology Primer (from NCBI)
 
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html What is a Cell]
 
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_cell.html What is a Cell]
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** Continuous-State Random Processes
 
** Continuous-State Random Processes
 
** Discrete-State Random Processes
 
** Discrete-State Random Processes
* {{BFS pdf|Bibliography and Index|bfs-backmatter|20Jul13}}
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* {{BFS pdf|Bibliography and Index|bfs-backmatter|05Dec13}}
 
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Revision as of 17:30, 5 December 2013

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


This textbook 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)

Contents

  • 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: 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 6: 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 7: Design Tradeoffs (PDF)
    • Metabolic Burden
    • Stochastic Effects: Design Tradeoffs between Retroactivity and Noise
  • Appendix A: Control Systems Primer
  • Bibliography and Index (PDF)

Additional Information