Difference between revisions of "Supplement: Biomolecular Feedback Systems"

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(Contents)
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** Dynamics and Control in the Cell
 
** Dynamics and Control in the Cell
 
** Control and Dynamical Systems Tools
 
** Control and Dynamical Systems Tools
 +
** Input/Output Modeling
 
** From Systems to Synthetic Biology
 
** From Systems to Synthetic Biology
 
* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|01Jan11}}
 
* Chapter 2: {{BFS pdf|Core Processes|bfs-coreproc|01Jan11}}
Line 42: Line 43:
 
** Stochastic Modeling of Biochemical Systems
 
** Stochastic Modeling of Biochemical Systems
 
** Simulation of Stochastic Systems
 
** Simulation of Stochastic Systems
** Linearized Modeling and Analysis
+
** Input/Output Linear Stochastic Systems
 
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
 
* Chapter 5: {{BFS pdf|Feedback Examples|bfs-fbkexamps|11Jul12}}
** The lac Operon
+
** The ''lac'' Operon
 
** (Heat shock)
 
** (Heat shock)
 
** (Phage <math>\lambda</math>)
 
** (Phage <math>\lambda</math>)
Line 51: Line 52:
 
| width=50% |
 
| width=50% |
 
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
 
* Chapter 6: {{BFS pdf|Biological Circuit Components|bfs-circuits|11Jul12}}
** Biological Circuit Design
+
** Introduction to Biological Circuit Design
** Introduction
+
** Negative Autoregulation
** Self-repressed Gene
+
 
** The Toggle Switch
 
** The Toggle Switch
 
** The Repressilator
 
** The Repressilator
 
** Activator-repressor Clock
 
** Activator-repressor Clock
 +
** An Incoherent Feedforward Loop (IFFL)
 
* Chapter 7: {{BFS pdf|Interconnecting Components|bfs-modules|11Jul12}}
 
* Chapter 7: {{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
** Retroactivity in Gene Transcriptional Circuits
+
** Retroactivity in Gene Circuits
 
** Retroactivity in Signaling Systems
 
** Retroactivity in Signaling Systems
** Insulation Devices to Enforce Modularity
+
** Insulation Devices: Retroactivity Attentuation
** Retroactivity and noise
+
Chapter 8: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|11Jul12}}
* Chapter 8: {{BFS pdf|Design Tradeoffs|bfs-tradeoffs|11Jul12}}
+
 
* 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]

Revision as of 18:09, 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

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
    • 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
    • (Heat shock)
    • (Phage )
    • Bacterial chemotaxis|bfs-chemotaxis
    • (Signaling pathways in yeast)
  • 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)

Additional Information