Difference between revisions of "Supplement: Biomolecular Feedback Systems"
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−  * {{BFS pdfPreface and Contentsbfsfrontmatter  +  * {{BFS pdfPreface and Contentsbfsfrontmatter11Jul12}} 
* Chapter 1: {{BFS pdfIntroductory Conceptsbfsintro01Jan11}}  * Chapter 1: {{BFS pdfIntroductory Conceptsbfsintro01Jan11}}  
** Systems Biology: Modeling, Analysis and the Role of Feedback  ** Systems Biology: Modeling, Analysis and the Role of Feedback  
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** PostTranscriptional Regulation  ** PostTranscriptional Regulation  
** Cellular Subsystems  ** Cellular Subsystems  
−  * Chapter 3: {{BFS pdfDynamic Behaviorbfsdynamics  +  * Chapter 3: {{BFS pdfDynamic Behaviorbfsdynamics11Jul12}} 
** Input/Output Modeling  ** Input/Output Modeling  
** Analysis Near Equilibria  ** Analysis Near Equilibria  
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** Bifurcations  ** Bifurcations  
** Model Reduction Techniques  ** Model Reduction Techniques  
−  * Chapter 4: {{BFS pdfStochastic Behaviorbfsstochastic  +  * Chapter 4: {{BFS pdfStochastic Behaviorbfsstochastic11Jul12}} 
** Stochastic Modeling of Biochemical Systems  ** Stochastic Modeling of Biochemical Systems  
** Simulation of Stochastic Systems  ** Simulation of Stochastic Systems  
** Linearized Modeling and Analysis  ** Linearized Modeling and Analysis  
−  * Chapter 5: Feedback Examples  +  * Chapter 5: {{BFS pdfFeedback Examplesbfsfbkexamps11Jul12}} 
** {{BFS pdfThe lac Operonbfslacoperon16Jan12}}  ** {{BFS pdfThe lac Operonbfslacoperon16Jan12}}  
** (Heat shock)  ** (Heat shock)  
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** (Signaling pathways in yeast)  ** (Signaling pathways in yeast)  
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−  * Chapter 6: {{BFS pdfBiological Circuit Componentsbfscircuits  +  * Chapter 6: {{BFS pdfBiological Circuit Componentsbfscircuits11Jul12}} 
** Biological Circuit Design  ** Biological Circuit Design  
** Introduction  ** Introduction  
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** The Repressilator  ** The Repressilator  
** Activatorrepressor Clock  ** Activatorrepressor Clock  
−  * Chapter 7: {{BFS pdfInterconnecting Componentsbfsmodules  +  * Chapter 7: {{BFS pdfInterconnecting Componentsbfsmodules11Jul12}} 
** Input/Output Modeling and the Modularity Assumption  ** Input/Output Modeling and the Modularity Assumption  
** Introduction to Retroactivity  ** Introduction to Retroactivity  
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** PID control  ** PID control  
** Limits of performance, Robust performance  ** Limits of performance, Robust performance  
−  * Appendix C: {{BFS pdfRandom Processesbfsrandom  +  * Appendix C: {{BFS pdfRandom Processesbfsrandom11Jul12}} 
** Random Variables  ** Random Variables  
** ContinuousState Random Processes  ** ContinuousState Random Processes 
Revision as of 17:31, 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
 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


Additional Information
 ASCC 2009 Workshop  Analysis and Design of Biomolecular Feedback Systems
 Engineering Principles in Biological Systems: 1012 December 2008, Cold Spring Harbor Laboratory
 Design Principles in Biological Systems: 2428 April 2008, Institute for Mathematics and Its Applications (IMA)
 Engineering Principles in Biological Systems: 68 December 2006, Cold Spring Harbor Laboratory