Difference between revisions of "Supplement: Biomolecular Feedback Systems"
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=== Examples ===  === Examples ===  
+  The material above is intended to be useful in analyzing a large variety of natural and engineered biomolecular feedback systems. Some of these examples will be included in the text, while others may be mentioned in exercises or simply left for the reader to explore on their own.  
+  
+  {  
+   valign=top  
+   width=50%   
+  * Repressilator: eqs, simulations, limit cycle stability using PB+ and Hastings  
+  * Toggle switch: eqs, nullclines and equilibria, stability, Lyapunov  
+  * Self repression: frequency response, time response  
+  * Self activation: dynamics plus Lyapunov  
+  * Activatorrepressor clock (two implementations): eqs, simulations, PB for the 2D model reduction, Hopf Bifurcation for the 4D (singular perturbation for the 2D reduction?)  
+  * Chemotaxis: integral feedback (Iglesias), modeling (incl methylation)  
+  * Input adaptation: MAPK with feedback? (Kholodenko?)  
+   width=50%   
+  * Development/differentiation: signal switching (Tomlin, Ashthagiri)  
+  * Sporalation, fate choice (Elowitz)  
+  * MAPK cascades (Sauro, Kholodenko)  
+  * Quorum Sensing (Weiss, ?), synchronization  
+  * Methabolic Pathways/engineering (yeast demand analysis, Hoffmeyer)  
+  * Hemoglobin (Kirshner) for allostery feedback?  
+  * Glucose/Lactose (Jacob and Monod)  
+  * Antisense switches (Smolke)  
+  * FFL (Alon)?  
+  * Heat Shock (El Samad)  
+  * Calcium Regulation (Khammash)  
+  }  
=== Additional Information ===  === Additional Information === 
Revision as of 03:07, 15 June 2008
Domitilla Del Vecchio (U. Mich) and Richard M. Murray (Caltech)
Contents 
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 {\em 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.
This page contains working notes for the material that is being prepared for the supplement. We anticipate that a preliminary version of the notes will be available by July 2009.
Outline
The current plan for the supplement is based on the following draft outline. Comments are welcome on topics that are missing.


Examples
The material above is intended to be useful in analyzing a large variety of natural and engineered biomolecular feedback systems. Some of these examples will be included in the text, while others may be mentioned in exercises or simply left for the reader to explore on their own.


Additional Information
 Engineering Principles in Biological Systems: 68 December 2006, Cold Spring Harbor Laboratory
 Design Principles in Biological Systems: 2428 April 2008, Institute for Mathematics and Its Applications (IMA)