Difference between revisions of "Supplement: Biomolecular Feedback Systems"
(→Contents) 
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** Input/Output Modeling  ** Input/Output Modeling  
** Analysis Near Equilibria  ** Analysis Near Equilibria  
+  ** Robustness  
** Analysis of Reaction Rate Equations  ** Analysis of Reaction Rate Equations  
** Limit Cycle Behavior  ** Limit Cycle Behavior  
−  
** Bifurcations  ** Bifurcations  
** Model Reduction Techniques  ** Model Reduction Techniques  
* Chapter 4: {{BFS pdfStochastic Behaviorbfsstochastic16Jan11}}  * Chapter 4: {{BFS pdfStochastic Behaviorbfsstochastic16Jan11}}  
** Stochastic Modeling of Biochemical Systems  ** Stochastic Modeling of Biochemical Systems  
−  **  +  ** Simulation of Stochastic Systems 
−  **  +  ** Linearized Modeling and Analysis 
−  +  
−  +  
−  +  
−  +  
 width=50%    width=50%   
* Chapter 5: Feedback Examples  * Chapter 5: Feedback Examples  
−  **  +  ** {{BFS pdfThe lac Operonbfslacoperon16Jan12}} 
−  ** Phage <math>\lambda</math>  +  ** (Heat shock) 
−  +  ** (Phage <math>\lambda</math>)  
** {{BFS pdfBacterial chemotaxisbfschemotaxis11Mar10}}  ** {{BFS pdfBacterial chemotaxisbfschemotaxis11Mar10}}  
+  ** (Signaling pathways in yeast)  
* Chapter 6: {{BFS pdfBiological Circuit Componentsbfscircuits30Mar10}}  * Chapter 6: {{BFS pdfBiological Circuit Componentsbfscircuits30Mar10}}  
** Biological Circuit Design  ** Biological Circuit Design  
+  ** Introduction  
** Selfrepressed Gene  ** Selfrepressed Gene  
** The Toggle Switch  ** The Toggle Switch  
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* Chapter 7: {{BFS pdfInterconnecting Componentsbfsmodules30Mar10}}  * Chapter 7: {{BFS pdfInterconnecting Componentsbfsmodules30Mar10}}  
** Input/Output Modeling and the Modularity Assumption  ** Input/Output Modeling and the Modularity Assumption  
−  **  +  ** Introduction to Retroactivity 
+  ** Retroactivity in Gene Transcriptional Circuits  
+  ** Retroactivity in Signaling Systems  
** Insulation Devices to Enforce Modularity  ** Insulation Devices to Enforce Modularity  
−  **  +  ** Retroactivity and noise 
−  +  * Chapter 8: Design Tradeoffs and Examples  
−  * Chapter 8: Design Tradeoffs  +  
−  +  
* 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]  
Line 77:  Line 75:  
** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]  ** [http://www.ncbi.nlm.nih.gov/About/primer/genetics_molecular.html Molecular Genetics: Piecing It Together]  
** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]  ** [http://www.genome.gov/Glossary/ NHGRI Talking Glossary]  
−  * Appendix B: A Primer on Control Theory  +  * Appendix B: {{BFS pdfA Primer on Control Theorybfscontrol16Jan12}} 
* Appendix C: {{BFS pdfRandom Processesbfsrandom26Dec10}}  * Appendix C: {{BFS pdfRandom Processesbfsrandom26Dec10}}  
* {{BFS pdfBibliography and Indexbfsbackmatter23Jan11}}  * {{BFS pdfBibliography and Indexbfsbackmatter23Jan11}} 
Revision as of 18:36, 16 January 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)
 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