Difference between revisions of "Supplement: Biomolecular Feedback Systems"
(→Contents) 

Line 24:  Line 24:  
** 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 pdfCore Processesbfscoreproc01Jan11}}  * Chapter 2: {{BFS pdfCore Processesbfscoreproc01Jan11}}  
Line 42:  Line 43:  
** Stochastic Modeling of Biochemical Systems  ** Stochastic Modeling of Biochemical Systems  
** Simulation of Stochastic Systems  ** Simulation of Stochastic Systems  
−  **  +  ** Input/Output Linear Stochastic Systems 
* Chapter 5: {{BFS pdfFeedback Examplesbfsfbkexamps11Jul12}}  * Chapter 5: {{BFS pdfFeedback Examplesbfsfbkexamps11Jul12}}  
−  ** 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 pdfBiological Circuit Componentsbfscircuits11Jul12}}  * Chapter 6: {{BFS pdfBiological Circuit Componentsbfscircuits11Jul12}}  
−  ** Biological Circuit Design  +  ** Introduction to Biological Circuit Design 
−  **  +  ** Negative Autoregulation 
−  +  
** The Toggle Switch  ** The Toggle Switch  
** The Repressilator  ** The Repressilator  
** Activatorrepressor Clock  ** Activatorrepressor Clock  
+  ** An Incoherent Feedforward Loop (IFFL)  
* Chapter 7: {{BFS pdfInterconnecting Componentsbfsmodules11Jul12}}  * 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  
−  ** Retroactivity in Gene  +  ** Retroactivity in Gene Circuits 
** Retroactivity in Signaling Systems  ** Retroactivity in Signaling Systems  
−  ** Insulation Devices  +  ** Insulation Devices: Retroactivity Attentuation 
−  +  Chapter 8: {{BFS pdfDesign Tradeoffsbfstradeoffs11Jul12}}  
−  +  
* 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

Chapter 8: Design Tradeoffs (PDF)

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