Introductory and Review papers
Physics
talk (slides) Nov 11, 2004
Emergent
complexity (slides) Nov 22, 2004 Georgia Tech
Old
IPAM slides
Complexity
and Robustness, JM Carlson
and J Doyle, PNAS, 99, Suppl. 1, 2538-2545 (pdf)
For more introductory papers on HOT, see Jean Carlson: http://www.physics.ucsb.edu/~carlson
Reverse
Engineering of Biological Complexity, ME Csete and J Doyle, Science, 295, 1664 (2002) (pdf)
Supplementary material
·
Biological examples (pdf)
·
Feedback examples (pdf)
·
Legos and protocols: Notes and
Pictures
·
Biology and protocols: Slides
·
Integral feedback: Proofs and
Notes
Links
·
Feedback Control Theory, by Doyle,
Francis and Tannenbaum (link)
·
Internet Protocols, Evolution, and Theory (link)
·
Systems Biology Workbench (SBW) and Markup
Language (SBML) (link)
Selected additional references:
Robust
Flow Stability: Theory, Computations and Experiments in Near Wall Turbulence, PhD thesis by Kumar Bobba (pdf)
Csete M.E. and J.C. Doyle, 2004, Bow ties, metabolism, and disease, Trends in Biotechnology, Vol 22, Issue 9, pg. 446-450 (pdf)
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J.
Doyle, 2004, Robustness of cellular
functions, Cell, October, 2004 (pdf)
H. El-Samad, H. Kurata , J.C. Doyle ,
Li, L., D. Alderson, J. Doyle, and W. Willinger. 2004. A First-Principles Approach to Understanding the Internet's Router-level Topology. Proc. ACM SIGCOMM
http://www.acm.org/sigs/sigcomm/sigcomm2004/papers.html#A_First_Principles
Mutation, specialization, and hypersensitivity in
highly optimized tolerance, Zhou, Carlson, and Doyle, PNAS (pdf)
PNAS 2002 99: 2049-2054; published online before print February 12 2002,
10.1073/pnas.261714399
Power laws, Highly Optimized Tolerance and generalized source coding, Doyle and Carlson, PRL, (pdf)
Highly Optimized Tolerance: A
Mechanism for Power Laws in Designed Systems, Carlson and Doyle, PRE, (pdf)
Robust perfect adaptation in bacterial chemotaxis through integral
feedback control, Yi, Huang, Simon, and Doyle, PNAS, (Link or PDF)
Structured semidefinite programs and semialgebraic geometry methods in robustness and optimization, Pablo Parrilo, PhD Thesis, Control and Dynamical Systems, Caltech, (Gzipped postscript)
Slides from old talks on Complexity and Robustness
1. CDC plenary slides (ppt)
2. Introduction to complex networks (ppt)
3. Allerton plenary (ppt)
4. Introduction to HOT (ppt)
A course in Robust Control Theory: A Convex Approach, Dullerud and Paganini, Springer
Essentials of Robust Control, Zhou, Prentice-Hall
Cells, Embryos, and Evolution, Gerhart and Kirschner
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