Complex networks

Introductory and review papers on complex networks, biological complexity and robustness.

Copied from "http://www.cds.caltech.edu/~doyle/CmplxNets/"

• 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)
• Reverse Engineering of Biological Complexity, ME Csete and J Doyle, Science, 295, 1664 (2002) (pdf)
• See also introductory papers on HOT

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]
• [Internet Protocols, Evolution, and Theory]
• [Systems Biology Workbench (SBW) and Markup Language (SBML)]

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 , C.A. Gross, and M. Khammash, 2004, Surviving Heat Shock: Control Strategies for Robustness and Performance, PNAS. Accepted, to appear.

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)

Feedback regulation of the heat shock response in E. Coli, Kurata, El-Samad, Yi, Khammash, and Doyle, draft, (PS (7M) or Zipped (300k))

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)

Additional recommended books

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

Related news and commentary items

• http://www.aip.org/enews/physnews/2000/split/pnu474-1.htm
• http://helix.nature.com/nsu/000323/000323-2.html
• The power of design, Mark Newman, Nature 405, 412-413 (2000)
• http://unisci.com/stories/20001/0314004.htm:
• http://www.pnas.org/cgi/content/full/97/10/5031