CDS 213

	The Architecture of Robust, Evolvable Networks
	Winter 2010

Instructor: John C. Doyle Course mailing list Lectures: TTh 4-5:30 pm, 107 Annenberg, changes emailed to course mailing list Course Schedule Week Date Topic Reading 1 Introduction to Network Architectures 12 Jan (T) IST Seminar: The Architecture of Robust, Evolvable Networks 14 Jan (Th) Internet Architecture Network is IPC: Day et al, 2008 (Paper); Matta (Slides); Implications PNA, Day, 2009 (Slides); Multihop/Multiparty influences on Net. Arch., Touch (Slides) 2 Network Architectures: Operating Systems and Cell Biology 19 Jan (T) Internet and Biology Architectures Assessing Security of a Clean Slate Internet Architecture , Boddapati, Day; Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle 21 Jan (Th) Robustness and Fragility, Hard Limits and Tradeoffs On Lossless Approximations, Fluctuation-Dissipation and Limitations of Measurements , Sandberg, Doyle 3 Case Studies: Cell Biology, Clothing and Legos 26 Jan (T) Network architecture and control of glycolysis; Clothing; Legos Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle; Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane , Campanella et al 28 Jan (Th) Heat Shock in cells; Clothing; Legos Surviving Heat Shock: Control strategies for robustness and performance , El-Samad, et al; Robustness of Cellular Functions Review, Stelling, et al; Reverse Engineering of Biological Complexity, Csete, Doyle 4 Naming, Addressing and Control in Cell Biology 2 Feb (T) Naming, Addressing and Control in Cell Biology Highly optimised global organisation of metabolic networks, R. Tanaka, M. Csete and J. Doyle;Quantitative evaluation of scale-rich metabolic networks, Tanaka, Doyle 4 Feb (Th) Signal Transduction Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon and Doyle; Chapter 7: Robustness of Protein Circuits: The Example of Bacterial Chemotaxis of "An Introduction to Systems Biology", Uri Alon 5 Architecture and Modeling in Cell Biology 9 Feb (T) Architecture and Layering in Cell Biology 11 Feb (Th) Modeling Bio Systems, Speaker: James Faeder Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek; Simulation of large-scale rule-based models, Colvin et al.; The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder;Rules for Modeling Signal-Transduction Systems, Hlavacek et al.; Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al. 6 Complexity and Fragility 16 Feb (T) Complexity and Fragility: Examples with NPP and Mandelbrot sets [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/DenniceConnections2006.pdf Studying the Logistic Map and the Mandelbrot Set using SOS Methods, Gayme, Fazel, Doyle];Complexity in Automation of SOS Proofs: An Illustrative Example, Gayme et al.,; [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/mandel2.pdf Optimization Based Methods for Determining Basins of Attraction in the Logistic Map and Set Membership in the Mandelbrot Set, Gayme et al. ] 18 Feb (Th) Course Projects There will be a course project to be discussed.