Organization (Networks & Collective Dynamics)

1. Networks:
   • Simple biological modules:
     • Transcription regulation; lac operon
     • Genetic switches
     • Signal transduction
     • Repressilator: a simple clock
   • Statistics of complex networks:
     • Random (Erdös-Rényi) networks
     • Percolation, diameter, degree distribution
     • Scale free networks, construction and properties
2. Dynamics on networks:
   • Fixed points and stability
     • Hopfield neural network
   • Cycles
     • The Belousov-Zhabotinsky Reaction
     • Biological clocks (animations from HMMI: The Drosophila Molecular Clock Model)
     • Synchronization (applet)
3. Biological patterns:
   • Turing instability
   • Cortical patterns

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