Emergence (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, offline)
  • Synchronization (applet-offline)

3. Biological patterns:

• Turing instability
• Cortical patterns