• Introduction & outline
• Evolving sequences, Master equation
• Population genetics, mutation, reproduction, selection
• Forward Kolmogorov equations, steady state

• Genetic drift, fixation
• Backward Kolmogorov equations, fixation
• Phylogeny, sequence matching
• Recursive algorithms, dynamic programming
• Significance of alignments, extreme value distribution

Lec. 3 (5/29)

• Forces and interactions
• Polymers, bending rigidity, entropic elasticity
• Interactions and Flory/mean-field theory
• Protein folding, random energy model

Lec. 4 (5/30)

• Nucleic acids
• Melting of DNA; Poland-Scheraga model
• Secondary structure of RNA
• Melting of an RNA hairpin

Lec. 5 (5/31)

• Dynamic Instability of microtubules, caps and catastrophes
• Molecular motors, ratchet and asymmetric hopping models
• Cell motility

Lec. 6 (6/3)

• Protein-DNA interactions
• Packing of DNA within cells
• Membranes

Lec. 7 (6/4)

• Biological networks
• Elements of networks: distance, diameter, degree distribution
• Random network (Erdos-Renyi), percolation
• Preferential attachment, The Barabasi-Albert model

Lec. 8 (6/5)

• Dynamics on networks: Fixed points
• The Hopfield model for associative memory
• Stability, bifurcations, and cycles
• Synchronization
• Turing Patterns