1. Biomolecular forces:
- Chemical bonds, van der Waals, hydrogen bonding
- Ionic interactions
2. Introduction to polymers:
3. Protein folding:
- Entropy and elasticity
- Interactions and the coil-globule transition
- Simple lattice models of protein folding
- Random Energy Model for freezing
4. DNA and RNA:
- Role of hydrophobicity and other interactions
- Secondary structure elements: alpha-helices & beta-sheets
- Classification of protein structures, and their evolution
- Dynamics of fast folding
- Watson-Crick pairing
- Energy/entropy considerations, and DNA melting
- RNA secondary structures
- Hartree equation for obtaining secondary structures without pseudo-knots
Tuesday September 24
L6: (MK) Phases of polymers
Thursday September 26
L7: (MK) Compact polymers and REM
Tuesday October 1
L8: (LM) Interactions in biology
Thursday October 3
L9: (LM) Protein folding energetics
Tuesday October 8
L10: (LM) Protein folding kinetics
Thursday October 10
L11: (MK) DNA
Thursday October 17
L12: (MK) RNA