1. Introduction to polymers:
2. DNA double helix:
- Entropy and elasticity
- Interactions and the coil-globule transition
- Ionic interactions
3. RNA strands:
- Watson-Crick pairs; symmetries
- Energy/entropy considerations, and melting
- Elasticity; bend, twist, and topology
- Unzipping; translocation, packing, ...
4. Protein folding:
- Varieties: mRNA, tRNA, ribosomal RNA, ...
- Hartree equation for obtaining secondary structures without pseudo-knots
- Kinetics folding (local minimum) vs thermodynamics hypothesis (global minimum)
- Sequence to Structure maps
5. Protein-Nucleic acid composites:
- Role of hydrophobicity and other interactions
- Secondary structure elements: alpha-helices & beta-sheets
- Classification of protein structures, and their evolution
- Simple lattice models of protein folding, solvation model
- Random Energy Model for freezing
- Dynamics of fast folding
- Folding in the cell: chaperones, co-translational, agregation and fibrils
- Hemoglobin: evolution, polymorphism, folding and fibrilation, function, regulation, ...
- Electrostatic interactions
- Specific and non-specific binding of factors to DNA regulatory elements
- Borg-von Hippel, wight matrices (profiles), information content
- Large scale packaging of DNA; histones, heterochromatin, ...