- Introduction to polymers:
- Entropy and elasticity
- Interactions and the coil-globule transition
- Ionic interactions
- DNA double helix:
- Watson-Crick pairs; symmetries
- Energy/entropy considerations, and melting
- Elasticity; bend, twist, and topology
- Unzipping; translocation, packing, …
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RNA strands:
- 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
- Protein folding:
- 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, …
- Protein-Nucleic acid composites:
- 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, …