Statistical Physics in Biology

Macromolecular Structure

1. Introduction to polymers:
   • Entropy and elasticity
   • Interactions and the coil-globule transition
   • Ionic interactions
2. DNA double helix:
   • Watson-Crick pairs; symmetries
   • Energy/entropy considerations, and melting
   • Elasticity; bend, twist, and topology
   • Unzipping; translocation, packing, …
3. 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)
4. Sequence to Structure maps
5. 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, …
6. 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, …

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