8.592J | Spring 2011 | Graduate

Statistical Physics in Biology

Introduction; Master Equation

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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As Taught In
Spring 2011
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