Macromolecular Structure

Introduction to Polymers:
- Entropy and Elasticity
- Interactions and the Coil-globule Transition
- Single Molecule Experiments, Optical Tweezers
DNA Double Helix:
- Watson-Crick Pairs; Symmetries
- Energy/entropy Considerations, and Melting
- Elasticity; Bend, Twist, and Topology
- Unzipping; Translocation, Packing, ...
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
- Sequence Evolution and Neutral Networks
Protein Folding:
- Role of Hydrophobicity and Other Interactions
- Secondary Structure Elements: Alpha-helices and 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, ...
- Structural Requirements of the Genome : Access; Duplication; ...
- Hemoglobin

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