1. Amino acids
2. Biomolecular Forces                                                                  
   • van der Waals interactions
   • hydrogen bonds
   • hydrophobic effect
3. Protein structure
   • secondary
   • 3D structure
4. Protein Folding Problem(s)
• Understand the physics of the folding problem (unique and reachable ground state) 
• Anfinsen Experiment
• Predict the native structure, given the sequence 
• Sequence-structure mapping and fold prediction
5. Lattice Model
   • The Random Energy Model (REM)
   • The freezing transition and associated singularities
   • Designed REM as a model of protein folding
6. Monte Carlo sequence design, detailed balance

1. Macroscopic properties of DNA; packaging into chromatin (eukaryotes)
2. Discovery of DNA Structure and Function: Watson and Crick, L. Pray, Nature Education 1, 1 (2008)
• Microscopic structure of DNA; the four nucleotides
• DNA Structure
• Importance of stacking interactions, binding energies
3. Denaturation, hybridization (similarity); renaturation (zippering)
4. (UV absorption) Melting curves for medium and long chains; general features and theoretical issues
5. The pair-stacking model; (Poland D & Scheraga HA. Theory of Helix-Coil Transitions in Biopolymers . Academic Press, New York, 1970)
6. Theoretical analysis of homopolymer denaturation (presentation by David Mukamel at ITP)

1. Structure and function of RNA
2. The `RNA world' hypothesis
3. Structural levels:
• primary, secondary, tertiary;
• Structural elements (stem, loop, bulge, ...)
• experimental methods
4. Representations without psuedoknots
5. Algorithms for finding optimal secondary structure: Nussinov (article), Zuker
6. Recursive (Hartree) calculation of partition function
7. RNA floding and Matrix Field Theory (McGenus)
8. Counting secondary structures. [Chandrasekhar, Rev. Mod. 15, 1 (1943)]
9. The melting of a hairpin

[Lecture Notes]

[Exercises]

Related links

• DNA-Inspired Electrostatics, Gelbart et al, Physics Today 53, 38 (2000).
• Electrostatics in DNA-peptide complexes; from a course on Principles of Protein Structure
• Ten years of tension: single-molecule DNA mechanic; Bustamante, et al, Nature 421, 423 (2003).
• On Electrostatic Screening; John Marko at Northwestern
• On DNA elasticity; Philip Nelson at UPenn
• The residual potential; Bruce Tidor at MIT
• Meltsim is a package to calculate melting temperature of specified DNA sequences.
• A DNA guide from University of Michigan
• The RNA world web-site
• The Zuker group's web-page
• The mfold Web Server
• The Vienna RNA package