Physics 498 BIO: Statistical Physics, Biological Information and Complexity

Nigel Goldenfeld

Course outline and schedule

 

Week 1 Aug 22, 24, 27 Why is biology hot?   Why is biology interesting to physicists?
What can physicists really do?  What should physicists not do?
Why is this the "century of biology"?
Chapter 0: The hierarchical nature of biological information
DNA, the universal genetic code
Week 2 Aug 29, 31, Sep 5. Making proteins, mitochondrial DNA
Chapter 1: The molecules of life
Three types of structure, DNA melting
Simple theory of DNA unzipping
Week 3 Sep 7, 10, 12 Statistical mechanics of polymers
Loops, polymer elasticity
Self-avoiding walks (Flory theory)
Week 4 Sep 14. 17, 19 Full theory of DNA melting
Week 5 Sep 21, 24, 26 DNA replication II, circular DNA, topoisomerases
Single molecule experiments on DNA
Week 6 Sep 28, Oct 1, 3 RNA secondary structure: prediction and dynamic programming
Week 7 Oct 5, 8, 10 Sequence specificity, energy landscape, protein folding
Chapter 2: Genes and bioinformatics
Week 8 Oct 12, 15, 17 Comparative methods for RNA secondary structure prediction
Week 9 Oct 19, 22, 24 Molecular evolution, molecular phylogenetic trees
Week 10 Oct 26, 29, 31 Student presentations
Week 11 Nov 2, 5, 7 Global and local sequence alignment, scoring matrices
Week 12 Nov 9, 12, 14 Dynamic programming, heuristics
Week 13 Nov 16, 26, 28 Statistical significance of alignment scores
Renormalization group approach to extremal statistics
Chapter 3: Biological complexity
Week 14 Nov 30, Dec 3, 5 Systems biology
Scaling laws in ecology, biodiversity
Macroevolution
Week 14 Dec 7