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 |