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 |