| 1 | Introduction; Master equation | |
| 2 | Elements of population genetics | |
| 3 | Evolving populations (forward Kolmogorov) | |
| 4 | Population genetics (fitness, selection, ...) | |
| 5 | Fixation (backward Kolmogorov) | |
| 6 | Introduction to sequence alignment | Assignment 1 due |
| 7 | Algorithms for sequence alignment | |
| 8 | Significance of alignments (extreme value distributions) | |
| 9 | Ionic interactions | Assignment 2 due |
| 10 | Polymer theory 1, entropy elasticity, collapse | |
| 11 | Polymer theory 2, collapse, Random energy model | |
| 12 | Protein folding I: elements of structure and forces | Assignment 3 due |
| 13 | Protein folding II: evolved (designed) foldable proteins | |
| 14 | Protein folding III: kinetics | Assignment 4 due |
| 15 | Protein folding IV:: kinetics | |
| 16 | DNA (melting) | |
| 17 | RNA (secondary structure) | Assignment 5 due |
| 18 | Protein-DNA interactions I: specific and non-specific binding | |
| 19 | Protein-DNA interactions II: sequence-dependence & kinetics | Assignment 6 due |
| 20 | Microtubules | |
| 21 | Molecular motors & cell motility | Assignment 7 due |
| 22 | Introduction to networks | |
| 23 | Dynamics on networks 1 | |
| 24 | Dynamics on networks 2 | Assignment 8 due |
| 25 | Packing of DNA inside cells | |
| 26 | Cooperativity: hemoglobin and transcription factors | Final Project due |
