Syllabus
Required text: Physical Biology of the Cell (2nd ed) by Phillips, Kondev, Theriot and Garcia (ISBN: 0815344503)
Note that the syllabus is tentative and subject to change. Check back regularly for the most recent version.
| Date | Week | Topic | Slides |
|---|---|---|---|
| Mon, Jan. 6 | 1 | Biological numeracy exam | Slides |
| Weds, Jan. 8 | 1 | Time scales in biology. What sets the time scale of division in bacteria? | Slides |
| Mon, Jan. 13 | 2 | What sets the time scale of division in bacteria continued. | - |
| Mon, Jan. 13 (6:30 PM) | 2 | (Make up #1) Diffusion as biology’s null hypothesis. Diffusion times and first encounter with dimensional analysis. | Slides |
| Weds, Jan. 15 | 2 | Diffusion continued. Diffusion as coin flips and binomial distribution as first of the great probability distributions. | Slides |
| Weds, Jan. 22 | 3 | Reaction-diffusion equations and pattern formation. Turing patterns. | - |
| Weds, Jan. 22 (6:30 PM) | 3 | (Make up #2) Diffusion continued. Continuum theory protocol. Experiments on 1D diffusion using molecular motors on cytoskeletal filaments. | - |
| Mon, Jan. 27 | 4 | Intro to dynamical systems. mRNA dynamics, cytoskeletal length dynamics. | - |
| Weds, Jan. 29 | 4 | Size control in biology - from the cytoskeleton to organelles | - |
| Mon, Feb. 3 | 4 | Active matter introduced - bird flocks. cytoskeleton-motor systems. What energy buys us in living matter. | - |
| Weds, Feb. 5 | 5 | Continuum theory protocol # 1 - elasticity theory in 1D, 2D and 3D | - |
| Weds, Feb. 5 (6:30 PM) | 5 | (Make up #3) Elasticity theory continued | - |
| Mon, Feb. 10 | 5 | Continuum theory protocol # 2 - hydrodynamics, Navier-Stokes equations, low and high Reynolds number | - |
| Weds, Feb. 12 | 6 | Hydrodynamics continued. Applications of hydrodynamics to biological problems. | - |
| Weds, Feb. 12 | 6 | (Make up #4) Active matter theory. | - |
| Weds, Feb. 19 | 7 | Entropy rules. The direction of spontaneous processes. The second law. | - |
| Mon, Feb. 24 | 8 | Boltzmann’s law and statistical mechanics. Biology of binding. | - |
| Weds, Feb. 26 | 8 | Examples of binding. Ligand-receptor problems. Gene expression as a binding problem. The MWC model and allostery. | - |
| Mon, Mar. 2 | 9 | Physical evolution. | - |
| Weds, Mar. 4 | 9 | The Biological Frontiers of Physics and Engineering. A look to the future. | - |