Textbooks
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Physical Biology of
the Cell (2nd ed) ISBN: 0815344503 |
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Cell Biology by the Numbers Link to the book here. Several readings will be assigned from this book as part of the homework. |
| DATE | TOPIC | READINGS DISCUSSED IN CLASS | HOMEWORK |
| Wednesday, Jan 4 | Lecture 1: Course introduction, A feeling for the numbers in biology. Thinking up an E. coli. | Schmidt et al. | HW1 out |
| Friday, Jan. 6 | Lecture 2: Ribosomes and the limit to the rate of cell division. A first look at diffusion in neurons. Pascal's triangle and path probabilities. | Stouthammer. | |
| Monday, Jan. 9 | Lecture 3: Diffusion in biology. Random walks in 1-D. Continuum diffusion equation. Fick's laws. Active transport. | ||
| Wednesday, Jan. 11 | Lecture 4: Diffusion in biology. The Central Dogma. Gene Expression. RNA Master Equation. The Full RNA Distribution. Protein to RNA Ratio. | ||
| Friday, Jan. 13 | No Class. | ||
| Monday, Jan. 16 | No Class. | ||
| Wednesday, Jan. 18 | No Class | ||
| Friday, Jan. 20 | No Class. | ||
| Monday, Jan. 23 | Lecture 5: Introduction to Boltzmann Weights and Statistical Mechanics. Stat Mech of Ion Channels and the Central Dogma. Introduction to Allostery. | ||
| Wednesday, Jan. 25 | Lecture 6: Statistical Mechanics of Allostery, Ion Channels, and the Central Dogma. Using Allostery to Consider Nucleosomes. Introduction to Induction. | ||
| Friday, Jan. 27 | Lecture 7: MWC model and Induction. Introduction to Genetic Switches and Cooperativity. Self-Activating Genes. | ||
| Monday, Jan. 30 | Lecture 8: Genetic Switches and the Mutual Repression Circuit. Phase Portrait Analysis of Genetic Switches. Body Plans in Flies. | Hwa. | |
| Wednesday, Feb. 1 | Lecture 9: Form of the gut. Morphogens in Flies and Establishing a Gradient. | Mahadevan. | |
| Friday, Feb. 3 | Lecture 10: Physics of Stress and Strain. Deformation of Rods. Buckling of Rods. | Yurke. | |
| Monday, Feb. 6 | Lecture 11: The Langmuir Trough. Mechanics of Lipids. Introduction to Membrane Physics. | ||
| Wednesday, Feb. 8 | No Class. | Garcia. | |
| Friday, Feb. 10 | No Class | ||
| Monday, Feb. 13 | Lecture 12: The Lipid Bilayer. Critical Concentration for Self-Assembly of Micelles. Curvature Energy of Membranes and Vesicles. | ||
| Wednesday, Feb. 15 | Lecture 13: Simple Model of Phase Separation. Membrane-less Organelles. | Brangwynne. | |
| Friday, Feb. 17 | Lecture 14: Biological Shape. | ||
| Monday, Feb. 20 | No Class. | ||
| Wednesday, Feb. 22 | Lecture 16: Energy Flow in Biology. structures | Kinetic Proofreading. | |
| Friday, Feb. 24 | Lecture 17: Energy Flow in Biology. | ||
| Monday, Feb. 27 | Lecture 18: Physical Evolution. | ||
| Wednesday, Mar. 1 | Lecture 19: Glycolysis in Wonderland and Optimality. Dispersal of species over distance. | Glycolysis in Wonderland. Allen. | |
| Friday, Mar. 3 | Lecture 20: Osmotic Pressure and the Dispersal of Frogs. | Nothing Makes Sense Except in the Light of Evolution. | |
| Monday, Mar. 6 | Lecture 21: The Chromosomal Theory of Inheritance. Genetic Drift as an Important Evolutionary Force. | ||
| Wednesday, Mar. 8 | Lecture 22: Evolution of Transcription Factor Binding Sites. Combining Genetic Drift, Selection, and Mutation. | Lassig. | |
| Friday, Mar. 10 | Lecture 23: Course wrap up. | The End of Theory Wigner. |