APH 161

General Information


Physical Biology of the Cell

Physical Biology of the Cell (2nd ed)
by Phillips, Kondev, Theriot and Garcia

ISBN: 0815344503

Cell Biology by the Numbers
by Ron Milo and Rob Phillips

Link to the book here.  Several readings will be assigned from this book as part of the homework.


Tentative Syllabus

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.