Following is a tentative course schedule, which is subject to change as the course progresses. Abbrevations for books: PBoC2 = Physical Biology of the Cell, 2nd Ed., but Phillips, et al. CBBTN = Cell Biology by the Numbers, by Milo and Phillips.
Weekly activities
- Lecture
- Mondays and Wednesdays, 2:30–4 pm, 100 Broad
- TA OHs
- Katherine: Mondays, 10:30–11:30 am, B123 Kerckhoff
- Jackie: Tuesdays, 7–8 pm, B123 Kerckhoff
- JB's OHs
- Fridays, 2:30-3:30 pm, B123 Kerckhoff
Homework due dates
- Homework 1 due 2:30 pm, Jan. 18
- Homework 2 due 2:30 pm, Jan. 25
- Homework 3 due 2:30 pm, Feb. 1
- Homework 4 due 2:30 pm, Feb. 8
- Homework 5 due 2:30 pm, Feb. 15
- Homework 6 due 2:30 pm, Feb. 22
- Homework 7 due 2:30 pm, Mar. 1
- Homework 8 due 2:30 pm, Mar. 8
- Homework 9 due 2:30 pm, Mar. 15
Lecture schedule
- Lecture 1
- (W 01/04) What is Physical Biology of the Cell?
Reading: PBoC2 Ch. 1, CBBTN "The Path to Biological Numeracy" - Lecture 2
- (M 01/09)
Cell biology by the numbers / Principles of estimation
Reading: PBoC2 2.1, 2.2., 3.1, 3.2 - Lecture 3
- (W 01/11) Mathematizing cartoons
- Lecture 4
- (W 01/18)Statistical mechanics of molecular interactions
Reading: PBoC2 Ch. 6 - Lecture 5
- (M 01/23)
Two-state models: Mscl case study
Reading: PBoC2 Ch. 7 - Lecture 6
- (W 01/25)
Allostery and the Monod-Wyman-Changeux model
Reading: Marzen, et al., 2013 - Lecture 7
- (M 01/30) Statistical mechanics of gene
expression regulation
Reading: PBoC2 19.1, 19.2, Bintu, et al., 2005 - Lecture 8
- (W 02/01)
Mass conservation, random walks, and diffusion
Reading: PBoC2 Ch. 13 - Lecture 9
- (M 02/06)
Introduction to biopolymers / Wormlike chain
Reading: PBoC2 8.1-8.3, 10.1-10.3 - Lecture 10
- (W 02/08)
DNA looping and packaging
Reading: PBoC2 10.4 - Lecture 11
- (M 02/13)
Actin and microtubules: buckling and length control
Reading: PBoC2 10.5, 15.1, 15.3-15.5 - Lecture 12
- (W 02/15) Molecular motors: active transport and force generation
Reading: PBoC2 Ch. 16 - Lecture 13
- (W 02/22) Mechanics of cell membranes (skipped)
Reading: PBoC2 Ch. 11 - Lecture 14
- (M 02/27) The cell as a material
Reading: Kasza, et al. 2007 - Lecture 15
- (W 03/01) Linear viscoelasticity
- Lecture 16
- (M 03/06) The tensorial equations of continuum mechanics
- Lecture 17
- (W 03/08) Stokes flow
- Lecture 18
- (M 03/13) The briefest of introductions to active matter