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
- Sara: Mondays, 10:30–11:30 am, B123 Kerckhoff
- Shichen: Tuesdays, 3–4 pm, B123 Kerckhoff
- JB's OHs
- Thursdays, 10:30–11:30 am, B123 Kerckhoff
Homework due dates
- Homework 1 due 2:30 pm, Jan. 15
- Homework 2 due 2:30 pm, Jan. 22
- Homework 3 due 2:30 pm, Jan. 29
- Homework 4 due 2:30 pm, Feb. 5
- Homework 5 due 2:30 pm, Feb. 12
- Homework 6 due 2:30 pm, Feb. 24
- Homework 7 due 2:30 pm, Feb. 26
- Homework 8 due 2:30 pm, Mar. 5
- Homework 9 due 2:30 pm, Mar. 12
- Homework 10 due 2:30 pm, Mar. 19
Lecture schedule
Lecture notes download. I will post lecture notes as they are available. I do not guarantee that all lecture notes will be available for download, but will post what I can.
- Lecture 1
- (M 01/06) What is Physical Biology of the Cell?
Reading: PBoC2 Ch. 1, CBBTN "The Path to Biological Numeracy" - Lecture 2
- (W 01/08)
Cell biology by the numbers / Principles of estimation
Reading: PBoC2 2.1, 2.2., 3.1, 3.2 - Lecture 3
- (M 01/13) Mathematizing cartoons
- Lecture 4
- (W 01/15) Statistical mechanics of gene
expression regulation
Reading: PBoC2 19.1, 19.2, Bintu, et al., 2005 - Lecture 5
- (W 01/22)
Mass conservation, random walks, and diffusion
Reading: PBoC2 Ch. 13 - Lecture 6
- (M 01/27)
Introduction to biopolymers / Wormlike chain
Reading: PBoC2 8.1-8.3, 10.1-10.3 - Lecture 7
- (W 01/29)
DNA looping and packaging
Reading: PBoC2 10.4 - Lecture 8
- (M 02/02)
Actin and microtubules: buckling and length control
Reading: PBoC2 10.5, 15.1, 15.3-15.5 - Lecture 9
- (W 02/05) Molecular motors: active transport and force generation
Reading: PBoC2 Ch. 16 - Lecture 10
- (M 02/10) Continuum mechanics I: Conservation of mass
- Lecture 11
- (W 02/11) Continuum mechanics II: Conservation of momentum
- Lecture 12
- (W 02/19) Life at low Reynolds number: Stokes flow
- Lecture 13
- (M 02/24) Dry active matter: Vicsek, Toner, and Tu
- Lecture 14
- (W 02/26) Continuum mechanics III: Active nematic gels
- Lecture 15
- (M 03/03) Linear viscoelasticity
- Lecture 16
- (W 03/05) Catch-up
- Lecture 17
- (M 03/10) Cell sorting and the differential adhesion hypothesis
- Lecture 18
- (W 03/11) Wrap-up