Mathematical Cell Biology; May 2012
Homework assignments:
Note: these assignments are being posted early so you can plan your work. They may undergo slight modification, depending on the week's material.- Homework and activities for Week 2 Set 1
(slightly edited)
- Homework and activities for Week 2 Set 2
(NEW: has been revised for clarity)
- There is also some HW on the site with Jun Allard's Material
Lectures and Course Material
You can find the topics covered, lecture notes, and links to material in the table below.Here is some reference material with some further details on topics covered on week 1 and few topics from week 2. Course Notes
Week 2
Guest lecturer for Week 2: Dr Jun Allard, UC Davis.
Link to Jun Allard's Material
| Dates | Topics | Rough Notes | Other Material | Lecture (video) |
|---|---|---|---|---|
| May 7-11 | Daily Lectures by Jun Allard |
Jun Allard's Material | See MathTube | |
| May 7-11 | Keshet Lectures (Slides include corrections) |
Slides: Lecture 5 (May 7) Lecture 6 (May 8) Lecture 7 (May 9) Lecture 8 (May 10) Lecture 9 (May 11) |
See MathTube | |
| May 7 | Oster-Odell Mechano-chemical model |
Slides | Prerecorded clip: Oster-Odell mechanochemical cell See also actual May 7 (Lecture 5) |
|
| May 7-11 | Introduction to Dimensional Analysis |
Chemostat Beta Cells |
See Chap 4 of Course Notes |
Prerecorded (YouTube) Lecture: Chemostat Example (6:23 min) Beta cells (2:52 min) |
| May 7-11 | Actin and the cytoskeleton | Julie Theriot's iBioSeminar | ||
| May 7-11 | Introduction to Polymerization |
Slides | Simple polymerization (6:24 min) | |
| May 7-11 | Polymer size distrib (with corrections) NEW! |
Notes:
Deriving the Eqs XPP files: asizedis.ode (OLD) asizedis2.ode (NEW) XPP Instructions |
Deriving the equations: Explanation (6:07 min) Simulating the polymer size distribution: XPP tutorial (6) (5:32 min) XPP tutorial (6.5)NEW (4.01 min) |
|
| May 7-11 | Microtubules: Dogterom-Leibler Eqs |
MTDogterom.ode | ||
| May 7-11 | Microtubule Movies | Structure Dynamic Instability MT and ER in vivo |
||
| May 7-11 | Molecular Motors: (1) Flagellar length control (2) SPB oscillations |
(1) Marshall JCB paper (2)Vogel PLoS paper (3)Odell and Foe paper Center for Cell Dynamics |
(1) Flagellae and cillia (2)Vogel movies (PLoS) (3) Odell simulations of motors on MT (4)Ron Vale ibioseminar: Motor proteins |
|
| May 7-11 | Prerecorded material: Actin Polymerization (1) Length distribution (2) In the lamellipod (3) |
Slides 1 Slides 2 Slides 3 |
Actin Basics (4:41 min) Filament length distribution (9:40 min) Actin recycling in cell motility (9:29 min) |
|
| May 7-11 | Reverse engineering a polymer assembly |
Slides | Reverse Engineering (8:06 min) |
Additional links
| Dates | Topics | Rough Notes | Other Material | Lecture (video) |
|---|---|---|---|---|
| May 4-11 | Cell Division and Cell Cycle Checkpoints |
Cell division Checkpoints |
||
| John Tyson's lectures | Tyson Lectures site Tyson:(1) Switches Tyson:(2) Cell Cycle |
Return to Course Home Page