Mathematical Cell Biology; May 2012

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
May 7-11 Daily Lectures by
Jun Allard
Jun Allard's Material See MathTube
May 7-11 Keshet Lectures
(Slides include corrections)
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
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
Slides Simple polymerization (6:24 min)
May 7-11 Polymer size distrib
(with corrections)
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
May 7-11 Microtubule Movies
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
May 4-11 Cell Division
and Cell Cycle Checkpoints
Cell division
John Tyson's lectures Tyson Lectures site
Tyson:(1) Switches
Tyson:(2) Cell Cycle

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