Math 593B/793F Fall 2014
Description: Mathematical Systems Biology.
Class schedule: Tuesdays, Thursdays, 8:30-9:45AM in Armstrong 313
Office hours: Tuesdays 5-6PM, Thursdays 2-3PM, and by appointment, in Armstrong Hall 305B
Info sheet containing more or less the stuff on this webpage.
Textbooks and resources
Useful free resources:
Linear algebra notes
- 30% Final exam on Tuesday December 11 2014, 11AM-1PM in Armstrong 315
- 25% Midterm exam
- 45% Homework assignments
- (793F only) 20% Project (homework, midterm and final are rescaled to sum up to 80%)
- Homework will be assigned once every three weeks, and due two weeks later (please see the course schedule below for exact dates).
- Late turn-ins will not be accepted.
- There will be one in-class midterm exam, on October 21.
- No make-up midterm will be given.
- Tuesday December 11 2014, 11AM-1PM in Armstrong 315.
- Final is cumulative.
Course Schedule (subject to changes)
|Aug 19||Introduction; exponential growth, logistic growth||1.1|
|Aug 21||Chemostat; Michaelis-Menten||1.1|
|Aug 26||Steady states; linear stability analysis||1.2|
|Aug 28||Vector fields; phase planes||1.4|
|Sep 2||Nullclines; local and global stability||1.4|
|Sep 4||SIRS model||1.5||HW 1 posted|
|Sep 9||Chemical kinetics||1.6|
|Sep 11||Interaction graph; Matlab interlude||1.5|
|Sep 16||Enzyme kinetics. QSSA||1.6|
|Sep 18||Inhibition||1.6||HW 1 due|
|Sep 23||Gene expression. Cooperativity||1.6|
|Sep 25||Deficiency theory|
|Sep 30||Hill kinetics. Ultrasensitivity||1.7|
|Oct 2||Goldbeter-Koshland model and ultrasensitivity. Bistability||1.7|
|Oct 7||Limit cycles||1.8||HW 2 posted|
|Oct 21||Midterm 1||Midterm solutions|
|Oct 23||Chapter 1 Review||1.9|
|Oct 28||Hopf bifurcations||1.9|
|Oct 30||Matlab. XPP||HW 2 due|
|Nov 6||Oscillating chemical networks|
|Nov 13||Graphical conditions for multistationarity: the DSR graph|
|Nov 18||Research project: dynamics of 2D chemical networks|
|Nov 20||Introduction to PDE models||2.1||HW 3 posted|
|Dec 11||Final exam||Solutions to final|
The West Virginia University community is committed to creating and fostering a positive learning and working environment based on open communication, mutual respect, and inclusion. If you are a person with a disability and anticipate needing any type of accommodation in order to participate in this class, please advise me and make appropriate arrangements with the Office of Accessibility Services (293-6700). For more information on West Virginia University's Diversity, Equity, and Inclusion initiatives, please see http://diversity.wvu.edu.