BINF 354 Foundations in Mathematical Biology
Fall, 2006
Mondays, Wednesday, 9-10:15 AM
Krasnow Institute Lecture Hall
Instructor: Dr. Kim L. Blackwell
Office Location: Krasnow Institute, Room 105
Office Hours: Wed 10:30-11:30 am or by appointment
Course Description:
Text:
Required: A Primer of Ecology, Nicholas Gotelli, 3d edition, Sinauer
Mathematical Physiology, Keener and Sneyd, Springer
Book of Genesis, Bower and Beeman, available on-line
Method of Instruction: Each class will consist of lectures explaining the material in the text. Mandatory reading should be completed prior to the lecture.
Homework is assigned weekly. Homework turned in one week late will be graded, but is penalized by one letter grade. Homework will not be accepted two or more weeks late.
Four different topics are covered, and there is one, non-cummulative exam for each topic. The exam will consist of problems similar to those assigned for homework.
The project:is a written report and oral presentation on a career that uses some aspect of mathematical biology. Include the following information: description of career, education required (degree and field), experience required, opportunities (number of positions), location, salary and benefits, and resources / bibliography.
1. Identify career (due 10/23)
2. Outline (due 11/06)
3. Expanded outline (one topic sentence for each expected paragraph, due 11/20)
4. Final report (due 12/04)
5. Oral presentation
Grading:
Homework: 20%
Project: 20%
Exams: 20% each (top three counted)
Important Dates: Sept 14: Last day to add, or drop with no tuition liability
Oct 1: Last day to drop with no academic liability
Honor Code: GMU Academic Policies apply in full (http://www3.gmu.edu/catalog/apolicies/).
SYLLABUS
Week,Date |
Topic |
Reading |
1M 08/28 |
Unit 1: Population Biology, 8/28 - 9/20 Introduction, Exponential Growth lecture |
Gotelli, Chapter 1 |
1W 08/30 |
Logistic Equation lecture |
Gotelli, Chapter 2 |
2W 09/06 |
Competition lecture |
Gotelli, Chapter 5 |
3M 09/11 |
Predator-Prey lecture |
Gotelli, Chapter 6 |
3W 09/13 |
Predator-Prey, Spatial, lecture |
Gotelli, Chapter 6 |
4M 09/18 |
Finish and review |
|
4W 09/20 |
Exam 1 |
|
5M 09/25 |
Unit 2: Biochemical Reactions, 9/25-10/18 Reactions and Kinetics, lecture |
Math Phys, p3-4 |
5W 09/27 |
Reaction Energetics, lecture |
Notes |
6M 10/02 |
No class, Yom Kippur |
|
6W 10/04 |
Enzymes, lecture |
Math Phys, p5-8 |
7M 10/09 |
Enzyme Inhibition, lecture |
Math Phys, p9-11 |
7W 10/11 |
Cooperativity, lecture |
Math Phys, p12-15 |
8M 10/16 |
Insights into Enzymes, Q&A (Harold Morowitz) |
|
8W 10/18 |
Exam 2 |
|
9M 10/23 |
Unit 3: Neurons & Action Potentials, 10/23 - 11/08 Neuron Overview lecture |
en.wikipedia.org/wiki/Neuron, vv.carleton.ca/~neil/neural/neuron-a.html |
9W 10/25 |
Resting potential & Nernst Equation 2 lectures |
pp 33-35, 51-53 |
10M 10/31 |
RC model of membrane, VM steady state |
pp 56-57, 74-76, BoG Chapter 2? |
10W 11/01 |
Action Potentials 2 lectures |
pp 103-108, BoG Chapter 4 |
11M 11/06 |
Hodgkin Huxley Equations |
pp 116-136, BoG Chapter 4 |
12Mon 11/13 |
Exam 3 - Moved To Monday!!! |
|
11Wed 11/08 |
Unit 4: Retina, 11/13-11/29 Anatomy and Physiology - Moved to Previous Wed lecture |
thalamus.wustl.edu/course/eyeret.html, webvision.med.utah.edu/ Part 1:2,3; Part 2: 1,2,4 |
12W 11/15 |
Light adaptation and visual psychophysics lecture |
pp 665-673, webvision.med.utah.edu/ Part IX: 1&4 |
13M 11/20 |
Receptive Fields, Constrast Sensitivity Functions next 2 lectures |
p 685-687; webvision.med.utah.edu/ Part 2, 6. Part IX 2; www.thebrain.mcgill.ca/flash/i/i_02/i_02_cl/i_02_cl_vis/i_02_cl_vis.html |
13W 11/22 |
Thanksgiving break |
|
14M 11/27 |
Linear Systems Modeling of Visual System |
pp692 -695, http://www.cns.nyu.edu/~david/linear-systems/linear-systems.html |
14W 11/29 |
Phototransduction lecture |
pp 675-679; http://dolphin.upenn.edu/~pugh/ Pugh, E.N., Jr. and Lamb, T.D. (2000) Phototransduction in Vertebrate Rods and Cones: Molecular Mechanisms of Amplification, Recovery and Light Adaptation |
12/04 |
Presentations |
|
12/06 |
Presentations |
|
Mon 12/18 |
Final exam |
|