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://www.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