Cellular Biophysics and Modeling
APSC 451/651, Fall 2005
Classroom: McGlothlin-Street Hall #20
Meeting times: Tues/Thur 3:30 - 4:50 PM

Instructor
Christopher A. Del Negro, Ph.D.
Office: McGlothlin-Street Hall #303
Lab: McGlothlin-Street Hall #318
Phone: 757-221-7808
e-mail: cadeln@wm.edu

Course Description
We examine the biophysics of cell membranes, focusing on electrical excitability and intracellular calcium signaling. Topics include membrane transport and diffusion, the origin of transmembrane potential (voltage), classical biophysics of the squid giant axon and the ionic basis of action potentials, the gating of voltage- and ligand-gated ion channels, bistability and voltage oscillations, buffered diffusion of intracellular calcium, the endoplasmic reticulum and calcium excitability, and geometric analysis of electrical- as well as calcium-related cell behaviors. The knowledge and techniques that Cellular Biophysics and Modeling teaches are directly applicable to contemporary research in neuroscience and cell biology.

This course uses techniques in nonlinear dynamics and ordinary differential equations. For each topic, we will review the biology and construct mathematical models that illustrate the biophysical principles underlying the phenomena and/or behaviors. Models will be simulated on computer, analyzed, and often simplified using techniques such as numerical integration, phase-plane analyses, bifurcation theory, and others. The mathematics will be presented and explained for students with a mostly biological background, and in a manner relevant to understanding the biological mechanisms in the most general terms.

This course is intended for advanced undergraduate and graduate students interested in biology, physics and applied mathematical research in neuroscience, cardiac electrophysiology, and cell biology.

Expectations
Class attendance is expected, but will not be monitored. Reading material includes textbooks and primary research literature, which is technically challenging. I will be available by telephone, email, or office visits to assist you in understanding the class material. Regular homework assignments will be problem sets, many of which will involve computer modeling and use of the software XPP-AUT and/or Berkeley Madonna. Homework will be collected and scored based on effort and participation, students should strive to get full credit on all homework assignments in order to augment their final grade. Keys to assignments will be posted to the course website. The College Honor Code must be upheld in all class-related activities; violations and violators will not be tolerated.

Grading
There will be one mid-term exam (30%), a final exam (50%), and homework assignments (20%). Final letter grades will be assigned according to the scale below: