Course Announcement

Math 6780 - Mathematical Biology (Mathematical Physiology)

Time: T Th 12:25-1:45 Room LCB 121


Keener and Sneyd, Mathematical Physiology, Volume 1 (Cell Physiology)

All proceeds from the sale of this text to students in this class will be donated to the Math Biology Development Fund in the Math Department.

Outline: This course will emphasize the mathematical modelling of cell physiology processes, with material drawn primarily from Volume 1 of Keener and Sneyd, Mathematical Physiology. Topics will include enzyme kinetics, ion channel dynamics, action potential generation and excitability, calcium handling, metabolism, bursting and endocrine secretion, cell cycle dynamics, synaptic transmission, muscle contraction and molecular motors, to name a few. Additional topics will be added according to student interest.

Lecture notes (from my Ipad) are posted here

Homework assignments will be posted and updated regularly at this .pdf file (with the .tex file here). Solutions for previous homework assignments are or will be posted here.

Notes: Here are xpp .ode files for the Selkov and Goldbeter-Lefever glycolysis models.

xpp file selkov.ode

xpp file Goldbeter_glycolysis.ode.

Here are .ode files for reduced HH equations, the Morris-Lecar mode and the full HH equationsl:

xpp file hhred.ode.

xpp file ML.ode.

xpp file HH.ode.

Here is the Matlab code to make plots for the Fire-Diffuse-Fire model fdf_plots.m

xpp files CK.ode. and CK2D.ode as well as notes on how to use thes files to make pretty pictures.

Here is a file for stochastic simulation of a Markov model of a potassium channel, using Gillespie algorithm: xpp file n_state_potassium.m.

Here are some notes modifying the explanation of closed time probability for the sodium ion channel model in Section 3.6.1.

For more information contact J. Keener, 1-6089