Math 6770 - Mathematical Biology (Mathematical Physiology)
Time: T Th 3:40-5:00pm Room JWB 208
Although we have a classroom and MOST lectures will be in person, the Lecture will also be available on zoom and projected onto the screen in the classroom (and recorded and postd on Canvas) Every week on Tue, Thu, until Dec 7, 2023, 31 occurrence(s)
Join Zoom Meeting
https://utah.zoom.us/j/92820647651
Meeting ID: 928 2064 7651
Passcode: 093063
Text:
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) as well as the zoom recording of the lecture will be posted on Canvas.
Homework assignments will also be posted and updated regularly on Canvas.
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
Important note: Because the instructor of this course is immunocompromised and is at risk of Covid infection and complications, the class will meet remotely (at the scheduled time) if not all students are vaccinated.
ADA Accommodations: The University of Utah will continue to accommodate students, faculty, and staff through the Americans with Disabilities Act (ADA). Given the nature of this course, attendance is required and adjustments cannot be granted to allow non-attendance. However, if you need to seek an ADA accommodation to request an exception to this attendance policy due to a disability, please contact the Center for Disability and Access (CDA). CDA will work to determine what, if any, ADA accommodations are reasonable and appropriate.