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Teaching cardiac electrophysiology modeling to undergraduate students: laboratory exercises and GPU programming for the study of arrhythmias and spiral wave dynamics

Authors :
James Glimm
Evan Closser
Dana Pardi
Kai Zhao
Nancy Griffeth
Gabriel Deards
Avessie Amedome
Elizabeth M. Cherry
Juan Castillo
Andrew B. Filipski
Joshua Rogers
Alan Joseph J. Caceres
Radu Grosu
Sandeep Sadhu
Terri Grosso-Applewhite
Cem Isbilir
Samuel Sanchez
Diquan Moore
Frederick B. von Stein
Robert F. Gilmour
Rupinder Singh
Joan K. Marc
Anoopa Singh
Pooja Sharma
Ezio Bartocci
Flavio H. Fenton
Andriy Goltsev
Scott A. Smolka
Aron Wolinetz
Edmund M. Clarke
Roumwelle Sta. Ines
Source :
Advances in Physiology Education. 35:427-437
Publication Year :
2011
Publisher :
American Physiological Society, 2011.

Abstract

As part of a 3-wk intersession workshop funded by a National Science Foundation Expeditions in Computing award, 15 undergraduate students from the City University of New York1collaborated on a study aimed at characterizing the voltage dynamics and arrhythmogenic behavior of cardiac cells for a broad range of physiologically relevant conditions using an in silico model. The primary goal of the workshop was to cultivate student interest in computational modeling and analysis of complex systems by introducing them through lectures and laboratory activities to current research in cardiac modeling and by engaging them in a hands-on research experience. The success of the workshop lay in the exposure of the students to active researchers and experts in their fields, the use of hands-on activities to communicate important concepts, active engagement of the students in research, and explanations of the significance of results as the students generated them. The workshop content addressed how spiral waves of electrical activity are initiated in the heart and how different parameter values affect the dynamics of these reentrant waves. Spiral waves are clinically associated with tachycardia, when the waves remain stable, and with fibrillation, when the waves exhibit breakup. All in silico experiments were conducted by simulating a mathematical model of cardiac cells on graphics processing units instead of the standard central processing units of desktop computers. This approach decreased the run time for each simulation to almost real time, thereby allowing the students to quickly analyze and characterize the simulated arrhythmias. Results from these simulations, as well as some of the background and methodology taught during the workshop, is presented in this article along with the programming code and the explanations of simulation results in an effort to allow other teachers and students to perform their own demonstrations, simulations, and studies.

Details

ISSN :
15221229 and 10434046
Volume :
35
Database :
OpenAIRE
Journal :
Advances in Physiology Education
Accession number :
edsair.doi.dedup.....d95f0e8d3de729c6f7f58336dec91198
Full Text :
https://doi.org/10.1152/advan.00034.2011