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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

Ezio Bartocci, Rupinder Singh, Frederick B. von Stein, Avessie Amedome, Alan Joseph J. Caceres, Juan Castillo, Evan Closser, Gabriel Deards, Andriy Goltsev, Roumwelle Sta. Ines, Cem Isbilir, Joan K. Marc, Diquan Moore, Dana Pardi, Sandeep Sadhu, Samuel Sanchez, Pooja Sharma, Anoopa Singh, Joshua Rogers, Aron Wolinetz, Terri Grosso-Applewhite, Kai Zhao, Andrew B. Filipski, Robert F. Gilmour, Jr., Radu Grosu, James Glimm, Scott A. Smolka, Elizabeth M. Cherry, Edmund M. Clarke, Nancy Griffeth, Flavio H. Fenton
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook
Advances in Physisology Education, vol. 35, no. 4, 427-437, 2011
@article{bartocci2011teaching,

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

   author={Bartocci, E. and Singh, R. and von Stein, F.B. and Amedome, A. and Caceres, A.J.J. and Castillo, J. and Closser, E. and Deards, G. and Goltsev, A. and Ines, R.S. and others},

   journal={Advances in physiology education},

   volume={35},

   number={4},

   pages={427–437},

   year={2011},

   publisher={Am Physiological Soc}

}

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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 York1 collaborated 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.
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