July 2014


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"Diane St. Germain" <[log in to unmask]>
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Diane St. Germain
Tue, 8 Jul 2014 15:26:10 +0000
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Dissertation Defense Announcement
To:  The George Mason University Community

Candidate: Hoang-Trong Minh Tuan

Program: PhD in Bioinformatics & Computational Biology

Date:   Monday July 21, 2014

Time:   11:00 a.m.

Place:  George Mason University
             Fairfax Campus<>

             Krasnow Institute, Room 229

Title: "Computational Studies of Ca2+ Dynamics in Cardiac Cells Using GPGPU"
Thesis Director: Dr. Moshin Saleet Jafri
Thesis Committee:  Dr. Avrama Blackwell, Dr. Dmitri Klimov, Dr. Eric Sobie, Dr. Huzefa Rangwala
A copy of the dissertation is available in the Johnson Center Library.  All are invited to attend the defense.
Calcium release in the heart plays a central role regulating and linking the electrical excitation of the heart with contraction.  The molecular and cellular processes that govern calcium release are stochastic in nature involving over 1,000,000 stochastic ion channels.  This creates a highly computationally expensive problem that necessitated the creation of novel algorithms that exploited advanced computational architectures. The studies presented in this dissertation started with introducing a fast, high-memory efficiency algorithm to simulate stochastic gatings of ion channels. The method was then implemented using the novel computing platform GPU which utilizes Compute Unified Device Architecture (CUDA) programming model, and to apply it in developping experimentally-based models of the rat ventricular myocytes. There are two levels of modelling were developed in this dissertation: the stochastic compartmental model that incorporate a mechanistic representation of the calcium-induced calcium-release (CICR) mechanism, and a stochastic temporal-spatial model that incorporate the spatial placement of all the calcium release units (CRU) in the myocyte. The presented work was used to answer specific scientific questions to the morphologies of ionic currents under heart failure (HF) condition, calcium alternans and the critical number of cells in order to trigger a spontaneous ectopic heartbeat. Then, the spatial model was used to study the dynamic changes in calcium sparks under atrial fibrillation (AF) conditions. The integrated whole-cell temporal spatial model for the rat was used to study calcium waves, which do not occur during normal conditions, but are important as they can cause membrane depolarizations under certain conditions as the result of the life threatening cardiac arrhythmias due.