@misc {27565,
	title = {Towards detailed Organ-Scale Simulations in Cardiac Electrophysiology},
	year = {2020},
	type = {Poster},
	address = {GPU Technology Conference (GTC), Silicon Valley, San Jose, USA},
	author = {Langguth, Johannes and Gaur, Namit and Arevalo, Hermenegild and Jarvis, Chad and Altanaite, Neringa and Lan, Qiang and Cai, Xing}
}
@article {24933,
	title = {Accelerating Detailed Tissue-Scale 3D Cardiac Simulations Using Heterogeneous CPU-Xeon Phi Computing},
	journal = {International Journal of Parallel Programming},
	year = {2016},
	month = {10/2016},
	pages = {1-23},
	publisher = {ACM/Springer},
	abstract = {We investigate heterogeneous computing, which involves both multicore CPUs and manycore Xeon Phi coprocessors, as a new strategy for computational cardiology. In particular, 3D tissues of the human cardiac ventricle are studied with a physiologically realistic model that has 10,000 calcium release units per cell and 100 ryanodine receptors per release unit, together with tissue-scale simulations of the electrical activity and calcium handling. In order to attain resource-efficient use of heterogeneous computing systems that consist of both CPUs and Xeon Phis, we first direct the coding effort at ensuring good performance on the two types of compute devices individually. Although SIMD code vectorization is the main theme of performance programming, the actual implementation details differ considerably between CPU and Xeon Phi. Moreover, in addition to combined OpenMP+MPI programming, a suitable division of the cells between the CPUs and Xeon Phis is important for resource-efficient usage of an entire heterogeneous system. Numerical experiments show that good resource utilization is indeed achieved and that such a heterogeneous simulator paves the way for ultimately understanding the mechanisms of arrhythmia. The uncovered good programming practices can be used by computational scientists who want to adopt similar heterogeneous hardware platforms for a wide variety of applications.},
	keywords = {Calcium handling, multiscale cardiac tissue simulation, supercomputing, Xeon Phi},
	doi = {10.1007/s10766-016-0461-2},
	author = {Langguth, Johannes and Lan, Qiang and Gaur, Namit and Cai, Xing}
}
@inproceedings {25016,
	title = {Enabling Tissue-Scale Cardiac Simulations Using Heterogeneous Computing on Tianhe-2},
	journal = {IEEE 22nd International Conference on Parallel and Distributed Systems (ICPADS)},
	year = {2016},
	month = {12/2016},
	pages = {843-852},
	publisher = {ACM/IEEE},
	abstract = {We develop a simulator for 3D tissue of the human cardiac ventricle with a physiologically realistic cell model and deploy it on the supercomputer Tianhe-2. In order to attain the full performance of the heterogeneous CPU-Xeon Phi design, we use carefully optimized codes for both devices and combine them to obtain suitable load balancing. Using a large number of nodes, we are able to perform tissue-scale simulations of the electrical activity and calcium handling in millions of cells, at a level of detail that tracks the states of trillions of ryanodine receptors. We can thus simulate arrythmogenic spiral waves and other complex arrhythmogenic patterns which arise from calcium handling deficiencies in human cardiac ventricle tissue. Due to extensive code tuning and parallelization via OpenMP, MPI, and SCIF/COI, large scale simulations of 10 heartbeats can be performed in a matter of hours. Test results indicate excellent scalability, thus paving the way for detailed whole-heart simulations in future generations of leadership class supercomputers.},
	keywords = {Calcium handling, multiscale cardiac tissue simulation, supercomputing, Xeon Phi},
	issn = {1521-9097},
	doi = {10.1109/ICPADS.2016.0114},
	author = {Langguth, Johannes and Lan, Qiang and Gaur, Namit and Cai, Xing and Wen, Mei},
	editor = {Zhang, Chunyuan}
}
@misc {23482,
	title = {Dysfunctional Sarcoplasmic Reticulum Ca2+ Release Underlies Arrhythmogenic Triggers in Catecholaminergic Polymorphic Ventricular Tachycardia: A Simulation Study in a Human Ventricular Myocyte Model},
	howpublished = {Gordons Research Conference on Cardiac Arrhythmia},
	year = {2015},
	publisher = {Gordons Research Conference on Cardiac Arrhythmia},
	address = {Lucca, Italy},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@inproceedings {23838,
	title = {Towards Detailed Tissue-Scale 3D Simulations of Electrical Activity and Calcium Handling in the Human Cardiac Ventricle},
	journal = {The 15th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2015)},
	year = {2015},
	month = {11/2015},
	pages = {79-92},
	publisher = {Lecture Notes in Computer Science, Springer Verlag},
	abstract = {We adopt a detailed human cardiac cell model, which has 10000 calcium release units, in connection with simulating the electrical activity and calcium handling at the tissue scale. This is a computationally intensive problem requiring a combination of efficient numerical algorithms and parallel programming. To this end, we use a method that is based on binomial distributions to collectively study the stochastic state transitions of the 100 ryanodine receptors inside every calcium release unit, instead of individually following each ryanodine receptor. Moreover, the implementation of the parallel simulator has incorporated optimizations in form of code vectorization and removing redundant calculations. Numerical experiments show very good parallel performance of the 3D simulator and demonstrate that various physiological behaviors are correctly reproduced. This work thus paves way for high-fidelity 3D simulations of human ventricular tissues, with the ultimate goal of understanding the mechanisms of arrhythmia.},
	keywords = {Calcium handling, multiscale cardiac tissue simulation, supercomputing},
	isbn = {978-3-319-27136-1},
	doi = {10.1007/978-3-319-27137-8_7},
	url = {http://link.springer.com/chapter/10.1007/978-3-319-27137-8_7},
	author = {Lan, Qiang and Gaur, Namit and Langguth, Johannes and Cai, Xing}
}
@misc {23364,
	title = {Arrhythmogenic Mechanisms and Therapeutic Targets for Catecholaminergic Polymorphic Ventricular Tachycardia: A Simulation Study in a Human Ventricular Myocyte},
	howpublished = {Simula Research Laboratory},
	year = {2014},
	type = {Cardiac Modeling Workshop},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@misc {23362,
	title = {Cellular Arrhythmogenesis in CPVT in a computational model of cardiac ventricular myocyte},
	year = {2014},
	month = {09/14},
	publisher = {European Working Group of Cardiac Cellular Electrophysiology},
	address = {Maastrich, Netherlands},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@misc {Simula.simula.3086,
	title = {Cellular Arrhythmogenesis in CPVT in a Computational Model of Cardiac Ventricular Myocyte},
	year = {2014},
	month = {08/2014},
	type = {Poster at Scandinavian Physiological Society Meeting},
	address = {Scandinavian Physiological Society Meeting},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@misc {23365,
	title = {Mathematical Modeling of Ca Handling and Computational Studies of Ca-related Arrhythmogenesis in Heart},
	howpublished = {National University of Defense Technology, China},
	year = {2014},
	type = {Workshop},
	address = {Changsha, China},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@misc {23361,
	title = {Spontaneous Ca2+ Release and Ca2+ Waves Underlie Early and Delayed Afterdepolarizations, and Triggered Activity in Ryanodine Receptor Mutation associated with Catecholaminergic Polymorphic Ventricular Tachycardia},
	year = {2014},
	month = {08/2014},
	address = {Scandinavian Physiological Society},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
@misc {Simula.simula.3084,
	title = {Spontaneous Ca2+ Release and Ca2+ Waves Underlie Early and Delayed Afterdepolarizations, and Triggered Activity, in Ryanodine Receptor Mutations Associated With Catecholaminergic Polymorphic Ventricular Tachycardia},
	year = {2014},
	month = {August},
	keywords = {Conference},
	author = {Gaur, Namit and Cai, Xing and Rudy, Yoram}
}
