Massively parallel models of the human circulatory system

Randles, Amanda; Draeger, Erik W.; Oppelstrup, Tomas; Krauss, Liam; Gunnels, John A.

doi:10.1145/2807591.2807676

Cited by 47 publications

(37 citation statements)

References 40 publications

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“…Indirect addressing is used to limit the required memory, as vascular geometries often occupy a small percentage of their bounding box volume. Global communication is not required and the lattice Boltzmann algorithm in HARVEY scales up to 1.5 million tasks [21, 22]. …”

Section: Methodsologymentioning

confidence: 99%

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Numerical simulation of a compound capsule in a constricted microchannel

Gounley

Draeger

Randles

2017

Procedia Computer Science

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Simulations of the passage of eukaryotic cells through a constricted channel aid in studying the properties of cancer cells and their transport in the bloodstream. Compound capsules, which explicitly model the outer cell membrane and nuclear lamina, have the potential to improve computational model fidelity. However, general simulations of compound capsules transiting a constricted microchannel have not been conducted and the influence of the compound capsule model on computational performance is not well known. In this study, we extend a parallel hemodynamics application to simulate the fluid-structure interaction between compound capsules and fluid. With this framework, we compare the deformation of simple and compound capsules in constricted microchannels, and explore how deformation depends on the capillary number and on the volume fraction of the inner membrane. The computational framework’s parallel performance in this setting is evaluated and future development lessons are discussed.

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Section: Methodsologymentioning

confidence: 99%

“…HARVEY is a massively parallel computational fluid dynamics solver, focused on hemodynamics and based on the lattice Boltzmann method [21, 22]. In this paper, we integrate HARVEY with FSI-functionality, using the immersed boundary method to couple a finite element model for deformable capsules to the fluid model.…”

Section: Introductionmentioning

confidence: 99%

Numerical simulation of a compound capsule in a constricted microchannel

Gounley

Draeger

Randles

2017

Procedia Computer Science

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“…In a study done by Randles et al 103 , the vasculature of a male adult XCAT phantom (50 th percentile) was converted by ScanIP into a FE model and then used to investigate fast computational methods to simulate flow in arterial networks, Fig. 15.…”

Section: Other Applicationsmentioning

confidence: 99%

Application of the 4-D XCAT Phantoms in Biomedical Imaging and Beyond

Segars

Tsui

Cai

et al. 2018

IEEE Trans. Med. Imaging

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The four dimensional (4D) eXtended CArdiac-Torso (XCAT) series of phantoms was developed to provide accurate computerized models of the human anatomy and physiology. The XCAT series encompasses a vast population of phantoms of varying ages from newborn to adult, each including parameterized models for the cardiac and respiratory motions. With great flexibility in the XCAT’s design, any number of body sizes, different anatomies, cardiac or respiratory motions or patterns, patient positions and orientations, and spatial resolutions can be simulated. As such, the XCAT phantoms are gaining a wide use in biomedical imaging research. There they can provide a virtual patient base from which to quantitatively evaluate and improve imaging instrumentation, data acquisition, techniques and image reconstruction and processing methods which can lead to improved image quality and more accurate clinical diagnoses. The phantoms have also found great use in radiation dosimetry, radiation therapy, medical device design, and even the security and defense industry. This review paper highlights some specific areas in which the XCAT phantoms have found use within biomedical imaging and other fields. From these examples, we illustrate the increasingly important role that computerized phantoms and computer simulation are playing in the research community.

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“…The computational demands of these simulations have historically restricted their size and scope, but advances in parallel algorithms and computer hardware have extended the reach of these simulations to much larger regions [30, 32–34]. High-performance computing (HPC) has extended the time-scale, domains, and fidelity that can be captured with CFD simulations.…”

Section: Computational Fluid Dynamicsmentioning

confidence: 99%

“…In 2013, Xiao and colleagues completed a key feasibility study for simulating flow in a full body simulation [35]. The largest 3D simulation to date simulated flow in all arteries of a human greater than 1 mm in diameter [34]. The flow was simulated at a 9 μ m resolution, required 509 billion grid points, and was modeled using 1.6 million processors.…”

Section: Computational Fluid Dynamicsmentioning

confidence: 99%

Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease

Randles

Leopold

2017

Trends in Biotechnology

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Non-invasive engineering models are now being used for diagnosing and planning the treatment of cardiovascular disease. Techniques in computational modeling and additive manufacturing have matured concurrently, and results from simulations can inform and enable the design and optimization of therapeutic devices and treatment strategies. The emerging synergy between large-scale simulations and 3D printing is having a two-fold benefit: first, 3D printing can be used to validate the complex simulations, and second, the flow models can be used to improve treatment planning for cardiovascular disease. In this review, we summarize and discuss recent methods and findings for leveraging advances in both additive manufacturing and patient-specific computational modeling, with an emphasis on new directions in these fields and remaining open questions.

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Massively parallel models of the human circulatory system

Cited by 47 publications

References 40 publications

Numerical simulation of a compound capsule in a constricted microchannel

Numerical simulation of a compound capsule in a constricted microchannel

Application of the 4-D XCAT Phantoms in Biomedical Imaging and Beyond

Computational Fluid Dynamics and Additive Manufacturing to Diagnose and Treat Cardiovascular Disease

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