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A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). (Computational Technology Laboratory)ORCID-id: 0000-0002-7342-1987
KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). BCAM - Basque Center for Applied Mathematics, Spain. (Computational Technology Laboratory)ORCID-id: 0000-0002-1695-8809
KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). (Computational Technology Laboratory)ORCID-id: 0000-0002-5020-1631
KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). BCAM - Basque Center for Applied Mathematics, Spain. (Computational Technology Laboratory)ORCID-id: 0000-0003-4256-0463
2015 (Engelska)Rapport (Övrigt vetenskapligt)
Abstract [en]

Progress in medical imaging, computational fluid dynamics and high performance computing (HPC) enables computer simulations to emerge as a significant tool to enhance our understanding of the relationship between cardiac diseases and hemodynamics. The field of cardiac modelling is diverse, covering different aspects on microscopic and macroscopic level. In our research, we develop a cardiac model which is embedded in a computational environment where specific properties of the heart such as fluid-structure interaction of the aortic valve can be modeled, or numerical and computational algorithms as parallel computing or adaptivity can be added in a modular way without extensive efforts. In this paper, we present a patient-specific Arbitrary Lagrangian-Eulerian (ALE) finite element framework for simulating the blood flow in the left ventricle of a human heart using HPC, which forms the core of our cardiac model. The mathematical model is described together with the discretization method, mesh smoothing algorithms, and the parallel implementation in Unicorn which is part of the open source software framework FEniCS-HPC. The parallel performance is demonstrated, a convergence study is conducted and intraventricular flow patterns are visualized. The results capture essential features observed with other computational models and imaging techniques, and thus indicate that our framework possesses the potential to provide relevant clinical information for diagnosis and medical treatment. Several studies have been conducted to simulate the three dimensional blood flow in the left ventricle of the human heart with prescribed wall movement. Our contribution to the field of cardiac research lies in establishing an open source framework modular both in modelling and numerical algorithms.

Ort, förlag, år, upplaga, sidor
KTH Royal Institute of Technology, 2015. , s. 17
Serie
CTL Technical Report ; 34
Nyckelord [en]
Finite element method, Arbitrary Lagrangian-Eulerian method, parallel algorithm, blood flow, left ventricle, patient-specific heart model
Nationell ämneskategori
Beräkningsmatematik
Identifikatorer
URN: urn:nbn:se:kth:diva-181110OAI: oai:DiVA.org:kth-181110DiVA, id: diva2:898808
Forskningsfinansiär
EU, Europeiska forskningsrådet, 202984VetenskapsrådetStiftelsen för strategisk forskning (SSF)
Anmärkning

QC 20160212

Tillgänglig från: 2016-01-29 Skapad: 2016-01-29 Senast uppdaterad: 2017-10-06Bibliografiskt granskad
Ingår i avhandling
1. Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
Öppna denna publikation i ny flik eller fönster >>Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
2017 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

Heart disease is the leading cause of death in the world. Therefore, numerous studies are undertaken to identify indicators which can be applied to discover cardiac dysfunctions at an early age. Among others, the fluid dynamics of the blood flow (hemodymanics) is considered to contain relevant information related to abnormal performance of the heart.This thesis presents a robust framework for numerical simulation of the fluid dynamics of the blood flow in the left ventricle of a human heart and the fluid-structure interaction of the blood and the aortic leaflets.We first describe a patient-specific model for simulating the intraventricular blood flow. The motion of the endocardial wall is extracted from data acquired with medical imaging and we use the incompressible Navier-Stokes equations to model the hemodynamics within the chamber. We set boundary conditions to model the opening and closing of the mitral and aortic valves respectively, and we apply a stabilized Arbitrary Lagrangian-Eulerian (ALE) space-time finite element method to simulate the blood flow. Even though it is difficult to collect in-vivo data for validation, the available data and results from other simulation models indicate that our approach possesses the potential and capability to provide relevant information about the intraventricular blood flow.To further demonstrate the robustness and clinical feasibility of our model, a semi-automatic pathway from 4D cardiac ultrasound imaging to patient-specific simulation of the blood flow in the left ventricle is developed. The outcome is promising and further simulations and analysis of large data sets are planned.In order to enhance our solver by introducing additional features, the fluid solver is extended by embedding different geometrical prototypes of both a native and a mechanical aortic valve in the outflow area of the left ventricle.Both, the contact as well as the fluid-structure interaction, are modeled as a unified continuum problem using conservation laws for mass and momentum. To use this ansatz for simulating the valvular dynamics is unique and has the expedient properties that the whole problem can be described with partial different equations and the same numerical methods for discretization are applicable.All algorithms are implemented in the high performance computing branch of Unicorn, which is part of the open source software framework FEniCS-HPC. The strong advantage of implementing the solvers in an open source software is the accessibility and reproducibility of the results which enhance the prospects of developing a method with clinical relevance.

Ort, förlag, år, upplaga, sidor
Stockholm: KTH Royal Institute of Technology, 2017. s. 51
Serie
TRITA-CSC-A, ISSN 1653-5723 ; 2017:21
Nyckelord
Finite element method, Arbitrary Lagrangian-Eulerian method, Fluid-Structure interaction, Contact model, parallel algorithm, blood flow, left ventricle, aortic valves, patient-specific heart model
Nationell ämneskategori
Beräkningsmatematik
Identifikatorer
urn:nbn:se:kth:diva-215277 (URN)978-91-7729-566-2 (ISBN)
Disputation
2017-10-27, Fantum, F-huset, plan 5, KTH Campus, Lindstedtsvägen 24, Stockholm, 10:00 (Engelska)
Opponent
Handledare
Forskningsfinansiär
Stiftelsen för strategisk forskning (SSF)VetenskapsrådetEU, Europeiska forskningsrådet, 202984
Anmärkning

QC 20171006

Tillgänglig från: 2017-10-06 Skapad: 2017-10-05 Senast uppdaterad: 2017-10-09Bibliografiskt granskad

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Spühler, Jeannette HiromiJansson, NiclasHoffman, Johan

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Spühler, Jeannette HiromiJansson, JohanJansson, NiclasHoffman, Johan
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