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Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). (Computational Technology Laboratory)ORCID iD: 0000-0002-7342-1987
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2017. , p. 51
Series
TRITA-CSC-A, ISSN 1653-5723 ; 2017:21
Keyword [en]
Finite element method, Arbitrary Lagrangian-Eulerian method, Fluid-Structure interaction, Contact model, parallel algorithm, blood flow, left ventricle, aortic valves, patient-specific heart model
National Category
Computational Mathematics
Identifiers
URN: urn:nbn:se:kth:diva-215277ISBN: 978-91-7729-566-2 (print)OAI: oai:DiVA.org:kth-215277DiVA, id: diva2:1147464
Public defence
2017-10-27, Fantum, F-huset, plan 5, KTH Campus, Lindstedtsvägen 24, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
Swedish Foundation for Strategic Research Swedish Research CouncilEU, European Research Council, 202984
Note

QC 20171006

Available from: 2017-10-06 Created: 2017-10-05 Last updated: 2017-10-09Bibliographically approved
List of papers
1. A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
Open this publication in new window or tab >>A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
2015 (English)Report (Other academic)
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.

Place, publisher, year, edition, pages
KTH Royal Institute of Technology, 2015. p. 17
Series
CTL Technical Report ; 34
Keyword
Finite element method, Arbitrary Lagrangian-Eulerian method, parallel algorithm, blood flow, left ventricle, patient-specific heart model
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-181110 (URN)
Funder
EU, European Research Council, 202984Swedish Research CouncilSwedish Foundation for Strategic Research
Note

QC 20160212

Available from: 2016-01-29 Created: 2016-01-29 Last updated: 2017-10-06Bibliographically approved
2. 3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE-FEM Model
Open this publication in new window or tab >>3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE-FEM Model
(English)Manuscript (preprint) (Other academic)
National Category
Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-215164 (URN)
Note

QC 20171006

Available from: 2017-10-03 Created: 2017-10-03 Last updated: 2017-10-09Bibliographically approved
3. A 3D full-friction contact model for fluid-structure interaction problems
Open this publication in new window or tab >>A 3D full-friction contact model for fluid-structure interaction problems
(English)Manuscript (preprint) (Other academic)
Keyword
Contact model, fluid-structure interaction, finite element method, Arbitrary Lagrangian-Eulerian method, parallel algorithm
National Category
Computational Mathematics
Research subject
Applied and Computational Mathematics
Identifiers
urn:nbn:se:kth:diva-215166 (URN)
Note

QC 20171006

Available from: 2017-10-03 Created: 2017-10-03 Last updated: 2018-05-08Bibliographically approved
4. Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
Open this publication in new window or tab >>Unicorn: Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
Show others...
2013 (English)In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 80, no SI, p. 310-319Article in journal (Refereed) Published
Abstract [en]

We present a framework for adaptive finite element computation of turbulent flow and fluid structure interaction, with focus on general algorithms that allow for complex geometry and deforming domains. We give basic models and finite element discretization methods, adaptive algorithms and strategies for efficient parallel implementation. To illustrate the capabilities of the computational framework, we show a number of application examples from aerodynamics, aero-acoustics, biomedicine and geophysics. The computational tools are free to download open source as Unicorn, and as a high performance branch of the finite element problem solving environment DOLFIN, both part of the FEniCS project.

Keyword
Unicorn, DOLFIN, FEniCS, Parallel adaptive finite element method, Open source software, Turbulent flow, Fluid structure interaction, Complex geometry, Deforming domain
National Category
Computer and Information Sciences
Identifiers
urn:nbn:se:kth:diva-124954 (URN)10.1016/j.compfluid.2012.02.003 (DOI)000320427200036 ()2-s2.0-84885190916 (Scopus ID)
Funder
EU, European Research CouncilSwedish Foundation for Strategic Research Swedish Research CouncilSwedish Energy Agency
Note

QC 20130803

Available from: 2013-08-02 Created: 2013-08-02 Last updated: 2018-05-08Bibliographically approved
5. Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging
Open this publication in new window or tab >>Patient-Specific Left Ventricular Flow Simulations From Transthoracic Echocardiography: Robustness Evaluation and Validation Against Ultrasound Doppler and Magnetic Resonance Imaging
Show others...
2017 (English)In: IEEE Transactions on Medical Imaging, ISSN 0278-0062, E-ISSN 1558-254X, Vol. 36, no 11, p. 2261-2275Article in journal (Refereed) Published
Abstract [en]

The combination of medical imaging with computational fluid dynamics (CFD) has enabled the study of 3D blood flow on a patient-specificlevel. However, with models based on gated high-resolution data, the study of transient flows, and any model implementation into routine cardiac care, is challenging. The present paper presents a novel pathway for patient-specific CFD modelling of the left ventricle (LV), using 4D transthoracic echocardiography (TTE) as input modality. To evaluate the clinical usability, two sub-studies were performed. First, a robustness evaluation was performed where repeated models with alternating input variables were generated for 6 subjects and changes in simulated output quantified. Second, a validation study was carried out where the pathway accuracy was evaluated against pulsed-wave Doppler (100 subjects), and 2D through-plane phase-contrast magnetic resonance imaging measurements over 7 intraventricular planes (6 subjects). The robustness evaluation indicated a model deviation of <12%, with highest regional and temporal deviations at apical segments and at peak systole, respectively. The validation study showed an error of < 11% (velocities < 10 cm/s) for all subjects, with no significant regional or temporal differences observed. With the patient-specific pathway shown to provide robust output with high accuracy, and with the pathway dependent only on 4DTTE, the method has a high potential to be used within future clinical studies on 3D intraventricular flowpatterns. To this, future model developments in the form of e.g. anatomically accurate LV valves may further enhance the clinical value of the simulations.

Place, publisher, year, edition, pages
Institute of Electrical and Electronics Engineers (IEEE), 2017
National Category
Medical Image Processing
Research subject
Medical Technology
Identifiers
urn:nbn:se:kth:diva-215187 (URN)10.1109/TMI.2017.2718218 (DOI)000414134200007 ()
Funder
Swedish Research Council, 2015-04237Swedish Foundation for Strategic Research , AM13-0049
Note

QC 20171006

Available from: 2017-10-04 Created: 2017-10-04 Last updated: 2017-12-12Bibliographically approved
6. Gestural 3D Interaction with a Beating Heart: Simulation Visualization and Interaction
Open this publication in new window or tab >>Gestural 3D Interaction with a Beating Heart: Simulation Visualization and Interaction
Show others...
2011 (English)In: Proceedings of SIGRAD 2011: Evaluations of Graphics and Visualization— Efficiency, Usefulness, Accessibility, Usability / [ed] Thomas Larsson, Lars Kjelldahl & Kai-Mikael Jää-Aro, Linköping University Electronic Press, 2011Conference paper, Published paper (Refereed)
Abstract [en]

The KTH School of Computer Science and Communication (CSC) established a strategic platform in Simulation-Visualization-Interaction (SimVisInt) in 2009, focused on the high potential in bringing together CSC core com-petences in simulation technology, visualization and interaction. The main part of the platform takes the form aset of new trans-disciplinary projects across established CSC research groups, within the theme of ComputationalHuman Modeling and Visualization: (i) interactive virtual biomedicine (HEART), (ii) simulation of human mo-tion (MOTION), and (iii) virtual prototyping of human hand prostheses (HAND). In this paper, we present recentresults from the HEART project that focused on gestural and haptic interaction with a heart simulation.

Place, publisher, year, edition, pages
Linköping University Electronic Press, 2011
National Category
Computational Mathematics Human Computer Interaction
Identifiers
urn:nbn:se:kth:diva-52832 (URN)978-91-7393-008-6 (ISBN)
Conference
SIGRAD 2011
Projects
Simulation Visualization Interaction (SimVisInt)
Note

QC 20120202

Available from: 2011-12-20 Created: 2011-12-20 Last updated: 2018-01-12Bibliographically approved

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