| 1. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(author)
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A finite element framework for high performance computer simulation of blood flow in the left ventricle of the human heart
- 2015
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Reports (other academic/artistic)abstract
- 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.
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| 2. |
- Degirmenci, Niyazi Cem, 1982-
(author)
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Adaptive Finite Element Methods for Fluid Structure Interaction Problems with Applications to Human Phonation
- 2018
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Doctoral thesis (other academic/artistic)abstract
- This work presents a unified framework for numerical solution of Fluid Structure Interaction (FSI) and acoustics problems with focus on human phonation. The Finite Element Method is employed for numerical investigation of partial differential equations that model conservation of momentum and mass. Since the resulting system of equations is very large, an efficient open source high performance implementation is constructed and provided. In order to gain accuracy for the numerical solutions, an adaptive mesh refinement strategy is employed which reduces the computational cost in comparison to a uniform refinement. Adaptive refinement of the mesh relies on computable error indicators which appear as a combination of a computable residual and the solution of a so-called dual problem acting as weights on computed residuals. The first main achievement of this thesis is to apply this strategy to numerical simulations of a benchmark problem for FSI. This FSI model is further extended for contact handling and applied to a realistic vocal folds geometry where the glottic wave formation was captured in the numerical simulations. This is the second achievement in the presented work. The FSI model is further coupled to an acoustics model through an acoustic analogy, for vocal folds with flow induced oscillations for a domain constructed to create the vowel /i/. The comparisons of the obtained pressure signal at specified points with respect to results from literature for the same vowel is reported, which is the final main result presented.
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| 3. |
- Nguyen, Van-Dang, 1985-
(author)
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High-Performance Finite Element Methods : with Application to Simulation of Diffusion MRI and Vertical Axis Wind Turbines
- 2018
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Licentiate thesis (other academic/artistic)abstract
- The finite element methods (FEM) have been developed over decades, and together with the growth of computer engineering, they become more and more important in solving large-scale problems in science and industry. The objective of this thesis is to develop high-performance finite element methods (HP-FEM), with two main applications in mind: computational diffusion magnetic resonance imaging (MRI), and simulation of the turbulent flow past a vertical axis wind turbine (VAWT). In the first application, we develop an efficient high-performance finite element framework HP-PUFEM based on a partition of unity finite element method to solve the Bloch-Torrey equation in heterogeneous domains. The proposed framework overcomes the difficulties that the standard approaches have when imposing the microscopic heterogeneity of the biological tissues. We also propose artificial jump conditions at the external boundaries to approximate the pseudo-periodic boundary conditions which allows for the water exchange at the external boundaries for non-periodic meshes. The framework is of a high level simplicity and efficiency that well facilitates parallelization. It can be straightforwardly implemented in different FEM software packages and it is implemented in FEniCS for moderate-scale simulations and in FEniCS-HPC for the large-scale simulations. The framework is validated against reference solutions, and implementation shows a strong parallel scalability. Since such a high-performance simulation framework is still missing in the field, it can become a powerful tool to uncover diffusion in complex biological tissues. In the second application, we develop an ALE-DFS method which combines advanced techniques developed in recent years to simulate turbulence. We apply a General Galerkin (G2) method which is continuous piecewise linear in both time and space, to solve the Navier-Stokes equations for a rotating turbine in an Arbitrary Lagrangian-Eulerian (ALE) framework. This method is enhanced with dual-based a posterior error control and automated mesh adaptation. Turbulent boundary layers are modeled by a slip boundary condition to avoid a full resolution which is impossible even with the most powerful computers available today. The method is validated against experimental data of parked turbines with good agreements. The thesis presents contributions in the form of both numerical methods for high-performance computing frameworks and efficient, tested software, published open source as part of the FEniCS-HPC platform.
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| 4. |
- Nguyen, Van Dang, 1985-
(author)
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High Performance Finite Element Methods with Application to Simulation of Vertical Axis Wind Turbines and Diffusion MRI
- 2019
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Doctoral thesis (other academic/artistic)abstract
- Finite element methods have been developed over decades, and together with the growth of computer power, they become more and more important in dealing with large-scale simulations in science and industry.The objective of this thesis is to develop high-performance finite element methods, with two concrete applications: computational fluid dynamics (CFD) with simulation of turbulent flow past a vertical axis wind turbine (VAWT), and computational diffusion magnetic resonance imaging (CDMRI). The thesis presents contributions in the form of both new numerical methods for high-performance computing frameworks and efficient, tested software, published open source as part of the FEniCS/FEniCS-HPC platform. More specifically, we have four main contributions through the thesis work.First, we develop a DFS-ALE method which combines the Direct finite element simulation method (DFS) with the Arbitrary Lagrangian-Eulerian method (ALE) to solve the Navier-Stokes equations for a rotating turbine. This method is enhanced with dual-based a posteriori error control and automated mesh adaptation. Turbulent boundary layers are modeled by a slip boundary condition to avoid a full resolution which is impossible even with the most powerful computers available today. The method is validated against experimental data with a good agreement.Second, we propose a partition of unity finite element method to tackle interface problems. In CFD, it allows for imposing slip velocity boundary conditions on conforming internal interfaces for a fluid-structure interaction model. In CDMRI, it helps to overcome the difficulties that the standard approaches have when imposing the microscopic heterogeneity of the biological tissues and allows for efficient solutions of the Bloch-Torrey equation in heterogeneous domains. The method facilitates a straightforward implementation on the FEniCS/ FEniCS-HPC platform. The method is validated against reference solutions, and the implementation shows a strong parallel scalability.Third, we propose a finite element discretization on manifolds in order to efficiently simulate the diffusion MRI signal in domains that have a thin layer or a thin tube geometrical structure. The method helps to significantly reduce the required simulation time, computer memory, and difficulties associated with mesh generation, while maintaining the accuracy. Thus, it opens the possibility to simulate complicated structures at a low cost, for a better understanding of diffusion MRI in the brain.Finally, we propose an efficient portable simulation framework that integrates recent advanced techniques in both mathematics and computer science to enable the users to perform simulations with the Cloud computing technology. The simulation framework consists of Python, IPython and C++ solvers working either on a web browser with Google Colaboratory notebooks or on the Google Cloud Platform with MPI parallelization.
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| 5. |
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| 6. |
- Nilsson, Elin, 1984-
(author)
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Where to shop? : understanding consumers' choices of grocery stores
- 2016
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Doctoral thesis (other academic/artistic)abstract
- For the last couple of decades consumer decision-making has been of increasing interest for retail as well as for consumer behaviour research. Food shopping constitutes a unique type of shopping behaviour. In comparison to other types of shopping, food is essential to life, and not often are there as many choices to be made in a short period of time as when shopping groceries.The purpose of this dissertation was to advance the knowledge of what influences consumers’ choices of grocery stores. More specifically, the main focus has been on how different situations (e.g., type of shopping) influence choices of grocery stores. Five papers, which build on three surveys on how consumers choose grocery stores in Sweden, are included in this dissertation.In the first paper a comprehensive set of ten aggregated attributes that determine store choices were developed. The second paper brought forward five consumer segments (Planning Suburbans, Social Shoppers, Pedestrians, City Dwellers, and Flexibles) based on where and how they shop. In the third paper it was shown that accessibility attributes (e.g., accessibility by car, availability) and attractiveness attributes (e.g., price, service) have different impacts on satisfaction, depending on consumer characteristics and shopping behaviour in supermarkets compared to convenience stores. In the fourth paper the result showed that satisfaction is affected by type of grocery shopping (major versus fill-in shopping) in conjunction with time pressure and which store attributes that are important for satisfaction. It was also shown that the effect of time pressure and type of shopping on satisfaction varied in different consumer segments. In the final paper it was shown that a store has to be more attractive in terms of attributes for a consumer to switch from the grocery store they usually patronage, even if the new store is situated right beside or closer than the consumer’s regular grocery store. The view of a “good location” is further developed in this dissertation, arguing that consumers’ mental distance to a store – their cognitive proximity – is much more important than the physical place of the store.In sum, this dissertation revealed that the situation is more important than previous research has shown. Depending on the situation, consumers will face different outcomes (different stores) and value different store attributes. Hence, stores need to manage different store attributes depending on which consumer groups the stores want to attract and what situation the consumers are facing. Therefore, consumers’ choices of grocery stores are situation-based choices.
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| 7. |
- Spühler, Jeannette Hiromi, 1981-
(author)
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Patient-Specific Finite Element Modeling of the Blood Flow in the Left Ventricle of a Human Heart
- 2017
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Doctoral thesis (other academic/artistic)abstract
- 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.
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| 8. |
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| 9. |
- Anderson, Johan, 1973-, et al.
(author)
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Fire Safety of Façades
- 2017
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Reports (other academic/artistic)abstract
- Façade fires do not occur often (in comparison to other major structure fires) but in recent years there have been a number of spectacular façade fires in high rise building such as the recent fire in Grenfell Tower, London.Under-ventilated compartment fires may cause flames to spill out of window openings impinging the façade, thus devastating façade fires may start on one floor leap-frogging to adjacent floors. It is therefore necessary to limit or delay fire spread to higher floors. Requirements built on large scale fire testing may decrease the risk of these types of fires provided that the building is constructed according to the specifications provided by the manufacturer. Different countries have different regulations and tests for façades. New materials and façade systems are continuously introduced which might call for an update of these tests and regulations.This report summarizes experimental and modelling efforts in characterizing the fire safety of façades using the Swedish SP Fire 105 and the British BS 8414 methods. Recent experimental results and modelling is presented exploring the variations in the fire exposure, fire load and the fuel used. The fire source and the heat exposure to the façade are characterized by additional temperatures measured by plate thermometers while some other aspects are only treated in the numerical study such as a change in fuel. It is found that the results from the BS 8414 are largely affected by wind and climate since the experimental test was performed outdoors, moreover fire spread on wooden façades is also briefly discussed.In order to obtain a deeper understanding of the test methods and the results CFD (Computational Fluid Dynamics) Modelling in FDS was used. The models were based on measured input parameters including uncertainties and an assessment of the impact of said uncertainties. The models could often reproduce the experimentally found temperatures qualitatively and quantitatively. A detailed discussion on the regulations and the tests that lead to the SP Fire 105 test method is also presented. Summaries of the façade testing methods and conditions in other European countries are presented in the appendices.Finally possible ways forward in updating the façade testing and regulations are discussed.
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| 10. |
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