| 61. |
- Nguyen, Van Dang, 1985-, et al.
(author)
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Diffusion MRI simulation in thin-layer and thin-tube media using a discretization on manifolds
- 2019
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In: Journal of magnetic resonance. - : Academic Press. - 1090-7807 .- 1096-0856. ; 299, s. 176-187
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Journal article (peer-reviewed)abstract
- The Bloch-Torrey partial differential equation can be used to describe the evolution of the transverse magnetization of the imaged sample under the influence of diffusion-encoding magnetic field gradients inside the MRI scanner. The integral of the magnetization inside a voxel gives the simulated diffusion MRI signal. This paper proposes 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 variable thickness of the three-dimensional domains is included in the weak formulation established on the manifolds. We conducted a numerical study of the proposed approach by simulating the diffusion MRI signals from the extracellular space (a thin layer medium) and from neurons (a thin tube medium), comparing the results with the reference signals obtained using a standard three-dimensional finite element discretization. We show good agreements between the simulated signals using our proposed method and the reference signals for a wide range of diffusion MRI parameters. The approximation becomes better as the diffusion time increases. The method helps to significantly reduce the required simulation time, computational memory, and difficulties associated with mesh generation, thus opening the possibilities to simulating complicated structures at low cost for a better understanding of diffusion MRI in the brain.
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| 62. |
- Nguyen, Van Dang, 1985-, et al.
(author)
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Direct Finite Element Simulation of the Turbulent Flow Past a Vertical Axis Wind Turbine
- 2019
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In: Renewable energy. - : Elsevier. - 0960-1481 .- 1879-0682. ; 135, s. 238-247
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Journal article (peer-reviewed)abstract
- There is today a significant interest in harvesting renewable energy, specifically wind energy, in offshore and urban environments. Vertical axis wind turbines get increasing attention since they are able to capture the wind from any direction. They are relatively easy to install and to transport, cheaper to build and maintain, and quite safe for humans and birds. Detailed computer simulations of the fluid dynamics of wind turbines provide an enhanced understanding of the technology and may guide design improvements. In this paper, we simulate the turbulent flow past a vertical axis wind turbine for a range of rotation angles in parked and rotating conditions. We propose the method of Direct Finite Element Simulation in a rotating ALE framework, abbreviated as DFS-ALE. The simulation results are validated against experimental data in the form of force measurements. We find that the simulation results are stable with respect to mesh refinement and that we capture well the general shape of the variation of force measurements over the rotation angles.
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| 63. |
- Nguyen, Van-Dang, 1985-
(author)
-
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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| 64. |
- Nguyen, Van Dang, 1985-
(author)
-
High Performance Finite Element Methods with Application to Simulation of Vertical Axis Wind Turbines and Diffusion MRI
- 2019
-
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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| 65. |
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| 66. |
- Nguyen, Van Dang, et al.
(author)
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Modelling Of Rotating Vertical Axis Turbines Using A Multiphase Finite Element Method
- 2017
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In: VII International Conference on Computational Methods in Marine Engineering (MARINE 2017). - : International Center for Numerical Methods in Engineering (CIMNE). - 9788494690983 ; , s. 950-959
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Conference paper (peer-reviewed)abstract
- We combine the unified continuum fluid-structure interaction method with a multiphase flow model to simulate turbulent flow and fluid-structure interaction of rotating vertical axis turbines in offshore environments. This work is part of a project funded by the Swedish Energy Agency, which focuses on energy systems combining ecological sustainability, competitiveness and reliability of supply. The numerical methods used comprise the Galerkin least-squares finite element method, coupled with the arbitrary Lagrangian-Eulerian method, in order to compute weak solutions of the Navier-Stokes equations for high Reynolds numbers on moving meshes. Mesh smoothing methods help to improve the mesh quality when the mesh undergoes large deformations. The simulations have been performed using the Unicorn solver in the FEniCS-HPC framework, which runs on supercomputers with near optimal weak and strong scaling up to thousands of cores.
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| 67. |
- Nguyen, Van Dang, 1985-, et al.
(author)
-
Portable simulation framework for diffusion MRI
- 2019
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In: Journal of magnetic resonance. - : Academic Press. - 1090-7807 .- 1096-0856. ; 309
-
Journal article (peer-reviewed)abstract
- The numerical simulation of the diffusion MRI signal arising from complex tissue micro-structures is helpful for understanding and interpreting imaging data as well as for designing and optimizing MRI sequences. The discretization of the Bloch-Torrey equation by finite elements is a more recently developed approach for this purpose, in contrast to random walk simulations, which has a longer history. While finite elements discretization is more difficult to implement than random walk simulations, the approach benefits from a long history of theoretical and numerical developments by the mathematical and engineering communities. In particular, software packages for the automated solutions of partial differential equations using finite elements discretization, such as FEniCS, are undergoing active support and development. However, because diffusion MRI simulation is a relatively new application area, there is still a gap between the simulation needs of the MRI community and the available tools provided by finite elements software packages. In this paper, we address two potential difficulties in using FEniCS for diffusion MRI simulation. First, we simplified software installation by the use of FEniCS containers that are completely portable across multiple platforms. Second, we provide a portable simulation framework based on Python and whose code is open source. This simulation framework can be seamlessly integrated with cloud computing resources such as Google Colaboratory notebooks working on a web browser or with Google Cloud Platform with MPI parallelization. We show examples illustrating the accuracy, the computational times, and parallel computing capabilities. The framework contributes to reproducible science and open-source software in computational diffusion MRI with the hope that it will help to speed up method developments and stimulate research collaborations.
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| 68. |
- Nguyen, Van Dang, 1985-, et al.
(author)
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Technical Report -- Comparison of Direct Finite Element Simulation with Actuator Line Models and Vortex Models for Simulation of Turbulent Flow Past a Vertical Axis wind Turbine
- 2019
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Reports (pop. science, debate, etc.)abstract
- We compare three different methodologies for simulation of turbulent flow past a vertical axis wind turbine: (i) full resolution of the turbine blades in a Direct Finite Element Simulation (DFS), (ii) implicit representation of the turbine blades in a 3D Actuator Line Method (ALM), and (iii) implicit representation of the turbine blades as sources in a Vortex Model (VM). The integrated normal force on one blade is computed for a range of azimuthal angles, and is compared to experimental data for the different tip speed ratios, 2.55, 3.44 and 4.09.
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| 69. |
- 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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| 70. |
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