| 1. |
- Ahlberg, Erik, et al.
(författare)
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"Vi klimatforskare stödjer Greta och skolungdomarna"
- 2019
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Ingår i: Dagens nyheter (DN debatt). - 1101-2447.
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- DN DEBATT 15/3. Sedan industrialiseringens början har vi använt omkring fyra femtedelar av den mängd fossilt kol som får förbrännas för att vi ska klara Parisavtalet. Vi har bara en femtedel kvar och det är bråttom att kraftigt reducera utsläppen. Det har Greta Thunberg och de strejkande ungdomarna förstått. Därför stödjer vi deras krav, skriver 270 klimatforskare.
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| 2. |
- Hoffman, Johan, 1974-, et al.
(författare)
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Computability and Adaptivity in CFD
- 2018
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Ingår i: Encyclopedia of Computational Mechanics. - : John Wiley & Sons.
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Bokkapitel (refereegranskat)
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| 3. |
- Hoffman, Johan, et al.
(författare)
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Computation of slat noise sources using adaptive FEM and lighthill's analogy
- 2013
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Ingår i: 19th AIAA/CEAS Aeroacoustics Conference.
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Konferensbidrag (refereegranskat)abstract
- This is a summary of preliminary results from simulations with the 30P30N high-lift device. We used the General Galerkin finite element method (G2), where no explicit subgrid model is used, and where the computational mesh is adaptively refined with respect to a posteriori error estimates for a quantity of interest. The mesh is fully unstructured and the solutions are time-resolved, which are key ingredients for solving challenging industrial applications in the field of aeroacoustics. We present preliminary results containing time-averaged quantities and snapshots of unsteady quantities, all reasonably agreeing with previous computational efforts. One important finding is that the use of adaptively generated meshes seems to be a more effcient way of computing aeroacoustic sources than by using "handmade" meshes.
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| 4. |
- Hoffman, Johan, et al.
(författare)
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FEniCS-HPC : Automated predictive high-performance finite element computing with applications in aerodynamics
- 2016
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Ingår i: Proceedings of the 11th International Conference on Parallel Processing and Applied Mathematics, PPAM 2015. - Cham : Springer-Verlag New York. ; , s. 356-365
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Konferensbidrag (refereegranskat)abstract
- Developing multiphysics nite element methods (FEM) andscalable HPC implementations can be very challenging in terms of soft-ware complexity and performance, even more so with the addition ofgoal-oriented adaptive mesh renement. To manage the complexity we inthis work presentgeneraladaptive stabilized methods withautomatedimplementation in the FEniCS-HPCautomatedopen source softwareframework. This allows taking the weak form of a partial dierentialequation (PDE) as input in near-mathematical notation and automati-cally generating the low-level implementation source code and auxiliaryequations and quantities necessary for the adaptivity. We demonstratenew optimal strong scaling results for the whole adaptive frameworkapplied to turbulent ow on massively parallel architectures down to25000 vertices per core with ca. 5000 cores with the MPI-based PETScbackend and for assembly down to 500 vertices per core with ca. 20000cores with the PGAS-based JANPACK backend. As a demonstration ofthe high impact of the combination of the scalability together with theadaptive methodology allowing prediction of gross quantities in turbulent ow we present an application in aerodynamics of a full DLR-F11 aircraftin connection with the HiLift-PW2 benchmarking workshop with goodmatch to experiments.
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| 5. |
- Hoffman, Johan, et al.
(författare)
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FEniCS-HPC: Coupled Multiphysics in Computational Fluid Dynamics
- 2017
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Ingår i: High-Performance Scientific Computing. - Cham : Springer. - 9783319538617 - 9783319538624 ; , s. 58-69
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Konferensbidrag (refereegranskat)abstract
- We present a framework for coupled multiphysics in computational fluid dynamics, targeting massively parallel systems. Our strategy is based on general problem formulations in the form of partial differential equations and the finite element method, which open for automation, and optimization of a set of fundamental algorithms. We describe these algorithms, including finite element matrix assembly, adaptive mesh refinement and mesh smoothing; and multiphysics coupling methodologies such as unified continuum fluid-structure interaction (FSI), and aeroacoustics by coupled acoustic analogies. The framework is implemented as FEniCS open source software components, optimized for massively parallel computing. Examples of applications are presented, including simulation of aeroacoustic noise generated by an airplane landing gear, simulation of the blood flow in the human heart, and simulation of the human voice organ.
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| 6. |
- Hoffman, Johan, et al.
(författare)
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Time-resolved adaptive FEM simulation of the DLR-F11 aircraft model at high Reynolds number
- 2014
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Ingår i: 52nd AIAA Aerospace Sciences Meeting - AIAA Science and Technology Forum and Exposition, SciTech 2014. - Reston, Virginia : American Institute of Aeronautics and Astronautics.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- We present a time-resolved, adaptive finite element method for aerodynamics, together with the results from the HiLiftPW-2 workshop, where this method is used to compute the flow past a DLR-F11 aircraft model at realistic Reynolds number. The mesh is automatically constructed by the method as part of the computation, and no explicit turbulence model is needed. The effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of the skin friction. In the extreme case of very high Reynolds numbers we approximate the small skin friction by zero skin friction, corresponding to a free slip boundary condition, which results in a computational model without any model parameter that needs tuning. Thus, the simulation methodology by- passes the main challenges posed by high Reynolds number CFD: the design of an optimal computational mesh, turbulence (or subgrid) modeling, and the cost of boundary layer res- olution. The results from HiLiftPW-2 presented in this report show good agreement with experimental data for a range of different angles of attack, while using orders of magnitude fewer degrees of freedom than what is needed in state of the art methods such as RANS.
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| 7. |
- Hoffman, Johan, et al.
(författare)
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Towards a parameter-free method for high Reynolds number turbulent flow simulation based on adaptive finite element approximation
- 2015
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Ingår i: Computer Methods in Applied Mechanics and Engineering. - : Elsevier. - 0045-7825 .- 1879-2138. ; 288, s. 60-74
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Tidskriftsartikel (refereegranskat)abstract
- We present work towards a parameter-free method for turbulent flow simulation based on adaptive finite element approximation of the Navier-Stokes equations at high Reynolds numbers. In this model, viscous dissipation is assumed to be dominated by turbulent dissipation proportional to the residual of the equations, and skin friction at solid walls is assumed to be negligible compared to inertial effects. The result is a computational model without empirical data, where the only parameter is the local size of the finite element mesh. Under adaptive refinement of the mesh based on a posteriori error estimation, output quantities of interest in the form of functionals of the finite element solution converge to become independent of the mesh resolution, and thus the resulting method has no adjustable parameters. No ad hoc design of the mesh is needed, instead the mesh is optimised based on solution features, in particular no bounder layer mesh is needed. We connect the computational method to the mathematical concept of a dissipative weak solution of the Euler equations, as a model of high Reynolds number turbulent flow, and we highlight a number of benchmark problems for which the method is validated.
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| 8. |
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| 9. |
- Hoffman, Johan, 1974-, et al.
(författare)
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Turbulent flow and Fluid–structure interaction
- 2012
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Ingår i: Lecture Notes in Computational Science and Engineering. - : Springer Science and Business Media Deutschland GmbH. ; , s. 543-552
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Bokkapitel (refereegranskat)abstract
- The FEniCS Project aims towards the goals of generality, efficiency, and simplicity, concerning mathematical methodology, implementation and application, and the Unicorn project is an implementation aimed at FSI and high Re turbulent flow guided by these principles. Unicorn is based on the DOLFIN/FFC/FIAT suite and the linear algebra package PETSc. We here present some key elements of Unicorn, and a set of computational results from applications. The details of the Unicorn implementation are described in Chapter 18.
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| 10. |
- Hoffman, Johan, et al.
(författare)
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Unicorn : Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- 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 e cient 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
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| 11. |
- Hoffman, Johan, et al.
(författare)
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Unicorn : Parallel adaptive finite element simulation of turbulent flow and fluid-structure interaction for deforming domains and complex geometry
- 2013
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Ingår i: Computers & Fluids. - : Elsevier BV. - 0045-7930 .- 1879-0747. ; 80:SI, s. 310-319
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 12. |
- Hoffman, Johan, 1974-, et al.
(författare)
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Unicorn : A unified continuum mechanics solver
- 2012
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Ingår i: Lecture Notes in Computational Science and Engineering. - : Springer Science and Business Media Deutschland GmbH. ; , s. 339-361
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Bokkapitel (refereegranskat)abstract
- This chapter provides a description of the technology of Unicorn focusing on simple, efficient and general algorithms and software for the Unified Continuum (UC) concept and the adaptive General Galerkin (G2) discretization as a unified approach to continuum mechanics. We describe how Unicorn fits into the FEniCS framework, how it interfaces to other FEniCS components, what interfaces and functionality Unicorn provides itself and how the implementation is designed. We also present some examples in fluid–structure interaction and adaptivity computed with Unicorn.
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| 13. |
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| 14. |
- Jansson, Anton, 1983, et al.
(författare)
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Humaniora i välfärdssamhället : En inledning
- 2023
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Ingår i: Humaniora i välfärdssamhället : Kunskapshistorier om efterkrigstiden - Kunskapshistorier om efterkrigstiden. - Göteborg : Makadam. - 2002-2131. - 9789170614019 - 9789170619014 ; 49, s. 9-29
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Bokkapitel (refereegranskat)
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| 15. |
- Jansson, Johan, 1978-, et al.
(författare)
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Simulation of 3D unsteady incompressible flow past a NACA 0012 wing section
- 2012
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- We present computational simulations of three-dimensional unsteady high Reynolds number incompressible flow past a NACA 0012 wing profile, for a range of angles of attack, from low lift through stall. A stabilized finite element method is used, referred to as General Galerkin (G2), with adaptive mesh refinement with respect to the error in target output, such as aerodynamic forces. Computational predictions of aerodynamic forces are validated against experimental data.
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| 16. |
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| 17. |
- Jansson, Johan, 1978-, et al.
(författare)
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Time-resolved Adaptive Direct FEM Simulation of High-lift Aircraft Configurations : Chapter in "Numerical Simulation of the Aerodynamics of High-Lift Configurations'", Springer
- 2018
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Ingår i: Numerical Simulation of the Aerodynamics of High-Lift Configurations. - Cham : Springer. - 9783319621364 - 9783319621357 ; , s. 67-92
-
Bokkapitel (refereegranskat)abstract
- We present an adaptive finite element method for time-resolved simulation of aerodynamics without any turbulence-model parameters, which is applied to a benchmark problem from the HiLiftPW-3workshop to compute the flowpast a JAXA Standard Model (JSM) aircraft model at realistic Reynolds numbers. The mesh is automatically constructed by the method as part of an adaptive algorithm based on a posteriori error estimation using adjoint techniques. No explicit turbulence model is used, and the effect of unresolved turbulent boundary layers is modeled by a simple parametrization of the wall shear stress in terms of a skin friction. In the case of very high Reynolds numbers, we approximate the small skin friction by zero skin friction, corresponding to a free-slip boundary condition, which results in a computational model without any model parameter to be tuned, and without the need for costly boundary-layer resolution. We introduce a numerical tripping-noise term to act as a seed for growth of perturbations; the results support that this triggers the correct physical separation at stall and has no significant pre-stall effect. We show that the methodology quantitavely and qualitatively captures the main features of the JSM experiment-aerodynamic forces and the stall mechanism-with a much coarser mesh resolution and lower computational cost than the state-of-the-art methods in the field, with convergence under mesh refinement by the adaptive method. Thus, the simulation methodology appears to be a possible answer to the challenge of reliably predicting turbulent-separated flows for a complete air vehicle.
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| 18. |
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| 19. |
- Jansson, Niclas, et al.
(författare)
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Framework For Massively Parallel Adaptive Finite Element Computational Fluid Dynamics On Tetrahedral Meshes
- 2012
-
Ingår i: SIAM Journal on Scientific Computing. - : Society for Industrial & Applied Mathematics (SIAM). - 1064-8275 .- 1095-7197. ; 34:1, s. C24-C42
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we describe a general adaptive finite element framework for unstructured tetrahedral meshes without hanging nodes suitable for large scale parallel computations. Our framework is designed to scale linearly to several thousands of processors, using fully distributed and efficient algorithms. The key components of our implementation, local mesh refinement and load balancing algorithms, are described in detail. Finally, we present a theoretical and experimental performance study of our framework, used in a large scale computational fluid dynamics computation, and we compare scaling and complexity of different algorithms on different massively parallel architectures.
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| 20. |
- Jansson, Niclas, 1983-
(författare)
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High Performance Adaptive Finite Element Methods : With Applications in Aerodynamics
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The massive computational cost for resolving all scales in a turbulent flow makes a direct numerical simulation of the underlying Navier-Stokes equations impossible in most engineering applications. Recent advances in adaptive finite element methods offer a new powerful tool in Computational Fluid Dynamics (CFD). The computational cost for simulating turbulent flow can be minimized by adaptively resolution of the mesh, based on a posteriori error estimation. Such adaptive methods have previously been implemented for efficient serial computations, but the extension to an efficient parallel solver is a challenging task. This work concerns the development of an adaptive finite element method that enables efficient computation of time resolved approximations of turbulent flow for complex geometries with a posteriori error control. We present efficient data structures and data decomposition methods for distributed unstructured tetrahedral meshes. Our work also concerns an efficient parallelization of local mesh refinement methods such as recursive longest edge bisection, and the development of an a priori predictive dynamic load balancing method, based on a weighted dual graph. We also address the challenges of emerging supercomputer architectures with the development of new hybrid parallel programming models, combining traditional message passing with lightweight one-sided communication. Our implementation has proven to be both general and efficient, scaling up to more than twelve thousands cores.
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| 21. |
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| 22. |
- Spühler, Jeannette H., et al.
(författare)
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3D Fluid-Structure Interaction Simulation of Aortic Valves Using a Unified Continuum ALE FEM Model
- 2018
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Ingår i: Frontiers in Physiology. - : Frontiers Media S.A.. - 1664-042X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Due to advances in medical imaging, computational fluid dynamics algorithms and high performance computing, computer simulation is developing into an important tool for understanding the relationship between cardiovascular diseases and intraventricular blood flow. The field of cardiac flow simulation is challenging and highly interdisciplinary. We apply a computational framework for automated solutions of partial differential equations using Finite Element Methods where any mathematical description directly can be translated to code. This allows us to develop a cardiac model where specific properties of the heart such as fluid-structure interaction of the aortic valve can be added in a modular way without extensive efforts. In previous work, we simulated the blood flow in the left ventricle of the heart. In this paper, we extend this model by placing prototypes of both a native and a mechanical aortic valve in the outflow region of the left ventricle. Numerical simulation of the blood flow in the vicinity of the valve offers the possibility to improve the treatment of aortic valve diseases as aortic stenosis (narrowing of the valve opening) or regurgitation (leaking) and to optimize the design of prosthetic heart valves in a controlled and specific way. The fluid-structure interaction and contact problem are formulated in a unified continuum model using the conservation laws for mass and momentum and a phase function. The discretization is based on an Arbitrary Lagrangian-Eulerian space-time finite element method with streamline diffusion stabilization, and it is implemented in the open source software Unicorn which shows near optimal scaling up to thousands of cores. Computational results are presented to demonstrate the capability of our framework.
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| 23. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(författare)
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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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Rapport (övrigt vetenskapligt/konstnärligt)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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| 24. |
- Spühler, Jeannette Hiromi, 1981-, et al.
(författare)
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A High Performance Computing Framework for Finite Element Simulation of Blood Flow in the Left Ventricle of the Human Heart
- 2020
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Ingår i: Lecture Notes in Computational Science and Engineering. - Cham : Springer. ; , s. 155-164
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Konferensbidrag (refereegranskat)abstract
- We present a high performance computing framework for finite element simulation of blood flow in the left ventricle of the human heart. The mathematical model is described together with the discretization method and the parallel implementation in Unicorn which is part of the open source software framework FEniCS-HPC. We show results based on patient-specific data that 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 other 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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| 25. |
- Attauabi, Mohamed, et al.
(författare)
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Influence of Genetics, Immunity and the Microbiome on the Prognosis of Inflammatory Bowel Disease (IBD Prognosis Study) : the protocol for a Copenhagen IBD Inception Cohort Study
- 2022
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Ingår i: BMJ Open. - : BMJ Publishing Group Ltd. - 2044-6055. ; 12:6, s. e055779-e055779
-
Tidskriftsartikel (refereegranskat)abstract
- Introduction: Inflammatory bowel diseases (IBD), encompassing Crohn's disease and ulcerative colitis, are chronic, inflammatory diseases of the gastrointestinal tract. We have initiated a Danish population-based inception cohort study aiming to investigate the underlying mechanisms for the heterogeneous course of IBD, including need for, and response to, treatment.Methods and analysis: IBD Prognosis Study is a prospective, population-based inception cohort study of unselected, newly diagnosed adult, adolescent and paediatric patients with IBD within the uptake area of Hvidovre University Hospital and Herlev University Hospital, Denmark, which covers approximately 1 050 000 inhabitants (~20% of the Danish population). The diagnosis of IBD will be according to the Porto diagnostic criteria in paediatric and adolescent patients or the Copenhagen diagnostic criteria in adult patients. All patients will be followed prospectively with regular clinical examinations including ileocolonoscopies, MRI of the small intestine, validated patient-reported measures and objective examinations with intestinal ultrasound. In addition, intestinal biopsies from ileocolonoscopies, stool, rectal swabs, saliva samples, swabs of the oral cavity and blood samples will be collected systematically for the analysis of biomarkers, microbiome and genetic profiles. Environmental factors and quality of life will be assessed using questionnaires and, when available, automatic registration of purchase data. The occurrence and course of extraintestinal manifestations will be evaluated by rheumatologists, dermatologists and dentists, and assessed by MR cholangiopancreatography, MR of the spine and sacroiliac joints, ultrasonography of peripheral joints and entheses, clinical oral examination, as well as panoramic radiograph of the jaws. Fibroscans and dual-energy X-ray absorptiometry scans will be performed to monitor occurrence and course of chronic liver diseases, osteopenia and osteoporosis.Ethics and dissemination: This study has been approved by Ethics Committee of the Capital Region of Denmark (approval number: H-20065831). Study results will be disseminated through publication in international scientific journals and presentation at (inter)national conferences.
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