| 1. |
- Gough, Leonie A., et al.
(författare)
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Data from: Specialists in ancient trees are more affected by climate than generalists
- 2016
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Annan publikationabstract
- Ancient trees are considered one of the most important habitats for biodiversity in Europe and North America. They support exceptional numbers of specialized species, including a range of rare and endangered wood-living insects. In this study, we use a dataset of 105 sites spanning a climatic gradient along the oak range of Norway and Sweden to investigate the importance of temperature and precipitation on beetle species richness in ancient, hollow oak trees. We expected that increased summer temperature would positively influence all wood-living beetle species whereas precipitation would be less important with a negligible or negative impact. Surprisingly, only oak-specialist beetles with a northern distribution increased in species richness with temperature. Few specialist beetles and no generalist beetles responded to the rise of 4°C in summer as covered by our climatic gradient. The negative effect of precipitation affected more specialist species than did temperature, whereas the generalists remained unaffected. In summary, we suggest that increased summer temperature is likely to benefit a few specialist beetles within this dead wood community, but a larger number of specialists are likely to decline due to increased precipitation. In addition, generalist species will remain unaffected. To minimize adverse impacts of climate change on this important community, long-term management plans for ancient trees are important.
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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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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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| 4. |
- 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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| 5. |
- 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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| 6. |
- 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
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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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| 7. |
- 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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| 8. |
- 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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| 9. |
- Almén, Niclas, 1971-, et al.
(författare)
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The reliability and factorial validity of the Swedish version of the Recovery Experience Questionnaire
- 2018
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Ingår i: Nordic Psychology. - : Informa UK Limited. - 1901-2276 .- 1904-0016. ; 70:4, s. 324-333
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Tidskriftsartikel (refereegranskat)abstract
- Recent research has indicated that recovery from work stress and effort might be crucial for health and well-being. Thus, a valid measurement of recovery becomes important. The main purpose of the present study was to empirically evaluate and seeking support for the hypothesized four-factor model of the Swedish version of Recovery Experience Questionnaire (REQ). The total sample (N = 680) was randomly split into two subsamples. The first subsample was used for finding the best-fitting model using an exploratory factor analysis and the second subsample was used to test the a priori model using confirmatory factor analysis. The results support the proposed four-factor structure of the scale for both males and females. Additionally, apart from high reliability estimates, this instrument proved to have good convergent and discriminant validity for all four factors. Implications for the use of the REQ in conjunction with recovery-focused interventions were discussed, as were limitations such as low response rate.
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| 10. |
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