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  • 1.
    Abrahamyan, Lilit
    et al.
    University of Amsterdam.
    Schaap, Jorrit A.
    Hoekstra, Alfons G.
    Shamonin, Denis
    M.A.Box, Frieke
    Van der Geest, Rob J.
    H.C. Reiber, Johan
    M.A. Sloot, Peter
    A Problem Solving Environment for Image-Based Computational Hemodynamics2005Konferensbidrag (Refereegranskat)
    Abstract [en]

    We introduce a complete problem solving environment designed for pulsatile flows in 3D complex geometries, especially arteries. Three-dimensional images from arteries, obtained from e.g. Magnetic Resonance Imaging, are segmented to obtain a geometrical description of the arteries of interest. This segmented artery is prepared for blood flow simulations in a 3D editing tool, allowing to define in- and outlets, to filter and crop part of the artery, to add certain structures ( e.g. a by-pass, or stents ), and to generate computational meshes as input to the blood flow simulators. Using dedicated fluid flow solvers the time dependent blood flow in the artery during one systole is computed. The resulting flow, pressure and shear stress fields are then analyzed using a number of visualization techniques. The whole environment can be operated from a desktop virtual reality system, and is embedded in a Grid computing environment.

  • 2.
    Apostolov, Rossen
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Axner, Lilit
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Agren, Hans
    Ayugade, Eduard
    Duta, Mihai
    Gelpi, Jose Luis
    Gimenez, Judit
    Goni, Ramon
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Jamitzky, Ferdinand
    Kranzmuller, Dieter
    Labarta, Jesus
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Orozco, Modesto
    Peterson, Magnus
    Satzger, Helmut
    Trefethen, Anne
    Scalable Software Services for Life Science2011Ingår i: Proceedings of 9th HealthGrid conference, 2011Konferensbidrag (Refereegranskat)
    Abstract [en]

    Life Science is developing into one of the largest e- Infrastructure users in Europe, in part due to the ever-growing amount of biological data. Modern drug design typically includes both sequence bioinformatics, in silico virtual screening, and free energy calculations, e.g. of drug binding. This development will accelerate tremendously, and puts high demands on simulation software and support services. e-Infrastructure projects such as PRACE/DEISA have made important advances on hardware and scalability, but have largely been focused on theoretical scalability for large systems, while typical life science applications rather concern small-to-medium size molecules. Here, we propose to address this with by implementing new techniques for efficient small-system parallelization combined with throughput and ensemble computing to enable the life science community to exploit the largest next-generation e-Infrastructures. We will also build a new cross-disciplinary Competence Network for all of life science, to position Europe as the world-leading community for development and maintenance of this software e-Infrastructure. Specifically, we will (1) develop new hierarchical parallelization approaches explicitly based on ensemble and high-throughput computing for new multi-core and streaming/GPU architectures, and establish open software standards for data storage and exchange, (2) implement, document, and maintain such techniques in pilot European open-source codes such as the widely used GROMACS & DALTON, a new application for ensemble simulation (DISCRETE), and large-scale bioinformatics protein annotation, (3) create a Competence Centre for scalable life science software to strengthen Europe as a major software provider and to enable the community to exploit e-Infrastructures to their full extent. This Competence Network will provide training and support infrastructure, and establish a long-term framework for maintenance and optimization of life science codes.

  • 3. Artoli, Abdel Monim
    et al.
    Abrahamyan, Lilit
    University of Amsterdam.
    Hoekstra, Alfons G.
    Accuracy versus Performance in Lattice Boltzmann BGK Accuracy versus Performance in Lattice Boltzmann BGK Simulations of Systolic Flows2004Ingår i: Lecture Notes in Computational Science and Engineering, ISSN 1439-7358, Vol. 3039, s. 548-555Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The aim of this work is to tune the lattice Boltzmann BGK (LBGK) simulation parameters in order to achieve optimum accuracy and performance for. time dependent flows. We present detailed analysis of the accuracy and performance of LBGK in simulating pulsatile Newtonian flow in a straight rigid 3D tube. We compare the obtained velocity profiles and shear stress to the analytic Womersley solutions. A curved boundary condition is used for the walls and the accuracy and performance are compared to that obtained by using the bounce-back on the links. A technique to reduce compressibility errors during simulations based on reducing the Mach number is presented.

  • 4.
    Axner, Lilit
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Bernsdorf, Joerg M.
    Zeiser, Thomas
    Lammers, Peter
    Linxweiler, Jan
    Hoekstra, Alfonsb G.
    Performance evaluation of a Parallel Sparse Lattice Boltzmann Solver2008Ingår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 227, nr 10, s. 4895-4911Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We develop a performance prediction model for a parallelized sparse lattice Boltzmann solver and present performance results for simulations of flow in a variety of complex geometries. A special focus is on partitioning and memory/load balancing strategy for geometries with a high solid fraction and/or complex topology such as porous media, fissured rocks and geometries from medical applications. The topology of the lattice nodes representing the fluid fraction of the computational domain is mapped on a graph. Graph decomposition is performed with both multilevel recursive-bisection and multilevel k-way schemes based on modified Kernighan–Lin and Fiduccia–Mattheyses partitioning algorithms. Performance results and optimization strategies are presented for a variety of platforms, showing a parallel efficiency of almost 80% for the largest problem size. A good agreement between the performance model and experimental results is demonstrated.

  • 5.
    Axner, Lilit
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Jeays, Adam
    Hoekstra, Alfons G
    Lawford, Pat
    Hose, Rod
    Sloot, Peter M.A
    Simulations of time harmonic blood flow in the Mesenteric artery: comparing finite element and lattice Boltzmann methods2009Ingår i: Biomedical engineering online, ISSN 1475-925X, E-ISSN 1475-925X, Vol. 8, nr 23, s. 28-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Systolic blood flow has been simulated in the abdominal aorta and the superior mesenteric artery. The simulations were carried out using two different computational hemodynamic methods: the finite element method to solve the Navier Stokes equations and the lattice Boltzmann method. Results: We have validated the lattice Boltzmann method for systolic flows by comparing the velocity and pressure profiles of simulated blood flow between methods. We have also analyzed flow-specific characteristics such as the formation of a vortex at curvatures and traces of flow. Conclusion: The lattice Boltzmann Method is as accurate as a Navier Stokes solver for computing complex blood flows. As such it is a good alternative for computational hemodynamics, certainly in situation where coupling to other models is required.

  • 6.
    Axner, Lilit
    et al.
    University of Amsterdam.
    Latt, Jonas
    Hoekstra, Alfons G.
    Chopard, Bastien
    Sloot, Peter M.A.
    Simulating Time Harmonic Flows with the Regularized L-BGK Method2007Ingår i: International Journal of Modern Physics C, ISSN 0129-1831, Vol. 18, nr 4, s. 661-666Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A recent improvement of the lattice BGK model, based on a regularization of the precollision distribution function, is applied to three dimensional Womersley flow. The accuracy and the stability of the model are essentially improved by using this regularization. A good agreement with analytical Womersley solution is presented, as well as an improvement of the accuracy over standard L-BGK. Numerical stability of the scheme for a range of Reynolds and Womersley numbers is also presented, demonstrating an enhancement of the stability range of L-BGK for this type of flows.

  • 7. Larsson, Torbjörn
    et al.
    Hammar, Johan
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Barth, Michaela
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Axner, Lilit
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    ENHANCING COMPUTATIONAL AERO-ACOUSTIC PROCESSES FOR GROUNDVEHICLES RESOLVING OPEN SOURCE CFD2018Ingår i: The 13th OpenFOAM Workshop, 2018, s. 1-4Konferensbidrag (Refereegranskat)
  • 8. Mascellaro, L.
    et al.
    Axner, Lilit
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Gong, Jing
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Monotricat® hull, first displacement naval hull navigating at speeds of planing hulls, on spray self-produced, at high hydrodynamic efficiency and energy recovery2015Ingår i: 18th International Conference on Ships and Shipping Research, NAV 2015, The European Marine Energy Centre Ltd , 2015, s. 38-47Konferensbidrag (Refereegranskat)
    Abstract [en]

    From the '50s, with the introduction of the first semi-planing hull of Nelson, which allowed to navigate with a certain tranquility at speeds higher than those of traditional hulls, and with the subsequent availability of more powerful engines, have been reached a speed equal to Fn greater than 0.6, which defines planing hulls. It was created so a clear distinction between displacement and planing hulls, in relation to the performances. The need to have naval units displacing faster has pushed the ship design to achieve increasingly high performance hulls, also focusing on the use of lightweight materials such as aluminum and more powerful engines, etc., but without substantially changing the traditional forms of hull. The patented hull Monotricat high hydrodynamic efficiency and energy saving represents the overcoming of this distinction between displacement and planing hulls, because, unlike previous solutions, is configured as the first hull that combines the characteristics of displacement and planning hull, since it presents an innovative architecture that could be defined as a hybrid between a monohull and catamaran, navigating on spray self-produced. This presentation will show how the hull Monotricat is the first displacement hull that can navigate at both displacement and planning speeds, with a resistance curve almost straight, maintaining the characteristics of a displacement hull. For these reasons the Monotricat hull is able to ensure: safety, comfort navigation, best seakeeping and maneuverability in restricted waters, stability, reduction of resistance to motion, cost management, regularity on the routes even in adverse weather-sea. These characteristics of the hull have been studied, tested and validated by leading research institutes and universities with more ameliorative results in each subsequent experimentation, reported in the present work, which demonstrated a greater hydrodynamic efficiency compared to conventional hulls tending to 20%.

  • 9.
    Zhang, Mengmeng
    et al.
    KTH.
    Melin, Tomas
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Barth, Michaela
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Axner, Lilit
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Mixed Fidelity Aerodynamic and Aero-Structural Optimization for Wings2018Ingår i: 2018 International Conference on High Performance Computing & Simulation, 2018, s. 476-483Konferensbidrag (Refereegranskat)
    Abstract [en]

    Automatic multidisciplinary design optimization is one of the challenges that are faced in the processes involved in designing efficient wings for aircraft. In this paper we present mixed fidelity aerodynamic and aero-structural optimization methods for designing wings. A novel shape design methodology has been developed - it is based on a mix of the automatic aerodynamic optimization for a reference aircraft model, and the aero-structural optimization for an uninhabited air vehicle (UAV) with a high aspect ratio wing. This paper is a significant step towards making it possible to perform all the core processes for aerodynamic and aero-structural optimization that require special skills in a fully automatic manner - this covers all the processes from creating the mesh for the wing simulation to executing the high-fidelity computational fluid dynamics (CFD) analysis code. Our results confirm that the simulation tools can make it possible for a far broader range of engineering researchers and developers to design aircraft in much simpler and more efficient ways. This is a vital step in the evolution of wing design processes as it means that the extremely expensive laboratory experiments that were traditionally used when designing the wings can now be replaced with more cost effective high performance computing (HPC) simulation that utilize accurate numerical methods.

  • 10. Zudilova-Seinstra, E.V.
    et al.
    Yang, N.
    Axner, Lilit
    Section Computational Science, Informatics Institute, University of Amsterdam.
    Wibisono, A.
    Vasunin, V.
    Service-Oriented Visualization applied to Medical Data Analysis2008Ingår i: Service Oriented Computing and Applications, ISSN 1863-2386, E-ISSN 1863-2394, Vol. 2, nr 4, s. 187-201Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    With the era of Grid computing, data driven experiments and simulations have become very advanced and complicated. To allow specialists from various domains to deal with large datasets, aside from developing efficient extraction techniques, it is necessary to have available computational facilities to visualize and interact with the results of an extraction process. Having this in mind, we developed an Interactive Visualization Framework, which supports a service-oriented architecture. This framework allows, on one hand visualization experts to construct visualizations to view and interact with large datasets, and on the other hand end-users (e.g., medical specialists) to explore these visualizations irrespective of their geographical location and available computing resources. The image-based analysis of vascular disorders served as a case study for this project. The paper presents main research findings and reports on the current implementation status.

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