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  • 201.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik.
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Optical properties of Naphthobischalcogenadiazoles from density functional perspectiveManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    In the present work the density functional calculations of two naphthobischalcogenadiazole (NXz) oligomers are shown. The oxygen- and sulphur-containing NXz trimers were optimized in a form of a neutral oligomer and a radical cation in order to investigate structural changes resulting from the polaron formation. The influence of polaron on band gaps is determined and supported with densities of states analysis together with absorption spectra. This manuscript used B3LYP and ωB97XD functionals in combination with 6-31+G(d) basis set.

  • 202.
    Mirsakiyeva, Amina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University,.
    Polaron formation and optical absorption in PEDOT and its selenium and tellurium derivatives: density functional calculationsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We present a density functional theory (DFT) study on polaron formation and optical properties of PEDOT and its selenium and tellurium derivatives. Comparing a number of combinations of basis set and approximations to the exchange-correlation functional, we find that the ωB97XD functional is an overall good choice giving well-localized polarons and optical spectra in good agreement with experiment. This functional has the correct long-range  asymptotic behavior, and also includes some short-range Hartree-Fock exchange. Despite the  long-range Hartree-Fock exchange part present in this functional, the spin contamination remains relatively limited and it also stably produces results that are virtually independent of the basis set used.

  • 203. Mohammad, Dara K.
    et al.
    Ali, Raja H.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för datavetenskap och kommunikation (CSC).
    Turunen, Janne J.
    Nore, Beston F.
    Smith, C. I. Edvard
    B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing2016Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 8, artikkel-id e0160255Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Protein kinase B (AKT) phosphorylates numerous substrates on the consensus motif RXRXXpS/T, a docking site for 14-3-3 interactions. To identify novel AKT-induced phosphorylation events following B cell receptor (BCR) activation, we performed proteomics, biochemical and bioinformatics analyses. Phosphorylated consensus motif-specific antibody enrichment, followed by tandem mass spectrometry, identified 446 proteins, containing 186 novel phosphorylation events. Moreover, we found 85 proteins with up regulated phosphorylation, while in 277 it was down regulated following stimulation. Up regulation was mainly in proteins involved in ribosomal and translational regulation, DNA binding and transcription regulation. Conversely, down regulation was preferentially in RNA binding, mRNA splicing and mRNP export proteins. Immunoblotting of two identified RNA regulatory proteins, RBM25 and MEF-2D, confirmed the proteomics data. Consistent with these findings, the AKT-inhibitor (MK-2206) dramatically reduced, while the mTORC-inhibitor PP242 totally blocked phosphorylation on the RXRXXpS/T motif. This demonstrates that this motif, previously suggested as an AKT target sequence, also is a substrate for mTORC1/2. Proteins with PDZ, PH and/or SH3 domains contained the consensus motif, whereas in those with an HMG-box, H15 domains and/or NF-X1-zinc-fingers, the motif was absent. Proteins carrying the consensus motif were found in all eukaryotic clades indicating that they regulate a phylogenetically conserved set of proteins.

  • 204.
    Monokrousos, Antonios
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mavriplis, Catherine
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Optimal disturbances above and upstream of a flat plate with an elliptic-type leading edge2014Inngår i: Theoretical and Computational Fluid Dynamics, ISSN 0935-4964, E-ISSN 1432-2250, Vol. 28, nr 2, s. 147-157Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Adjoint-based iterative methods are employed to compute linear optimal disturbances in a spatially growing boundary layer around an elliptic leading edge. The Lagrangian approach is used where an objective function is chosen and constraints are assigned. The optimisation problem is solved using power iterations combined with a matrix-free formulation, where the state is marched forward in time with a standard direct numerical simulation solver and backward with the adjoint solver until a chosen convergence criterion is fulfilled. We consider the global and, more relevant to receptivity studies, the upstream localised optimal initial condition leading to the largest possible energy amplification at time T. We find that the two-dimensional initial condition with the largest potential for growth is a Tollmien-Schlichting-like wave packet that includes the Orr mechanism and is located inside the boundary layer downstream of the leading edge. Three-dimensional optimal disturbances induce streaks by the lift-up mechanism. Requiring the optimal initial condition to be localised upstream of the plate enables us to better study the effects of the leading edge on the boundary layer receptivity mechanisms. Two-dimensional upstream disturbances are inefficient at triggering unstable eigenmodes, whereas three-dimensional disturbances induce streamwise streaks with significant growth.

  • 205. Moruz, Luminita
    et al.
    Hoopmann, Michael R.
    Rosenlund, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Granholm, Viktor
    Moritz, Robert L.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mass Fingerprinting of Complex Mixtures: Protein Inference from High-Resolution Peptide Masses and Predicted Retention Times2013Inngår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 12, nr 12, s. 5730-5741Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In typical shotgun experiments, the mass spectrometer records the masses of a large set of ionized analytes but fragments only a fraction of them. In the subsequent analyses, normally only the fragmented ions are used to compile a set of peptide identifications, while the unfragmented ones are disregarded. In this work, we show how the unfragmented ions, here denoted MS1-features, can be used to increase the confidence of the proteins identified in shotgun experiments. Specifically, we propose the usage of in silico mass tags, where the observed MS1-features are matched against de novo predicted masses and retention times for all peptides derived from a sequence database. We present a statistical model to assign protein-level probabilities based on the MS1-features and combine this data with the fragmentation spectra. Our approach was evaluated for two triplicate data sets from yeast and human, respectively, leading to up to 7% more protein identifications at a fixed protein-level false discovery rate of 1%. The additional protein identifications were validated both in the context of the mass spectrometry data and by examining their estimated transcript levels generated using RNA-Seq. The proposed method is reproducible, straightforward to apply, and can even be used to reanalyze and increase the yield of existing data sets.

  • 206. Moruz, Luminita
    et al.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    GradientOptimizer: An open-source graphical environment for calculating optimized gradients in reversed-phase liquid chromatography2014Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 14, nr 12, s. 1464-1466Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We here present GradientOptimizer, an intuitive, lightweight graphical user interface to design nonlinear gradients for separation of peptides by reversed-phase liquid chromatography. The software allows to calculate three types of nonlinear gradients, each of them optimizing a certain retention time distribution of interest. GradientOptimizer is straightforward to use, requires minimum processing of the input files, and is supported under Windows, Linux, and OS X platforms. The software is open-source and can be downloaded under an Apache 2.0 license at https://github.com/statisticalbiotechnology/NonlinearGradientsUI.

  • 207. Moruz, Luminita
    et al.
    Pichler, Peter
    Stranzl, Thomas
    Mechtler, Karl
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Optimized Nonlinear Gradients for Reversed-Phase Liquid Chromatography in Shotgun Proteomics2013Inngår i: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 85, nr 16, s. 7777-7785Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Reversed-phase liquid chromatography has become the preferred method for separating peptides in most of the mass spectrometry-based proteomics workflows of today. In the way the technique is typically applied, the peptides are released from the chromatography column by the gradual addition of an organic buffer according to a linear function. However, when applied to complex peptide mixtures, this approach leads to unequal spreads of the peptides over the chromatography time. To address this, we investigated the use of nonlinear gradients, customized for each setup at hand. We developed an algorithm to generate optimized gradient functions for shotgun proteomics experiments and evaluated it for two data sets consisting each of four replicate runs of a human complex sample. Our results show that the optimized gradients produce a more even spread of the peptides over the chromatography run, while leading to increased numbers of confident peptide identifications. In addition, the list of peptides identified using nonlinear gradients differed considerably from those found with the linear ones, suggesting that such gradients can be a valuable tool for increasing the proteome coverage of mass spectrometry-based experiments.

  • 208. Motamed, M.
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    A wavefront-based Gaussian beam method for computing high frequency wave propagation problems2015Inngår i: Computers and Mathematics with Applications, ISSN 0898-1221, E-ISSN 1873-7668, Vol. 69, nr 9, s. 949-963Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a novel wavefront method based on Gaussian beams for computing high frequency wave propagation problems. Unlike standard geometrical optics, Gaussian beams compute the correct solution of the wave field also at caustics. The method tracks a front of two canonical beams with two particular initial values for width and curvature. In a fast post-processing step, from the canonical solutions we recreate any other Gaussian beam with arbitrary initial data on the initial front. This provides a simple mechanism to include a variety of optimization processes, including error minimization and beam width minimization, for a posteriori selection of optimal beam initial parameters. The performance of the method is illustrated with two numerical examples.

  • 209.
    Muhle, Franz
    et al.
    Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, As, Norway..
    Schottler, Jannik
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany..
    Bartl, Jan
    Norwegian Univ Sci & Technol, Dept Energy & Proc Engn, Trondheim, Norway..
    Futrzynski, Romain
    Siemens PLM Software, London, England..
    Evans, Steve
    Siemens PLM Software, London, England..
    Bernini, Luca
    Politecn Milan, Dept Mech Engn, Milan, Italy..
    Schito, Paolo
    Politecn Milan, Dept Mech Engn, Milan, Italy..
    Draper, Martin
    Univ Republica, Fac Ingn, Montevideo, Uruguay..
    Guggeri, Andres
    Univ Republica, Fac Ingn, Montevideo, Uruguay..
    Kleusberg, Elektra
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holling, Michael
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany..
    Peinke, Joachim
    Carl von Ossietzky Univ Oldenburg, ForWind Ctr Wind Energy, Inst Phys, Oldenburg, Germany.;Fraunhofer IWES, Oldenburg, Germany..
    Adaramola, Muyiwa S.
    Norwegian Univ Life Sci, Fac Environm Sci & Nat Resource Management, As, Norway..
    Saetran, Lars
    Norwegian Univ Sci & Technol, Dept Energy & Proc Engn, Trondheim, Norway..
    Blind test comparison on the wake behind a yawed wind turbine2018Inngår i: Wind Energy Science, ISSN 2213-3968, E-ISSN 2366-7443, Vol. 3, nr 2, s. 883-903Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This article summarizes the results of the "Blind test 5" workshop, which was held in Visby, Sweden, in May 2017. This study compares the numerical predictions of the wake flow behind a model wind turbine operated in yaw to experimental wind tunnel results. Prior to the workshop, research groups were invited to predict the turbine performance and wake flow properties using computational fluid dynamics (CFD) methods. For this purpose, the power, thrust, and yaw moments for a 30 degrees yawed model turbine, as well as the wake's mean and turbulent streamwise and vertical flow components, were measured in the wind tunnel at the Norwegian University of Science and Technology (NTNU). In order to increase the complexity, a non-yawed downstream turbine was added in a second test case, while a third test case challenged the modelers with a new rotor and turbine geometry. Four participants submitted predictions using different flow solvers, three of which were based on large eddy simulations (LES) while another one used an improved delayed detached eddy simulation (IDDES) model. The performance of a single yawed turbine was fairly well predicted by all simulations, both in the first and third test cases. The scatter in the downstream turbine performance predictions in the second test case, however, was found to be significantly larger. The complex asymmetric shape of the mean streamwise and vertical velocities was generally well predicted by all the simulations for all test cases. The largest improvement with respect to previous blind tests is the good prediction of the levels of TKE in the wake, even for the complex case of yaw misalignment. These very promising results confirm the mature development stage of LES/DES simulations for wind turbine wake modeling, while competitive advantages might be obtained by faster computational methods.

  • 210.
    Murail, Samuel
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Howard, Rebecca J.
    Trudell, James R.
    Bertaccini, Edward
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tracing the Closing of a Ligand-Gated Ion Channel in Atomic Detail: An Unconstrained Four-Microsecond Simulation of GLIC Leads to a Closed State Remarkably Similar to ELIC2012Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, nr 3, s. 113A-114AArtikkel i tidsskrift (Annet vitenskapelig)
  • 211.
    Murail, Samuel
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wallner, Björn
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Trudell, James R.
    Bertaccini, Edward
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Microsecond Simulations Indicate that Ethanol Binds between Subunits and Could Stabilize an Open-State Model of a Glycine Receptor2011Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, nr 7, s. 1642-1650Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cys-loop receptors constitute a superfamily of ion channels gated by ligands such as acetylcholine, serotonin, glycine, and gamma-aminobutyric acid. All of these receptors are thought to share structural characteristics, but due to high sequence variation and limited structure availability, our knowledge about allosteric binding sites is still limited. These sites are frequent targets of anesthetic and alcohol molecules, and are of high pharmacological importance. We used molecular simulations to study ethanol binding and equilibrium exchange for the homomeric alpha 1 glycine receptor (GlyR alpha 1), modeled on the structure of the Gloeobacter violaceus pentameric ligand-gated channel. Ethanol has a well-known potentiating effect and can be used in high concentrations. By performing two microsecond-scale simulations of GlyR with/without ethanol, we were able to observe spontaneous binding in cavities and equilibrium ligand exchange. Of interest, it appears that there are ethanol-binding sites both between and within the GlyR transmembrane subunits, with the intersubunit site having the highest occupancy and slowest exchange (similar to 200 ns). This model site involves several residues that were previously identified via mutations as being crucial for potentiation. Finally, ethanol appears to stabilize the GlyR model built on a presumably open form of the ligand-gated channel. This stabilization could help explain the effects of allosteric ligand binding in Cys-loop receptors.

  • 212.
    Nakane, Takanori
    et al.
    MRC Lab Mol Biol, Cambridge, England..
    Kimanius, Dari
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Scheres, Sjors H. W.
    MRC Lab Mol Biol, Cambridge, England..
    Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION2018Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 7, artikkel-id e36861Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.

  • 213.
    Narangifard, A.
    et al.
    KI, Dept Med, Solna MedS, Stockholm, Sweden.;ERCO Pharma AB, Sci Life Lab, Stockholm, Sweden..
    den Hollander, L.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Wennberg, Christian L.
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lundborg, M.
    ERCO Pharma AB, Sci Life Lab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Iwai, I.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Han, H.
    Max Planck Inst Mol Physiol, Syst Cell Biol, Dortmund, Germany..
    Masich, S.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Daneholt, B.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden..
    Norlen, L.
    Karolinska Inst, Dept Cell & Mol Biol CMB, SE-17177 Stockholm, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Stockholm, Sweden..
    Human skin barrier formation takes place via a cubic to lamellar lipid phase transition as analyzed by cryo-electron microscopy and EM-simulation2018Inngår i: Experimental Cell Research, ISSN 0014-4827, E-ISSN 1090-2422, Vol. 366, nr 2, s. 139-151Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The skin's permeability barrier consists of stacked lipid sheets of splayed ceramides, cholesterol and free fatty acids, positioned intercellularly in the stratum corneum. We report here on the early stage of skin barrier formation taking place inside the tubuloreticular system in the secretory cells of the topmost viable epidermis and in the intercellular space between viable epidermis and stratum corneum. The barrier formation process was analysed in situ in its near-native state, using cryo-EM combined with molecular dynamics modeling and EM simulation. Stacks of lamellae appear towards the periphery of the tubuloreticular system and they are closely associated with granular regions. Only models based on a bicontinuous cubic phase organization proved compatible with the granular cryo-EM patterns. Only models based on a dehydrated lamellar phase organization agreed with the lamellar cryo-EM patterns. The data support that human skin barrier formation takes place via a cubic to lamellar lipid phase transition.

  • 214. Nason, F.
    et al.
    Zhu, Lailai
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Dubini, G.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Numerical simulation of a deformable cell in microchannels2013Inngår i: Computational Methods for Coupled Problems in Science and Engineering V: A Conference Celebrating the 60th Birthday of Eugenio Onate, COUPLED PROBLEMS 2013, 2013, s. 685-695Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The main goal of this work is to numerically investigate the behavior of a cell flowing in a microfluidic system. In particular, we want to model flow-induced deformations of an isolated cell to quantitatively evaluate the cell response when subjected to a representative range of flow rates in a realistic geometry, with specific interest in the case of cell trapping. This research will help optimize operating conditions as well as the design of cell manipulation/culture micro-devices, so as to guarantee cell viability and ultimately improve high-throughput performance.

  • 215.
    Negi, Prabal
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Boundary layers over wing sections2017Licentiatavhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The understanding of developing boundary layers over wings is an important topic from the perspective of industrial applications. An increased understanding would be consequential not only for achieving higher fuel efficiency but also in the design of aircraft control strategies. With these aims in mind, the current work aims to further the understanding of developing boundary layer over wingsections. The study is performed with two particular perspectives in mind -unsteady aerodynamic effects in a pitching airfoil and turbulent boundary layerstructure in non-equilibrium boundary layers over a stationary airfoil.The boundary layer evolution in unsteady natural laminar flow airfoils undergoing small-amplitude pitch-oscillations is investigated. For high Reynolds numbers the origins of the non-linear unsteady aerodynamic response of laminar airfoils is explained on the basis of quasi-steady assumptions. Temporal nonlinearitiesin aerodynamic forces are shown to be inherently linked to thenon-linearities of static aerodynamic force coefficients and that a simple phaselagconcept can model the observed non-linear unsteady response. On the other hand at lower Reynolds numbers, when there exists an unstable leading edgelaminar separation bubble, the unsteady response is dynamically rich and changes in boundary layer characteristics can be abrupt. Such quasi-steadyphase-lag concepts are no longer appropriate to explain the unsteady flow physics in such a case. For the case of stationary airfoils, flow statistics for flow around an airfoil at two different Reynolds numbers are compared to assess Reynolds number effects in non-equilibrium flows. Pressure gradient effects found to be stronger at low Reynolds numbers, leading to higher energy in the larger structures present  in the outer part of the turbulent boundary layer.

  • 216.
    Negi, Prabal
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Dynamic response of laminar flow airfoils2017Rapport (Annet vitenskapelig)
  • 217.
    Negi, Prabal
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center, SeRC.
    A re-examination of filter-based stabilization for spectral-element methods2017Rapport (Annet vitenskapelig)
  • 218.
    Negi, Prabal Singh
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    LES of the unsteady response of a natural laminar flow airfoil2018Inngår i: 2018 Applied Aerodynamics Conference, American Institute of Aeronautics and Astronautics, 2018Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Large-eddy simulations are performed to investigate the dynamic response of a natural laminar flow airfoil undergoing harmonic pitch oscillations at a chord based Reynolds number of Rec= 750, 000. Large changes in the transition location are observed throughout the pitch cycles which leads to a non-linear response of the aerodynamic force coefficients. Preliminary results show that the evolution of the boundary layer over the airfoil can be modeled by using a simple phase-lag concept which implies that the boundary-layer evolution is quasi-steady in nature. A simple empirical model is developed based on this quasi-steady, phase-lag assumption which fits very well with the measured experimental data.

  • 219.
    Negi, Prabal Singh
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mishra, Maneesh
    Nanyang Technol Univ, Sch Mech & Aerosp Engn, Singapore 639798, Singapore..
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Skote, Martin
    Cranfield Univ, Sch Aerosp Transport & Mfg, Cranfield MK43 OAL, Beds, England..
    Bypass transition delay using oscillations of spanwise wall velocity2019Inngår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 4, nr 6, artikkel-id 063904Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Large eddy simulations are performed to investigate the possibility of bypass transition delay in spatially developing boundary layers. An open loop wall control mechanism is employed which consists of either spatial or temporal oscillations of the spanwise wall velocity. Both spatial and temporal oscillations show a delay in the sharp rise in skin friction coefficient which is characteristic of laminar-turbulent transition. An insight into the mechanism is offered based on a secondary filtering of the continuous Orr-Sommerfeld-Squire (OSQ) modes provided by the Stokes layer, and it is shown that the control mechanism selectively affects the low-frequency penetrating modes of the OSQ spectrum. This perspective clarifies the limitations of the mechanism's capability to create transition delay. Furthermore, we extend the two-mode model of bypass transition proposed by T. Zaki and P. Durbin [j Fluid Mech. 531, 85 (2005)] to cases with wall control and illustrate the selective action of the wall oscillations on the penetrating mode in this simplified case.

  • 220.
    Negi, Prabal Singh
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Unsteady aerodynamic effects in small-amplitude pitch oscillations of an airfoil2018Inngår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, s. 378-391Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    High-fidelity wall-resolved large-eddy simulations (LES) are utilized to investigate the flow-physics of small-amplitude pitch oscillations of an airfoil at Rec=100,000. The investigation of the unsteady phenomenon is done in the context of natural laminar flow airfoils, which can display sensitive dependence of the aerodynamic forces on the angle of attack in certain “off-design” conditions. The dynamic range of the pitch oscillations is chosen to be in this sensitive region. Large variations of the transition point on the suction-side of the airfoil are observed throughout the pitch cycle resulting in a dynamically rich flow response. Changes in the stability characteristics of a leading-edge laminar separation bubble has a dominating influence on the boundary layer dynamics and causes an abrupt change in the transition location over the airfoil. The LES procedure is based on a relaxation-term which models the dissipation of the smallest unresolved scales. The validation of the procedure is provided for channel flows and for a stationary wing at Rec=400,000.

  • 221.
    Negi, Prabal
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Philipp, Schlatter
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish e-Science Research Center (SeRC).
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Unsteady aerodynamic effects in small-amplitude pitch oscillations of an airfoilManuskript (preprint) (Annet vitenskapelig)
  • 222.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Abouali, Omid
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. School of Mechanical Engineering, Shiraz University.
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Heat transfer in laminar Couette flow laden with rigid spherical particles2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 834, s. 308-334Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study heat transfer in plane Couette flow laden with rigid spherical particles by means of direct numerical simulations. In the simulations we use a direct-forcing immersed boundary method to account for the dispersed phase together with a volume-of-fluid approach to solve the temperature field inside and outside the particles. We focus on the variation of the heat transfer with the particle Reynolds number, total volume fraction (number of particles) and the ratio between the particle and fluid thermal diffusivity, quantified in terms of an effective suspension diffusivity. We show that, when inertia at the particle scale is negligible, the heat transfer increases with respect to the unladen case following an empirical correlation recently proposed in the literature. In addition, an average composite diffusivity can be used to approximate the effective diffusivity of the suspension in the inertialess regime when varying the molecular diffusion in the two phases. At finite particle inertia, however, the heat transfer increase is significantly larger, smoothly saturating at higher volume fractions. By phase-ensemble-averaging we identify the different mechanisms contributing to the total heat transfer and show that the increase of the effective conductivity observed at finite inertia is due to the increase of the transport associated with fluid and particle velocity. We also show that the contribution of the heat conduction in the solid phase to the total wall-normal heat flux reduces when increasing the particle Reynolds number, so that particles of low thermal diffusivity weakly alter the total heat flux in the suspension at finite particle Reynolds numbers. On the other hand, a higher particle thermal diffusivity significantly increases the total heat transfer.

  • 223.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Asmar, L. A.
    Picano, F.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Numerical study of heat transfer in laminar and turbulent pipe flow with finite-size spherical particles2018Inngår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, s. 189-199Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Controlling heat and mass transfer in particulate suspensions has many applications in fuel combustion, food industry, pollution control and life science. We perform direct numerical simulations (DNS) to study the heat transfer within a suspension of neutrally buoyant, finite-size spherical particles in laminar and turbulent pipe flows, using the immersed boundary method (IBM) to account for the solid fluid interactions and a volume of fluid (VoF) method to resolve the temperature equation both inside and outside the particles. Particle volume fractions up to 40% are simulated for different pipe to particle diameter ratios. We show that a considerable heat transfer enhancement (up to 330%) can be achieved in the laminar regime by adding spherical particles. The heat transfer is observed to increase significantly as the pipe to particle diameter ratio decreases for the parameter range considered here. Larger particles are found to have a greater impact on the heat transfer enhancement than on the wall-drag increase. In the turbulent regime, however, only a transient increase in the heat transfer is observed and the process decelerates in time below the values in single-phase flows as high volume fractions of particles laminarize the core region of the pipe. A heat transfer enhancement, measured with respect to the single phase flow, is only achieved at volume fractions as low as 5% in a turbulent flow.

  • 224.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Turbulence modulation in channel flow of finite-size spheroidal particles2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 859, s. 887-901Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Finite-size particles modulate wall-bounded turbulence, leading, for the case of spherical particles, to increased drag also owing to the formation of a particle wall layer. Here, we study the effect of particle shape on the turbulence in suspensions of spheroidal particles at volume fraction phi = 10 % and show how the near-wall particle dynamics deeply changes with the particle aspect ratio and how this affects the global suspension behaviour. Direct numerical simulations are performed using a direct-forcing immersed boundary method to account for the dispersed phase, combined with a soft-sphere collision model and lubrication corrections for short-range particle-particle and particle-wall interactions. The turbulence reduces with the aspect ratio of oblate particles, leading to drag reduction with respect to the single-phase flow for particles with aspect ratio AR <= 1/3, when the significant reduction in Reynolds shear stress is more than the compensation by the additional stresses, induced by the solid phase. Oblate particles are found to avoid the region close to the wall, travelling parallel to it with small angular velocities, while preferentially sampling high-speed fluid in the wall region. Prolate particles also tend to orient parallel to the wall and avoid its vicinity. Their reluctance to rotate around the spanwise axis reduces the wall-normal velocity fluctuation of the flow and therefore the turbulence Reynolds stress, similar to oblates; however, they undergo rotations in wall-parallel planes which increase the additional solid stresses due to their relatively larger angular velocities compared to the oblates. These larger additional stresses compensate for the reduction in turbulence activity and lead to a wall drag similar to that of single-phase flows. Spheres on the other hand, form a layer close to the wall with large angular velocities in the spanwise direction, which increases the turbulence activity in addition to exerting the largest solid stresses on the suspension, in comparison to the other studied shapes. Spherical particles therefore increase the wall drag with respect to the single-phase flow.

  • 225.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Costa, Pedro
    Breugem, Wim Paul
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Drag reduction in turbulent channel flow laden with finite-size oblate spheroids2017Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 816, s. 43-70Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study suspensions of oblate rigid particles in a viscous fluid for different values of the particle volume fractions.Direct numerical simulations have been performed using a direct-forcing immersed boundary method to account for the dispersed phase, combined with a soft-sphere collision model and lubrication corrections for short-range particle-particle and particle-wall interactions. With respect to the single phase flow, we show that in flows laden with oblate spheroids the drag is reduced and the turbulent fluctuations attenuated.In particular, the turbulence activity decreases to lower values than those obtained by only accounting for the effective suspension viscosity.To explain the observed drag reduction we consider the particle dynamics and the interactions of the particles with the turbulent velocity field and show that the particle wall layer, previously observed and found to be responsible for the increased dissipation in suspensions of spheres, disappears in the case of oblate particles.These rotate significantly slower than spheres near the wall and tend to stay with their major axes parallel to the wall, which leads to a decrease of the Reynolds stresses and turbulence production and so to the overall drag reduction.

  • 226.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rosti, Marco E.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Turbulent  flow of finite-size spherical particles with viscous hyper-elastic walls2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Annet vitenskapelig)
  • 227.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rosti, Marco Edoardo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Turbulent flow of finite-size spherical particles in channels with viscous hyper-elastic walls2019Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 873, s. 410-440, artikkel-id PII S0022112019004130Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study single-phase and particle-laden turbulent channel flows bounded by two incompressible hyper-elastic walls with different deformability at bulk Reynolds number $5600$ . The solid volume fraction of finite-size neutrally buoyant rigid spherical particles considered is $10\,\%$ . The elastic walls are assumed to be of a neo-Hookean material. A fully Eulerian formulation is employed to model the elastic walls together with a direct-forcing immersed boundary method for the coupling between the fluid and the particles. The data show a significant drag increase and the enhancement of the turbulence activity with growing wall elasticity for both the single-phase and particle-laden flows when compared with the single-phase flow over rigid walls. Drag reduction and turbulence attenuation is obtained, on the other hand, with highly elastic walls when comparing the particle-laden flow with the single-phase flow for the same wall properties; the opposite effect, drag increase, is observed upon adding particles to the flow over less elastic walls. This is explained by investigating the near-wall turbulence, where the strong asymmetry in the magnitude of the wall-normal velocity fluctuations (favouring positive $v<^>{\prime }$ ), is found to push the particles towards the channel centre. The particle layer close to the wall contributes to turbulence production by increasing the wall-normal velocity fluctuations, so that in the absence of this layer, smaller wall deformations and in turn turbulence attenuation is observed. For a moderate wall elasticity, we increase the particle volume fraction up to $20\,\%$ and find that particle migration away from the wall is the cause of turbulence attenuation with respect to the flow over rigid walls. However, for this higher volume fractions, the particle induced stress compensates for the decreasing Reynolds shear stress, resulting in a higher overall drag for the case with elastic walls. The effect of the wall elasticity on the overall drag reduces significantly with increasing particle volume fraction.

  • 228.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Karp-Boss, Lee
    School of Marine Sciences, University of Maine.
    Bearon, Rachel
    Department of Mathematical Sciences, University of Liverpool.
    Variano, Evan
    Department of Civil and Environmental Engineering, University of California.
    Sedimentation of inertia-less prolate spheroids in homogenous isotropic turbulence with application to non-motile phytoplankton2017Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 831, s. 655-674Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Phytoplankton are the foundation of aquatic food webs. Through photosynthesis, phytoplankton draw down $CO_2$ at magnitudes equivalent to forests and other terrestrial plants and convert it to organic material that is then consumed by other organisms of phytoplankton in higher trophic levels. Mechanisms that affect local concentrations and velocities are of primary significance to many encounter-based processes in the plankton including prey-predator interactions, fertilization and aggregate formation. We report results from simulations of sinking phytoplankton, considered as elongated spheroids, in homogenous isotropic turbulence to answer the question of whether trajectories and velocities of sinking phytoplankton are altered by turbulence. We show in particular that settling spheroids with physical characteristics similar to those of diatoms weakly cluster and preferentially sample regions of down-welling flow, corresponding to an increase of the mean settling speed with respect to the mean settling speed in quiescent fluid.  We explain how different parameters can affect the settling speed and what underlying mechanisms might be involved.  Interestingly, we observe that the increase in the aspect ratio of the prolate spheroids can affect the clustering and the average settling speed of particles by two mechanisms: first is the effect of aspect ratio on the rotation rate of the particles, which saturates faster than the second mechanism of increasing drag anisotropy.   

  • 229. Nogueira, P. A. S.
    et al.
    Cavalieri, A. V. G.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Resolvent-based control of streaks in boundary layers2018Inngår i: 31st Congress of the International Council of the Aeronautical Sciences, ICAS 2018, International Council of the Aeronautical Sciences , 2018Konferansepaper (Fagfellevurdert)
    Abstract [en]

    In the present work, we investigate efficient placement of sensors and actuators for closed-loop control of boundary-layer flows. The focus of this work is on the transitional flow cases where perturbation field is dominated by streaks. This is done using a reduced-order model based on resolvent analysis, an approach that also allows us to analyse the sensitivity of the flow response to control. A numerical sensitivity analysis was performed in this first approach, leading to conclusions about best choices of velocity components to be sensed and directions to be forced. Afterwards, we compared the performance between gaussian and shear sensors at the wall, focusing on the damping of the first resolvent gain using these devices. We close the work with the analysis of a plasma actuator, a configuration closer to standard choices for this kind of problem in both simulations and experiments. 

  • 230.
    Noorani, Azad
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Particle dispersion in turbulent curved pipe flowManuskript (preprint) (Annet vitenskapelig)
  • 231.
    Noorani, Azad
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Particle transport in turbulent curved pipe flow2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 793, s. 248-279Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Direct numerical simulations (DNS) of particle-laden turbulent flow in straight, mildly curved and strongly bent pipes are performed in which the solid phase is modelled as small heavy spherical particles. A total of seven populations of dilute particles with different Stokes numbers, one-way coupled with their carrier phase, are simulated. The objective is to examine the effect of the curvature on micro-particle transport and accumulation. It is shown that even a slight non-zero curvature in the flow configuration strongly impact the particle concentration map such that the concentration of inertial particles with hulk Stokes number 0.45 (based on hulk velocity and pipe radius) at the inner bend wall of mildly curved pipe becomes 12.8 times larger than that in the viscous sublayer of the straight pipe. Near-wall helicoidal particle streaks are observed in the curved configurations with their inclination varying with the strength of the secondary motion of the carrier phase. A reflection layer, as previously observed in particle laden turbulent S-shaped channels, is also apparent in the strongly curved pipe with heavy particles. In addition, depending on the curvature, the central regions of the mean Dean vortices appear to he completely depleted of particles, as observed also in the partially relaminarised region at the inner bend. The turbophoretic drift of the particles is shown to he affected by weak and strong secondary motions of the carrier phase and geometry-induced centrifugal forces. The first- and second-order moments of the velocity and acceleration of the particulate phase in the same configurations are addressed in a companion paper by the same authors. The current data set will be useful for modelling particles advected in wall-bounded turbulent flows where the effects of the curvature are not negligible.

  • 232.
    Noorani, Azad
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sardina, Gaetano
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Particle Velocity and Acceleration in Turbulent Bent Pipe Flows2015Inngår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 95, nr 2-3, s. 539-559Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the dynamics of dilute micro-size inertial particles in turbulent curved pipe flows of different curvature by means of direct numerical simulations with one-way coupled Lagrangian particle tracking. The focus of this work is on the first and second order moments of the velocity and acceleration of the particulate phase, relevant statistics for any modelling effort, whereas the particle distribution is analysed in a previous companion paper. The aim is to understand the role of the cross-stream secondary motions (Dean vortices) on the particle dynamics. We identify the mean Dean vortices associated to the motion of the particles and show that these are moved towards the side-walls and, interestingly, more intense than those of the mean flow. Analysis of the streamwise particle flux reveals a substantial increase due to the secondary motions that brings particles towards the pipe core while moving them towards the outer bend. The in-plane particle flux, most intense in the flow viscous sub-layer along the side walls, increases with particle inertia and pipe curvature. The particle reflections at the outer bend, previously observed also in other strongly curved configurations, locally alter the particle axial and wall-normal velocity and increase turbulent kinetic energy.

  • 233.
    Noorani, Azad
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Evidence of sublaminar drag naturally occurring in a curved pipe2015Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 27, nr 3, artikkel-id 035105Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Steady and unsteady flows in a mildly curved pipe for a wide range of Reynolds numbers are examined with direct numerical simulation. It is shown that in a range of Reynolds numbers in the vicinity of Re-b approximate to 3400, based on bulk velocity and pipe diameter, a marginally turbulent flow is established in which the friction drag naturally reduces below the laminar solution at the same Reynolds number. The obtained values for friction drag for the laminar and turbulent (sublaminar) flows turn out to be in excellent agreement with experimental measurements in the literature. Our results are also in agreement with Fukagata et al. ["On the lower bound of net driving power in controlled duct flows," Phys. D 238, 1082 (2009)], as the lower bound of net power required to drive the flow, i.e., the pressure drop of the Stokes solution, is still lower than our marginally turbulent flow. A large-scale traveling structure that is thought to be responsible for that behaviour is identified in the instantaneous field. This mode could also be extracted using proper orthogonal decomposition. The effect of this mode is to redistribute the mean flow in the circular cross section which leads to lower gradients at the wall compared to the laminar flow.

  • 234.
    Noorani, Azad
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Swirl-switching phenomenon in turbulent flow through toroidal pipes2015Inngår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Direct numerical simulations (DNS) are performed to investigate turbulent flows in toroidal pipes with mild and strong curvature. By means of proper orthogonal decomposition (POD), dominant structures in the flow field are identified. The most energetic structures in the strongly curved pipes (κ = 0.1 and κ = 0.3) are very similar in both configurations studied here. These modes (shape and frequency) also match the coherent structures responsible for swirl switching phenomenon found earlier in experimental and numerical studies of turbulent flow in spatially developing 90° bends with which the current results are compared. The observed swirl switching in toroidal pipes, which is isolated from any upstream and separation conditions, may challenge the current hyphothesis regarding the origin of swirl switching mechanism.

  • 235. Nowbahar, Arash
    et al.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Turbophoresis attenuation in a turbulent channel flow with polymer additives2013Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 732, s. 706-719Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Turbophoresis occurs in wall-bounded turbulent flows where it induces a preferential accumulation of inertial particles towards the wall and is related to the spatial gradients of the turbulent velocity fluctuations. In this work, we address the effects of drag-reducing polymer additives on turbophoresis in a channel flow. The analysis is based on data from a direct numerical simulation of the turbulent flow of a viscoelastic fluid modelled with the FENE-P closure and laden with particles of different inertia. We show that polymer additives decrease the particle preferential wall accumulation and demonstrate with an analytical model that the turbophoretic drift is reduced because the wall-normal variation of the wall-normal fluid velocity fluctuations decreases. As this is a typical feature of drag reduction in turbulent flows, an attenuation of turbophoresis and a corresponding increase in the particle streamwise flux are expected to be observed in all of these flows, e. g. fibre or bubble suspensions and magnetohydrodynamics.

  • 236. Nyblom, Maria
    et al.
    Poulsen, Hanne
    Gourdon, Pontus
    Reinhard, Linda
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Fedosova, Natalya
    Nissen, Poul
    Crystal Structure of Na+, K+-ATPase in the Na+-Bound State2013Inngår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, nr 6154, s. 123-127Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Na+, K+-adenosine triphosphatase (ATPase) maintains the electrochemical gradients of Na+ and K+ across the plasma membrane-a prerequisite for electrical excitability and secondary transport. Hitherto, structural information has been limited to K+-bound or ouabain-blocked forms. We present the crystal structure of a Na+-bound Na+, K+-ATPase as determined at 4.3 angstrom resolution. Compared with the K+-bound form, large conformational changes are observed in the a subunit whereas the beta and gamma subunit structures are maintained. The locations of the three Na+ sites are indicated with the unique site III at the recently suggested IIIb, as further supported by electrophysiological studies on leak currents. Extracellular release of the third Na+ from IIIb through IIIa, followed by exchange of Na+ for K+ at sites I and II, is suggested.

  • 237.
    Offermans, Nicolas
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Marin, O.
    Schanen, M.
    Gong, Jing
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fischer, P.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    On the strong scaling of the spectral element solver Nek5000 on petascale systems2016Inngår i: Proceedings of the 2016 Exascale Applications and Software Conference (EASC2016): April 25-29 2016, Stockholm, Sweden, Association for Computing Machinery (ACM), 2016, artikkel-id a5Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The present work is targeted at performing a strong scaling study of the high-order spectral element uid dynamics solver Nek5000. Prior studies such as [5] indicated a recommendable metric for strong scalability from a theoretical viewpoint, which we test here extensively on three parallel machines with different performance characteristics and interconnect networks, namely Mira (IBM Blue Gene/Q), Beskow (Cray XC40) and Titan (Cray XK7). The test cases considered for the simulations correspond to a turbulent ow in a straight pipe at four different friction Reynolds numbers Reτ = 180, 360, 550 and 1000. Considering the linear model for parallel communication we quantify the machine characteristics in order to better assess the scaling behaviors of the code. Subsequently sampling and profiling tools are used to measure the computation and communication times over a large range of compute cores. We also study the effect of the two coarse grid solvers XXT and AMG on the computational time. Super-linear scaling due to a reduction in cache misses is observed on each computer. The strong scaling limit is attained for roughly 5000 - 10; 000 degrees of freedom per core on Mira, 30; 000 - 50; 0000 on Beskow, with only a small impact of the problem size for both machines, and ranges between 10; 000 and 220; 000 depending on the problem size on Titan. This work aims at being a reference for Nek5000 users and also serves as a basis for potential issues to address as the community heads towards exascale supercomputers.

  • 238. Olivieri, S.
    et al.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Iudicone, D.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    The effect of the Basset history force on particle clustering in homogeneous and isotropic turbulence2014Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 26, nr 4, s. 041704-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the effect of the Basset history force on the dynamics of small particles transported in homogeneous and isotropic turbulence and show that this term, often neglected in previous numerical studies, reduces the small-scale clustering typical of inertial particles. The contribution of this force to the total particle acceleration is, on average, responsible for about 10% of the total acceleration and particularly relevant during rare strong events. At moderate density ratios, i.e., sand or metal powder in water, its presence alters the balance of forces determining the particle acceleration.

  • 239.
    Otero, Evelyn
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg.
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Min, Misun
    Argonne National Laboratory.
    Fischer, Paul
    Argonne National Laboratory.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Laure, Erwin
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    OpenACC accelerator for the Pn-Pn-2 algorithm in Nek50002018Inngår i: Proceedings of the 5th International Conference on Exascale Applications and Software, 2018Konferansepaper (Fagfellevurdert)
  • 240.
    Otero, Evelyn
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg, Aerodynamik. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Marin, Oana
    Argonne Natl Lab, MCS, Lemont, IL 60439 USA..
    Laure, Erwin
    PDC KTH, Ctr High Performance Comp, SE-10044 Stockholm, Sweden..
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Lossy Data Compression Effects on Wall-bounded Turbulence: Bounds on Data Reduction2018Inngår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 101, nr 2, s. 365-387Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Postprocessing and storage of large data sets represent one of the main computational bottlenecks in computational fluid dynamics. We assume that the accuracy necessary for computation is higher than needed for postprocessing. Therefore, in the current work we assess thresholds for data reduction as required by the most common data analysis tools used in the study of fluid flow phenomena, specifically wall-bounded turbulence. These thresholds are imposed a priori by the user in L (2)-norm, and we assess a set of parameters to identify the minimum accuracy requirements. The method considered in the present work is the discrete Legendre transform (DLT), which we evaluate in the computation of turbulence statistics, spectral analysis and resilience for cases highly-sensitive to the initial conditions. Maximum acceptable compression ratios of the original data have been found to be around 97%, depending on the application purpose. The new method outperforms downsampling, as well as the previously explored data truncation method based on discrete Chebyshev transform (DCT).

  • 241. Otten, Matthew
    et al.
    Gong, Jing
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mametjanov, Azamat
    Vose, Aaron
    Levesque, John
    Fischer, Paul
    Min, Misun
    An MPI/OpenACC implementation of a high-order electromagnetics solver with GPUDirect communication2016Inngår i: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, nr 3, s. 320-334Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present performance results and an analysis of a message passing interface (MPI)/OpenACC implementation of an electromagnetic solver based on a spectral-element discontinuous Galerkin discretization of the time-dependent Maxwell equations. The OpenACC implementation covers all solution routines, including a highly tuned element-by-element operator evaluation and a GPUDirect gather-scatter kernel to effect nearest neighbor flux exchanges. Modifications are designed to make effective use of vectorization, streaming, and data management. Performance results using up to 16,384 graphics processing units of the Cray XK7 supercomputer Titan show more than 2.5x speedup over central processing unit-only performance on the same number of nodes (262,144 MPI ranks) for problem sizes of up to 6.9 billion grid points. We discuss performance-enhancement strategies and the overall potential of GPU-based computing for this class of problems.

  • 242. Ottosson, Nina E.
    et al.
    Ejneby, Malin Silvera
    Wu, Xiongyu
    Yazdi, Samira
    Konradsson, Peter
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Elinder, Fredrik
    A drug pocket at the lipid bilayer-potassium channel interface2017Inngår i: Science Advances, ISSN 0036-8156, E-ISSN 2375-2548, Vol. 3, nr 10, artikkel-id e1701099Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Many pharmaceutical drugs against neurological and cardiovascular disorders exert their therapeutic effects by binding to specific sites on voltage-gated ion channels of neurons or cardiomyocytes. To date, all molecules targeting known ion channel sites bind to protein pockets that are mainly surrounded by water. We describe a lipid-protein drug-binding pocket of a potassium channel. We synthesized and electrophysiologically tested 125 derivatives, analogs, and related compounds to dehydroabietic acid. Functional data in combination with docking and molecular dynamics simulations mapped a binding site for small-molecule compounds at the interface between the lipid bilayer and the transmembrane segments S3 and S4 of the voltage-sensor domain. This fundamentally new binding site for small-molecule compounds paves the way for the design of new types of drugs against diseases caused by altered excitability.

  • 243.
    Pan, Fan
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Chico, Jonathan
    Delin, Anna
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. Uppsala Univ, Sweden.
    Bergman, Anders
    Bergqvist, Lars
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Extended spin model in atomistic simulations of alloys2017Inngår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, nr 18, artikkel-id 184432Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An extended atomistic spin model allowing for studies of the finite-temperature magnetic properties of alloys is proposed. The model is obtained by extending the Heisenberg Hamiltonian via a parametrization from a first-principles basis, interpolating from both the low-temperature ferromagnetic and the high-temperature paramagnetic reference states. This allows us to treat magnetic systems with varying degree of itinerant character within the model. Satisfactory agreement with both previous theoretical studies and experiments are obtained in terms of Curie temperatures and paramagnetic properties. The proposed model is not restricted to elements but is also applied to binary alloys, such as the technologically important material permalloy, where significant differences in the finite magnetic properties of Fe and Ni magnetic moments are found. The proposed model strives to find the right compromise between accuracy and computational feasibility for accurate modeling, even for complex magnetic alloys and compounds.

  • 244.
    Pan, Fan
    et al.
    KTH, Skolan för teknikvetenskap (SCI). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Chico, Jonathan
    Delin, Anna
    Bergman, Anders
    Bergqvist, Lars
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Tidigare Institutioner, Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Finite temperature properties of transition metal alloys using extended spin modelManuskript (preprint) (Annet vitenskapelig)
  • 245.
    Pan, Fan
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Chico, Jonathan
    Hellsvik, Johan
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Bergman, Anders
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Systematic study of magnetodynamic properties at finite temperatures in doped permalloy from first-principles calculations2016Inngår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 94, nr 21, artikkel-id 214410Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By means of first-principles calculations, we have systematically investigated how the magnetodynamic properties Gilbert damping, magnetization, and exchange stiffness are affected when permalloy (Py) (Fe0.19Ni0.81) is doped with 4d or 5d transition metal impurities. We find that the trends in the Gilbert damping can be understood from relatively few basic parameters such as the density of states at the Fermi level, the spin-orbit coupling, and the impurity concentration. The temperature dependence of the Gilbert damping is found to be very weak which we relate to the lack of intraband transitions in alloys. Doping with 4d elements has no major impact on the studied Gilbert damping, apart from diluting the host. However, the 5d elements have a profound effect on the damping and allow it to be tuned over a large interval while maintaining the magnetization and exchange stiffness. As regards the spin stiffness, doping with early transition metals results in considerable softening, whereas late transition metals have a minor impact. Our result agree well with earlier calculations where available. In comparison to experiments, the computed Gilbert damping appears slightly underestimated, whereas the spin stiffness shows a general good agreement.

  • 246.
    Pan, Fan
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. Department of Physics and Astronomy,Uppsala University.
    Bergman, Anders
    Bergqvist, Lars
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Magnon properties of random alloysManuskript (preprint) (Annet vitenskapelig)
  • 247. Panda, S. K.
    et al.
    Bhowal, S.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Eriksson, O.
    Dasgupta, I.
    Effect of spin orbit coupling and Hubbard U on the electronic structure of IrO22014Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, nr 15, s. 155102-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have studied in detail the electronic structure of IrO2 including spin orbit coupling (SOC) and electronelectron interaction, both within the generalized gradient approximation plus Hubbard U (GGA+ U) and GGA plus dynamical mean field theory (GGA+ DMFT) approximations. Our calculations reveal that the Ir t(2g) states at the Fermi level largely retain the J(eff) = 1/2 character, suggesting that this complex spin orbit entangled state may be robust even in metallic IrO2. We have calculated the phase diagram for the ground state of IrO2 as a function of U and find a metal insulator transition that coincides with a magnetic phase change, where the effect of SOC is only to reduce the critical values of U necessary for the transition. We also find that dynamic correlations, as given by the GGA+ DMFT calculations, tend to suppress the spin- splitting, yielding a Pauli paramagnetic metal for moderate values of the Hubbard U. Our calculated optical spectra and photoemission spectra including SOC are in good agreement with experiment, demonstrating the importance of SOC in IrO2.

  • 248. Panda, S. K.
    et al.
    Di Marco, I.
    Delin, Anna
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Eriksson, O.
    Correlated electronic structure of CeN2016Inngår i: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 208, s. 111-115Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have studied in detail the electronic structure of CeN including spin orbit coupling (SOC) and electron electron interaction, within the dynamical mean-field theory combined with density-functional theory in generalized gradient approximation (GGA+DMFT). The effective impurity problem has been solved through the spin-polarized T-matrix fluctuation-exchange (SPTF) solver and the Hubbard I approximation (HIA). The calculated l-projected atomic partial densities of states and the converged potential were used to obtain the X-ray-photoemission-spectra (XPS) and Bremstrahlung Isochromat spectra (BIS). Following the spirit of Gunnarsson-Schonhammer model, we have coupled the SPTF and HIA 4f spectral functions to explain the various spectroscopic manifestations of CeN. Our computed spectra in such a coupled scheme explain the experimental data remarkably well, establishing the validity of our theoretical model in analyzing the electronic structure of CeN. The contribution of the various l-states in the total spectra and the importance of cross sections are also analyzed in detail.

  • 249. Panda, S. K.
    et al.
    Pal, Banabir
    Mandal, Suman
    Gorgoi, Mihaela
    Das, Shyamashis
    Sarkar, Indranil
    Drube, Wolfgang
    Sun, Weiwei
    Di Marco, I.
    Lindblad, Andreas
    Thunstroem, P.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Karis, Olof
    Kvashnin, Y. O.
    van Schilfgaarde, M.
    Eriksson, O.
    Sarma, D. D.
    High photon energy spectroscopy of NiO: Experiment and theory2016Inngår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, nr 23, artikkel-id 235138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have revisited the valence band electronic structure of NiO by means of hard x-ray photoemission spectroscopy (HAXPES) together with theoretical calculations using both the GW method and the local density approximation + dynamical mean-field theory (LDA+DMFT) approaches. The effective impurity problem in DMFT is solved through the exact diagonalization (ED) method. We show that the LDA+DMFT method in conjunction with the standard fully localized limit (FLL) and around mean field (AMF) double-counting alone cannot explain all the observed structures in the HAXPES spectra. GW corrections are required for the O bands and Ni-s and p derived states to properly position their binding energies. Our results establish that a combination of the GW and DMFT methods is necessary for correctly describing the electronic structure of NiO in a proper ab initio framework. We also demonstrate that the inclusion of photoionization cross section is crucial to interpret the HAXPES spectra of NiO. We argue that our conclusions are general and that the here suggested approach is appropriate for any complex transition metal oxide.

  • 250. Panda, S. K.
    et al.
    Thunstrom, P.
    Di Marco, I.
    Schott, J.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Dasgupta, I.
    Eriksson, O.
    Sarma, D. D.
    A charge self-consistent LDA plus DMFT study of the spectral properties of hexagonal NiS2014Inngår i: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 16, s. 093049-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electronic structure and spectral properties of hexagonal NiS have been studied in the high temperature paramagnetic phase and low temperature anti-ferromagnetic phase. The calculations have been performed using charge self-consistent density-functional theory in local density approximation combined with dynamical mean-field theory (LDA+DMFT). The photoemission spectra (PES) and optical properties have been computed and compared with the experimental data. Our results show that the dynamical correlation effects are important to understand the spectral and optical properties of NiS. These effects have been analyzed in detail by means of the computed real and imaginary part of the self-energy.

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