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  • 151.
    Heusser, Stephanie A.
    et al.
    SciLifeLab, Solna, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Yoluk, Ozge
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 433A-433AArtikel i tidskrift (Övrigt vetenskapligt)
  • 152. Heusser, Stephanie
    et al.
    Yoluk, Özge
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Klement, Goran
    Reiderer, Erika
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Howard, Rebecca
    Functional Characterization of Neurotransmitter Activation and Modulation in a Nematode Model Ligand-gated Ion Channel2016Ingår i: Journal of Neurochemistry, ISSN 0022-3042, E-ISSN 1471-4159, Vol. 138, nr 2, s. 243-253Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The superfamily of pentameric ligand-gated ion channels includes neurotransmitter receptors that mediate fast synaptic transmission in vertebrates, and are targets for drugs including alcohols, anesthetics, benzodiazepines and anticonvulsants. However, the mechanisms of ion channel opening, gating and modulation in these receptors leave many open questions, despite their pharmacological importance. Subtle conformational changes in both the extracellular and transmembrane domains are likely to influence channel opening, but have been difficult to characterize given the limited structural data available for human membrane proteins. Recent crystal structures of a modifiedCaenorhabditis elegans glutamate-gated chloride channel (GluCl) in multiple states offer an appealing model system for structure-function studies. However, the pharmacology of the crystallographic GluCl construct is not well established. To establish the functional relevance of this system, we used two-electrode voltage-clamp electrophysiology in Xenopus oocytes to characterize activation of crystallographic and native-like GluCl constructs by L-glutamate and ivermectin. We also tested modulation by ethanol and other anesthetic agents, and used site-directed mutagenesis to explore the role of a region of Loop F which was implicated in ligand gating by molecular dynamics simulations. Our findings indicate that the crystallographic construct functionally models concentration-dependent agonism and allosteric modulation of pharmacologically relevant receptors. Specific substitutions at residue Leu174 in loop F altered direct L-glutamate activation, consistent with computational evidence for this region's role in ligand binding. These insights demonstrate conservation of activation and modulation properties in this receptor family, and establish a framework for GluCl as a model system, including new possibilities for drug discovery.

  • 153.
    Holmgaard List, Nanna
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Knoops, Jeremie
    Rubio-Magnieto, Jenifer
    Ide, Julien
    Beljonne, David
    Norman, Patrick
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Surin, Mathieu
    Linares, Mathieu
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder2017Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, nr 42, s. 14947-14953Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI-DNA interactions.

  • 154.
    Hosseini, Seyed M.
    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.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Swedish Defense Research Agency, FOI, Sweden.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Direct numerical simulation of the flow around a wing section at moderate Reynolds number2016Ingår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 61, s. 117-128Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Abstract A three-dimensional direct numerical simulation has been performed to study the turbulent flow around the asymmetric NACA4412 wing section at a moderate chord Reynolds number of R e c = 400 , 000 , with an angle of attack of A o A = 5 ∘ . The mesh was optimized to properly resolve all relevant scales in the flow, and comprises around 3.2 billion grid points. The incompressible spectral-element Navier–Stokes solver Nek5000 was used to carry out the simulation. An unsteady volume force is used to trip the flow to turbulence on both sides of the wing at 10% of the chord. Full turbulence statistics are computed in addition to collection of time history data in selected regions. The Reynolds numbers on the suction side reach Reτ ≃ 373 and R e Ξ = 2 , 800 with the pressure-gradient parameter ranging from β ≈ 0.0 to β ≈ 85. Similarly, on the pressure side, the Reynolds numbers reach Reτ ≈ 346 and R e Ξ = 818 while β changes from β ≈ 0.0 to β ≈ − 0.25 . The effect of adverse pressure gradients on the mean flow is consistent with previous observations, namely a steeper incipient log law, a more prominent wake region and a lower friction. The turbulence kinetic energy profiles show a progressively larger inner peak for increasing pressure gradient, as well as the emergence and development of an outer peak with stronger APGs. The present simulation shows the potential of high-order (spectral) methods in simulating complex external flows at moderately high Reynolds numbers.

  • 155.
    Howard, Rebecca J.
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Zhuang, Yuxuan
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Heusser, Stephanie A.
    Univ Copenhagen, Dept Drug Design & Pharmacol, Copenhagen, Denmark..
    Bergh, Cathrine
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH Royal Inst Tech, Appl Phys, Stockholm, Sweden..
    Rovsnik, Urska
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Orellana, Laura
    Stockholm Univ, Dept Biochem & Biophys, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Tidigare Institutioner (före 2005), Fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH Royal Inst Tech, Appl Phys, Stockholm, Sweden..
    Allosteric Gating Determinants in the Transmembrane Domain of Pentameric Ligand-Gated Ion Channels2020Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 118, nr 3, s. 584A-584AArtikel i tidskrift (Övrigt vetenskapligt)
  • 156.
    Hufnagel, Lorenz
    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.
    Canton, Jacopo
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Marin, Oana
    Merzari, Elia
    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.
    The three-dimensional structure of swirl-switching in bent pipe flow2017Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 835, s. 86-101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Swirl-switching is a low-frequency oscillatory phenomenon which affects the Dean vortices in bent pipes and may cause fatigue in piping systems. Despite thirty years worth of research, the mechanism that causes these oscillations and the frequencies that characterise them remain unclear. Here we show that a three-dimensional wave-like structure is responsible for the low-frequency switching of the dominant Dean vortex. The present study, performed via direct numerical simulation, focuses on the turbulent flow through a 90 degrees pipe bend preceded and followed by straight pipe segments. A pipe with curvature 0.3 (defined as ratio between pipe radius and bend radius) is studied for a bulk Reynolds number Re = 11 700, corresponding to a friction Reynolds number Re-tau approximate to 360. Synthetic turbulence is generated at the inflow section and used instead of the classical recycling method in order to avoid the interference between recycling and swirl-switching frequencies. The flow field is analysed by three-dimensional proper orthogonal decomposition (POD) which for the first time allows the identification of the source of swirl-switching: a wave-like structure that originates in the pipe bend. Contrary to some previous studies, the flow in the upstream pipe does not show any direct influence on the swirl-switching modes. Our analysis further shows that a three-dimensional characterisation of the modes is crucial to understand the mechanism, and that reconstructions based on two-dimensional POD modes are incomplete.

  • 157.
    Huttmann, Felix
    et al.
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Rothenbach, Nico
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Kraus, Stefan
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Ollefs, Katharina
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Arruda, Lucas M.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Bernien, Matthias
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Thonig, Danny
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden..
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fransson, Jonas
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden..
    Kummer, Kurt
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS40220, F-38043 Grenoble 9, France..
    Brookes, Nicholas B.
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS40220, F-38043 Grenoble 9, France..
    Eriksson, Olle
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden.;Orebro Univ, Sch Sci & Technol, SE-70182 Orebro, Sweden..
    Kuch, Wolfgang
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Michely, Thomas
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Wende, Heiko
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Europium Cyclooctatetraene Nanowire Carpets: A Low-Dimensional, Organometallic, and Ferromagnetic Insulator2019Ingår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, nr 5, s. 911-917Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We investigate the magnetic and electronic properties of europium cyclooctatetraene (EuCot) nanowires by means of low-temperature X-ray magnetic circular dichroism (XMCD) and scanning tunneling microscopy (STM) and spectroscopy (STS). The EuCot nanowires are prepared in situ on a graphene surface. STS measurements identify EuCot as an insulator with a minority band gap of 2.3 eV. By means of Eu M-5,M-4 edge XMCD, orbital and spin magnetic moments of (-0.1 +/- 0.3)mu(B) and (+7.0 +/- 0.6)mu(B), respectively, were determined. Field-dependent measurements of the XMCD signal at the Eu M-5 edge show hysteresis for grazing X-ray incidence at 5 K, thus confirming EuCot as a ferromagnetic material. Our density functional theory calculations reproduce the experimentally observed minority band gap. Modeling the experimental results theoretically, we find that the effective interatomic exchange interaction between Eu atoms is on the order of millielectronvolts, that magnetocrystalline anisotropy energy is roughly half as big, and that dipolar energy is approximately ten times lower.

  • 158.
    Häggblad, Jon
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk analys, NA (stängd 2012-06-30).
    Runborg, Olof
    KTH, Skolan för datavetenskap och kommunikation (CSC), Numerisk analys, NA (stängd 2012-06-30). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Accuracy of staircase approximations in finite-difference methods for wave propagation2014Ingår i: Numerische Mathematik, ISSN 0029-599X, E-ISSN 0945-3245, Vol. 128, nr 4, s. 741-771Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    While a number of increasingly sophisticated numerical methods have been developed for time-dependent problems in electromagnetics, the Yee scheme is still widely used in the applied fields, mainly due to its simplicity and computational efficiency. A fundamental drawback of the method is the use of staircase boundary approximations, giving inconsistent results. Usually experience of numerical experiments provides guidance of the impact of these errors on the final simulation result. In this paper, we derive exact discrete solutions to the Yee scheme close to the staircase approximated boundary, enabling a detailed theoretical study of the amplitude, phase and frequency errors created. Furthermore, we show how evanescent waves of amplitude occur along the boundary. These characterize the inconsistencies observed in electromagnetic simulations and the locality of the waves explain why, in practice, the Yee scheme works as well as it does. The analysis is supported by detailed proofs and numerical examples.

  • 159.
    Ivanov, Ilya
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Akhmetova, Dana
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Peng, Ivy Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Machado, Rui
    Rahn, Mirko
    Bartsch, Valeria
    Hart, Alistair
    Fischer, Paul
    Evaluation of Parallel Communication Models in Nekbone, a Nek5000 mini-application2015Ingår i: 2015 IEEE International Conference on Cluster Computing, IEEE , 2015, s. 760-767Konferensbidrag (Refereegranskat)
    Abstract [en]

    Nekbone is a proxy application of Nek5000, a scalable Computational Fluid Dynamics (CFD) code used for modelling incompressible flows. The Nekbone mini-application is used by several international co-design centers to explore new concepts in computer science and to evaluate their performance. We present the design and implementation of a new communication kernel in the Nekbone mini-application with the goal of studying the performance of different parallel communication models. First, a new MPI blocking communication kernel has been developed to solve Nekbone problems in a three-dimensional Cartesian mesh and process topology. The new MPI implementation delivers a 13% performance improvement compared to the original implementation. The new MPI communication kernel consists of approximately 500 lines of code against the original 7,000 lines of code, allowing experimentation with new approaches in Nekbone parallel communication. Second, the MPI blocking communication in the new kernel was changed to the MPI non-blocking communication. Third, we developed a new Partitioned Global Address Space (PGAS) communication kernel, based on the GPI-2 library. This approach reduces the synchronization among neighbor processes and is on average 3% faster than the new MPI-based, non-blocking, approach. In our tests on 8,192 processes, the GPI-2 communication kernel is 3% faster than the new MPI non-blocking communication kernel. In addition, we have used the OpenMP in all the versions of the new communication kernel. Finally, we highlight the future steps for using the new communication kernel in the parent application Nek5000.

  • 160.
    Ivanov, Ilya
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Machado, Rui
    Rahn, Mirko
    Akhmetova, Dana
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    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.
    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.
    Fischer, Paul
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Evaluating New Communication Models in the Nek5000 Code for Exascale2015Konferensbidrag (Övrigt vetenskapligt)
  • 161.
    Izbassarov, Daulet
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    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.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Sarabian, Mohammad
    Hormozi, Sarah
    Brandt, Luca
    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, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik.
    Tammisola, Outi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Computational modeling of multiphase viscoelastic and elastoviscoplastic flows2018Ingår i: International Journal for Numerical Methods in Fluids, ISSN 0271-2091, E-ISSN 1097-0363, Vol. 88, nr 12, s. 521-543Artikel i tidskrift (Refereegranskat)
  • 162.
    Jarlebring, Elias
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    BROYDEN'S METHOD FOR NONLINEAR EIGENPROBLEMS2019Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 41, nr 2, s. A989-A1012Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Broyden's method is a general method commonly used for nonlinear systems of equations when very little information is available about the problem. We develop an approach based on Broyden's method for the structure appearing in nonlinear eigenvalue problems. Our approach is designed for problems where the evaluation of a matrix vector product is computationally expensive, essentially as expensive as solving the corresponding linear system of equations. We show how the structure of the Jacobian matrix can be incorporated into the algorithm to improve convergence. The algorithm exhibits local superlinear convergence for simple eigenvalues, and we characterize the convergence. We show how deflation can be integrated and combined such that the method can be used to compute several eigenvalues. A specific problem in machine tool milling, coupled with a PDE, is used to illustrate the approach. The simulations were carried out using the Julia programming language, and the simulation software is provided publicly for reproducibility.

  • 163.
    Jarlebring, Elias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Koskela, Antti
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Mele, Giampaolo
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Disguised and new quasi-Newton methods for nonlinear eigenvalue problems2018Ingår i: Numerical Algorithms, ISSN 1017-1398, E-ISSN 1572-9265, Vol. 79, nr 1, s. 311-335Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In this paper, we take a quasi-Newton approach to nonlinear eigenvalue problems (NEPs) of the type M(λ)v = 0, where (Formula presented.) is a holomorphic function. We investigate which types of approximations of the Jacobian matrix lead to competitive algorithms, and provide convergence theory. The convergence analysis is based on theory for quasi-Newton methods and Keldysh’s theorem for NEPs. We derive new algorithms and also show that several well-established methods for NEPs can be interpreted as quasi-Newton methods, and thereby, we provide insight to their convergence behavior. In particular, we establish quasi-Newton interpretations of Neumaier’s residual inverse iteration and Ruhe’s method of successive linear problems.

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  • 164.
    Jarlebring, Elias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mele, Giampaolo
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Palitta, Davide
    Univ Bologna, Dipartimento Matemat, Piazza Porta S Donato,5, I-40127 Bologna, Italy..
    Ringh, Emil
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Krylov methods for low-rank commuting generalized Sylvester equations2018Ingår i: Numerical Linear Algebra with Applications, ISSN 1070-5325, E-ISSN 1099-1506, Vol. 25, nr 6, artikel-id e2176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider generalizations of the Sylvester matrix equation, consisting of the sum of a Sylvester operator and a linear operator pi with a particular structure. More precisely, the commutators of the matrix coefficients of the operator pi and the Sylvester operator coefficients are assumed to be matrices with low rank. We show (under certain additional conditions) low-rank approximability of this problem, that is, the solution to this matrix equation can be approximated with a low-rank matrix. Projection methods have successfully been used to solve other matrix equations with low-rank approximability. We propose a new projection method for this class of matrix equations. The choice of the subspace is a crucial ingredient for any projection method for matrix equations. Our method is based on an adaption and extension of the extended Krylov subspace method for Sylvester equations. A constructive choice of the starting vector/block is derived from the low-rank commutators. We illustrate the effectiveness of our method by solving large-scale matrix equations arising from applications in control theory and the discretization of PDEs. The advantages of our approach in comparison to other methods are also illustrated.

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  • 165.
    Jarlebring, Elias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mele, Giampaolo
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The waveguide eigenvalue problem and the tensor infinite Arnoldi method2017Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 39, nr 3, s. A1062-A1088Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a new computational approach for a class of large-scale nonlinear eigenvalue problems (NEPs) that are nonlinear in the eigenvalue. The contribution of this paper is two fold. We derive a new iterative algorithm for NEPs, the tensor infinite Arnoldi method (TIAR), which is applicable to a general class of NEPs, and we show how to specialize the algorithm to a specific NEP: the waveguide eigenvalue problem. The waveguide eigenvalue problem arises from a finite-element discretization of a partial differential equation used in the study waves propagating in a periodic medium. The algorithm is successfully applied to accurately solve benchmark problems as well as complicated waveguides. We study the complexity of the specialized algorithm with respect to the number of iterations "m" and the size of the problem "n", both from a theoretical perspective and in practice. For the waveguide eigenvalue problem, we establish that the computationally dominating part of the algorithm has complexity O(nm^2+sqrt(n)m^3). Hence, the asymptotic complexity of TIAR applied to the waveguide eigenvalue problem, for n→ ∞, is the same as for Arnoldi’s method for standard eigenvalue problems.

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  • 166.
    Jarlebring, Elias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Poloni, F.
    Iterative methods for the delay Lyapunov equation with T-Sylvester preconditioning2019Ingår i: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 135, s. 173-185Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The delay Lyapunov equation is an important matrix boundary-value problem which arises as an analogue of the Lyapunov equation in the study of time-delay systems x˙(t)=A0x(t)+A1x(t−τ)+B0u(t). We propose a new algorithm for the solution of the delay Lyapunov equation. Our method is based on the fact that the delay Lyapunov equation can be expressed as a linear system of equations, whose unknown is the value U(τ/2)∈Rn×n, i.e., the delay Lyapunov matrix at time τ/2. This linear matrix equation with n2 unknowns is solved by adapting a preconditioned iterative method such as GMRES. The action of the n2×n2 matrix associated to this linear system can be computed by solving a coupled matrix initial-value problem. A preconditioner for the iterative method is proposed based on solving a T-Sylvester equation MX+XTN=C, for which there are methods available in the literature. We prove that the preconditioner is effective under certain assumptions. The efficiency of the approach is illustrated by applying it to a time-delay system stemming from the discretization of a partial differential equation with delay. Approximate solutions to this problem can be obtained for problems of size up to n≈1000, i.e., a linear system with n2≈106 unknowns, a dimension which is outside of the capabi© 2018 IMACS

  • 167.
    Johansson, Petter
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Carlson, Andreas
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Water-substrate physico-chemistry in wetting dynamics2015Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 781, s. 695-711Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider the wetting of water droplets on substrates with different chemical composition and molecular spacing, but with an identical equilibrium contact angle. A combined approach of large-scale molecular dynamics simulations and a continuum phase field model allows us to identify and quantify the influence of the microscopic physics at the contact line on the macroscopic droplet dynamics. We show that the substrate physico-chemistry, in particular hydrogen bonding, can significantly alter the flow. Since the material parameters are systematically derived from the atomistic simulations, our continuum model has only one adjustable parameter, which appears as a friction factor at the contact line. The continuum model approaches the atomistic wetting rate only when we adjust this contact line friction factor. However, the flow appears to he qualitatively different when comparing the atomistic and continuum models, highlighting that non-trivial continuum effects can come into play near the interface of the wetting front.

  • 168.
    Johansson, Petter
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI).
    Electrowetting diminishes contact line friction in dynamic wettingManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    We use large-scale molecular dynamics to study dynamics at the three-phase contact line in electrowetting of water and electrolytes on no-slip substrates. Under the applied electrostatic potential the line friction at the contact line is diminished. The effect is consistent for droplets of different sizes as well as for both pure water and electrolyte solution droplets. We analyze the electric field at the contact line to show how it assists ions and dipolar molecules to advance the contact line. Without an electric field, the interaction between a substrate and a liquid has a very short range, mostly affecting the bottom, immobilized layer of liquid molecules which leads to high friction since mobile molecules are not pulled towards the surface. In electrowetting, the electric field attractscharged and polar molecules over a longer range which diminishes the friction.

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  • 169.
    Johansson, Petter
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Hess, Berk
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Molecular origin of contact line friction in dynamic wetting2018Ingår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, nr 7, artikel-id 074201Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact line can advance during wetting. Using large-scale molecular dynamics simulations we show that the contact line advances by single molecules moving ahead of the contact line through two distinct processes: either moving over or displacing other liquid molecules. In both processes friction occurs at the molecular scale. We measure the energy dissipation at the contact line and show that it is of the same magnitude as the dissipation in the bulk of a droplet. The friction increases significantly as the contact angle decreases, which suggests suggests thermal activation plays a role. We provide a simple model that is consistent with the observations.

  • 170.
    Kametani, Yukinori
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Fukagata, K.
    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.
    Drag reduction in spatially developing turbulent boundary layers by blowing at constant mass-flux2015Ingår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    A series of large-eddy simulations of spatially developing turbulent boundary layers with uniform blowing at moderate Reynolds numbers (based on free-stream velocity, U∞ and momentum thickness, θ) up to Reθ ∼ 2500 were performed with the special focus on the effect of intermittent (separated in streamwise direction) blowing sections. The number of blowing sections, N, investigated is set to be 3, 6, 20, 30 and compared to N = 1, which constitutes the reference case, while the total wall-mass flux is constrained to be the same for all considered cases, corresponding to a blowing amplitude of 0.1% of U∞ for the reference case. Results indicate that the reference case provides a net-energy saving rate of around 18%, which initially decreases at most 2 percentage points for N = 3 but recovers with increasing N. The initial reduction of the drag reduction is due to the shorter streamwise length of intermittent blowing sections. The physical decomposition of the skin friction drag through the FIK identity (Fukagata et at, 2002), shows that the distribution of all components over each blowing section has similar trends, resulting in similar averaged values over the whole control region.

  • 171. Karlsson, A.
    et al.
    Olofsson, N.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Clements, M.
    A parallel microsimulation package for modelling cancer screening policies2017Ingår i: Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, IEEE, 2017, s. 323-330Konferensbidrag (Refereegranskat)
    Abstract [en]

    Microsimulation with stochastic life histories is an important tool in the development of public policies. In this article, we use microsimulation to evaluate policies for prostate cancer testing. We implemented the microsimulations as an R package, with pre- and post-processing in R and with the simulations written in C++. Calibrating a microsimulation model with a large population can be computationally expensive. To address this issue, we investigated four forms of parallelism: (i) shared memory parallelism using R; (ii) shared memory parallelism using OpenMP at the C++ level; (iii) distributed memory parallelism using R; and (iv) a hybrid shared/distributed memory parallelism using OpenMP at the C++ level and MPI at the R level. The close coupling between R and C++ offered advantages for ease of software dissemination and the use of high-level R parallelisation methods. However, this combination brought challenges when trying to use shared memory parallelism at the C++ level: the performance gained by hybrid OpenMP/MPI came at the cost of significant re-factoring of the existing code. As a case study, we implemented a prostate cancer model in the microsimulation package. We used this model to investigate whether prostate cancer testing with specific re-testing protocols would reduce harms and maintain any mortality benefit from prostate-specific antigen testing. We showed that four-yearly testing would have a comparable effectiveness and a marked decrease in costs compared with two-yearly testing and current testing. In summary, we developed a microsimulation package in R and assessed the cost-effectiveness of prostate cancer testing. We were able to scale up the microsimulations using a combination of R and C++, however care was required when using shared memory parallelism at the C++ level.

  • 172.
    Kawata, Takuya
    et al.
    Tokyo Univ Sci, Yamazaki 2641, Noda, Chiba 2788510, Japan..
    Alfredsson, P. Henrik
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Strömningsfysik. KTH, Skolan för industriell teknik och management (ITM), Centra, Competence Center for Gas Exchange (CCGEx). KTH, Skolan för teknikvetenskap (SCI), Hållfasthetslära (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Inverse Interscale Transport of the Reynolds Shear Stress in Plane Couette Turbulence2018Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 120, nr 24, artikel-id 244501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Interscale interaction between small-scale structures near the wall and large-scale structures away from the wall plays an increasingly important role with increasing Reynolds number in wall-bounded turbulence. While the top-down influence from the large-to small-scale structures is well known, it has been unclear whether the small scales near the wall also affect the large scales away from the wall. In this Letter we show that the small-scale near-wall structures indeed play a role to maintain the large-scale structures away from the wall, by showing that the Reynolds shear stress is transferred from small to large scales throughout the channel. This is in contrast to the turbulent kinetic energy transport which is from large to small scales. Such an "inverse" interscale transport of the Reynolds shear stress eventually supports the turbulent energy production at large scales.

  • 173.
    Khan, Mehmood Alam
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, Skolan för datavetenskap och kommunikation (CSC). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Sweden.
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lateral gene transfer events2016Ingår i: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 17, artikel-id 431Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. Results: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. Conclusions: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.

  • 174.
    Khan, Mehmood
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lataral gene transfer eventsManuskript (preprint) (Övrigt vetenskapligt)
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  • 175.
    Khapko, Taras
    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.
    Kreilos, T.
    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.
    Duguet, Y.
    Eckhardt, B.
    Henningson, Dan Stefan
    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.
    Edge states as mediators of bypass transition in boundary-layer flows2016Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 801, artikel-id R2Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The concept of edge states is investigated in the asymptotic suction boundary layer in relation to the receptivity process to noisy perturbations and the nucleation of turbulent spots. Edge tracking is first performed numerically, without imposing any discrete symmetry, in a large computational domain allowing for full spatial localisation of the perturbation velocity. The edge state is a three-dimensional localised structure recurrently characterised by a single low-speed streak that experiences erratic bursts and planar shifts. This recurrent streaky structure is then compared with predecessors of individual spot nucleation events, triggered by non-localised initial noise. The present results suggest a nonlinear picture, rooted in dynamical systems theory, of the nucleation process of turbulent spots in boundary-layer flows, in which the localised edge state plays the role of state-space mediator.

  • 176.
    Khapko, Taras
    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.
    Kreilos, Tobias
    Emergent Complexity in Physical Systems Laboratory (ECPS), École Polytechnique Fédérale de Lausanne.
    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.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    Eckhardt, Bruno
    Fachbereich Physik, Philipps-Universität Marburg.
    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.
    Edge states as mediators of bypass transition in boundary-layer flows2016Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The concept of edge state is investigated in the asymptotic suction boundary layer in relation with the receptivity process to noisy perturbations and the nucleation of turbulent spots. Edge tracking is first performed numerically, without imposing any discrete symmetry, in a large computational domain allowing for full spatial localisation of the perturbation velocity. The edge state is a three-dimensional localised structure recurrently characterised by a single low-speed streak that experiences erratic bursts and planar shifts. This recurrent streaky structure is then compared with predecessors of individual spot nucleation events, triggered by non-localised initial noise. The present results suggest a nonlinear picture, rooted in dynamical systems theory, of the nucleation process of turbulent spots in boundary-layer flows, in which the localised edge states play the role of state-space mediator.

  • 177.
    Khapko, Taras
    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.
    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.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    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.
    Turbulence collapse in a suction boundary layer2016Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 795, s. 356-379Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Turbulence in the asymptotic suction boundary layer is investigated numerically at the verge of laminarisation using direct numerical simulation. Following an adiabatic protocol, the Reynolds number Re is decreased in small steps starting from a fully turbulent state until laminarisation is observed. Computations in a large numerical domain allow in principle for the possible coexistence of laminar and turbulent regions. However, contrary to other subcritical shear flows, no laminar–turbulent coexistence is observed, even near the onset of sustained turbulence. High-resolution computations suggest a critical Reynolds number Reg≈270, below which turbulence collapses, based on observation times of O(105) inertial time units. During the laminarisation process, the turbulent flow fragments into a series of transient streamwise-elongated structures, whose interfaces do not display the characteristic obliqueness of classical laminar–turbulent patterns. The law of the wall, i.e. logarithmic scaling of the velocity profile, is retained down to Reg, suggesting a large-scale wall-normal transport absent in internal shear flows close to the onset. In order to test the effect of these large-scale structures on the near-wall region, an artificial volume force is added to damp spanwise and wall-normal fluctuations above y+=100, in viscous units. Once the largest eddies have been suppressed by the forcing, and thus turbulence is confined to the near-wall region, oblique laminar–turbulent interfaces do emerge as inother wall-bounded flows, however only transiently. These results suggest that oblique stripes at the onset are a prevalent feature of internal shear flows, but will not occur in canonical boundary layers, including the spatially growing ones.

  • 178. Kieri, Emil
    et al.
    Kreiss, Gunilla
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Coupling of Gaussian Beam and Finite Difference Solvers for Semiclassical Schrodinger Equations2015Ingår i: Advances in Applied Mathematics and Mechanics, ISSN 2070-0733, E-ISSN 2075-1354, Vol. 7, nr 6, s. 687-714Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the semiclassical regime, solutions to the time-dependent Schrodinger equation for molecular dynamics are highly oscillatory. The number of grid points required for resolving the oscillations may become very large even for simple model problems, making solution on a grid intractable. Asymptotic methods like Gaussian beams can resolve the oscillations with little effort and yield good approximations when the atomic nuclei are heavy and the potential is smooth. However, when the potential has variations on a small length-scale, quantum phenomena become important. Then asymptotic methods are less accurate. The two classes of methods perform well in different parameter regimes. This opens for hybrid methods, using Gaussian beams where we can and finite differences where we have to. We propose a new method for treating the coupling between the finite difference method and Gaussian beams. The new method reduces the needed amount of overlap regions considerably compared to previous methods, which improves the efficiency.

  • 179. Kimanius, Dari
    et al.
    Forsberg, Bjorn O.
    Scheres, Sjors H. W.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm University, Sweden.
    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-22016Ingår i: eLIFE, E-ISSN 2050-084X, Vol. 5, artikel-id e18722Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

  • 180.
    Kleine, Vitor
    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. Instituto Tecnológico de Aeronáutica, Praça Marechal Eduardo Gomes, 50, Vila das Acácias, São Josédos Campos SP, 12228-900, Brazil.
    Kleusberg, Elektra
    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.
    Tip-vortex instabilities of two in-line wind turbines2019Ingår i: Wake Conference 201922–24 May 2019, Visby, Sweden, Institute of Physics Publishing (IOPP), 2019, Vol. 1256, nr 1, artikel-id 012015Konferensbidrag (Refereegranskat)
    Abstract [en]

    The hydrodynamic stability of a vortex system behind two in-line wind turbines operating at low tip-speed ratios is investigated using the actuator-line method in conjunction with the spectral-element flow solver Nek5000. To this end, a simplified setup with two identical wind turbine geometries rotating at the same tip-speed ratio is simulated and compared with a single turbine wake. Using the rotating frame of reference, a steady solution is obtained, which serves as a base state to study the growth mechanisms of induced perturbations to the system. It is shown that, already in the steady state, the tip vortices of the two turbines interact with each other, exhibiting the so-called overtaking phenomenon. Hereby, the tip vortices of the upstream turbine overtake those of the downstream turbine repeatedly. By applying targeted harmonic excitations at the upstream turbine's blade tips a variety of modes are excited and grow with downstream distance. Dynamic mode decomposition of this perturbed flow field showed that the unstable out-of-phase mode is dominant, both with and without the presence of the second turbine. The perturbations of the upstream turbine's helical vortex system led to the destabilization of the tip vortices shed by the downstream turbine. Two distinct mechanisms were observed: for certain frequencies the downstream turbine's vortices oscillate in phase with the vortex system of the upstream turbine while for other frequencies a clear out-of-phase behaviour is observed. Further, short-wave instabilities were shown to grow in the numerical simulations, similar to existing experimental studies [1].

  • 181.
    Kleusberg, Elektra
    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.
    Benard, Sabrina
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Ecole Normale Supérieure Paris-Saclay, Cachan, France.
    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.
    Tip-vortex breakdown of wind turbines subject to shear2019Ingår i: Wind Energy, ISSN 1095-4244, E-ISSN 1099-1824, Vol. 22, nr 12, s. 1789-1799Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Sheared velocity profiles pervade all wind-turbine applications, thus making it important to understand their effect on the wake. In this study, a single wind turbine is modeled using the actuator-line method in the incompressible Navier–Stokes equations. The tip vortices are perturbed harmonically, and the growth rate of the response is evaluated under uniform inflow and a linear velocity profile. Whereas previous investigations of this kind were conducted in the rotating frame of reference, this study evaluates the excitation response in the fixed frame of reference, thus necessitating a frequency transformation. It is shown that increasing the shear decreases the spatial growth rate in the upper half of the wake while increasing it in the lower half. When scaled with the local tip vortex parameters, the growth rate along the entire azimuth collapses to a single value for the investigated wavenumbers. We conclude that even though the tip-vortex breakdown is asymmetric in sheared flow, the scaled growth rates follow the behavior of axisymmetric helical vortices. An excitation amplitude reduction by an order of magnitude extends the linear growth region of the wake by one radius for uniform inflow. In the sheared setup, the linear growth region is extended further in the top half than in the bottom half because of the progressive distortion of the helical tip vortices. An existing model to determine the stable wake length was shown to be in close agreement with the observed numerical results when adjusted for shear.

  • 182.
    Kleusberg, Elektra
    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.
    Mikkelsen, R. F.
    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.
    Ivanell, Stefan
    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. Uppsala University, Sweden.
    Henningson, Dan S.
    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.
    High-Order Numerical Simulations of Wind Turbine Wakes2017Ingår i: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 854, nr 1, artikel-id 012025Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Previous attempts to describe the structure of wind turbine wakes and their mutual interaction were mostly limited to large-eddy and Reynolds-averaged Navier-Stokes simulations using finite-volume solvers. We employ the higher-order spectral-element code Nek5000 to study the influence of numerical aspects on the prediction of the wind turbine wake structure and the wake interaction between two turbines. The spectral-element method enables an accurate representation of the vortical structures, with lower numerical dissipation than the more commonly used finite-volume codes. The wind-turbine blades are modeled as body forces using the actuator-line method (ACL) in the incompressible Navier-Stokes equations. Both tower and nacelle are represented with appropriate body forces. An inflow boundary condition is used which emulates homogeneous isotropic turbulence of wind-tunnel flows. We validate the implementation with results from experimental campaigns undertaken at the Norwegian University of Science and Technology (NTNU Blind Tests), investigate parametric influences and compare computational aspects with existing numerical simulations. In general the results show good agreement between the experiments and the numerical simulations both for a single-turbine setup as well as a two-turbine setup where the turbines are offset in the spanwise direction. A shift in the wake center caused by the tower wake is detected similar to experiments. The additional velocity deficit caused by the tower agrees well with the experimental data. The wake is captured well by Nek5000 in comparison with experiments both for the single wind turbine and in the two-turbine setup. The blade loading however shows large discrepancies for the high-turbulence, two-turbine case. While the experiments predicted higher thrust for the downstream turbine than for the upstream turbine, the opposite case was observed in Nek5000.

  • 183.
    Kleusberg, Elektra
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Sarmast, S.
    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.
    Ivanell, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Uppsala University, Wind Energy Section, Campus Gotland, SE-621 67 Visby, Sweden.
    Henningson, Dan Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Actuator line simulations of a Joukowsky and Tjæreborg rotor using spectral element and finite volume methods2016Ingår i: SCIENCE OF MAKING TORQUE FROM WIND (TORQUE 2016), Institute of Physics (IOP), 2016, Vol. 753, nr 8, artikel-id 082011Konferensbidrag (Refereegranskat)
    Abstract [en]

    The wake structure behind a wind turbine, generated by the spectral element code Nek5000, is compared with that from the finite volume code EllipSys3D. The wind turbine blades are modeled using the actuator line method. We conduct the comparison on two different setups. One is based on an idealized rotor approximation with constant circulation imposed along the blades corresponding to Glauert's optimal operating condition, and the other is the Tjffireborg wind turbine. The focus lies on analyzing the differences in the wake structures entailed by the different codes and corresponding setups. The comparisons show good agreement for the defining parameters of the wake such as the wake expansion, helix pitch and circulation of the helical vortices. Differences can be related to the lower numerical dissipation in Nek5000 and to the domain differences at the rotor center. At comparable resolution Nek5000 yields more accurate results. It is observed that in the spectral element method the helical vortices, both at the tip and root of the actuator lines, retain their initial swirl velocity distribution for a longer distance in the near wake. This results in a lower vortex core growth and larger maximum vorticity along the wake. Additionally, it is observed that the break down process of the spiral tip vortices is significantly different between the two methods, with vortex merging occurring immediately after the onset of instability in the finite volume code, while Nek5000 simulations exhibit a 2-3 radii period of vortex pairing before merging.

  • 184.
    Koskela, Antti
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Jarlebring, Elias
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hochstenbach, M. E.
    Krylov approximation of linear odes with polynomial parameterization2016Ingår i: SIAM Journal on Matrix Analysis and Applications, ISSN 0895-4798, E-ISSN 1095-7162, Vol. 37, nr 2, s. 519-538Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We propose a new numerical method to solve linear ordinary differential equations of the type δu/δt (t, ϵ) = A(ϵ) u(t,ϵ), where A: C → Cn×n is a matrix polynomial with large and sparse matrix coefficients. The algorithm computes an explicit parameterization of approximations of u(t, ϵ) such that approximations for many different values of ϵ and t can be obtained with a very small additional computational effort. The derivation of the algorithm is based on a reformulation of the parameterization as a linear parameter-free ordinary differential equation and on approximating the product of the matrix exponential and a vector with a Krylov method. The Krylov approximation is generated with Arnoldi's method and the structure of the coefficient matrix turns out to be independent of the truncation parameter so that it can also be interpreted as Arnoldi's method applied to an infinite dimensional matrix. We prove the super linear convergence of the algorithm and provide a posteriori error estimates to be used as termination criteria. The behavior of the algorithm is illustrated with examples stemming from spatial discretizations of partial differential equations.

  • 185. Kreilos, T.
    et al.
    Khapko, Taras
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schneider, T. M.
    Veble, G.
    Duguet, Y.
    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.
    Henningson, Dan S.
    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.
    Eckhardt, B.
    Turbulence transition in the asymptotic suction boundary layer2013Ingår i: International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013, TSFP-8 , 2013Konferensbidrag (Refereegranskat)
    Abstract [en]

    We study the transition to turbulence in the asymptotic suction boundary layer (ASBL) by direct numerical simulation. Tracking the motion of trajectories intermediate between laminar and turbulent states we can identify the invariant object inside the laminar-Turbulent boundary, the edge state. In small domains, the flow behaves like a travelling wave over short time intervals. On longer times one notes that the energy shows strong bursts at regular time intervals. During the bursts the streak structure is lost, but it reforms, translated in the spanwise direction by half the domain size. Varying the suction velocity allows to embed the flow into a family of flows that interpolate between plane Couette flow and the ASBL. Near the plane Couette limit, the edge state is a travelling wave. Increasing the suction, the travelling wave and a symmetry-related copy of it undergo a saddle-node infinite-period (SNIPER) bifurcation that leads to bursting and discrete-symmetry shifts. In wider domains, the structures localize in the spanwise direction, and the flow in the active region is similar to the one in small domains. There are still periodic bursts at which the flow structures are shifted, but the shift-distance is no longer connected to a discrete symmetry of the flow geometry. Two different states are found by edge tracking techniques, one where structures are shifted to the same side at every burst and one where they are alternatingly shifted to the left and to the right.

  • 186.
    Kreilos, Tobias
    et al.
    Emergent Complexity in Physical Systems Laboratory (ECPS), École Polytechnique Fédérale de Lausanne.
    Khapko, Taras
    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. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    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.
    Eckhardt, Bruno
    Fachbereich Physik, Philipps-Universität Marburg.
    Bypass transition and spot nucleation in boundary layers2016Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    The spatio-temporal aspects of the transition to turbulence are considered in the case of a boundary-layer flow developing above a flat plate exposed to free-stream turbulence. Combining results on the receptivity to free-stream turbulence with the nonlinear concept of a transition threshold, a physically motivated model suggests a spatial distribution of spot nucleation events. To describe the evolution of turbulent spots a probabilistic cellular automaton is introduced, with all parameters directly fitted from numerical simulations of the boundary layer. The nucleation rates are then combined with the cellular automaton model, yielding excellent quantitative agreement with the statistical characteristics for different free-stream turbulence levels. We thus show how the recent theoretical progress on transitional wall-bounded flows can be extended to the much wider class of spatially developing boundary-layer flows.

  • 187. Kudrnovsky, J.
    et al.
    Drchal, V.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rusz, J.
    Turek, I.
    Unified approach to electronic, thermodynamical, and transport properties of Fe3Si and Fe3Al alloys2014Ingår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, nr 13, s. 134408-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The electronic, thermodynamical, and transport properties of ordered Fe3X (X = Al, Si) alloys are studied from first principles. We present here a unified approach to the phase stability, the estimate of the Curie temperature, the temperature dependence of sublattice magnetizations, magnon spectra, the spin-stiffnesses, and residual resistivities. An important feature of the present study is that all calculated physical properties are determined in the framework of the same first-principles electronic structure model combined with the effective Ising and Heisenberg Hamiltonians used for study of the thermodynamical properties of alloys. Curie temperatures, spin-stiffnesses, and magnon spectra are determined using the same calculated exchange integrals. Finally, the transport properties are calculated using the linear-response theory. Our theoretical estimates compare well with available experimental data. In particular, calculations predict (in agreement with experiment) the ordered D0(3) phase as the ground-state alloy structure, demonstrate that a correct relation of Curie temperatures of Fe3Al/Fe3Si alloys can be obtained only by going beyond a simple mean-field approximation, provide reasonable estimates of spin-stiffnesses, and give resistivities compatible with structural disorder observed in the experiment. Although the calculated temperature dependences of the Fe magnetization on different sublattices are similar, they nevertheless deviate more than in the experiment, and we discuss a possible origin.

  • 188. Kumar, Ankit
    et al.
    Pan, Fan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Husain, Sajid
    Akansel, Serkan
    Brucas, Rimantas
    Bergqvist, Lars
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Chaudhary, Sujeet
    Svedlindh, Peter
    Temperature-dependent Gilbert damping of Co2FeAl thin films with different degree of atomic order2017Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 96, nr 22, artikel-id 224425Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Half-metallicity and low magnetic damping are perpetually sought for spintronics materials, and full Heusler compounds in this respect provide outstanding properties. However, it is challenging to obtain the well-ordered half-metallic phase in as-deposited full Heusler compound thin films, and theory has struggled to establish a fundamental understanding of the temperature-dependent Gilbert damping in these systems. Here we present a study of the temperature-dependent Gilbert damping of differently ordered as-deposited Co2FeAl full Heusler compound thin films. The sum of inter-and intraband electron scattering in conjunction with the finite electron lifetime in Bloch states governs the Gilbert damping for the well-ordered phase, in contrast to the damping of partially ordered and disordered phases which is governed by interband electronic scattering alone. These results, especially the ultralow room-temperature intrinsic damping observed for the well-ordered phase, provide fundamental insights into the physical origin of the Gilbert damping in full Heusler compound thin films.

  • 189.
    Käll, Lukas
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Krogh, Anders
    Sonnhammer, Erik L. L.
    Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server2007Ingår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, nr Web Server issue, 1, s. W429-W432Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all predicted transmembrane topologies overlap. This impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.

  • 190.
    König, Carolin
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Skanberg, Robin
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Hotz, Ingrid
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Ynnerman, Anders
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Norman, P.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Linares, Mathieu
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, nr 24, s. 3030-3033Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 191.
    Lacis, Ugis
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Johansson, Petter
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fullana, Tomas
    Sorbonne Université.
    Hess, Berk
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI).
    Amberg, Gustav
    KTH, Tidigare Institutioner (före 2005), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Södertorn University, Stockholm, Sweden.
    Bagheri, Shervin
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Zaleski, Stephane
    Sorbonne Université.
    Steady moving contact line of water over a no-slip substrateManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    The movement of the triple contact line plays a crucial role inmany applications such as ink-jet printing, liquid coating and drainage(imbibition) in porous media. To design accurate computational toolsfor these applications, predictive models of the moving contact line areneeded. However, the basic mechanisms responsible for movement ofthe triple contact line are not well understood but still debated. We investigatethe movement of the contact line between water, vapour anda silica-like solid surface under steady conditions in low capillary numberregime. We use molecular dynamics (MD) with an atomistic watermodel to simulate a nanoscopic drop between two moving plates. Weinclude hydrogen bonding between the water molecules and the solidsubstrate, which leads to a sub-molecular slip length. We benchmarktwo continuum methods, the Cahn{Hilliard phase-eld (PF) model anda volume-of-uid (VOF) model, against MD results.We show that bothcontinuum models reproduce the statistical measures obtained fromMD reasonably well, with a trade-o in accuracy. We demonstrate theimportance of the phase-eld mobility parameter and the local sliplength in accurately modelling the moving contact line.

  • 192.
    Lambert, Ruth A.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    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.
    Active suspensions in thin films: nutrient uptake and swimmer motion2013Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 733, s. 528-557Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A numerical study of swimming particle motion and nutrient transport is conducted for a semidilute to dense suspension in a thin film. The steady squirmer model is used to represent the motion of living cells in suspension with the nutrient uptake by swimming particles modelled using a first-order kinetic equation representing the absorption process that occurs locally at the particle surface. An analysis of the dynamics of the neutral squirmers inside the film shows that the vertical motion is reduced significantly. The mean nutrient uptake for both isolated and populations of swimmers decreases for increasing swimming speeds when nutrient advection becomes relevant as less time is left for the nutrient to diffuse to the surface. This finding is in contrast to the case where the uptake is modelled by imposing a constant nutrient concentration at the cell surface and the mass flux results to be an increasing monotonic function of the swimming speed. In comparison to non-motile particles, the cell motion has a negligible influence on nutrient uptake at lower particle absorption rates since the process is rate limited. At higher absorption rates, the swimming motion results in a large increase in the nutrient uptake that is attributed to the movement of particles and increased mixing in the fluid. As the volume fraction of swimming particles increases, the squirmers consume slightly less nutrients and require more power for the same swimming motion. Despite this increase in energy consumption, the results clearly demonstrate that the gain in nutrient uptake make swimming a winning strategy for micro-organism survival also in relatively dense suspensions.

  • 193. 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)
  • 194.
    Lashgari, Iman
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Niazi Ardekani, Mehdi
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Banerjee, Indradumna
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Inertial migration of spherical and oblate particles in straight ductsIngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study numerically the inertial migration of a single rigid sphere and an oblate spheroid in straight square and rectangular ducts. A highly accurate interface-resolved numerical algorithm is employed to analyse the entire migration dynamics of the oblate particle and compare it with that of the sphere. Similarly to the inertial focusing of spheres, the oblate particle reaches one of the four face-centred equilibrium positions, however they are vertically aligned with the axis of symmetry in the spanwise direction. In addition, the lateral trajectories of spheres and oblates collapse into an equilibrium manifold before ending at the equilibrium positions, with the equilibrium manifold tangential to lines of constant background shear for both sphere and oblate particles. The differences between the migration of the oblate and sphere are also presented, in particular the oblate may focus on the diagonal symmetry line of the duct cross-section, close to one of the corners, if its diameter is larger than a certain threshold. Moreover, we show that the final orientation and rotation of the oblate exhibit a chaotic behaviour for Reynolds numbers beyond a critical value. Finally, we document that the lateral motion of the oblate particle is less uniform than that of the spherical particle due to its evident tumbling motion throughout the migration. In a square duct, the strong tumbling motion of the oblate in the first stage of the migration results in a lower lateral velocity and consequently longer focusing length with respect to that of the spherical particle. The opposite is true in a rectangular duct where the higher lateral velocity of the oblate in the second stage of the migration, with negligible tumbling, gives rise to shorter focusing lengths.These results can help the design of microfluidic systems for bio-applications.

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  • 195.
    Lashgari, Iman
    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.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Padova, Italy.
    Breugem, W. -P
    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.
    Transition to Turbulence in the Presence of Finite Size Particles2015Ingår i: Procedia IUTAM, Elsevier, 2015, s. 211-217Konferensbidrag (Refereegranskat)
    Abstract [en]

    We study the transition from laminar to turbulent flow in a channel seeded with finite-size neutrally buoyant particles. A fixed ratio of 10 between the channel height and the particle diameter is considered. The flow is examined in the range of Reynolds numbers 500 ≤ Re ≤; 5000 and the particle volume fractions 0.001 ≤ Φ ≤; 0.3. We report a non-monotonic behavior of the threshold value of the Reynolds number above which the flow becomes turbulent, in agreement with previous experimental studies. The mean square velocity fluctuations and Reynolds shear stress of the fluid phase are reduced by increasing the particle volume fraction at a fixed Re=1500, while the mean square velocities of the solid phase are enhanced monotonically suggesting a transition from fluid to particle dominated dynamics at high volume fraction.

  • 196.
    Lashgari, Iman
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. University of Padova, Italy.
    Breugem, Wim Paul
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Channel flow of rigid sphere suspensions: Particle dynamics in the inertial regime2016Ingår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 78, s. 12-24Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We consider suspensions of neutrally-buoyant finite-size rigid spherical particles in channel flow and investigate the relation between the particle dynamics and the mean bulk behavior of the mixture for Reynolds numbers 500 ≤ Re ≤ 5000 and particle volume fraction 0 ≤ Φ ≤ 0.3, via fully resolved numerical simulations. Analysis of the momentum balance reveals the existence of three different regimes: laminar, turbulent and inertial shear-thickening depending on which of the stress terms, viscous, Reynolds or particle stress, is the major responsible for the momentum transfer across the channel. We show that both Reynolds and particle stress dominated flows fall into the Bagnoldian inertial regime and that the Bagnold number can predict the bulk behavior although this is due to two distinct physical mechanisms. A turbulent flow is characterized by larger particle dispersion and a more uniform particle distribution, whereas the particulate-dominated flows is associated with a significant particle migration towards the channel center where the flow is smooth laminar-like and dispersion low. Interestingly, the collision kernel shows similar values in the different regimes, although the relative particle velocity and clustering clearly vary with inertia and particle concentration.

  • 197.
    Lashgari, Iman
    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.
    Picano, Francesco
    Costa, Pedro
    Breugem, Wim-Paul
    Brandt, L.uca
    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 channel flow of a dense binary mixture of rigid particles2017Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 818, s. 623-645Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We study turbulent channel flow of a binary mixture of finite-sized neutrally buoyant rigid particles by means of interface-resolved direct numerical simulations. We fix the bulk Reynolds number and total solid volume fraction, Re-b = 5600 and Phi = 20 %, and vary the relative fraction of small and large particles. The binary mixture consists of particles of two different sizes, 2h/d(l) = 20 and 2h/d(s) = 30 where h is the half-channel height and d(l) and d(s) the diameters of the large and small particles. While the particulate flow statistics exhibit a significant alteration of the mean velocity profile and turbulent fluctuations with respect to the unladen flow, the differences between the mono-disperse and bi-disperse cases are small. However, we observe a clear segregation of small particles at the wall in binary mixtures, which affects the dynamics of the near-wall region and thus the overall drag. This results in a higher drag in suspensions with a larger number of large particles. As regards bi-disperse effects on the particle dynamics, a non-monotonic variation of the particle dispersion in the spanwise (homogeneous) direction is observed when increasing the percentage of small/large particles. Finally, we note that particles of the same size tend to cluster more at contact whereas the dynamics of the large particles gives the highest collision kernels due to a higher approaching speed.

  • 198.
    Lashgari, Iman
    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.
    Tammisola, Outi
    Department of Engineering, University of Cambridge, Cambridge, UK.
    Citro, Vincenzo
    DIIN, University of Salerno, Fisciano, Italy.
    Juniper, Matthew P.
    Department of Engineering, Univerisyt of Cambridge, Cambridge, UK.
    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.
    The planar X-junction flow: stability analysis and control2014Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 753, s. 1-28Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The bifurcations and control of the flow in a planar X-junction are studied via linear stability analysis and direct numerical simulations. This study reveals the instability mechanisms in a symmetric channel junction and shows how these can be stabilized or destabilized by boundary modification. We observe two bifurcations as the Reynolds number increases. They both scale with the inlet speed of the two side channels and are almost independent of the inlet speed of the main channel. Equivalently, both bifurcations appear when the recirculation zones reach a critical length. A two-dimensional stationary global mode becomes unstable first, changing the flow from a steady symmetric state to a steady asymmetric state via a pitchfork bifurcation. The core of this instability, whether defined by the structural sensitivity or by the disturbance energy production, is at the edges of the recirculation bubbles, which are located symmetrically along the walls of the downstream channel. The energy analysis shows that the first bifurcation is due to a lift-up mechanism. We develop an adjustable control strategy for the first bifurcation with distributed suction or blowing at the walls. The linearly optimal wall-normal velocity distribution is computed through a sensitivity analysis and is shown to delay the first bifurcation from Re = 82.5 to Re = 150. This stabilizing effect arises because blowing at the walls weakens the wall-normal gradient of the streamwise velocity around the recirculation zone and hinders the lift-up. At the second bifurcation, a three-dimensional stationary global mode with a spanwise wavenumber of order unity becomes unstable around the asymmetric steady state. Nonlinear three-dimensional simulations at the second bifurcation display transition to a nonlinear cycle involving growth of a three-dimensional steady structure, time-periodic secondary instability and nonlinear breakdown restoring a two-dimensional flow. Finally, we show that the sensitivity to wall suction at the second bifurcation is as large as it is at the first bifurcation, providing a possible mechanism for destabilization.

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  • 199.
    Laure, Erwin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holmgren, Sverker
    Preface2013Ingår i: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, nr 8, s. 2115-2116Artikel i tidskrift (Refereegranskat)
  • 200.
    Lazeroms, Werner
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brethouwer, Gert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Wallin, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Nonlinear features in explicit algebraic models for turbulent flows with active scalars2015Ingår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    A detailed discussion of explicit algebraic turbulence models in the case of active scalars is given. In particular, we discuss the appearance of nonlinearities in the models and the need for explicit solutions of the resulting nonlinear equations. Focussing on a recently published model for two-dimensional stratified flows, we present an intuitive way of approximating the solution of a sixth-order polynomial equation for the production-to-dissipation ratio (p + g)/e of turbulent kinetic energy K. This formulation is shown to be consistent for turbulent channel flow with stable and unstable stratification. The result is important for obtaining a robust model with a correct behaviour of the turbulence production in different limits of shear and buoyancy. The results have recently been published in Lazeroms et al. (2015).

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