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  • 1.
    af Klinteberg, Ludvig
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Tornberg, Anna-Karin
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    A fast integral equation method for solid particles in viscous flow using quadrature by expansion2016In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 326, 420-445 p.Article in journal (Refereed)
    Abstract [en]

    Boundary integral methods are advantageous when simulating viscous flow around rigid particles, due to the reduction in number of unknowns and straightforward handling of the geometry. In this work we present a fast and accurate framework for simulating spheroids in periodic Stokes flow, which is based on the completed double layer boundary integral formulation. The framework implements a new method known as quadrature by expansion (QBX), which uses surrogate local expansions of the layer potential to evaluate it to very high accuracy both on and off the particle surfaces. This quadrature method is accelerated through a newly developed precomputation scheme. The long range interactions are computed using the spectral Ewald (SE) fast summation method, which after integration with QBX allows the resulting system to be solved in M log M time, where M is the number of particles. This framework is suitable for simulations of large particle systems, and can be used for studying e.g. porous media models.

    The full text will be freely available from 2018-09-09 10:45
  • 2. Agarwal, Akshat
    et al.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Zaki, Tamer A.
    Linear and nonlinear evolution of a localized disturbance in polymeric channel flow2014In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 760, 278-303 p.Article in journal (Refereed)
    Abstract [en]

    The evolution of an initially localized disturbance in polymeric channel flow is investigated, with the FENE-P model used to characterize the viscoelastic behaviour of the flow. In the linear growth regime, the flow response is stabilized by viscoelasticity, and the maximum attainable disturbance energy amplification is reduced with increasing polymer concentration. The reduction in the energy growth rate is attributed to the polymer work, which plays a dual role. First, a spanwise polymer-work term develops, and is explained by the tilting action of the wall-normal voracity on the mean streamwise conformation tensor. This resistive term weakens the spanwise velocity perturbation thus reducing the energy of the localized disturbance. The second action of the polymer is analogous, with a wall-normal polymer work term that weakens the vertical velocity perturbation. Its indirect effect on energy growth is substantial since it reduces the production of Reynolds shear stress and in turn of the streamwise velocity perturbation, or streaks. During the early stages of nonlinear growth, the dominant effect of the polymer is to suppress the large-scale streaky structures which are strongly amplified in Newtonian flows. As a result, the process of transition to turbulence is prolonged and, after transition, a drag-reduced turbulent state is attained.

  • 3.
    Aguilar, Xavier
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fürlinger, K.
    Laure, Erwin
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Online MPI trace compression using event flow graphs and wavelets2016In: Procedia Computer Science, Elsevier, 2016, 1497-1506 p.Conference paper (Refereed)
    Abstract [en]

    Performance analysis of scientific parallel applications is essential to use High Performance Computing (HPC) infrastructures efficiently. Nevertheless, collecting detailed data of large-scale parallel programs and long-running applications is infeasible due to the huge amount of performance information generated. Even though there are no technological constraints in storing Terabytes of performance data, the constant flushing of such data to disk introduces a massive overhead into the application that makes the performance measurements worthless. This paper explores the use of Event flow graphs together with wavelet analysis and EZW-encoding to provide MPI event traces that are orders of magnitude smaller while preserving accurate information on timestamped events. Our mechanism compresses the performance data online while the application runs, thus, reducing the pressure put on the I/O system due to buffer flushing. As a result, we achieve lower application perturbation, reduced performance data output, and the possibility to monitor longer application runs. © The Authors. Published by Elsevier B.V.

  • 4.
    Aguilar, Xavier
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gimenez, Judit
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Scalability analysis of Dalton, a molecular structure program2013In: Future generations computer systems, ISSN 0167-739X, Vol. 29, no 8, 2197-2204 p.Article in journal (Refereed)
    Abstract [en]

    Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.

  • 5. Aidas, Kestutis
    et al.
    Angeli, Celestino
    Bak, Keld L.
    Bakken, Vebjorn
    Bast, Radovan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Boman, Linus
    Christiansen, Ove
    Cimiraglia, Renzo
    Coriani, Sonia
    Dahle, Pal
    Dalskov, Erik K.
    Ekstrom, Ulf
    Enevoldsen, Thomas
    Eriksen, Janus J.
    Ettenhuber, Patrick
    Fernandez, Berta
    Ferrighi, Lara
    Fliegl, Heike
    Frediani, Luca
    Hald, Kasper
    Halkier, Asger
    Hattig, Christof
    Heiberg, Hanne
    Helgaker, Trygve
    Hennum, Alf Christian
    Hettema, Hinne
    Hjertenaes, Eirik
    Host, Stinne
    Hoyvik, Ida-Marie
    Iozzi, Maria Francesca
    Jansik, Branislav
    Jensen, Hans Jorgen Aa.
    Jonsson, Dan
    Jorgensen, Poul
    Kauczor, Joanna
    Kirpekar, Sheela
    Kjrgaard, Thomas
    Klopper, Wim
    Knecht, Stefan
    Kobayashi, Rika
    Koch, Henrik
    Kongsted, Jacob
    Krapp, Andreas
    Kristensen, Kasper
    Ligabue, Andrea
    Lutnaes, Ola B.
    Melo, Juan I.
    Mikkelsen, Kurt V.
    Myhre, Rolf H.
    Neiss, Christian
    Nielsen, Christian B.
    Norman, Patrick
    Olsen, Jeppe
    Olsen, Jogvan Magnus H.
    Osted, Anders
    Packer, Martin J.
    Pawlowski, Filip
    Pedersen, Thomas B.
    Provasi, Patricio F.
    Reine, Simen
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ruden, Torgeir A.
    Ruud, Kenneth
    Rybkin, Vladimir V.
    Salek, Pawel
    Samson, Claire C. M.
    de Meras, Alfredo Sanchez
    Saue, Trond
    Sauer, Stephan P. A.
    Schimmelpfennig, Bernd
    Sneskov, Kristian
    Steindal, Arnfinn H.
    Sylvester-Hvid, Kristian O.
    Taylor, Peter R.
    Teale, Andrew M.
    Tellgren, Erik I.
    Tew, David P.
    Thorvaldsen, Andreas J.
    Thogersen, Lea
    Vahtras, Olav
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Watson, Mark A.
    Wilson, David J. D.
    Ziolkowski, Marcin
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    The Dalton quantum chemistry program system2014In: Wiley Interdisciplinary Reviews. Computational Molecular Science, ISSN 1759-0876, Vol. 4, no 3, 269-284 p.Article in journal (Refereed)
    Abstract [en]

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.

  • 6.
    Ali, Raja Hashim
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Bark, Mikael
    KTH, School of Information and Communication Technology (ICT).
    Miró, Jorge
    KTH, School of Information and Communication Technology (ICT).
    Muhammad, Sayyed Auwn
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sjöstrand, J.
    Zubair, Syed M.
    KTH, School of Electrical Engineering (EES), Communication Networks. University of Balochistan, Pakistan.
    Abbas, R. M.
    Arvestad, L.
    VMCMC: A graphical and statistical analysis tool for Markov chain Monte Carlo traces2017In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 18, no 1, 97Article in journal (Refereed)
    Abstract [en]

    Background: MCMC-based methods are important for Bayesian inference of phylogeny and related parameters. Although being computationally expensive, MCMC yields estimates of posterior distributions that are useful for estimating parameter values and are easy to use in subsequent analysis. There are, however, sometimes practical difficulties with MCMC, relating to convergence assessment and determining burn-in, especially in large-scale analyses. Currently, multiple software are required to perform, e.g., convergence, mixing and interactive exploration of both continuous and tree parameters. Results: We have written a software called VMCMC to simplify post-processing of MCMC traces with, for example, automatic burn-in estimation. VMCMC can also be used both as a GUI-based application, supporting interactive exploration, and as a command-line tool suitable for automated pipelines. Conclusions: VMCMC is a free software available under the New BSD License. Executable jar files, tutorial manual and source code can be downloaded from https://bitbucket.org/rhali/visualmcmc/.

  • 7.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Imayama, Shintaro
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Revisiting the stability analysis of the flow over a rotating disk2014Report (Other academic)
    Abstract [en]

    Local linear stability analysis applied to the rotating-disk flow is discussed.This flow case is an exact similarity solution to the cylindrical incompressibleNavier–Stokes equations also called the von Karman flow. The laminar mean velocity profiles are obtained by solving the resulting ordinary differential equa-tions assuming the flow is axisymmetric and time independent. Two stability-analyses methods are used to investigate the local linear stability of this flow: i)the ‘shooting method’; and ii) the ‘Chebyshev polynomial method’. This the-oretical investigation focuses on convectively unstable disturbances. Resultsobtained from the two methods are compared and the methods are shown togive similar results. These theoretical results are also compared with directnumerical simulations and experimental results showing good agreement.

  • 8.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Imayama, Shintaro
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Revisiting the stability analysis of the flow over a rotating diskManuscript (preprint) (Other academic)
    Abstract [en]

    Local linear stability analysis applied to the rotating-disk flow is discussed.This flow case is an exact similarity solution to the cylindrical incompressible Navier–Stokes equations also called the von K ́arm ́an flow. The laminar mean velocity profiles are obtained by solving the resulting ordinary differential equations assuming the flow is axisymmetric and time independent. Two stability-analyses methods are used to investigate the local linear stability of this flow: i)the ‘shooting method’; and ii) the ‘Chebyshev polynomial method’. This theoretical investigation focuses on convectively unstable disturbances. Results obtained from the two methods are compared and the methods are shown togive similar results. These theoretical results are also compared with direct numerical simulations and experimental results showing good agreement.

  • 9.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Imayama, Shintaro
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Alfredsson, Henrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Lingwood, Rebecca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Simulating the linear behaviour of the flow over a rotating disk due to roughness elements2014Report (Other academic)
  • 10.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philip
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Alfredsson, P. Henrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Lingwood, Rebecca J.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. University of London, United Kingdom.
    On the global nonlinear instability of the rotating-disk flow over a finite domain2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 803, 332-355 p.Article in journal (Refereed)
    Abstract [en]

    Direct numerical simulations based on the incompressible nonlinear Navier-Stokes equations of the flow over the surface of a rotating disk have been conducted. An impulsive disturbance was introduced and its development as it travelled radially outwards and ultimately transitioned to turbulence has been analysed. Of particular interest was whether the nonlinear stability is related to the linear stability properties. Specifically three disk-edge conditions were considered; (i) a sponge region forcing the flow back to laminar flow, (ii) a disk edge, where the disk was assumed to be infinitely thin and (iii) a physically realistic disk edge of finite thickness. This work expands on the linear simulations presented by Appelquist el al. (J. Fluid. Mech., vol. 765, 2015, pp. 612-631), where, for case (i), this configuration was shown to be globally linearly unstable when the sponge region effectively models the influence of the turbulence on the flow field. In contrast, case (ii) was mentioned there to he linearly globally stable, and here, where nonlinearity is included, it is shown that both cases (ii) and (iii) are nonlinearly globally unstable. The simulations show that the flow can he globally linearly stable if the linear wavepacket has a positive front velocity. However, in the same flow field, a nonlinear global instability can emerge, which is shown to depend on the outer turbulent region generating a linear inward-travelling mode that sustains a transition front within the domain. The results show that the front position does not approach the critical Reynolds number for the local absolute instability, R = 507. Instead, the front approaches R = 583 and both the temporal frequency and spatial growth rate correspond to a global mode originating at this position.

  • 11.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Simulating the laminar von Karman flow in Nek50002014Report (Other academic)
    Abstract [en]

    The laminar incompressible boundary layer over a rotating disk, also called the von Karman flow, is investigated. The goal is to set up a direct numericalsimulation (DNS) environment for further use to investigate the transition from laminar to turbulent flow for this boundary layer. For this the spectral-element code Nek5000 is used. A set of ODE-equations are first derived from the incompressible cylindrical Navier–Stokes equations, which are solved for the exact von Karman solution. Further, Nek5000 is prepared to solve for the same laminar solution. Comparing the two solutions give a quantification of the accuracy of the DNS solver Nek5000. Different scalings of the equations are investigated, together with quantifications of how good the different available boundary conditions are, also investigating different reference frames and grid dependency of the solution. The general conclusion is that the von K ́rm ́na aflow is possible to simulate in Nek5000. The method was robust when it cameto using different scalings, reference frames and resolutions.

  • 12.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Alfredsson, Henrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Lingwood, Rebecca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Global linear instability and the radial boundary of the rotating-disk flowManuscript (preprint) (Other academic)
  • 13.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Alfredsson, Henrik
    KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lingwood, Rebecca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. nstitute of Continuing Education, University of Cambridge, Madingley Hall, Madingley Cambridge, United Kingdom .
    Global linear instability of the rotating-disk flow investigated through simulations2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 765, 612-631 p.Article in journal (Refereed)
    Abstract [en]

    Numerical simulations of the flow developing on the surface of a rotating disk are presented based on the linearized incompressible Navier-Stokes equations. The boundary-layer flow is perturbed by an impulsive disturbance within a linear global framework, and the effect of downstream turbulence is modelled by a damping region further downstream. In addition to the outward-travelling modes, inward-travelling disturbances excited at the radial end of the simulated linear region, r(end), by the modelled turbulence are included within the simulations, potentially allowing absolute instability to develop. During early times the flow shows traditional convective behaviour, with the total energy slowly decaying in time. However, after the disturbances have reached r(end), the energy evolution reaches a turning point and, if the location of r(end) is at a Reynolds number larger than approximately R = 594 (radius non-dimensionalized by root v/Omega*, where v is the kinematic viscosity and Omega* is the rotation rate of the disk), there will be global temporal growth. The global frequency and mode shape are clearly imposed by the conditions at r(end). Our results suggest that the linearized Ginzburg-Landau model by Healey (J. Fluid Mech., vol. 663, 2010, pp. 148-159) captures the (linear) physics of the developing rotating-disk flow, showing that there is linear global instability provided the Reynolds number of r(end) is sufficiently larger than the critical Reynolds number for the onset of absolute instability.

  • 14. Araujo-Cabarcas, J. C.
    et al.
    Engström, C.
    Jarlebring, Elias
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    Efficient resonance computations for Helmholtz problems based on a Dirichlet-to-Neumann map2018In: Journal of Computational and Applied Mathematics, ISSN 0377-0427, E-ISSN 1879-1778, Vol. 330, 177-192 p.Article in journal (Refereed)
    Abstract [en]

    We present an efficient procedure for computing resonances and resonant modes of Helmholtz problems posed in exterior domains. The problem is formulated as a nonlinear eigenvalue problem (NEP), where the nonlinearity arises from the use of a Dirichlet-to-Neumann map, which accounts for modeling unbounded domains. We consider a variational formulation and show that the spectrum consists of isolated eigenvalues of finite multiplicity that only can accumulate at infinity. The proposed method is based on a high order finite element discretization combined with a specialization of the Tensor Infinite Arnoldi method (TIAR). Using Toeplitz matrices, we show how to specialize this method to our specific structure. In particular we introduce a pole cancellation technique in order to increase the radius of convergence for computation of eigenvalues that lie close to the poles of the matrix-valued function. The solution scheme can be applied to multiple resonators with a varying refractive index that is not necessarily piecewise constant. We present two test cases to show stability, performance and numerical accuracy of the method. In particular the use of a high order finite element discretization together with TIAR results in an efficient and reliable method to compute resonances. 

  • 15.
    Ardekani, Mehdi Niazi
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Costa, Pedro
    Breugem, Wim Paul
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Numerical study of the sedimentation of spheroidal particles2016In: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 87, 16-34 p.Article in journal (Refereed)
    Abstract [en]

    The gravity-driven motion of-rigid particles in a viscous fluid is relevant in many natural and industrial processes, yet this has mainly been investigated for spherical particles. We therefore consider the sedimentation of non-spherical (spheroidal) isolated and particle pairs in a viscous fluid via numerical simulations using the Immersed Boundary Method. The simulations performed here show that the critical Galileo number for the onset of secondary motions decreases as the spheroid aspect ratio departs from 1. Above this critical threshold, oblate particles perform a zigzagging motion whereas prolate particles rotate around, the vertical axis while having their broad side facing the falling direction. Instabilities of the vortices in the wake follow when farther increasing the Galileo number. We also study the drafting kissing-tumbling associated with the settling of particle pairs. We find that the interaction time increases significantly for non-spherical particles and, more interestingly, spheroidal particles are attracted from larger lateral displacements. This has important implications for the estimation of collision kernels and can result its increasing clustering in suspensions of sedimenting spheroids.

  • 16.
    Arjmand, Doghonay
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Analysis of heterogeneous multiscale methods for long time wave propagation problems2014In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 12, no 3, 1135-1166 p.Article in journal (Refereed)
    Abstract [en]

    In this paper, we analyze a multiscale method developed under the heterogeneous multiscale method (HMM) framework for numerical approximation of multiscale wave propagation problems in periodic media. In particular, we are interested in the long time O(epsilon(-2)) wave propagation, where e represents the size of the microscopic variations in the media. In large time scales, the solutions of multiscale wave equations exhibit O(1) dispersive effects which are not observed in short time scales. A typical HMM has two main components: a macromodel and a micromodel. The macromodel is incomplete and lacks a set of local data. In the setting of multiscale PDEs, one has to solve for the full oscillatory problem over local microscopic domains of size eta = O(epsilon) to upscale the parameter values which are missing in the macroscopic model. In this paper, we prove that if the microproblems are consistent with the macroscopic solutions, the HMM approximates the unknown parameter values in the macromodel up to any desired order of accuracy in terms of epsilon/eta..

  • 17. Arjmand, Doghonay
    et al.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Estimates for the upscaling error in heterogeneous multiscale methods for wave propagation problems in locally periodic media2017In: Multiscale Modeling & simulation, ISSN 1540-3459, E-ISSN 1540-3467, Vol. 15, no 2, 948-976 p.Article in journal (Refereed)
    Abstract [en]

    This paper concerns the analysis of a multiscale method for wave propagation problems in microscopically nonhomogeneous media. A direct numerical approximation of such problems is prohibitively expensive as it requires resolving the microscopic variations over a much larger physical domain of interest. The heterogeneous multiscale method (HMM) is an efficient framework to approximate the solutions of multiscale problems. In the HMM, one assumes an incomplete macroscopic model which is coupled to a known but expensive microscopic model. The micromodel is solved only locally to upscale the parameter values which are missing in the macro model. The resulting macroscopic model can then be solved at a cost independent of the small scales in the problem. In general, the accuracy of the HMM is related to how good the upscaling step approximates the right macroscopic quantities. The analysis of the method that we consider here was previously addressed only in purely periodic media, although the method itself is numerically shown to be applicable to more general settings. In the present study, we consider a more realistic setting by assuming a locally periodic medium where slow and fast variations are allowed at the same time. We then prove that the HMM captures the right macroscopic effects. The generality of the tools and ideas in the analysis allows us to establish convergence rates in a multidimensional setting. The theoretical findings here imply an improved convergence rate in one dimension, which also justifies the numerical observations from our earlier study.

  • 18.
    Arjmand, Doghonay
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Stohrer, Christian
    A FINITE ELEMENT HETEROGENEOUS MULTISCALE METHOD WITH IMPROVED CONTROL OVER THE MODELING ERROR2016In: Communications in Mathematical Sciences, ISSN 1539-6746, E-ISSN 1945-0796, Vol. 14, no 2, 463-487 p.Article in journal (Refereed)
    Abstract [en]

    Multiscale partial differential equations (PDEs) are difficult to solve by traditional numerical methods due to the need to resolve the small wavelengths in the media over the entire computational domain. We develop and analyze a Finite Element Heterogeneous Multiscale Method (FE-HMM) for approximating the homogenized solutions of multiscale PDEs of elliptic, parabolic, and hyperbolic type. Typical multiscale methods require a coupling between a micro and a macro model. Inspired from the homogenization theory, traditional FE-HMM schemes use elliptic PDEs as the micro model. We use, however, the second order wave equation as our micro model independent of the type of the problem on the macro level. This allows us to control the modeling error originating from the coupling between the different scales. In a spatially fully discrete a priori error analysis we prove that the modeling error can be made arbitrarily small for periodic media, even if we do not know the exact period of the oscillations in the media. We provide numerical examples in one and two dimensions confirming the theoretical results. Further examples show that the method captures the effective solutions in general non-periodic settings as well.

  • 19.
    Atwa, Mohamed M.
    et al.
    KTH, School of Information and Communication Technology (ICT), Electronics, Integrated devices and circuits.
    Alaskalany, Ahmed
    KTH, School of Information and Communication Technology (ICT), Electronics, Integrated devices and circuits. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Elgammal, Karim
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Smith, Anderson D.
    Hammar, Mattias
    KTH, Superseded Departments (pre-2005), Microelectronics and Information Technology, IMIT. KTH, Superseded Departments (pre-2005), Electronics.
    Östling,
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits. KTH, School of Information and Communication Technology (ICT), Electronics, Integrated devices and circuits.
    Trilayer Graphene as a Candidate Material for Phase-Change Memory Applications2016In: MRS ADVANCES, ISSN 2059-8521, Vol. 1, no 20, 1487-1494 p.Article in journal (Refereed)
    Abstract [en]

    There is pressing need in computation of a universal phase change memory consolidating the speed of RAM with the permanency of hard disk storage. A potentiated scanning tunneling microscope tip traversing the soliton separating a metallic, ABA-stacked phase and a semiconducting ABC-stacked phase in trilayer graphene has been shown to permanently transform ABA-stacked regions to ABC-stacked regions. In this study, we used density functional theory (DFT) calculations to assess the energetics of this phase-change and explore the possibility of organic functionalization using s-triazine to facilitate a reverse phase-change from rhombohedral back to Bernal in graphene trilayers. A significant deviation in the energy per simulated atom arises when s-triazine is adsorbed, favoring the transformation of the ABC phase to the ABA phase once more. A phase change memory device utilizing rapid, energy-efficient, reversible, field-induced phase-change in graphene trilayers could potentially revolutionize digital memory industry.

  • 20.
    Banaei, Arash Alizad
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Loiseau, Jean-Christophe
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lashgari, Iman
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, L.uca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Numerical simulations of elastic capsules with nucleus in shear flow2017In: EUROPEAN JOURNAL OF COMPUTATIONAL MECHANICS, ISSN 1779-7179, Vol. 26, no 1-2, 131-153 p.Article in journal (Refereed)
    Abstract [en]

    The shear-induced deformation of a capsule with a stiff nucleus, a model of eukaryotic cells, is studied numerically. The membrane of the cell and of its nucleus are modelled as a thin elastic material obeying a Neo-Hookean constitutive law. The fluid-structure coupling is obtained using an immersed boundary method. The variations induced by the presence of the nucleus on the cell deformation are investigated when varying the viscosity ratio between the inner and outer fluids, the membrane elasticity and its bending stiffness. The deformation of the eukaryotic cell is smaller than that of the prokaryotic one. The reduction in deformation increases for larger values of the capillary number. The eukaryotic cell remains thicker in itsmiddle part compared to the prokaryotic one, thus making it less flexible to pass through narrow capillaries. For a viscosity ratio of 5, the deformation of the cell is smaller than in the case of uniform viscosity. In addition, for non-zero bending stiffness of the membrane, the deformation decreases and the shape is closer to an ellipsoid. Finally, we compare the results obtained modelling the nucleus as an inner stiffer membrane with those obtained using a rigid particle.

  • 21. Basile, Walter
    et al.
    Sachenkova, Oxana
    Light, Sara
    Elofsson, Arne
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    High GC content causes orphan proteins to be intrinsically disordered2017In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, no 3, e1005375Article in journal (Refereed)
    Abstract [en]

    De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population These orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC) and Drosophila (high GC). GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.

  • 22. Bergman, Anders
    et al.
    Hellsvik, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Bessarab, Pavel F.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Iceland, Iceland.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Spin relaxation signature of colossal magnetic anisotropy in platinum atomic chains2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, 36872Article in journal (Refereed)
    Abstract [en]

    Recent experimental data demonstrate emerging magnetic order in platinum atomically thin nanowires. Furthermore, an unusual form of magnetic anisotropy-colossal magnetic anisotropy (CMA)-was earlier predicted to exist in atomically thin platinum nanowires. Using spin dynamics simulations based on first-principles calculations, we here explore the spin dynamics of atomically thin platinum wires to reveal the spin relaxation signature of colossal magnetic anisotropy, comparing it with other types of anisotropy such as uniaxial magnetic anisotropy (UMA). We find that the CMA alters the spin relaxation process distinctly and, most importantly, causes a large speed-up of the magnetic relaxation compared to uniaxial magnetic anisotropy. The magnetic behavior of the nanowire exhibiting CMA should be possible to identify experimentally at the nanosecond time scale for temperatures below 5 K. This time-scale is accessible in e.g., soft x-ray free electron laser experiments.

  • 23.
    Bobke, Alexandra
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Simulations of turbulent boundary layers with suction and pressure gradients2016Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The focus of the present licentiate thesis is on the effect of suction and pressure gradients on turbulent boundary-layer flows, which are investigated separately through performing numerical simulations.The first part aims at assessing history and development effects on adverse pressure-gradient (APG) turbulent boundary layers (TBL). A suitable set-up was developed to study near-equilibrium conditions for a boundary layer developingon a flat plate by setting the free-stream velocity at the top of the domain following a power law. The computational box size and the correct definition of the top-boundary condition were systematically tested. Well-resolved large-eddy simulations were performed to keep computational costs low. By varying the free-stream velocity distribution parameters, e.g. power-law exponent and virtual origin, pressure gradients of different strength and development were obtained. The magnitude of the pressure gradient is quantified in terms of the Clauser pressure-gradient parameter β. The effect of the APG is closely related to its streamwise development, hence, TBLs with non-constant and constant β were investigated. The effect was manifested in the mean flow through a much more pronounced wake region and in the Reynolds stresses through the existence of an outer peak. The terms of the turbulent kinetic energy budgets indicate the influence of the APG on the distribution of the transfer mechanism across the boundary layer. Stronger and more energetic structures were identified in boundary layers with relatively stronger pressure gradients in their development history. Due to the difficulty of determining the boundary-layer thickness in flows with strong pressure gradients or over a curvedsurface, a new method based on the diagnostic-plot concept was introduced to obtain a robust estimation of the edge of a turbulent boundary layer.

    In the second part, large-eddy simulations were performed on temporally developing turbulent asymptotic suction boundary layers (TASBLs). Findings from previous studies about the effect of suction could be confirmed, e.g. the reduction of the fluctuation levels and Reynolds shear stresses. Furthermore, the importance of the size of the computational domain and the time development were investigated. Both parameters were found to have a large impact on the results even on low-order statistics. While the mean velocity profile collapses in the inner layer irrespective of box size and development time, a wake region occurs for too small box sizes or early development time and vanishes once sufficiently large domains and/or integration times are chosen. The asymptotic state is charactersized by surprisingly thick boundary layers even for moderateReynolds numbers Re (based on free-stream velocity and laminar displacement thickness); for instance, Re = 333 gives rise to a friction Reynolds number Reτ = 2000. Similarly, the flow gives rise to very large structures in the outer region. These findings have important ramifications for experiments, since very large facilities are required to reach the asymptotic state even for low Reynolds numbers.

  • 24.
    Bobke, Alexandra
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    History effects and near-equilibrium in adverse-pressure-gradient turbulent boundary layersManuscript (preprint) (Other academic)
    Abstract [en]

    This study deals with turbulent boundary layers under adverse-pressure gradients. Well-resolved large-eddy simulations (LES) were performed to assess the influence of the streamwise pressure development. The pressure gradient is imposed by prescribing the free-stream velocity in the free-stream above the layer. In order to fulfill the near-equilibrium conditions, the free-stream velocity has to follow a power-law distribution. The turbulence statistics pertaining tocases with a constant Clauser pressure-gradient parameter β were compared with cases with a non-constant pressure distribution at matched β and friction Reynolds number  Reτ. It was noticed that the non-constant cases appear toconverge slowly to a certain state of the boundary layer, which is uniquelycharacterised by β and Reτ . The investigations on the flat plate were extended to the flow around a wing section. Comparisons with the flat-plate cases revealed some interesting features: In turbulent boundary layers with strong pressure gradients in the development history the energy-carrying structures in the outerregion are strongly enhanced, which can be detected by the pronounced wake inthe mean velocity as well as the large second peak in the Reynolds stresses. This was also confirmed by one-dimensional energy spectra, where more energetic large structures were identified in the outer region for stronger pressure gradients overall. A scaling law suggested by Kitsios et al. (2015) was tested on a constant pressure gradient case. The mean velocity and Reynolds stress profiles were found to be dependent on the downstream development when they were scaled with the edge velocity and displacement thickness.

  • 25.
    Bobke, Alexandra
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Large-eddy simulations of adverse pressure gradient turbulent boundary layersManuscript (preprint) (Other academic)
    Abstract [en]

    Adverse pressure-gradient (APG) turbulent boundary layers (TBL) are studied by performing well-resolved large-eddy simulations. The pressure gradient is imposed by defining the free-stream velocity distribution with the description of a power law. Different inflow conditions, box sizes and upper boundary conditions are tested in order to determine the final set-up. The statistics ofturbulent boundary layers with three different power-law coefficients and thus magnitudes of adverse pressure gradients are then compared to zero pressure-gradient (ZPG) data. The effect of the APG on TBLs is manifested in the mean flow through a much more prominent wake region and in the Reynolds stresses through the existence of an outer peak. The pre-multiplied energy budgets shows the APG influence on the distribution of the turbulent kinetic energy transfer mechanism across the boundary layer.

  • 26.
    Bobke, Alexandra
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Simulations of turbulent asymptotic suction boundary layers2015In: Journal of turbulence, ISSN 1468-5248, E-ISSN 1468-5248, Vol. 17, 157-180 p.Article in journal (Refereed)
    Abstract [en]

    A series of large-eddy simulations of a turbulent asymptotic suction boundary layer (TASBL) was performed in a periodic domain, on which uniform suction was applied over a flat plate. Three Reynolds numbers (defined as ratio of free-stream and suction velocity) of Re = 333, 400 and 500 and a variety of domain sizes were considered in temporal simulations in order to investigate the turbulence statistics, the importance of the computational domain size, the arising flow structures as well as temporal development length required to achieve the asymptotic state. The effect of these two important parameters was assessed in terms of their influence on integral quantities, mean velocity, Reynolds stresses, higher order statistics, amplitude modulation and spectral maps. While the near-wall region up to the buffer region appears to scale irrespective of Re and domain size, the parameters of the logarithmic law (i.e. von Kármán and additive coefficient) decrease with increasing Re, while the wake strength decreases with increasing spanwise domain size and vanishes entirely once the spanwise domain size exceeds approximately two boundary-layer thicknesses irrespective of Re. The wake strength also reduces with increasing simulation time. The asymptotic state of the TASBL is characterised by surprisingly large friction Reynolds numbers and inherits features of wall turbulence at numerically high Re. Compared to a turbulent boundary layer (TBL) or a channel flow without suction, the components of the Reynolds-stress tensor are overall reduced, but exhibit a logarithmic increase with decreasing suction rates, i.e. increasing Re. At the same time, the anisotropy is increased compared to canonical wall-bounded flows without suction. The reduced amplitudes in turbulence quantities are discussed in light of the amplitude modulation due to the weakened larger outer structures. The inner peak in the spectral maps is shifted to higher wavelength and the strength of the outer peak is much less than for TBLs. An additional spatial simulation was performed, in order to relate the simulation results to wind tunnel experiments, which – in accordance with the results from the temporal simulation – indicate that a truly TASBL is practically impossible to realise in a wind tunnel. Our unique data set agrees qualitatively with existing literature results for both numerical and experimental studies, and at the same time sheds light on the fact why the asymptotic state could not be established in a wind tunnel experiment, viz. because experimental studies resemble our simulation results from too small simulation boxes or insufficient development times.

  • 27. Bongo, Lars Ailo
    et al.
    Ciegis, Raimondas
    Frasheri, Neki
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Kimovski, Dragi
    Kropf, Peter
    Margenov, Svetozar
    Mihajlovic, Milan
    Neytcheva, Maya
    Rauber, Thomas
    Rünger, Gudula
    Trobec, Roman
    Wuyts, Roel
    Wyrzykowski, Roman
    Applications for Ultrascale Computing2015In: Supercomputing Frontiers and Innovations, ISSN 2409-6008, Vol. 2, no 1, 19-48 p.Article in journal (Refereed)
    Abstract [en]

    Studies of complex physical and engineering systems, represented by multi-scale and multi-physics computer simulations have an increasing demand for computing power, especially when the simulations of realistic problems are considered. This demand is driven by the increasing size and complexity of the studied systems or the time constraints. Ultrascale computing systems offer a possible solution to this problem. Future ultrascale systems will be large-scale complex computing systems combining technologies from high performance computing, distributed systems, big data, and cloud computing. Thus, the challenge of developing and programming complex algorithms on these systems is twofold. Firstly, the complex algorithms have to be either developed from scratch, or redesigned in order to yield high performance, while retaining correct functional behaviour. Secondly, ultrascale computing systems impose a number of non-functional cross-cutting concerns, such as fault tolerance or energy consumption, which can significantly impact the deployment of applications on large complex systems. This article discusses the state-of-the-art of programming for current and future large scale systems with an emphasis on complex applications. We derive a number of programming and execution support requirements by studying several computing applications that the authors are currently developing and discuss their potential and necessary upgrades for ultrascale execution.

  • 28.
    Borlenghi, Simone
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Lepri, Stefano
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Thermomagnonic diode: Rectification of energy and magnetization currents2014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 5, 054428- p.Article in journal (Refereed)
    Abstract [en]

    We investigate the dynamics of two coupled macrospins connected to thermal baths at different temperatures. The system behaves like a diode which allows the propagation of energy and magnetization currents in one direction only. This effect is described by a simple model of two coupled nonlinear oscillators interacting with two independent reservoirs. It is shown that the rectification phenomenon can be interpreted as a a stochastic phase synchronization of the two spin oscillators. A brief comparison with realistic micromagnetic simulations is presented. This new effect yields promising opportunities in spin caloritronics and nanophononic devices.

  • 29. Borlenghi, Simone
    et al.
    Mahani, M. R.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Fangohr, Hans
    Franchin, M.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Fransson, Jonas
    Micromagnetic simulations of spin-torque driven magnetization dynamics with spatially resolved spin transport and magnetization texture2017In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 96, no 9, 094428Article in journal (Refereed)
    Abstract [en]

    We present a simple and fast method to simulate spin-torque driven magnetization dynamics in nanopillar spin-valve structures. The approach is based on the coupling between a spin transport code based on random matrix theory and a micromagnetics finite-elements software. In this way the spatial dependence of both spin transport and magnetization dynamics is properly taken into account. Our results are compared with experiments. The excitation of the spin-wave modes, including the threshold current for steady-state magnetization precession and the nonlinear frequency shift of the modes are reproduced correctly. The giant magneto resistance effect and the magnetization switching also agree with experiment. The similarities with recently described spin-caloritronics devices are also discussed.

  • 30. Borlenghi, Simone
    et al.
    Mahani, M. Reza
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Fransson, Jonas
    Nanoscale control of heat and spin conduction in artificial spin chains2016In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 94, no 13, 134419Article in journal (Refereed)
    Abstract [en]

    We describe a mechanism to control the energy and magnetization currents in an artificial spin chain, consisting of an array of permalloy nanodisks coupled through a magnetodipolar interaction. The chain is kept out of equilibrium by two thermal baths with different temperatures connected to its ends, which control the current propagation. Transport is enhanced by applying a uniform radio-frequency pump field resonating with some of the spin-wave modes of the chain. Moreover, the two currents can be controlled independently by tuning the static field applied on the chain. Thus we describe two effective means for the independent control of coupled currents and the enhancement of thermal and spin-wave conductivity in a realistic magnonics device, suggesting that similar effects could be observed in a large class of nonlinear oscillating systems.

  • 31.
    Borlenghi, Simone
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Wang, Weiwei
    Fangohr, Hans
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Designing a Spin-Seebeck Diode2014In: Physical Review Letters, ISSN 0031-9007, Vol. 112, no 4, 047203- p.Article in journal (Refereed)
    Abstract [en]

    Using micromagnetic simulations, we have investigated spin dynamics in a spin-valve bilayer in the presence of a thermal gradient. The direction and the intensity of the gradient allow us to excite the spin wave modes of each layer selectively. This permits us to synchronize the magnetization precession of the two layers and to rectify the flows of energy and magnetization through the system. Our study yields promising opportunities for applications in spin caloritronics and nanophononics devices.

  • 32. Branca, Rui M. M.
    et al.
    Orre, Lukas M.
    Johansson, Henrik J.
    Granholm, Viktor
    Huss, Mikael
    Perez-Bercoff, Åsa
    Forshed, Jenny
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lehtiö, Janne
    HiRIEF LC-MSMS enables deep proteome coverage and unbiased proteogenomics2014In: Nature Methods, ISSN 1548-7091, E-ISSN 1548-7105, Vol. 11, no 1, 59- p.Article in journal (Refereed)
    Abstract [en]

    We present a liquid chromatography-mass spectrometry (LC-MSMS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.

  • 33.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The lift-up effect: The linear mechanism behind transition and turbulence in shear flows2014In: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 47, 80-96 p.Article in journal (Refereed)
    Abstract [en]

    The formation and amplification of streamwise velocity perturbations induced by cross-stream disturbances is ubiquitous in shear flows. This disturbance growth mechanism, so neatly identified by Ellingsen and Palm in 1975, is a key process in transition to turbulence and self-sustained turbulence. In this review, we first present the original derivation and early studies and then discuss the non-modal growth of streaks, the result of the lift-up process, in transitional and turbulent shear flows. In the second part, the effects on the lift-up process of additives in the fluid and of a second phase are discussed and new results presented with emphasis on particle-laden shear flows. For all cases considered, we see the lift-up process to be a very robust process, always present as a first step in subcritical transition.

  • 34.
    Brandt, L.uca
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ardekani, Mehdi Niazi
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Picano, F.
    Costa, P.
    Breugem, W. -P
    Numerical study of turbulent channel flow laden with finite-size non-spherical particles2017In: 10th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2017, International Symposium on Turbulence and Shear Flow Phenomena, TSFP10 , 2017, Vol. 4Conference paper (Refereed)
    Abstract [en]

    We present interface-resolved numerical simulations of turbulent channel flow laden with non-spherical rigid and neutrally-buoyant particles. We first focus on the case of oblate particles of aspect ratio 1/3 at volume fractions up to 15% and show that the turbulent drag is decreasing when increasing the particle volume fraction although the effective viscosity of the suspension actually increases. We relate the observed drag reduction to turbulence attenuation and to particle migration away from the near-wall region. Particles tend to align parallel to the wall with rotation rates significantly lower than those reported for spheres. In the second part of the study, we examine the effect of the particle slenderness on the observed drag reduction and show that the drag increases for flatter particles.

  • 35.
    Brethouwer, Geert
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Duguet, Yohann
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Johansson, Arne V.
    KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Recurrent Bursts via Linear Processes in Turbulent Environments2014In: Physical Review Letters, ISSN 0031-9007, Vol. 112, no 14, 144502- p.Article in journal (Refereed)
    Abstract [en]

    Large-scale instabilities occurring in the presence of small-scale turbulent fluctuations are frequently observed in geophysical or astrophysical contexts but are difficult to reproduce in the laboratory. Using extensive numerical simulations, we report here on intense recurrent bursts of turbulence in plane Poiseuille flow rotating about a spanwise axis. A simple model based on the linear instability of the mean flow can predict the structure and time scale of the nearly periodic and self-sustained burst cycles. Poiseuille flow is suggested as a prototype for future studies of low-dimensional dynamics embedded in strongly turbulent environments.

  • 36.
    Brynjell-Rahkola, Mattias
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Shahriari, Nima
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Stability and sensitivity of a cross-flow-dominated Falkner-Skan-Cooke boundary layer with discrete surface roughness2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 826, 830-850 p.Article in journal (Refereed)
    Abstract [en]

    With the motivation of determining the critical roughness size, a global stability and sensitivity analysis of a three-dimensional Falkner-Skan-Cooke (FSC) boundary layer with a cylindrical surface roughness is performed. The roughness size is chosen such that breakdown to turbulence is initiated by a global version of traditional secondary instabilities of the cross-flow (CF) vortices instead of an immediate flow tripping at the roughness. The resulting global eigenvalue spectra of the systems are found to be very sensitive to numerical parameters and domain size. This sensitivity to numerical parameters is quantified using the epsilon-pseudospectrum, and the dependency on the domain is analysed through an impulse response, structural sensitivity analysis and an energy budget. It is shown that while the frequencies remain relatively unchanged, the growth rates increase with domain size, which originates from the inclusion of stronger CF vortices in the baseflow. This is reflected in a change in the rate of advective energy transport by the baseflow. It is concluded that the onset of global instability in a FSC boundary layer as the roughness height is increased does not correspond to an immediate flow tripping behind the roughness, but occurs for lower roughness heights if sufficiently long domains are considered. However, the great sensitivity results in an inability to accurately pinpoint the exact parameter values for the bifurcation, and the large spatial growth of the disturbances in the long domains eventually becomes larger than can be resolved using finite-precision arithmetic.

  • 37.
    Brynjell-Rahkola, Mattias
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Shahriari, Nima
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish Defence Research Agency, Sweden.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Stability and sensitivity of a crossflow-dominated Falkner–Skan–Cooke boundary layer with discrete surface roughness2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Article in journal (Refereed)
    Abstract [en]

    With the motivation of determining the critical roughness size, a global stability and sensitivity analysis of a three-dimensional Falkner–Skan–Cooke (FSC) boundary layer with a cylindrical surface roughness is performed. The roughness size is chosen such that breakdown to turbulence is initiated by a global version of traditional secondary instabilities of the crossflow (CF) vortices, instead of an immediate flow tripping at the roughness. The resulting global eigenvalue spectra of the systems are found to be very sensitive to numerical parameters and domain size. This sensitivity to numerical parameters is quantified using the "-pseudospectrum, and the dependency on the domain is analysed through an impulse response and an energy budget. It is shown that the growth rates increase with domain size, which originates from the inclusion of stronger CF vortices in the baseflow. This is reflected in a change in the rate of advective energy transport by the baseflow. It is concluded that the onset of global instability in a FSC boundary layer as the roughness height is increased does not correspond to an immediate flow tripping behind the roughness, but occurs for lower roughness heights if su ciently long domains are considered. However, the great sensitivity results in an inability to accurately pinpoint the exact parameter values for the bifurcation, and the large spatial growth of the disturbances in the long domains eventually becomes larger than what can be resolved using finite precision arithmetics. 

  • 38.
    Bäbler, Matthäus
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemical Engineering and Technology, Energy Processes.
    Biferale, Luca
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Feudel, Ulrike
    Guseva, Ksenia
    Lanotte, Alessandra S.
    Marchioli, Cristian
    Picano, Francesco
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. University of Padua, Italy.
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Soldati, Alfredo
    Toschi, Federico
    Numerical simulations of aggregate breakup in bounded and unbounded turbulent flows2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 766Article in journal (Refereed)
    Abstract [en]

    Breakup of small aggregates in fully developed turbulence is studied by means of direct numerical simulations in a series of typical bounded and unbounded flow configurations, such as a turbulent channel flow, a developing boundary layer and homogeneous isotropic turbulence. The simplest criterion for breakup is adopted, whereby aggregate breakup occurs when the local hydrodynamic stress sigma similar to epsilon(1/2), with epsilon being the energy dissipation at the position of the aggregate, overcomes a given threshold sigma(cr), which is characteristic for a given type of aggregate. Results show that the breakup rate decreases with increasing threshold. For small thresholds, it develops a scaling behaviour among the different flows. For high thresholds, the breakup rates show strong differences between the different flow configurations, highlighting the importance of non-universal mean-flow properties. To further assess the effects of flow inhomogeneity and turbulent fluctuations, the results are compared with those obtained in a smooth stochastic flow. Furthermore, we discuss the limitations and applicability of a set of independent proxies.

  • 39.
    Canton, Jacopo
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Modal instability of the flow in a toroidal pipe2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 792, 894-909 p.Article in journal (Refereed)
    Abstract [en]

    The modal instability encountered by the incompressible flow inside a toroidal pipe is studied, for the first time, by means of linear stability analysis and direct numerical simulation (DNS). In addition to the unquestionable aesthetic appeal, the torus represents the smallest departure from the canonical straight pipe flow, at least for low curvatures. The flow is governed by only two parameters: the Reynolds number (Formula presented.) and the curvature of the torus (Formula presented.), i.e. the ratio between pipe radius and torus radius. The absence of additional features, such as torsion in the case of a helical pipe, allows us to isolate the effect that the curvature has on the onset of the instability. Results show that the flow is linearly unstable for all curvatures investigated between 0.002 and unity, and undergoes a Hopf bifurcation at (Formula presented.) of about 4000. The bifurcation is followed by the onset of a periodic regime, characterised by travelling waves with wavelength (Formula presented.) pipe diameters. The neutral curve associated with the instability is traced in parameter space by means of a novel continuation algorithm. Tracking the bifurcation provides a complete description of the modal onset of instability as a function of the two governing parameters, and allows a precise calculation of the critical values of (Formula presented.) and (Formula presented.). Several different modes are found, with differing properties and eigenfunction shapes. Some eigenmodes are observed to belong to groups with a set of common characteristics, deemed ‘families’, while others appear as ‘isolated’. Comparison with nonlinear DNS shows excellent agreement, confirming every aspect of the linear analysis, its accuracy, and proving its significance for the nonlinear flow. Experimental data from the literature are also shown to be in considerable agreement with the present results.

  • 40.
    Canton, Jacopo
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Chin, Cheng
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Reynolds number dependence of large-scale friction control in turbulent channel flow2016In: PHYSICAL REVIEW FLUIDS, ISSN 2469-990X, Vol. 1, no 8, 081501Article in journal (Refereed)
    Abstract [en]

    The present work investigates the effectiveness of the control strategy introduced by Schoppa and Hussain [Phys. Fluids 10, 1049 (1998)] as a function of Reynolds number (Re). The skin-friction drag reduction method proposed by these authors, consisting of streamwise-invariant, counter-rotating vortices, was analyzed by Canton et al. [Flow, Turbul. Combust. 97, 811 (2016)] in turbulent channel flows for friction Reynolds numbers (Re t) corresponding to the value of the original study (i.e., 104) and 180. For these Re, a slightly modified version of the method proved to be successful and was capable of providing a drag reduction of up to 18%. The present study analyzes the Reynolds number dependence of this drag-reducing strategy by performing two sets of direct numerical simulations (DNS) for Re-tau = 360 and 550. A detailed analysis of the method as a function of the control parameters (amplitude and wavelength) and Re confirms, on the one hand, the effectiveness of the large-scale vortices at low Re and, on the other hand, the decreasing and finally vanishing effectiveness of this method for higher Re. In particular, no drag reduction can be achieved for Re t = 550 for any combination of the parameters controlling the vortices. For low Reynolds numbers, the large-scale vortices are able to affect the near-wall cycle and alter the wall-shear-stress distribution to cause an overall drag reduction effect, in accordance with most control strategies. For higher Re, instead, the present method fails to penetrate the near-wall region and cannot induce the spanwise velocity variation observed in other more established control strategies, which focus on the near-wall cycle. Despite the negative outcome, the present results demonstrate the shortcomings of the control strategy and show that future focus should be on methods that directly target the near-wall region or other suitable alternatives.

  • 41.
    Canton, Jacopo
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Characterisation of the steady, laminar incompressible flow in toroidal pipes covering the entire curvature range2017In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 66, 95-107 p.Article in journal (Refereed)
    Abstract [en]

    This work is concerned with a detailed investigation of the steady (laminar), incompressible flow inside bent pipes. In particular, a toroidal pipe is considered in an effort to isolate the effect of the curvature, δ, on the flow features, and to compare the present results to available correlations in the literature. More than 110 000 numerical solutions are computed, without any approximation, spanning the entire curvature range, 0 ≤ δ ≤ 1, and for bulk Reynolds numbers Re up to 7 000, where the flow is known to be unsteady. Results show that the Dean number De provides a meaningful non-dimensional group only below very strict limits on the curvature and the Dean number itself. For δ>10−6 and De > 10, in fact, not a single flow feature is found to scale well with the Dean number. These considerations are also valid for quantities, such as the Fanning friction factor, that were previously considered Dean-number dependent only. The flow is therefore studied as a function of two equally important, independent parameters: the curvature of the pipe and the Reynolds number. The analysis shows that by increasing the curvature the flow is fundamentally changed. Moderate to high curvatures are not only quantitatively, but also qualitatively different from low δ cases. A complete description of some of the most relevant flow quantities is provided. Most notably the friction factor f for laminar flow in curved pipes by Ito [J. Basic Eng. 81:123–134 (1959)] is reproduced, the influence of the curvature on f is quantified and the scaling is discussed. A complete database including all the computed solutions is available at www.flow.kth.se.

  • 42. Capuccini, Marco
    et al.
    Ahmed, Laeeq
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schaal, Wesley
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Spjuth, Ola
    Large-scale virtual screening on public cloud resources with Apache Spark2017In: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 9, 15Article in journal (Refereed)
    Abstract [en]

    Background: Structure-based virtual screening is an in-silico method to screen a target receptor against a virtual molecular library. Applying docking-based screening to large molecular libraries can be computationally expensive, however it constitutes a trivially parallelizable task. Most of the available parallel implementations are based on message passing interface, relying on low failure rate hardware and fast network connection. Google's MapReduce revolutionized large-scale analysis, enabling the processing of massive datasets on commodity hardware and cloud resources, providing transparent scalability and fault tolerance at the software level. Open source implementations of MapReduce include Apache Hadoop and the more recent Apache Spark. Results: We developed a method to run existing docking-based screening software on distributed cloud resources, utilizing the MapReduce approach. We benchmarked our method, which is implemented in Apache Spark, docking a publicly available target receptor against similar to 2.2 M compounds. The performance experiments show a good parallel efficiency (87%) when running in a public cloud environment. Conclusion: Our method enables parallel Structure-based virtual screening on public cloud resources or commodity computer clusters. The degree of scalability that we achieve allows for trying out our method on relatively small libraries first and then to scale to larger libraries.

  • 43. Cedervall, Johan
    et al.
    Andersson, Mikael Svante
    Sarkar, Tapati
    Delczeg-Czirjak, Erna K.
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hansen, Thomas C.
    Beran, Premysl
    Nordblad, Per
    Sahlberg, Martin
    Magnetic structure of the magnetocaloric compound AlFe2B22016In: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 664, 784-791 p.Article in journal (Refereed)
    Abstract [en]

    The crystal and magnetic structures of AlFe2B2 have been studied with a combination of X-ray and neutron diffraction and electronic structure calculations. The magnetic and magnetocaloric properties have been investigated by magnetisation measurements. The samples have been produced using high temperature synthesis and subsequent heat treatments. The compound crystallises in the orthorhombic crystal system Cmmm and it orders ferromagnetically at 285 K through a second order phase transition. At temperatures below the magnetic transition the magnetic moments align along the crystallographic a-axis. The magnetic entropy change from 0 to 800 kA/m was found to be - 1.3 J/K kg at the magnetic transition temperature.

  • 44.
    Chattopadhyaya, Mausumi
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Murugan, N. Arul
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study2016In: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, no 36, 7175-7182 p.Article in journal (Refereed)
    Abstract [en]

    We study the linear and nonlinear optical properties of a well-known acid base indicator, bromophenol blue (BPB), in aqueous solution by employing static and integrated approaches. In the static approach, optical properties have been calculated using time-dependent density functional theory (TD-DFT) on the fully relaxed geometries of the neutral and different unprotonated forms of BPB. Moreover, both closed and open forms of BPB were considered. In the integrated approach, the optical properties have been computed over many snapshots extracted from molecular dynamics simulation using a hybrid time-dependent density functional theory/molecular mechanics approach. The static approach suggests closed neutral double right arrow anionic interconversion as the dominant mechanism for the red shift in the absorption spectra of BPB due to a change from acidic to basic pH. It is found by employing an integrated approach that the two interconversions, namely open neutral double right arrow anionic and open neutral double right arrow dianionic, can contribute to the pH- dependent shift in the absorption spectra of BPB. Even though both static and integrated approaches reproduce the pH-dependent red shift in the absorption spectra of BPB, the latter one is suitable to determine both the spectra and spectral broadening. Finally, the computed static first hyperpolarizability for various protonated and deprotonated forms of BPB reveals that this molecule can be used as a nonlinear optical probe for pH sensing in addition to its highly exploited use as an optical probe.

  • 45. Citro, Vincenzo
    et al.
    Giannetti, Flavio
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Luchini, Paolo
    Linear three-dimensional global and asymptotic stability analysis of incompressible open cavity flow2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 768Article in journal (Refereed)
    Abstract [en]

    The viscous and inviscid linear stability of the incompressible flow past a square open cavity is studied numerically. The analysis shows that the flow first undergoes a steady three-dimensional bifurcation at a critical Reynolds number of 1370. The critical mode is localized inside the cavity and has a flat roll structure with a spanwise wavelength of about 0.47 cavity depths. The adjoint global mode reveals that the instability is most efficiently triggered in the thin region close to the upstream tip of the cavity. The structural sensitivity analysis identifies the wavemaker as the region located inside the cavity and spatially concentrated around a closed orbit. As the flow outside the cavity plays no role in the generation mechanisms leading to the bifurcation, we confirm that an appropriate parameter to describe the critical conditions in open cavity flows is the Reynolds number based on the average velocity between the two upper edges. Stabilization is achieved by a decrease of the total momentum inside the shear layer that drives the core vortex within the cavity. The mechanism of instability is then studied by means of a short-wavelength approximation considering pressureless inviscid modes. The closed streamline related to the maximum inviscid growth rate is found to be the same as that around which the global wavemaker is concentrated. The structural sensitivity field based on direct and adjoint eigenmodes, computed at a Reynolds number far higher than that of the base flow, can predict the critical orbit on which the main instabilities inside the cavity arise. Further, we show that the sub-leading unstable time-dependent modes emerging at supercritical conditions are characterized by a period that is a multiple of the revolution time of Lagrangian particles along the orbit of maximum growth rate. The eigenfrequencies of these modes, computed by global stability analysis, are in very good agreement with the asymptotic results.

  • 46. Costa, Pedro
    et al.
    Picano, Francesco
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Universal Scaling Laws for Dense Particle Suspensions in Turbulent Wall-Bounded Flows2016In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 117, no 13, 134501Article in journal (Refereed)
    Abstract [en]

    The macroscopic behavior of dense suspensions of neutrally buoyant spheres in turbulent plane channel flow is examined. We show that particles larger than the smallest turbulence scales cause the suspension to deviate from the continuum limit in which its dynamics is well described by an effective suspension viscosity. This deviation is caused by the formation of a particle layer close to the wall with significant slip velocity. By assuming two distinct transport mechanisms in the near-wall layer and the turbulence in the bulk, we define an effective wall location such that the flow in the bulk can still be accurately described by an effective suspension viscosity. We thus propose scaling laws for the mean velocity profile of the suspension flow, together with a master equation able to predict the increase in drag as a function of the particle size and volume fraction.

  • 47. Delczeg-Czirjak, E. K.
    et al.
    Pereiro, M.
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kvashnin, Y. O.
    Di Marco, I
    Li, Guijiang
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Uppsala Univ, Div Mat Theory, Dept Phys & Astron, Sweden.
    Eriksson, O.
    Origin of the magnetostructural coupling in FeMnP0.75Si0.252014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, no 21, 214436- p.Article in journal (Refereed)
    Abstract [en]

    The strong coupling between the crystal structure and magnetic state (ferromagnetic or helical antiferromagnetic) of FeMnP0.75Si0.25 is investigated using density functional theory in combination with atomistic spin dynamics. We find many competing energy minima for drastically different ferromagnetic and noncollinear magnetic configurations. We also find that the appearance of a helical spin-spiral magnetic structure at finite temperature is strongly related to one of the crystal structures reported for this material. Shorter Fe-Fe distances are found to lead to a destabilized ferromagnetic coupling, while out-of-plane Mn-Mn exchange interactions become negative with the shortening of the interatomic distances along the c axis, implying an antiferromagnetic coupling for the nearest-neighbor Mn-Mn interactions. The impact of the local dynamical correlations is also discussed.

  • 48. Di, Yana
    et al.
    Popovic, Jelena
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    AN ADAPTIVE FAST INTERFACE TRACKING METHOD2015In: Journal of Computational Mathematics, ISSN 0254-9409, E-ISSN 1991-7139, Vol. 33, no 6, 576-586 p.Article in journal (Refereed)
    Abstract [en]

    An adaptive numerical scheme is developed for the propagation of an interface in a velocity field based on the fast interface tracking method proposed in [2]. A multiresolution stategy to represent the interface instead of point values, allows local grid refinement while controlling the approximation error on the interface. For time integration, we use an explicit Runge-Kutta scheme of second-order with a multiscale time step, which takes longer time steps for finer spatial scales. The implementation of the algorithm uses a dynamic tree data structure to represent data in the computer memory. We briefly review first the main algorithm, describe the essential data structures, highlight the adaptive scheme, and illustrate the computational efficiency by some numerical examples.

  • 49. Duguet, Yohann
    et al.
    Monokrousos, Antonios
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Minimal transition thresholds in plane Couette flow2013In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 25, no 8, 084103- p.Article in journal (Refereed)
    Abstract [en]

    Subcritical transition to turbulence requires finite-amplitude perturbations. Using a nonlinear optimisation technique in a periodic computational domain, we identify the perturbations of plane Couette flow transitioning with least initial kinetic energy for Re <= 3000. We suggest a new scaling law E-c = O(Re-2.7) for the energy threshold vs. the Reynolds number, in quantitative agreement with experimental estimates for pipe flow. The route to turbulence associated with such spatially localised perturbations is analysed in detail for Re = 1500. Several known mechanisms are found to occur one after the other: Orr mechanism, oblique wave interaction, lift-up, streak bending, streak breakdown, and spanwise spreading. The phenomenon of streak breakdown is analysed in terms of leading finite-time Lyapunov exponents of the associated edge trajectory.

  • 50. Durrenfeld, P.
    et al.
    Gerhard, F.
    Chico, J.
    Dumas, R. K.
    Ranjbar, M.
    Bergman, A.
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Gould, C.
    Molenkamp, L. W.
    Åkerman, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. University of Gothenburg, Sweden; NanOsc AB, Sweden.
    Tunable damping, saturation magnetization, and exchange stiffness of half-Heusler NiMnSb thin films2015In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, no 21, 214424Article in journal (Refereed)
    Abstract [en]

    The half-metallic half-Heusler alloy NiMnSb is a promising candidate for applications in spintronic devices due to its low magnetic damping and its rich anisotropies. Here we use ferromagnetic resonance (FMR) measurements and calculations from first principles to investigate how the composition of the epitaxially grown NiMnSb influences the magnetodynamic properties of saturation magnetization M-S, Gilbert damping alpha, and exchange stiffness A. M-S and A are shown to have a maximum for stoichiometric composition, while the Gilbert damping is minimum. We find excellent quantitative agreement between theory and experiment for M-S and alpha. The calculated A shows the same trend as the experimental data but has a larger magnitude. In addition to the unique in-plane anisotropy of the material, these tunabilities of the magnetodynamic properties can be taken advantage of when employing NiMnSb films in magnonic devices.

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