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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, p. 420-445Article 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.

  • 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, p. 278-303Article 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, p. 1497-1506Conference 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, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Jordan, H.
    Heller, T.
    Hirsch, A.
    Fahringer, T.
    Laure, Erwin
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    An On-Line Performance Introspection Framework for Task-Based Runtime Systems2019In: 19th International Conference on Computational Science, ICCS 2019, Springer Verlag , 2019, p. 238-252Conference paper (Refereed)
    Abstract [en]

    The expected high levels of parallelism together with the heterogeneity and complexity of new computing systems pose many challenges to current software. New programming approaches and runtime systems that can simplify the development of parallel applications are needed. Task-based runtime systems have emerged as a good solution to cope with high levels of parallelism, while providing software portability, and easing program development. However, these runtime systems require real-time information on the state of the system to properly orchestrate program execution and optimise resource utilisation. In this paper, we present a lightweight monitoring infrastructure developed within the AllScale Runtime System, a task-based runtime system for extreme scale. This monitoring component provides real-time introspection capabilities that help the runtime scheduler in its decision-making process and adaptation, while introducing minimum overhead. In addition, the monitoring component provides several post-mortem reports as well as real-time data visualisation that can be of great help in the task of performance debugging.

  • 5.
    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, E-ISSN 1872-7115, Vol. 29, no 8, p. 2197-2204Article 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.

  • 6. 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, p. 269-284Article 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.

  • 7.
    Alghalibi, Dhiya
    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. Kufa Univ, Coll Engn, Al Najaf, Iraq..
    Numerical study of particle suspensions in Newtonian and non-Newtonian fluids2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Solid or deformable particles suspended in a viscous fluid are of scientific and technological interest in a broad range of applications. Pyroclastic flows from volcanoes, sedimentation flows in river bed, food industries, oil-well drilling, as well as blood flow in the human body and the motion of suspended micro-organisms in water (like plankton) are among the possible examples. Often, in these particulate flows, the carrier fluid might exhibit an inelastic or a visco-elastic non-Newtonian behavior. Understanding the behavior of these suspensions is a very difficult task. Indeed, the complexities and challenges of multiphase flows are mainly due to the large number of governing parameters such as the physical properties of the particles (e.g., shape, size, stiffness, density difference with suspended fluid, solid volume fraction), the large set of interactions among particles and the properties of the carrier fluid (Newtonian or non-Newtonian); variations of each of these parameters may provide substantial quantitative and qualitative changes in the behavior of the suspension and affect the overall dynamics in several and sometimes surprising ways. The aim of this work is therefore to provide a deeper understanding of the behavior of particle suspensions in laminar Newtonian and non-Newtonian (inelastic and/or visco-elastic) fluid flows for a wide range of different parameters. To this purpose, particle-resolved direct numerical simulations of spherical particles are performed, using an efficient and accurate numerical tool. The code is based on the Immersed Boundary Method (IBM) for the fluid-solid interactions with lubrication, friction and collision models for the close range particle-particle (particle-wall) interactions. Both inelastic (Carreau and power-law), and visco-elastic models (Oldroyd-B and Giesekus) are employed to investigate separately the shear-thinning, shear-thickening, viscoelastic and combined shear-thinning visco-elastic features of the most commonly encountered non-Newtonian fluids. Moreover, a fully Eulerian numerical algorithm based on the one-continuum formulation is used to examine the case of an hyper-elastic neo-Hookean deformable particle suspended in a Newtonian flows.

    Firstly, we have investigated suspensions of solid spheres in Newtonian, shear thinning and shear thickening fluids in the simple shear flow created by two walls moving in opposite directions, considering various solid volume fractions and particle Reynolds numbers, thus including inertial effects. The results show that that the non-dimensional relative viscosity of of the suspension and the mean value of the local shear-rate can be well predicted by homogenization theory, more accurately for lower particle concentrations. Moreover, we show that in the presence of inertia, the effective viscosity of these suspensions deviates from that of Stokesian suspensions.

    We also examine the role of fluid elasticity, shear-thinning and combined shear-thinning visco-elastic effects on the simple linear Couette shear flow of neutrally-buoyant rigid spherical particles. It is found that the effective viscosity grows monotonically with the solid volume fraction and that all the Non-Newtonian cases exhibit a lower effective viscosity than the Newtonian ones; in addition, we show that elastic effects dominate at low elasticity whereas shear thinning is predominant at high applied shear rates. These variations in the effective viscosity are mainly due to changes in the particle-induced shear stress component.

    We then study the settling of spherical particles in quiescent wall-bounded Newtonian and shear-thinning fluids at three different solid volume fractions. We find that the mean settling velocities decrease with the particle concentration as a consequence of the hindering effect and thatthe mean settling speed is always larger in the shear thinning fluid than in the Newtonian one, due to the reduction of the local fluid viscosity around the particles which leads to a lower drag force acting on the particles.

    Finally, the inertial migration of hyper-elastic deformable particle in laminar pipe flows is also investigated. We consider different flow rates and various levels of particle elasticity. We observe that the particle deforms and experiences a lateral movement while traveling downstream through the pipe, always finding a stable position at the pipe centerline.

  • 8.
    Alghalibi, Dhiya
    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. College of Engineering, University of Kufa, Al Najaf, Iraq.
    Fornari, Walter
    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.
    Rosti, Marco E.
    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.
    Sedimentation of finite-size particles in quiescent wall-bounded shear-thinning and Newtonian fluidsIn: Journal of International Journal of Multiphase Flow, ISSN 0301-9322Article in journal (Refereed)
  • 9.
    Alghalibi, Dhiya
    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. Kufa Univ, Coll Engn, Al Najaf, Iraq..
    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.
    Hormozi, Sarah
    Ohio Univ, Dept Mech Engn, Athens, OH 45701 USA..
    Interface-resolved simulations of particle suspensions in Newtonian, shear thinning and shear thickening carrier fluids2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 852, p. 329-357Article in journal (Refereed)
    Abstract [en]

    We present a numerical study of non-colloidal spherical and rigid particles suspended in Newtonian, shear thinning and shear thickening fluids employing an immersed boundary method. We consider a linear Couette configuration to explore a wide range of solid volume fractions (0.1 <= Phi <= 0.4) and particle Reynolds numbers (0.1 <= Re<INF>p</INF><INF></INF> <= 10). We report the distribution of solid and fluid phase velocity and solid volume fraction and show that close to the boundaries inertial effects result in a significant slip velocity between the solid and fluid phase. The local solid volume fraction profiles indicate particle layering close to the walls, which increases with the nominal Phi. This feature is associated with the confinement effects. We calculate the probability density function of local strain rates and compare the latter's mean value with the values estimated from the homogenisation theory of Chateau et al. (J. Rheol., vol. 52, 2008, pp. 489-506), indicating a reasonable agreement in the Stokesian regime. Both the mean value and standard deviation of the local strain rates increase primarily with the solid volume fraction and secondarily with the Re<INF>p</INF>. The wide spectrum of the local shear rate and its dependency on Phi and Re<INF>p</INF> point to the deficiencies of the mean value of the local shear rates in estimating the rheology of these non-colloidal complex suspensions. Finally, we show that in the presence of inertia, the effective viscosity of these non-colloidal suspensions deviates from that of Stokesian suspensions. We discuss how inertia affects the microstructure and provide a scaling argument to give a closure for the suspension shear stress for both Newtonian and power-law suspending fluids. The stress closure is valid for moderate particle Reynolds numbers, O(Re<INF>p</INF>) similar to 10.

  • 10.
    Alghalibi, Dhiya
    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. College of Engineering, University of Kufa, Al Najaf, Iraq.
    Rosti, Marco E.
    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.
    Inertial migration of a deformable particle in pipe flow2019In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 4, no 10, article id 104201Article in journal (Refereed)
    Abstract [en]

    We perform fully Eulerian numerical simulations of an initially spherical hyperelastic particle suspended in a Newtonian pressure-driven flow in a cylindrical straight pipe. We study the full particle migration and deformation for different Reynolds numbers and for various levels of particle elasticity, to disentangle the interplay of inertia and elasticity on the particle focusing. We observe that the particle deforms and undergoes a lateral displacement while traveling downstream through the pipe, finally focusing at the pipe centerline. We note that the migration dynamics and the final equilibrium position are almost independent of the Reynolds number, while they strongly depend on the particle elasticity; in particular, the migration is faster as the elasticity increases (i.e., the particle is more deformable), with the particle reaching the final equilibrium position at the centerline in shorter times. Our simulations show that the results are not affected by the particle initial conditions, position, and velocity. Finally, we explain the particle migration by computing the total force acting on the particle and its different components, viscous and elastic.

  • 11.
    Alghalibi, Dhiya
    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. College of Engineering, Kufa University, Al Najaf, Iraq.
    Rosti, Marco E.
    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. Department of Mechanical Engineering, The University of Tokyo, Tokyo, Japan.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Superseded Departments (pre-2005), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Interface-resolved simulations of particle suspensions in visco-elastic carrier fluidsIn: Journal of Fluid Mechanics, ISSN 0022-1120, EISSN 1469-7645Article in journal (Refereed)
    Abstract [en]

    We study the rheology of a suspension of neutrally buoyant rigid particles subject touniform shear in different kinds of non-Newtonian fluids, chosen in order to disentanglethe effect of elasticity and shear thinning on the macroscopic system behavior. In par-ticular, we adopt the inelastic Carreau, viscoelastic Oldroyd-B and Giesekus models forthe carrier fluid. The rheology of the suspension is analyzed for a wide range of particlevolume fractions, Weissenberg and Reynolds numbers, comparing the results with thoseobtained for a Newtonian carrier fluid. We report here that the effective viscosity per-taining all the non-Newtonian cases is always lower than that of the suspension in theNewtonian carrier fluid and grows monotonically with the solid volume fraction. Theshear-thinning viscoelastic Giesekus fluid behaves similarly to the Oldroyd-B fluid at lowWeissenberg numbers and to the Carreau fluid at high Weissenberg numbers, indicatingthat elastic effects dominate at low Weissenberg and shear thinning is predominant athigh Weissenberg number. These variations in the effective viscosity are mainly due tochanges in the particle induced shear stress component. These data show that, at highshear rates, a viscoelastic carrier fluid can be modelled as a simple shear-thinning fluidfor which theoretical closures exists, while new models are needed at low Weissenbergnumbers to account for elastic effects such as decreased particle stress. Finally, when theinertia is increased, the suspension effective viscosity grows with the particle Reynoldsnumber at the same rate as in a Newtonian fluid for the Oldroyd-B case, while in ashear-thinning fluid the growth is less than in the Newtonian fluid. Also in the presenceof inertia, therefore, the shear-thinning behaviour dominates the suspension dynamics atrelatively high values of the imposed shear rate and elasticity effects saturate.

  • 12.
    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, article id 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/.

  • 13.
    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.

  • 14.
    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.

  • 15.
    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)
  • 16.
    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, p. 332-355Article 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.

  • 17.
    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.

  • 18.
    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)
  • 19.
    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, p. 612-631Article 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.

  • 20.
    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, P. 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. Queen Mary University of London, Mile End Road, London, United Kingdom.
    Turbulence in the rotating-disk boundary layer investigated through direct numerical simulations2018In: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 70, p. 6-18Article in journal (Refereed)
    Abstract [en]

    Direct numerical simulations (DNS) are reported for the turbulent rotating-disk boundary layer for the first time. Two turbulent simulations are presented with overlapping small and large Reynolds numbers, where the largest corresponds to a momentum-loss Reynolds number of almost 2000. Simulation data are compared with experimental data from the same flow case reported by Imayama et al. (2014), and also a comparison is made with a numerical simulation of a two-dimensional turbulent boundary layer (2DTBL) over a flat plate reported by Schlatter and Örlü (2010). The agreement of the turbulent statistics between experiments and simulations is in general very good, as well as the findings of a missing wake region and a lower shape factor compared to the 2DTBL. The simulations also show rms-levels in the inner region similar to the 2DTBL. The simulations validate Imayama et al.’s results showing that the rotating-disk turbulent boundary layer in the near-wall region contains shorter streamwise (azimuthal) wavelengths than the 2DTBL, probably due to the outward inclination of the low-speed streaks. Moreover, all velocity components are available from the simulations, and hence the local flow angle, Reynolds stresses and all terms in the turbulent kinetic energy equation are also discussed. However there are in general no large differences compared to the 2DTBL, hence the three-dimensional effects seem to have only a small influence on the turbulence.

  • 21. 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, p. 177-192Article 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. 

  • 22.
    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, p. 16-34Article 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.

  • 23.
    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, p. 1135-1166Article 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..

  • 24. 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, p. 948-976Article 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.

  • 25.
    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, p. 463-487Article 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.

  • 26.
    Atwa, Mohamed M.
    et al.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Alaskalany, Ahmed
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Elgammal, Karim
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Smith, Anderson D.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Hammar, Mattias
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Östling, Mikael
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Trilayer Graphene as a Candidate Material for Phase-Change Memory Applications2016In: MRS Advances, ISSN 2316-7858, E-ISSN 1610-191X, Vol. 1, no 20, p. 1487-1494Article 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.

  • 27.
    Atzori, Marco
    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.
    Vinuesa, Ricardo
    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.
    Lozano-Durán, A.
    Schlatter, Philipp
    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.
    Characterization of turbulent coherent structures in square duct flow2018In: Journal of Physics: Conference Series, Institute of Physics Publishing (IOPP), 2018, Vol. 1001, no 1Conference paper (Refereed)
    Abstract [en]

    This work is aimed at a first characterization of coherent structures in turbulent square duct flows. Coherent structures are defined as connected components in the domain identified as places where a quantity of interest (such as Reynolds stress or vorticity) is larger than a prescribed non-uniform threshold. Firstly, we qualitatively discuss how a percolation analysis can be used to assess the effectiveness of the threshold function, and how it can be affected by statistical uncertainty. Secondly, various physical quantities that are expected to play an important role in the dynamics of the secondary flow of Prandtl's second kind are studied. Furthermore, a characterization of intense Reynolds-stress events in square duct flow, together with a comparison of their shape for analogous events in channel flow at the same Reynolds number, is presented.

  • 28.
    Bagheri, Shervin
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Liu, Q.ingyun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Bergstrand, Jan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Pu, R.
    Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information.
    Zhan, Q.
    Centre for Optical and Electromagnetic Research, Guangdong Provincial Key Laboratory of Optical Information.
    Ara, M. H. M.
    Photonics Laboratory, Physics Department, Kharazmi University, Tehran, Iran.
    Ågren, Hans
    KTH, Superseded Departments (pre-2005), Biotechnology. KTH, Superseded Departments (pre-2005), Chemistry. KTH, School of Biotechnology (BIO), Centres, Albanova VinnExcellence Center for Protein Technology, ProNova. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Liu, Haichun
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum and Biophotonics.
    Change in the emission saturation and kinetics of upconversion nanoparticles under different light irradiations2019In: Optical materials (Amsterdam), ISSN 0925-3467, E-ISSN 1873-1252, Vol. 97, article id 109389Article in journal (Refereed)
    Abstract [en]

    Nd3+-sensitized upconversion nanoparticles (UCNPs) can be excited by both 980 and 808 nm light, which is regarded as a particularly advantageous property of these particles. In this work, we demonstrate that the nanoparticles can exhibit significantly different response when excited at these two excitation wavelengths, showing dependence on the intensity of the excitation light and the way it is distributed in time. Specifically, with 808 nm excitation saturation in the emitted luminescence is more readily reached with increasing excitation intensities than upon 980 nm excitation. This is accompanied by delayed upconversion luminescence (UCL) kinetics and weaker UCL intensities. The different luminescence response at 808 and 980 nm excitation reported in this work is relevant in a manifold of applications using UCNPs as labels and sensors. This could also open new possibilities for multi-wavelength excitable UCNPs for upconversion color display and in laser-scanning microscopy providing selective readouts and sub-sectioning of samples.

  • 29.
    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, p. 131-153Article 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.

  • 30.
    Banerjee, Indradumna
    et al.
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Rosti, Marco Eduardo
    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.
    Niazi Ardekani, Mehdi
    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.
    Kumar, Tharagan
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    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, 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.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Dynamics of Inertial migration of particles in straight channels2017Conference paper (Refereed)
    Abstract [en]

    SUMMARY

    We study numerically the entire migration dynamics of spherical and oblate particles in straight rectangular and square cross sectional ducts. The reported results can help in design of straight duct channel based microfluidic systems.

     

    KEYWORDS: Inertial microfluidics, Lateral migration, Oblate particles, Straight particles.

     

    INTRODUCTION

    We  simulate spherical and oblate rigid particles in straight ducts of different aspect ratios using an Immersed Boundary Method. To the best of our knowledge, this is the first time not only the equilibrium position of particles is described, but also the entire migration dynamics of the particle from the initial to final position, including particle trajectory, velocity, rotation and orientation, are investigated.

     

    EXPERIMENTAL

     The fluid is considered incompressible and its motion is governed by the Navier Stokes and Continuity equations. The numerical approach employed is an Immersed Boundary Method (IBM) with two sets of grid points: an equispaced Eulerian mesh for the fluid flow, and Lagrangian grid points uniformly distributed on the surface of the particle. The flow is set up in square and rectangular cross section ducts with no slip and no penetration boundary conditions (Fig.1).

     

    RESULTS AND DISCUSSION

    We examine the lateral motion of spherical and oblate particles using the IBM method mentioned above. While simulating three different spheres in a square duct of duct width to sphere diameter ratio H/Ds= [3.5, 5, 10], we find that the particles focus at closest face-cantered equilibrium position from their point of introduction(Fig.2a). We also show the downstream length needed for a sphere to focus, focusing length, as a function of the distance from the vertical duct symmetry line and as a function of Reynolds number(Fig.2b and c respectively). Spherical particles in rectangular duct tend to move laterally toward the longer length wall and then slowly moves towards the equilibrium position at the face-centre along the long wall(fig.3a). We also observe that the focusing length is longer for spherical particles in a rectangular duct, about three times longer than that in square duct (fig. 3b). In case of an oblate particle flowing through a square duct, the lateral motion towards the face centred equilibrium position is similar to that of a sphere (fig.4a), however there is significant tumbling motion of the particle as it tries to reach equilibrium(fig.4b).In a rectangular duct of aspect ratio 2, the oblate particle reaches a steady configuration on the duct symmetry line at the center of the different faces (fig.5a). The focusing length surprisingly is shorter in a rectangular duct for an oblate particle in contrast to its focusing length in a square duct. This is attributed to the higher lateral velocity of the oblate in the second stage of the migration, that with negligible tumbling(fig.5b). The behavior of three oblate particles in a square duct of duct width to longer diameter ratio H/Ds= [3.5, 5, 10] is different compared to a sphere as the largest oblate tend to focus at the duct cross section diagonals compared to the other two which are at face centred equilibrium as in case of a sphere(fig.6a). We attribute this to the rotation rate of the larger particle which is initially increasing and then decreasing(fig.6b).When it comes to focusing lengths, the smaller particles need longer times to reach their final equilibrium(fig.6c). Another interesting behavior we see is the effect of Reynolds number, where it can be seen that the oblate particles show a tilt of 21 degrees when focusing at equilibrium at certain high Reynolds number (fig.7).

     

    CONCLUSION

    The results presented employ a highly accurate interface-resolved numerical algorithm, based on the Immersed Boundary Method to study the entire inertial migration of an oblate particle in both square and rectangular ducts and compare it with that of a single sphere. Currently, we apply a volume penalization method and polymeric drag component to the code to solve for viscoelastic effects in circular microcapillaries.

     

    ACKNOWLEDGEMENTS

    This work was supported by the European Research Council Grant no. ERC-2013-CoG-616186, TRITOS and by the Swedish Research Council Grant no. VR 2014-5001, COST Action MP1305: Flowing matter, and computation time from SNIC.

     REFERENCES : Lashgari, Iman, et al. Journal of Fluid Mechanics 819 (2017): 540-561.

  • 31. 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, article id 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.

  • 32.
    Beneitez Galan, Miguel
    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.
    Duguet, Yohann
    LIMSI-CNRS, UPR 3251, Université Paris-Saclay, Orsay, F-91403, France Abstract.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. 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.
    Edge tracking in spatially developing boundary layer flows2019In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 881, p. 164-181Article in journal (Refereed)
    Abstract [en]

    Recent progress in understanding subcritical transition to turbulence is based on the concept of the edge, the manifold separating the basins of attraction of the laminar and the turbulent state. Originally developed in numerical studies of parallel shear flows with a linearly stable base flow, this concept is adapted here to the case of a spatially developing Blasius boundary layer. Longer time horizons fundamentally change the nature of the problem due to the loss of stability of the base flow due to Tollmien-Schlichting (TS) waves. We demonstrate, using a moving box technique, that efficient long-time tracking of edge trajectories is possible for the parameter range relevant to bypass transition, even if the asymptotic state itself remains out of reach. The flow along the edge trajectory features streak switching observed for the first time in the Blasius boundary layer. At long enough times, TS waves co-exist with the coherent structure characteristic of edge trajectories. In this situation we suggest a reinterpretation of the edge as a manifold dividing the state space between the two main types of boundary layer transition, i.e. bypass transition and classical transition.

  • 33. 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, article id 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.

  • 34.
    Bergqvist, Lars
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Bergman, Anders
    Realistic finite temperature simulations of magnetic systems using quantum statistics2018In: Physical Review Materials, ISSN 2475-9953, Vol. 2, no 1, article id 013802Article in journal (Refereed)
    Abstract [en]

    We have performed realistic atomistic simulations at finite temperatures using Monte Carlo and atomistic spin dynamics simulations incorporating quantum (Bose-Einstein) statistics. The description is much improved at low temperatures compared to classical (Boltzmann) statistics normally used in these kind of simulations, while at higher temperatures the classical statistics are recovered. This corrected low-temperature description is reflected in both magnetization and the magnetic specific heat, the latter allowing for improved modeling of the magnetic contribution to free energies. A central property in the method is the magnon density of states at finite temperatures, and we have compared several different implementations for obtaining it. The method has no restrictions regarding chemical and magnetic order of the considered materials. This is demonstrated by applying the method to elemental ferromagnetic systems, including Fe and Ni, as well as Fe-Co random alloys and the ferrimagnetic system GdFe3.

  • 35. Bessarab, Pavel F.
    et al.
    Mueller, Gideon P.
    Lobanov, Igor S.
    Rybakov, Filipp N.
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics.
    Kiselev, Nikolai S.
    Jonsson, Hannes
    Uzdin, Valery M.
    Blugel, Stefan
    Bergqvist, Lars
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lifetime of racetrack skyrmions2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 3433Article in journal (Refereed)
    Abstract [en]

    The skyrmion racetrack is a promising concept for future information technology. There, binary bits are carried by nanoscale spin swirls-skyrmions-driven along magnetic strips. Stability of the skyrmions is a critical issue for realising this technology. Here we demonstrate that the racetrack skyrmion lifetime can be calculated from first principles as a function of temperature, magnetic field and track width. Our method combines harmonic transition state theory extended to include Goldstone modes, with an atomistic spin Hamiltonian parametrized from density functional theory calculations. We demonstrate that two annihilation mechanisms contribute to the skyrmion stability: At low external magnetic field, escape through the track boundary prevails, but a crossover field exists, above which the collapse in the interior becomes dominant. Considering a Pd/Fe bilayer on an Ir(111) substrate as a well-established model system, the calculated skyrmion lifetime is found to be consistent with reported experimental measurements. Our simulations also show that the Arrhenius pre-exponential factor of escape depends only weakly on the external magnetic field, whereas the pre-exponential factor for collapse is strongly field dependent. Our results open the door for predictive simulations, free from empirical parameters, to aid the design of skyrmion-based information technology.

  • 36. Biancofiore, L.
    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, T. A.
    Streak instability in viscoelastic Couette flow2017In: PHYSICAL REVIEW FLUIDS, ISSN 2469-990X, Vol. 2, no 4, article id 043304Article in journal (Refereed)
    Abstract [en]

    The secondary instability of nonlinear streaks and transition to turbulence in viscoelastic Couette flow are studied using direct numerical simulations. Viscoelasticity is modeled using the FENE-P constitutive equations. Both the polymer concentration beta and Weissenberg number Wi are varied in order to assess their effects on transition at moderate Reynolds number. The base streaks are obtained from nonlinear simulations of the Couette flow response to a streamwise vortex. We select the initial amplitude of the vortex which yields a desired maximum amplitude of the nonlinear streaks during their temporal evolution. The development of streaks in both Newtonian and non-Newtonian flows is primarily due to the action of streamwise vorticity onto the mean shear. In the viscoelastic case, it is also affected by the polymer torque, which opposes the vorticity and becomes more pronounced at large Weissenberg number. Streaks with the same maximum streamwise velocity perturbation can therefore have different total kinetic energy at higher Weissenberg number. At every streak amplitude of interest, harmonic forcing is introduced along the transverse direction to trigger the secondary instability and breakdown to turbulence. We demonstrate that the critical amplitude of the forcing, A(d), increases at large Weissenberg number. The degree of stabilization due to elasticity depends on the initial streak intensity, A(s),(in). For weak streaks the critical amplitude for secondary instability is more sensitive to Wi than for strong ones. This is explained by the existence of two different mechanisms that can trigger transition to turbulence. The perturbation to weak streaks is initially stabilized by the polymer torque which acts to oppose the amplification of wall-normal vorticity and, as a result, delays breakdown to turbulence. The secondary instability of strong streaks, on the other hand, is more immune to this stabilizing influence of the polymer.

  • 37.
    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.

  • 38.
    Bobke, Alexandra
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vinuesa, Ricardo
    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.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. 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.
    History effects and near equilibrium in adverse-pressure-gradient turbulent boundary layers2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 820, p. 667-692Article in journal (Refereed)
    Abstract [en]

    Turbulent boundary layers under adverse pressure gradients are studied using well-resolved large-eddy simulations (LES) with the goal of assessing the influence of the streamwise pressure-gradient development. Near-equilibrium boundary layers were characterized through the Clauser pressure-gradient parameter β. In order to fulfil the near-equilibrium conditions, the free stream velocity was prescribed such that it followed a power-law distribution. The turbulence statistics pertaining to cases with a constant value of β (extending up to approximately 40 boundary-layer thicknesses) were compared with cases with non-constant β distributions at matched values of β and friction Reynolds number Reδ∗. An additional case at matched Reynolds number based on displacement thickness Reδ∗ was also considered. It was noticed that non-constant β cases appear to approach the conditions of equivalent constant β cases after long streamwise distances (approximately 7 boundary-layer thicknesses). The relevance of the constant β cases lies in the fact that they define a 'canonical' state of the boundary layer, uniquely characterized by β and Re. The investigations on the flat plate were extended to the flow around a wing section overlapping in terms of β and Re. Comparisons with the flat-plate cases at matched values of β and Re revealed that the different development history of the turbulent boundary layer on the wing section leads to a less pronounced wake in the mean velocity as well as a weaker second peak in the Reynolds stresses. This is due to the weaker accumulated effect of the β history. Furthermore, a scaling law suggested by Kitsios et al. (Intl J. Heat Fluid Flow, vol. 61, 2016, pp. 129-136), proposing the edge velocity and the displacement thickness as scaling parameters, was tested on two constant-pressure-gradient parameter cases. The mean velocity and Reynolds-stress profiles were found to be dependent on the downstream development. The present work is the first step towards assessing history effects in adverse-pressure-gradient turbulent boundary layers and highlights the fact that the values of the Clauser pressure-gradient parameter and the Reynolds number are not sufficient to characterize the state of the boundary layer.

  • 39.
    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.

  • 40.
    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.

  • 41.
    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, p. 157-180Article 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.

  • 42. 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, p. 19-48Article 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.

  • 43.
    Borlenghi, Simone
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Boman, Magnus
    KTH, School of Electrical Engineering and Computer Science (EECS), Software and Computer systems, SCS. RISE SICS, Electrum 229, SE-16429 Kista, Sweden..
    Delin, Anna
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Modeling reservoir computing with the discrete nonlinear Schrodinger equation2018In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, no 5, article id 052101Article in journal (Refereed)
    Abstract [en]

    We formulate, using the discrete nonlinear Schrodinger equation (DNLS), a general approach to encode and process information based on reservoir computing. Reservoir computing is a promising avenue for realizing neuromorphic computing devices. In such computing systems, training is performed only at the output level by adjusting the output from the reservoir with respect to a target signal. In our formulation, the reservoir can be an arbitrary physical system, driven out of thermal equilibrium by an external driving. The DNLS is a general oscillator model with broad application in physics, and we argue that our approach is completely general and does not depend on the physical realization of the reservoir. The driving, which encodes the object to be recognized, acts as a thermodynamic force, one for each node in the reservoir. Currents associated with these thermodynamic forces in turn encode the output signal from the reservoir. As an example, we consider numerically the problem of supervised learning for pattern recognition, using as a reservoir a network of nonlinear oscillators.

  • 44.
    Borlenghi, Simone
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Stochastic Thermodynamics of Oscillators' Networks2018In: Entropy, ISSN 1099-4300, E-ISSN 1099-4300, Vol. 20, no 12, article id 992Article in journal (Refereed)
    Abstract [en]

    We apply the stochastic thermodynamics formalism to describe the dynamics of systems of complex Langevin and Fokker-Planck equations. We provide in particular a simple and general recipe to calculate thermodynamical currents, dissipated and propagating heat for networks of nonlinear oscillators. By using the Hodge decomposition of thermodynamical forces and fluxes, we derive a formula for entropy production that generalises the notion of non-potential forces and makes transparent the breaking of detailed balance and of time reversal symmetry for states arbitrarily far from equilibrium. Our formalism is then applied to describe the off-equilibrium thermodynamics of a few examples, notably a continuum ferromagnet, a network of classical spin-oscillators and the Frenkel-Kontorova model of nano friction.

  • 45.
    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, p. 054428-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.

  • 46. 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, article id 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.

  • 47. 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, article id 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.

  • 48.
    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, E-ISSN 1079-7114, Vol. 112, no 4, p. 047203-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.

  • 49. 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, p. 59-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.

  • 50.
    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, p. 80-96Article 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.

1234567 1 - 50 of 415
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