kth.sePublications
Change search
Refine search result
1234567 1 - 50 of 765
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1. Abdulrazaq, Muhammed
    et al.
    Shahmardi, Armin
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Edoardo Rost, Marco
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. Department of Energy and Process Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
    Numerical modelling of the extensional dynamics in elastoviscoplastic fluidsManuscript (preprint) (Other academic)
    Abstract [en]

    The extensional dynamics of an elasto-viscoplastic (EVP) fluid is studied by means of numerical simulations closely modelling an experimental configuration.  Specifically, we track the interface between the EVP material and the Newtonian medium using an algebraic volume of fluid method (MTHINC-VOF) and employ a fully Eulerian immersed boundary method (IBM) to model the motion of the piston responsible of the extension of the material.

    We investigate the role of different values of the yield stress, surface tension at the interface between the EVP material and the surrounding fluid, polymer viscosity ratio, and extension rates on the necking thickness of the material, extensional viscosity, and yielding of the material. 

     The results of the simulations reveal that when the yield stress of the EVP material is much larger than the viscous stresses, the material undergoes an elastic deformation, regardless of the selected values of extension rate, interfacial forces, and viscosity ratio. Moreover, increasing the ratio of the polymeric viscosity to the total viscosity of the system accelerates the EVP rupture due to the high stress concentration in the central part of the material sample. Specific and novel to our study, we show that interfacial forces cannot be ignored when the surface tension coefficient is such that a Capillary number based on the extensional rate is order 1. For large values of the surface tension coefficient, the EVP material fails sooner, with a clear deviation from the exponential reduction in the neck thickness.

  • 2.
    Abdulrazaq, Muhammed
    et al.
    Eindhoven Univ Technol, Dept Appl Phys, Fluids & Flows Grp, POB 513, NL-5600 MB Eindhoven, Netherlands..
    Shahmardi, Armin
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Rosti, Marco Edoardo
    Grad Univ, Okinawa Inst Sci & Technol, Complex Fluids & Flows Unit, 1919-1 Tancha, Onna Son, Okinawa 9040495, Japan..
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Numerical modelling of the extensional dynamics in elastoviscoplastic fluids2023In: Journal of Non-Newtonian Fluid Mechanics, ISSN 0377-0257, E-ISSN 1873-2631, Vol. 318, article id 105060Article in journal (Refereed)
    Abstract [en]

    The extensional dynamics of an elasto-viscoplastic (EVP) fluid is studied by means of numerical simulations modelling an experimental configuration. Specifically, we track the interface between the EVP material and the Newtonian medium using an algebraic volume of fluid method (MTHINC-VOF) and employ a fully Eulerian immersed boundary method (IBM) to model the motion of the piston responsible for the extension of the material. We investigate the role of different values of the yield stress, surface tension at the interface between the EVP material and the surrounding fluid, polymer viscosity ratio, and extension rates on the necking thickness of the material, extensional viscosity, and yielding of the material for two sets of parameter with low and high elasticity. The results of the simulations reveal that when the yield stress of the EVP material is much larger than the viscous stresses, the material undergoes an elastic deformation, regardless of the selected values of the extension rate, interfacial forces, and viscosity ratio. Moreover, by increasing the ratio of the polymeric viscosity to the total viscosity of the system, the EVP material produces stronger strain hardening and reaches the minimum resolvable width sooner. Specific and novel to our study, we show that interfacial forces cannot be ignored when the surface tension coefficient is such that a Capillary number based on the extensional rate is of order 1. For large values of the surface tension coefficient, the EVP material fails sooner, with a clear deviation from the exponential reduction in the neck thickness. Moreover, our results suggest that the role of the yield stress value on the dynamics of the material is more pronounced at lower elasticity.

  • 3. Abreu, L. I.
    et al.
    Cavalieri, A. V. G.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Reduced-order models to analyse coherent structures in turbulent pipe flow2019In: 11th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2019, International Symposium on Turbulence and Shear Flow Phenomena, TSFP , 2019Conference paper (Refereed)
    Abstract [en]

    Fully resolved direct numerical simulations, performed with a high-order spectral-element method, are used to study coherent structures in turbulent pipe flow at friction Reynolds numbers Reτ = 180 and 550 (El Khoury et al., 2013). The database was analysed using spectral proper orthogonal decomposition (SPOD) so as to identify dominant coherent structures, most of which are of streaky shape. As a reduced-order model for such structures, the linearised flow response to harmonic forcing was computed, and the analysed singular modes of the resolvent operator were analysed. For turbulent flows, this approach amounts to considering the non-linear terms in the Navier–Stokes system as an unknown forcing, treated convenienty as external. Resolvent analysis then allows an identification of the optimal forcing and most amplified flow response; the latter may be related to observed relevant structures obtained by SPOD, especially if the gain between forcing and response is much larger than what is found for suboptimal forcings or if the non-linear forcing is white noise. Results from SPOD and resolvent analysis were extracted for several combinations of frequencies, streamwise and azimuthal wavenumbers. For both Reynolds numbers, good agreement between SPOD and resolvent modes was observed for parameter combinations where the lift-up mechanism is present: optimal forcing from resolvent analysis represents streamwise vortices and the associated response are streaky structures.

  • 4.
    Abreu, Leandra I.
    et al.
    Divisão de Engenharia Aeronáutica, Instituto Tecnológico de Aeronáutica, 12228-900, São José dos Campos, SP, Brazil.
    Tanarro, Alvaro
    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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Cavalieri, André V.G.
    Divisão de Engenharia Aeronáutica, Instituto Tecnológico de Aeronáutica, 12228-900, São José dos Campos, SP, Brazil.
    Schlatter, Philipp
    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.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Superseded Departments (pre-2005), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wavepackets in turbulent flows around airfoilsManuscript (preprint) (Other academic)
    Abstract [en]

    Motivated by the recent analysis by Sano et al. 2019, Phys. Rev. Fluids, vol. 4, p. 094602, of spanwise-coherent structures in the turbulent flow around airfoils and their connection to trailing-edge noise, we carry out a thorough characterisation of such structures in three simulation databases. We analyse two different numerical simulations of incompressible flow in turbulent regime, both at chord Reynolds number of 400,000: a large-eddy simulation for a NACA 0012 profile at zero angle of attack, and a direct numerical simulation for a NACA 4412 airfoil with an angle of attack of 5 degrees. Snapshots of the flow field were analysed using Spectral Proper Orthogonal Decomposition (SPOD), in order to extract the dominant coherent structures of the flow. Focus is given to  the aforementioned spanwise-coherent fluctuations, which two-dimensional disturbances in the computational domain due to the use of periodic boundary conditions. The leading SPOD modes show that the most energetic coherent structures are wavepackets, extending over the whole turbulent boundary layers around the airfoils with significant amplitudes near the trailing-edge. Higher amplitudes are observed in the region of  stronger adverse pressure gradient at the suction side of the NACA 4412 airfoil. To understand how such structures in the turbulent field can be modelled, the linear response of the flow using the singular value decomposition of the linearised resolvent operator was performed, using the mean field as a base flow and considering a locally parallel approximation. Such analysis shows that the leading SPOD modes can be associated to optimal, linearised flow responses, particularly for stations far from the trailing edge; the latter introduces a discontinuity in boundary conditions, and the locally parallel approximation becomes questionable. We then focus on evaluating the dependence of such wavepackets on the domain size, to ensure that these structures are not an artifact of the use of periodic boundary conditions in small computational boxes. To do so, we performed an incompressible LES of a zero-pressure gradient turbulent boundary layer (ZPGTBL), for three different spanwise sizes: Lz=32 δ*, Lz=64 δ* and Lz=128 δ*, where δ* is a reference displacement thickness in a region of developed turbulent flow, with Reynolds number matching the values in the airfoil simulations. The signature of such wavepackets is seen in non-premultiplied spanwise wavenumber spectra, which reaches, for the three domain sizes, a plateau for spanwise wavelengths going to infinity (or wavenumbers going to zero); this plateau is representative of the spanwise-coherent structures seen in the airfoil simulations. Similar SPOD and resolvent analyses were carried out for the zero spanwise wavenumber of the ZPGTBL, and the same coherent wavepackets were observed for the three domains, with very similar amplitudes. Such wavepackets were also accurately modelled using the optimal resolvent response. These results confirm that the spanwise-elongated structures are not domain-size dependent for the studied simulations, and are thus a feature of turbulent boundary layers.

  • 5.
    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.

    Download full text (pdf)
    Post-print
  • 6. 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.

  • 7.
    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.

  • 8.
    Aguilar, Xavier
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, 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), Computer Science, 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.

  • 9.
    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.

  • 10.
    Ahmed, Zaheer
    et al.
    Koc Univ, Dept Mech Engn, Istanbul, Turkey..
    Izbassarov, Daulet
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Lu, Jiacai
    Johns Hopkins Univ, Dept Mech Engn, Baltimore, MD 21218 USA..
    Tryggvason, Gretar
    Johns Hopkins Univ, Dept Mech Engn, Baltimore, MD 21218 USA..
    Muradoglu, Metin
    Koc Univ, Dept Mech Engn, Istanbul, Turkey..
    Tammisola, Outi
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Effects of soluble surfactant on lateral migration of a bubble in a pressure driven channel flow2020In: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 126, article id 103251Article in journal (Refereed)
    Abstract [en]

    The effects of soluble surfactant on the lateral migration of a bubble in a pressure-driven channel flow are examined by interface-resolved numerical simulations. The interfacial and bulk surfactant concentration evolution equations are solved fully coupled with the incompressible Navier-Stokes equations. A non-linear equation of state is used to relate interfacial surface tension to surfactant concentration at the interface. Extensive computations are performed to investigate the bubble dynamics for a wide range of parameters. It is found that surfactant dramatically changes the bubble dynamics. In the clean case, the bubble position depends on its deformability, characterized by the Eotvos (Eo) and the capillary (Ca) numbers. The spherical bubble moves towards the wall, while the deformable one migrates away from it. On the other hand, in the presence of the surfactant, even the spherical bubble moves away from the wall. It is also found that the contaminated bubble stays away from the wall for Eo = 0.1 and Eo = 1.5 while it migrates towards the wall for 0.1 < Eo < 1.5. Also, at high Eo, the onset of path instability is observed for both the clean and the contaminated cases. However, adding surfactant to the system triggers the path instability earlier and amplifies the oscillations afterwards.

  • 11.
    Aho, Noora
    et al.
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Buslaev, Pavel
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Jansen, Anton
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Bauer, Paul
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Groenhof, Gerrit
    Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Scalable Constant pH Molecular Dynamics in GROMACS2022In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 18, no 10, p. 6148-6160Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the λ-dynamics approach by Brooks and co-workers [Kong, X.; Brooks III, C. L. J. Chem. Phys.1996, 105, 2414–2423] was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the λ-coordinates, not only reduces the complexity associated with parametrizing the intramolecular interactions between the sites but also is easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

  • 12. 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.

  • 13.
    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.

    Download full text (pdf)
    fulltext
  • 14.
    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)
    Abstract [en]

    We study the sedimentaion of finite-size particles in a quiescent wall-boundedNewtonian and shear-thinning fluids. The problem is studied numerically bymeans of direct numerical simulations with the presence of the particles ac-counted for with an immersed boundary method. The supensions are Non-Brownian rigid spherical particles with particle to fluid density ratio ρ p /ρ f =1.5; three different solid volume fractions Φ = 1%, 5% and 20% are considered.The Archimedes number is kept constant to Ar = 36 for all shear-thinning fluidcases, while it is changed to Ar = 97 for the Newtonian fluid to reproduce thesame terminal velocity of a single particle sedimenting in the shear-thinningfluid. We show that the mean settling velocities decrease with the particle con-centration as a consequence of the hindering effect and that the mean settlingspeed is always larger in the shear thinning fluid than in the Newtonian one.This is due to the decrease of the mean viscosity of the fluid which leads to alower drag force acting on the particles. We show that particles tend to formaggregates in the middle of the channel in a shear-thinning fluid, preferentiallypositioning in the wake of neighboring particles or aside them, resulting in lowerlevels of fluctuation in the gravity direction than in a Newtonian fluid.

  • 15.
    Alghalibi, Dhiya
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. 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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. 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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Complex Fluids and Flows Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. 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 fluids2020In: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 129, article id 103291Article in journal (Refereed)
    Abstract [en]

    We study the sedimentation of finite-size particles in quiescent wall-bounded Newtonian and shear-thinning fluids by interface resolved numerical simulations. The suspended phase consists of Non-Brownian rigid spherical particles with particle to fluid density ratio ρp/ρf=1.5 at three different solid volume fractions Φ=1%, 5% and 20%. Firstly, to focus on the effect of shear-thinning on the particle dynamics and interactions, the Archimedes number is increased for a single particle to have the same settling speed in the Newtonian fluid as in the shear-thinning fluid. Secondly, we consider fixed Archimedes and vary the shear-thinning properties of the fluid. Overall, we report a twofold effect of shear thinning. First and more important, the substantial increase of the particle sedimentation velocity in the shear-thinning case due to the increase of the shear rate around the particles, which reduces the local viscosity leading to a reduced particle drag. Secondly, the shear-thinning fluid reduces the level of particle interactions, causing a reduction of velocity fluctuations and resulting in particles sedimenting at approximately the same speed. Moreover, the mean settling velocities decrease with the particle concentration as a consequence of the hindering effect. Particles tend to sediment in the middle of the channel, preferentially positioning in the wake of neighbouring particles or aside them, resulting in lower levels of fluid velocity fluctuations in the gravity direction in the shear-thinning fluid.

  • 16.
    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.

  • 17.
    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.

  • 18.
    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, 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, E-ISSN 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.

  • 19.
    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, 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/.

  • 20.
    Ali, Raja Hashim
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Muhammad, Sayyed Auwn
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Khan, Mehmodd Alam
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Stockholms universitet.
    Quantitative synteny scoring improves homology inference and partitioning of gene families2013In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 14, p. S12-Article in journal (Refereed)
    Abstract [en]

    Background: Clustering sequences into families has long been an important step in characterization of genes and proteins. There are many algorithms developed for this purpose, most of which are based on either direct similarity between gene pairs or some sort of network structure, where weights on edges of constructed graphs are based on similarity. However, conserved synteny is an important signal that can help distinguish homology and it has not been utilized to its fullest potential. Results: Here, we present GenFamClust, a pipeline that combines the network properties of sequence similarity and synteny to assess homology relationship and merge known homologs into groups of gene families. GenFamClust identifies homologs in a more informed and accurate manner as compared to similarity based approaches. We tested our method against the Neighborhood Correlation method on two diverse datasets consisting of fully sequenced genomes of eukaryotes and synthetic data. Conclusions: The results obtained from both datasets confirm that synteny helps determine homology and GenFamClust improves on Neighborhood Correlation method. The accuracy as well as the definition of synteny scores is the most valuable contribution of GenFamClust.

    Download full text (pdf)
    fulltext
  • 21.
    Alizad Banaei, Arash
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Rahmani, Mona
    Univ British Columbia, Dept Math, Vancouver, BC V6T 1Z2, Canada..
    Martinez, D. Mark
    Univ British Columbia, Dept Chem & Biol Engn, Vancouver, BC V6T 1Z3, Canada..
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Inertial settling of flexible fiber suspensions2020In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 5, no 2, article id 024301Article in journal (Refereed)
    Abstract [en]

    We study the inertial settling of suspensions of flexible and rigid fibers using an immersed boundary method. The fibers considered are inextensible and slender, with an aspect ratio of 20. For a single Galileo number of Ga = 160, we examine a range of dimensionless bending rigidities 0.1 < gamma < 20 and fiber concentrations 0.5 < nL(3) < 25, with n being the fiber number density and L the fiber length, that spans dilute and semidilute regimes. The settling fibers form streamers, regions where the fibers are packed and settle faster than the average settling velocity of the suspension, for nL(3) > 10. In the low-concentration regions outside the streamers, the fibers either go upward or have low settling velocities. Flexible fibers exhibit higher packing inside the streamers and smaller streamers compared to the streamers formed by the rigid fibers. Due to this higher packing, the flexible fibers settle faster compared to the rigid fibers. The formation of the streamers counterbalances the hindering of the settling velocity at higher concentrations. At higher nL(3), however, the maximum local concentration of fibers relative to a uniform distribution diminishes for both flexible and rigid fibers as the mobility of the fibers becomes limited due to the presence of other fibers in their vicinity. Due to this limited mobility, the deformation of the fibers and their settling orientation become insensitive to nL(3) for nL(3) > 7. In both the dilute and semidilute regimes, flexible fibers are more aligned with the direction perpendicular to gravity compared to rigid fibers.

  • 22.
    Amini, Kasra
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Mishra, Ases Akas
    Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
    Sivakumar, Amit Kumar
    Department of Chemistry and Chemical Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
    Arlov, Dragana
    Tetra Pak Processing Systems, 221 86 Lund, Sweden.
    Innings, Fredrik
    Tetra Pak Processing Systems, 221 86 Lund, Sweden.
    Kádár, Roland
    Department of Industrial and Materials Science, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
    Tammisola, Outi
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Scaling laws for near-wall flows of thixo-elasto-viscoplastic fluids in a millifluidic channel2024In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 36, no 2, article id 023107Article in journal (Refereed)
    Abstract [en]

    Thixo-elasto-viscoplastic (TEVP) fluids are very complex fluids. In addition to elasticity and viscoplasticity, they exhibit thixotropy, i.e., time-dependent rheology due to breakdown and recovery of internal structures at different length- and timescales. General and consistent methods for a priori flow prediction of TEVP fluids based on rheological characteristics are yet to be developed. We report a combined study of the rheology and flow of 18 samples of different TEVP fluids (three yogurts and three concentrations of Laponite and Carbopol, respectively, in water in both the unstirred and a stirred state). The rheology is determined both with standard protocols and with an ex situ protocol aiming at reproducing the shear history of the fluid in the flow. Micrometer resolution flow measurements in a millimeter scale rectangular duct are performed with Doppler Optical Coherence Tomography (D-OCT). As expected, the results show the existence of a plug flow region for samples with sufficiently high yield stress. At low flow rates, the plug extends almost all the way to the wall and the extent of the plug decreases not only with increased flow rate but also with increased thixotropy. The ex situ rheology protocol enables estimation of the shear rate and shear stress close to the wall, making it possible to identify two scaling laws that relates four different non-dimensional groups quantifying the key properties wall-shear stress and slip velocity. The scaling laws are suggested as an ansatz for a priori prediction of the near-wall flow of TEVP fluids based on shear flow-curves obtained with a rheometer.

  • 23.
    Andersson, Måns
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Markidis, Stefano
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    A Case Study on DaCe Portability & Performance for Batched Discrete Fourier Transforms2023In: Proceedings of the International Conference on High Performance Computing in Asia-Pacific Region: 2023, Association for Computing Machinery (ACM) , 2023Conference paper (Refereed)
    Abstract [en]

    With the emergence of new computer architectures, portability and performance-portability become significant concerns for developing HPC applications. This work reports our experience and lessons learned using DaCe to create and optimize batched Discrete Fourier Transform (DFT) calculations on different single node computer systems. The batched DFT calculation is an essential component in FFT algorithms and is widely used in computer science, numerical analysis, and signal processing. We implement the batched DFT with three complex-value array data layouts and compare them with the native complex type implementation. We use DaCe, which relies on Stateful DataFlow multiGraphs (SDFG) as an intermediate representation (IR) which can be optimized through transforms and then generates code for different architectures. We present several performance results showcasing the potential of DaCe for expressing HPC applications on different computer systems.

  • 24.
    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.

    Download full text (pdf)
    fulltext
  • 25.
    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.

    Download full text (pdf)
    Technical report
  • 26.
    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)
  • 27.
    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.

  • 28.
    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.

    Download full text (pdf)
    Technical report
  • 29.
    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)
  • 30.
    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.

  • 31.
    Appelquist, Ellinor
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Alfredsson, P. Henrik
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Industrial Engineering and Management (ITM), Centres, Competence Center for Gas Exchange (CCGEx). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lingwood, Rebecca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Transition to turbulence in the rotating-disk boundary layer2020In: ETC 2013 - 14th European Turbulence Conference, Zakon Group LLC , 2020Conference paper (Refereed)
    Abstract [en]

    The development of the flow over a rotating disk is investigated by direct numerical simulations using both the linearised and fully nonlinear Navier-Stokes equations. The nonlinear simulations allow investigation of the transition to turbulence of the realistic spatially-developing boundary layer, and these simulations can be directly validated by physical experiments of the same case. The current research aims to elucidate further the global stability properties of the flow. So far, there are no conclusive simulations available in the literature for the fully nonlinear case for this flow, and since the nonlinearity is particularly relevant for transition to turbulence an increased understanding of this process is expected. 

  • 32.
    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.

  • 33. 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. 

  • 34.
    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.

  • 35.
    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..

  • 36. 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.

  • 37.
    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.

  • 38.
    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, E-ISSN 2059-8521, 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.

  • 39.
    Atzori, Marco
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Köpp, Wiebke
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Chien, Wei Der
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Theoretical Computer Science, TCS. KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Massaro, Daniele
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Mallor, Fermin
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Peplinski, Adam
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Rezaei, Mohammadtaghi
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Jansson, Niclas
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Markidis, Stefano
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Laure, E.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Weinkauf, Tino
    KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
    In situ visualization of large-scale turbulence simulations in Nek5000 with ParaView Catalyst2022In: Journal of Supercomputing, ISSN 0920-8542, E-ISSN 1573-0484, Vol. 78, no 3, p. 3605-3620Article in journal (Refereed)
    Abstract [en]

    In situ visualization on high-performance computing systems allows us to analyze simulation results that would otherwise be impossible, given the size of the simulation data sets and offline post-processing execution time. We develop an in situ adaptor for Paraview Catalyst and Nek5000, a massively parallel Fortran and C code for computational fluid dynamics. We perform a strong scalability test up to 2048 cores on KTH’s Beskow Cray XC40 supercomputer and assess in situ visualization’s impact on the Nek5000 performance. In our study case, a high-fidelity simulation of turbulent flow, we observe that in situ operations significantly limit the strong scalability of the code, reducing the relative parallel efficiency to only ≈ 21 % on 2048 cores (the relative efficiency of Nek5000 without in situ operations is ≈ 99 %). Through profiling with Arm MAP, we identified a bottleneck in the image composition step (that uses the Radix-kr algorithm) where a majority of the time is spent on MPI communication. We also identified an imbalance of in situ processing time between rank 0 and all other ranks. In our case, better scaling and load-balancing in the parallel image composition would considerably improve the performance of Nek5000 with in situ capabilities. In general, the result of this study highlights the technical challenges posed by the integration of high-performance simulation codes and data-analysis libraries and their practical use in complex cases, even when efficient algorithms already exist for a certain application scenario.

  • 40.
    Atzori, Marco
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Mallor, Fermin
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Pozuelo, Ramon
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Fukagata, Koji
    Department of Mechanical Engineering, Keio University, 223-8522 Yokohama, Japan.
    Vinuesa, Ricardo
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Schlatter, Philipp
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    A new perspective on skin-friction contributions in adverse-pressure-gradient turbulent boundary layersManuscript (preprint) (Other academic)
    Abstract [en]

    For adverse-pressure-gradient turbulent boundary layers, the study of integral skin-friction contributions still poses significant challenges. Beyond questions related to the integration boundaries and the derivation procedure, which have been thoroughly investigated in the literature, an important issue is how different terms should be aggregated. The nature of these flows, which exhibit significant in-homogeneity in the streamwise direction, usually results in cancellation between several contributions with high absolute values. We propose a formulation of the identity derived by Fukagata, Iwamoto \& Kasagi (Phys. Fluids, vol. 14, 2002, pp. 73--76), which we obtained from the convective form of the governing equations. A new skin-friction contribution is defined, considering wall-tangential convection and pressure gradient together. This contribution is related to the evolution of the dynamic pressure in the mean flow. The results of the decomposition are examined for a broad range of pressure-gradient conditions and different flow-control strategies. We found that the new formulation of the identity allows to readily identify the different regimes of near-equilibrium conditions and approaching separation. It also provides a more effective description of control effects. A similar aggregation between convection and pressure-gradient terms is also possible for any other decomposition where in-homogeneity contributions are considered explicitly. 

  • 41.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Fahland, G.
    Stroh, A.
    Gatti, D.
    Frohnapfel, B.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Aerodynamic Effects of Uniform Blowing and Suction on a NACA4412 Airfoil2020In: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987Article in journal (Refereed)
    Abstract [en]

    We carried out high-fidelity large-eddy simulations to investigate the effects of uniform blowing and uniform suction on the aerodynamic efficiency of a NACA4412 airfoil at the moderate Reynolds number based on chord length and incoming velocity of Rec= 200 , 000. We found that uniform blowing applied at the suction side reduces the aerodynamics efficiency, while uniform suction increases it. This result is due to the combined impact of blowing and suction on skin friction, pressure drag and lift. When applied to the pressure side, uniform blowing improves aerodynamic efficiency. The Reynolds-number dependence of the relative contributions of pressure and friction to the total drag for the reference case is analysed via Reynolds-averaged Navier–Stokes simulations up to Rec= 10 , 000 , 000. The results suggest that our conclusions on the control effect can tentatively be extended to a broader range of Reynolds numbers. 

  • 42.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. 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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gatti, D.
    Stroh, A.
    Frohnapfel, B.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Effects of Different Friction Control Techniques on Turbulence Developing Around Wings2020In: ERCOFTAC Workshop Direct and Large Eddy Simulation: Direct and Large Eddy Simulation XII, Springer, 2020, p. 305-311Chapter in book (Refereed)
    Abstract [en]

    Developing efficient flow control techniques remain a challenging task due to the complexity of turbulent flows in industrial applications, a relevant example of which are turbulent boundary layers (TBL) subjected to pressure gradients. In the present study, we employ high-fidelity numerical simulations to assess the impact of different control strategies on the flow around a NACA4412 airfoil at a Reynolds number Rec=200,000 based on the chord length c and the inflow velocity U∞. The choice of this specific study case is motivated by the relatively weak dependence of the pressure distribution around the airfoil on the Reynolds number [6], which allows distinguishing the effects of increasing Reynolds number and those of the non-uniform adverse pressure gradient (APG).

  • 43.
    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.

  • 44.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    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), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Lozano-Durán, A.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Contribution of Reynolds-stress structures to the secondary flow in turbulent ducts2019In: 11th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2019, International Symposium on Turbulence and Shear Flow Phenomena, TSFP , 2019Conference paper (Refereed)
    Abstract [en]

    The present work is aimed at evaluating the contribution to the secondary flow in duct flow with square and rectangular cross section from three-dimensional coherent structures, defined as intense Reynolds-stress events. The contribution to a certain mean quantity is defined as the ensemble average over the detected coherent structures, weighted with their own occupied volume fraction. Our analysis unveils that the contribution to the cross-stream components of the mean velocity is either very similar to the same contribution in channel flow, or almost negligible in respect to the contribution from the portion of the domain not occupied by coherent structures. These results suggest that the most intense events are not directly responsible for the secondary flow.

  • 45.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering 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), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Lozano-Durán, Adrián
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Coherent structures in turbulent boundary layers over an airfoil2020In: Journal of Physics: Conference Series, ISSN 1742-6588, Vol. 1522, article id 012020Article in journal (Refereed)
    Abstract [en]

    This preliminary study is concerned with the identification of three-dimensional coherent structures, defined as intense Reynolds-stress events, in the turbulent boundary layer developing over the suction side of a NACA4412 airfoil at a Reynolds number based on the chord length and the incoming velocity of $Re_c=200,000$. The scientific interest for such flows originates from the non-uniform adverse pressure gradient that affects the boundary-layer development. Firstly, we assess different methods to identify the turbulent-non-turbulent interface, in order to exclude the irrotational region from the analysis. Secondly, we evaluate the contribution of the considered coherent structures to the enhanced wall-normal velocity, characteristic of adverse pressure gradients. Our results show that it is necessary to limit the detection of coherent structures to the turbulent region of the domain, and that the structures reveal qualitative differences between the contributions of intense events to the wall-normal velocity in adverse-pressure-gradient and zero-pressure-gradient turbulent boundary layers.

  • 46.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering 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), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Lozano-Durán, Adrián
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics.
    Intense Reynolds-stress events in turbulent ducts2021In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 89, article id 108802Article in journal (Refereed)
    Abstract [en]

    The aim of the present work is to investigate the role of intense Reynolds shear-stress events in the generation of the secondary flow in turbulent ducts. We consider the connected regions of flow where the product of the instantaneous fluctuations of two velocity components is higher than a threshold based on the long-time turbulence statistics, in the spirit of the three-dimensional quadrant analysis proposed by Lozano-Dur\'an \textit{et al.} (\textit{J.~Fluid Mech.}, vol. 694, 2012, pp. 100--130). We examine both the geometrical properties of these structures and their contribution to the mean in-plane velocity components, and we perform a comparison with turbulent channel flow at similar Reynolds number. The contribution to a certain mean quantity is defined as the ensemble average over the detected coherent structures, weighted with their own occupied volume fraction. In the core region of the duct, the contribution of intense events to the wall-normal component of the mean velocity is in very good agreement with that in the channel, despite the presence of the secondary flow in the former. Additionally, the shapes of the three-dimensional objects do not differ significantly in both flows. In the corner region of the duct, the proximity of the walls affects both the geometrical properties of the coherent structures and the contribution to the mean component of the vertical velocity. However, such contribution is less relevant than that of the complementary portion of the flow not included in such objects. Our results show that strong Reynolds shear-stress events are affected by the presence of a corner but, despite the important role of these structures in the dynamics of wall-bounded turbulent flows, their contribution to the secondary flow is relatively low, both in the core and in the corner.

  • 47.
    Atzori, Marco
    et al.
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Engineering Mechanics, Fluid Mechanics and Engineering Acoustics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Control effects on coherent structures in a non-uniform adverse-pressure-gradient boundary layer2021Report (Other academic)
    Abstract [en]

    In the present report, we examine the effects of three control strategies, namely uniform blowing, uniform suction, and body-force damping, on the intense Reynolds-stress events in the turbulent boundary layer (TBL) developing on the suction side of a NACA4412 airfoil. This flow is subjected to a non-uniform adverse pressure gradient (APG), which substantially modifies its turbulence statistics with respect to a zero-pressure-gradient (ZPG) boundary layer, and it also changes how control strategies affect the flow. We found that the strong APG results in intense events that are shorter and more often detached from the wall than in ZPG TBLs, and it also modified the contributions of different quadrants. Ejections remain the most relevant structures, but sweeps become more important than in ZPG TBLs, a fact that results in a lower contribution to the wall-normal vertical velocity from intense events. We found that control effects are relatively less important on intense events than on the turbulent statistics. Uniform blowing has an impact similar to that of an even more intense APG, while uniform suction has more complex effects, most likely due to the particular behavior of the wall-normal velocity component near the wall. Body-force damping also reduces the probability of occurrence of very-large attached structures and, not surprisingly, that of intense events in the proximity of the actuation region. 

  • 48.
    Azimi-Mousolou, Vahid
    et al.
    Univ Isfahan, Fac Math & Stat, Dept Appl Math & Comp Sci, Esfahan 8174673441, Iran.;Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Bergman, Anders
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Alballova Univ Ctr, Sch Engn Sci.
    Eriksson, Olle
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Örebro Univ, Sch Sci & Technol, SE-70182 Örebro, Sweden..
    Pereiro, Manuel
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Thonig, Danny
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden.;Örebro Univ, Sch Sci & Technol, SE-70182 Örebro, Sweden..
    Sjoqvist, Erik
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Entanglement duality in spin-spin interactions2022In: Physical Review A: covering atomic, molecular, and optical physics and quantum information, ISSN 2469-9926, E-ISSN 2469-9934, Vol. 106, no 3, article id 032407Article in journal (Refereed)
    Abstract [en]

    We examine entanglement of thermal states for spin-1/2 dimers in external magnetic fields. Entanglement transition in the temperature-magnetic-field plane demonstrates a duality in spin-spin interactions. This identifies a pair of dual categories of symmetric and antisymmetric dimers with each category classified into toric entanglement classes. The entanglement transition line is preserved from each toric entanglement class to its dual toric class. The toric classification is an indication of the topological signature of the entanglement, which bring about topological stability that could be relevant for quantum information processing.

  • 49.
    Azimi-Mousolou, Vahid
    et al.
    Department of Applied Mathematics and Computer Science, Faculty of Mathematics and Statistics, University of Isfahan, Isfahan 81746-73441, Iran; Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden, Box 516.
    Bergman, Anders
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden, Box 516.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Eriksson, Olle
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden, Box 516.
    Pereiro, Manuel
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden, Box 516.
    Thonig, Danny
    School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden.
    Sjöqvist, Erik
    Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden, Box 516.
    Transmon probe for quantum characteristics of magnons in antiferromagnets2023In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 108, no 9, article id 094430Article in journal (Refereed)
    Abstract [en]

    The detection of magnons and their quantum properties, especially in antiferromagnetic (AFM) materials, is a substantial step to realize many ambitious advances in the study of nanomagnetism and the development of energy efficient quantum technologies. The recent development of hybrid systems based on superconducting circuits provides the possibility to engineer quantum sensors that exploit different degrees of freedom. Here, we examine the magnon-photon-transmon hybridization based on bipartite AFM materials, which gives rise to an effective coupling between a transmon qubit and magnons in a bipartite AFM. We demonstrate how magnon modes, their chiralities, and quantum properties, such as nonlocality and two-mode magnon entanglement in bipartite AFMs, can be characterized through the Rabi frequency of the superconducting transmon qubit.

  • 50.
    Bagge, Joar
    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.
    Rosén, Tomas
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Engineering Mechanics.
    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.
    Parabolic velocity profile causes shape-selective drift of inertial ellipsoids2021In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 926, article id A24Article in journal (Refereed)
    Abstract [en]

    Understanding particle drift in suspension flows is of the highest importance in numerous engineering applications where particles need to be separated and filtered out from the suspending fluid. Commonly known drift mechanisms such as the Magnus force, Saffman force and Segre-Silberberg effect all arise only due to inertia of the fluid, with similar effects on all non-spherical particle shapes. In this work, we present a new shape-selective lateral drift mechanism, arising from particle inertia rather than fluid inertia, for ellipsoidal particles in a parabolic velocity profile. We show that the new drift is caused by an intermittent tumbling rotational motion in the local shear flow together with translational inertia of the particle, while rotational inertia is negligible. We find that the drift is maximal when particle inertial forces are of approximately the same order of magnitude as viscous forces, and that both extremely light and extremely heavy particles have negligible drift. Furthermore, since tumbling motion is not a stable rotational state for inertial oblate spheroids (nor for spheres), this new drift only applies to prolate spheroids or tri-axial ellipsoids. Finally, the drift is compared with the effect of gravity acting in the directions parallel and normal to the flow. The new drift mechanism is stronger than gravitational effects as long as gravity is less than a critical value. The critical gravity is highest (i.e. the new drift mechanism dominates over gravitationally induced drift mechanisms) when gravity acts parallel to the flow and the particles are small.

1234567 1 - 50 of 765
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf