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  • 201.
    Niazi Ardekani, Mehdi
    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.
    Abouali, Omid
    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. School of Mechanical Engineering, Shiraz University.
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    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.
    Heat transfer in laminar Couette flow laden with rigid spherical particles2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 834, p. 308-334Article in journal (Refereed)
    Abstract [en]

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

  • 202.
    Niazi Ardekani, Mehdi
    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.
    Asmar, L. A.
    Picano, F.
    Brandt, L.uca
    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.
    Numerical study of heat transfer in laminar and turbulent pipe flow with finite-size spherical particles2018In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 71, p. 189-199Article in journal (Refereed)
    Abstract [en]

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

  • 203.
    Niazi Ardekani, Mehdi
    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
    Picano, Francesco
    University of Padova, Department of Industrial Engineering.
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Drag reduction in turbulent channel flow laden with finite-size oblate spheroids2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 816, p. 43-70Article in journal (Refereed)
    Abstract [en]

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

  • 204.
    Niazi Ardekani, Mehdi
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Brandt, Luca
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Karp-Boss, Lee
    School of Marine Sciences, University of Maine.
    Bearon, Rachel
    Department of Mathematical Sciences, University of Liverpool.
    Variano, Evan
    Department of Civil and Environmental Engineering, University of California.
    Sedimentation of inertia-less prolate spheroids in homogenous isotropic turbulence with application to non-motile phytoplankton2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 831, p. 655-674Article in journal (Refereed)
    Abstract [en]

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

  • 205.
    Noorani, Azad
    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.
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Particle dispersion in turbulent curved pipe flowManuscript (preprint) (Other academic)
  • 206.
    Noorani, Azad
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Particle transport in turbulent curved pipe flow2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 793, p. 248-279Article in journal (Refereed)
    Abstract [en]

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

  • 207.
    Noorani, Azad
    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.
    Sardina, Gaetano
    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.
    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.
    Particle Velocity and Acceleration in Turbulent Bent Pipe Flows2015In: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 95, no 2-3, p. 539-559Article in journal (Refereed)
    Abstract [en]

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

  • 208.
    Noorani, Azad
    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.
    Evidence of sublaminar drag naturally occurring in a curved pipe2015In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 27, no 3, article id 035105Article in journal (Refereed)
    Abstract [en]

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

  • 209.
    Noorani, Azad
    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), Mechanics.
    Swirl-switching phenomenon in turbulent flow through toroidal pipes2015In: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Conference paper (Refereed)
    Abstract [en]

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

  • 210. Nowbahar, Arash
    et al.
    Sardina, Gaetano
    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.
    Picano, Francesco
    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.
    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.
    Turbophoresis attenuation in a turbulent channel flow with polymer additives2013In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 732, p. 706-719Article in journal (Refereed)
    Abstract [en]

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

  • 211. Nyblom, Maria
    et al.
    Poulsen, Hanne
    Gourdon, Pontus
    Reinhard, Linda
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fedosova, Natalya
    Nissen, Poul
    Crystal Structure of Na+, K+-ATPase in the Na+-Bound State2013In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 342, no 6154, p. 123-127Article in journal (Refereed)
    Abstract [en]

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

  • 212.
    Offermans, Nicolas
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Marin, O.
    Schanen, M.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fischer, P.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics.
    On the strong scaling of the spectral element solver Nek5000 on petascale systems2016In: Proceedings of the 2016 Exascale Applications and Software Conference (EASC2016): April 25-29 2016, Stockholm, Sweden, Association for Computing Machinery (ACM), 2016, article id a5Conference paper (Refereed)
    Abstract [en]

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

  • 213. Olivieri, S.
    et al.
    Picano, Francesco
    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.
    Sardina, Gaetano
    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.
    Iudicone, D.
    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.
    The effect of the Basset history force on particle clustering in homogeneous and isotropic turbulence2014In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 26, no 4, p. 041704-Article in journal (Refereed)
    Abstract [en]

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

  • 214.
    Orellana, Laura
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Yoluk, Ozge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Carrillo, Oliver
    Orozco, Modesto
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed)
    Abstract [en]

    Protein conformational changes are at the heart of cell functions, from signalling to ion transport. However, the transient nature of the intermediates along transition pathways hampers their experimental detection, making the underlying mechanisms elusive. Here we retrieve dynamic information on the actual transition routes from principal component analysis (PCA) of structurally-rich ensembles and, in combination with coarse-grained simulations, explore the conformational landscapes of five well-studied proteins. Modelling them as elastic networks in a hybrid elastic-network Brownian dynamics simulation (eBDIMS), we generate trajectories connecting stable end-states that spontaneously sample the crystallographic motions, predicting the structures of known intermediates along the paths. We also show that the explored non-linear routes can delimit the lowest energy passages between end-states sampled by atomistic molecular dynamics. The integrative methodology presented here provides a powerful framework to extract and expand dynamic pathway information from the Protein Data Bank, as well as to validate sampling methods in general.

  • 215.
    Otero, Evelyn
    et al.
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering.
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Min, Misun
    Argonne National Laboratory.
    Fischer, Paul
    Argonne National Laboratory.
    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.
    Laure, Erwin
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    OpenACC accelerator for the Pn-Pn-2 algorithm in Nek50002018In: Proceedings of the 5th International Conference on Exascale Applications and Software, 2018Conference paper (Refereed)
  • 216.
    Otero, Evelyn
    et al.
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, Aerodynamics. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Marin, Oana
    Argonne Natl Lab, MCS, Lemont, IL 60439 USA..
    Laure, Erwin
    PDC KTH, Ctr High Performance Comp, SE-10044 Stockholm, Sweden..
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Mechanics of Industrial Processes. KTH Mech, Linne FLOW Ctr, SE-10044 Stockholm, Sweden.;Swedish E Sci Res Ctr SeRC, Stockholm, Sweden..
    Lossy Data Compression Effects on Wall-bounded Turbulence: Bounds on Data Reduction2018In: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 101, no 2, p. 365-387Article in journal (Refereed)
    Abstract [en]

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

  • 217. Otten, Matthew
    et al.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Mametjanov, Azamat
    Vose, Aaron
    Levesque, John
    Fischer, Paul
    Min, Misun
    An MPI/OpenACC implementation of a high-order electromagnetics solver with GPUDirect communication2016In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, no 3, p. 320-334Article in journal (Refereed)
    Abstract [en]

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

  • 218. Ottosson, Nina E.
    et al.
    Ejneby, Malin Silvera
    Wu, Xiongyu
    Yazdi, Samira
    Konradsson, Peter
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Physics.
    Elinder, Fredrik
    A drug pocket at the lipid bilayer-potassium channel interface2017In: Science Advances, ISSN 0036-8156, E-ISSN 2375-2548, Vol. 3, no 10, article id e1701099Article in journal (Refereed)
    Abstract [en]

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

  • 219.
    Pan, Fan
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Chico, Jonathan
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. Uppsala Univ, Sweden.
    Bergman, Anders
    Bergqvist, Lars
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics.
    Extended spin model in atomistic simulations of alloys2017In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 95, no 18, article id 184432Article in journal (Refereed)
    Abstract [en]

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

  • 220.
    Pan, Fan
    et al.
    KTH, School of Engineering Sciences (SCI). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Chico, Jonathan
    Delin, Anna
    Bergman, Anders
    Bergqvist, Lars
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Superseded Departments, Materials Science and Engineering. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Finite temperature properties of transition metal alloys using extended spin modelManuscript (preprint) (Other academic)
  • 221.
    Pan, Fan
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Chico, Jonathan
    Hellsvik, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Bergman, Anders
    Bergqvist, Lars
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Systematic study of magnetodynamic properties at finite temperatures in doped permalloy from first-principles calculations2016In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 94, no 21, article id 214410Article in journal (Refereed)
    Abstract [en]

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

  • 222.
    Pan, Fan
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics. Department of Physics and Astronomy,Uppsala University.
    Bergman, Anders
    Bergqvist, Lars
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Magnon properties of random alloysManuscript (preprint) (Other academic)
  • 223. Panda, S. K.
    et al.
    Bhowal, S.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Eriksson, O.
    Dasgupta, I.
    Effect of spin orbit coupling and Hubbard U on the electronic structure of IrO22014In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 89, no 15, p. 155102-Article in journal (Refereed)
    Abstract [en]

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

  • 224. Panda, S. K.
    et al.
    Di Marco, I.
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Eriksson, O.
    Correlated electronic structure of CeN2016In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 208, p. 111-115Article in journal (Refereed)
    Abstract [en]

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

  • 225. Panda, S. K.
    et al.
    Pal, Banabir
    Mandal, Suman
    Gorgoi, Mihaela
    Das, Shyamashis
    Sarkar, Indranil
    Drube, Wolfgang
    Sun, Weiwei
    Di Marco, I.
    Lindblad, Andreas
    Thunstroem, P.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Sweden.
    Karis, Olof
    Kvashnin, Y. O.
    van Schilfgaarde, M.
    Eriksson, O.
    Sarma, D. D.
    High photon energy spectroscopy of NiO: Experiment and theory2016In: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 93, no 23, article id 235138Article in journal (Refereed)
    Abstract [en]

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

  • 226. Panda, S. K.
    et al.
    Thunstrom, P.
    Di Marco, I.
    Schott, J.
    Delin, Anna
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Dasgupta, I.
    Eriksson, O.
    Sarma, D. D.
    A charge self-consistent LDA plus DMFT study of the spectral properties of hexagonal NiS2014In: New Journal of Physics, ISSN 1367-2630, E-ISSN 1367-2630, Vol. 16, p. 093049-Article in journal (Refereed)
    Abstract [en]

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

  • 227. Paredes, P.
    et al.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics. FOI, Sweden.
    Theofilis, V.
    Henningson, Dan Stefan
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The Nonlinear PSE-3D Concept for Transition Prediction in Flows with a Single Slowly-varying Spatial Direction2015In: Procedia IUTAM, Elsevier, 2015, p. 36-44Conference paper (Refereed)
    Abstract [en]

    A number of flow cases of practical significance exhibit a predominant spatial direction, along which the mean properties of the flow field vary slowly while having fast variations on the cross-sectional planes. This property is taken into account when the three- dimensional parabolized stability equations (PSE-3D) are derived. These equations represent the most efficient approach for the solution of the instability problem of such flows. In this work, the linear PSE-3D are extended to predict the nonlinear development of perturbations in this kind of complex three-dimensional flows. The newly developed method is formulated and verified for different flow problems of interest. Firstly, it has been verified by computing the evolution of linear and nonlinear Tollmien- Schlichting waves in Blasius boundary layer, showing excellent agreement with traditional nonlinear PSE predictions. Also, the evolution of optimal streaks is simulated and compared against direct numerical simulations. Finally, the nonlinear development of stationary crossflow instabilities in a three-dimensional boundary layer is monitored using a non-orthogonal coordinate system to follow the instability trajectory, showing again a very good agreement with PSE results.

  • 228.
    Parviainen, Pekka
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Farahani, H. S.
    Lagergren, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Learning bounded tree-width Bayesian networks using integer linear programming2014In: Journal of machine learning research, ISSN 1532-4435, E-ISSN 1533-7928, Vol. 33, p. 751-759Article in journal (Refereed)
    Abstract [en]

    In many applications one wants to compute conditional probabilities given a Bayesian network. This inference problem is NP-hard in general but becomes tractable when the network has low tree-width. Since the inference problem is common in many application areas, we provide a practical algorithm for learning bounded tree-width Bayesian networks. We cast this problem as an integer linear program (ILP). The program can be solved by an anytime algorithm which provides upper bounds to assess the quality of the found solutions. A key component of our program is a novel integer linear formulation for bounding tree-width of a graph. Our tests clearly indicate that our approach works in practice, as our implementation was able to find an optimal or nearly optimal network for most of the data sets.

  • 229. Paul, S.
    et al.
    Iuşan, D.
    Thunström, P.
    Kvashnin, Y. O.
    Hellsvik, Johan
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics.
    Pereiro, M.
    Delin, Anna
    KTH, School of Engineering Sciences (SCI), Applied Physics, Materials and Nanophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Knut, R.
    Phuyal, D.
    Lindblad, A.
    Karis, O.
    Sanyal, B.
    Eriksson, O.
    Investigation of the spectral properties and magnetism of BiFeO3 by dynamical mean-field theory2018In: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 97, no 12, article id 125120Article in journal (Refereed)
    Abstract [en]

    Using the local density approximation plus dynamical mean-field theory (LDA+DMFT), we have computed the valence-band photoelectron spectra and magnetic excitation spectra of BiFeO3, one of the most studied multiferroics. Within the DMFT approach, the local impurity problem is tackled by the exact diagonalization solver. The solution of the impurity problem within the LDA+DMFT method for the paramagnetic and magnetically ordered phases produces result in agreement with the experimental data on electronic and magnetic structures. For comparison, we also present results obtained by the LDA+U approach which is commonly used to compute the physical properties of this compound. Our LDA+DMFT derived electronic spectra match adequately with the experimental hard x-ray photoelectron spectroscopy and resonant photoelectron spectroscopy for Fe 3d states, whereas the LDA+U method fails to capture the general features of the measured spectra. This indicates the importance of accurately incorporating the dynamical aspect of electronic correlation among Fe 3d orbitals to reproduce the experimental excitation spectra. Specifically, the LDA+DMFT derived density of states exhibits a significant amount of Fe 3d states at the position of Bi lone pairs, implying that the latter are not alone in the spectral scenario. This fact might modify our interpretation about the origin of ferroelectric polarization in this material. Our study demonstrates that the combination of orbital cross sections for the constituent elements and broadening schemes for the spectral functions are crucial to explain the detailed structures of the experimental electronic spectra. Our magnetic excitation spectra computed from the LDA+DMFT result conform well with the inelastic neutron scattering data.

  • 230.
    Peplinski, Adam
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    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.
    Henningson, Dan Stefan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Global stability and optimal perturbation for a jet in cross-flow2015In: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 49, p. 438-447Article in journal (Refereed)
    Abstract [en]

    We study the stability of a jet in cross-flow at low values of the jet to cross-flow velocity ratio R using direct numerical simulations (DNS) and global linear stability analysis adopting a time-stepper method. For the simplified setup without a meshed pipe in the simulations we compare results of a fully-spectral code SIMSON with a spectral-element code Nek5000. We find the use of periodic domains, even with the fringe method, unsuitable due to the large sensitivity of the eigenvalues and due to the large spatial growth of the corresponding eigenmodes. However, we observe a similar sensitivity to reflection from the outflow boundary in the inflow/outflow configuration, and therefore we use an extended domain where reflections are minimal. We apply in our studies both modal and non-modal linear analyses investigating transient effects and their asymptotic fate, and we find a transient wavepacket to develop almost identically in both the globally stable and unstable cases. The final results of the global stability analysis for our numerical setup show the critical value of R, at which the first bifurcation occurs, to lie in the range between 1.5 and 1.6.

  • 231.
    Peplinski, Adam
    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.
    Henningson, Dan Stefan
    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.
    Investigations of stability and transition of a jet in crossflow using DNS2015In: Instability and Control of Massively Separated Flows: Proceedings of the International Conference on Instability and Control of Massively Separated Flows, held in Prato, Italy, from 4-6 September 2013, Kluwer Academic Publishers, 2015, Vol. 107, p. 7-18Conference paper (Refereed)
    Abstract [en]

    We study the stability of a jet in crossflow at low values of the jet-tocrossflow velocity ratio R focusing on direct numerical simulations (DNS) and the global linear stability analysis adopting a time-stepper method. For the simplified setup neglecting a meshed pipe in the simulations, we compare results of the fullyspectral code SIMSON with the spectral-element code Nek5000. We find the calculated critical value R for the first bifurcation to be dependent on the numerical method used. This result is related to a large sensitivity of the eigenvalues and to the large spatial growth of the corresponding eigenmodes, making the use of periodic domains, even with the fringe method, difficult. However, we observe a similar sensitivity to reflection from the outflow boundary in the inflow/outflow configuration as well.We apply in our studies both modal and non-modal analyses investigating transient effects and their asymptotic fate, and we find transient wavepacket that develop almost identically in the stable and unstable cases. Finally, we compare these results with the simulation including the pipe in the computational domain finding the latter one to be much more unstable.

  • 232. Peters, Lars
    et al.
    Ghosh, Saurabh
    Sanyal, Biplab
    van Dijk, Chris
    Bowlan, John
    de Heer, Walt
    Delin, Anna
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. Uppsala Universitet, Sweden.
    Di Marco, Igor
    Eriksson, Olle
    Katsnelson, Mikhail I.
    Johansson, Borje
    Kirilyuk, Andrei
    Magnetism and exchange interaction of small rare-earth clusters; Tb as a representative2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 19676Article in journal (Refereed)
    Abstract [en]

    Here we follow, both experimentally and theoretically, the development of magnetism in Tb clusters from the atomic limit, adding one atom at a time. The exchange interaction is, surprisingly, observed to drastically increase compared to that of bulk, and to exhibit irregular oscillations as a function of the interatomic distance. From electronic structure theory we find that the theoretical magnetic moments oscillate with cluster size in exact agreement with experimental data. Unlike the bulk, the oscillation is not caused by the RKKY mechanism. Instead, the inter-atomic exchange is shown to be driven by a competition between wave-function overlap of the 5d shell and the on-site exchange interaction, which leads to a competition between ferromagnetic double-exchange and antiferromagnetic super-exchange. This understanding opens up new ways to tune the magnetic properties of rare-earth based magnets with nano-sized building blocks.

  • 233. Picano, F.
    et al.
    Costa, P.
    Breugem, W. -P
    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.
    Turbulence modulation by dense suspensions in channel flows2017In: 10th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2017, International Symposium on Turbulence and Shear Flow Phenomena, TSFP10 , 2017, Vol. 1Conference paper (Refereed)
    Abstract [en]

    Dense suspensions are usually investigated in the laminar limit where inertial effects are insignificant. In this regime, the main effect of the suspended phase is to alter the rheological behavior of the flow which always displays higher effective viscosity with respect to the carrier fluid. When the flow rate is high enough, i.e. at high Reynolds number, the flow may become turbulent and the interaction between solid and liquid phase modifies the turbulent dynamics that we know in single-phase fluids. In the present work, we study turbulent channel flows laden with finite-size particles at high volume fraction (F = 0:2) by means of Direct Numerical Simulations. A direct-forcing Immersed Boundary Method has been adopted to couple liquid and solid phases. The two-phase simulations have been performed fixing the bulk Reynolds number at Reb = Ub 2h=n = 12000 (Ub bulk velocity, h channel half-width and n the fluid kinematic viscosity). The particle size is relatively large with respect to the viscous length, i.e. 10 and 20 times, but smaller than large scales. We will present a detailed comparison of the statistical behavior of the particle-laden flow and the corresponding single-phase flow. The presence of the solid phase strongly alters the wall turbulence dynamics and its effect cannot be accounted only considering the higher rheological effective viscosity.

  • 234.
    Picano, Francesco
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Turbulent channel flow of dense suspensions of neutrally buoyant spheres2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 764, p. 463-487Article in journal (Refereed)
    Abstract [en]

    Dense particle suspensions are widely encountered in many applications and in environmental flows. While many previous studies investigate their rheological properties in laminar flows, little is known on the behaviour of these suspensions in the turbulent/inertial regime. The present study aims to fill this gap by investigating the turbulent flow of a Newtonian fluid laden with solid neutrally-buoyant spheres at relatively high volume fractions in a plane channel. Direct numerical simulation (DNS) are performed in the range of volume fractions Phi=0-0.2 with an immersed boundary method (IBM) used to account for the dispersed phase. The results show that the mean velocity profiles are significantly altered by the presence of a solid phase with a decrease of the von Karman constant in the log-law. The overall drag is found to increase with the volume fraction, more than one would expect if just considering the increase of the system viscosity due to the presence of the particles. At the highest volume fraction investigated here, Phi = 0.2, the velocity fluctuation intensities and the Reynolds shear stress are found to decrease. The analysis of the mean momentum balance shows that the particle-induced stresses govern the dynamics at high Phi and are the main responsible of the overall drag increase. In the dense limit, we therefore find a decrease of the turbulence activity and a growth of the particle induced stress, where the latter dominates for the Reynolds numbers considered here.

  • 235.
    Picano, Francesco
    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.
    Breugem, Wim-Paul
    Mitra, Dhrubaditya
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    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.
    Shear Thickening in Non-Brownian Suspensions: An Excluded Volume Effect2013In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 111, no 9, p. 098302-Article in journal (Refereed)
    Abstract [en]

    Shear thickening appears as an increase of the viscosity of a dense suspension with the shear rate, sometimes sudden and violent at high volume fraction. Its origin for noncolloidal suspension with non-negligible inertial effects is still debated. Here we consider a simple shear flow and demonstrate that fluid inertia causes a strong microstructure anisotropy that results in the formation of a shadow region with no relative flux of particles. We show that shear thickening at finite inertia can be explained as an increase of the effective volume fraction when considering the dynamically excluded volume due to these shadow regions.

  • 236. Popovic, Jelena
    et al.
    Runborg, Olof
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mathematics (Dept.).
    Adaptive fast interface tracking methods2017In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 337, p. 42-61Article in journal (Refereed)
    Abstract [en]

    In this paper, we present a fast time adaptive numerical method for interface tracking. The method uses an explicit multiresolution description of the interface, which is represented by wavelet vectors that correspond to the details of the interface on different scale levels. The complexity of standard numerical methods for interface tracking, where the interface is described by N marker points, is 0 (N/Delta t),when a time step At is used. The methods that we propose in this paper have 0 (TOL-1/P log N + N log N) computational cost, at least for uniformly smooth problems, where TOL is some given tolerance and p is the order of the time stepping method that is used for time advection of the interface. The adaptive method is robust in the sense that it can handle problems with both smooth and piecewise smooth interfaces (e.g. interfaces with corners) while keeping a low computational cost. We show numerical examples that verify these properties.

  • 237.
    Poppi, Stefano
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology. KTH, Centres, SeRC - Swedish e-Science Research Centre. Dalarna University, Sweden.
    Bales, Chris
    Techno-Economic Analysis of a Novel Solar Thermal and Air-Source Heat Pump System2016Conference paper (Other academic)
    Abstract [en]

    This paper presents a techno-economic analysis of a novel solar thermal and air source heat pump system. The system was designed for relatively high operating temperatures in the space heating circuit and included the use of a heat pump with vapor injection cycle and vacuum insulation on the storage tank. The system model was validated against measurements in laboratory and simulated in TRNSYS 17. Annual simulations were performed for the combination of two climates (Carcassonne and Zurich) and two house standards (SFH45 and SFH100) and the best results were achieved for the boundary conditions the system was designed for. For those conditions (Zurich and SFH100), the novel system showed potential for being cost-effective compared to state of art solar and heat pump system. The “additional investment limit”, i.e. the maximum extra investment cost for the novel system in comparison to a state of art benchmark system that gives a break even result for a period of 10 years, varied between 827 € and 2482 € depending on electricity price. The results of a sensitivity analysis showed that variations in electricity price affected the additional investment limit far more than the other economic parameters.

  • 238.
    Poppi, Stefano
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology. KTH, Centres, SeRC - Swedish e-Science Research Centre. Dalarna University, Sweden.
    Sommerfeldt, Nelson
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology.
    Bales, Chris
    Madani, Hatef
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Applied Thermodynamics and Refrigeration.
    Lundqvist, Per
    KTH, School of Industrial Engineering and Management (ITM), Energy Technology, Applied Thermodynamics and Refrigeration.
    Techno-economic review of solar heat pump systems for residential heating applications2018In: Renewable & sustainable energy reviews, ISSN 1364-0321, E-ISSN 1879-0690, Vol. 81, p. 22-32Article, review/survey (Refereed)
    Abstract [en]

    Solar heat pump systems (SHPs) have been investigated for several decades and have been proven to increase the share of renewable energy and reduce electric energy demand in residential heating applications. Many review articles have been published on the subject, however literature discussing the techno-economics of different solar technologies (thermal, photovoltaic and hybrid thermal/photovoltaic) in combination with heat pumps is lacking, and thus to directly compare the merits of different SHPs is not an easy task. The objectives of this study are: a) review the different system boundaries and the main performance indicators used for assessing energetic and economic performances; b) review techno-economic studies in the literature and identify which studies give enough information and are compatible enough for making an economic inter-comparison; c) present an economic inter-comparison based on the identified systems. The results show that there is a lack of studies including an economic assessment of solar photovoltaic and heat pump systems. Additionally, there are no consistent boundaries or approaches to the study structures, making comparisons between systems difficult. In conclusion, a standardized or broadly accepted definition of technical and economic performance for SHPs is needed. Despite this, the study has shown that there are clear trends for decreasing payback times for SHPs, both solar thermal (ST) and photovoltaic (PV), with decreasing heating degree-days and with increasing solar resource.

  • 239.
    Pouya, Iman
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pronk, Sander
    KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, M.
    Lindahl, Erik R.
    KTH, School of Engineering Sciences (SCI), Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient large-scale ensemble sampling2017In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 71, p. 18-31Article in journal (Refereed)
    Abstract [en]

    Compute-intensive applications have gradually changed focus from massively parallel supercomputers to capacity as a resource obtained on-demand. This is particularly true for the large-scale adoption of cloud computing and MapReduce in industry, while it has been difficult for traditional high-performance computing (HPC) usage in scientific and engineering computing to exploit this type of resources. However, with the strong trend of increasing parallelism rather than faster processors, a growing number of applications target parallelism already on the algorithm level with loosely coupled approaches based on sampling and ensembles. While these cannot trivially be formulated as MapReduce, they are highly amenable to throughput computing. There are many general and powerful frameworks, but in particular for sampling-based algorithms in scientific computing there are some clear advantages from having a platform and scheduler that are highly aware of the underlying physical problem. Here, we present how these challenges are addressed with combinations of dataflow programming, peer-to-peer techniques and peer-to-peer networks in the Copernicus platform. This allows automation of sampling-focused workflows, task generation, dependency tracking, and not least distributing these to a diverse set of compute resources ranging from supercomputers to clouds and distributed computing (across firewalls and fragile networks). Workflows are defined from modules using existing programs, which makes them reusable without programming requirements. The system achieves resiliency by handling node failures transparently with minimal loss of computing time due to checkpointing, and a single server can manage hundreds of thousands of cores e.g. for computational chemistry applications.

  • 240.
    Pronk, Sander
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Pouya, Iman
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lundborg, Magnus
    Rotskoff, Grant
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wesén, Björn
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kasson, Peter M.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, SE-10691 Stockholm, Sweden.
    Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform2015In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, no 6, p. 2600-2608Article in journal (Refereed)
    Abstract [en]

    Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide mote processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.

  • 241.
    Páll, Szilard
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A flexible algorithm for calculating pair interactions on SIMD architectures2013In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 184, no 12, p. 2641-2650Article in journal (Refereed)
    Abstract [en]

    Calculating interactions or correlations between pairs of particles is typically the most time-consuming task in particle simulation or correlation analysis. Straightforward implementations using a double loop over particle pairs have traditionally worked well, especially since compilers usually do a good job of unrolling the inner loop. In order to reach high performance on modern CPU and accelerator architectures, single-instruction multiple-data (SIMD) parallelization has become essential. Avoiding memory bottlenecks is also increasingly important and requires reducing the ratio of memory to arithmetic operations. Moreover, when pairs only interact within a certain cut-off distance, good SIMD utilization can only be achieved by reordering input and output data, which quickly becomes a limiting factor. Here we present an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters. Calculating all interactions between particles in a pair of such clusters improves data reuse compared to the traditional scheme and results in a more efficient SIMD parallelization. Adjusting the cluster size allows the algorithm to map to SIMD units of various widths. This flexibility not only enables fast and efficient implementation on current CPUs and accelerator architectures like GPUs or Intel MIC, but it also makes the algorithm future-proof. We present the algorithm with an application to molecular dynamics simulations, where we can also make use of the effective buffering the method introduces.

  • 242.
    Quaranta, Hugo Umberto
    et al.
    Airbus Helicopters, Aerodynamics Department, Marignane, France.
    Brynjell-Rahkola, Mattias
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Leweke, Thomas
    CNRS, Aix-Marseille Universit ́e, Centrale Marseille, IRPHE, Marseille, France.
    Henningson, Dan S.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Long-wave instabilities of two interlaced helical vortices2017Manuscript (preprint) (Other academic)
    Abstract [en]

    We investigate theoretically and experimentally the stability of two interlaced helical vortices with respect to displacement perturbations having wavelengths that are large compared to the size of the vortex cores. First, existing theoretical results are recalled and applied to the present configuration. Various modes of unstable perturbations, involving different phase relationships between the two vortices, are identified and their growth rates are calculated. They lead to a local pairing of neighbouring helix loops, or to a uniform pairing with one helix expanding and the other one contracting. A relation is established between this instability and the three-dimensional pairing of arrays of straight parallel vortices, and a striking quantitative agreement concerning the growth rates is found, showing that the local pairing of vortices is the driving mechanism behind the instability of the helix system. Second, an experimental study designed to observe these instabilities in a real flow is presented. Two helical vortices are generated by a two-bladed rotor in a water channel and characterised through dye visualisations and PIV measurements. Unstable displacement modes are triggered individually, either by varying the rotation frequency of the rotor, or by imposing a small rotor eccentricity. The observed unstable mode structure, and the corresponding growth rates obtained from advanced processing of visualisation sequences, are in good agreement with theoretical predictions. The non-linear late stages of the instability are also documented experimentally. Whereas local pairing leads to strong deformations and subsequent break-up of the vortices, uniform pairing results in a leapfrogging phenomenon, which intermittently restores the initial double-helix geometry, in agreement with recent observations from numerical simulations.

  • 243.
    Rasam, Amin
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering.
    Wallin, Stefan
    KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Brethouwer, Gert
    KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Johansson, Arne V.
    KTH, School of Engineering Sciences (SCI), Mechanics, Turbulence. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Large-eddy simulation using the explicit algebraic subgrid model in complex geometries2013In: International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013, TSFP-8 , 2013Conference paper (Refereed)
    Abstract [en]

    In Rasam et al. (2011) we compared the performance of the explicit algebraic subgrid-scale (SGS) model (EASSM) (Marstorp et al., 2009) with that of the conventional dynamic Smagorinsky model (DSM) in large eddy simulation (LES) of channel flow using a pseudo-spectral Navier-Stokes solver. We showed that, due to the better prediction of the individual SGS stresses in a wide range of grid resolutions and due to the nonlinear SGS stress contribution by the model, the EASSM predictions were less resolution dependent and more accurate than those of the DSM. As the first step in this study towards LES in complex geometries, we extend our previous study and perform LES of turbulent channel flow at Ret = 590 using the EASSM and the code Saturne, which is an unstructured finite volume solver suitable for LES in complex geometries. The results are compared to those of the DSM and show that the EASSM predictions of the wall shear and the Reynolds stresses are more accurate. LES results using the EASSM obtained from the code Saturne are also compared to those obtained using the pseudo-spectral solver obtained in our previous study (Rasam et al., 2013). As the next step, we are performing LES of flow over periodic hill using the EASSM and the code Saturne. The results will be compared with those of the DSM and the reference LES and will be presented at the conference.

  • 244.
    Ray, Arjun
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Wallner, B.
    Improved model quality assessment using ProQ22012In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 13, no 1, p. 224-Article in journal (Refereed)
    Abstract [en]

    Background: Employing methods to assess the quality of modeled protein structures is now standard practice in bioinformatics. In a broad sense, the techniques can be divided into methods relying on consensus prediction on the one hand, and single-model methods on the other. Consensus methods frequently perform very well when there is a clear consensus, but this is not always the case. In particular, they frequently fail in selecting the best possible model in the hard cases (lacking consensus) or in the easy cases where models are very similar. In contrast, single-model methods do not suffer from these drawbacks and could potentially be applied on any protein of interest to assess quality or as a scoring function for sampling-based refinement.Results: Here, we present a new single-model method, ProQ2, based on ideas from its predecessor, ProQ. ProQ2 is a model quality assessment algorithm that uses support vector machines to predict local as well as global quality of protein models. Improved performance is obtained by combining previously used features with updated structural and predicted features. The most important contribution can be attributed to the use of profile weighting of the residue specific features and the use features averaged over the whole model even though the prediction is still local.Conclusions: ProQ2 is significantly better than its predecessors at detecting high quality models, improving the sum of Z-scores for the selected first-ranked models by 20% and 32% compared to the second-best single-model method in CASP8 and CASP9, respectively. The absolute quality assessment of the models at both local and global level is also improved. The Pearson's correlation between the correct and local predicted score is improved from 0.59 to 0.70 on CASP8 and from 0.62 to 0.68 on CASP9; for global score to the correct GDT_TS from 0.75 to 0.80 and from 0.77 to 0.80 again compared to the second-best single methods in CASP8 and CASP9, respectively. ProQ2 is available at http://proq2.wallnerlab.org.

  • 245. Ren, J.
    et al.
    Fu, S.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Swedish Defence Research Agency.
    Stabilization of the hypersonic boundary layer by finite-amplitude streaks2016In: 54th AIAA Aerospace Sciences Meeting, 2016Conference paper (Refereed)
    Abstract [en]

    Stabilization of two-dimensional disturbances in hypersonic boundary layer flows by finite-amplitude streaks is investigated using nonlinear parabolized stability equations. The boundary-layer flows at Mach numbers 4.5 and 6.0 are studied in which both the first-and second modes are supported. The streaks considered here are driven either by the so-called optimal perturbations (Klebanoff-type) or the centrifugal instability (Görtler-type). When the streak amplitude is in an appropriate range, i.e., large enough to modulate the laminar boundary layer but low enough to not trigger secondary instability, both the first-and second modes can effectively be suppressed.

  • 246. Ren, Jie
    et al.
    Fu, Song
    Hanifi, Ardeshir
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Swedish Def Res Agcy FOI, Stockholm, Sweden.
    Stabilization of the hypersonic boundary layer by finite-amplitude streaks2016In: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 28, no 2, article id 024110Article in journal (Refereed)
    Abstract [en]

    Stabilization of two-dimensional disturbances in hypersonic boundary layer flows by finite-amplitude streaks is investigated using nonlinear parabolized stability equations. The boundary-layer flows at Mach numbers 4.5 and 6.0 are studied in which both first and second modes are supported. The streaks considered here are driven either by the so-called optimal perturbations (Klebanoff-type) or the centrifugal instability (Gortler-type). When the streak amplitude is in an appropriate range, i.e., large enough to modulate the laminar boundary layer but low enough to not trigger secondary instability, both first and second modes can effectively be suppressed. (C) 2016 AIP Publishing LLC.

  • 247. Rezaeiravesh, S.
    et al.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Liefvendahl, M.
    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.
    Assessment of uncertainties in hot-wire anemometry and oil-film interferometry measurements for wall-bounded turbulent flows2018In: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 72, p. 57-73Article in journal (Refereed)
    Abstract [en]

    In this study, the sources of uncertainty of hot-wire anemometry (HWA) and oil-film interferometry (OFI) measurements are assessed. Both statistical and classical methods are used for the forward and inverse problems, so that the contributions to the overall uncertainty of the measured quantities can be evaluated. The correlations between the parameters are taken into account through the Bayesian inference with error-in-variable (EiV) model. In the forward problem, very small differences were found when using Monte Carlo (MC), Polynomial Chaos Expansion (PCE) and linear perturbation methods. In flow velocity measurements with HWA, the results indicate that the estimated uncertainty is lower when the correlations among parameters are considered, than when they are not taken into account. Moreover, global sensitivity analyses with Sobol indices showed that the HWA measurements are most sensitive to the wire voltage, and in the case of OFI the most sensitive factor is the calculation of fringe velocity. The relative errors in wall-shear stress, friction velocity and viscous length are 0.44%, 0.23% and0.22%, respectively. Note that these values are lower than the ones reported in other wall-bounded turbulence studies. Note that in most studies of wall-bounded turbulence the correlations among parameters are not considered, and the uncertainties from the various parameters are directly added when determining the overall uncertainty of the measured quantity. In the present analysis we account for these correlations, which may lead to a lower overall uncertainty estimate due to error cancellation Furthermore, our results also indicate that the crucial aspect when obtaining accurate inner-scaled velocity measurements is the wind-tunnel flow quality, which is more critical than the accuracy in wall-shear stress measurements.

  • 248.
    Rinaldi, Enrico
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Patel, A.
    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.
    Pecnik, R.
    Linear stability of buffer layer streaks in turbulent channels with variable density and viscosity2017In: Physical Review Fluids, ISSN 2469-990X, Vol. 2, no 11, article id 113903Article in journal (Refereed)
    Abstract [en]

    We investigate the stability of streaks in the buffer layer of turbulent channel flows with temperature-dependent density and viscosity by means of linear theory. The adopted framework consists of an extended set of the Orr-Sommerfeld-Squire equations that accounts for density and viscosity nonuniformity in the direction normal to the walls. The base flow profiles for density, viscosity, and velocity are averaged from direct numerical simulations (DNSs) of fully developed turbulent channel flows. We find that the inner scaling based on semilocal quantities provides an effective parametrization of the effect of variable properties on the linearized flow. The spanwise spacing of optimal buffer layer streaks scales to λz,opt≈90 for all cases considered and the maximum energy amplification decreases, compared to the one for a flow with constant properties, if the semilocal Reynolds number Reτ increases away from the walls, consistently with less energetic streaks observed in DNSs of turbulent channels. A secondary stability analysis of the two-dimensional velocity profile formed by the mean turbulent velocity and the nonlinearly saturated optimal streaks predicts a streamwise instability mode with wavelength λx,cr≈230 in semilocal units, regardless of the fluid property distribution across the channel. The threshold for the onset of the secondary instability is reduced, compared to a constant property flow, if Reτ increases away from the walls, which explains the more intense ejection events reported in DNSs. The opposite behavior is predicted by the linear theory for decreasing Reτ, in accord with DNS observations. We finally show that the phase velocity of the critical mode of secondary instability agrees well with the convection velocity calculated by DNSs in the near-wall region for both constant and variable viscosity flows.

  • 249.
    Rinaldi, Enrico
    et al.
    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, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Bagheri, Shervin
    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.
    Edge state modulation by mean viscosity gradients2018In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 838, p. 379-403Article in journal (Refereed)
    Abstract [en]

    Motivated by the relevance of edge state solutions as mediators of transition, we use direct numerical simulations to study the effect of spatially non-uniform viscosity on their energy and stability in minimal channel flows. What we seek is a theoretical support rooted in a fully nonlinear framework that explains the modified threshold for transition to turbulence in flows with temperature-dependent viscosity. Consistently over a range of subcritical Reynolds numbers, we find that decreasing viscosity away from the walls weakens the streamwise streaks and the vortical structures responsible for their regeneration. The entire self-sustained cycle of the edge state is maintained on a lower kinetic energy level with a smaller driving force, compared to a flow with constant viscosity. Increasing viscosity away from the walls has the opposite effect. In both cases, the effect is proportional to the strength of the viscosity gradient. The results presented highlight a local shift in the state space of the position of the edge state relative to the laminar attractor with the consequent modulation of its basin of attraction in the proximity of the edge state and of the surrounding manifold. The implication is that the threshold for transition is reduced for perturbations evolving in the neighbourhood of the edge state in the case that viscosity decreases away from the walls, and vice versa.

  • 250.
    Rinkevicius, Zilvinas
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rosal Sandberg, Jaime Axel
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Mikkelsen, Kurt V.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments2014In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, no 3, p. 989-1003Article in journal (Refereed)
    Abstract [en]

    We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

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