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  • 51.
    Brynjell-Rahkola, Mattias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Shahriari, Nima
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Swedish Defence Research Agency, Sweden.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Stability and sensitivity of a crossflow-dominated Falkner–Skan–Cooke boundary layer with discrete surface roughness2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 52.
    Brynjell-Rahkola, Mattias
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tuckerman, L. S.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Computing Optimal Forcing Using Laplace Preconditioning2017Inngår i: Communications in Computational Physics, ISSN 1815-2406, E-ISSN 1991-7120, Vol. 22, nr 5, s. 1508-1532Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    For problems governed by a non-normal operator, the leading eigenvalue of the operator is of limited interest and a more relevant measure of the stability is obtained by considering the harmonic forcing causing the largest system response. Various methods for determining this so-called optimal forcing exist, but they all suffer from great computational expense and are hence not practical for large-scale problems. In the present paper a new method is presented, which is applicable to problems of arbitrary size. The method does not rely on timestepping, but on the solution of linear systems, in which the inverse Laplacian acts as a preconditioner. By formulating the search for the optimal forcing as an eigenvalue problem based on the resolvent operator, repeated system solves amount to power iterations, in which the dominant eigenvalue is seen to correspond to the energy amplification in a system for a given frequency, and the eigenfunction to the corresponding forcing function. Implementation of the method requires only minor modifications of an existing timestepping code, and is applicable to any partial differential equation containing the Laplacian, such as the Navier-Stokes equations. We discuss the method, first, in the context of the linear Ginzburg-Landau equation and then, the two-dimensional lid-driven cavity flow governed by the Navier-Stokes equations. Most importantly, we demonstrate that for the lid-driven cavity, the optimal forcing can be computed using a factor of up to 500 times fewer operator evaluations than the standard method based on exponential timestepping.

  • 53.
    Bäbler, Matthäus
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemiteknik, Energiprocesser.
    Biferale, Luca
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Feudel, Ulrike
    Guseva, Ksenia
    Lanotte, Alessandra S.
    Marchioli, Cristian
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Padua, Italy.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Soldati, Alfredo
    Toschi, Federico
    Numerical simulations of aggregate breakup in bounded and unbounded turbulent flows2015Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 766Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 54.
    Canton, Jacopo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Strömningsfysik. KTH, Skolan för industriell teknik och management (ITM), Centra, Competence Center for Gas Exchange (CCGEx). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Linear stability of the flow in a toroidal pipe2015Inngår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    While hydrodynamic stability and transition to turbulence in straight pipes - being one of the most fundamental problems in fluid mechanics - has been studied extensively, the stability of curved pipes has received less attention. In the present work, the first (linear) instability of the canonical flow inside a toroidal pipe is investigated as a first step in the study of the related laminar-turbulent transition process. The impact of the curvature of the pipe, in the range 8 e [0.002,1], on the stability properties of the flow is studied in the framework of linear stability analysis. Results show that the flow is indeed modally unstable for all curvatures investigated and that the wave number corresponding to the critical mode depends on the curvature, as do several other features of this problem. The critical modes are mainly located in the region of the Dean vortices, and are characterised by oscillations which are symmetric or antisymmetric as a function of the curvature. The neutral curve associated with the first bifurcation is the result of a complex interaction between isolated modes and branches composed by several modes characterised by a common structure. This behaviour is in obvious contrast to that of straight pipes, which are linearly stable for all Reynolds numbers.

  • 55.
    Canton, Jacopo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Modal instability of the flow in a toroidal pipe2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 792, s. 894-909Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 56.
    Canton, Jacopo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Chin, Cheng
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Reynolds number dependence of large-scale friction control in turbulent channel flow2016Inngår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 1, nr 8, artikkel-id 081501Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 57.
    Canton, Jacopo
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Strömningsfysik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Characterisation of the steady, laminar incompressible flow in toroidal pipes covering the entire curvature range2017Inngår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 66, s. 95-107Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 58. Capuccini, Marco
    et al.
    Ahmed, Laeeq
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Schaal, Wesley
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Spjuth, Ola
    Large-scale virtual screening on public cloud resources with Apache Spark2017Inngår i: Journal of Cheminformatics, ISSN 1758-2946, E-ISSN 1758-2946, Vol. 9, artikkel-id 15Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 59. Cedervall, Johan
    et al.
    Andersson, Mikael Svante
    Sarkar, Tapati
    Delczeg-Czirjak, Erna K.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hansen, Thomas C.
    Beran, Premysl
    Nordblad, Per
    Sahlberg, Martin
    Magnetic structure of the magnetocaloric compound AlFe2B22016Inngår i: Journal of Alloys and Compounds, ISSN 0925-8388, E-ISSN 1873-4669, Vol. 664, s. 784-791Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 60.
    Chattopadhyaya, Mausumi
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Murugan, N. Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Origin of the Absorption Band of Bromophenol Blue in Acidic and Basic pH: Insight from a Combined Molecular Dynamics and TD-DFT/MM Study2016Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 120, nr 36, s. 7175-7182Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 61. Chen, Yuxi
    et al.
    Toth, Gabor
    Cassak, Paul
    Jia, Xianzhe
    Gombosi, Tamas I.
    Slavin, James A.
    Markidis, Stefano
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Peng, Ivy Bo
    KTH.
    Jordanova, Vania K.
    Henderson, Michael G.
    Global Three-Dimensional Simulation of Earth's Dayside Reconnection Using a Two-Way Coupled Magnetohydrodynamics With Embedded Particle-in-Cell Model: Initial Results2017Inngår i: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 122, nr 10, s. 10318-10335Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We perform a three-dimensional (3-D) global simulation of Earth's magnetosphere with kinetic reconnection physics to study the flux transfer events (FTEs) and dayside magnetic reconnection with the recently developed magnetohydrodynamics with embedded particle-in-cell model. During the 1 h long simulation, the FTEs are generated quasi-periodically near the subsolar point and move toward the poles. We find that the magnetic field signature of FTEs at their early formation stage is similar to a "crater FTE," which is characterized by a magnetic field strength dip at the FTE center. After the FTE core field grows to a significant value, it becomes an FTE with typical flux rope structure. When an FTE moves across the cusp, reconnection between the FTE field lines and the cusp field lines can dissipate the FTE. The kinetic features are also captured by our model. A crescent electron phase space distribution is found near the reconnection site. A similar distribution is found for ions at the location where the Larmor electric field appears. The lower hybrid drift instability (LHDI) along the current sheet direction also arises at the interface of magnetosheath and magnetosphere plasma. The LHDI electric field is about 8 mV/m, and its dominant wavelength relative to the electron gyroradius agrees reasonably with Magnetospheric Multiscale (MMS) observations.

  • 62. Citro, Vincenzo
    et al.
    Giannetti, Flavio
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Luchini, Paolo
    Linear three-dimensional global and asymptotic stability analysis of incompressible open cavity flow2015Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 768Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 63.
    Costa, Pedro
    et al.
    Delft Univ Technol, Proc & Energy Dept Multiphase Syst, Leeghwaterstr 21, NL-2621 CA Delft, Netherlands..
    Picano, Francesco
    Univ Padua, Dept Ind Engn, Via Venezia 1, I-35131 Padua, Italy..
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Breugem, Wim-Paul
    Delft Univ Technol, Proc & Energy Dept Multiphase Syst, Leeghwaterstr 21, NL-2621 CA Delft, Netherlands..
    Effects of the finite particle size in turbulent wall-bounded flows of dense suspensions2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 843, s. 450-478Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We use interface-resolved numerical simulations to study finite-size effects in turbulent channel flow of neutrally buoyant spheres. Two cases with particle sizes differing by a factor of two, at the same solid volume fraction of 20% and bulk Reynolds number are considered. These are complemented with two reference single-phase flows: the unladen case, and the flow of a Newtonian fluid with the effective suspension viscosity of the same mixture in the laminar regime. As recently highlighted in Costa etal. (Phys. Rev. Lett., vol.117, 2016, 134501), a particle-wall layer is responsible for deviations of the mesoscale-averaged statistics from what is observed in the continuum limit where the suspension is modelled as a Newtonian fluid with (higher) effective viscosity. Here we investigate in detail the fluid and particle dynamics inside this layer and in the bulk. In the particle-wall layer, the near-wall inhomogeneity has an influence on the suspension microstructure over a distance proportional to the particle size. In this layer, particles have a significant (apparent) slip velocity that is reflected in the distribution of wall shear stresses. This is characterized by extreme events (both much higher and much lower than the mean). Based on these observations we provide a scaling for the particle-to-fluid apparent slip velocity as a function of the flow parameters. We also extend the scaling laws in Costa etal. (Phys. Rev. Lett., vol.117, 2016, 134501) to second-order Eulerian statistics in the homogeneous suspension region away from the wall. The results show that finite-size effects in the bulk of the channel become important for larger particles, while negligible for lower-order statistics and smaller particles. Finally, we study the particle dynamics along the wall-normal direction. Our results suggest that single-point dispersion is dominated by particle-turbulence (and not particle-particle) interactions, while differences in two-point dispersion and collisional dynamics are consistent with a picture of shear-driven interactions.

  • 64. Costa, Pedro
    et al.
    Picano, Francesco
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    Universal Scaling Laws for Dense Particle Suspensions in Turbulent Wall-Bounded Flows2016Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 117, nr 13, artikkel-id 134501Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 65.
    Dadfar, Reza
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Control of instabilities in an unswept wing boundary layer2018Inngår i: AIAA Journal, ISSN 0001-1452, E-ISSN 1533-385X, Vol. 56, nr 5, s. 1750-1759Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Linear control theory is used to construct an output feedback controller to attenuate the amplitude of the Tollmien–Schlichting waves inside the boundary layer developing over an unswept wing. The analysis is based on direct numerical simulations. The studied scenario includes the impulse response of the system to a generic disturbance in the freestream, which triggers a Tollmien–Schlichting wave packet inside the boundary layer. The performance of a linear quadratic Gaussian controller is analyzed to suppress the amplitude of the Tollmien–Schlichting wave packet using a row of sensors and plasma actuators localized at the wall. The target of the controller is chosen as a subset of proper orthogonal decomposition modes describing the dynamics of the unstable disturbances. The plasma actuators are implemented as volume forcing. To account for the limitations of the plasma actuators concerning a unidirectional forcing, several strategies are implemented in the linear quadratic Gaussian framework. Their performances are compared with that for classical linear quadratic Gaussian controller. These controllers successfully reduced the amplitude of the wave packet.

  • 66. De Aguiar Quintanilha Junior, H. R.
    et al.
    Kataras, P. B.
    Theofilis, V.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg, MWL Marcus Wallenberg Laboratoriet.
    Nonmodal stability analysis of the HIFiRE-5 elliptic cone model flow in different flight altitudes2018Inngår i: 58th Israel Annual Conference on Aerospace Sciences, IACAS 2018, Israel Annual Conference on Aerospace Sciences , 2018, s. 1543-1555Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Nonmodal instability analysis is carried out for a 2:1 elliptic cone with base flow conditions selected for a Ma=7 and two different ight altitudes, namely 33km and 21km with unit Reynolds number Re′ = 1.89 x 106 m-1 and Re′ = 1.015 x 107 m-1, respectively. The aim is to analyze the effects of transiently growing optimal disturbances and their possible relation to instability mechanisms that have been confirmed to exist in previous modal crossow. Local linear stability results obtained at several streamwise locations on the cone surface indicate that transient growth in the crossow region may be correlated to streamwise oriented structures having spanwise spacing of the same order of magnitude as which have long been known to exist in this flow.

  • 67.
    De Vita, Francesco
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rosti, Marco E.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Izbassarov, Daulet
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Duffo, L.
    Tammisola, Outi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hormozi, S.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elastoviscoplastic flows in porous media2018Inngår i: Journal of Non-Newtonian Fluid Mechanics, ISSN 0377-0257, E-ISSN 1873-2631, Vol. 258, s. 10-21Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigate the elastoviscoplastic flow through porous media by numerical simulations. We solve the Navier–Stokes equations combined with the elastoviscoplastic model proposed by Saramito for the stress tensor evolution [1]. In this model, the material behaves as a viscoelastic solid when unyielded, and as a viscoelastic Oldroyd-B fluid for stresses higher than the yield stress. The porous media is made of a symmetric array of cylinders, and we solve the flow in one periodic cell. We find that the solution is time-dependent even at low Reynolds numbers as we observe oscillations in time of the unyielded region especially at high Bingham numbers. The volume of the unyielded region slightly decreases with the Reynolds number and strongly increases with the Bingham number; up to 70% of the total volume is unyielded for the highest Bingham numbers considered here. The flow is mainly shear dominated in the yielded region, while shear and elongational flow are equally distributed in the unyielded region. We compute the relation between the pressure drop and the flow rate in the porous medium and present an empirical closure as function of the Bingham and Reynolds numbers. The apparent permeability, normalized with the case of Newtonian fluids, is shown to be greater than 1 at low Bingham numbers, corresponding to lower pressure drops due to the flow elasticity, and smaller than 1 for high Bingham numbers, indicating larger dissipation in the flow owing to the presence of the yielded regions. Finally we investigate the effect of the Weissenberg number on the distribution of the unyielded regions and on the pressure gradient.

  • 68. Delczeg-Czirjak, E. K.
    et al.
    Pereiro, M.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Kvashnin, Y. O.
    Di Marco, I
    Li, Guijiang
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik.
    Vitos, Levente
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. Uppsala Univ, Div Mat Theory, Dept Phys & Astron, Sweden.
    Eriksson, O.
    Origin of the magnetostructural coupling in FeMnP0.75Si0.252014Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, nr 21, s. 214436-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 69. Di, Yana
    et al.
    Popovic, Jelena
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    AN ADAPTIVE FAST INTERFACE TRACKING METHOD2015Inngår i: Journal of Computational Mathematics, ISSN 0254-9409, E-ISSN 1991-7139, Vol. 33, nr 6, s. 576-586Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 70. Duguet, Yohann
    et al.
    Monokrousos, Antonios
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Minimal transition thresholds in plane Couette flow2013Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 25, nr 8, s. 084103-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 71. Durrenfeld, P.
    et al.
    Gerhard, F.
    Chico, J.
    Dumas, R. K.
    Ranjbar, M.
    Bergman, A.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Gould, C.
    Molenkamp, L. W.
    Åkerman, Johan
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. University of Gothenburg, Sweden; NanOsc AB, Sweden.
    Tunable damping, saturation magnetization, and exchange stiffness of half-Heusler NiMnSb thin films2015Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, nr 21, artikkel-id 214424Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 72. Dörr, P. C.
    et al.
    Kloker, M. J.
    Hanifi, Ardeshir
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Effect of upstream flow deformation using plasma actuators on crossflow transition induced by unsteady vortical free-stream disturbances2017Inngår i: 47th AIAA Fluid Dynamics Conference, 2017, American Institute of Aeronautics and Astronautics, 2017Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Upstream flow deformation (UFD) has been shown to be an effective technique to delay roughness induced laminar-turbulent transition at low free-stream turbulence level in three-dimensional boundary-layer flows. Beneficial steady crossflow vortex (CFV) control modes are excited and the resulting nonlinear CFVs induce a useful mean-flow distortion. We recently showed by direct numerical simulations that plasma actuators, modeled by localized steady volume forcing, can be employed to excite the UFD control modes. In the current work we investigate the same actuator set-ups to control transition caused by traveling CFVs that are excited by single unsteady vortical free-stream disturbances (FSDs) impinging on the boundary layer. FSDs of various wavenumbers and frequencies are imposed either upstream or downstream, or at the position of the actuators to also scrutinize if the volume forcing has a direct unfavorable effect on the receptivity to the FSDs that adds to the stabilization by the UFD. For all investigated cases we show that a significant transition delay is achieved.

  • 73.
    Eitel-Amor, Georg
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Strömningsfysik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Strömningsfysik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Simulation and validation of a spatially evolving turbulent boundary layer up to Reθ = 83002014Inngår i: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 47, s. 57-69Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Results of a finely resolved large-eddy simulation (LES) of a spatially developing zero-pressure-gradient turbulent boundary layer up to a Reynolds number of Reθ = 8300 are presented. The very long computational domain provides substantial assessment for suggested high Reynolds number (Re) trends. Statistics, integral quantities and spectral data are validated using high quality direct numerical simulation (DNS) ranging up to Reθ = 4300 and hot-wire measurements covering the remaining Re-range. The mean velocity, turbulent fluctuations, skin friction, and shape factor show excellent agreement with the reference data. Through utilisation of filtered DNS, subtle differences between the LES and DNS could to a large extent be explained by the reduced spanwise resolution of the LES. Spectra and correlations for the streamwise velocity and the wall-shear stress evidence a clear scale-separation and a footprint of large outer scales on the near-wall small scales. While the inner peak decreases in importance and reduces to 4% of the total energy at the end of the domain, the energy of the outer peak scales in outer units. In the near-wall region a clear k - 1 region emerges. Consideration of the two-dimensional spectra in time and spanwise space reveals that an outer time scale λt ≈ 10δ99 / U∞, with the boundary layer thickness δ99 and free-stream velocity U∞, is the correct scale throughout the boundary layer rather than the transformed streamwise wavelength multiplied by a (scale independent) convection velocity. Maps for the covariance of small scale energy and large scale motions exhibit a stronger linear Re dependence for the amplitude of the off-diagonal peak compared to the diagonal one, thereby indicating that the strength of the amplitude modulation can only qualitatively be assessed through the diagonal peak. In addition, the magnitude of the wall-pressure fluctuations confirms mixed scaling, and pressure spectra at the highest Re give a first indication of a -7/3 wave number dependence. © 2014 Elsevier Inc.

  • 74.
    Eitel-Amor, Georg
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Flores, O.
    Hairpin vortices in turbulent boundary layers2015Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 27, nr 2, artikkel-id 025108Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The present work presents a number of parallel and spatially developing simulations of boundary layers to address the question of whether hairpin vortices are a dominant feature of near-wall turbulence, and which role they play during transition. In the first part, the parent-offspring regeneration mechanism is investigated in parallel (temporal) simulations of a single hairpin vortex introduced in a mean shear flow corresponding to either turbulent channels or boundary layers (Re-tau less than or similar to 590). The effect of a turbulent background superimposed on the mean flow is considered by using an eddy viscosity computed from resolved simulations. Tracking the vortical structure downstream, it is found that secondary hairpins are only created shortly after initialization, with all rotational structures decaying for later times. For hairpins in a clean (laminar) environment, the decay is relatively slow, while hairpins in weak turbulent environments (10% of nu(t)) dissipate after a couple of eddy turnover times. In the second part, the role of hairpin vortices in laminar-turbulent transition is studied using simulations of spatial boundary layers tripped by hairpin vortices. These vortices are generated by means of specific volumetric forces representing an ejection event, creating a synthetic turbulent boundary layer initially dominated by hairpin-like vortices. These hairpins are advected towards the wake region of the boundary layer, while a sinusoidal instability of the streaks near the wall results in rapid development of a turbulent boundary layer. For Re-theta > 400, the boundary layer is fully developed, with no evidence of hairpin vortices reaching into the wall region. The results from both the parallel and spatial simulations strongly suggest that the regeneration process is rather short-lived and may not sustain once a turbulent background is developed. From the transitional flow simulations, it is conjectured that the forest of hairpins reported in former direct numerical simulation studies is reminiscent of the transitional boundary layer and may not be connected to some aspects of the dynamics of the fully developed wall-bounded turbulence.

  • 75.
    El Khoury, George K.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Noorani, Azad
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul F.
    Brethouwer, Geert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Direct Numerical Simulation of Turbulent Pipe Flow at Moderately High Reynolds Numbers2013Inngår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 91, nr 3, s. 475-495Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fully resolved direct numerical simulations (DNSs) have been performed with a high-order spectral element method to study the flow of an incompressible viscous fluid in a smooth circular pipe of radius R and axial length 25R in the turbulent flow regime at four different friction Reynolds numbers Re (tau) = 180, 360, 550 and . The new set of data is put into perspective with other simulation data sets, obtained in pipe, channel and boundary layer geometry. In particular, differences between different pipe DNS are highlighted. It turns out that the pressure is the variable which differs the most between pipes, channels and boundary layers, leading to significantly different mean and pressure fluctuations, potentially linked to a stronger wake region. In the buffer layer, the variation with Reynolds number of the inner peak of axial velocity fluctuation intensity is similar between channel and boundary layer flows, but lower for the pipe, while the inner peak of the pressure fluctuations show negligible differences between pipe and channel flows but is clearly lower than that for the boundary layer, which is the same behaviour as for the fluctuating wall shear stress. Finally, turbulent kinetic energy budgets are almost indistinguishable between the canonical flows close to the wall (up to y (+) a parts per thousand aEuro parts per thousand 100), while substantial differences are observed in production and dissipation in the outer layer. A clear Reynolds number dependency is documented for the three flow configurations.

  • 76.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Materialfysik, MF.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Tidigare Institutioner (före 2005), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Adsorption of carbon dioxide and water molecules on graphene on top of silica substrates: dispersion corrected density functional calculationsManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We report on systematic computational studies of carbon dioxide and water molecule adsorption on graphene, with the graphene layer deposited on top of a substrate. Specifically, we address the influence of cristobalite and quartz substrates, i.e. two different types of silicon dioxide. The computations are based on density functional theory (DFT), with a nonempirical nonlocal van der Waals density functional included to account for dispersion forces.We calculate the binding energies and equilibrium positions of the molecules, as well as charge transfer and how the charge density of the graphene layer changes due to the interactions with the substrate and the molecules. The molecule-graphene bonding distances are found to be in the range 3.3-3.4 Å, and the graphene-substrate bonding distances around 3.6 Å. These values are slightly larger than what we have found previously, using an empirical expression for the van der Waals density functional. At the same time, the values for the binding energies are increased, compared to what we have obtained in a previous study. We find, in all cases, a net electron transfer from the adsorbed molecule to the graphene+substrate system. For quartz, the total charge transfer is between 0.1 and 0.2 electrons per adsorbed molecule. For cristobalite, it is only about a tenth of that. Our findings are consistent with earlier calculations as well as experimental data.

  • 77.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Materialfysik, MF.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Tidigare Institutioner (före 2005), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Graphene adhesion on surfaces: a van der Waals density functional studyManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    We present a van der Waals density functional (vdW-DF) calculations study of graphene adhesion to different types of substrates with different surface conditions. The study expands to both metal and semiconductor substrates with different surface endings. All substrate surfaces were the 111 surfaces where they have hexagonal lattice parameters perfectly matching with the graphene's. Adsorption geometries, energies, bader charges, dipole moments and electronic structure in terms of density of states are investigated. The results are showing a general agrement with both experimental results as well as theoritical findings done with similar setup. The results reveal that the degree of adhesive of graphene to different surfaces can affect the electronic structure of graphene ending in having different applications when designing graphene in building nano-electronic devices.

  • 78.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hugosson, Håkan W.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar. Chalmers Institute of Technology, Sweden.
    Råsander, Mikael
    Bergqvist, Lars
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Density functional calculations of graphene-based humidity and carbon dioxide sensors: effect of silica and sapphire substrates2017Inngår i: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 663, s. 23-30Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present dispersion-corrected density functional calculations of water and carbon dioxide molecules adsorption on graphene residing on silica and sapphire substrates. The equilibrium positions and bonding distances for the molecules are determined. Water is found to prefer the hollow site in the center of the graphene hexagon, whereas carbon dioxide prefers sites bridging carbon-carbon bonds as well as sites directly on top of carbon atoms. The energy differences between different sites are however minute - typically just a few tenths of a millielectronvolt. Overall, the molecule-graphene bonding distances are found to be in the range 3.1-3.3 (A) over circle. The carbon dioxide binding energy to graphene is found to be almost twice that of the water binding energy (around 0.17 eV compared to around 0.09 eV). The present results compare well with previous calculations, where available. Using charge density differences, we also qualitatively illustrate the effect of the different substrates and molecules on the electronic structure of the graphene sheet.

  • 79.
    Elgammal, Karim
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hugosson, Håkan W.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Integrerade komponenter och kretsar.
    Råsander, Mikael
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Density functional theory calculations of graphene-based humidity and carbon dioxide sensors: effect of silica and sapphire substratesManuskript (preprint) (Annet vitenskapelig)
  • 80.
    Elofsson, Arne
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Hess, Berk
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Onufriev, Alexey
    Virginia Tech, Dept Comp Sci, Ctr Soft Matter & Biol Phys, Blacksburg, VA USA.;Virginia Tech, Dept Phys, Ctr Soft Matter & Biol Phys, Blacksburg, VA USA..
    van der Spoel, David
    Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala Ctr Computat Chem, Uppsala, Sweden..
    Wallqvist, Anders
    US Army Med Res & Mat Command, Dept Def Biotechnol High Performance Comp Softwar, Telemed & Adv Technol Res Ctr, Ft Detrick, MD USA..
    Ten simple rules on how to create open access and reproducible molecular simulations of biological systems2019Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 15, nr 1, artikkel-id e1006649Artikkel i tidsskrift (Annet vitenskapelig)
  • 81. Engquist, Björn
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tsai, Y. -HR.
    Preface2012Inngår i: Workshop on Numerical Analysis and Multiscale Computations, 2009, Springer Verlag , 2012Konferansepaper (Fagfellevurdert)
  • 82.
    Eriksson, Olivia
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Jauhiainen, Alexandra
    AstraZeneca, IMED Biotech Unit, Early Clin Dev, Biometr, Gothenburg, Sweden..
    Sasane, Sara Maad
    Lund Univ, Ctr Math Sci, Lund, Sweden..
    Kramer, Andrei
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Nair, Anu G.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sartorius, Carolina
    Lund Univ, Ctr Math Sci, Lund, Sweden..
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models2019Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, nr 2, s. 284-292Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Motivation: Dynamical models describing intracellular phenomena are increasing in size and complexity as more information is obtained from experiments. These models are often over-parameterized with respect to the quantitative data used for parameter estimation, resulting in uncertainty in the individual parameter estimates as well as in the predictions made from the model. Here we combine Bayesian analysis with global sensitivity analysis (GSA) in order to give better informed predictions; to point out weaker parts of the model that are important targets for further experiments, as well as to give guidance on parameters that are essential in distinguishing different qualitative output behaviours. Results: We used approximate Bayesian computation (ABC) to estimate the model parameters from experimental data, as well as to quantify the uncertainty in this estimation (inverse uncertainty quantification), resulting in a posterior distribution for the parameters. This parameter uncertainty was next propagated to a corresponding uncertainty in the predictions (forward uncertainty propagation), and a GSA was performed on the predictions using the posterior distribution as the possible values for the parameters. This methodology was applied on a relatively large model relevant for synaptic plasticity, using experimental data from several sources. We could hereby point out those parameters that by themselves have the largest contribution to the uncertainty of the prediction as well as identify parameters important to separate between qualitatively different predictions. This approach is useful both for experimental design as well as model building.

  • 83.
    Ezhova, Ekaterina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Helsinki, Finland.
    Cenedese, C.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Dynamics of a turbulent Buoyant Plume in a stratified fluid: An idealized model of subglacial discharge in Greenland Fjords2017Inngår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 47, nr 10, s. 2611-2630Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study reports the results of large-eddy simulations of an axisymmetric turbulent buoyant plume in a stratified fluid. The configuration used is an idealized model of the plume generated by a subglacial discharge at the base of a tidewater glacier with an ambient stratification typical of Greenland fjords. The plume is discharged from a round source of various diameters and characteristic stratifications for summer and winter are considered. The classical theory for the integral parameters of a turbulent plume in a homogeneous fluid gives accurate predictions in the weakly stratified lower layer up to the pycnocline, and the plume dynamics are not sensitive to changes in the source diameter. In winter, when the stratification is similar to an idealized two-layer case, turbulent entrainment and generation of internal waves by the plume top are in agreement with the theoretical and numerical results obtained for turbulent jets in a two-layer stratification. In summer, instead, the stratification is more complex and turbulent entrainment by the plume top is significantly reduced. The subsurface layer in summer is characterized by a strong density gradient and the oscillating plume generates internal waves that might serve as an indicator of submerged plumes not penetrating to the surface.

  • 84.
    Ezhova, Ekaterina
    et al.
    Univ Helsinki, Inst Atmospher & Earth Syst Res, Helsinki, Finland.;Univ Helsinki, Dept Phys, Fac Sci, Helsinki, Finland..
    Cenedese, Claudia
    Woods Hole Oceanog Inst, Dept Phys Oceanog, Woods Hole, MA 02543 USA..
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik. Royal Inst Technol, Linne FLOW Ctr, Stockholm, Sweden.;Royal Inst Technol, Swedish E Sci Res Ctr, Dept Mech, Stockholm, Sweden..
    Dynamics of Three-Dimensional Turbulent Wall Plumes and Implications for Estimates of Submarine Glacier Melting2018Inngår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 48, nr 9, s. 1941-1950Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Subglacial discharges have been observed to generate buoyant plumes along the ice face of Greenland tidewater glaciers. These plumes have been traditionally modeled using classical plume theory, and their characteristic parameters (e.g., velocity) are employed in the widely used three-equation melt parameterization. However, the applicability of plume theory for three-dimensional turbulent wall plumes is questionable because of the complex near-wall plume dynamics. In this study, corrections to the classical plume theory are introduced to account for the presence of a wall. In particular, the drag and entrainment coefficients are quantified for a three-dimensional turbulent wall plume using data from direct numerical simulations. The drag coefficient is found to be an order of magnitude larger than that for a boundary layer flow over a flat plate at a similar Reynolds number. This result suggests a significant increase in the melting estimates by the current parameterization. However, the volume flux in a wall plume is found to be one-half that of a conical plume that has 2 times the buoyancy flux. This finding suggests that the total entrainment (per unit area) of ambient water is the same and that the plume scalar characteristics (i.e., temperature and salinity) can be predicted reasonably well using classical plume theory.

  • 85.
    Ezhova, Ekaterina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Cenedese, Claudia
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Interaction between a Vertical Turbulent Jet and a Thermocline2016Inngår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 46, nr 11, s. 3415-3437Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The behavior of an axisymmetric vertical turbulent jet in an unconfined stratified environment is studied by means of well-resolved, large-eddy simulations. The stratification is two uniform layers separated by a thermocline. This study considers two cases: when the thermocline thickness is small and on the order of the jet diameter at the thermocline entrance. The Froude number of the jet at the thermocline varies from 0.6 to 1.9, corresponding to the class of weak fountains. The mean jet penetration, stratified turbulent entrainment, jet oscillations, and the generation of internal waves are examined. The mean jet penetration is predicted well by a simple model based on the conservation of the source energy in the thermocline. The entrainment coefficient for the thin thermocline is consistent with the theoretical model for a two-layer stratification with a sharp interface, while for the thick thermocline entrainment is larger at low Froude numbers. The data reveal the presence of a secondary horizontal flow in the upper part of the thick thermocline, resulting in the entrainment of fluid from the thermocline rather than from the upper stratification layer. The spectra of the jet oscillations in the thermocline display two peaks, at the same frequencies for both stratifications at fixed Froude number. For the thick thermocline, internal waves are generated only at the lower frequency, since the higher peak exceeds the maximal buoyancy frequency. For the thin thermocline, conversely, the spectra of the internal waves show the two peaks at low Froude numbers, whereas only one peak at the lower frequency is observed at higher Froude numbers.

  • 86.
    Fan, Xuge
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Elgammal, Karim
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar.
    Östling, Mikael
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University, Box 516, SE-75120 Uppsala, Sweden.
    Lemme, Max C.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar. Department of Electronic Devices, RWTH Aachen University, 52074 Aachen, Germany.
    Niklaus, Frank
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Humidity and CO2 gas sensing properties of double-layer graphene2018Inngår i: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 127, s. 576-587Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Graphene has interesting gas sensing properties with strong responses of the graphene resistance when exposed to gases. However, the resistance response of double-layer graphene when exposed to humidity and gasses has not yet been characterized and understood. In this paper we study the resistance response of double-layer graphene when exposed to humidity and CO2, respectively. The measured response and recovery times of the graphene resistance to humidity are on the order of several hundred milliseconds. For relative humidity levels of less than ~ 3% RH, the resistance of double-layer graphene is not significantly influenced by the humidity variation. We use such a low humidity atmosphere to investigate the resistance response of double-layer graphene that is exposed to pure CO2 gas, showing a consistent response and recovery behaviour. The resistance of the double-layer graphene decreases linearly with increase of the concentration of pure CO2 gas. Density functional theory simulations indicate that double-layer graphene has a weaker gas response compared to single-layer graphene, which is in agreement with our experimental data. Our investigations contribute to improved understanding of the humidity and CO2 gas sensing properties of double-layer graphene which is important for realizing viable graphene-based gas sensors in the future.

  • 87.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Chaudhuri, Pinaki
    Umbert López, Cyan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mitra, Dhrubaditya
    Picano, Francesco
    Rheology of extremely confined non-Brownian suspensions2016Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 116, nr 1, artikkel-id 018301Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    We study the rheology of confined suspensions of  neutrally buoyant rigid monodisperse spheres in plane-Couetteflow using Direct Numerical Simulations.We find that if the width of the channel is a (small) integer multiple of the spherediameter, the spheres self-organize into two-dimensional layersthat slide on each other and the effective viscosity of the suspension  issignificantly reduced.  Each two-dimensional layer is found to be structurallyliquid-like but its dynamics is frozen in time.

  • 88.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Formenti, A.
    Picano, F.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The effect of particle density in turbulent channel flow laden with finite size particles in semi-dilute conditions2016Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 28, nr 3, artikkel-id 033301Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the effect of varying the mass and volume fraction of a suspension of rigid spheres dispersed in a turbulent channel flow. We performed several direct numerical simulations using an immersed boundary method for finite-size particles changing the solid to fluid density ratio R, the mass fraction χ, and the volume fraction φ. We find that varying the density ratio R between 1 and 10 at constant volume fraction does not alter the flow statistics as much as when varying the volume fraction φ at constant R and at constant mass fraction. Interestingly, the increase in overall drag found when varying the volume fraction is considerably higher than that obtained for increasing density ratios at same volume fraction. The main effect at density ratios R of the order of 10 is a strong shear-induced migration towards the centerline of the channel. When the density ratio R is further increased up to 1000, the particle dynamics decouple from that of the fluid. The solid phase behaves as a dense gas and the fluid and solid phase statistics drastically change. In this regime, the collision rate is high and dominated by the normal relative velocity among particles.

  • 89.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Kazerooni, Hamid Tabaei
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. Ruhr-Universität Bochum, Department of Hydraulic Fluid Machinery, Universitätsstrae 150, Bochum, Germany.
    Hussong, Jeanette
    Ruhr Univ Bochum, Chair Hydraul Fluid Machinery, Univ Str 150, D-44801 Bochum, Germany..
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Suspensions of finite-size neutrally buoyant spheres in turbulent duct flow2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 851, s. 148-186Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the turbulent square duct flow of dense suspensions of neutrally buoyant spherical particles. Direct numerical simulations (DNS) are performed in the range of volume fractions phi = 0-0.2, using the immersed boundary method (IBM) to account for the dispersed phase. Based on the hydraulic diameter a Reynolds number of 5600 is considered. We observe that for phi = 0.05 and 0.1, particles preferentially accumulate on the corner bisectors, close to the corners, as also observed for laminar square duct flows of the same duct-to-particle size ratio. At the highest volume fraction, particles preferentially accumulate in the core region. For plane channel flows, in the absence of lateral confinement, particles are found instead to be uniformly distributed across the channel. The intensity of the cross-stream secondary flows increases (with respect to the unladen case) with the volume fraction up to phi = 0.1, as a consequence of the high concentration of particles along the corner bisector. For phi = 0.2 the turbulence activity is reduced and the intensity of the secondary flows reduces to below that of the unladen case. The friction Reynolds number increases with phi in dilute conditions, as observed for channel flows. However, for phi = 0.2 the mean friction Reynolds number is similar to that for phi = 0.1. By performing the turbulent kinetic energy budget, we see that the turbulence production is enhanced up to phi = 0.1, while for phi = 0.2 the production decreases below the values for phi = 0.05. On the other hand, the dissipation and the transport monotonically increase with phi The interphase interaction term also contributes positively to the turbulent kinetic energy budget and increases monotonically with phi, in a similar way as the mean transport. Finally, we show that particles move on average faster than the fluid. However, there are regions close to the walls and at the corners where they lag behind it. In particular, for phi = 0.05, 0.1, the slip velocity distribution at the corner bisectors seems correlated to the locations of maximum concentration: the concentration is higher where the slip velocity vanishes. The wall-normal hydrodynamic and collision forces acting on the particles push them away from the corners. The combination of these forces vanishes around the locations of maximum concentration. The total mean forces are generally low along the corner bisectors and at the core, also explaining the concentration distribution for phi = 0.2.

  • 90.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik.
    Clustering and increased settling speed of oblate particles at finite Reynolds number2017Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Fagfellevurdert)
  • 91.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Clustering and increased settling speed of oblate particles at finite Reynolds number2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 848, s. 696-721Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the settling of rigid oblates in a quiescent fluid using interface-resolved direct numerical simulations. In particular, an immersed boundary method is used to account for the dispersed solid phase together with lubrication correction and collision models to account for short-range particle-particle interactions. We consider semi-dilute suspensions of oblate particles with aspect ratio AR = 1/3 and solid volume fractions (Phi = 0.5-10%. The solid-to-fluid density ratio R = 1.02 and the Galileo number (i.e. the ratio between buoyancy and viscous forces) based on the diameter of a sphere with equivalent volume Ga = 60. With this choice of parameters, an isolated oblate falls vertically with a steady wake with its broad side perpendicular to the gravity direction. At this Ga, the mean settling speed of spheres is a decreasing function of the volume Phi and is always smaller than the terminal velocity of the isolated particle, V-t. On the contrary, in dilute suspensions of oblate particles (with Phi <= 1 %), the mean settling speed is approximately 33 % larger than V-t. At higher concentrations, the mean settling speed decreases becoming smaller than the terminal velocity V-t between (Phi = 5 % and 10%. The increase of the mean settling speed is due to the formation of particle clusters that for Phi = 0.5-1 % appear as columnar-like structures. From the pair distribution function we observe that it is most probable to find particle pairs almost vertically aligned. However, the pair distribution function is non-negligible all around the reference particle indicating that there is a substantial amount of clustering at radial distances between 2 and 6c (with c the polar radius of the oblate). Above Phi = 5 %, the hindrance becomes the dominant effect, and the mean settling speed decreases below V-t. As the particle concentration increases, the mean particle orientation changes and the mean pitch angle (the angle between the particle axis of symmetry and gravity) increases from 23 degrees to 47 degrees . Finally, we increase Ga from 60 to 140 for the case with (Phi = 0.5 % and find that the mean settling speed (normalized by V-t) decreases by less than 1 % with respect to Ga = 60. However, the fluctuations of the settling speed around the mean are reduced and the probability of finding vertically aligned particle pairs increases.

  • 92.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Picano, Francesco
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The effect of polydispersity in a turbulent channel flow laden with finite-size particles2018Inngår i: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 67, s. 54-64Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study turbulent channel flows of monodisperse and polydisperse suspensions of finite-size spheres by means of Direct Numerical Simulations using an immersed boundary method to account for the dispersed phase. Suspensions with 3 different Gaussian distributions of particle radii are considered (i.e. 3 different standard deviations). The distributions are centered on the reference particle radius of the monodisperse suspension. In the most extreme case, the radius of the largest particles is 4 times that of the smaller particles. We consider two different solid volume fractions, 2% and 10%. We find that for all polydisperse cases, both fluid and particles statistics are not substantially altered with respect to those of the monodisperse case. Mean streamwise fluid and particle velocity profiles are almost perfectly overlapping. Slightly larger differences are found for particle velocity fluctuations. These increase close to the wall and decrease towards the centerline as the standard deviation of the distribution is increased. Hence, the behavior of the suspension is mostly governed by excluded volume effects regardless of particle size distribution (at least for the radii here studied). Due to turbulent mixing, particles are uniformly distributed across the channel. However, smaller particles can penetrate more into the viscous and buffer layer and velocity fluctuations are therein altered. Non trivial results are presented for particle-pair statistics.

    Fulltekst tilgjengelig fra 2020-02-29 15:45
  • 93.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Picano, Francesco
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Reduced particle settling speed in turbulence2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 808, s. 153-167Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the settling of finite-size rigid spheres in sustained homogeneous isotropic turbulence (1111) by direct numerical simulations using an immersed boundary method to account for the dispersed solid phase. We study semi-dilute suspensions at different Galileo numbers, Ga. The Galileo number is the ratio between buoyancy and viscous forces, and is here varied via the solid-to-fluid density ratio rho(p)/rho(f), The focus is on particles that are slightly heavier than the fluid. We find that in HIT, the mean settling speed is less than that in quiescent fluid; in particular, it reduces by 6 %-60 % with respect to the terminal velocity of an isolated sphere in quiescent fluid as the ratio between the latter and the turbulent velocity fluctuations it is decreased. Analysing the fluid particle relative motion, we find that the mean settling speed is progressively reduced while reducing rho(p)/rho(f) due to the increase of the vertical drag induced by the particle cross-flow velocity. Unsteady effects contribute to the mean overall drag by about 6%-10%. The probability density functions of particle velocities and accelerations reveal that these are closely related to the features of the turbulent flow. The particle mean-square displacement in the settling direction is found to be similar for all Ga if time is scaled by (2a)/u' (where 2a is the particle diameter and a is the turbulence velocity root mean square).

  • 94.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tabaei Kazerooni, Hamid
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Hussong, Jeanette
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Suspensions of finite-size neutrally buoyant spheres in turbulent duct flow2017Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Fagfellevurdert)
  • 95.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Zade, Sagar
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Picano, Francesco
    Department of Industrial EngineeringUniversity of PadovaPaduaItaly.
    Settling of finite-size particles in turbulence at different volume fractions2018Inngår i: Acta Mechanica, ISSN 0001-5970, E-ISSN 1619-6937, Vol. 230, nr 2, s. 413-430Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the settling of finite-size rigid spheres in quiescent fluid and in sustained homogeneous isotropic turbulence (HIT) by direct numerical simulations using an immersed boundary method to account for the dispersed solid phase. We consider semi-dilute and dense suspensions of rigid spheres with solid volume fractions ϕ= 0.5 - 10 % , solid-to-fluid density ratio R= 1.02 , and Galileo number (i.e., the ratio between buoyancy and viscous forces) Ga= 145. In HIT, the nominal Reynolds number based on the Taylor microscale is Re λ ≃ 90 , and the ratio between the particle diameter and the nominal Kolmogorov scale is (2 a) / η≃ 12 (being a the particle radius). We find that in HIT the mean settling speed is less than that in quiescent fluid for all ϕ. For ϕ= 0.5 % , the mean settling speed in HIT is 8 % less than in quiescent fluid. However, by increasing the volume fraction the difference in the mean settling speed between quiescent fluid and HIT cases reduces, being only 1.7 % for ϕ= 10 %. Indeed, while at low ϕ the settling speed is strongly altered by the interaction with turbulence, at large ϕ this is mainly determined by the (strong) hindering effect. This is similar in quiescent fluid and in HIT, leading to similar mean settling speeds. On the contrary, particle angular velocities are always found to increase with ϕ. These are enhanced by the interaction with turbulence, especially at low ϕ. In HIT, the correlations of particle lateral velocity fluctuations oscillate around zero before decorrelating completely. The time period of the oscillation seems proportional to the ratio between the integral lengthscale of turbulence and the particle characteristic terminal velocity. Regarding the mean square particle displacement, we find that it is strongly enhanced by turbulence in the direction perpendicular to gravity, even at the largest ϕ. Finally, we investigate the collision statistics for all cases and find the interesting result that the collision frequency is larger in quiescent fluid than in HIT for ϕ= 0.5 - 1 %. This is due to frequent drafting–kissing–tumbling events in quiescent fluid. The collision frequency becomes instead larger in HIT than in still fluid for ϕ= 5 - 10 % , due to the larger relative approaching velocities in HIT, and to the less intense drafting–kissing–tumbling events in quiescent fluid. The collision frequency also appears to be almost proportional to the estimate for small inertial particles uniformly distributed in space, though much smaller. Concerning the turbulence modulation, we find that the mean energy dissipation increases almost linearly with ϕ, leading to a large reduction of Re λ .

  • 96.
    Fourati, Zaineb
    et al.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Heusser, Stephanie A.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Hu, Haidai
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France.;UPMC Univ Paris 6, Sorbonne Univ, F-75005 Paris, France..
    Ruza, Reinis R.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Sauguet, Ludovic
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.
    Delarue, Marc
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels2018Inngår i: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 23, nr 4, s. 993-1004Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.

  • 97. Fouxon, Itzhak
    et al.
    Ge, Zhouyang
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Leshansky, Alexander
    Integral representation of channel flow with interacting particles2017Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, nr 6, artikkel-id 063110Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We construct a boundary integral representation for the low-Reynolds-number flow in a channel in the presence of freely suspended particles (or droplets) of arbitrary size and shape. We demonstrate that lubrication theory holds away from the particles at horizontal distances exceeding the channel height and derive a multipole expansion of the flow which is dipolar to the leading approximation. We show that the dipole moment of an arbitrary particle is a weighted integral of the stress and the flow at the particle surface, which can be determined numerically. We introduce the equation of motion that describes hydrodynamic interactions between arbitrary, possibly different, distant particles, with interactions determined by the product of the mobility matrix and the dipole moment. Further, the problem of three identical interacting spheres initially aligned in the streamwise direction is considered and the experimentally observed "pair exchange" phenomenon is derived analytically and confirmed numerically. For nonaligned particles, we demonstrate the formation of a configuration with one particle separating from a stable pair. Our results suggest that in a dilute initially homogenous particulate suspension flowing in a channel the particles will eventually separate into singlets and pairs.

  • 98.
    Frecus, Bogdan
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 25, s. 10466-10471Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The character and value of spin labels for probing environments like double-stranded DNA depends on the degree of changeof the spin Hamiltonian parameters of the spin label induced by the environment. Herein we provide a systematic theoreticalinvestigation of this issue, based on a density functional theory method applied to a spin labeled DNA model system, focusingon the dependence of the EPR properties of the spin label on the π stacking and hydrogen bonding that occur upon incorporatingthe spin label into selected base pair inside DNA. It is found that the EPR spin Hamiltonian parameters of the spin label is onlynegligibly affected by its incorporation into DNA, when compared to the its free form. This result gives theoretical ground forthe common empirical assumption regarding the behaviour of spin Hamiltonian parameters made in EPR based measurementsof distance between spin labels incorporated into DNA.

  • 99. Frånberg, Mattias
    et al.
    Gertow, Karl
    Hamsten, Anders
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests2015Inngår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, nr 9, artikkel-id e1005502Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite the success of genome-wide association studies in medical genetics, the underlying genetics of many complex diseases remains enigmatic. One plausible reason for this could be the failure to account for the presence of genetic interactions in current analyses. Exhaustive investigations of interactions are typically infeasible because the vast number of possible interactions impose hard statistical and computational challenges. There is, therefore, a need for computationally efficient methods that build on models appropriately capturing interaction. We introduce a new methodology where we augment the interaction hypothesis with a set of simpler hypotheses that are tested, in order of their complexity, against a saturated alternative hypothesis representing interaction. This sequential testing provides an efficient way to reduce the number of non-interacting variant pairs before the final interaction test. We devise two different methods, one that relies on a priori estimated numbers of marginally associated variants to correct for multiple tests, and a second that does this adaptively. We show that our methodology in general has an improved statistical power in comparison to seven other methods, and, using the idea of closed testing, that it controls the family-wise error rate. We apply our methodology to genetic data from the PRO-CARDIS coronary artery disease case/control cohort and discover three distinct interactions. While analyses on simulated data suggest that the statistical power may suffice for an exhaustive search of all variant pairs in ideal cases, we explore strategies for a priori selecting subsets of variant pairs to test. Our new methodology facilitates identification of new disease-relevant interactions from existing and future genome-wide association data, which may involve genes with previously unknown association to the disease. Moreover, it enables construction of interaction networks that provide a systems biology view of complex diseases, serving as a basis for more comprehensive understanding of disease pathophysiology and its clinical consequences.

  • 100.
    Frånberg, Mattias
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS). KTH, Centra, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.
    Lagergren, Jens
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
    BESIQ: A tool for discovering gene-gene and gene-environment interactions in genome-wide association studiesManuskript (preprint) (Annet vitenskapelig)
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