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  • 351.
    Vinuesa, Ricardo
    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.
    Bobke, Alexandra
    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, 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.
    Scaling of adverse-pressure-gradient turbulent boundary layers in near-equilibrium conditions2017Inngår i: Progress in Turbulence VII, Springer, 2017, Vol. 196, s. 73-78Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Well-resolved large-eddy simulations are used to study adverse-pressure-gradient (APG) turbulent boundary layers (TBLs) under near-equilibrium conditions. In particular, we focus on two near-equilibrium cases where the power-law freestream velocity distribution is adjusted in order to produce long regions with a constant value of the Clauser pressure-gradient parameter β. In the first case we obtain an APG TBL with a constant value of β ≃ 1 over 37 average boundary-layer thicknesses, and in the second one a constant value of β ≃ 2 for around 28 average boundary-layer thicknesses. The scaling law suggested by Kitsios et al. (Int J Heat Fluid Flow 61:117–128, 2016, [10]), proposing the edge velocity and the displacement thickness as scaling parameters, was tested on the two constant-pressure-gradient parameter cases. The mean velocity and Reynolds-stress profiles were found to be dependent on the downstream development, a conclusion in agreement with classical theory.

  • 352.
    Vinuesa, Ricardo
    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.
    Hosseini, Seyed M.
    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.
    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.
    Pressure-gradient turbulent boundary layers developing around a wing section2017Inngår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 99, nr 3-4, s. 613-641Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A direct numerical simulation database of the flow around a NACA4412 wing section at R e (c) = 400,000 and 5(ay) angle of attack (Hosseini et al. Int. J. Heat Fluid Flow 61, 117-128, 2016), obtained with the spectral-element code Nek5000, is analyzed. The Clauser pressure-gradient parameter beta ranges from ae integral 0 and 85 on the suction side, and from 0 to - 0.25 on the pressure side of the wing. The maximum R e (oee integral) and R e (tau) values are around 2,800 and 373 on the suction side, respectively, whereas on the pressure side these values are 818 and 346. Comparisons between the suction side with zero-pressure-gradient turbulent boundary layer data show larger values of the shape factor and a lower skin friction, both connected with the fact that the adverse pressure gradient present on the suction side of the wing increases the wall-normal convection. The adverse-pressure-gradient boundary layer also exhibits a more prominent wake region, the development of an outer peak in the Reynolds-stress tensor components, and increased production and dissipation across the boundary layer. All these effects are connected with the fact that the large-scale motions of the flow become relatively more intense due to the adverse pressure gradient, as apparent from spanwise premultiplied power-spectral density maps. The emergence of an outer spectral peak is observed at beta values of around 4 for lambda (z) ae integral 0.65 delta (99), closer to the wall than the spectral outer peak observed in zero-pressure-gradient turbulent boundary layers at higher R e (oee integral) . The effect of the slight favorable pressure gradient present on the pressure side of the wing is opposite the one of the adverse pressure gradient, leading to less energetic outer-layer structures.

  • 353.
    Vinuesa, Ricardo
    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.
    Negi, Prabal
    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.
    Henningson, Dan
    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.
    High-fidelity simulations of the flow around wings at high Reynolds numbers2017Manuskript (preprint) (Annet vitenskapelig)
  • 354.
    Vinuesa, Ricardo
    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.
    Nagib, H. M.
    IIT, MMAE Dept, Chicago, IL 60616 USA.
    Secondary flow in turbulent ducts with increasing aspect ratio2018Inngår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, nr 5, artikkel-id 054606Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Direct numerical simulations of turbulent duct flows with aspect ratios 1, 3, 5, 7, 10, and 14.4 at a center-plane friction Reynolds number Re-tau,Re- c similar or equal to 180, and aspect ratios 1 and 3 at Re-tau,Re- c similar or equal to 360, were carried out with the spectral-element code NEK5000. The aim of these simulations is to gain insight into the kinematics and dynamics of Prandtl's secondary flow of the second kind and its impact on the flow physics of wall-bounded turbulence. The secondary flow is characterized in terms of the cross-plane component of the mean kinetic energy, and its variation in the spanwise direction of the flow. Our results show that averaging times of around 3000 convective time units (based on duct half-height h) are required to reach a converged state of the secondary flow, which extends up to a spanwise distance of around similar or equal to 5h measured from the side walls. We also show that if the duct is not wide enough to accommodate the whole extent of the secondary flow, then its structure is modified as reflected through a different spanwise distribution of energy. Another confirmation of the extent of the secondary flow is the decay rate of kinetic energy of any remnant secondary motions for z(c)/h > 5 (where z(c) is the spanwise distance from the corner) in aspect ratios 7, 10, and 14.4, which exhibits a decreasing level of energy with increasing averaging time t(a), and in its rapid rate of decay given by similar to t(a)(-1). This is the same rate of decay observed in a spanwise-periodic channel simulation, which suggests that at the core, the kinetic energy of the secondary flow integrated over the cross-sectional area, < K >(yz), behaves as a random variable with zero mean, with rate of decay consistent with central limit theorem. Long-time averages of statistics in a region of rectangular ducts extending about the width of a well-designed channel simulation (i.e., extending about similar or equal to 3h on each side of the center plane) indicate that ducts or experimental facilities with aspect ratios larger than 10 may, if properly designed, exhibit good agreement with results obtained from spanwise-periodic channel computations.

  • 355.
    von Malottki, Stephan
    et al.
    Univ Kiel, Inst Theoret Phys & Astrophys, Leibnizstr 15, D-24098 Kiel, Germany..
    Bessarab, Pavel F.
    Univ Kiel, Inst Theoret Phys & Astrophys, Leibnizstr 15, D-24098 Kiel, Germany.;ITMO Univ, St Petersburg 197101, Russia..
    Haldar, Soumyajyoti
    Univ Kiel, Inst Theoret Phys & Astrophys, Leibnizstr 15, D-24098 Kiel, Germany..
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala Univ, Dept Phys & Astron, Uppsala, Sweden.
    Heinze, Stefan
    Univ Kiel, Inst Theoret Phys & Astrophys, Leibnizstr 15, D-24098 Kiel, Germany..
    Skyrmion lifetime in ultrathin films2019Inngår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 99, nr 6, artikkel-id 060409Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We show that thermal stability of skyrmions due to entropic effects can be strongly affected by external control parameters such as magnetic field and interface composition. The lifetimes of isolated skyrmions in atomic Pd/Fe bilayers on Ir(111) and on Rh(111) are calculated in the framework of harmonic transition state theory based on an atomistic spin model parametrized from density functional theory. Depending on the system the attempt frequency for skyrmion collapse can change by up to nine orders of magnitude with the strength of the applied magnetic field. We demonstrate that this effect is due to a drastic change of entropy with skyrmion radius which opens a route toward stabilizing sub-10-nm skyrmions at room temperature.

  • 356.
    Wei, Liang
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brethouwer, Gert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elsinga, G. E.
    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.
    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.
    Scaling of small-scale motions in wall-bounded turbulent flows2013Inngår i: International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013, TSFP-8 , 2013Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The objective is to investigate flow topology and related Reynolds-number scaling in the eigenframe of the strain-rate tensor for wall-bounded turbulent flows. The databases used in the current study are from direct numerical simulations (DNS) of fully developed channel flow up to friction Reynolds number Ret ≈ 1500, and a spatially developing, zero-pressure-gradient turbulent boundary layer up to Reθ ≈ 4300 (Ret ≈ 1400)., and a spatially developing, zero-pressure-gradient turbulent boundary layer up to Reθ ≈ 4300 (Ret ≈ 1400).. It is found that for all cases considered, the averaged flow patterns in the local strainrate eigenframe appear universal: large scale motions are separated by a shear layer with a pair of vortices. Based on Kolmogorov (η,uη), Taylor (lt) and integral length scales, Reynolds-number scalings of the averaged flow patterns, including the thickness and strength of the shear layer, the distance between the two vortical regions, and the velocity distribution along the most compressing and stretching directions are considered. It is found that the Taylor scaling of the profiles for the thickness of the shear layer seems more suitable than the Kolmogorov scaling, and the integral scaling collapses well away from the shear layer, which confirms that those patterns represent large scales. Generally speaking, the scaling profiles based on the Kolmogorov length and velocity collapse well near the origin, but the Taylor scaling seems best suited in a broader region.

  • 357.
    Wei, Liang
    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.
    Elsinga, Gerrit E.
    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.
    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.
    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.
    Universality and scaling phenomenology of small-scale turbulence in wall-bounded flows2014Inngår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 26, nr 3, s. 035107-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The Reynolds number scaling of flow topology in the eigenframe of the strain-rate tensor is investigated for wall-bounded flows, which is motivated by earlier works showing that such topologies appear to be qualitatively universal across turbulent flows. The databases used in the current study are from direct numerical simulations (DNS) of fully developed turbulent channel flow (TCF) up to friction Reynolds number Re-tau approximate to 1500, and a spatially developing, zero-pressure-gradient turbulent boundary layer (TBL) up to Re-theta approximate to 4300 (Re-tau approximate to 1400). It is found that for TCF and TBL at different Reynolds numbers, the averaged flow patterns in the local strain-rate eigenframe appear the same consisting of a pair of co-rotating vortices embedded in a finite-size shear layer. It is found that the core of the shear layer associated with the intense vorticity region scales on the Kolmogorov length scale, while the overall height of the shear layer and the distance between the vortices scale well with the Taylor micro scale. Moreover, the Taylor micro scale collapses the height of the shear layer in the direction of the vorticity stretching. The outer region of the averaged flow patterns approximately scales with the macro scale, which indicates that the flow patterns outside of the shear layer mainly are determined by large scales. The strength of the shear layer in terms of the peak tangential velocity appears to scale with a mixture of the Kolmogorov velocity and root-mean-square of the streamwise velocity scaling. A quantitative universality in the reported shear layers is observed across both wall-bounded flows for locations above the buffer region.

  • 358. Wen, Bo
    et al.
    Du, Chaoqin
    Li, Guilin
    Ghali, Fawaz
    Jones, Andrew R.
    Käll, Lukas
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Xu, Shaohang
    Zhou, Ruo
    Ren, Zhe
    Feng, Qiang
    Xu, Xun
    Wang, Jun
    IPeak: An open source tool to combine results from multiple MS/MS search engines2015Inngår i: Proteomics, ISSN 1615-9853, E-ISSN 1615-9861, Vol. 15, nr 17, s. 2916-2920Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/.

  • 359.
    Weng, Chenyang
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg, MWL Marcus Wallenberg Laboratoriet.
    Boij, Susann
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Farkost och flyg, MWL Marcus Wallenberg Laboratoriet.
    Hanifi, Ardeshir
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. FOI, Swedish Def Res Agcy,Sweden.
    Numerical and theoretical investigation of pulsatile turbulent channel flows2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 792, s. 98-133Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A turbulent channel flow subjected to imposed harmonic oscillations is studied by direct numerical simulation (DNS) and theoretical models. Simulations have been performed for different pulsation frequencies. The time- and phase-averaged data have been used to analyse the flow. The onset of nonlinear effects during the production of the perturbation Reynolds stresses is discussed based on the DNS data, and new physical features observed in the DNS are reported. A linear model proposed earlier by the present authors for the coherent perturbation Reynolds shear stress is reviewed and discussed in depth. The model includes the non-equilibrium effects during the response of the Reynolds stress to the imposed periodic shear straining, where a phase lag exists between the stress and the strain. To validate the model, the perturbation velocity and Reynolds shear stress from the model are compared with the DNS data. The performance of the model is found to be good in the frequency range where quasi-static assumptions are invalid. The viscoelastic characteristics of the turbulent eddies implied by the model are supported by the DNS data. Attempts to improve the model are also made by incorporating the DNS data in the model.

  • 360.
    Wennberg, Christian L.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Murtola, Teemu
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Improved Accuracy and Performance of Lennard-Jones Lattice Summation in GromacsManuskript (preprint) (Annet vitenskapelig)
  • 361.
    Wennberg, Christian L.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Murtola, Teemu
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties2013Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 9, nr 8, s. 3527-3537Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The accuracy of electrostatic interactions in molecular dynamics advanced tremendously with the introduction of particle-mesh Ewald (PME) summation almost 20 years ago. Lattice summation electrostatics is now the de facto standard for most types of biomolecular simulations, and in particular, for lipid bilayers, it has been a critical improvement due to the large charges typically present in zwitterionic lipid headgroups. In contrast, Lennard-Jones interactions have continued to be handled with increasingly longer cutoffs, partly because few alternatives have been available despite significant difficulties in tuning cutoffs and parameters to reproduce lipid properties. Here, we present a new Lennard-Jones PME implementation applied to lipid bilayers. We confirm that long-range contributions are well approximated by dispersion corrections in simple systems such as pentadecane (which makes parameters transferable), but for inhomogeneous and anisotropic systems such as lipid bilayers there are large effects on surface tension, resulting in up to 5.5% deviations in area per lipid and order parameters-far larger than many differences for which reparameterization has been attempted. We further propose an approximation for combination rules in reciprocal space that significantly reduces the computational cost of Lennard-Jones PME and makes accurate treatment of all nonbonded interactions competitive with simulations employing long cutoffs. These results could potentially have broad impact on important applications such as membrane proteins and free energy calculations.

  • 362.
    Wennberg, Christian L.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Murtola, Teemu
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Pall, Szilard
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Abraham, Mark James
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Direct-Space Corrections Enable Fast and Accurate Lorentz-Berthelot Combination Rule Lennard-Jones Lattice Summation2015Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 11, nr 12, s. 5737-5746Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Long-range lattice summation techniques such as the particle-mesh Ewald (PME) algorithm for electrostatics have been revolutionary to the precision and accuracy of molecular simulations in general. Despite the performance penalty associated with lattice summation electrostatics, few biomolecular simulations today are performed without it. There are increasingly strong arguments for moving in the same direction for Lennard-Jones (LJ) interactions, and by using geometric approximations of the combination rules in reciprocal space, we have been able to make a very high-performance implementation available in GROMACS. Here, we present a new way to correct for these approximations to achieve exact treatment of Lorentz-Berthelot combination rules within the cutoff, and only a very small approximation error remains outside the cutoff (a part that would be completely ignored without LJ-PME). This not only improves accuracy by almost an order of magnitude but also achieves absolute biomolecular simulation performance that is an order of magnitude faster than any other available lattice summation technique for LJ interactions. The implementation includes both CPU and GPU acceleration, and its combination with improved scaling LJ-PME simulations now provides performance close to the truncated potential methods in GROMACS but with much higher accuracy.

  • 363.
    Wennberg, Christian
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Murtola, Teemu
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lattice Summation of Lennard-Jones Interactions in Bilayer Simulations has Critical Effects on Surface Tension2012Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, nr 3, s. 172A-173AArtikkel i tidsskrift (Annet vitenskapelig)
  • 364. Williams, A. J.
    et al.
    Ekins, S.
    Spjuth, Ola
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Willighagen, Egon L.
    Accessing, using, and creating chemical property databases for computational toxicology modeling2012Inngår i: Computational Toxicology: Volume I, Springer , 2012, s. 221-241Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    Toxicity data is expensive to generate, is increasingly seen as precompetitive, and is frequently used for the generation of computational models in a discipline known as computational toxicology. Repositories of chemical property data are valuable for supporting computational toxicologists by providing access to data regarding potential toxicity issues with compounds as well as for the purpose of building structure-toxicity relationships and associated prediction models. These relationships use mathematical, statistical, and modeling computational approaches and can be used to understand the mechanisms by which chemicals cause harm and, ultimately, enable prediction of adverse effects of these chemicals to human health and/or the environment. Such approaches are of value as they offer an opportunity to prioritize chemicals for testing. An increasing amount of data used by computational toxicologists is being published into the public domain and, in parallel, there is a greater availability of Open Source software for the generation of computational models. This chapter provides an overview of the types of data and software available and how these may be used to produce predictive toxicology models for the community.

  • 365. Xia, Zhenhua
    et al.
    Brethouwer, Gert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Chen, Shiyi
    High-order moments of streamwise fluctuations in a turbulent channel flow with spanwise rotation2018Inngår i: PHYSICAL REVIEW FLUIDS, ISSN 2469-990X, Vol. 3, nr 2, artikkel-id 022601Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    It is well known that the spanwise rotation in turbulent channel flow alters the mean velocity distribution to a linear law. In the present work, we have studied the higher-order moments of the streamwise fluctuations in a turbulent channel flow with spanwise rotation. Our results show that in a significant part of the channel the 2p-order moments, raised by the power 1/p with p = 1,2, ... ,6, also follow linear behavior according to <(u'(+))(2p)>(1/p) = a(p) (y/h) + b(p). Here, u'(+) is the streamwise velocity fluctuation normalized by the global friction velocity, h is the channel half width, and b(p) and a(p) are the intercept and the slope, respectively, which vary with Reynolds and rotation numbers. The linear regions can be extended by introducing a self-similar scaling, that is, 2p-order moments as a function of 2q-order moments. The slopes in the self-similar scaling a(p)/a(1) do not reveal sub-Gaussian behavior as in nonrotating wall-bounded flows, but rather Gaussian or super-Gaussian behaviors.

  • 366. Yazdi, Sammy
    et al.
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elinder, Fredrik
    Stein, Matthias
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Molecular Characterization of the Binding of Polyunsaturated Fatty Acids to a Voltage-Gated Potassium Channel2014Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 739A-739AArtikkel i tidsskrift (Annet vitenskapelig)
  • 367. Yin, Yuli
    et al.
    Pan, Fan
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ahlberg, Martina
    Ranjbar, Mojtaba
    Duerrenfeld, Philipp
    Houshang, Afshin
    Haidar, Mohammad
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Zhai, Ya
    Dumas, Randy K.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Åkerman, Johan
    University of Gothenburg, Sweden.
    Tunable permalloy-based films for magnonic devices2015Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, nr 2, artikkel-id 024427Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Using both broadband ferromagnetic resonance (FMR) spectroscopy and ab initio calculations, we study the magnetodynamic properties of permalloy (Py, Ni80Fe20) and Py100-x M-x films with M as platinum (Pt), gold (Au), or silver (Ag). From the uniform FMR mode, we extract the saturation magnetization (M-S), damping (alpha), and inhomogeneous broadening (Delta H-0); from the first perpendicular standing spin-wave (PSSW) mode, we extract the exchange stiffness (A). M-S and A are found to decrease with increasing alloying, most strongly for Au and less so for Pt. On the other hand, alpha increases rapidly with both Pt and Au content, while being virtually independent of Ag content. The physical origins of the observed trends in alpha, M-S, and A are analyzed and explained using density functional theory calculations in the coherent potential approximation. The calculated trends quantitatively agree with the experimental observations. The drastically different impacts of Pt, Au, and Ag on the various fundamental magnetodynamic properties will allow for significant design freedom, where different properties can be varied independently of others through careful combinations of the Pt, Au, and Ag contents of Py100-x M-x films. By empirical approximations of each property's concentration dependence, we can dial in any desired combination of magnetodynamic properties within this parameter space. As a proof-of-principle demonstration we design a set of Py100-x-yPtxAgy films, where the saturation magnetization stays constant throughout the set and the damping can be tuned by a factor of 4.

  • 368.
    Yoluk, Ozge
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Heusser, Stephanie
    SciLifeLab, Solna, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Orellana, Laura
    KTH.
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Stockholm, Sweden..
    Gating Ritual: Simulations of Gating in Glutamate-Gated Chloride Channel2015Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 431A-431AArtikkel i tidsskrift (Annet vitenskapelig)
  • 369.
    Yoluk, Ozge
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Stockholm, Sweden..
    Orellana, L
    KTH.
    Lindahl, E
    KTH.
    Microsecond time-scale dynamics of the pentameric ligand-gated ion channels: a comparative study2015Inngår i: European Biophysics Journal, ISSN 0175-7571, E-ISSN 1432-1017, Vol. 44, s. S219-S219Artikkel i tidsskrift (Annet vitenskapelig)
  • 370.
    Yoluk, Özge
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brömstrup, Torben
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Bertaccini, Edward J.
    Trudell, James R.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Stabilization of the GluCl Ligand-Gated Ion Channel in the Presence and Absence of Ivermectin2013Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 105, nr 3, s. 640-647Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Improving our understanding of the mechanisms and effects of anesthetics is a critically important part of neuroscience. The currently dominant theory is that anesthetics and similar molecules act by binding to Cys-loop receptors in the postsynaptic terminal of nerve cells and potentiate or inhibit their function. Although structures for some of the most important mammalian channels have still not been determined, a number of important results have been derived from work on homologous cationic channels in bacteria. However, partly due to the lack of a nervous system in bacteria, there are a number of questions about how these results relate to higher organisms. The recent determination of a structure of the eukaryotic chloride channel, GluCl, is an important step toward accurate modeling of mammalian channels, because it is more similar in function to human Cys-loop receptors such as GABA(A)R or GlyR. One potential issue with using GluCl to model other receptors is the presence of the large ligand ivermectin (IVM) positioned between all five subunits. Here, we have performed a series of microsecond molecular simulations to study how the dynamics and structure of GluCl change in the presence versus absence of IVM. When the ligand is removed, subunits move at least 2 angstrom closer to each other compared to simulations with IVM bound. In addition, the pore radius shrinks to 1.2 angstrom, all of which appears to support a model where IVM binding between subunits stabilizes an open state, and that the relaxed nonIVM conformations might be suitable for modeling other channels. Interestingly, the presence of IVM also has an effect on the structure of the important loop C located at the neurotransmitter-binding pocket, which might help shed light on its partial agonist behavior.

  • 371. Yu, Xue Qin
    et al.
    Luo, Qingwei
    Smith, David P.
    Clements, Mark S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    O'Connell, Dianne L.
    Prostate cancer prevalence in New South Wales Australia: A population-based study2015Inngår i: Cancer Epidemiology, ISSN 1877-7821, E-ISSN 1877-783X, Vol. 39, nr 1, s. 29-36Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Information on the current and future numbers of Australian men living with prostate cancer is limited. We describe a method for estimating complete prevalence of prostate cancer to provide a measure of the burden of prostate cancer in Australia. Methods: Prostate cancer data from the New South Wales (NSW) Central Cancer Registry were used with PIAMOD (Prevalence and Incidence Analysis MODel) software to estimate future prostate cancer prevalence in NSW. We first fitted parametric incidence and survival models then used the modelled incidence and survival estimates to calculate complete prevalence. The estimated and projected prevalence incorporate past observed trends and take into account different assumptions about future survival trends. These models were validated against observed prevalence from the counting method. Results: Based on data for 1996-2007, the number of men living with prostate cancer in NSW was estimated to rise by 59% to 73%, from 38,322 in 2007 to 60,910-66,160 in 2017. The increasing incidence rates and the ageing population were the major contributors to this estimated increase. Validation suggested that these projections were reasonable, as the estimated prevalence in 1996-2007 was in good agreement with the corresponding prevalence calculated using the direct counting method, and the incidence models were supported by the recent data on prostate-specific antigen testing. Conclusions: As the number of men living with prostate cancer is expected to increase dramatically in the next decade in Australia, representing a significant challenge to the health system, careful planning and development of a healthcare system able to respond to this increased demand is required. These projections are useful for addressing the challenge in meeting the cancer care needs of men with prostate cancer.

  • 372. Yu, Xue Qin
    et al.
    Luo, Qingwei
    Smith, David P.
    Clements, Mark S.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Patel, Manish I.
    O'Connell, Dianne L.
    Phase of care prevalence for prostate cancer in New South Wales, Australia: A population-based modelling study2017Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 2, artikkel-id e0171013Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objective To develop a method for estimating the future numbers of prostate cancer survivors requiring different levels of care. Design, setting and participants Analysis of population-based cancer registry data for prostate cancer cases (aged 18-84 years) diagnosed in 1996-2007, and a linked dataset with hospital admission data for men with prostate cancer diagnosed during 2005-2007 in New South Wales (NSW), Australia. Methods Cancer registry data (1996-2007) were used to project complete prostate cancer prevalence in NSW, Australia for 2008-2017, and treatment information from hospital records (2005-2007) was used to estimate the inpatient care needs during the first year after diagnosis. The projected complete prevalence was divided into care needs-based groups. We first divided the cohort into two groups based on patient's age (<75 and 75-84 years). The younger cohort was further divided into initial care and monitoring phases. Cause of death data were used as a proxy for patients requiring last year of life prostate cancer care. Finally, episode data were used to estimate the future number of cases with metastatic progression. Results Of the estimated total of 60,910 men with a previous diagnosis of prostate cancer in 2017, the largest groups will be older patients (52.0%) and younger men who require monitoring (42.5%). If current treatment patterns continue, in the first year post-diagnosis 41% (1380) of patients (<75 years) will have a radical prostatectomy, and 52.6% (1752) will be likely to have either active surveillance, external beam radiotherapy or androgen deprivation therapy. About 3% will require care for subsequent metastases, and 1288 men with prostate cancer are likely to die from the disease in 2017. Conclusions This method extends the application of routinely collected population-based data, and can contribute much to the knowledge of the number of men with prostate cancer and their health care requirements. This could be of significant use in planning future cancer care services and facilities in Australia.

  • 373.
    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.
    Experimental studies of large particles in Newtonian and non-Newtonian fluids2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    In everyday human life, laminar flow is arguably an exception whereas turbulent flow is the norm. Yet, the former has been much better understood, naturally since laminar flow renders itself to treatment in a relatively easier fashion compared to turbulence with its chaotic dynamics across multiple scales in space and time. A parallel analogy in terms of sophistication of dynamics can be drawn between single phase and multiphase flows; the latter being the norm yet poorly understood due to numerous complexities arising on account of the huge parameter space involved. It is also remarkable that numerical studies are more prevalent in this field and there is a dearth of experimental results, which are important for both validation purposes and as a beacon to navigate research in practically relevant directions. This work has emerged to address the above issues. The attention has been largely directed towards understanding the flow of spherical particles in a square duct at moderately high concentrations using Particle Image Velocimetry (PIV) with refractive-index-matched (RIM) hydrogel particles. Fluids with Newtonian, viscoelastic and elastoviscoplastic rheology have been investigated due to their presence in natural and industrially relevant flows. Experiments and Direct Numerical Simulations (DNS) with spherical particles in a round pipe with turbulent flow of a Newtonian fluid are also conducted to extend and generalise the observations made in the square duct.

    With the ability to optically interrogate the bulk of the flow at high particle concentrations (20\% in this work), many interesting measurements are made possible, focussing on the turbulent regime. For the Newtonian fluid, the pressure drop or, equivalently, the energy required to pump the fluid-particle mixture is a complex function of particle size and concentration in the duct. This phenomenon arises due to the particle concentration distribution, with a local maxima at the core and the walls, and its resulting effect on the dominant stresses in the system i.e.\ the Reynolds shear stress and particle-induced stress. Particles also migrate in a similar fashion in a turbulent flow of viscoelastic suspending fluid but, with a larger tendency to accumulate in the core compared to its Newtonian counterpart at the same Reynolds number leading to a faster rise in total stress with concentration. Finally, for the \textit{thick} elastoviscoplastic fluid, the single-phase flow is laminar but it exhibits turbulence-like fluctuations when particles are added, which are distributed in exotic configurations depending on the interplay between the viscoelastic forces and the ensuing secondary flows as well as inertial forces. On the other hand, a quantitative comparison between simulations and experiments for particles transported along the floor of the duct under turbulent conditions has helped in reinforcing confidence in both approaches.

    We believe that these results will establish more confidence in the experimental usage of hydrogel particles for studying the flow of moderately dense suspensions. A natural extension would be the investigation of flow geometries more complex than a pipe or a square duct. Our results at higher Reynolds numbers is expected to motivate numerical simulations which are capable of investigating the detailed causes behind these observations, which are still unclear as of now. The information provided about the overall drag and the associated particle concentration and stress distribution will be helpful in painting a unified picture of turbulent suspension dynamics for a comprehensive range of flow rates and particle sizes. Future studies, either experimental or numerical, bearing similarities or deviations from our observations would also be constructive, for e.g.\ in assessing the sensitivity of the system to parameters that may be overlooked in the present study.

  • 374.
    Zade, Sagar
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH Mech, Linne Flow Ctr, SE-10044 Stockholm, Sweden.;KTH Mech, SeRC Swedish E Sci Res Ctr, SE-10044 Stockholm, Sweden..
    Costa, Pedro
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH Mech, Linne Flow Ctr, SE-10044 Stockholm, Sweden.;KTH Mech, SeRC Swedish E Sci Res Ctr, SE-10044 Stockholm, Sweden..
    Fornari, Walter
    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. KTH Mech, Linne Flow Ctr, SE-10044 Stockholm, Sweden.;KTH Mech, SeRC Swedish E Sci Res Ctr, SE-10044 Stockholm, Sweden..
    Lundell, Fredrik
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH Mech, Linne Flow Ctr, SE-10044 Stockholm, Sweden.;KTH Mech, SeRC Swedish E Sci Res Ctr, SE-10044 Stockholm, Sweden..
    Brandt, Luca
    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. KTH Mech, Linne Flow Ctr, SE-10044 Stockholm, Sweden.;KTH Mech, SeRC Swedish E Sci Res Ctr, SE-10044 Stockholm, Sweden..
    Experimental investigation of turbulent suspensions of spherical particles in a squareduct2018Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 857, s. 748-783Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We report experimental observations of turbulent flow with spherical particles in a square duct. Three particle sizes, namely 2H/d(p) = 40, 16 and 9 (2H being the duct full height and d(p) being the particle diameter), are investigated. The particles are nearly neutrally buoyant with a density ratio of 1.0035 and 1.01 with respect to the suspending fluid. Refractive index matched-particle image velocimetry (RIM-PIV) is used for fluid velocity measurement even at the highest particle volume fraction (20 %) and particle tracking velocimetry (PTV) for the particle velocity statistics for the flows seeded with particles of the two largest sizes, whereas only pressure measurements are reported for the smallest particles. Settling effects are seen at the lowest bulk Reynolds number R-e2H approximate to 10 000, whereas, at the highest R-e2H approximate to 27 000, particles are in almost full suspension. The friction factor of the suspensions is found to be significantly larger than that of single-phase duct flow at the lower R-e2H investigated; however, the difference decreases when increasing the flow rate and the total drag approaches the values of the single-phase flow at the higher Reynolds number considered, R-e2H = 27 000. The pressure drop is found to decrease with the particle diameter for volume fractions lower than (sic) = 10% for nearly all R-e2H investigated. However, at the highest volume fraction (sic) = 20 %, we report a peculiar non-monotonic behaviour: the pressure drop first decreases and then increases with increasing particle size. The decrease of the turbulent drag with particle size at the lowest volume fractions is related to an attenuation of the turbulence. The drag increase for the two largest particle sizes at (sic) = 20 %, however, occurs despite this large reduction of the turbulent stresses, and it is therefore due to significant particle-induced stresses. At the lowest Reynolds number, the particles reside mostly in the bottom half of the duct, where the mean velocity significantly decreases; the flow is similar to that in a moving porous bed near the bottom wall and to turbulent duct flow with low particle concentration near the top wall.

  • 375.
    Zade, Sagar
    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.
    Lundell, Fredrik
    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.
    Turbulence modulation by finite-size spherical particles in Newtonian and viscoelastic fluids2019Inngår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 112, s. 116-129Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We experimentally investigate the influence of finite-size spherical particles in turbulent flows of a Newtonian and a drag reducing viscoelastic fluid at varying particle volume fractions and fixed Reynolds number. Experiments are performed in a square duct at a Reynolds number Re2H of nearly 1.1 × 104, Weissenberg number Wi for single phase flow is between 1 and 2 and results in a drag-reduction of 43% compared to a Newtonian flow (at the same Re2H). Particles are almost neutrally-buoyant hydrogel spheres having a density ratio of 1.0035 ± 0.0003 and a duct height 2H to particle diameter dp ratio of around 10. We measure flow statistics for four different volume fractions ϕ namely 5, 10, 15 and 20% by using refractive-index-matched Particle Image Velocimetry (PIV). For both Newtonian Fluid (NF) and Visceolastic Fluid (VEF), the drag monotonically increases with ϕ. For NF, the magnitude of drag increase due to particle addition can be reasonably estimated using a concentration dependent effective viscosity for volume fractions below 10%. The drag increase is, however, underestimated at higher ϕ. For VEF, the absolute value of drag is lower than NF but, its rate of increase with ϕ is higher. Similar to particles in a NF, particles in VEF tend to migrate towards the center of the duct and form a layer of high concentration at the wall. Interestingly, relatively higher migration towards the center and lower migration towards the walls is observed for VEF. The primary Reynolds shear stress reduces with increasing ϕ throughout the duct height for both types of fluid.

  • 376.
    Zalesny, Robert
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Murugan, Natarajan Arul
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Gel'mukhanov, Faris
    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.
    Osmialowski, Borys
    Bartkowiak, Wojciech
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Toward Fully Nonempirical Simulations of Optical Band Shapes of Molecules in Solution: A Case Study of Heterocyclic Ketoimine Difluoroborates2015Inngår i: Journal of Physical Chemistry A, ISSN 1089-5639, E-ISSN 1520-5215, Vol. 119, nr 21, s. 5145-5152Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This study demonstrates that a hybrid density functional theory/molecular mechanics approach can be successfully combined with time-dependent wavepacket approach to predict the shape of optical bands for molecules in solutions, including vibrational fine structure. A key step in this treatment is the estimation of the inhomogeneous broadening based on the hybrid approach, where the polarization between solute and atomically decomposed solvent is taken into account in a self-consistent manner. The potential of this approach is shown by predicting optical absorption bands for three heterocyclic ketoimine difluoroborates in solution.

  • 377.
    Zhan, Caijuan
    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.
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lushi, Enkeleida
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Accumulation of motile elongated micro-organisms in turbulence2014Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 739, s. 22-36Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the effect of turbulence on marine life by performing numerical simulations of motile micro-organisms, modelled as prolate spheroids, in isotropic homogeneous turbulence. We show that the clustering and patchiness observed in laminar flows, linear shear and vortex flows, are significantly reduced in a three-dimensional turbulent flow mainly because of the complex topology; elongated micro-organisms show some level of clustering in the case of swimmers without any preferential alignment whereas spherical swimmers remain uniformly distributed. Micro-organisms with one preferential swimming direction (e.g. gyrotaxis) still show significant clustering if spherical in shape, whereas prolate swimmers remain more uniformly distributed. Due to their large sensitivity to the local shear, these elongated swimmers react more slowly to the action of vorticity and gravity and therefore do not have time to accumulate in a turbulent flow. These results show how purely hydrodynamic effects can alter the ecology of micro-organisms that can vary their shape and their preferential orientation.

  • 378. Zhang, Bo
    et al.
    Pirmoradian, Mohammad
    Zubarev, Roman
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences2017Inngår i: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 16, nr 5, s. 936-948Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Most implementations of mass spectrometry-based proteomics involve enzymatic digestion of proteins, expanding the analysis to multiple proteolytic peptides for each protein. Currently, there is no consensus of how to summarize peptides' abundances to protein concentrations, and such efforts are complicated by the fact that error control normally is applied to the identification process, and do not directly control errors linking peptide abundance measures to protein concentration. Peptides resulting from suboptimal digestion or being partially modified are not representative of the protein concentration. Without a mechanism to remove such unrepresentative peptides, their abundance adversely impacts the estimation of their protein's concentration. Here, we present a relative quantification approach, Diffacto, that applies factor analysis to extract the covariation of peptides' abundances. The method enables a weighted geometrical average summarization and automatic elimination of incoherent peptides. We demonstrate, based on a set of controlled label-free experiments using standard mixtures of proteins, that the covariation structure extracted by the factor analysis accurately reflects protein concentrations. In the 1% peptide-spectrum match-level FDR data set, as many as 11% of the peptides have abundance differences incoherent with the other peptides attributed to the same protein. If not controlled, such contradicting peptide abundance have a severe impact on protein quantifications. When adding the quantities of each protein's three most abundant peptides, we note as many as 14% of the proteins being estimated as having a negative correlation with their actual concentration differences between samples. Diffacto reduced the amount of such obviously incorrectly quantified proteins to 1.6%. Furthermore, by analyzing clinical data sets from two breast cancer studies, our method revealed the persistent proteomic signatures linked to three subtypes of breast cancer. We conclude that Diffacto can facilitate the interpretation and enhance the utility of most types of proteomics data.

  • 379.
    Zhang, Mengmeng
    et al.
    KTH.
    Melin, Tomas
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Barth, Michaela
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Axner, Lilit
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Mixed Fidelity Aerodynamic and Aero-Structural Optimization for Wings2018Inngår i: 2018 International Conference on High Performance Computing & Simulation, 2018, s. 476-483Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Automatic multidisciplinary design optimization is one of the challenges that are faced in the processes involved in designing efficient wings for aircraft. In this paper we present mixed fidelity aerodynamic and aero-structural optimization methods for designing wings. A novel shape design methodology has been developed - it is based on a mix of the automatic aerodynamic optimization for a reference aircraft model, and the aero-structural optimization for an uninhabited air vehicle (UAV) with a high aspect ratio wing. This paper is a significant step towards making it possible to perform all the core processes for aerodynamic and aero-structural optimization that require special skills in a fully automatic manner - this covers all the processes from creating the mesh for the wing simulation to executing the high-fidelity computational fluid dynamics (CFD) analysis code. Our results confirm that the simulation tools can make it possible for a far broader range of engineering researchers and developers to design aircraft in much simpler and more efficient ways. This is a vital step in the evolution of wing design processes as it means that the extremely expensive laboratory experiments that were traditionally used when designing the wings can now be replaced with more cost effective high performance computing (HPC) simulation that utilize accurate numerical methods.

  • 380.
    Zhang, Mengqi
    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.
    Lashgari, Iman
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Zaki, Tamer A.
    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.
    Linear stability analysis of channel flow of viscoelastic Oldroyd-B and FENE-P fluids2013Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 737, s. 249-279Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study the modal and non-modal linear instability of inertia-dominated channel flow of viscoelastic fluids modelled by the Oldroyd-B and FENE-P closures. The effects of polymer viscosity and relaxation time are considered for both fluids, with the additional parameter of the maximum possible extension for the FENE-P. We find that the parameter explaining the effect of the polymer on the instability is the ratio between the polymer relaxation time and the characteristic instability time scale (the frequency of a modal wave and the time over which the disturbance grows in the non-modal case). Destabilization of both modal and non-modal instability is observed when the polymer relaxation time is shorter than the instability time scale, whereas the flow is more stable in the opposite case. Analysis of the kinetic energy budget reveals that in both regimes the production of perturbation kinetic energy due to the work of the Reynolds stress against the mean shear is responsible for the observed effects where polymers act to alter the correlation between the streamwise and wall-normal velocity fluctuations. In the subcritical regime, the non-modal amplification of streamwise elongated structures is still the most dangerous disturbance-growth mechanism in the flow and this is slightly enhanced by the presence of polymers. However, viscoelastic effects are found to have a stabilizing effect on the amplification of oblique modes.

  • 381.
    Zhu, Lailai
    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.
    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.
    The motion of a deforming capsule through a corner2015Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 770, s. 374-397Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A three-dimensional deformable capsule convected through a square duct with a corner is studied via numerical simulations. We develop an accelerated boundary integral implementation adapted to general geometries and boundary conditions. A global spectral method is adopted to resolve the dynamics of the capsule membrane developing elastic tension according to the neo-Hookean constitutive law and bending moments in an inertialess flow. The simulations show that the trajectory of the capsule closely follows the underlying streamlines independently of the capillary number. The membrane deformability, on the other hand, significantly influences the relative area variations, the advection velocity and the principal tensions observed during the capsule motion. The evolution of the capsule velocity displays a loss of the time-reversal symmetry of Stokes flow due to the elasticity of the membrane. The velocity decreases while the capsule is approaching the corner, as the background flow does, reaches a minimum at the corner and displays an overshoot past the corner due to the streamwise elongation induced by the flow acceleration in the downstream branch. This velocity overshoot increases with confinement while the maxima of the major principal tension increase linearly with the inverse of the duct width. Finally, the deformation and tension of the capsule are shown to decrease in a curved corner.

  • 382.
    Zhu, Lailai
    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. Ecole Polytech Fed Lausanne, Lab Fluid Mech & Instabil, CH-1015 Lausanne, Switzerland.;Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08540 USA.
    Gallaire, Francois
    Ecole Polytech Fed Lausanne, Lab Fluid Mech & Instabil, CH-1015 Lausanne, Switzerland..
    Bifurcation Dynamics of a Particle-Encapsulating Droplet in Shear Flow2017Inngår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 119, nr 6, artikkel-id 064502Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To understand the behavior of composite fluid particles such as nucleated cells and double emulsions in flow, we study a finite-size particle encapsulated in a deforming droplet under shear flow as a model system. In addition to its concentric particle-droplet configuration, we numerically explore other eccentric and time-periodic equilibrium solutions, which emerge spontaneously via supercritical pitchfork and Hopf bifurcations. We present the loci of these solutions around the codimension-two point. We adopt a dynamic system approach to model and characterize the coupled behavior of the two bifurcations. By exploring the flow fields and hydrodynamic forces in detail, we identify the role of hydrodynamic particle-droplet interaction which gives rise to these bifurcations.

  • 383.
    Zhu, Lailai
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Laboratory of Fluid Mechanics and Instabilities, Switzerland .
    Rorai, Cecilia
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, Nordic Institute for Theoretical Physics NORDITA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mitra, Dhrubaditya
    KTH, Centra, Nordic Institute for Theoretical Physics NORDITA.
    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.
    A microfluidic device to sort capsules by deformability: a numerical study2014Inngår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 10, nr 39, s. 7705-7711Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Guided by extensive numerical simulations, we propose a microfluidic device that can sort elastic capsules by their deformability. The device consists of a duct embedded with a semi-cylindrical obstacle, and a diffuser which further enhances the sorting capability. We demonstrate that the device can operate reasonably well under changes in the initial position of the capsule. The efficiency of the device remains essentially unaltered under small changes of the obstacle shape (from semi-circular to semi-elliptic cross-section). Confinement along the direction perpendicular to the plane of the device increases its efficiency. This work is the first numerical study of cell sorting by a realistic microfluidic device.

  • 384.
    Zhu, Lailai
    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. Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA.
    Stone, Howard A.
    Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA..
    Propulsion driven by self-oscillation via an electrohydrodynamic instability2019Inngår i: Physical Review Fluids, ISSN 2469-990X, Vol. 4, nr 6, artikkel-id 061701Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Oscillations of flagella and cilia play an important role in biology, which motivates the idea of functional mimicry as part of bioinspired applications. Nevertheless, it still remains challenging to drive their artificial counterparts to oscillate via a steady, homogeneous stimulus. Combining theory and simulations, we demonstrate a strategy to achieve this goal by using an elastoelectrohydrodynamic instability (based on the Quincke rotation instability). In particular, we show that applying a uniform dc electric field can produce self-oscillatory motion of a microrobot composed of a dielectric particle and an elastic filament. Upon tuning the electric field and filament elasticity, the microrobot exhibits three distinct behaviors: a stationary state, undulatory swimming, and steady spinning, where the swimming behavior stems from an instability emerging through a Hopf bifurcation. Our results imply the feasibility of engineering self-oscillations by leveraging the elastoviscous response to control the type of bifurcation and the form of instability. We anticipate that our strategy will be useful in a broad range of applications imitating self-oscillatory natural phenomena and biological processes.

  • 385.
    Zivanov, Jasenko
    et al.
    MRC, Lab Mol Biol, Cambridge, England..
    Nakane, Takanori
    MRC, Lab Mol Biol, Cambridge, England..
    Forsberg, Björn O.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Kimanius, Dari
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Hagen, Wim J. H.
    European Mol Biol Lab, Struct & Computat Biol Unit, Heidelberg, Germany.;European Mol Biol Lab, Cryoelectron Microscopy Serv Platform, Heidelberg, Germany..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Scheres, Sjors H. W.
    MRC, Lab Mol Biol, Cambridge, England..
    New tools for automated high-resolution cryo-EM structure determination in RELION-32018Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 7, artikkel-id e42166Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2-0.7 angstrom compared to previous RELION versions.

5678 351 - 385 of 385
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