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  • 151.
    Khan, Mehmood
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lataral gene transfer eventsManuskript (preprint) (Annet vitenskapelig)
  • 152.
    Khapko, Taras
    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.
    Kreilos, T.
    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.
    Duguet, Y.
    Eckhardt, B.
    Henningson, Dan Stefan
    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.
    Edge states as mediators of bypass transition in boundary-layer flows2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 801, artikkel-id R2Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The concept of edge states is investigated in the asymptotic suction boundary layer in relation to the receptivity process to noisy perturbations and the nucleation of turbulent spots. Edge tracking is first performed numerically, without imposing any discrete symmetry, in a large computational domain allowing for full spatial localisation of the perturbation velocity. The edge state is a three-dimensional localised structure recurrently characterised by a single low-speed streak that experiences erratic bursts and planar shifts. This recurrent streaky structure is then compared with predecessors of individual spot nucleation events, triggered by non-localised initial noise. The present results suggest a nonlinear picture, rooted in dynamical systems theory, of the nucleation process of turbulent spots in boundary-layer flows, in which the localised edge state plays the role of state-space mediator.

  • 153.
    Khapko, Taras
    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.
    Kreilos, Tobias
    Emergent Complexity in Physical Systems Laboratory (ECPS), École Polytechnique Fédérale de Lausanne.
    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.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    Eckhardt, Bruno
    Fachbereich Physik, Philipps-Universität Marburg.
    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.
    Edge states as mediators of bypass transition in boundary-layer flows2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The concept of edge state is investigated in the asymptotic suction boundary layer in relation with the receptivity process to noisy perturbations and the nucleation of turbulent spots. Edge tracking is first performed numerically, without imposing any discrete symmetry, in a large computational domain allowing for full spatial localisation of the perturbation velocity. The edge state is a three-dimensional localised structure recurrently characterised by a single low-speed streak that experiences erratic bursts and planar shifts. This recurrent streaky structure is then compared with predecessors of individual spot nucleation events, triggered by non-localised initial noise. The present results suggest a nonlinear picture, rooted in dynamical systems theory, of the nucleation process of turbulent spots in boundary-layer flows, in which the localised edge states play the role of state-space mediator.

  • 154.
    Khapko, Taras
    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.
    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.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    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.
    Turbulence collapse in a suction boundary layer2016Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 795, s. 356-379Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Turbulence in the asymptotic suction boundary layer is investigated numerically at the verge of laminarisation using direct numerical simulation. Following an adiabatic protocol, the Reynolds number Re is decreased in small steps starting from a fully turbulent state until laminarisation is observed. Computations in a large numerical domain allow in principle for the possible coexistence of laminar and turbulent regions. However, contrary to other subcritical shear flows, no laminar–turbulent coexistence is observed, even near the onset of sustained turbulence. High-resolution computations suggest a critical Reynolds number Reg≈270, below which turbulence collapses, based on observation times of O(105) inertial time units. During the laminarisation process, the turbulent flow fragments into a series of transient streamwise-elongated structures, whose interfaces do not display the characteristic obliqueness of classical laminar–turbulent patterns. The law of the wall, i.e. logarithmic scaling of the velocity profile, is retained down to Reg, suggesting a large-scale wall-normal transport absent in internal shear flows close to the onset. In order to test the effect of these large-scale structures on the near-wall region, an artificial volume force is added to damp spanwise and wall-normal fluctuations above y+=100, in viscous units. Once the largest eddies have been suppressed by the forcing, and thus turbulence is confined to the near-wall region, oblique laminar–turbulent interfaces do emerge as inother wall-bounded flows, however only transiently. These results suggest that oblique stripes at the onset are a prevalent feature of internal shear flows, but will not occur in canonical boundary layers, including the spatially growing ones.

  • 155. Kieri, Emil
    et al.
    Kreiss, Gunilla
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Coupling of Gaussian Beam and Finite Difference Solvers for Semiclassical Schrodinger Equations2015Inngår i: Advances in Applied Mathematics and Mechanics, ISSN 2070-0733, E-ISSN 2075-1354, Vol. 7, nr 6, s. 687-714Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the semiclassical regime, solutions to the time-dependent Schrodinger equation for molecular dynamics are highly oscillatory. The number of grid points required for resolving the oscillations may become very large even for simple model problems, making solution on a grid intractable. Asymptotic methods like Gaussian beams can resolve the oscillations with little effort and yield good approximations when the atomic nuclei are heavy and the potential is smooth. However, when the potential has variations on a small length-scale, quantum phenomena become important. Then asymptotic methods are less accurate. The two classes of methods perform well in different parameter regimes. This opens for hybrid methods, using Gaussian beams where we can and finite differences where we have to. We propose a new method for treating the coupling between the finite difference method and Gaussian beams. The new method reduces the needed amount of overlap regions considerably compared to previous methods, which improves the efficiency.

  • 156. Kimanius, Dari
    et al.
    Forsberg, Bjorn O.
    Scheres, Sjors H. W.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm University, Sweden.
    Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-22016Inngår i: eLIFE, E-ISSN 2050-084X, Vol. 5, artikkel-id e18722Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By reaching near-atomic resolution for a wide range of specimens, single-particle cryo-EM structure determination is transforming structural biology. However, the necessary calculations come at large computational costs, which has introduced a bottleneck that is currently limiting throughput and the development of new methods. Here, we present an implementation of the RELION image processing software that uses graphics processors (GPUs) to address the most computationally intensive steps of its cryo-EM structure determination workflow. Both image classification and high-resolution refinement have been accelerated more than an order-of-magnitude, and template-based particle selection has been accelerated well over two orders-of-magnitude on desktop hardware. Memory requirements on GPUs have been reduced to fit widely available hardware, and we show that the use of single precision arithmetic does not adversely affect results. This enables high-resolution cryo-EM structure determination in a matter of days on a single workstation.

  • 157.
    Kleine, Vitor
    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. Instituto Tecnológico de Aeronáutica, Praça Marechal Eduardo Gomes, 50, Vila das Acácias, São Josédos Campos SP, 12228-900, Brazil.
    Kleusberg, Elektra
    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.
    Tip-vortex instabilities of two in-line wind turbines2019Inngår i: Wake Conference 201922–24 May 2019, Visby, Sweden, Institute of Physics Publishing (IOPP), 2019, Vol. 1256, nr 1, artikkel-id 012015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The hydrodynamic stability of a vortex system behind two in-line wind turbines operating at low tip-speed ratios is investigated using the actuator-line method in conjunction with the spectral-element flow solver Nek5000. To this end, a simplified setup with two identical wind turbine geometries rotating at the same tip-speed ratio is simulated and compared with a single turbine wake. Using the rotating frame of reference, a steady solution is obtained, which serves as a base state to study the growth mechanisms of induced perturbations to the system. It is shown that, already in the steady state, the tip vortices of the two turbines interact with each other, exhibiting the so-called overtaking phenomenon. Hereby, the tip vortices of the upstream turbine overtake those of the downstream turbine repeatedly. By applying targeted harmonic excitations at the upstream turbine's blade tips a variety of modes are excited and grow with downstream distance. Dynamic mode decomposition of this perturbed flow field showed that the unstable out-of-phase mode is dominant, both with and without the presence of the second turbine. The perturbations of the upstream turbine's helical vortex system led to the destabilization of the tip vortices shed by the downstream turbine. Two distinct mechanisms were observed: for certain frequencies the downstream turbine's vortices oscillate in phase with the vortex system of the upstream turbine while for other frequencies a clear out-of-phase behaviour is observed. Further, short-wave instabilities were shown to grow in the numerical simulations, similar to existing experimental studies [1].

  • 158.
    Kleusberg, Elektra
    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.
    Benard, Sabrina
    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 Normale Supérieure Paris-Saclay, Cachan, France.
    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.
    Tip-vortex breakdown of wind turbines subject to shear2019Inngår i: Wind Energy, ISSN 1095-4244, E-ISSN 1099-1824, Vol. 22, nr 12, s. 1789-1799Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Sheared velocity profiles pervade all wind-turbine applications, thus making it important to understand their effect on the wake. In this study, a single wind turbine is modeled using the actuator-line method in the incompressible Navier–Stokes equations. The tip vortices are perturbed harmonically, and the growth rate of the response is evaluated under uniform inflow and a linear velocity profile. Whereas previous investigations of this kind were conducted in the rotating frame of reference, this study evaluates the excitation response in the fixed frame of reference, thus necessitating a frequency transformation. It is shown that increasing the shear decreases the spatial growth rate in the upper half of the wake while increasing it in the lower half. When scaled with the local tip vortex parameters, the growth rate along the entire azimuth collapses to a single value for the investigated wavenumbers. We conclude that even though the tip-vortex breakdown is asymmetric in sheared flow, the scaled growth rates follow the behavior of axisymmetric helical vortices. An excitation amplitude reduction by an order of magnitude extends the linear growth region of the wake by one radius for uniform inflow. In the sheared setup, the linear growth region is extended further in the top half than in the bottom half because of the progressive distortion of the helical tip vortices. An existing model to determine the stable wake length was shown to be in close agreement with the observed numerical results when adjusted for shear.

  • 159.
    Kleusberg, Elektra
    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.
    Mikkelsen, R. F.
    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.
    Ivanell, Stefan
    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. Uppsala University, 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.
    High-Order Numerical Simulations of Wind Turbine Wakes2017Inngår i: Journal of Physics, Conference Series, ISSN 1742-6588, E-ISSN 1742-6596, Vol. 854, nr 1, artikkel-id 012025Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Previous attempts to describe the structure of wind turbine wakes and their mutual interaction were mostly limited to large-eddy and Reynolds-averaged Navier-Stokes simulations using finite-volume solvers. We employ the higher-order spectral-element code Nek5000 to study the influence of numerical aspects on the prediction of the wind turbine wake structure and the wake interaction between two turbines. The spectral-element method enables an accurate representation of the vortical structures, with lower numerical dissipation than the more commonly used finite-volume codes. The wind-turbine blades are modeled as body forces using the actuator-line method (ACL) in the incompressible Navier-Stokes equations. Both tower and nacelle are represented with appropriate body forces. An inflow boundary condition is used which emulates homogeneous isotropic turbulence of wind-tunnel flows. We validate the implementation with results from experimental campaigns undertaken at the Norwegian University of Science and Technology (NTNU Blind Tests), investigate parametric influences and compare computational aspects with existing numerical simulations. In general the results show good agreement between the experiments and the numerical simulations both for a single-turbine setup as well as a two-turbine setup where the turbines are offset in the spanwise direction. A shift in the wake center caused by the tower wake is detected similar to experiments. The additional velocity deficit caused by the tower agrees well with the experimental data. The wake is captured well by Nek5000 in comparison with experiments both for the single wind turbine and in the two-turbine setup. The blade loading however shows large discrepancies for the high-turbulence, two-turbine case. While the experiments predicted higher thrust for the downstream turbine than for the upstream turbine, the opposite case was observed in Nek5000.

  • 160.
    Kleusberg, Elektra
    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.
    Sarmast, 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.
    Ivanell, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Uppsala University, Wind Energy Section, Campus Gotland, SE-621 67 Visby, Sweden.
    Henningson, Dan Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Actuator line simulations of a Joukowsky and Tjæreborg rotor using spectral element and finite volume methods2016Inngår i: SCIENCE OF MAKING TORQUE FROM WIND (TORQUE 2016), Institute of Physics (IOP), 2016, Vol. 753, nr 8, artikkel-id 082011Konferansepaper (Fagfellevurdert)
    Abstract [en]

    The wake structure behind a wind turbine, generated by the spectral element code Nek5000, is compared with that from the finite volume code EllipSys3D. The wind turbine blades are modeled using the actuator line method. We conduct the comparison on two different setups. One is based on an idealized rotor approximation with constant circulation imposed along the blades corresponding to Glauert's optimal operating condition, and the other is the Tjffireborg wind turbine. The focus lies on analyzing the differences in the wake structures entailed by the different codes and corresponding setups. The comparisons show good agreement for the defining parameters of the wake such as the wake expansion, helix pitch and circulation of the helical vortices. Differences can be related to the lower numerical dissipation in Nek5000 and to the domain differences at the rotor center. At comparable resolution Nek5000 yields more accurate results. It is observed that in the spectral element method the helical vortices, both at the tip and root of the actuator lines, retain their initial swirl velocity distribution for a longer distance in the near wake. This results in a lower vortex core growth and larger maximum vorticity along the wake. Additionally, it is observed that the break down process of the spiral tip vortices is significantly different between the two methods, with vortex merging occurring immediately after the onset of instability in the finite volume code, while Nek5000 simulations exhibit a 2-3 radii period of vortex pairing before merging.

  • 161.
    Koskela, Antti
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Jarlebring, Elias
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hochstenbach, M. E.
    Krylov approximation of linear odes with polynomial parameterization2016Inngår i: SIAM Journal on Matrix Analysis and Applications, ISSN 0895-4798, E-ISSN 1095-7162, Vol. 37, nr 2, s. 519-538Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We propose a new numerical method to solve linear ordinary differential equations of the type δu/δt (t, ϵ) = A(ϵ) u(t,ϵ), where A: C → Cn×n is a matrix polynomial with large and sparse matrix coefficients. The algorithm computes an explicit parameterization of approximations of u(t, ϵ) such that approximations for many different values of ϵ and t can be obtained with a very small additional computational effort. The derivation of the algorithm is based on a reformulation of the parameterization as a linear parameter-free ordinary differential equation and on approximating the product of the matrix exponential and a vector with a Krylov method. The Krylov approximation is generated with Arnoldi's method and the structure of the coefficient matrix turns out to be independent of the truncation parameter so that it can also be interpreted as Arnoldi's method applied to an infinite dimensional matrix. We prove the super linear convergence of the algorithm and provide a posteriori error estimates to be used as termination criteria. The behavior of the algorithm is illustrated with examples stemming from spatial discretizations of partial differential equations.

  • 162. Kreilos, T.
    et al.
    Khapko, Taras
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schneider, T. M.
    Veble, G.
    Duguet, Y.
    Schlatter, Philipp
    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.
    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.
    Eckhardt, B.
    Turbulence transition in the asymptotic suction boundary layer2013Inngår i: International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2013, TSFP-8 , 2013Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We study the transition to turbulence in the asymptotic suction boundary layer (ASBL) by direct numerical simulation. Tracking the motion of trajectories intermediate between laminar and turbulent states we can identify the invariant object inside the laminar-Turbulent boundary, the edge state. In small domains, the flow behaves like a travelling wave over short time intervals. On longer times one notes that the energy shows strong bursts at regular time intervals. During the bursts the streak structure is lost, but it reforms, translated in the spanwise direction by half the domain size. Varying the suction velocity allows to embed the flow into a family of flows that interpolate between plane Couette flow and the ASBL. Near the plane Couette limit, the edge state is a travelling wave. Increasing the suction, the travelling wave and a symmetry-related copy of it undergo a saddle-node infinite-period (SNIPER) bifurcation that leads to bursting and discrete-symmetry shifts. In wider domains, the structures localize in the spanwise direction, and the flow in the active region is similar to the one in small domains. There are still periodic bursts at which the flow structures are shifted, but the shift-distance is no longer connected to a discrete symmetry of the flow geometry. Two different states are found by edge tracking techniques, one where structures are shifted to the same side at every burst and one where they are alternatingly shifted to the left and to the right.

  • 163.
    Kreilos, Tobias
    et al.
    Emergent Complexity in Physical Systems Laboratory (ECPS), École Polytechnique Fédérale de Lausanne.
    Khapko, Taras
    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. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Duguet, Yohann
    LIMSI, CNRS, Université Paris-Saclay.
    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.
    Eckhardt, Bruno
    Fachbereich Physik, Philipps-Universität Marburg.
    Bypass transition and spot nucleation in boundary layers2016Manuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The spatio-temporal aspects of the transition to turbulence are considered in the case of a boundary-layer flow developing above a flat plate exposed to free-stream turbulence. Combining results on the receptivity to free-stream turbulence with the nonlinear concept of a transition threshold, a physically motivated model suggests a spatial distribution of spot nucleation events. To describe the evolution of turbulent spots a probabilistic cellular automaton is introduced, with all parameters directly fitted from numerical simulations of the boundary layer. The nucleation rates are then combined with the cellular automaton model, yielding excellent quantitative agreement with the statistical characteristics for different free-stream turbulence levels. We thus show how the recent theoretical progress on transitional wall-bounded flows can be extended to the much wider class of spatially developing boundary-layer flows.

  • 164. Kudrnovsky, J.
    et al.
    Drchal, V.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Rusz, J.
    Turek, I.
    Unified approach to electronic, thermodynamical, and transport properties of Fe3Si and Fe3Al alloys2014Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 90, nr 13, s. 134408-Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The electronic, thermodynamical, and transport properties of ordered Fe3X (X = Al, Si) alloys are studied from first principles. We present here a unified approach to the phase stability, the estimate of the Curie temperature, the temperature dependence of sublattice magnetizations, magnon spectra, the spin-stiffnesses, and residual resistivities. An important feature of the present study is that all calculated physical properties are determined in the framework of the same first-principles electronic structure model combined with the effective Ising and Heisenberg Hamiltonians used for study of the thermodynamical properties of alloys. Curie temperatures, spin-stiffnesses, and magnon spectra are determined using the same calculated exchange integrals. Finally, the transport properties are calculated using the linear-response theory. Our theoretical estimates compare well with available experimental data. In particular, calculations predict (in agreement with experiment) the ordered D0(3) phase as the ground-state alloy structure, demonstrate that a correct relation of Curie temperatures of Fe3Al/Fe3Si alloys can be obtained only by going beyond a simple mean-field approximation, provide reasonable estimates of spin-stiffnesses, and give resistivities compatible with structural disorder observed in the experiment. Although the calculated temperature dependences of the Fe magnetization on different sublattices are similar, they nevertheless deviate more than in the experiment, and we discuss a possible origin.

  • 165. Kumar, Ankit
    et al.
    Pan, Fan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Husain, Sajid
    Akansel, Serkan
    Brucas, Rimantas
    Bergqvist, Lars
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Chaudhary, Sujeet
    Svedlindh, Peter
    Temperature-dependent Gilbert damping of Co2FeAl thin films with different degree of atomic order2017Inngår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 96, nr 22, artikkel-id 224425Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Half-metallicity and low magnetic damping are perpetually sought for spintronics materials, and full Heusler compounds in this respect provide outstanding properties. However, it is challenging to obtain the well-ordered half-metallic phase in as-deposited full Heusler compound thin films, and theory has struggled to establish a fundamental understanding of the temperature-dependent Gilbert damping in these systems. Here we present a study of the temperature-dependent Gilbert damping of differently ordered as-deposited Co2FeAl full Heusler compound thin films. The sum of inter-and intraband electron scattering in conjunction with the finite electron lifetime in Bloch states governs the Gilbert damping for the well-ordered phase, in contrast to the damping of partially ordered and disordered phases which is governed by interband electronic scattering alone. These results, especially the ultralow room-temperature intrinsic damping observed for the well-ordered phase, provide fundamental insights into the physical origin of the Gilbert damping in full Heusler compound thin films.

  • 166.
    Käll, Lukas
    et al.
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Krogh, Anders
    Sonnhammer, Erik L. L.
    Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server2007Inngår i: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 35, nr Web Server issue, 1, s. W429-W432Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30-65% of all predicted signal peptides and 25-35% of all predicted transmembrane topologies overlap. This impairs predictions of 5-10% of the proteome, hence this is an important issue in protein annotation. To address this problem, we previously designed a hidden Markov model, Phobius, that combines transmembrane topology and signal peptide predictions. The method makes an optimal choice between transmembrane segments and signal peptides, and also allows constrained and homology-enriched predictions. We here present a web interface (http://phobius.cgb.ki.se and http://phobius.binf.ku.dk) to access Phobius.

  • 167.
    König, Carolin
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Skanberg, Robin
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Hotz, Ingrid
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Ynnerman, Anders
    Linkopings Univ, Dept Media & Informat Technol, Norrkoping, Sweden..
    Norman, P.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Linares, Mathieu
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations2018Inngår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, nr 24, s. 3030-3033Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A very stable binding site for the interaction between a pentameric oligothiophene and an amyloid-(1-42) fibril has been identified by means of non-biased molecular dynamics simulations. In this site, the probe is locked in an all-trans conformation with a Coulombic binding energy of 1200 kJ mol(-1) due to the interactions between the anionic carboxyl groups of the probe and the cationic epsilon-amino groups in the lysine side chain. Upon binding, the conformationally restricted probes show a pronounced increase in molecular planarity. This is in line with the observed changes in luminescence properties that serve as the foundation for their use as biomarkers.

  • 168.
    Lambert, Ruth A.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Breugem, Wim-Paul
    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.
    Active suspensions in thin films: nutrient uptake and swimmer motion2013Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 733, s. 528-557Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A numerical study of swimming particle motion and nutrient transport is conducted for a semidilute to dense suspension in a thin film. The steady squirmer model is used to represent the motion of living cells in suspension with the nutrient uptake by swimming particles modelled using a first-order kinetic equation representing the absorption process that occurs locally at the particle surface. An analysis of the dynamics of the neutral squirmers inside the film shows that the vertical motion is reduced significantly. The mean nutrient uptake for both isolated and populations of swimmers decreases for increasing swimming speeds when nutrient advection becomes relevant as less time is left for the nutrient to diffuse to the surface. This finding is in contrast to the case where the uptake is modelled by imposing a constant nutrient concentration at the cell surface and the mass flux results to be an increasing monotonic function of the swimming speed. In comparison to non-motile particles, the cell motion has a negligible influence on nutrient uptake at lower particle absorption rates since the process is rate limited. At higher absorption rates, the swimming motion results in a large increase in the nutrient uptake that is attributed to the movement of particles and increased mixing in the fluid. As the volume fraction of swimming particles increases, the squirmers consume slightly less nutrients and require more power for the same swimming motion. Despite this increase in energy consumption, the results clearly demonstrate that the gain in nutrient uptake make swimming a winning strategy for micro-organism survival also in relatively dense suspensions.

  • 169. Larsson, Torbjörn
    et al.
    Hammar, Johan
    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.
    ENHANCING COMPUTATIONAL AERO-ACOUSTIC PROCESSES FOR GROUNDVEHICLES RESOLVING OPEN SOURCE CFD2018Inngår i: The 13th OpenFOAM Workshop, 2018, s. 1-4Konferansepaper (Fagfellevurdert)
  • 170.
    Lashgari, Iman
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Niazi Ardekani, Mehdi
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Banerjee, Indradumna
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Russom, Aman
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Brandt, Luca
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Inertial migration of spherical and oblate particles in straight ductsInngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study numerically the inertial migration of a single rigid sphere and an oblate spheroid in straight square and rectangular ducts. A highly accurate interface-resolved numerical algorithm is employed to analyse the entire migration dynamics of the oblate particle and compare it with that of the sphere. Similarly to the inertial focusing of spheres, the oblate particle reaches one of the four face-centred equilibrium positions, however they are vertically aligned with the axis of symmetry in the spanwise direction. In addition, the lateral trajectories of spheres and oblates collapse into an equilibrium manifold before ending at the equilibrium positions, with the equilibrium manifold tangential to lines of constant background shear for both sphere and oblate particles. The differences between the migration of the oblate and sphere are also presented, in particular the oblate may focus on the diagonal symmetry line of the duct cross-section, close to one of the corners, if its diameter is larger than a certain threshold. Moreover, we show that the final orientation and rotation of the oblate exhibit a chaotic behaviour for Reynolds numbers beyond a critical value. Finally, we document that the lateral motion of the oblate particle is less uniform than that of the spherical particle due to its evident tumbling motion throughout the migration. In a square duct, the strong tumbling motion of the oblate in the first stage of the migration results in a lower lateral velocity and consequently longer focusing length with respect to that of the spherical particle. The opposite is true in a rectangular duct where the higher lateral velocity of the oblate in the second stage of the migration, with negligible tumbling, gives rise to shorter focusing lengths.These results can help the design of microfluidic systems for bio-applications.

  • 171.
    Lashgari, Iman
    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
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Padova, Italy.
    Breugem, W. -P
    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.
    Transition to Turbulence in the Presence of Finite Size Particles2015Inngår i: Procedia IUTAM, Elsevier, 2015, s. 211-217Konferansepaper (Fagfellevurdert)
    Abstract [en]

    We study the transition from laminar to turbulent flow in a channel seeded with finite-size neutrally buoyant particles. A fixed ratio of 10 between the channel height and the particle diameter is considered. The flow is examined in the range of Reynolds numbers 500 ≤ Re ≤; 5000 and the particle volume fractions 0.001 ≤ Φ ≤; 0.3. We report a non-monotonic behavior of the threshold value of the Reynolds number above which the flow becomes turbulent, in agreement with previous experimental studies. The mean square velocity fluctuations and Reynolds shear stress of the fluid phase are reduced by increasing the particle volume fraction at a fixed Re=1500, while the mean square velocities of the solid phase are enhanced monotonically suggesting a transition from fluid to particle dominated dynamics at high volume fraction.

  • 172.
    Lashgari, Iman
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Picano, Francesco
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. University of Padova, Italy.
    Breugem, Wim Paul
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Channel flow of rigid sphere suspensions: Particle dynamics in the inertial regime2016Inngår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 78, s. 12-24Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We consider suspensions of neutrally-buoyant finite-size rigid spherical particles in channel flow and investigate the relation between the particle dynamics and the mean bulk behavior of the mixture for Reynolds numbers 500 ≤ Re ≤ 5000 and particle volume fraction 0 ≤ Φ ≤ 0.3, via fully resolved numerical simulations. Analysis of the momentum balance reveals the existence of three different regimes: laminar, turbulent and inertial shear-thickening depending on which of the stress terms, viscous, Reynolds or particle stress, is the major responsible for the momentum transfer across the channel. We show that both Reynolds and particle stress dominated flows fall into the Bagnoldian inertial regime and that the Bagnold number can predict the bulk behavior although this is due to two distinct physical mechanisms. A turbulent flow is characterized by larger particle dispersion and a more uniform particle distribution, whereas the particulate-dominated flows is associated with a significant particle migration towards the channel center where the flow is smooth laminar-like and dispersion low. Interestingly, the collision kernel shows similar values in the different regimes, although the relative particle velocity and clustering clearly vary with inertia and particle concentration.

  • 173.
    Lashgari, Iman
    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
    Costa, Pedro
    Breugem, Wim-Paul
    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.
    Turbulent channel flow of a dense binary mixture of rigid particles2017Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 818, s. 623-645Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We study turbulent channel flow of a binary mixture of finite-sized neutrally buoyant rigid particles by means of interface-resolved direct numerical simulations. We fix the bulk Reynolds number and total solid volume fraction, Re-b = 5600 and Phi = 20 %, and vary the relative fraction of small and large particles. The binary mixture consists of particles of two different sizes, 2h/d(l) = 20 and 2h/d(s) = 30 where h is the half-channel height and d(l) and d(s) the diameters of the large and small particles. While the particulate flow statistics exhibit a significant alteration of the mean velocity profile and turbulent fluctuations with respect to the unladen flow, the differences between the mono-disperse and bi-disperse cases are small. However, we observe a clear segregation of small particles at the wall in binary mixtures, which affects the dynamics of the near-wall region and thus the overall drag. This results in a higher drag in suspensions with a larger number of large particles. As regards bi-disperse effects on the particle dynamics, a non-monotonic variation of the particle dispersion in the spanwise (homogeneous) direction is observed when increasing the percentage of small/large particles. Finally, we note that particles of the same size tend to cluster more at contact whereas the dynamics of the large particles gives the highest collision kernels due to a higher approaching speed.

  • 174.
    Lashgari, Iman
    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.
    Tammisola, Outi
    Department of Engineering, University of Cambridge, Cambridge, UK.
    Citro, Vincenzo
    DIIN, University of Salerno, Fisciano, Italy.
    Juniper, Matthew P.
    Department of Engineering, Univerisyt of Cambridge, Cambridge, UK.
    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 planar X-junction flow: stability analysis and control2014Inngår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 753, s. 1-28Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The bifurcations and control of the flow in a planar X-junction are studied via linear stability analysis and direct numerical simulations. This study reveals the instability mechanisms in a symmetric channel junction and shows how these can be stabilized or destabilized by boundary modification. We observe two bifurcations as the Reynolds number increases. They both scale with the inlet speed of the two side channels and are almost independent of the inlet speed of the main channel. Equivalently, both bifurcations appear when the recirculation zones reach a critical length. A two-dimensional stationary global mode becomes unstable first, changing the flow from a steady symmetric state to a steady asymmetric state via a pitchfork bifurcation. The core of this instability, whether defined by the structural sensitivity or by the disturbance energy production, is at the edges of the recirculation bubbles, which are located symmetrically along the walls of the downstream channel. The energy analysis shows that the first bifurcation is due to a lift-up mechanism. We develop an adjustable control strategy for the first bifurcation with distributed suction or blowing at the walls. The linearly optimal wall-normal velocity distribution is computed through a sensitivity analysis and is shown to delay the first bifurcation from Re = 82.5 to Re = 150. This stabilizing effect arises because blowing at the walls weakens the wall-normal gradient of the streamwise velocity around the recirculation zone and hinders the lift-up. At the second bifurcation, a three-dimensional stationary global mode with a spanwise wavenumber of order unity becomes unstable around the asymmetric steady state. Nonlinear three-dimensional simulations at the second bifurcation display transition to a nonlinear cycle involving growth of a three-dimensional steady structure, time-periodic secondary instability and nonlinear breakdown restoring a two-dimensional flow. Finally, we show that the sensitivity to wall suction at the second bifurcation is as large as it is at the first bifurcation, providing a possible mechanism for destabilization.

  • 175.
    Laure, Erwin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holmgren, Sverker
    Preface2013Inngår i: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 29, nr 8, s. 2115-2116Artikkel i tidsskrift (Fagfellevurdert)
  • 176.
    Lazeroms, Werner
    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.
    Wallin, Stefan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Nonlinear features in explicit algebraic models for turbulent flows with active scalars2015Inngår i: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A detailed discussion of explicit algebraic turbulence models in the case of active scalars is given. In particular, we discuss the appearance of nonlinearities in the models and the need for explicit solutions of the resulting nonlinear equations. Focussing on a recently published model for two-dimensional stratified flows, we present an intuitive way of approximating the solution of a sixth-order polynomial equation for the production-to-dissipation ratio (p + g)/e of turbulent kinetic energy K. This formulation is shown to be consistent for turbulent channel flow with stable and unstable stratification. The result is important for obtaining a robust model with a correct behaviour of the turbulence production in different limits of shear and buoyancy. The results have recently been published in Lazeroms et al. (2015).

  • 177. Lehtio, J.
    et al.
    Branca, M.
    Johansson, H.
    Orre, M.
    Granholm, Viktor
    KTH.
    Forshed, J.
    Perez-Bercoff, M.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Genome Wide Proteomics Using Peptide High Resolution Isoelectric Focusing Hirief-Ms Allows Detection New Human Gene Models2012Inngår i: Annals of Oncology, ISSN 0923-7534, E-ISSN 1569-8041, Vol. 23, s. 33-34Artikkel i tidsskrift (Annet vitenskapelig)
  • 178.
    Li, Xin
    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.
    Electronic Circular Dichroism of Surface-Adsorbed Molecules by Means of Quantum Mechanics Capacitance Molecular Mechanics2014Inngår i: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 118, nr 11, s. 5833-5840Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    To promote a more comprehensive understanding of the influence of metal-adsorbate interaction for molecules at metallo surfaces or metallo nanoparticles in solvent environments on their electronic circular dichroism (ECD) spectra, we evaluate the application of a recently derived quantum mechanics capacitance molecular mechanics (QMCMM) model for ECD. Using helicene absorbed on gold surfaces in protic and aprotic solvents as illustration, we elucidate the detailed effects on excitation energies, transition moments, rotatory strengths, orientation dependence of ECD spectra, and the different roles of aprotic and protic solvents and the induced charge distribution patterns on the surface. These changes are decomposed in terms of surface alone, solvent alone, and combined surface solvent influence, and furthermore into the indirect contributions by the surface-induced restructuring of the helicene. Much of the salient changes of the ECD can be rationalized to the substantial redistribution of charge at the gold surface induced by the presence of the helicene. The study indicates that through the QMCMNI model the effects of a metallic surface on the circular dichroism spectra of adsorbed organic molecules can be tackled by extended QM calculations coupled to polarizability-capacitance force fields for large metallic clusters representing surfaces or nanoparticles.

  • 179.
    Li, Xin
    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.
    Two-Photon Absorption of Metal-Assisted Chromophores2014Inngår i: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 10, nr 12, s. 5630-5639Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aiming to understand the effect of a metal surface on nonlinear optical properties and the combined effects of surface and solvent environments on such properties, we present a multiscale response theory study, integrated with dynamics of the two-photon absorption of 4-nitro-4'-amino-trans-stilbene physisorbed on noble metal surfaces, considering two such surfaces, Ag(111) and Au(111), and two solvents, cyclohexane and water, as cases for demonstration. A few conclusions of general character could be drawn: While the geometrical change of the chromophore induced by the environment was found to notably alter (diminish) the two-photon absorption cross section in the polar medium, the effects of the metal surface and solvent on the electronic structure of the chromophore surpasses the geometrical effects and leads to a considerably enhanced two-photon absorption cross section in the polar solvent. This enhancement of two-photon absorption arises essentially from the metal charge image induced enlargement of the difference between the dipole moment of the excited state and the ground state. The orientation-dependence of the two-photon absorption is found to connect with the lateral rotation of the chromophore, where the two-photon absorption reaches its maximum when the polarization of the incident light coincides with the long-axis of the chromophore. Our results demonstrate a distinct enhancement of the two-photon absorption by a metal surface and a polar medium and envisage the employment of metal-chromophore composite materials for future development of nonlinear optical materials with desirable properties.

  • 180. Liin, Sara
    et al.
    Gabrielsson, Anders
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elinder, Fredrik
    Lindahl, Erik
    The Molecular Mechanism of the Dual Spider Toxin Effect on Voltage Gated K+ Channels2016Inngår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 107A-107AArtikkel i tidsskrift (Annet vitenskapelig)
  • 181.
    Linares, Mathieu
    et al.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sun, Haofan
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi. East China Univ Sci & Technol, Shanghai Key Lab Funct Mat Chem, Dept Chem & Mol Engn, Shanghai 200237, Peoples R China.
    Biler, Michal
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Andreasson, Joakim
    Chalmers Univ Technol, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Norman, P.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Teoretisk kemi och biologi.
    Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra2019Inngår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 21, nr 7, s. 3637-3643Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.

  • 182.
    Lindahl, V.
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Lidmar, Jack
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Fysik.
    Riemann metric approach to optimal sampling of multidimensional free-energy landscapes2018Inngår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 98, nr 2, artikkel-id 023312Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%-70%.

  • 183.
    Lindahl, Viveca
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hess, Berk
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Permeability and ammonia selectivity in aquaporin TIP2;1: linking structure to function2018Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, artikkel-id 2995Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Aquaporin TIP2;1 is a protein channel permeable to both water and ammonia. The structural origin of ammonia selectivity remains obscure, but experiments have revealed that a double mutation renders it impermeable to ammonia without affecting water permeability. Here, we aim to reproduce and explain these observations by performing an extensive mutational study using microsecond long molecular dynamics simulations, applying the two popular force fields CHARMM36 and Amber ff99SB-ILDN. We calculate permeabilities and free energies along the channel axis for ammonia and water. For one force field, the permeability of the double mutant decreases by a factor of 2.5 for water and 4 for ammonia, increasing water selectivity by a factor of 1.6. We attribute this effect to decreased entropy of water in the pore, due to the observed increase in pore-water interactions and narrower pore. Additionally, we observe spontaneous opening and closing of the pore on the cytosolic side, which suggests a gating mechanism for the pore. Our results show that sampling methods and simulation times are sufficient to delineate even subtle effects of mutations on structure and function and to capture important long-timescale events, but also underline the importance of improving models further.

  • 184.
    Lindahl, Viveca
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Villa, Alessandra
    Hess, Berk
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sequence dependency of canonical base pair opening in the DNA double helix2017Inngår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 13, nr 4, artikkel-id e1005463Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm. The simulation is guided back and forth along the coordinate, allowing for multiple opening pathways. We compare the calculated free energies with those from an NMR study and check assumptions of the model used for interpreting the NMR data. Our results further show that the neighboring sequence is an important factor for the opening free energy, but also indicates that other sequence effects may play a role. All base pairs are observed to have a propensity for opening toward the major groove. The preferred opening base is cytosine for GC base pairs, while for AT there is sequence dependent competition between the two bases. For AT opening, we identify two non-canonical base pair interactions contributing to a local minimum in the free energy profile. For both AT and CG we observe long-lived interactions with water and with sodium ions at specific sites on the open base pair.

  • 185.
    Lindvall, Jenny
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden..
    Svensson, Gunilla
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden.
    Caballero, Rodrigo
    KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Bolin Ctr Climate Res, Dept Meteorol, Stockholm, Sweden.
    The impact of changes in parameterizations of surface drag and vertical diffusion on the large-scale circulation in the Community Atmosphere Model (CAM5)2017Inngår i: Climate Dynamics, ISSN 0930-7575, E-ISSN 1432-0894, Vol. 48, nr 11, s. 3741-3758Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Simulations with the Community Atmosphere Model version 5 (CAM5) are used to analyze the sensitivity of the large-scale circulation to changes in parameterizations of orographic surface drag and vertical diffusion. Many GCMs and NWP models use enhanced turbulent mixing in stable conditions to improve simulations, while CAM5 cuts off all turbulence at high stabilities and instead employs a strong orographic surface stress parameterization, known as turbulent mountain stress (TMS). TMS completely dominates the surface stress over land and reduces the near-surface wind speeds compared to simulations without TMS. It is found that TMS is generally beneficial for the large-scale circulation as it improves zonal wind speeds, Arctic sea level pressure and zonal anomalies of the 500-hPa stream function, compared to ERA-Interim. It also alleviates atmospheric blocking frequency biases in the Northern Hemisphere. Using a scheme that instead allows for a modest increase of turbulent diffusion at higher stabilities only in the planetary boundary layer (PBL) appears to in some aspects have a similar, although much smaller, beneficial effect as TMS. Enhanced mixing throughout the atmospheric column, however, degrades the CAM5 simulation. Evaluating the simulations in comparison with detailed measurements at two locations reveals that TMS is detrimental for the PBL at the flat grassland ARM Southern Great Plains site, giving too strong wind turning and too deep PBLs. At the Sodankyla forest site, the effect of TMS is smaller due to the larger local vegetation roughness. At both sites, all simulations substantially overestimate the boundary layer ageostrophic flow.

  • 186. Liu, H.
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, N. M.
    Sobolev and max norm error estimates for Gaussian beam superpositions2016Inngår i: Communications in Mathematical Sciences, ISSN 1539-6746, E-ISSN 1945-0796, Vol. 14, nr 7, s. 2037-2072Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    This work is concerned with the accuracy of Gaussian beam superpositions, which are asymptotically valid high frequency solutions to linear hyperbolic partial differential equations and the Schrödinger equation. We derive Sobolev and max norms estimates for the difference between an exact solution and the corresponding Gaussian beam approximation, in terms of the short wavelength e. The estimates are performed for the scalar wave equation and the Schrödinger equation. Our result demonstrates that a Gaussian beam superposition with kth order beams converges to the exact solution as O(εk/2-s) in order s Sobolev norms. This result is valid in any number of spatial dimensions and it is unaffected by the presence of caustics in the solution. In max norm, we show that away from caustics the convergence rate is O(ε⌈k/2⌉) and away from the essential support of the solution, the convergence is spectral in ε. However, in the neighborhood of a caustic point we are only able to show the slower, and dimensional dependent, rate O(ε(k-n)/2) in n spatial dimensions.

  • 187. Liu, Hailiang
    et al.
    Ralston, James
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, Nicolay M.
    Gaussian beam methods for the helmholtz equation2014Inngår i: SIAM Journal on Applied Mathematics, ISSN 0036-1399, E-ISSN 1095-712X, Vol. 74, nr 3, s. 771-793Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work we construct Gaussian beam approximations to solutions of the high frequency Helmholtz equation with a localized source. Under the assumption of nontrapping rays we show error estimates between the exact outgoing solution and Gaussian beams in terms of the wave number k, both for single beams and superposition of beams. The main result is that the relative local L-2 error in the beam approximations decay as k(-N/2) independent of dimension and presence of caustics for Nth order beams.

  • 188. Liu, Hailiang
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tanushev, Nicolay M.
    Error estimates for Gaussian beam superpositions2013Inngår i: Mathematics of Computation, ISSN 0025-5718, E-ISSN 1088-6842, Vol. 82, nr 282, s. 919-952Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gaussian beams are asymptotically valid high frequency solutions to hyperbolic partial differential equations, concentrated on a single curve through the physical domain. They can also be extended to some dispersive wave equations, such as the Schrodinger equation. Superpositions of Gaussian beams provide a powerful tool to generate more general high frequency solutions that are not necessarily concentrated on a single curve. This work is concerned with the accuracy of Gaussian beam superpositions in terms of the wavelength epsilon. We present a systematic construction of Gaussian beam superpositions for all strictly hyperbolic and Schrodinger equations subject to highly oscillatory initial data of the form Ae(i Phi/) (epsilon). Through a careful estimate of an oscillatory integral operator, we prove that the k-th order Gaussian beam superposition converges to the original wave field at a rate proportional to epsilon(k/2) in the appropriate norm dictated by the well-posedness estimate. In particular, we prove that the Gaussian beam superposition converges at this rate for the acoustic wave equation in the standard, epsilon-scaled, energy norm and for the Schrodinger equation in the L-2 norm. The obtained results are valid for any number of spatial dimensions and are unaffected by the presence of caustics. We present a numerical study of convergence for the constant coefficient acoustic wave equation in R-2 to analyze the sharpness of the theoretical results.

  • 189.
    Liu, Ying
    et al.
    Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA..
    Rallabandi, Bhargav
    Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA.;Univ Calif Riverside, Dept Mech Engn, Riverside, CA 92521 USA..
    Zhu, Lailai
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA..
    Gupta, Ankur
    Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA..
    Stone, Howard A.
    Princeton Univ, Dept Mech & Aerosp Engn, Princeton, NJ 08544 USA..
    Pattern formation in oil-in-water emulsions exposed to a salt gradient2019Inngår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 4, nr 8, artikkel-id 084307Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Flow instabilities can occur in a fluid system with two components that have significantly different diffusivities and that have opposite effects on the fluid density, as is the scenario in traditional double-diffusive convection. Here, we experimentally show that an oil-in-water emulsion exposed to salt concentration gradients generates a flowerlike pattern driven by vertical and azimuthal instabilities. We also report numerical and analytical studies to elaborate on the mechanism, the instability criteria, and the most unstable modes that determine the details of the observed patterns. We find that the instability is driven by buoyancy and stems from the differential transport between the dissolved salt and the suspended oil droplets, which have opposing effects on the density of the medium. Consequently, we identify a criterion for the development of the instability that involves the relative densities and concentrations of the salt and oil droplets. We also argue that the typical wave number of the pattern formed scales with the Peclet number of the salt, which here is equivalent to the Rayleigh number since the flow is driven by buoyancy. We find good agreement of these predictions with both experiments and numerical simulations.

  • 190.
    Lizarraga, Raquel
    et al.
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap.
    Pan, Fan
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Bergqvist, Lars
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Holmstrom, Erik
    Gercsi, Zsolt
    Vitos, Levente
    First Principles Theory of the hcp-fcc Phase Transition in Cobalt2017Inngår i: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, artikkel-id 3778Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Identifying the forces that drive a phase transition is always challenging. The hcp-fcc phase transition that occurs in cobalt at similar to 700 K has not yet been fully understood, although early theoretical studies have suggested that magnetism plays a main role in the stabilization of the fcc phase at high temperatures. Here, we perform a first principles study of the free energies of these two phases, which we break into contributions arising from the vibration of the lattice, electronic and magnetic systems and volume expansion. Our analysis of the energy of the phases shows that magnetic effects alone cannot drive the fcc-hcp transition in Co and that the largest contribution to the stabilization of the fcc phase comes from the vibration of the ionic lattice. By including all the contributions to the free energy considered here we obtain a theoretical transition temperature of 825 K.

  • 191. Locht, I. L. M.
    et al.
    Di Marco, I.
    Garnerone, S.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Battiato, M.
    Ultrafast magnetization dynamics: Microscopic electronic configurations and ultrafast spectroscopy2015Inngår i: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 92, nr 6, artikkel-id 064403Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We provide an approach for the identification of the electronic and magnetic configurations of ferromagnetic Fe after an ultrafast decrease or increase of the magnetization. The model is based on the well-grounded assumption that, after an ultrafast variation of the magnetization, the system achieves a partial thermal equilibrium. With statistical arguments we show that the magnetic configurations are qualitatively different in the case of reduced or increased magnetization. The predicted magnetic configurations are then used to compute the dielectric response at the 3p (M) absorption edge, which is directly related to the changes observed in the experimental T-MOKE data. The good qualitative agreement between theory and experiment offers a substantial support for the validity of the model, and to the very existence of an ultrafast increase of the magnetization.

  • 192. Locht, I. L. M.
    et al.
    Kvashnin, Y. O.
    Rodrigues, D. C. M.
    Pereiro, 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.
    Lichtenstein, A. I.
    Katsnelson, M. I.
    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.
    Klautau, A. B.
    Johansson, Börje
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. Uppsala University, Sweden.
    Di Marco, I.
    Eriksson, O.
    Standard model of the rare earths analyzed from the Hubbard I approximation2016Inngår i: PHYSICAL REVIEW B, ISSN 2469-9950, Vol. 94, nr 8, artikkel-id 085137Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this work we examine critically the electronic structure of the rare-earth elements by use of the so-called Hubbard I approximation. From the theoretical side all measured features of both occupied and unoccupied states are reproduced, without significant deviations between observations and theory. We also examine cohesive properties like the equilibrium volume and bulk modulus, where we find, in general, a good agreement between theory andmeasurements. In addition, we have reproduced the spin and orbital moments of these elements as they are reflected from measurements of the saturation moment. We have also employed the Hubbard I approximation to extract the interatomic exchange parameters of an effective spin Hamiltonian for the heavy rare earths. We show that the Hubbard I approximation gives results which are consistent with calculations where 4f electrons are treated as core states for Gd. The latter approach was also used to address the series of the heavy/late rare earths. Via Monte Carlo simulations we obtained ordering temperatures which reproduce measurements within about 20%. We have further illustrated the accuracy of these exchange parameters by comparing measured and calculated magnetic configurations for the heavy rare earths and the magnon dispersion for Gd. The Hubbard I approximation is compared to other theories of the electronic structure, and we argue that it is superior. We discuss the relevance of our results in general and how this makes it possible to treat the electronic structure of materials containing rare-earth elements, such as permanent magnets, magnetostrictive compounds, photovoltaics, optical fibers, topological insulators, and molecular magnets.

  • 193.
    Lundborg, Magnus
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Apostolov, Rossen
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Spångberg, Daniel
    Gärdenäs, Anders
    van der Spoel, David
    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.
    An Efficient and Extensible Format, Library, and API for Binary Trajectory Data from Molecular Simulations2014Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 35, nr 3, s. 260-269Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high-performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost-efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present Trajectory Next Generation (TNG)a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state-of-the-art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes.

  • 194.
    Lundborg, Magnus
    et al.
    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. Center for Biomembrane Research, Stockholm University, Sweden .
    Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 3, s. 810-823Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.

  • 195.
    Lundborg, Magnus
    et al.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Narangifard, Ali
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden.;Karolinska Inst, Dept Med, Solna MedS, Solna, Sweden..
    Wennberg, Christian L.
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.
    Daneholt, Bertil
    Karolinska Inst, Dept Cell & Mol Biol CMB, Stockholm, Sweden..
    Norlén, Lars
    Karolinska Inst, Dept Cell & Mol Biol CMB, Stockholm, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Stockholm, Sweden..
    Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation2018Inngår i: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 203, nr 2, s. 149-161Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In the present study we have analyzed the molecular structure and function of the human skin's permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin. The skin's barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin - the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure's detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial. Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models' lipid composition was to that reported in human stratum corneum, the better was the match between the models' simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model's calculated water permeability and thermotropic behaviour were found compatible with that of human skin. The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems.

  • 196.
    Lundborg, Magnus
    et al.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Wennberg, Christian L.
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden..
    Narangifard, Ali
    ERCO Pharma AB, Sci Life Lab, Solna, Sweden.;Karolinska Inst, Solna MedS, Dept Med, Solna, Sweden..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.
    Norlén, Lars
    Karolinska Inst, Dept Cell & Mol Biol CMB, Solna, Sweden.;Karolinska Univ Hosp, Dermatol Clin, Solna, Sweden..
    Predicting drug permeability through skin using molecular dynamics simulation2018Inngår i: Journal of Controlled Release, ISSN 0168-3659, E-ISSN 1873-4995, Vol. 283, s. 269-279Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Understanding and predicting permeability of compounds through skin is of interest for transdermal delivery of drugs and for toxicity predictions of chemicals. We show, using a new atomistic molecular dynamics model of the skin's barrier structure, itself validated against near-native cryo-electron microscopy data from human skin, that skin permeability to the reference compounds benzene, DMSO (dimethyl sulfoxide), ethanol, codeine, naproxen, nicotine, testosterone and water can be predicted. The permeability results were validated against skin permeability data in the literature. We have investigated the relation between skin barrier molecular organization and permeability using atomistic molecular dynamics simulation. Furthermore, it is shown that the calculated mechanism of action differs between the five skin penetration enhancers Azone, DMSO, oleic acid, stearic acid and water. The permeability enhancing effect of a given penetration enhancer depends on the permeating compound and on the concentration of penetration enhancer inside the skin's barrier structure. The presented method may open the door for computer based screening of the permeation of drugs and toxic compounds through skin.

  • 197.
    Lupo, Giandomenico
    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.
    Duwig, Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Uncertainty quantification of multispecies droplet evaporation modelsManuskript (preprint) (Annet vitenskapelig)
  • 198.
    Lupo, Giandomenico
    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.
    Gruber, Andrea
    SINTEF Energy Research, Thermal Energy Department, Trondheim, Norway.
    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. Department of Energy and Process Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
    Duwig, Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Direct numerical simulation of spray evaporation in hot turbulent channel flowManuskript (preprint) (Annet vitenskapelig)
  • 199.
    Lupo, Giandomenico
    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.
    Guglielmino, Stefano
    Dipartimento di Ingegneria Civile e Industriale, Università di Pisa, Pisa, Italy.
    Viacava, Francesco
    Dipartimento di Ingegneria Civile e Industriale, Università di Pisa, Pisa, Italy.
    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. Department of Energy and Process Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
    Duwig, Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Immersed boundary method for direct numerical simulation of multicomponent droplet evaporationManuskript (preprint) (Annet vitenskapelig)
  • 200.
    Lupo, Giandomenico
    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, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    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. Norwegian Univ Sci & Technol NTNU, Dept Energy & Proc Engn, Stockholm, Sweden..
    Duwig, Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    An Immersed Boundary Method for flows with evaporating droplets2019Inngår i: International Journal of Heat and Mass Transfer, ISSN 0017-9310, E-ISSN 1879-2189, Vol. 143, artikkel-id 118563Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present a new Immersed Boundary Method (IBM) for the interface resolved simulation of spherical droplet evaporation in gas flow. The method is based on the direct numerical simulation of the coupled momentum, energy and species transport in the gas phase, while the exchange of these quantities with the liquid phase is handled through global mass, energy and momentum balances for each droplet. This approach, applicable in the limit of small spherical droplets, allows for accurate and efficient phase coupling without direct solution of the liquid phase fields, thus saving computational cost. We provide validation results, showing that all the relevant physical phenomena and their interactions are correctly captured, both for laminar and turbulent gas flow. Test cases include fixed rate and free evaporation of a static droplet, displacement of a droplet by Stefan flow, and evaporation of a hydrocarbon droplet in homogeneous isotropic turbulence. The latter case is validated against experimental data, showing the feasibility of the method towards the treatment of conditions representative of real life spray fuel applications.

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