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  • 101.
    Fornari, Walter
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Picano, Francesco
    Sardina, Gaetano
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Reduced particle settling speed in turbulence2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 808, p. 153-167Article in journal (Refereed)
    Abstract [en]

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

  • 102.
    Fornari, Walter
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Tabaei Kazerooni, Hamid
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Hussong, Jeanette
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Suspensions of finite-size neutrally buoyant spheres in turbulent duct flow2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Article in journal (Refereed)
  • 103.
    Fornari, Walter
    et al.
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Zade, Sagar
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics.
    Picano, Francesco
    Department of Industrial EngineeringUniversity of PadovaPaduaItaly.
    Settling of finite-size particles in turbulence at different volume fractions2018In: Acta Mechanica, ISSN 0001-5970, E-ISSN 1619-6937, Vol. 230, no 2, p. 413-430Article in journal (Refereed)
    Abstract [en]

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

  • 104.
    Fourati, Zaineb
    et al.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Heusser, Stephanie A.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Hu, Haidai
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France.;UPMC Univ Paris 6, Sorbonne Univ, F-75005 Paris, France..
    Ruza, Reinis R.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Sauguet, Ludovic
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.
    Delarue, Marc
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels2018In: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 23, no 4, p. 993-1004Article in journal (Refereed)
    Abstract [en]

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

  • 105. Fouxon, Itzhak
    et al.
    Ge, Zhouyang
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Leshansky, Alexander
    Integral representation of channel flow with interacting particles2017In: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, no 6, article id 063110Article in journal (Refereed)
    Abstract [en]

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

  • 106.
    Frecus, Bogdan
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Rinkevicius, Zilvinas
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013In: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, no 25, p. 10466-10471Article in journal (Refereed)
    Abstract [en]

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

  • 107. Frånberg, Mattias
    et al.
    Gertow, Karl
    Hamsten, Anders
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests2015In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, no 9, article id e1005502Article in journal (Refereed)
    Abstract [en]

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

  • 108.
    Frånberg, Mattias
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS). KTH, Centres, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.
    Lagergren, Jens
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
    BESIQ: A tool for discovering gene-gene and gene-environment interactions in genome-wide association studiesManuscript (preprint) (Other academic)
  • 109.
    Frånberg, Mattias
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS). KTH, Centres, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ; Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden ; .
    Sabater-Lleal, Maria
    Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ; Unit of Genomics of Complex Diseases, Institut d’Investigació Biomèdica Sant Pau (IIB-Sant Pau), Barcelona, Spain.
    Hamsten, Anders
    Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
    Lagergren, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Electrical Engineering and Computer Science (EECS).
    Sennblad, Bengt
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ; .
    Discovering gene-environment interactions with LassoManuscript (preprint) (Other academic)
  • 110. Fukada, T.
    et al.
    Fornari, Walter
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Takeuchi, S.
    Kajishima, T.
    A numerical approach for particle-vortex interactions based on volume-averaged equations2018In: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 104, p. 188-205Article in journal (Refereed)
    Abstract [en]

    To study the dynamics of particles in turbulence when their sizes are comparable to the smallest eddies in the flow, the Kolmogorov length scale, efficient and accurate numerical models for the particle-fluid interaction are still missing. Therefore, we here extend the treatment of the particle feedback on the fluid based on the volume-averaged fluid equations (VA simulation) in the previous study of the present authors, by estimating the fluid force correlated with the disturbed flow. We validate the model against interface-resolved simulations using the immersed-boundary method. Simulations of single particles show that the history effect is well captured by the present estimation method based on the disturbed flow. Similarly, the simulation of the flow around a rotating particle demonstrates that the lift force is also well captured by the proposed method. We also consider the interaction between non-negligible size particles and an array of Taylor–Green vortices. For density ratios ρd /ρc ≥ 10, the results show that the particle motion captured by the VA approach is closer to that of the fully-resolved simulations than that obtained with a traditional two-way coupling simulation. The flow disturbance is also well represented by the VA simulation. In particular, it is found that history effects enhance the curvature of the trajectory in vortices and this enhancement increases with the particle size. Furthermore, the flow field generated by a neighboring particle at distances of around ten particle diameters significantly influences particle trajectories. The computational cost of the VA simulation proposed here is considerably lower than that of the interface-resolved simulation.

  • 111.
    Gaaf, Sarah W.
    et al.
    TU Eindhoven.
    Jarlebring, Elias
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The infinite Bi-Lanczos method for nonlinear eigenvalue problems2017In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 39, p. S898-S919Article in journal (Refereed)
  • 112.
    Gallino, Giacomo
    et al.
    Ecole Polytech Fed Lausanne, Lab Fluid Mech & Instabil, CH-1015 Lausanne, Switzerland..
    Zhu, Lailai
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Gallaire, Francois
    Ecole Polytech Fed Lausanne, Lab Fluid Mech & Instabil, CH-1015 Lausanne, Switzerland..
    The Hydrodynamics of a Micro-Rocket Propelled by a Deformable Bubble2019In: FLUIDS, ISSN 2311-5521, Vol. 4, no 1, article id 48Article in journal (Refereed)
    Abstract [en]

    We perform simulations to study the hydrodynamics of a conical-shaped swimming micro-robot that ejects catalytically produced bubbles from its inside. We underline the nontrivial dependency of the swimming velocity on the bubble deformability and on the geometry of the swimmer. We identify three distinct phases during the bubble evolution: immediately after nucleation the bubble is spherical and its inflation barely affects the swimming speed; then the bubble starts to deform due to the confinement gradient generating a force that propels the swimmer; while in the last phase, the bubble exits the cone, resulting in an increase in the swimmer velocity. Our results shed light on the fundamental hydrodynamics of the propulsion of catalytic conical swimmers and may help to improve the efficiency of these micro-machines.

  • 113.
    Ge, Zhouyang
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Holmgren, Hanna
    Uppsala Univ, Dept Informat Technol, Div Sci Comp, Box 337, S-75105 Uppsala, Sweden..
    Kronbichler, Martin
    Tech Univ Munich, Inst Computat Mech, Boltzmannstr 15, D-85748 Garching, Germany..
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kreiss, Gunilla
    Uppsala Univ, Dept Informat Technol, Div Sci Comp, Box 337, S-75105 Uppsala, Sweden..
    Effective slip over partially filled microcavities and its possible failure2018In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, no 5, article id 054201Article in journal (Refereed)
    Abstract [en]

    Motivated by the emerging applications of liquid-infused surfaces (LIS), we study the drag reduction and robustness of transverse flows over two-dimensional microcavities partially filled with an oily lubricant. Using separate simulations at different scales, characteristic contact line velocities at the fluid-solid intersection are first extracted from nanoscale phase field simulations and then applied to micronscale two-phase flows, thus introducing a multiscale numerical framework to model the interface displacement and deformation within the cavities. As we explore the various effects of the lubncant-toouter-fluid viscosity ratio A2/A0 th(mu)over tilde( )c(mu)over tilde(1), thary number Ca, the static contact angle A> and t theta(s), filling fraction of the cavity <5, we f delta d that the effective slip is most sensitive to the parameter S. The effects of A2/A1 an(mu)over tilde( )A(mu)over tilde(a )re ge theta(s)erally intertwined but weakened if <5 < 1. delta M 1er, for an initial filling fraction S = 0.94 delta our results show that the effective slip is nearly independent of the capillary number when it is small. Further increasing Ca to about O.OIA1/A20.01(mu)over tilde(1)/(mu)over tilde(2)ntify a possible failure mode, associated with lubricants draining from the LIS, for A2/A1 A (mu)over tilde(2)1(mu)over tilde(1)V less than or similar to y viscous lubricants (e.g., A2/A1 > (mu)over tilde()),(mu)over tilde(h)owever, are immune to such failure due to their generally larger contact line velocity.

  • 114.
    Ge, Zhouyang
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Loiseau, Jean Christophe
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Arts et Métiers ParisTech, France.
    Tammisola, Outi
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    An efficient mass-preserving interface-correction level set/ghost fluid method for droplet suspensions under depletion forces2018In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 353, p. 435-459Article in journal (Refereed)
    Abstract [en]

    Aiming for the simulation of colloidal droplets in microfluidic devices, we present here a numerical method for two-fluid systems subject to surface tension and depletion forces among the suspended droplets. The algorithm is based on an efficient solver for the incompressible two-phase Navier–Stokes equations, and uses a mass-conserving level set method to capture the fluid interface. The four novel ingredients proposed here are, firstly, an interface-correction level set (ICLS) method; global mass conservation is achieved by performing an additional advection near the interface, with a correction velocity obtained by locally solving an algebraic equation, which is easy to implement in both 2D and 3D. Secondly, we report a second-order accurate geometric estimation of the curvature at the interface and, thirdly, the combination of the ghost fluid method with the fast pressure-correction approach enabling an accurate and fast computation even for large density contrasts. Finally, we derive a hydrodynamic model for the interaction forces induced by depletion of surfactant micelles and combine it with a multiple level set approach to study short-range interactions among droplets in the presence of attracting forces.

  • 115.
    Ge, Zhouyang
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Tammisola, Outi
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH Mech, INTERFACE Ctr, SE-10044 Stockholm, Sweden..
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH Mech, INTERFACE Ctr, SE-10044 Stockholm, Sweden..
    Flow-assisted droplet assembly in a 3D microfluidic channel2019In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 15, no 16, p. 3451-3460Article in journal (Refereed)
    Abstract [en]

    Self-assembly of soft matter, such as droplets or colloids, has become a promising scheme to engineer novel materials, model living matter, and explore non-equilibrium statistical mechanics. In this article, we present detailed numerical simulations of few non-Brownian droplets in various flow conditions, specifically, focusing on their self-assembly within a short distance in a three-dimensional (3D) microfluidic channel, cf. [Shen et al., Adv. Sci., 2016, 3(6), 1600012]. Contrary to quasi two-dimensional (q2D) systems, where dipolar interaction is the key mechanism for droplet rearrangement, droplets in 3D confinement produce much less disturbance to the underlying flow, thus experiencing weaker dipolar interactions. Using confined simple shear and Poiseuille flows as reference flows, we show that the droplet dynamics is mostly affected by the shear-induced cross-stream migration, which favors chain structures if the droplets are under an attractive depletion force. For more compact clusters, such as three droplets in a triangular shape, our results suggest that an inhomogeneous cross-sectional inflow profile is further required. Overall, the accelerated self-assembly of a small-size droplet cluster results from the combined effects of strong depletion forces, confinement-mediated shear alignments, and fine-tuned inflow conditions. The deterministic nature of the flow-assisted self-assembly implies the possibility of large throughputs, though calibration of all different effects to directly produce large droplet crystals is generally difficult.

  • 116.
    Ghosh, Souvik
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH Mech, SeRC Swedish eSci Res Ctr, SE-10044 Stockholm, Sweden..
    Loiseau, Jean-Christophe
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Breugem, Wim-Paul
    Delft Univ Technol, Proc & Energy Dept, NL-2628 CB Delft, Netherlands..
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Modal and non-modal linear stability of Poiseuille flow through a channel with a porous substrate2019In: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 75, p. 29-43Article in journal (Refereed)
    Abstract [en]

    We present modal and non-modal linear stability analyses of Poiseuille flow through a plane channel with a porous substrate modeled using the Volume Averaged Navier-Stokes (VANS) equations. Modal stability analysis shows the destabilization of the flow with increasing porosity of the layer. The instability mode originates from the homogeneous fluid region of the channel for all the values of porosity considered but the governing mechanism changes. Perturbation kinetic energy analysis reveals the importance of viscous dissipation at low porosity values while dissipation in the porous substrate becomes significant at higher porosity. Scaling analysis highlights the invariance of the critical wavenumber with changing porosity. On the other hand, the critical Reynolds number remains invariant at low porosity and scales as Re-c similar to (H/delta)(1.4) at high porosity where delta is the typical thickness of the vorticity layer at the fluid-porous interface. This reveals the existence of a Tollmien-Schlichting-like viscous instability mechanism at low porosity values, and Rayleigh analysis shows the presence of an inviscid instability mechanism at high porosity. For the whole range of porosities considered, the non-modal analysis shows that the optimal mechanism responsible for transient energy amplification is the lift-up effect, giving rise to streaky structure as in single-phase plane Poiseuille flow. The present results strongly suggest that the transition to turbulence follows the same path as that of classical Poiseuille flow at low porosity values, while it is dictated by the modal instability for high porosity values. SAS. All rights reserved.

  • 117.
    Gomez-Blanco, J.
    et al.
    McGill Univ, Dept Anat & Cell Biol, Montreal, PQ, Canada..
    de la Rosa-Trevin, J. M.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Marabini, R.
    Univ Autonoma Madrid, Escuela Politecn Super, E-28049 Madrid, Spain..
    del Cano, L.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Jimenez, A.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Martinez, M.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Melero, R.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Majtner, T.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Maluenda, D.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Mota, J.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Rancel, Y.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Ramirez-Aportela, E.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Vilas, J. L.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Carroni, M.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Fleischmann, S.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Stockholm, Sweden.;KTH Royal Inst Technol, Swedish E Sci Res Ctr, Stockholm, Sweden..
    Ashton, A. W.
    Harwell Sci & Innovat Campus, Diamond Light Source, Didcot OX11 0DE, Oxon, England..
    Basham, M.
    Harwell Sci & Innovat Campus, Diamond Light Source, Didcot OX11 0DE, Oxon, England..
    Clare, D. K.
    Harwell Sci & Innovat Campus, Diamond Light Source, Didcot OX11 0DE, Oxon, England..
    Savage, K.
    Harwell Sci & Innovat Campus, Diamond Light Source, Didcot OX11 0DE, Oxon, England..
    Siebert, C. A.
    Harwell Sci & Innovat Campus, Diamond Light Source, Didcot OX11 0DE, Oxon, England..
    Sharov, G. G.
    MRC, Lab Mol Biol, Francis Crick Ave, Cambridge CB2 OQH, England..
    Sorzano, C. O. S.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Conesa, P.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Carazo, J. M.
    CSIC, Natl Ctr Biotechnol, Biocomp Unit, C Darwin 3,Campus Univ Autonoma, Madrid 28049, Spain..
    Using Scipion for stream image processing at Cryo-EM facilities2018In: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 204, no 3, p. 457-463Article in journal (Refereed)
    Abstract [en]

    Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevfn et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

  • 118.
    Gong, Jing
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Cray Inc..
    Henty, David
    University of Edinburgh.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fischer, Paul
    Argonne National Laboratory.
    Heisey, Katherine
    Argonne National Laboratory.
    OpenACC Acceleration of Nek5000: a Spectral Element Code2013Conference paper (Other academic)
  • 119.
    Gong, Jing
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Otten, Matthew
    Fischer, Paul
    Min, Misun
    Nekbone performance on GPUs with OpenACC and CUDA Fortran implementations2016In: Journal of Supercomputing, ISSN 0920-8542, E-ISSN 1573-0484, Vol. 72, no 11, p. 4160-4180Article in journal (Refereed)
    Abstract [en]

    We present a hybrid GPU implementation and performance analysis of Nekbone, which represents one of the core kernels of the incompressible Navier-Stokes solver Nek5000. The implementation is based on OpenACC and CUDA Fortran for local parallelization of the compute-intensive matrix-matrix multiplication part, which significantly minimizes the modification of the existing CPU code while extending the simulation capability of the code to GPU architectures. Our discussion includes the GPU results of OpenACC interoperating with CUDA Fortran and the gather-scatter operations with GPUDirect communication. We demonstrate performance of up to 552 Tflops on 16, 384 GPUs of the OLCF Cray XK7 Titan.

  • 120.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Cebamanos, Luis
    Hart, Alistair
    Min, Misun
    Fischer, Paul
    NekBone with Optimizaed OpenACC directives2015Conference paper (Refereed)
    Abstract [en]

    Accelerators and, in particular, Graphics Processing Units (GPUs) have emerged as promising computing technologies which may be suitable for the future Exascale systems. Here, we present performance results of NekBone, a benchmark of the Nek5000 code, implemented with optimized OpenACC directives and GPUDirect communications. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. Results of an optimized NekBone version lead to 78 Gflops performance on a single node. In addition, a performance result of 609 Tflops has been reached on 16, 384 GPUs of the Titan supercomputer at Oak Ridge National Laboratory.

     

  • 121.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Peplinski, Adam
    Hart, Alistair
    Doleschal, Jens
    Henty, David
    Fischer, Paul
    Nek5000 with OpenACC2015In: Solving software challenges for exascale, 2015, p. 57-68Conference paper (Refereed)
    Abstract [en]

    Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flows. We follow up on an earlier study which ported the simplified version of Nek5000 to a GPU-accelerated system by presenting the hybrid CPU/GPU implementation of the full Nek5000 code using OpenACC. The matrix-matrix multiplication, the Nek5000 gather-scatter operator and a preconditioned Conjugate Gradient solver have implemented using OpenACC for multi-GPU systems. We report an speed-up of 1.3 on single node of a Cray XK6 when using OpenACC directives in Nek5000. On 512 nodes of the Titan supercomputer, the speed-up can be approached to 1.4. A performance analysis of the Nek5000 code using Score-P and Vampir performance monitoring tools shows that overlapping of GPU kernels with host-accelerator memory transfers would considerably increase the performance of the OpenACC version of Nek5000 code.

  • 122. Granholm, V.
    et al.
    Kim, S.
    Fernandez Navarro, José
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Sjölund, E.
    Smith, R. D.
    Käll, Lukas
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fast and accurate database searches with MS-GF+percolator2014In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, no 2, p. 890-897Article in journal (Refereed)
    Abstract [en]

    One can interpret fragmentation spectra stemming from peptides in mass-spectrometry-based proteomics experiments using so-called database search engines. Frequently, one also runs post-processors such as Percolator to assess the confidence, infer unique peptides, and increase the number of identifications. A recent search engine, MS-GF+, has shown promising results, due to a new and efficient scoring algorithm. However, MS-GF+ provides few statistical estimates about the peptide-spectrum matches, hence limiting the biological interpretation. Here, we enabled Percolator processing for MS-GF+ output and observed an increased number of identified peptides for a wide variety of data sets. In addition, Percolator directly reports p values and false discovery rate estimates, such as q values and posterior error probabilities, for peptide-spectrum matches, peptides, and proteins, functions that are useful for the whole proteomics community.

  • 123.
    Griss, Johannes
    et al.
    Med Univ Vienna, Dept Dermatol, Div Immunol Allergy & Infect Dis, Wahringer Gurtel 18-20, A-1090 Vienna, Austria.;EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England..
    Perez-Riverol, Yasset
    EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England..
    The, Matthew
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Käll, Lukas
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Vizcaino, Juan Antonio
    EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England..
    Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra"2018In: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, no 5, p. 1993-1996Article in journal (Refereed)
    Abstract [en]

    In the recent benchmarking article entitled "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra", Rieder et al. compared several different approaches to cluster MS/MS spectra. While we certainly recognize the value of the manuscript, here, we report some shortcomings detected in the original analyses. For most analyses, the authors clustered only single MS/MS runs. In one of the reported analyses, three MS/MS runs were processed together, which already led to computational performance issues in many of the tested approaches. This fact highlights the difficulties of using many of the tested algorithms on the nowadays produced average proteomics data sets. Second, the authors only processed identified spectra when merging MS runs. Thereby, all unidentified spectra that are of lower quality were already removed from the data set and could not influence the clustering results. Next, we found that the authors did not analyze the effect of chimeric spectra on the clustering results. In our analysis, we found that 3% of the spectra in the used data sets were chimeric, and this had marked effects on the behavior of the different clustering algorithms tested. Finally, the authors' choice to evaluate the MS-Cluster and spectra-cluster algorithms using a precursor tolerance of 5 Da for high-resolution Orbitrap data only was, in our opinion, not adequate to assess the performance of MS/MS clustering approaches.

  • 124. Gronberg, Christina
    et al.
    Sitsel, Oleg
    Lindahl, Erik
    Gourdon, Pontus
    Andersson, Magnus
    KTH, School of Engineering Sciences (SCI), Theoretical Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, no 11, p. 2417-2429Article in journal (Refereed)
    Abstract [en]

    Cu+-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu+-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu+ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu+ delivery. Mutational analyses and simulations in the presence and absence of Cu+ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu+-transporting P-type ATPases.

  • 125. Hadikhani, P.
    et al.
    Hashemi, S. M. H.
    Balestra, G.
    Zhu, Lailai
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre. Princeton University, United States.
    Modestino, M. A.
    Gallaire, F.
    Psaltis, D.
    Inertial manipulation of bubbles in rectangular microfluidic channels2018In: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 18, no 7, p. 1035-1046Article in journal (Refereed)
    Abstract [en]

    Inertial microfluidics is an active field of research that deals with crossflow positioning of the suspended entities in microflows. Until now, the majority of the studies have focused on the behavior of rigid particles in order to provide guidelines for microfluidic applications such as sorting and filtering. Deformable entities such as bubbles and droplets are considered in fewer studies despite their importance in multiphase microflows. In this paper, we show that the trajectory of bubbles flowing in rectangular and square microchannels can be controlled by tuning the balance of forces acting on them. A T-junction geometry is employed to introduce bubbles into a microchannel and analyze their lateral equilibrium position in a range of Reynolds (1 < Re < 40) and capillary numbers (0.1 < Ca < 1). We find that the Reynolds number (Re), the capillary number (Ca), the diameter of the bubble (D), and the aspect ratio of the channel are the influential parameters in this phenomenon. For instance, at high Re, the flow pushes the bubble towards the wall while large Ca or D moves the bubble towards the center. Moreover, in the shallow channels, having aspect ratios higher than one, the bubble moves towards the narrower sidewalls. One important outcome of this study is that the equilibrium position of bubbles in rectangular channels is different from that of solid particles. The experimental observations are in good agreement with the performed numerical simulations and provide insights into the dynamics of bubbles in laminar flows which can be utilized in the design of flow based multiphase flow reactors.

  • 126.
    Hess, Berk
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Pall, Szilard
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Peplinski, Adam
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control.
    Highly Tuned Small Matrix Multiplications Applied to Spectral Element Code Nek50002016Conference paper (Refereed)
  • 127.
    Heusser, Stephanie A.
    et al.
    Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Lycksell, Marie
    Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Wang, Xueqing
    Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    McComas, Sarah E.
    Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 42, p. 10672-10677Article in journal (Refereed)
    Abstract [en]

    Theories of general anesthesia have shifted in focus from bulk lipid effects to specific interactions with membrane proteins. Target receptors include several subtypes of pentameric ligand-gated ion channels; however, structures of physiologically relevant proteins in this family have yet to define anesthetic binding at high resolution. Recent cocrystal structures of the bacterial protein GLIC provide snapshots of state-dependent binding sites for the common surgical agent propofol (PFL), offering a detailed model system for anesthetic modulation. Here, we combine molecular dynamics and oocyte electrophysiology to reveal differential motion and modulation upon modification of a transmembrane binding site within each GLIC subunit. WT channels exhibited net inhibition by PFL, and a contraction of the cavity away from the pore-lining M2 helix in the absence of drug. Conversely, in GLIC variants exhibiting net PFL potentiation, the cavity was persistently expanded and proximal to M2. Mutations designed to favor this deepened site enabled sensitivity even to subclinical concentrations of PFL, and a uniquely prolonged mode of potentiation evident up to similar to 30 min after washout. Dependence of these prolonged effects on exposure time implicated the membrane as a reservoir for a lipid-accessible binding site. However, at the highest measured concentrations, potentiation appeared to be masked by an acute inhibitory effect, consistent with the presence of a discrete, water-accessible site of inhibition. These results support a multisite model of transmembrane allosteric modulation, including a possible link between lipid- and receptor-based theories that could inform the development of new anesthetics.

  • 128.
    Heusser, Stephanie A.
    et al.
    SciLifeLab, Solna, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Yoluk, Ozge
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 433A-433AArticle in journal (Other academic)
  • 129. Heusser, Stephanie
    et al.
    Yoluk, Özge
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Klement, Goran
    Reiderer, Erika
    Lindahl, Erik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Howard, Rebecca
    Functional Characterization of Neurotransmitter Activation and Modulation in a Nematode Model Ligand-gated Ion Channel2016In: Journal of Neurochemistry, ISSN 0022-3042, E-ISSN 1471-4159, Vol. 138, no 2, p. 243-253Article in journal (Refereed)
    Abstract [en]

    The superfamily of pentameric ligand-gated ion channels includes neurotransmitter receptors that mediate fast synaptic transmission in vertebrates, and are targets for drugs including alcohols, anesthetics, benzodiazepines and anticonvulsants. However, the mechanisms of ion channel opening, gating and modulation in these receptors leave many open questions, despite their pharmacological importance. Subtle conformational changes in both the extracellular and transmembrane domains are likely to influence channel opening, but have been difficult to characterize given the limited structural data available for human membrane proteins. Recent crystal structures of a modifiedCaenorhabditis elegans glutamate-gated chloride channel (GluCl) in multiple states offer an appealing model system for structure-function studies. However, the pharmacology of the crystallographic GluCl construct is not well established. To establish the functional relevance of this system, we used two-electrode voltage-clamp electrophysiology in Xenopus oocytes to characterize activation of crystallographic and native-like GluCl constructs by L-glutamate and ivermectin. We also tested modulation by ethanol and other anesthetic agents, and used site-directed mutagenesis to explore the role of a region of Loop F which was implicated in ligand gating by molecular dynamics simulations. Our findings indicate that the crystallographic construct functionally models concentration-dependent agonism and allosteric modulation of pharmacologically relevant receptors. Specific substitutions at residue Leu174 in loop F altered direct L-glutamate activation, consistent with computational evidence for this region's role in ligand binding. These insights demonstrate conservation of activation and modulation properties in this receptor family, and establish a framework for GluCl as a model system, including new possibilities for drug discovery.

  • 130.
    Holmgaard List, Nanna
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Knoops, Jeremie
    Rubio-Magnieto, Jenifer
    Ide, Julien
    Beljonne, David
    Norman, Patrick
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Surin, Mathieu
    Linares, Mathieu
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Origin of DNA-Induced Circular Dichroism in a Minor-Groove Binder2017In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 139, no 42, p. 14947-14953Article in journal (Refereed)
    Abstract [en]

    Induced circular dichroism (ICD) of DNA-binding ligands is well known to be strongly influenced by the specific mode of binding, but the relative importance of the possible mechanisms has remained undetermined. With a combination of molecular dynamics simulations, CD response calculations, and experiments on an AT-sequence, we show that the ICD of minor-groove-bound 4',6-diamidino-2-phenylindole (DAPI) originates from an intricate interplay between the chiral imprint of DNA, off-resonant excitonic coupling to nucleobases, charge-transfer, and resonant excitonic coupling between DAPIs. The significant contributions from charge-transfer and the chiral imprint to the ICD demonstrate the inadequacy of a standard Frenkel exciton theory of the DAPI-DNA interactions.

  • 131.
    Hosseini, Seyed M.
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Vinuesa, Ricardo
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Hanifi, Ardeshir
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Swedish Defense Research Agency, FOI, Sweden.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Direct numerical simulation of the flow around a wing section at moderate Reynolds number2016In: International Journal of Heat and Fluid Flow, ISSN 0142-727X, E-ISSN 1879-2278, Vol. 61, p. 117-128Article in journal (Other academic)
    Abstract [en]

    Abstract A three-dimensional direct numerical simulation has been performed to study the turbulent flow around the asymmetric NACA4412 wing section at a moderate chord Reynolds number of R e c = 400 , 000 , with an angle of attack of A o A = 5 ∘ . The mesh was optimized to properly resolve all relevant scales in the flow, and comprises around 3.2 billion grid points. The incompressible spectral-element Navier–Stokes solver Nek5000 was used to carry out the simulation. An unsteady volume force is used to trip the flow to turbulence on both sides of the wing at 10% of the chord. Full turbulence statistics are computed in addition to collection of time history data in selected regions. The Reynolds numbers on the suction side reach Reτ ≃ 373 and R e Ξ = 2 , 800 with the pressure-gradient parameter ranging from β ≈ 0.0 to β ≈ 85. Similarly, on the pressure side, the Reynolds numbers reach Reτ ≈ 346 and R e Ξ = 818 while β changes from β ≈ 0.0 to β ≈ − 0.25 . The effect of adverse pressure gradients on the mean flow is consistent with previous observations, namely a steeper incipient log law, a more prominent wake region and a lower friction. The turbulence kinetic energy profiles show a progressively larger inner peak for increasing pressure gradient, as well as the emergence and development of an outer peak with stronger APGs. The present simulation shows the potential of high-order (spectral) methods in simulating complex external flows at moderately high Reynolds numbers.

  • 132.
    Hufnagel, Lorenz
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Canton, Jacopo
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Marin, Oana
    Merzari, Elia
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The three-dimensional structure of swirl-switching in bent pipe flow2017In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 835, p. 86-101Article in journal (Refereed)
    Abstract [en]

    Swirl-switching is a low-frequency oscillatory phenomenon which affects the Dean vortices in bent pipes and may cause fatigue in piping systems. Despite thirty years worth of research, the mechanism that causes these oscillations and the frequencies that characterise them remain unclear. Here we show that a three-dimensional wave-like structure is responsible for the low-frequency switching of the dominant Dean vortex. The present study, performed via direct numerical simulation, focuses on the turbulent flow through a 90 degrees pipe bend preceded and followed by straight pipe segments. A pipe with curvature 0.3 (defined as ratio between pipe radius and bend radius) is studied for a bulk Reynolds number Re = 11 700, corresponding to a friction Reynolds number Re-tau approximate to 360. Synthetic turbulence is generated at the inflow section and used instead of the classical recycling method in order to avoid the interference between recycling and swirl-switching frequencies. The flow field is analysed by three-dimensional proper orthogonal decomposition (POD) which for the first time allows the identification of the source of swirl-switching: a wave-like structure that originates in the pipe bend. Contrary to some previous studies, the flow in the upstream pipe does not show any direct influence on the swirl-switching modes. Our analysis further shows that a three-dimensional characterisation of the modes is crucial to understand the mechanism, and that reconstructions based on two-dimensional POD modes are incomplete.

  • 133.
    Huttmann, Felix
    et al.
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Rothenbach, Nico
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Kraus, Stefan
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Ollefs, Katharina
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Arruda, Lucas M.
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Bernien, Matthias
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Thonig, Danny
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden..
    Delin, Anna
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fransson, Jonas
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden..
    Kummer, Kurt
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS40220, F-38043 Grenoble 9, France..
    Brookes, Nicholas B.
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS40220, F-38043 Grenoble 9, France..
    Eriksson, Olle
    Uppsala Univ, Dept Phys & Astron, Mat Theory, SE-75120 Uppsala, Sweden.;Orebro Univ, Sch Sci & Technol, SE-70182 Orebro, Sweden..
    Kuch, Wolfgang
    Free Univ Berlin, Inst Expt Phys, Arnimallee 14, D-14195 Berlin, Germany..
    Michely, Thomas
    Univ Cologne, Inst Phys 2, Zulpicher Str 77, D-50937 Cologne, Germany..
    Wende, Heiko
    Univ Duisburg Essen, Fak Phys, Lotharstr 1, D-47057 Duisburg, Germany.;Ctr Nanointegrat Duisburg Essen CENIDE, Lotharstr 1, D-47057 Duisburg, Germany..
    Europium Cyclooctatetraene Nanowire Carpets: A Low-Dimensional, Organometallic, and Ferromagnetic Insulator2019In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 10, no 5, p. 911-917Article in journal (Refereed)
    Abstract [en]

    We investigate the magnetic and electronic properties of europium cyclooctatetraene (EuCot) nanowires by means of low-temperature X-ray magnetic circular dichroism (XMCD) and scanning tunneling microscopy (STM) and spectroscopy (STS). The EuCot nanowires are prepared in situ on a graphene surface. STS measurements identify EuCot as an insulator with a minority band gap of 2.3 eV. By means of Eu M-5,M-4 edge XMCD, orbital and spin magnetic moments of (-0.1 +/- 0.3)mu(B) and (+7.0 +/- 0.6)mu(B), respectively, were determined. Field-dependent measurements of the XMCD signal at the Eu M-5 edge show hysteresis for grazing X-ray incidence at 5 K, thus confirming EuCot as a ferromagnetic material. Our density functional theory calculations reproduce the experimentally observed minority band gap. Modeling the experimental results theoretically, we find that the effective interatomic exchange interaction between Eu atoms is on the order of millielectronvolts, that magnetocrystalline anisotropy energy is roughly half as big, and that dipolar energy is approximately ten times lower.

  • 134.
    Häggblad, Jon
    et al.
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30).
    Runborg, Olof
    KTH, School of Computer Science and Communication (CSC), Numerical Analysis, NA (closed 2012-06-30). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Accuracy of staircase approximations in finite-difference methods for wave propagation2014In: Numerische Mathematik, ISSN 0029-599X, E-ISSN 0945-3245, Vol. 128, no 4, p. 741-771Article in journal (Refereed)
    Abstract [en]

    While a number of increasingly sophisticated numerical methods have been developed for time-dependent problems in electromagnetics, the Yee scheme is still widely used in the applied fields, mainly due to its simplicity and computational efficiency. A fundamental drawback of the method is the use of staircase boundary approximations, giving inconsistent results. Usually experience of numerical experiments provides guidance of the impact of these errors on the final simulation result. In this paper, we derive exact discrete solutions to the Yee scheme close to the staircase approximated boundary, enabling a detailed theoretical study of the amplitude, phase and frequency errors created. Furthermore, we show how evanescent waves of amplitude occur along the boundary. These characterize the inconsistencies observed in electromagnetic simulations and the locality of the waves explain why, in practice, the Yee scheme works as well as it does. The analysis is supported by detailed proofs and numerical examples.

  • 135.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Peng, Ivy Bo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Machado, Rui
    Rahn, Mirko
    Bartsch, Valeria
    Hart, Alistair
    Fischer, Paul
    Evaluation of Parallel Communication Models in Nekbone, a Nek5000 mini-application2015In: 2015 IEEE International Conference on Cluster Computing, IEEE , 2015, p. 760-767Conference paper (Refereed)
    Abstract [en]

    Nekbone is a proxy application of Nek5000, a scalable Computational Fluid Dynamics (CFD) code used for modelling incompressible flows. The Nekbone mini-application is used by several international co-design centers to explore new concepts in computer science and to evaluate their performance. We present the design and implementation of a new communication kernel in the Nekbone mini-application with the goal of studying the performance of different parallel communication models. First, a new MPI blocking communication kernel has been developed to solve Nekbone problems in a three-dimensional Cartesian mesh and process topology. The new MPI implementation delivers a 13% performance improvement compared to the original implementation. The new MPI communication kernel consists of approximately 500 lines of code against the original 7,000 lines of code, allowing experimentation with new approaches in Nekbone parallel communication. Second, the MPI blocking communication in the new kernel was changed to the MPI non-blocking communication. Third, we developed a new Partitioned Global Address Space (PGAS) communication kernel, based on the GPI-2 library. This approach reduces the synchronization among neighbor processes and is on average 3% faster than the new MPI-based, non-blocking, approach. In our tests on 8,192 processes, the GPI-2 communication kernel is 3% faster than the new MPI non-blocking communication kernel. In addition, we have used the OpenMP in all the versions of the new communication kernel. Finally, we highlight the future steps for using the new communication kernel in the parent application Nek5000.

  • 136.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Machado, Rui
    Rahn, Mirko
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Evaluating New Communication Models in the Nek5000 Code for Exascale2015Conference paper (Other academic)
  • 137.
    Izbassarov, Daulet
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Rosti, Marco E.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Niazi Ardekani, Mehdi
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Sarabian, Mohammad
    Hormozi, Sarah
    Brandt, Luca
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Mechanics, Physicochemical Fluid Mechanics. KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Mechanics of Industrial Processes.
    Tammisola, Outi
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Computational modeling of multiphase viscoelastic and elastoviscoplastic flows2018In: International Journal for Numerical Methods in Fluids, ISSN 0271-2091, E-ISSN 1097-0363, Vol. 88, no 12, p. 521-543Article in journal (Refereed)
  • 138.
    Jarlebring, Elias
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    BROYDEN'S METHOD FOR NONLINEAR EIGENPROBLEMS2019In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 41, no 2, p. A989-A1012Article in journal (Refereed)
    Abstract [en]

    Broyden's method is a general method commonly used for nonlinear systems of equations when very little information is available about the problem. We develop an approach based on Broyden's method for the structure appearing in nonlinear eigenvalue problems. Our approach is designed for problems where the evaluation of a matrix vector product is computationally expensive, essentially as expensive as solving the corresponding linear system of equations. We show how the structure of the Jacobian matrix can be incorporated into the algorithm to improve convergence. The algorithm exhibits local superlinear convergence for simple eigenvalues, and we characterize the convergence. We show how deflation can be integrated and combined such that the method can be used to compute several eigenvalues. A specific problem in machine tool milling, coupled with a PDE, is used to illustrate the approach. The simulations were carried out using the Julia programming language, and the simulation software is provided publicly for reproducibility.

  • 139.
    Jarlebring, Elias
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Koskela, Antti
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA.
    Mele, Giampaolo
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Disguised and new quasi-Newton methods for nonlinear eigenvalue problems2018In: Numerical Algorithms, ISSN 1017-1398, E-ISSN 1572-9265, Vol. 79, no 1, p. 311-335Article in journal (Refereed)
    Abstract [en]

    In this paper, we take a quasi-Newton approach to nonlinear eigenvalue problems (NEPs) of the type M(λ)v = 0, where (Formula presented.) is a holomorphic function. We investigate which types of approximations of the Jacobian matrix lead to competitive algorithms, and provide convergence theory. The convergence analysis is based on theory for quasi-Newton methods and Keldysh’s theorem for NEPs. We derive new algorithms and also show that several well-established methods for NEPs can be interpreted as quasi-Newton methods, and thereby, we provide insight to their convergence behavior. In particular, we establish quasi-Newton interpretations of Neumaier’s residual inverse iteration and Ruhe’s method of successive linear problems.

  • 140.
    Jarlebring, Elias
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Mele, Giampaolo
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Palitta, Davide
    Univ Bologna, Dipartimento Matemat, Piazza Porta S Donato,5, I-40127 Bologna, Italy..
    Ringh, Emil
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Krylov methods for low-rank commuting generalized Sylvester equations2018In: Numerical Linear Algebra with Applications, ISSN 1070-5325, E-ISSN 1099-1506, Vol. 25, no 6, article id e2176Article in journal (Refereed)
    Abstract [en]

    We consider generalizations of the Sylvester matrix equation, consisting of the sum of a Sylvester operator and a linear operator pi with a particular structure. More precisely, the commutators of the matrix coefficients of the operator pi and the Sylvester operator coefficients are assumed to be matrices with low rank. We show (under certain additional conditions) low-rank approximability of this problem, that is, the solution to this matrix equation can be approximated with a low-rank matrix. Projection methods have successfully been used to solve other matrix equations with low-rank approximability. We propose a new projection method for this class of matrix equations. The choice of the subspace is a crucial ingredient for any projection method for matrix equations. Our method is based on an adaption and extension of the extended Krylov subspace method for Sylvester equations. A constructive choice of the starting vector/block is derived from the low-rank commutators. We illustrate the effectiveness of our method by solving large-scale matrix equations arising from applications in control theory and the discretization of PDEs. The advantages of our approach in comparison to other methods are also illustrated.

  • 141.
    Jarlebring, Elias
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Mele, Giampaolo
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Runborg, Olof
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.), Numerical Analysis, NA. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    The waveguide eigenvalue problem and the tensor infinite Arnoldi method2017In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 39, no 3, p. A1062-A1088Article in journal (Refereed)
    Abstract [en]

    We present a new computational approach for a class of large-scale nonlinear eigenvalue problems (NEPs) that are nonlinear in the eigenvalue. The contribution of this paper is two fold. We derive a new iterative algorithm for NEPs, the tensor infinite Arnoldi method (TIAR), which is applicable to a general class of NEPs, and we show how to specialize the algorithm to a specific NEP: the waveguide eigenvalue problem. The waveguide eigenvalue problem arises from a finite-element discretization of a partial differential equation used in the study waves propagating in a periodic medium. The algorithm is successfully applied to accurately solve benchmark problems as well as complicated waveguides. We study the complexity of the specialized algorithm with respect to the number of iterations "m" and the size of the problem "n", both from a theoretical perspective and in practice. For the waveguide eigenvalue problem, we establish that the computationally dominating part of the algorithm has complexity O(nm^2+sqrt(n)m^3). Hence, the asymptotic complexity of TIAR applied to the waveguide eigenvalue problem, for n→ ∞, is the same as for Arnoldi’s method for standard eigenvalue problems.

  • 142.
    Jarlebring, Elias
    et al.
    KTH, School of Engineering Sciences (SCI), Mathematics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Poloni, F.
    Iterative methods for the delay Lyapunov equation with T-Sylvester preconditioning2019In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 135, p. 173-185Article in journal (Refereed)
    Abstract [en]

    The delay Lyapunov equation is an important matrix boundary-value problem which arises as an analogue of the Lyapunov equation in the study of time-delay systems x˙(t)=A0x(t)+A1x(t−τ)+B0u(t). We propose a new algorithm for the solution of the delay Lyapunov equation. Our method is based on the fact that the delay Lyapunov equation can be expressed as a linear system of equations, whose unknown is the value U(τ/2)∈Rn×n, i.e., the delay Lyapunov matrix at time τ/2. This linear matrix equation with n2 unknowns is solved by adapting a preconditioned iterative method such as GMRES. The action of the n2×n2 matrix associated to this linear system can be computed by solving a coupled matrix initial-value problem. A preconditioner for the iterative method is proposed based on solving a T-Sylvester equation MX+XTN=C, for which there are methods available in the literature. We prove that the preconditioner is effective under certain assumptions. The efficiency of the approach is illustrated by applying it to a time-delay system stemming from the discretization of a partial differential equation with delay. Approximate solutions to this problem can be obtained for problems of size up to n≈1000, i.e., a linear system with n2≈106 unknowns, a dimension which is outside of the capabi© 2018 IMACS

  • 143.
    Johansson, Petter
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics.
    Carlson, Andreas
    Hess, Berk
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Water-substrate physico-chemistry in wetting dynamics2015In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 781, p. 695-711Article in journal (Refereed)
    Abstract [en]

    We consider the wetting of water droplets on substrates with different chemical composition and molecular spacing, but with an identical equilibrium contact angle. A combined approach of large-scale molecular dynamics simulations and a continuum phase field model allows us to identify and quantify the influence of the microscopic physics at the contact line on the macroscopic droplet dynamics. We show that the substrate physico-chemistry, in particular hydrogen bonding, can significantly alter the flow. Since the material parameters are systematically derived from the atomistic simulations, our continuum model has only one adjustable parameter, which appears as a friction factor at the contact line. The continuum model approaches the atomistic wetting rate only when we adjust this contact line friction factor. However, the flow appears to he qualitatively different when comparing the atomistic and continuum models, highlighting that non-trivial continuum effects can come into play near the interface of the wetting front.

  • 144.
    Johansson, Petter
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Hess, Berk
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Molecular origin of contact line friction in dynamic wetting2018In: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, no 7, article id 074201Article in journal (Refereed)
    Abstract [en]

    A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact line can advance during wetting. Using large-scale molecular dynamics simulations we show that the contact line advances by single molecules moving ahead of the contact line through two distinct processes: either moving over or displacing other liquid molecules. In both processes friction occurs at the molecular scale. We measure the energy dissipation at the contact line and show that it is of the same magnitude as the dissipation in the bulk of a droplet. The friction increases significantly as the contact angle decreases, which suggests suggests thermal activation plays a role. We provide a simple model that is consistent with the observations.

  • 145.
    Kametani, Yukinori
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Örlü, Ramis
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Fukagata, K.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Drag reduction in spatially developing turbulent boundary layers by blowing at constant mass-flux2015In: 9th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2015, TSFP-9 , 2015Conference paper (Refereed)
    Abstract [en]

    A series of large-eddy simulations of spatially developing turbulent boundary layers with uniform blowing at moderate Reynolds numbers (based on free-stream velocity, U∞ and momentum thickness, θ) up to Reθ ∼ 2500 were performed with the special focus on the effect of intermittent (separated in streamwise direction) blowing sections. The number of blowing sections, N, investigated is set to be 3, 6, 20, 30 and compared to N = 1, which constitutes the reference case, while the total wall-mass flux is constrained to be the same for all considered cases, corresponding to a blowing amplitude of 0.1% of U∞ for the reference case. Results indicate that the reference case provides a net-energy saving rate of around 18%, which initially decreases at most 2 percentage points for N = 3 but recovers with increasing N. The initial reduction of the drag reduction is due to the shorter streamwise length of intermittent blowing sections. The physical decomposition of the skin friction drag through the FIK identity (Fukagata et at, 2002), shows that the distribution of all components over each blowing section has similar trends, resulting in similar averaged values over the whole control region.

  • 146. Karlsson, A.
    et al.
    Olofsson, N.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Clements, M.
    A parallel microsimulation package for modelling cancer screening policies2017In: Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, IEEE, 2017, p. 323-330Conference paper (Refereed)
    Abstract [en]

    Microsimulation with stochastic life histories is an important tool in the development of public policies. In this article, we use microsimulation to evaluate policies for prostate cancer testing. We implemented the microsimulations as an R package, with pre- and post-processing in R and with the simulations written in C++. Calibrating a microsimulation model with a large population can be computationally expensive. To address this issue, we investigated four forms of parallelism: (i) shared memory parallelism using R; (ii) shared memory parallelism using OpenMP at the C++ level; (iii) distributed memory parallelism using R; and (iv) a hybrid shared/distributed memory parallelism using OpenMP at the C++ level and MPI at the R level. The close coupling between R and C++ offered advantages for ease of software dissemination and the use of high-level R parallelisation methods. However, this combination brought challenges when trying to use shared memory parallelism at the C++ level: the performance gained by hybrid OpenMP/MPI came at the cost of significant re-factoring of the existing code. As a case study, we implemented a prostate cancer model in the microsimulation package. We used this model to investigate whether prostate cancer testing with specific re-testing protocols would reduce harms and maintain any mortality benefit from prostate-specific antigen testing. We showed that four-yearly testing would have a comparable effectiveness and a marked decrease in costs compared with two-yearly testing and current testing. In summary, we developed a microsimulation package in R and assessed the cost-effectiveness of prostate cancer testing. We were able to scale up the microsimulations using a combination of R and C++, however care was required when using shared memory parallelism at the C++ level.

  • 147.
    Kawata, Takuya
    et al.
    Tokyo Univ Sci, Yamazaki 2641, Noda, Chiba 2788510, Japan..
    Alfredsson, P. Henrik
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics. KTH, School of Industrial Engineering and Management (ITM), Centres, Competence Center for Gas Exchange (CCGEx). KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Inverse Interscale Transport of the Reynolds Shear Stress in Plane Couette Turbulence2018In: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 120, no 24, article id 244501Article in journal (Refereed)
    Abstract [en]

    Interscale interaction between small-scale structures near the wall and large-scale structures away from the wall plays an increasingly important role with increasing Reynolds number in wall-bounded turbulence. While the top-down influence from the large-to small-scale structures is well known, it has been unclear whether the small scales near the wall also affect the large scales away from the wall. In this Letter we show that the small-scale near-wall structures indeed play a role to maintain the large-scale structures away from the wall, by showing that the Reynolds shear stress is transferred from small to large scales throughout the channel. This is in contrast to the turbulent kinetic energy transport which is from large to small scales. Such an "inverse" interscale transport of the Reynolds shear stress eventually supports the turbulent energy production at large scales.

  • 148.
    Khan, Mehmood Alam
    et al.
    KTH, School of Computer Science and Communication (CSC). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, School of Computer Science and Communication (CSC). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, School of Computer Science and Communication (CSC). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, Centres, SeRC - Swedish e-Science Research Centre. Stockholm Univ, Sweden.
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lateral gene transfer events2016In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 17, article id 431Article in journal (Refereed)
    Abstract [en]

    Background: Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. Results: In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify "highways" of LGT. Conclusions: Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples.

  • 149.
    Khan, Mehmood
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Mahmudi, Owais
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ulah, Ikram
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Arvestad, Lars
    Lagergren, Jens
    KTH, School of Computer Science and Communication (CSC), Computational Biology, CB. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Probabilistic inference of lataral gene transfer eventsManuscript (preprint) (Other academic)
  • 150.
    Khapko, Taras
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Kreilos, T.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Duguet, Y.
    Eckhardt, B.
    Henningson, Dan Stefan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Edge states as mediators of bypass transition in boundary-layer flows2016In: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 801, article id R2Article in journal (Refereed)
    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.

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