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  • 101.
    Eitel-Amor, Georg
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Flores, O.
    Hairpin vortices in turbulent boundary layers2015Ingår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 27, nr 2, artikel-id 025108Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 102.
    El Khoury, George K.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Noorani, Azad
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul F.
    Brethouwer, Geert
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Johansson, Arne V.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Turbulens. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Direct Numerical Simulation of Turbulent Pipe Flow at Moderately High Reynolds Numbers2013Ingår i: Flow Turbulence and Combustion, ISSN 1386-6184, E-ISSN 1573-1987, Vol. 91, nr 3, s. 475-495Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 103.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Materialfysik, MF.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Tidigare Institutioner (före 2005), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Adsorption of carbon dioxide and water molecules on graphene on top of silica substrates: dispersion corrected density functional calculationsManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

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

  • 104.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Materialfysik, MF.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Tidigare Institutioner (före 2005), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Graphene adhesion on surfaces: a van der Waals density functional studyManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

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

  • 105.
    Elgammal, Karim
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hugosson, Håkan W.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar. Chalmers Institute of Technology, Sweden.
    Råsander, Mikael
    Bergqvist, Lars
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University, Sweden.
    Density functional calculations of graphene-based humidity and carbon dioxide sensors: effect of silica and sapphire substrates2017Ingår i: Surface Science, ISSN 0039-6028, E-ISSN 1879-2758, Vol. 663, s. 23-30Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 106.
    Elgammal, Karim
    et al.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hugosson, Håkan W.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Integrerade komponenter och kretsar.
    Råsander, Mikael
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF.
    Bergqvist, Lars
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Delin, Anna
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Material- och nanofysik, Materialfysik, MF. KTH, Centra, SeRC - Swedish e-Science Research Centre. Uppsala University.
    Density functional theory calculations of graphene-based humidity and carbon dioxide sensors: effect of silica and sapphire substratesManuskript (preprint) (Övrigt vetenskapligt)
  • 107.
    Elofsson, Arne
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Hess, Berk
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Onufriev, Alexey
    Virginia Tech, Dept Comp Sci, Ctr Soft Matter & Biol Phys, Blacksburg, VA USA.;Virginia Tech, Dept Phys, Ctr Soft Matter & Biol Phys, Blacksburg, VA USA..
    van der Spoel, David
    Uppsala Univ, Dept Cell & Mol Biol, Sci Life Lab, Uppsala Ctr Computat Chem, Uppsala, Sweden..
    Wallqvist, Anders
    US Army Med Res & Mat Command, Dept Def Biotechnol High Performance Comp Softwar, Telemed & Adv Technol Res Ctr, Ft Detrick, MD USA..
    Ten simple rules on how to create open access and reproducible molecular simulations of biological systems2019Ingår i: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 15, nr 1, artikel-id e1006649Artikel i tidskrift (Övrigt vetenskapligt)
  • 108. Engquist, Björn
    et al.
    Runborg, Olof
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tsai, Y. -HR.
    Preface2012Ingår i: Workshop on Numerical Analysis and Multiscale Computations, 2009, Springer Verlag , 2012Konferensbidrag (Refereegranskat)
  • 109.
    Eriksson, Olivia
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Jauhiainen, Alexandra
    AstraZeneca, IMED Biotech Unit, Early Clin Dev, Biometr, Gothenburg, Sweden..
    Sasane, Sara Maad
    Lund Univ, Ctr Math Sci, Lund, Sweden..
    Kramer, Andrei
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Nair, Anu G.
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sartorius, Carolina
    Lund Univ, Ctr Math Sci, Lund, Sweden..
    Hellgren Kotaleski, Jeanette
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Uncertainty quantification, propagation and characterization by Bayesian analysis combined with global sensitivity analysis applied to dynamical intracellular pathway models2019Ingår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, nr 2, s. 284-292Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 110.
    Ezhova, Ekaterina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. University of Helsinki, Finland.
    Cenedese, C.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Dynamics of a turbulent Buoyant Plume in a stratified fluid: An idealized model of subglacial discharge in Greenland Fjords2017Ingår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 47, nr 10, s. 2611-2630Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 111.
    Ezhova, Ekaterina
    et al.
    Univ Helsinki, Inst Atmospher & Earth Syst Res, Helsinki, Finland.;Univ Helsinki, Dept Phys, Fac Sci, Helsinki, Finland..
    Cenedese, Claudia
    Woods Hole Oceanog Inst, Dept Phys Oceanog, Woods Hole, MA 02543 USA..
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Processteknisk strömningsmekanik. Royal Inst Technol, Linne FLOW Ctr, Stockholm, Sweden.;Royal Inst Technol, Swedish E Sci Res Ctr, Dept Mech, Stockholm, Sweden..
    Dynamics of Three-Dimensional Turbulent Wall Plumes and Implications for Estimates of Submarine Glacier Melting2018Ingår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 48, nr 9, s. 1941-1950Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 112.
    Ezhova, Ekaterina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Cenedese, Claudia
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Interaction between a Vertical Turbulent Jet and a Thermocline2016Ingår i: Journal of Physical Oceanography, ISSN 0022-3670, E-ISSN 1520-0485, Vol. 46, nr 11, s. 3415-3437Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 113.
    Fallenius, Bengt E. G.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Örlü, Ramis
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Skolan för industriell teknik och management (ITM), Centra, Competence Center for Gas Exchange (CCGEx). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Bellani, G.
    Martini, A.
    Troncossi, M.
    Mascotelli, L.
    Fransson, Jens H. M.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Talamelli, A.
    Alfredsson, P. Henrik
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Assessment of wall vibrations in the long pipe facility at CICLoPE2019Ingår i: Springer Proceedings in Physics, Springer Science and Business Media, LLC , 2019, s. 203-208Konferensbidrag (Refereegranskat)
    Abstract [en]

    The present investigation aims at finding out whether there are pipe vibrations in the higher Reynolds number range at the Long Pipe Facility at the CICLoPE facility and to quantify their amplitude and frequency. Since vibrations are natural to any wind-tunnel facility, similar vibration measurements have also been performed in an established high-quality wind-tunnel facility, viz. the Minimum Turbulence Level (MTL) wind tunnel at KTH Royal Institute of Technology, in order to provide reference data. Results affirm that the amplitudes observed in Willert et al. (J Fluid Mech 826, 2017) are most likely the result of an amplification due to the optical set-up that is attached to the window plug, rather than vibrations of the pipe structure.

  • 114.
    Fan, Xuge
    et al.
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Elgammal, Karim
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Smith, Anderson D.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar.
    Östling, Mikael
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar.
    Delin, Anna
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap. KTH, Centra, SeRC - Swedish e-Science Research Centre. Department of Physics and Astronomy, Materials Theory Division, Uppsala University, Box 516, SE-75120 Uppsala, Sweden.
    Lemme, Max C.
    KTH, Skolan för informations- och kommunikationsteknik (ICT), Elektronik, Integrerade komponenter och kretsar. Department of Electronic Devices, RWTH Aachen University, 52074 Aachen, Germany.
    Niklaus, Frank
    KTH, Skolan för elektro- och systemteknik (EES), Mikro- och nanosystemteknik.
    Humidity and CO2 gas sensing properties of double-layer graphene2018Ingår i: Carbon, ISSN 0008-6223, E-ISSN 1873-3891, Vol. 127, s. 576-587Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 115.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Chaudhuri, Pinaki
    Umbert López, Cyan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Mitra, Dhrubaditya
    Picano, Francesco
    Rheology of extremely confined non-Brownian suspensions2016Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 116, nr 1, artikel-id 018301Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

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

  • 116.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Formenti, A.
    Picano, F.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The effect of particle density in turbulent channel flow laden with finite size particles in semi-dilute conditions2016Ingår i: Physics of fluids, ISSN 1070-6631, E-ISSN 1089-7666, Vol. 28, nr 3, artikel-id 033301Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 117.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Kazerooni, Hamid Tabaei
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. Ruhr-Universität Bochum, Department of Hydraulic Fluid Machinery, Universitätsstrae 150, Bochum, Germany.
    Hussong, Jeanette
    Ruhr Univ Bochum, Chair Hydraul Fluid Machinery, Univ Str 150, D-44801 Bochum, Germany..
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Suspensions of finite-size neutrally buoyant spheres in turbulent duct flow2018Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 851, s. 148-186Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 118.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Brandt, L.uca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik.
    Clustering and increased settling speed of oblate particles at finite Reynolds number2017Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikel i tidskrift (Refereegranskat)
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    fulltext
  • 119.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Niazi Ardekani, Mehdi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Clustering and increased settling speed of oblate particles at finite Reynolds number2018Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 848, s. 696-721Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

  • 120.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Picano, Francesco
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The effect of polydispersity in a turbulent channel flow laden with finite-size particles2018Ingår i: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 67, s. 54-64Artikel i tidskrift (Refereegranskat)
    Abstract [en]

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

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    fulltext
  • 121.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Picano, Francesco
    Sardina, Gaetano
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Reduced particle settling speed in turbulence2016Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645, Vol. 808, s. 153-167Artikel i tidskrift (Refereegranskat)
    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).

  • 122.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Fysiokemisk strömningsmekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tabaei Kazerooni, Hamid
    KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Hussong, Jeanette
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Suspensions of finite-size neutrally buoyant spheres in turbulent duct flow2017Ingår i: Journal of Fluid Mechanics, ISSN 0022-1120, E-ISSN 1469-7645Artikel i tidskrift (Refereegranskat)
    Ladda ner fulltext (pdf)
    fulltext
  • 123.
    Fornari, Walter
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Zade, Sagar
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Picano, Francesco
    Department of Industrial EngineeringUniversity of PadovaPaduaItaly.
    Settling of finite-size particles in turbulence at different volume fractions2018Ingår i: Acta Mechanica, ISSN 0001-5970, E-ISSN 1619-6937, Vol. 230, nr 2, s. 413-430Artikel i tidskrift (Refereegranskat)
    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 .

  • 124.
    Fourati, Zaineb
    et al.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Heusser, Stephanie A.
    Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.;Stockholm Univ, Sci Life Lab, S-17165 Solna, Sweden..
    Hu, Haidai
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France.;UPMC Univ Paris 6, Sorbonne Univ, F-75005 Paris, France..
    Ruza, Reinis R.
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Sauguet, Ludovic
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-17165 Solna, Sweden.
    Delarue, Marc
    Inst Pasteur, Unit Struct Dynam Macromol, F-75015 Paris, France.;CNRS, UMR 3528, F-75015 Paris, France..
    Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels2018Ingår i: Cell reports, ISSN 2211-1247, E-ISSN 2211-1247, Vol. 23, nr 4, s. 993-1004Artikel i tidskrift (Refereegranskat)
    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.

  • 125. Fouxon, Itzhak
    et al.
    Ge, Zhouyang
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Leshansky, Alexander
    Integral representation of channel flow with interacting particles2017Ingår i: Physical review. E, ISSN 2470-0045, E-ISSN 2470-0053, Vol. 96, nr 6, artikel-id 063110Artikel i tidskrift (Refereegranskat)
    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.

  • 126.
    Frecus, Bogdan
    et al.
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    Rinkevicius, Zilvinas
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Ågren, Hans
    KTH, Skolan för bioteknologi (BIO), Teoretisk kemi och biologi.
    π –stacking effects on the EPR parameters of a prototypical DNA spin label2013Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 15, nr 25, s. 10466-10471Artikel i tidskrift (Refereegranskat)
    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.

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    manuscript_pi_stacking_EPR_DNA.pdf
  • 127. Frånberg, Mattias
    et al.
    Gertow, Karl
    Hamsten, Anders
    Lagergren, Jens
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsbiologi, CB. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests2015Ingår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 11, nr 9, artikel-id e1005502Artikel i tidskrift (Refereegranskat)
    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.

  • 128.
    Frånberg, Mattias
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS). KTH, Centra, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm, Sweden.
    Lagergren, Jens
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Sennblad, Bengt
    Cardiovascular Medicine Unit, Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden ; Dept of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
    BESIQ: A tool for discovering gene-gene and gene-environment interactions in genome-wide association studiesManuskript (preprint) (Övrigt vetenskapligt)
  • 129.
    Frånberg, Mattias
    et al.
    KTH, Skolan för elektroteknik och datavetenskap (EECS). KTH, Centra, 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, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS).
    Sennblad, Bengt
    KTH, Centra, Science for Life Laboratory, SciLifeLab. Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden ; .
    Discovering gene-environment interactions with LassoManuskript (preprint) (Övrigt vetenskapligt)
  • 130. Fukada, T.
    et al.
    Fornari, Walter
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Takeuchi, S.
    Kajishima, T.
    A numerical approach for particle-vortex interactions based on volume-averaged equations2018Ingår i: International Journal of Multiphase Flow, ISSN 0301-9322, E-ISSN 1879-3533, Vol. 104, s. 188-205Artikel i tidskrift (Refereegranskat)
    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.

  • 131.
    Gaaf, Sarah W.
    et al.
    TU Eindhoven.
    Jarlebring, Elias
    KTH, Skolan för teknikvetenskap (SCI), Matematik (Inst.), Numerisk analys, NA. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    The infinite Bi-Lanczos method for nonlinear eigenvalue problems2017Ingår i: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 39, s. S898-S919Artikel i tidskrift (Refereegranskat)
  • 132.
    Gallino, Giacomo
    et al.
    Ecole Polytech Fed Lausanne, Lab Fluid Mech & Instabil, CH-1015 Lausanne, Switzerland..
    Zhu, Lailai
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, 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 Bubble2019Ingår i: FLUIDS, ISSN 2311-5521, Vol. 4, nr 1, artikel-id 48Artikel i tidskrift (Refereegranskat)
    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.

  • 133.
    Ge, Zhouyang
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    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, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, 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 failure2018Ingår i: Physical Review Fluids, E-ISSN 2469-990X, Vol. 3, nr 5, artikel-id 054201Artikel i tidskrift (Refereegranskat)
    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.

  • 134.
    Ge, Zhouyang
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Loiseau, Jean Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Arts et Métiers ParisTech, France.
    Tammisola, Outi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    An efficient mass-preserving interface-correction level set/ghost fluid method for droplet suspensions under depletion forces2018Ingår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 353, s. 435-459Artikel i tidskrift (Refereegranskat)
    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.

  • 135.
    Ge, Zhouyang
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Tammisola, Outi
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH Mech, INTERFACE Ctr, SE-10044 Stockholm, Sweden..
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH Mech, INTERFACE Ctr, SE-10044 Stockholm, Sweden..
    Flow-assisted droplet assembly in a 3D microfluidic channel2019Ingår i: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 15, nr 16, s. 3451-3460Artikel i tidskrift (Refereegranskat)
    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.

  • 136.
    Gharpure, Anant
    et al.
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA..
    Teng, Jinfeng
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA..
    Zhuang, Yuxuan
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-17121 Solna, Sweden..
    Noviello, Colleen M.
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA..
    Walsh, Richard M., Jr.
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA.;Harvard Med Sch, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA..
    Cabuco, Rico
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA..
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-17121 Solna, Sweden..
    Zaveri, Nurulain T.
    Astraea Therapeut, Mountain View, CA 94043 USA..
    Lindahl, Erik
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Hibbs, Ryan E.
    Univ Texas Southwestern Med Ctr Dallas, Dept Neurosci, Dallas, TX 75390 USA..
    Agonist Selectivity and Ion Permeation in the alpha 3 beta 4 Ganglionic Nicotinic Receptor2019Ingår i: Neuron, ISSN 0896-6273, E-ISSN 1097-4199, Vol. 104, nr 3, s. 501-+Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The alpha 3 beta 4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the alpha 3 beta 4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the alpha 3 beta 4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.

  • 137.
    Ghosh, Souvik
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH Mech, SeRC Swedish eSci Res Ctr, SE-10044 Stockholm, Sweden..
    Loiseau, Jean-Christophe
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Breugem, Wim-Paul
    Delft Univ Technol, Proc & Energy Dept, NL-2628 CB Delft, Netherlands..
    Brandt, Luca
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Modal and non-modal linear stability of Poiseuille flow through a channel with a porous substrate2019Ingår i: European journal of mechanics. B, Fluids, ISSN 0997-7546, E-ISSN 1873-7390, Vol. 75, s. 29-43Artikel i tidskrift (Refereegranskat)
    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.

  • 138.
    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, Centra, 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 facilities2018Ingår i: Journal of Structural Biology, ISSN 1047-8477, E-ISSN 1095-8657, Vol. 204, nr 3, s. 457-463Artikel i tidskrift (Refereegranskat)
    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.

  • 139.
    Gong, Jing
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Cray Inc..
    Henty, David
    University of Edinburgh.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Fischer, Paul
    Argonne National Laboratory.
    Heisey, Katherine
    Argonne National Laboratory.
    OpenACC Acceleration of Nek5000: a Spectral Element Code2013Konferensbidrag (Övrigt vetenskapligt)
  • 140.
    Gong, Jing
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Otten, Matthew
    Fischer, Paul
    Min, Misun
    Nekbone performance on GPUs with OpenACC and CUDA Fortran implementations2016Ingår i: Journal of Supercomputing, ISSN 0920-8542, E-ISSN 1573-0484, Vol. 72, nr 11, s. 4160-4180Artikel i tidskrift (Refereegranskat)
    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.

  • 141.
    Gong, Jing
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Cebamanos, Luis
    Hart, Alistair
    Min, Misun
    Fischer, Paul
    NekBone with Optimizaed OpenACC directives2015Konferensbidrag (Refereegranskat)
    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.

     

  • 142.
    Gong, Jing
    et al.
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Peplinski, Adam
    Hart, Alistair
    Doleschal, Jens
    Henty, David
    Fischer, Paul
    Nek5000 with OpenACC2015Ingår i: Solving software challenges for exascale, 2015, s. 57-68Konferensbidrag (Refereegranskat)
    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.

  • 143. Granholm, V.
    et al.
    Kim, S.
    Fernandez Navarro, José
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Sjölund, E.
    Smith, R. D.
    Käll, Lukas
    KTH, Skolan för bioteknologi (BIO), Genteknologi. KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Fast and accurate database searches with MS-GF+percolator2014Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 13, nr 2, s. 890-897Artikel i tidskrift (Refereegranskat)
    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.

  • 144.
    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, Centra, Science for Life Laboratory, SciLifeLab.
    Käll, Lukas
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, 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"2018Ingår i: Journal of Proteome Research, ISSN 1535-3893, E-ISSN 1535-3907, Vol. 17, nr 5, s. 1993-1996Artikel i tidskrift (Refereegranskat)
    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.

  • 145. Gronberg, Christina
    et al.
    Sitsel, Oleg
    Lindahl, Erik
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, nr 11, s. 2417-2429Artikel i tidskrift (Refereegranskat)
    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.

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  • 146.
    Guastoni, L.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Srinivasan, P. A.
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Azizpour, Hossein
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för elektroteknik och datavetenskap (EECS).
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    Vinuesa, Ricardo
    KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Mekanik.
    On the use of recurrent neural networks for predictions of turbulent flows2019Ingår i: 11th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2019, International Symposium on Turbulence and Shear Flow Phenomena, TSFP , 2019Konferensbidrag (Refereegranskat)
    Abstract [en]

    In this paper, the prediction capabilities of recurrent neural networks are assessed in the low-order model of near-wall turbulence by Moehlis et al. (New J. Phys. 6, 56, 2004). Our results show that it is possible to obtain excellent predictions of the turbulence statistics and the dynamic behavior of the flow with properly trained long short-term memory (LSTM) networks, leading to relative errors in the mean and the fluctuations below 1%. We also observe that using a loss function based only on the instantaneous predictions of the flow may not lead to the best predictions in terms of turbulence statistics, and it is necessary to define a stopping criterion based on the computed statistics. Furthermore, more sophisticated loss functions, including not only the instantaneous predictions but also the averaged behavior of the flow, may lead to much faster neural network training.

  • 147.
    Gupta, Rahul
    et al.
    Uppsala Univ, Dept Engn Sci, Box 534, SE-75121 Uppsala, Sweden..
    Behera, Nilamani
    Uppsala Univ, Dept Engn Sci, Box 534, SE-75121 Uppsala, Sweden..
    Venugopal, Vijay A.
    Seagate Technol, 1 Disc Dr, Springtown BT48 0BF, North Ireland..
    Basu, Swaraj
    Seagate Technol, 1 Disc Dr, Springtown BT48 0BF, North Ireland..
    Puri, Anil K.
    Seagate Technol, 1 Disc Dr, Springtown BT48 0BF, North Ireland..
    Strom, Petter
    Uppsala Univ, Dept Phys & Astron, Box 516, SE-75120 Uppsala, Sweden..
    Gubbins, Mark A.
    Seagate Technol, 1 Disc Dr, Springtown BT48 0BF, North Ireland..
    Bergqvist, Lars
    KTH, Skolan för industriell teknik och management (ITM), Materialvetenskap, Tillämpad materialfysik. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Brucas, Rimantas
    Uppsala Univ, Dept Engn Sci, Box 534, SE-75121 Uppsala, Sweden..
    Svedlindh, Peter
    Uppsala Univ, Dept Engn Sci, Box 534, SE-75121 Uppsala, Sweden..
    Kumar, Ankit
    Uppsala Univ, Dept Engn Sci, Box 534, SE-75121 Uppsala, Sweden..
    Engineering of spin mixing conductance at Ru/FeCo/Ru interfaces: Effect of Re doping2020Ingår i: Physical Review B, ISSN 2469-9950, E-ISSN 2469-9969, Vol. 101, nr 2, artikel-id 024401Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have deposited polycrystalline Re-doped (Fe65Co35)((100-x))Re-x (0 <= x <= 12.6 at. %) thin films grown under identical conditions and sandwiched between thin layers of Ru in order to study the phenomenon of spin pumping as a function of Re concentration. In-plane and out-of-plane ferromagnetic resonance spectroscopy results show an enhancement of the Gilbert damping with an increase in Re doping. We find 98% enhancement in the real part of effective spin mixing conductance [Re(g(eff)(up arrow down arrow))] with Re doping. Conversely, the Re(g(eff)(up arrow down arrow)) does not change with Re doping in Fe65Co35 thin films which are seeded and capped with Cu layers. The enhancement in Re(g(eff)(up arrow down arrow)) of Re-doped Fe65Co35 thin films sandwiched between thin layers of Ru is linked to the Re doping-induced change of the interface electronic structure in the nonmagnetic Ru layer. The saturation magnetization decreases 35% with increasing Re doping up to 12.6 at. %. This study opens a direction of tuning the spin mixing conductance in magnetic heterostructures by doping of the ferromagnetic layer, which is essential for the realization of energyefficient operation of spintronic devices.

  • 148. Hadikhani, P.
    et al.
    Hashemi, S. M. H.
    Balestra, G.
    Zhu, Lailai
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW. KTH, Centra, SeRC - Swedish e-Science Research Centre. Princeton University, United States.
    Modestino, M. A.
    Gallaire, F.
    Psaltis, D.
    Inertial manipulation of bubbles in rectangular microfluidic channels2018Ingår i: Lab on a Chip, ISSN 1473-0197, E-ISSN 1473-0189, Vol. 18, nr 7, s. 1035-1046Artikel i tidskrift (Refereegranskat)
    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.

  • 149.
    Hess, Berk
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Pall, Szilard
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Schlatter, Philipp
    KTH, Skolan för teknikvetenskap (SCI), Mekanik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för teknikvetenskap (SCI), Centra, Linné Flow Center, FLOW.
    Peplinski, Adam
    KTH, Skolan för teknikvetenskap (SCI), Mekanik, Stabilitet, Transition, Kontroll.
    Highly Tuned Small Matrix Multiplications Applied to Spectral Element Code Nek50002016Konferensbidrag (Refereegranskat)
  • 150.
    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, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, 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 cavity2018Ingår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, nr 42, s. 10672-10677Artikel i tidskrift (Refereegranskat)
    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.

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