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  • 1. Aad, G.
    et al.
    Grahn, Karl-Johan
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Lund-Jensen, Bengt
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    Strandberg, Jonas
    University of Chicago.
    Zwalinski, L.
    Lafaye, Remi
    KTH, School of Engineering Sciences (SCI), Physics, Particle and Astroparticle Physics.
    et, al
    Measurement of the inelastic proton-proton cross-section at root s=7 TeV with the ATLAS detector2011In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 2, p. 463-Article in journal (Refereed)
    Abstract [en]

    The dependence of the rate of proton-proton interactions on the centre-of-mass collision energy, root s, is of fundamental importance for both hadron collider physics and particle astrophysics. The dependence cannot yet be calculated from first principles; therefore, experimental measurements are needed. Here we present the first measurement of the inelastic proton-proton interaction cross-section at a centre-of-mass energy, root s, of 7 TeV using the ATLAS detector at the Large Hadron Collider. Events are selected by requiring hits on scintillation counters mounted in the forward region of the detector. An inelastic crosssection of 60.3 +/- 2.1 mb is measured for xi > 5x10(-6), where xi is calculated from the invariant mass, M(X), of hadrons selected using the largest rapidity gap in the event. For diffractive events, this corresponds to requiring at least one of the dissociation masses to be larger than 15.7 GeV.

  • 2. Aghion, S.
    et al.
    Ahlén, O.
    Amsler, C.
    Ariga, A.
    Ariga, T.
    Belov, A. S.
    Berggren, Karl
    Physics Department, European Organisation for Nuclear Research, Switzerland.
    Bonomi, G.
    Bräunig, P.
    Bremer, J.
    Brusa, R. S.
    Cabaret, L.
    Canali, C.
    Caravita, R.
    Castelli, F.
    Cerchiari, G.
    Cialdi, S.
    Comparat, D.
    Consolati, G.
    Derking, H.
    Di Domizio, S.
    Di Noto, L.
    Doser, M.
    Dudarev, A.
    Ereditato, A.
    Ferragut, R.
    Fontana, A.
    Genova, P.
    Giammarchi, M.
    Gligorova, A.
    Gninenko, S. N.
    Haider, S.
    Huse, T.
    Jordan, E.
    Jørgensen, L. V.
    Kaltenbacher, T.
    Kawada, J.
    Kellerbauer, A.
    Kimura, M.
    Knecht, A.
    Krasnický, D.
    Lagomarsino, V.
    Lehner, S.
    Magnani, A.
    Malbrunot, C.
    Mariazzi, S.
    Matveev, V. A.
    Moia, F.
    Nebbia, G.
    Nédélec, P.
    Oberthaler, M. K.
    Pacifico, N.
    Petràček, V.
    Pistillo, C.
    Prelz, F.
    Prevedelli, M.
    Regenfus, C.
    Riccardi, C.
    Røhne, O.
    Rotondi, A.
    Sandaker, H.
    Scampoli, P.
    Storey, J.
    Vasquez, M.A. Subieta
    Špaček, M.
    Testera, G.
    Vaccarone, R.
    Widmann, E.
    Zavatarelli, S.
    Zmeskal, J.
    A moiré deflectometer for antimatter2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, article id 2538Article in journal (Refereed)
    Abstract [en]

    The precise measurement of forces is one way to obtain deep insight into the fundamental interactions present in nature. In the context of neutral antimatter, the gravitational interaction is of high interest, potentially revealing new forces that violate the weak equivalence principle. Here we report on a successful extension of a tool from atom optics—the moiré deflectometer—for a measurement of the acceleration of slow antiprotons. The setup consists of two identical transmission gratings and a spatially resolving emulsion detector for antiproton annihilations. Absolute referencing of the observed antimatter pattern with a photon pattern experiencing no deflection allows the direct inference of forces present. The concept is also straightforwardly applicable to antihydrogen measurements as pursued by the AEgIS collaboration. The combination of these very different techniques from high energy and atomic physics opens a very promising route to the direct detection of the gravitational acceleration of neutral antimatter.

  • 3. Andersson, Sandra
    et al.
    Sundberg, Marten
    Pristovsek, Nusa
    Ibrahim, Ahmed
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Natl Res Ctr, Egypt.
    Jonsson, Philip
    Katona, Borbala
    Clausson, Carl-Magnus
    Zieba, Agata
    Ramstrom, Margareta
    Soderberg, Ola
    Williams, Cecilia
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Univ Houston, USA; Karolinska Inst, Sweden.
    Asplund, Anna
    Insufficient antibody validation challenges oestrogen receptor beta research2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15840Article in journal (Refereed)
    Abstract [en]

    The discovery of oestrogen receptor beta (ER beta/ESR2) was a landmark discovery. Its reported expression and homology with breast cancer pharmacological target ER alpha (ESR1) raised hopes for improved endocrine therapies. After 20 years of intense research, this has not materialized. We here perform a rigorous validation of 13 anti-ER beta antibodies, using well-characterized controls and a panel of validation methods. We conclude that only one antibody, the rarely used monoclonal PPZ0506, specifically targets ER beta in immunohistochemistry. Applying this antibody for protein expression profiling in 44 normal and 21 malignant human tissues, we detect ER beta protein in testis, ovary, lymphoid cells, granulosa cell tumours, and a subset of malignant melanoma and thyroid cancers. We do not find evidence of expression in normal or cancerous human breast. This expression pattern aligns well with RNA-seq data, but contradicts a multitude of studies. Our study highlights how inadequately validated antibodies can lead an exciting field astray.

  • 4. Arabi, A.
    et al.
    Ullah, K.
    Branca, R. M. M.
    Johansson, J.
    Bandarra, D.
    Haneklaus, M.
    Fu, J.
    Ariës, I.
    Nilsson, Peter
    KTH, School of Biotechnology (BIO), Proteomics (closed 20130101). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Den Boer, M. L.
    Pokrovskaja, K.
    Grandér, D.
    Xiao, G.
    Rocha, S.
    Lehtiö, J.
    Sangfelt, O.
    Proteomic screen reveals Fbw7 as a modulator of the NF-kappa B pathway2012In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 3, p. 976-Article in journal (Refereed)
    Abstract [en]

    Fbw7 is a ubiquitin-ligase that targets several oncoproteins for proteolysis, but the full range of Fbw7 substrates is not known. Here we show that by performing quantitative proteomics combined with degron motif searches, we effectively screened for a more complete set of Fbw7 targets. We identify 89 putative Fbw7 substrates, including several disease-associated proteins. The transcription factor NF-κB2 (p100/p52) is one of the candidate Fbw7 substrates. We show that Fbw7 interacts with p100 via a conserved degron and that it promotes degradation of p100 in a GSK3 2 phosphorylation-dependent manner. Fbw7 inactivation increases p100 levels, which in the presence of NF-κB pathway stimuli, leads to increased p52 levels and activity. Accordingly, the apoptotic threshold can be increased by loss of Fbw7 in a p100-dependent manner. In conclusion, Fbw7-mediated destruction of p100 is a regulatory component restricting the response to NF-κB2 pathway stimulation.

  • 5. Bagnoud, Alexandre
    et al.
    Chourey, Karuna
    Hettich, Robert L.
    de Bruijn, Ino
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    Leupin, Olivier X.
    Schwyn, Bernhard
    Bernier-Latmani, Rizlan
    Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 12770Article in journal (Refereed)
    Abstract [en]

    The Opalinus Clay formation will host geological nuclear waste repositories in Switzerland. It is expected that gas pressure will build-up due to hydrogen production from steel corrosion, jeopardizing the integrity of the engineered barriers. In an in situ experiment located in the Mont Terri Underground Rock Laboratory, we demonstrate that hydrogen is consumed by microorganisms, fuelling a microbial community. Metagenomic binning and metaproteomic analysis of this deep subsurface community reveals a carbon cycle driven by autotrophic hydrogen oxidizers belonging to novel genera. Necromass is then processed by fermenters, followed by complete oxidation to carbon dioxide by heterotrophic sulfate-reducing bacteria, which closes the cycle. This microbial metabolic web can be integrated in the design of geological repositories to reduce pressure build-up. This study shows that Opalinus Clay harbours the potential for chemolithoautotrophic-based system, and provides a model of microbial carbon cycle in deep subsurface environments where hydrogen and sulfate are present.

  • 6. Belotelov, V. I.
    et al.
    Kreilkamp, L. E.
    Akimov, I. A.
    Kalish, A. N.
    Bykov, D. A.
    Kasture, S.
    Yallapragada, V. J.
    Gopal, Achanta Venu
    Grishin, Alexander M.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Khartsev, Sergiy I.
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Nur-E-Alam, M.
    Vasiliev, M.
    Doskolovich, L. L.
    Yakovlev, D. R.
    Alameh, K.
    Zvezdin, A. K.
    Bayer, M.
    Plasmon-mediated magneto-optical transparency2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 2128-Article in journal (Refereed)
    Abstract [en]

    Magnetic field control of light is among the most intriguing methods for modulation of light intensity and polarization on sub-nanosecond timescales. The implementation in nanostructured hybrid materials provides a remarkable increase of magneto-optical effects. However, so far only the enhancement of already known effects has been demonstrated in such materials. Here we postulate a novel magneto-optical phenomenon that originates solely from suitably designed nanostructured metal-dielectric material, the so-called magneto-plasmonic crystal. In this material, an incident light excites coupled plasmonic oscillations and a waveguide mode. An in-plane magnetic field allows excitation of an orthogonally polarized waveguide mode that modifies optical spectrum of the magneto-plasmonic crystal and increases its transparency. The experimentally achieved light intensity modulation reaches 24%. As the effect can potentially exceed 100%, it may have great importance for applied nanophotonics. Further, the effect allows manipulating and exciting waveguide modes by a magnetic field and light of proper polarization.

  • 7.
    Berglund, Emelie
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Maaskola, Jonas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Schultz, Niklas
    Friedrich, Stefanie
    Marklund, Maja
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Bergenstrahle, Joseph
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Tarish, Firas
    Tanoglidi, Anna
    Vickovic, Sanja
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Larsson, Ludvig
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
    Salmén, Fredrik
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ogris, Christoph
    Wallenborg, Karolina
    Lagergren, Jens
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Ståhl, Patrik
    Sonnhammer, Erik
    Helleday, Thomas
    Lundeberg, Joakim
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 2419Article in journal (Refereed)
    Abstract [en]

    Intra-tumor heterogeneity is one of the biggest challenges in cancer treatment today. Here we investigate tissue-wide gene expression heterogeneity throughout a multifocal prostate cancer using the spatial transcriptomics (ST) technology. Utilizing a novel approach for deconvolution, we analyze the transcriptomes of nearly 6750 tissue regions and extract distinct expression profiles for the different tissue components, such as stroma, normal and PIN glands, immune cells and cancer. We distinguish healthy and diseased areas and thereby provide insight into gene expression changes during the progression of prostate cancer. Compared to pathologist annotations, we delineate the extent of cancer foci more accurately, interestingly without link to histological changes. We identify gene expression gradients in stroma adjacent to tumor regions that allow for re-stratification of the tumor microenvironment. The establishment of these profiles is the first step towards an unbiased view of prostate cancer and can serve as a dictionary for future studies.

  • 8.
    Biltmo, Anders
    et al.
    KTH, School of Engineering Sciences (SCI), Theoretical Physics.
    Henelius, Patrik
    KTH, School of Engineering Sciences (SCI), Theoretical Physics, Condensed Matter Theory.
    Unreachable glass transition in dilute dipolar magnet2012In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 3, p. 857-Article in journal (Refereed)
    Abstract [en]

    In magnetic systems the combined effects of disorder and frustration may cause the moments to freeze into a disordered state at a spin-glass transition. Recent experiments have shown that the rare earth compound LiHo0.045Y0.955F4 freezes, but that the transition is unreachable because of dynamics that are 10(7) times slower than in ordinary spin-glass materials. This conclusion refutes earlier investigations reporting a speed-up of the dynamics into an exotic anti-glass phase caused by entanglement of quantum dipoles. Here we present a theory, backed by numerical simulations, which describes the material in terms of classical dipoles governed by Glauber dynamics. The dipoles freeze and we find that the ultra-slow dynamics are caused by rare, strongly ordered clusters, which give rise to a previously predicted, but hitherto unobserved, Griffths phase between the paramagnetic and spin-glass phases. In addition, the hyperfine interaction creates a high energy barrier to flipping the electronic spin, resulting in a clear signature in the dynamic correlation function.

  • 9. Bonetti, Stefano
    et al.
    Kukreja, R
    Chen, Z
    Macià, F
    Hernàndez, J. M.
    Eklund, Anders
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Backes, D
    Frisch, J
    Katine, J
    Malm, Gunnar
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Urazhdin, S
    Kent, A. D.
    Stöhr, J.
    Ohldag, H.
    Dürr, H. A.
    Direct observation and imaging of a spin-wave soliton with p−like symmetry2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 8889Article in journal (Refereed)
    Abstract [en]

    The prediction and realization of magnetic excitations driven by electrical currents via the spin transfer torque effect, enables novel magnetic nano-devices where spin-waves can be used to process and store information. The functional control of such devices relies on understanding the properties of non-linear spin-wave excitations. It has been demonstrated that spin waves can show both an itinerant character, but also appear as localized solitons. So far, it was assumed that localized solitons have essentially cylindrical, s−like symmetry. Using a newly developed high-sensitivity time-resolved magnetic x-ray microscopy, we instead observe the emergence of a novel localized soliton excitation with a nodal line, i.e. with p−like symmetry. Micromagnetic simulations identify the physical mechanism that controls the transition from s− to p−like solitons. Our results suggest a potential new pathway to design artificial atoms with tunable dynamical states using nanoscale magnetic devices.

  • 10.
    Borgström, Erik
    et al.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Redin, David
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lundin, Sverker
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berglund, Emelie
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Andersson, Anders F.
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Ahmadian, Afshin
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Phasing of single DNA molecules by massively parallel barcoding2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7173Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing platforms mainly produce short-read data, resulting in a loss of phasing information for many of the genetic variants analysed. For certain applications, it is vital to know which variant alleles are connected to each individual DNA molecule. Here we demonstrate a method for massively parallel barcoding and phasing of single DNA molecules. First, a primer library with millions of uniquely barcoded beads is generated. When compartmentalized with single DNA molecules, the beads can be used to amplify and tag any target sequences of interest, enabling coupling of the biological information from multiple loci. We apply the assay to bacterial 16S sequencing and up to 94% of the hypothesized phasing events are shown to originate from single molecules. The method enables use of widely available short-read-sequencing platforms to study long single molecules within a complex sample, without losing phase information.

  • 11. Bovo, L.
    et al.
    Twengström, Mikael
    KTH, School of Engineering Sciences (SCI), Physics.
    Petrenko, O. A.
    Fennell, T.
    Gingras, M. J. P.
    Bramwell, S. T.
    Henelius, Patrik
    KTH, School of Engineering Sciences (SCI), Physics.
    Special temperatures in frustrated ferromagnets2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, article id 1999Article in journal (Refereed)
    Abstract [en]

    The description and detection of unconventional magnetic states, such as spin liquids, is a recurring topic in condensed matter physics. While much of the efforts have traditionally been directed at geometrically frustrated antiferromagnets, recent studies reveal that systems featuring competing antiferromagnetic and ferromagnetic interactions are also promising candidate materials. We find that this competition leads to the notion of special temperatures, analogous to those of gases, at which the competing interactions balance, and the system is quasi-ideal. Although induced by weak perturbing interactions, these special temperatures are surprisingly high and constitute an accessible experimental diagnostic of eventual order or spin-liquid properties. The well characterised Hamiltonian and extended low-temperature susceptibility measurement of the canonical frustrated ferromagnet Dy2Ti2O7 enables us to formulate both a phenomenological and microscopic theory of special temperatures for magnets. Other members of this class of magnets include kapellasite Cu3Zn(OH)6Cl2 and the spinel GeCo2O4.

  • 12. Brasko, Csilla
    et al.
    Smith, Kevin
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Molnar, Csaba
    Farago, Nora
    Hegedus, Lili
    Balind, Arpad
    Balassa, Tamas
    Szkalisity, Abel
    Sukosd, Farkas
    Kocsis, Katalin
    Balint, Balazs
    Paavolainen, Lassi
    Enyedi, Marton Z.
    Nagy, Istvan
    Puskas, Laszlo G.
    Haracska, Lajos
    Tamas, Gabor
    Horvath, Peter
    Intelligent image-based in situ single-cell isolation2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 226Article in journal (Refereed)
    Abstract [en]

    Quantifying heterogeneities within cell populations is important for many fields including cancer research and neurobiology; however, techniques to isolate individual cells are limited. Here, we describe a high-throughput, non-disruptive, and cost-effective isolation method that is capable of capturing individually targeted cells using widely available techniques. Using high-resolution microscopy, laser microcapture microscopy, image analysis, and machine learning, our technology enables scalable molecular genetic analysis of single cells, targetable by morphology or location within the sample.

  • 13.
    C. Couto, Rafael
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Vaz da Cruz, Vinícius
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ertan, Emelie
    Eckert, Sebastian
    Fondell, Mattis
    Dantz, Marcus
    Kennedy, Brian
    Schmitt, Thorsten
    Pietzsch, Annette
    F. Guimarães, Freddy
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel’mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Odelius, Michael
    Kimberg, Victor
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Föhlisch, Alexander
    Selective gating to vibrational modes through resonant X-ray scattering2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, p. 14165-1-14165-7Article in journal (Refereed)
    Abstract [en]

    The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations.

  • 14. Carreras-Puigvert, J.
    et al.
    Zitnik, M.
    Jemth, A. -S
    Carter, M.
    Unterlass, J. E.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Loseva, O.
    Karem, Z.
    Calderón-Montanõ, J. M.
    Lindskog, C.
    Edqvist, P. -H
    Matuszewski, D. J.
    Ait Blal, Hammou
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Berntsson, R. P. A.
    Häggblad, M.
    Martens, U.
    Studham, M.
    Lundgren, B.
    Wählby, C.
    Sonnhammer, E. L. L.
    Lundberg, Emma
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Stenmark, P.
    Zupan, B.
    Helleday, T.
    A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 1541Article in journal (Refereed)
    Abstract [en]

    The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes. To a certain extent, their substrate preference redundancies correlate with structural classes, thus linking structure and activity relationships. To elucidate interdependence among the NUDIX hydrolases, we pairwise deplete them generating an epistatic interaction map, evaluate cell cycle perturbations upon knockdown in normal and cancer cells, and analyse their protein and mRNA expression in normal and cancer tissues. Using a novel FUSION algorithm, we integrate all data creating a comprehensive NUDIX enzyme profile map, which will prove fundamental to understanding their biological functionality.

  • 15. Chang, J.
    et al.
    Månsson, Martin
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Pailhes, S.
    Claesson, Thomas
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Lipscombe, O. J.
    Hayden, S. M.
    Patthey, L.
    Tjernberg, Oscar
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF.
    Mesot, J.
    Anisotropic breakdown of Fermi liquid quasiparticle excitations in overdoped La2-xSrxCuO42013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 2559-Article in journal (Refereed)
    Abstract [en]

    High-temperature superconductivity emerges from an un-conventional metallic state. This has stimulated strong efforts to understand exactly how Fermi liquids breakdown and evolve into an un-conventional metal. A fundamental question is how Fermi liquid quasiparticle excitations break down in momentum space. Here we show, using angle-resolved photoemission spectroscopy, that the Fermi liquid quasiparticle excitations of the overdoped superconducting cuprate La1.77Sr0.23CuO4 is highly anisotropic in momentum space. The quasiparticle scattering and residue behave differently along the Fermi surface and hence the Kadowaki-Wood's relation is not obeyed. This kind of Fermi liquid breakdown may apply to a wide range of strongly correlated metal systems where spin fluctuations are present.

  • 16. Chen, Gefei
    et al.
    Abelein, Axel
    Nilsson, Harriet E.
    KTH, School of Technology and Health (STH), Medical Engineering, Structural Biotechnology.
    Leppert, Axel
    Andrade-Talavera, Yuniesky
    Tambaro, Simone
    Hemmingsson, Lovisa
    Roshan, Firoz
    Landreh, Michael
    Biverstal, Henrik
    Koeck, Philip J. B.
    KTH, School of Technology and Health (STH), Medical Engineering, Structural Biotechnology.
    Presto, Jenny
    Hebert, Hans
    Fisahn, Andre
    Johansson, Jan
    Bri2 BRICHOS client specificity and chaperone activity are governed by assembly state2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 2081Article in journal (Refereed)
    Abstract [en]

    . Protein misfolding and aggregation is increasingly being recognized as a cause of disease. In Alzheimer's disease the amyloid-beta peptide (A beta) misfolds into neurotoxic oligomers and assembles into amyloid fibrils. The Bri2 protein associated with Familial British and Danish dementias contains a BRICHOS domain, which reduces A beta fibrillization as well as neurotoxicity in vitro and in a Drosophila model, but also rescues proteins from irreversible nonfibrillar aggregation. How these different activities are mediated is not known. Here we show that Bri2 BRICHOS monomers potently prevent neuronal network toxicity of A beta, while dimers strongly suppress A beta fibril formation. The dimers assemble into high-molecular-weight oligomers with an apparent two-fold symmetry, which are efficient inhibitors of non-fibrillar protein aggregation. These results indicate that Bri2 BRICHOS affects qualitatively different aspects of protein misfolding and toxicity via different quaternary structures, suggesting a means to generate molecular chaperone diversity.

  • 17.
    Chen, Shula
    et al.
    Linkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Sweden..
    Huang, Yuqing
    Linkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Sweden..
    Visser, Dennis
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Anand, Srinivasan
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Buyanova, Irina A.
    Linkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Sweden..
    Chen, Weimin M.
    Linkoping Univ, Dept Phys Chem & Biol, SE-58183 Linkoping, Sweden..
    Room-temperature polarized spin-photon interface based on a semiconductor nanodisk-in-nanopillar structure driven by few defects2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3575Article in journal (Refereed)
    Abstract [en]

    Owing to their superior optical properties, semiconductor nanopillars/nanowires in one-dimensional (1D) geometry are building blocks for nano-photonics. They also hold potential for efficient polarized spin-light conversion in future spin nano-photonics. Unfortunately, spin generation in 1D systems so far remains inefficient at room temperature. Here we propose an approach that can significantly enhance the radiative efficiency of the electrons with the desired spin while suppressing that with the unwanted spin, which simultaneously ensures strong spin and light polarization. We demonstrate high optical polarization of 20%, inferring high electron spin polarization up to 60% at room temperature in a 1D system based on a GaNAs nanodisk-in-GaAs nanopillar structure, facilitated by spin-dependent recombination via merely 2-3 defects in each nanodisk. Our approach points to a promising direction for realization of an interface for efficient spin-photon quantum information transfer at room temperature-a key element for future spin-photonic applications.

  • 18. Cherifi-Hertel, S.
    et al.
    Bulou, H.
    Hertel, R.
    Taupier, G.
    Dorkenoo, K. D. H.
    Andreas, C.
    Guyonnet, J.
    Gaponenko, I.
    Gallo, Katia
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Electronics and Quantum Optics, QEO.
    Paruch, P.
    Non-Ising and chiral ferroelectric domain walls revealed by nonlinear optical microscopy2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15768Article in journal (Refereed)
    Abstract [en]

    The properties of ferroelectric domain walls can significantly differ from those of their parent material. Elucidating their internal structure is essential for the design of advanced devices exploiting nanoscale ferroicity and such localized functional properties. Here, we probe the internal structure of 180° ferroelectric domain walls in lead zirconate titanate (PZT) thin films and lithium tantalate bulk crystals by means of second-harmonic generation microscopy. In both systems, we detect a pronounced second-harmonic signal at the walls. Local polarimetry analysis of this signal combined with numerical modelling reveals the existence of a planar polarization within the walls, with Néel and Bloch-like configurations in PZT and lithium tantalate, respectively. Moreover, we find domain wall chirality reversal at line defects crossing lithium tantalate crystals. Our results demonstrate a clear deviation from the ideal Ising configuration that is traditionally expected in uniaxial ferroelectrics, corroborating recent theoretical predictions of a more complex, often chiral structure.

  • 19.
    Chung, Sunjae
    et al.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. Univ Gothenburg, Sweden.
    Eklund, Anders
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Iacocca, Ezio
    Mohseni, Seyed Majid
    Sani, Sohrab R.
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics.
    Bookman, Lake
    Hoefer, Mark A.
    Dumas, Randy K.
    Åkerman, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics. Univ Gothenburg, Sweden.
    Magnetic droplet nucleation boundary in orthogonal spin-torque nano-oscillators2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11209Article in journal (Refereed)
    Abstract [en]

    Static and dynamic magnetic solitons play a critical role in applied nanomagnetism. Magnetic droplets, a type of non-topological dissipative soliton, can be nucleated and sustained in nanocontact spin-torque oscillators with perpendicular magnetic anisotropy free layers. Here, we perform a detailed experimental determination of the full droplet nucleation boundary in the current-field plane for a wide range of nanocontact sizes and demonstrate its excellent agreement with an analytical expression originating from a stability analysis. Our results reconcile recent contradicting reports of the field dependence of the droplet nucleation. Furthermore, our analytical model both highlights the relation between the fixed layer material and the droplet nucleation current magnitude, and provides an accurate method to experimentally determine the spin transfer torque asymmetry of each device.

  • 20. Coucheron, David A.
    et al.
    Fokine, Michael
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Patil, Nilesh
    Breiby, Dag Werner
    Buset, Ole Tore
    Healy, Noel
    Peacock, Anna C.
    Hawkins, Thomas
    Jones, Max
    Ballato, John
    Gibson, Ursula J.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Laser recrystallization and inscription of compositional microstructures in crystalline SiGe-core fibres2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 13265Article in journal (Refereed)
    Abstract [en]

    Glass fibres with silicon cores have emerged as a versatile platform for all-optical processing, sensing and microscale optoelectronic devices. Using SiGe in the core extends the accessible wavelength range and potential optical functionality because the bandgap and optical properties can be tuned by changing the composition. However, silicon and germanium segregate unevenly during non-equilibrium solidification, presenting new fabrication challenges, and requiring detailed studies of the alloy crystallization dynamics in the fibre geometry. We report the fabrication of SiGe-core optical fibres, and the use of CO2 laser irradiation to heat the glass cladding and recrystallize the core, improving optical transmission. We observe the ramifications of the classic models of solidification at the microscale, and demonstrate suppression of constitutional undercooling at high solidification velocities. Tailoring the recrystallization conditions allows formation of long single crystals with uniform composition, as well as fabrication of compositional microstructures, such as gratings, within the fibre core.

  • 21. Das, Tanmoy
    et al.
    Balatsky, Alexander V.
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Engineering three-dimensional topological insulators in Rashba-type spin-orbit coupled heterostructures2013In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, p. 1972-Article in journal (Refereed)
    Abstract [en]

    Topological insulators represent a new class of quantum phase defined by invariant symmetries and spin-orbit coupling that guarantees metallic Dirac excitations at its surface. The discoveries of these states have sparked the hope of realizing non-trivial excitations and novel effects such as a magnetoelectric effect and topological Majorana excitations. Here we develop a theoretical formalism to show that a three-dimensional topological insulator can be designed artificially via stacking bilayers of two-dimensional Fermi gases with opposite Rashba-type spin-orbit coupling on adjacent layers, and with interlayer quantum tunneling. We demonstrate that in the stack of bilayers grown along a (001)-direction, a non-trivial topological phase transition occurs above a critical number of Rashba bilayers. In the topological phase, we find the formation of a single spin-polarized Dirac cone at the G-point. This approach offers an accessible way to design artificial topological insulators in a set up that takes full advantage of the atomic layer deposition approach. This design principle is tunable and also allows us to bypass limitations imposed by bulk crystal geometry.

  • 22.
    Dellantonio, Luca
    et al.
    Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark.;Univ Copenhagen, Niels Bohr Inst, Ctr Hybrid Quantum Networks Hy Q, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Kyriienko, Oleksandr
    KTH, Centres, Nordic Institute for Theoretical Physics NORDITA. Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Marquardt, Florian
    Univ Erlangen Nurnberg, Inst Theoret Phys, Staudstr 7, D-91058 Erlangen, Germany.;Max Planck Inst Sci Light, Gunther Scharowsky Str 1, D-91058 Erlangen, Germany..
    Sorensen, Anders S.
    Univ Copenhagen, Niels Bohr Inst, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark.;Univ Copenhagen, Niels Bohr Inst, Ctr Hybrid Quantum Networks Hy Q, Blegdamsvej 17, DK-2100 Copenhagen O, Denmark..
    Quantum nondemolition measurement of mechanical motion quanta2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3621Article in journal (Refereed)
    Abstract [en]

    The fields of optomechanics and electromechanics have facilitated numerous advances in the areas of precision measurement and sensing, ultimately driving the studies of mechanical systems into the quantum regime. To date, however, the quantization of the mechanical motion and the associated quantum jumps between phonon states remains elusive. For optomechanical systems, the coupling to the environment was shown to make the detection of the mechanical mode occupation difficult, typically requiring the single-photon strong coupling regime. Here, we propose and analyse an electromechanical setup, which allows us to overcome this limitation and resolve the energy levels of a mechanical oscillator. We found that the heating of the membrane, caused by the interaction with the environment and unwanted couplings, can be suppressed for carefully designed electromechanical systems. The results suggest that phonon number measurement is within reach for modern electromechanical setups.

  • 23.
    Dubois, Valentin J.
    et al.
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Raja, Shyamprasad Natarajan
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Gehring, Pascal
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    Caneva, Sabina
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    van der Zant, Herre S. J.
    Delft Univ Technol, Kavli Inst Nanosci, Lorentzweg 1, NL-2628 CJ Delft, Netherlands..
    Niklaus, Frank
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems.
    Stemme, Göran
    KTH, School of Electrical Engineering and Computer Science (EECS), Micro and Nanosystems. KTH Royal Inst Technol, Sch Elect Engn & Comp Sci EECS, Dept Micro & Nanosyst MST, SE-10044 Stockholm, Sweden..
    Massively parallel fabrication of crack-defined gold break junctions featuring sub-3 nm gaps for molecular devices2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3433Article in journal (Refereed)
    Abstract [en]

    Break junctions provide tip-shaped contact electrodes that are fundamental components of nano and molecular electronics. However, the fabrication of break junctions remains notoriously time-consuming and difficult to parallelize. Here we demonstrate true parallel fabrication of gold break junctions featuring sub-3 nm gaps on the wafer-scale, by relying on a novel self-breaking mechanism based on controlled crack formation in notched bridge structures. We achieve fabrication densities as high as 7 million junctions per cm(2), with fabrication yields of around 7% for obtaining crack-defined break junctions with sub-3 nm gaps of fixed gap width that exhibit electron tunneling. We also form molecular junctions using dithiol-terminated oligo(phenylene ethynylene) (OPE3) to demonstrate the feasibility of our approach for electrical probing of molecules down to liquid helium temperatures. Our technology opens a whole new range of experimental opportunities for nano and molecular electronics applications, by enabling very large-scale fabrication of solid-state break junctions.

  • 24.
    Edfors, Fredrik
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Andreas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Linderbäck, Klas
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Maddalo, Gianluca
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Azimi, Alireza
    Karolinska Inst, Karolinska Univ Hosp, Dept Oncol Pathol, SE-17177 Stockholm, Sweden..
    Sivertsson, Åsa
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Tegel, Hanna
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Hober, Sophia
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Al-Khalili Szigyarto, Cristina
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fagerberg, Linn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    von Feilitzen, Kalle
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Oksvold, Per
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Lindskog, Cecilia
    Uppsala Univ, Dept Immunol Genet & Pathol, SE-75185 Uppsala, Sweden..
    Forsström, Björn
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Uhlén, Mathias
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science. KTH, Centres, Science for Life Laboratory, SciLifeLab. Biosustainabil, DK-2970 Horsholm, Denmark..
    Enhanced validation of antibodies for research applications2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4130Article in journal (Refereed)
    Abstract [en]

    There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.

  • 25.
    Elshaari, Ali W.
    et al.
    KTH, School of Electrical Engineering (EES).
    Zadeh, Iman Esmaeil
    Fognini, Andreas
    Reimer, Michael E.
    Dalacu, Dan
    Poole, Philip J.
    Zwiller, Val
    KTH, School of Engineering Sciences (SCI), Applied Physics. KTH, School of Electrical Engineering (EES).
    Jöns, Klaus D.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Quantum Nano Photonics.
    On-chip single photon filtering and multiplexing in hybrid quantum photonic circuits2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 379Article in journal (Refereed)
    Abstract [en]

    Quantum light plays a pivotal role in modern science and future photonic applications. Since the advent of integrated quantum nanophotonics different material platforms based on III-V nanostructures-, colour centers-, and nonlinear waveguides as on-chip light sources have been investigated. Each platform has unique advantages and limitations; however, all implementations face major challenges with filtering of individual quantum states, scalable integration, deterministic multiplexing of selected quantum emitters, and on-chip excitation suppression. Here we overcome all of these challenges with a hybrid and scalable approach, where single III-V quantum emitters are positioned and deterministically integrated in a complementary metal-oxide-semiconductor-compatible photonic circuit. We demonstrate reconfigurable on-chip single-photon filtering and wavelength division multiplexing with a foot print one million times smaller than similar table-top approaches, while offering excitation suppression of more than 95 dB and efficient routing of single photons over a bandwidth of 40 nm. Our work marks an important step to harvest quantum optical technologies' full potential.

  • 26.
    Etcheverry, Sebastian
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Faridi, Muhammad Asim
    KTH. mafaridi@kth.se.
    Ramachandraiah, Harisha
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Margulis, Walter
    Laurell, Fredrik
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Russom, Aman
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology.
    Optical Fiber inertial focusing based micro FlowcytometerIn: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed)
    Abstract [en]

    Flow cytometry is a powerful method for analysis of cells and particles. Fueled by the need for point of care diagnostic applications, a significant effort has been made to miniaturize flow cytometry. However, despite recent advances, current microflow cytometers remain less versatile and much slower than their large-scale counterparts. Here, we present a portable all-silica optofluidic device that integrates particle focusing in flow through cylindrical silica capillaries and light delivery in optical fibers to simultaneously measure fluorescence and scattering from cells and particles at a rate of 2500 particles/s – a throughput comparable to conventional cytometers. Precise 3D cell focusing and ordering is accomplished using extended elasto-inertial focusing (EEF), a key enabler for eliminating the sheath fluid commonly employed in flow cytometry with maintained high throughput. We demonstrate simultaneously two-color fluorescence and scattering measurement of different sized particles and cells. This robust and low-cost optofluidic device, assembled without the need of clean-room facilities, is ideal suited for point of care applications.

  • 27.
    Fan, Ke
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Chen, Hong
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Ji, Yongfei
    Huang, Hui
    Claesson, Per Martin
    Daniel, Quentin
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Philippe, Bertrand
    Rensmo, Hakan
    Li, Fusheng
    Luo, Yi
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Nickel-vanadium monolayer double hydroxide for efficient electrochemical water oxidation2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11981Article in journal (Refereed)
    Abstract [en]

    Highly active and low-cost electrocatalysts for water oxidation are required due to the demands on sustainable solar fuels; however, developing highly efficient catalysts to meet industrial requirements remains a challenge. Herein, we report a monolayer of nickel-vanadium-layered double hydroxide that shows a current density of 27 mA cm(-2) (57 mA cm(-2) after ohmic-drop correction) at an overpotential of 350 mV for water oxidation. Such performance is comparable to those of the best-performing nickel-iron-layered double hydroxides for water oxidation in alkaline media. Mechanistic studies indicate that the nickel-vanadium-layered double hydroxides can provide high intrinsic catalytic activity, mainly due to enhanced conductivity, facile electron transfer and abundant active sites. This work may expand the scope of cost-effective electrocatalysts for water splitting.

  • 28.
    Forchheimer, Daniel
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Forchheimer, Robert
    Linköping University.
    Haviland, David B.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Nanostructure Physics.
    Improving image contrast and material discrimination with nonlinear response in bimodal atomic force microscopy2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 6270Article in journal (Refereed)
    Abstract [en]

    Atomic force microscopy has recently been extented to bimodal operation, where increased image contrast is achieved through excitation and measurement of two cantilever eigenmodes. This enhanced material contrast is advantageous in analysis of complex heterogeneous materials with phase separation on the micro or nanometre scale. Here we show that much greater image contrast results from analysis of nonlinear response to the bimodal drive, at harmonics and mixing frequencies. The amplitude and phase of up to 17 frequencies are simultaneously measured in a single scan. Using a machine-learning algorithm we demonstrate almost threefold improvement in the ability to separate material components of a polymer blend when including this nonlinear response. Beyond the statistical analysis performed here, analysis of nonlinear response could be used to obtain quantitative material properties at high speeds and with enhanced resolution.

  • 29. Frye, M.
    et al.
    Taddei, A.
    Dierkes, C.
    Martinez-Corral, I.
    Fielden, Matthew
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Ortsäter, H.
    Kazenwadel, J.
    Calado, D. P.
    Ostergaard, P.
    Salminen, M.
    He, L.
    Harvey, N. L.
    Kiefer, F.
    Mäkinen, T.
    Matrix stiffness controls lymphatic vessel formation through regulation of a GATA2-dependent transcriptional program2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, article id 1511Article in journal (Refereed)
    Abstract [en]

    Tissue and vessel wall stiffening alters endothelial cell properties and contributes to vascular dysfunction. However, whether extracellular matrix (ECM) stiffness impacts vascular development is not known. Here we show that matrix stiffness controls lymphatic vascular morphogenesis. Atomic force microscopy measurements in mouse embryos reveal that venous lymphatic endothelial cell (LEC) progenitors experience a decrease in substrate stiffness upon migration out of the cardinal vein, which induces a GATA2-dependent transcriptional program required to form the first lymphatic vessels. Transcriptome analysis shows that LECs grown on a soft matrix exhibit increased GATA2 expression and a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including VEGFR3. Analyses of mouse models demonstrate a cell-autonomous function of GATA2 in regulating LEC responsiveness to VEGF-C and in controlling LEC migration and sprouting in vivo. Our study thus uncovers a mechanism by which ECM stiffness dictates the migratory behavior of LECs during early lymphatic development.

  • 30.
    Fuchs, Gabriel
    et al.
    Dept. of Physiology and Pharmacology, Karolinska Institutet ; Department of Cardiology, Sundsvall’s Hospital.
    Berg, Niclas
    KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics.
    Broman, Mikael
    Dept. of Physiology and Pharmacology, Karolinska Institutet ; ECMO Centre Karolinska, Pediatric Perioperative Medicine and Intensive Care, Karolinska University Hospital.
    Prahl Wittberg, Lisa
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics, Fluid Physics. KTH, School of Engineering Sciences (SCI), Mechanics, Biomechanics.
    Modeling sensitivity and uncertainties in platelet activation models applied on centrifugal pumps for extracorporeal life supportIn: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed)
  • 31.
    Gandini, Rosaria
    et al.
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Reichenbach, Tom
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Tan, Tien-Chye
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Divne, Christina
    KTH, School of Biotechnology (BIO), Industrial Biotechnology.
    Structural basis for dolichylphosphate mannose biosynthesis2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 120Article in journal (Refereed)
    Abstract [en]

    Protein glycosylation is a critical protein modification. In biogenic membranes of eukaryotes and archaea, these reactions require activated mannose in the form of the lipid conjugate dolichylphosphate mannose (Dol-P-Man). The membrane protein dolichylphosphate mannose synthase (DPMS) catalyzes the reaction whereby mannose is transferred from GDP-mannose to the dolichol carrier Dol-P, to yield Dol-P-Man. Failure to produce or utilize Dol-P-Man compromises organism viability, and in humans, several mutations in the human dpm1 gene lead to congenital disorders of glycosylation (CDG). Here, we report three high-resolution crystal structures of archaeal DPMS from Pyrococcus furiosus, in complex with nucleotide, donor, and glycolipid product. The structures offer snapshots along the catalytic cycle, and reveal how lipid binding couples to movements of interface helices, metal binding, and acceptor loop dynamics to control critical events leading to Dol-P-Man synthesis. The structures also rationalize the loss of dolichylphosphate mannose synthase function in dpm1-associated CDG.The generation of glycolipid dolichylphosphate mannose (Dol-P-Man) is a critical step for protein glycosylation and GPI anchor synthesis. Here the authors report the structure of dolichylphosphate mannose synthase in complex with bound nucleotide and donor to provide insight into the mechanism of Dol-P-Man synthesis.

  • 32.
    Horio, M.
    et al.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Matt, C. E.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland.;Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland.;Harvard Univ, Dept Phys, Cambridge, MA 02138 USA..
    Kramer, K.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Sutter, D.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Cook, A. M.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Sassa, Y.
    Uppsala Univ, Dept Phys & Astron, SE-75121 Uppsala, Sweden..
    Hauser, K.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Månsson, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Plumb, N. C.
    Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Shi, M.
    Paul Scherrer Inst, Swiss Light Source, CH-5232 Villigen, Switzerland..
    Lipscombe, O. J.
    Univ Bristol, HH Wills Phys Lab, Bristol BS8 1TL, Avon, England..
    Hayden, S. M.
    Univ Bristol, HH Wills Phys Lab, Bristol BS8 1TL, Avon, England..
    Neupert, T.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Chang, J.
    Univ Zurich, Phys Inst, Winterthurerstr 190, CH-8057 Zurich, Switzerland..
    Two-dimensional type-II Dirac fermions in layered oxides2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3252Article in journal (Refereed)
    Abstract [en]

    Relativistic massless Dirac fermions can be probed with high-energy physics experiments, but appear also as low-energy quasi-particle excitations in electronic band structures. In condensed matter systems, their massless nature can be protected by crystal symmetries. Classification of such symmetry-protected relativistic band degeneracies has been fruitful, although many of the predicted quasi-particles still await their experimental discovery. Here we reveal, using angle-resolved photoemission spectroscopy, the existence of two-dimensional type-II Dirac fermions in the high-temperature superconductor La1.77Sr0.23CuO4. The Dirac point, constituting the crossing of d(x2-y2) and d(z2) bands, is found approximately one electronvolt below the Fermi level (E-F) and is protected by mirror symmetry. If spin-orbit coupling is considered, the Dirac point degeneracy is lifted and the bands acquire a topologically non-trivial character. In certain nickelate systems, band structure calculations suggest that the same type-II Dirac fermions can be realised near EF.

  • 33.
    Houshangh, A.
    et al.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, S-16440 Kista, Sweden..
    Khymyn, R.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Fulara, H.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Gangwar, A.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Haidar, M.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Etesami, S. R.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Ferreira, R.
    Int Iberian Nanotechnol Lab, P-4715330 Braga, Portugal..
    Freitas, P. P.
    Int Iberian Nanotechnol Lab, P-4715330 Braga, Portugal..
    Dvornik, M.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Dumas, R. K.
    Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden..
    Åkerman, Johan
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Engineering Material Physics. Univ Gothenburg, Phys Dept, S-41296 Gothenburg, Sweden.;NanOsc AB, S-16440 Kista, Sweden..
    Spin transfer torque driven higher-order propagating spin waves in nano-contact magnetic tunnel junctions2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4374Article in journal (Refereed)
    Abstract [en]

    Short wavelength exchange-dominated propagating spin waves will enable magnonic devices to operate at higher frequencies and higher data transmission rates. While giant magnetoresistance (GMR)-based magnetic nanocontacts are efficient injectors of propagating spin waves, the generated wavelengths are 2.6 times the nano-contact diameter, and the electrical signal strength remains too weak for applications. Here we demonstrate nano-contact-based spin wave generation in magnetic tunnel junctions and observe large-frequency steps consistent with the hitherto ignored possibility of second-and third-order propagating spin waves with wavelengths of 120 and 74 nm, i.e., much smaller than the 150-nm nanocontact. Mutual synchronization is also observed on all three propagating modes. These higher-order propagating spin waves will enable magnonic devices to operate at much higher frequencies and greatly increase their transmission rates and spin wave propagating lengths, both proportional to the much higher group velocity.

  • 34. Huang, M.
    et al.
    Bao, J.
    Hallström, Björn M.
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Petranovic, D.
    Nielsen, Jens
    KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Efficient protein production by yeast requires global tuning of metabolism2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, no 1, article id 1131Article in journal (Refereed)
    Abstract [en]

    The biotech industry relies on cell factories for production of pharmaceutical proteins, of which several are among the top-selling medicines. There is, therefore, considerable interest in improving the efficiency of protein production by cell factories. Protein secretion involves numerous intracellular processes with many underlying mechanisms still remaining unclear. Here, we use RNA-seq to study the genome-wide transcriptional response to protein secretion in mutant yeast strains. We find that many cellular processes have to be attuned to support efficient protein secretion. In particular, altered energy metabolism resulting in reduced respiration and increased fermentation, as well as balancing of amino-acid biosynthesis and reduced thiamine biosynthesis seem to be particularly important. We confirm our findings by inverse engineering and physiological characterization and show that by tuning metabolism cells are able to efficiently secrete recombinant proteins. Our findings provide increased understanding of which cellular regulations and pathways are associated with efficient protein secretion.

  • 35.
    Huang, Shuo
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Huang, He
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Science and Technology on Surface Physics and Chemistry Laboratory, Mianyang, 621900, PR China.
    Li, Wei
    Department of Physics and Astronomy, Division of Materials Theory, Uppsala University, SE-75120, Uppsala, Sweden.
    Kim, Dongyoo
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics. Department of Physics, Pukyung National University, Busan, 608-737, Republic of Korea.
    Lu, Song
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Li, Xiaoqing
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Holmström, E.
    Kwon, S. K.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Twinning in metastable high-entropy alloys2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, article id 2381Article in journal (Refereed)
    Abstract [en]

    Twinning is a fundamental mechanism behind the simultaneous increase of strength and ductility in medium- and high-entropy alloys, but its operation is not yet well understood, which limits their exploitation. Since many high-entropy alloys showing outstanding mechanical properties are actually thermodynamically unstable at ambient and cryogenic conditions, the observed twinning challenges the existing phenomenological and theoretical plasticity models. Here, we adopt a transparent approach based on effective energy barriers in combination with first-principle calculations to shed light on the origin of twinning in high-entropy alloys. We demonstrate that twinning can be the primary deformation mode in metastable face-centered cubic alloys with a fraction that surpasses the previously established upper limit. The present advance in plasticity of metals opens opportunities for tailoring the mechanical response in engineering materials by optimizing metastable twinning in high-entropy alloys. 

  • 36.
    Håkansson, Karl
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Fall, Andreas
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Fibre Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Yu, Sun
    DESY, Hamburg Germany.
    Krywka, Christina
    Institute of experimental and applied physics. Kiel Germany.
    Roth, Stephan
    DESY, Hamburg Germany.
    Santoro, Gonzalo
    DESY, Hamburg Germany.
    Kvick, Mathias
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Prahl Wittberg, Lisa
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Wågberg, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology, Fibre Technology. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center.
    Söderberg, Daniel
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Chemical Science and Engineering (CHE), Centres, Wallenberg Wood Science Center. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. Innventia AB, Stockholm Sweden.
    Hydrodynamic alignment and assembly of nanofibrils resulting in strong cellulose filaments2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 4018-Article in journal (Refereed)
    Abstract [en]

    Cellulose nanofibrils can be obtained from trees and have considerable potential as a building block for biobased materials. In order to achieve good properties of these materials, the nanostructure must be controlled. Here we present a process combining hydrodynamic alignment with a dispersion-gel transition that produces homogeneous and smooth filaments from a low-concentration dispersion of cellulose nanofibrils in water. The preferential fibril orientation along the filament direction can be controlled by the process parameters. The specific ultimate strength is considerably higher than previously reported filaments made of cellulose nanofibrils. The strength is even in line with the strongest cellulose pulp fibres extracted from wood with the same degree of fibril alignment. Successful nanoscale alignment before gelation demands a proper separation of the timescales involved. Somewhat surprisingly, the device must not be too small if this is to be achieved.

  • 37. Jin, Chiming
    et al.
    Li, Zi-An
    Kovacs, Andras
    Caron, Jan
    Zheng, Fengshan
    Rybakov, Filipp N.
    KTH, School of Engineering Sciences (SCI), Physics, Statistical Physics. Ural federal university, Russian Federation.
    Kiselev, Nikolai S.
    Du, Haifeng
    Bluegel, Stefan
    Tian, Mingliang
    Zhang, Yuheng
    Farle, Michael
    Dunin-Borkowski, Rafal E.
    Control of morphology and formation of highly geometrically confined magnetic skyrmions2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15569Article in journal (Refereed)
    Abstract [en]

    The ability to controllably manipulate magnetic skyrmions, small magnetic whirls with particle-like properties, in nanostructured elements is a prerequisite for incorporating them into spintronic devices. Here, we use state-of-the-art electron holographic imaging to directly visualize the morphology and nucleation of magnetic skyrmions in a wedge-shaped FeGe nanostripe that has a width in the range of 45-150 nm. We find that geometrically-confined skyrmions are able to adopt a wide range of sizes and ellipticities in a nanostripe that are absent in both thin films and bulk materials and can be created from a helical magnetic state with a distorted edge twist in a simple and efficient manner. We perform a theoretical analysis based on a three-dimensional general model of isotropic chiral magnets to confirm our experimental results. The flexibility and ease of formation of geometrically confined magnetic skyrmions may help to optimize the design of skyrmion-based memory devices.

  • 38.
    Kazemzadeh, Amin
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Eriksson, Anders
    KTH, School of Engineering Sciences (SCI), Mechanics.
    Madou, Marc
    Univ Calif Irvine, Dept Mech & Aerosp Engn, Irvine, CA 92697 USA..
    Russom, Aman
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Nano Biotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    A micro-dispenser for long-term storage and controlled release of liquids2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, no 1, article id 189Article in journal (Refereed)
    Abstract [en]

    The success of lab-on-a-chip systems may depend on a low-cost device that incorporates on-chip storage and fluidic operations. To date many different methods have been developed that cope separately with on-chip storage and fluidic operations e. g., hydrophobic and capillary valves pneumatic pumping and blister storage packages. The blister packages seem difficult to miniaturize and none of the existing liquid handling techniques despite their variety are capable of proportional repeatable dispensing. We report here on an inexpensive robust and scalable micro-dispenser that incorporates long-term storage and aliquoting of reagents on different microfluidics platforms. It provides long-term shelf-life for different liquids enables precise dispensing on lab-on-a-disc platforms and less accurate but proportional dispensing when operated by finger pressure. Based on this technology we introduce a method for automation of blood plasma separation and multi-step bioassay procedures. This micro-dispenser intends to facilitate affordable portable diagnostic devices and accelerate the commercialization of lab-on-a-chip devices.

  • 39. Kronqvist, Nina
    et al.
    Otikovs, Martins
    Chmyrov, Volodymyr
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Chen, Gefei
    Andersson, Marlene
    Nordling, Kerstin
    Landreh, Michael
    Sarr, Médoune
    Jörnvall, Hans
    Wennmalm, Stefan
    Widengren, Jerker
    KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
    Meng, Qing
    Rising, Anna
    Otzen, Daniel Erik Rik
    Knight, Stefan
    Jaudzems, Kristaps
    Johansson, Jan Ove
    Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 3254-Article in journal (Refereed)
    Abstract [en]

    The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.

  • 40. Kronqvist, Nina
    et al.
    Sarr, Medoune
    Lindqvist, Anton
    Nordling, Kerstin
    Otikovs, Martins
    Venturi, Luca
    Pioselli, Barbara
    Purhonen, Pasi
    Landreh, Michael
    Biverstal, Henrik
    Toleikis, Zigmantas
    Sjöberg, Lisa
    Robinson, Carol V.
    Pelizzi, Nicola
    Jornvall, Hans
    Hebert, Hans
    KTH, School of Technology and Health (STH), Basic Science and Biomedicine, Structural Biotechnology. Karolinska Institutet, Sverige.
    Jaudzems, Kristaps
    Curstedt, Tore
    Rising, Anna
    Johansson, Jan
    Efficient protein production inspired by how spiders make silk2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 15504Article in journal (Refereed)
    Abstract [en]

    Membrane proteins are targets of most available pharmaceuticals, but they are difficult to produce recombinantly, like many other aggregation-prone proteins. Spiders can produce silk proteins at huge concentrations by sequestering their aggregation-prone regions in micellar structures, where the very soluble N-terminal domain (NT) forms the shell. We hypothesize that fusion to NT could similarly solubilize non-spidroin proteins, and design a charge-reversed mutant (NT star) that is pH insensitive, stabilized and hypersoluble compared to wildtype NT. NT star-transmembrane protein fusions yield up to eight times more of soluble protein in Escherichia coli than fusions with several conventional tags. NT star enables transmembrane peptide purification to homogeneity without chromatography and manufacture of low-cost synthetic lung surfactant that works in an animal model of respiratory disease. NT star also allows efficient expression and purification of non-transmembrane proteins, which are otherwise refractory to recombinant production, and offers a new tool for reluctant proteins in general.

  • 41.
    Lacis, Ugis
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Brosse, Nicolas
    KTH, School of Engineering Sciences (SCI), Solid Mechanics (Dept.). KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Ingremeau, F.
    Mazzino, A.
    Lundell, Fredrik
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Kellay, H.
    Bagheri, Shervin
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Passive appendages generate drift through symmetry breaking2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 5310-Article in journal (Refereed)
    Abstract [en]

    Plants and animals use plumes, barbs, tails, feathers, hairs and fins to aid locomotion. Many of these appendages are not actively controlled, instead they have to interact passively with the surrounding fluid to generate motion. Here, we use theory, experiments and numerical simulations to show that an object with a protrusion in a separated flow drifts sideways by exploiting a symmetry-breaking instability similar to the instability of an inverted pendulum. Our model explains why the straight position of an appendage in a fluid flow is unstable and how it stabilizes either to the left or right of the incoming flow direction. It is plausible that organisms with appendages in a separated flow use this newly discovered mechanism for locomotion; examples include the drift of plumed seeds without wind and the passive reorientation of motile animals.

  • 42. Li, Y.
    et al.
    Zakharov, D.
    Zhao, S.
    Tappero, R.
    Jung, U.
    Elsen, A.
    Baumann, Ph.
    Nuzzo, Ralph G.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Surface and Corrosion Science.
    Stach, E. A.
    Frenkel, A. I.
    Complex structural dynamics of nanocatalysts revealed in Operando conditions by correlated imaging and spectroscopy probes2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7583Article in journal (Refereed)
    Abstract [en]

    Understanding how heterogeneous catalysts change size, shape and structure during chemical reactions is limited by the paucity of methods for studying catalytic ensembles in working state, that is, in operando conditions. Here by a correlated use of synchrotron X-ray absorption spectroscopy and scanning transmission electron microscopy in operando conditions, we quantitatively describe the complex structural dynamics of supported Pt catalysts exhibited during an exemplary catalytic reaction-ethylene hydrogenation. This work exploits a microfabricated catalytic reactor compatible with both probes. The results demonstrate dynamic transformations of the ensemble of Pt clusters that spans a broad size range throughout changing reaction conditions. This method is generalizable to quantitative operando studies of complex systems using a wide variety of X-ray and electron-based experimental probes.

  • 43. Lundqvist, Mikael
    et al.
    Herman, Pawel
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Warden, Melissa R.
    Brincat, Scott L.
    Miller, Earl K.
    Gamma and beta bursts during working memory readout suggest roles in its volitional control2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 394Article in journal (Refereed)
    Abstract [en]

    Working memory (WM) activity is not as stationary or sustained as previously thought. There are brief bursts of gamma (similar to 50-120 Hz) and beta (similar to 20-35 Hz) oscillations, the former linked to stimulus information in spiking. We examined these dynamics in relation to readout and control mechanisms of WM. Monkeys held sequences of two objects in WM to match to subsequent sequences. Changes in beta and gamma bursting suggested their distinct roles. In anticipation of having to use an object for the match decision, there was an increase in gamma and spiking information about that object and reduced beta bursting. This readout signal was only seen before relevant test objects, and was related to premotor activity. When the objects were no longer needed, beta increased and gamma decreased together with object spiking information. Deviations from these dynamics predicted behavioral errors. Thus, beta could regulate gamma and the information in WM.

  • 44. Maccaferri, Nicolo
    et al.
    Gregorczyk, Keith E.
    de Oliveira, Thales V. A. G.
    Kataja, Mikko
    van Dijken, Sebastiaan
    Pirzadeh, Zhaleh
    Dmitriev, Alexandre
    Akerman, Johan
    KTH, School of Information and Communication Technology (ICT), Materials- and Nano Physics, Material Physics, MF. Department of Physics, University of Gothenburg, Sweden .
    Knez, Mato
    Vavassori, Paolo
    Ultrasensitive and label-free molecular-level detection enabled by light phase control in magnetoplasmonic nanoantennas2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 6150Article in journal (Refereed)
    Abstract [en]

    Systems allowing label-free molecular detection are expected to have enormous impact on biochemical sciences. Research focuses on materials and technologies based on exploiting localized surface plasmon resonances in metallic nanostructures. The reason for this focused attention is their suitability for single-molecule sensing, arising from intrinsically nanoscopic sensing volume and the high sensitivity to the local environment. Here we propose an alternative route, which enables radically improved sensitivity compared with recently reported plasmon-based sensors. Such high sensitivity is achieved by exploiting the control of the phase of light in magnetoplasmonic nanoantennas. We demonstrate a manifold improvement of refractometric sensing figure-of-merit. Most remarkably, we show a raw surface sensitivity (that is, without applying fitting procedures) of two orders of magnitude higher than the current values reported for nanoplasmonic sensors. Such sensitivity corresponds to a mass of similar to 0.8 ag per nanoantenna of polyamide-6.6 (n = 1.51), which is representative for a large variety of polymers, peptides and proteins.

  • 45. Mardinoglu, Adil
    et al.
    Ågren, Rasmus
    Kampf, Caroline
    Asplund, Anna
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Nielsen, Jens
    KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 3083-Article in journal (Refereed)
    Abstract [en]

    Several liver disorders result from perturbations in the metabolism of hepatocytes, and their underlying mechanisms can be outlined through the use of genome-scale metabolic models (GEMs). Here we reconstruct a consensus GEM for hepatocytes, which we call iHepatocytes2322, that extends previous models by including an extensive description of lipid metabolism. We build iHepatocytes2322 using Human Metabolic Reaction 2.0 database and proteomics data in Human Protein Atlas, which experimentally validates the incorporated reactions. The reconstruction process enables improved annotation of the proteomics data using the network centric view of iHepatocytes2322. We then use iHepatocytes2322 to analyse transcriptomics data obtained from patients with non-alcoholic fatty liver disease. We show that blood concentrations of chondroitin and heparan sulphates are suitable for diagnosing non-alcoholic steatohepatitis and for the staging of non-alcoholic fatty liver disease. Furthermore, we observe serine deficiency in patients with NASH and identify PSPH, SHMT1 and BCAT1 as potential therapeutic targets for the treatment of non-alcoholic steatohepatitis.

  • 46.
    Marino, Raffaele
    et al.
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST). KTH, Centres, Nordic Institute for Theoretical Physics NORDITA.
    Parisi, G.
    Ricci-Tersenghi, F.
    The backtracking survey propagation algorithm for solving random K-SAT problems2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 12996Article in journal (Refereed)
    Abstract [en]

    Discrete combinatorial optimization has a central role in many scientific disciplines, however, for hard problems we lack linear time algorithms that would allow us to solve very large instances. Moreover, it is still unclear what are the key features that make a discrete combinatorial optimization problem hard to solve. Here we study random K-satisfiability problems with K=3,4, which are known to be very hard close to the SAT-UNSAT threshold, where problems stop having solutions. We show that the backtracking survey propagation algorithm, in a time practically linear in the problem size, is able to find solutions very close to the threshold, in a region unreachable by any other algorithm. All solutions found have no frozen variables, thus supporting the conjecture that only unfrozen solutions can be found in linear time, and that a problem becomes impossible to solve in linear time when all solutions contain frozen variables.

  • 47.
    Masullo, Luciano A.
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Boden, Andreas
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Pennacchietti, Francesca
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Coceano, Giovanna
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Ratz, Michael
    Karolinska Inst, Dept Cell & Mol Biol, S-17176 Stockholm, Sweden..
    Testa, Ilaria
    KTH, School of Engineering Sciences (SCI), Applied Physics.
    Enhanced photon collection enables four dimensional fluorescence nanoscopy of living systems2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 3281Article in journal (Refereed)
    Abstract [en]

    The theoretically unlimited spatial resolution of fluorescence nanoscopy often comes at the expense of time, contrast and increased dose of energy for recording. Here, we developed MoNaLISA, for Molecular Nanoscale Live Imaging with Sectioning Ability, a nanoscope capable of imaging structures at a scale of 45-65 nm within the entire cell volume at low light intensities (W-kW cm(-2)). Our approach, based on reversibly switchable fluorescent proteins, features three distinctly modulated illumination patterns crafted and combined to gain fluorescence ON-OFF switching cycles and image contrast. By maximizing the detected photon flux, MoNaLISA enables prolonged (40-50 frames) and large (50 x 50 mu m(2)) recordings at 0.3-1.3 Hz with enhanced optical sectioning ability. We demonstrate the general use of our approach by 4D imaging of organelles and fine structures in epithelial human cells, colonies of mouse embryonic stem cells, brain cells, and organotypic tissues.

  • 48. Matt, C. E.
    et al.
    Sutter, D.
    Cook, A. M.
    Sassa, Y.
    Månsson, Martin
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Tjernberg, Oscar
    KTH, School of Engineering Sciences (SCI), Applied Physics, Material Physics, MF.
    Das, L.
    Horio, M.
    Destraz, D.
    Fatuzzo, C. G.
    Hauser, K.
    Shi, M.
    Kobayashi, M.
    Strocov, V. N.
    Schmitt, T.
    Dudin, P.
    Hoesch, M.
    Pyon, S.
    Takayama, T.
    Takagi, H.
    Lipscombe, O. J.
    Hayden, S. M.
    Kurosawa, T.
    Momono, N.
    Oda, M.
    Neupert, T.
    Chang, J.
    Direct observation of orbital hybridisation in a cuprate superconductor2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 972Article in journal (Refereed)
    Abstract [en]

    The minimal ingredients to explain the essential physics of layered copper-oxide (cuprates) materials remains heavily debated. Effective low-energy single-band models of the copper-oxygen orbitals are widely used because there exists no strong experimental evidence supporting multi-band structures. Here, we report angle-resolved photoelectron spectroscopy experiments on La-based cuprates that provide direct observation of a two-band structure. This electronic structure, qualitatively consistent with density functional theory, is parametrised by a two-orbital (d(x2-y2) and d(z2)) tight-binding model. We quantify the orbital hybridisation which provides an explanation for the Fermi surface topology and the proximity of the van-Hove singularity to the Fermi level. Our analysis leads to a unification of electronic hopping parameters for single-layer cuprates and we conclude that hybridisation, restraining d-wave pairing, is an important optimisation element for superconductivity.

  • 49. Miron, Catalin
    et al.
    Miao, Quan
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Nicolas, Christophe
    Bozek, John D.
    Andralojc, Witold
    Patanen, Minna
    Simoes, Grazieli
    Travnikova, Oksana
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Gel'mukhanov, Faris
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Site-selective photoemission from delocalized valence shells induced by molecular rotation2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, p. 3816-Article in journal (Refereed)
    Abstract [en]

    Due to the generally delocalized nature of molecular valence orbitals, valence-shell spectroscopies do not usually allow to specifically target a selected atom in a molecule. However, in X-ray electron spectroscopy, the photoelectron momentum is large and the recoil angular momentum transferred to the molecule is larger when the photoelectron is ejected from a light atom compared with a heavy one. This confers an extreme sensitivity of the rotational excitation to the ionization site. Here we show that, indeed, the use of high-energy photons to photoionize valence-shell electrons of hydrogen chloride offers an unexpected way to decrypt the atomic composition of the molecular orbitals due to the rotational dependence of the photoionization profiles. The analysis of the site-specific rotational envelopes allows us to disentangle the effects of the two main mechanisms of rotational excitation, based on angular momentum exchange between the molecule and either the incoming photon or the emitted electron.

  • 50.
    Nyström, Gustav
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Marais, Andrew
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Karabulut, Erdem
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Wågberg, Lars
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Cui, Yi
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Hamedi, Mahiar
    Self-assembled three-dimensional and compressible interdigitated thin-film supercapacitors and batteries2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, p. 7259-Article in journal (Refereed)
    Abstract [en]

    Traditional thin-film energy-storage devices consist of stacked layers of active films on two-dimensional substrates and do not exploit the third dimension. Fully three-dimensional thin-film devices would allow energy storage in bulk materials with arbitrary form factors and with mechanical properties unique to bulk materials such as compressibility. Here we show three-dimensional energy-storage devices based on layer-by-layer self-assembly of interdigitated thin films on the surface of an open-cell aerogel substrate. We demonstrate a reversibly compressible three-dimensional supercapacitor with carbon nanotube electrodes and a three-dimensional hybrid battery with a copper hexacyanoferrate ion intercalating cathode and a carbon nanotube anode. The three-dimensional supercapacitor shows stable operation over 400 cycles with a capacitance of 25â €‰Fâ €‰g â '1 and is fully functional even at compressions up to 75%. Our results demonstrate that layer-by-layer self-assembly inside aerogels is a rapid, precise and scalable route for building high-surface-area 3D thin-film devices.

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