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  • 1.
    Acosta Navarro, J. C.
    et al.
    Stockholm University, Sweden .
    Smolander, S.
    University of Helsinki, Finland .
    Struthers, Hamish
    Linköping University, National Supercomputer Centre (NSC).
    Zorita, E.
    Institute for Coastal Research, Geesthacht, Germany.
    Ekman, A. M. L.
    Stockholm University, Sweden .
    Kaplan, J. O.
    Ecole Polytechnique Federal de Lausanne, Switzerland.
    Guenther, A.
    PNNL, Richland, WA USA .
    Arneth, A.
    Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany.
    Riipinen, I.
    Stockholm University, Sweden .
    Global emissions of terpenoid VOCs from terrestrial vegetation in the last millennium2014In: Journal of Geophysical Research - Atmospheres, ISSN 2169-897X, E-ISSN 2169-8996, Vol. 119, no 11, p. 6867-6885Article in journal (Refereed)
    Abstract [en]

    We investigated the millennial variability (1000 A.D.-2000 A.D.) of global biogenic volatile organic compound (BVOC) emissions by using two independent numerical models: The Model of Emissions of Gases and Aerosols from Nature (MEGAN), for isoprene, monoterpene, and sesquiterpene, and Lund-Potsdam-Jena-General Ecosystem Simulator (LPJ-GUESS), for isoprene and monoterpenes. We found the millennial trends of global isoprene emissions to be mostly affected by land cover and atmospheric carbon dioxide changes, whereas monoterpene and sesquiterpene emission trends were dominated by temperature change. Isoprene emissions declined substantially in regions with large and rapid land cover change. In addition, isoprene emission sensitivity to drought proved to have significant short-term global effects. By the end of the past millennium MEGAN isoprene emissions were 634 TgC yr-1 (13% and 19% less than during 1750-1850 and 1000-1200, respectively), and LPJ-GUESS emissions were 323 TgC yr-1(15% and 20% less than during 1750-1850 and 1000-1200, respectively). Monoterpene emissions were 89 TgC yr-1(10% and 6% higher than during 1750-1850 and 1000-1200, respectively) in MEGAN, and 24 TgC yr-1 (2% higher and 5% less than during 1750-1850 and 1000-1200, respectively) in LPJ-GUESS. MEGAN sesquiterpene emissions were 36 TgC yr-1(10% and 4% higher than during 1750-1850 and 1000-1200, respectively). Although both models capture similar emission trends, the magnitude of the emissions are different. This highlights the importance of building better constraints on VOC emissions from terrestrial vegetation.

  • 2.
    Acosta Navarro, J. C.
    et al.
    Stockholm University, Sweden.
    Varma, V.
    Stockholm University, Sweden.
    Riipinen, I.
    Stockholm University, Sweden.
    Seland, O.
    Norwegian Meteorol Institute, Norway.
    Kirkevag, A.
    Norwegian Meteorol Institute, Norway.
    Struthers, Hamish
    Linköping University, National Supercomputer Centre (NSC). Stockholm University, Sweden.
    Iversen, T.
    Norwegian Meteorol Institute, Norway.
    Hansson, H. -C.
    Stockholm University, Sweden; Stockholm University, Sweden.
    Ekman, A. M. L.
    Stockholm University, Sweden.
    Amplification of Arctic warming by past air pollution reductions in Europe2016In: Nature Geoscience, ISSN 1752-0894, E-ISSN 1752-0908, Vol. 9, no 4, p. 277-281Article in journal (Refereed)
    Abstract [en]

    The Arctic region is warming considerably faster than the rest of the globe(1), with important consequences for the ecosystems(2) and human exploration of the region(3). However, the reasons behind this Arctic amplification are not entirely clear(4). As a result of measures to enhance air quality, anthropogenic emissions of particulate matter and its precursors have drastically decreased in parts of the Northern Hemisphere over the past three decades(5). Here we present simulations with an Earth system model with comprehensive aerosol physics and chemistry that show that the sulfate aerosol reductions in Europe since 1980 can potentially explain a significant fraction of Arctic warming over that period. Specifically, the Arctic region receives an additional 0.3Wm(-2) of energy, and warms by 0.5 degrees C on annual average in simulations with declining European sulfur emissions in line with historical observations, compared with a model simulation with fixed European emissions at 1980 levels. Arctic warming is amplified mainly in fall and winter, but the warming is initiated in summer by an increase in incoming solar radiation as well as an enhanced poleward oceanic and atmospheric heat transport. The simulated summertime energy surplus reduces sea-ice cover, which leads to a transfer of heat from the Arctic Ocean to the atmosphere. We conclude that air quality regulations in the Northern Hemisphere, the ocean and atmospheric circulation, and Arctic climate are inherently linked.

  • 3.
    Engel, Philipp
    et al.
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
    Kwong, Waldan K.
    Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA; Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
    McFrederick, Quinn
    Department of Entomology, University of California, Riverside, California, USA.
    Anderson, Kirk E.
    USDA, Carl Hayden Bee Research Center, Tucson, Arizona, USA.
    Barribeau, Seth Michael
    Department of Biology, East Carolina University, Greenville, North Carolina, USA.
    Angus Chandler, James
    Department of Microbiology, California Academy of Sciences, San Francisco, California, USA.
    Cornman, R. Scott
    U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA.
    Dainat, Jacques
    Linköping University, National Supercomputer Centre (NSC). Department of Medical Biochemistry and Microbiology Uppsala University, Uppsala, Sweden.
    de Miranda, Joachim R.
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Doublet, Vincent
    Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
    Emery, Olivier
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
    Evans, Jay D.
    USDA, ARS Bee Research Laboratory, Beltsville, Maryland, USA.
    Farinelli, Laurent
    Fasteris SA, Switzerland.
    Flenniken, Michelle L.
    Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA.
    Granberg, Fredrik
    Department of Biomedical Sciences and Veterinary Public Health, Virology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Grasis, Juris A.
    Department of Biology, North Life Sciences, San Diego State University, San Diego, California, USA.
    Gauthier, Laurent
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland; Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.
    Hayer, Juliette
    Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden.
    Koch, Hauke
    Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA; Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom.
    Kocher, Sarah
    Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge , Massachusetts , USA.
    Martinson, Vincent G.
    Department of Biology, University of Rochester, Rochester, New York, USA.
    Moran, Nancy
    Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
    Munoz-Torres, Monica
    Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley , California , USA.
    Newton, Irene
    Department of Biology, Indiana University, Bloomington, Indiana, USA.
    Paxton, Robert J.
    Institute for Biology, Martin Luther University Halle-Wittenberg, Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
    Powell, Eli
    Department of Integrative Biology, University of Texas at Austin, Austin, Texas, USA.
    Sadd, Ben M.
    School of Biological Sciences, Illinois State University, Normal, Illinois, USA.
    Schmid-Hempel, Paul
    ETHZ Institut für Integrative Biologie, Zurich, Switzerland.
    Schmid-Hempel, Regula
    ETHZ Institut für Integrative Biologie, Zurich, Switzerland.
    Jin Song, Se
    University of Colorado at Boulder, Boulder, Colorado, USA.
    Schwarz, Ryan S.
    USDA, ARS Bee Research Laboratory, Beltsville, Maryland, USA.
    vanEngelsdorp, Dennis
    Department of Entomology, University of Maryland, College Park, Maryland, USA.
    Dainat, Benjamin
    Agroscope, Swiss Bee Research Centre, Bern, Switzerland; Bee Health Extension Service, Apiservice, Bern , Switzerland.
    The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions2016In: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 7, no 2, article id e02164-15Article, review/survey (Refereed)
    Abstract [en]

    As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the micro biome. The bee micro biome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee micro biome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

  • 4.
    Fallqvist, Amie
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Department of Science and Technology. Linköping University, Faculty of Science & Engineering.
    Olovsson, Weine
    Linköping University, National Supercomputer Centre (NSC). Linköping University, Faculty of Science & Engineering.
    Alling, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Max Planck Inst Eisenforsch GmbH, Germany.
    Palisaitis, Justinas
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Belov, M. P.
    Natl Univ Sci and Technol MISIS, Russia.
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Hultman, Lars
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Persson, Per O A
    Linköping University, Department of Physics, Chemistry and Biology, Thin Film Physics. Linköping University, Faculty of Science & Engineering.
    Resolving the debated atomic structure of the metastable cubic SiNx tissue phase in nanocomposites with TiN2018In: Physical Review Materials, ISSN 2475-9953, Vol. 2, no 9, article id 093608Article in journal (Refereed)
    Abstract [en]

    The TiN/SiNx nanocomposite and nanolaminate systems are the archetype for super if not ultrahard materials. Yet, the nature of the SiNx tissue phase is debated. Here, we show by atomically resolved electron microscopy methods that SiNx is epitaxially stabilized in a NaCl structure on the adjacent TiN(001) surfaces. Additionally, electron energy loss spectroscopy, supported by first-principles density functional theory calculations infer that SiNx hosts Si vacancies.

  • 5.
    Hartung, Kerstin
    et al.
    Stockholm Univ, Sweden; Swedish E Sci Res Ctr, Sweden.
    Svensson, Gunilla
    Stockholm Univ, Sweden; Swedish E Sci Res Ctr, Sweden.
    Struthers, Hamish
    Linköping University, National Supercomputer Centre (NSC).
    Deppenmeier, Anna-Lena
    Wageningen Univ, Netherlands; Royal Netherlands Meteorol Inst KNMI, Netherlands.
    Hazeleger, Wilco
    Wageningen Univ, Netherlands; Netherlands eSci Ctr, Netherlands.
    An EC-Earth coupled atmosphere-ocean single-column model (AOSCM.v1_EC-Earth3) for studying coupled marine and polar processes2018In: Geoscientific Model Development, ISSN 1991-959X, E-ISSN 1991-9603, Vol. 11, no 10, p. 4117-4137Article in journal (Refereed)
    Abstract [en]

    Single-column models (SCMs) have been used as tools to help develop numerical weather prediction and global climate models for several decades. SCMs decouple small-scale processes from large-scale forcing, which allows the testing of physical parameterisations in a controlled environment with reduced computational cost. Typically, either the ocean, sea ice or atmosphere is fully modelled and assumptions have to be made regarding the boundary conditions from other subsystems, adding a potential source of error. Here, we present a fully coupled atmosphere-ocean SCM (AOSCM), which is based on the global climate model EC-Earth3. The initial configuration of the AOSCM consists of the Nucleus for European Modelling of the Ocean (NEMO3.6) (ocean), the Louvain-la-Neuve Sea Ice Model (LIM3) (sea ice), the Open Integrated Forecasting System (OpenIFS) cycle 40r1 (atmosphere), and OASIS3-MCT (coupler). Results from the AOSCM are presented at three locations: the tropical Atlantic, the midlatitude Pacific and the Arctic. At all three locations, in situ observations are available for comparison. We find that the coupled AOSCM can capture the observed atmospheric and oceanic evolution based on comparisons with buoy data, soundings and ship-based observations. The model evolution is sensitive to the initial conditions and forcing data imposed on the column. Comparing coupled and uncoupled configurations of the model can help disentangle model feedbacks. We demonstrate that the AOSCM in the current set-up is a valuable tool to advance our understanding in marine and polar boundary layer processes and the interactions between the individual components of the system (atmosphere, sea ice and ocean).

  • 6.
    Herberthson, Magnus
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Johansson, KarinLinköping University, Department of Mathematics. Linköping University, Faculty of Science & Engineering.Kozlov, VladimirLinköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.Ljungkvist, EmmaLinköping University, National Supercomputer Centre (NSC).Singull, MartinLinköping University, Department of Mathematics, Mathematical Statistics . Linköping University, Faculty of Science & Engineering.
    Proceedings from Workshop: Mathematics in Biology and Medicine, 11-12 May 2017, Linköping University2017Conference proceedings (editor) (Refereed)
  • 7.
    Silvearv, Fredrik
    et al.
    Luleå University of Technology, Sweden; Uppsala University, Sweden.
    Larsson, Peter
    Linköping University, National Supercomputer Centre (NSC).
    Jones, Sarah. L. T.
    National University of Ireland University of Coll Cork, Ireland.
    Ahuja, Rajeev
    Uppsala University, Sweden; Royal Institute Technology KTH, Sweden.
    Larsson, J. Andreas
    Luleå University of Technology, Sweden; Uppsala University, Sweden; National University of Ireland University of Coll Cork, Ireland.
    Establishing the most favorable metal-carbon bond strength for carbon nanotube catalysts2015In: Journal of Materials Chemistry C, ISSN 2050-7526, E-ISSN 2050-7534, Vol. 3, no 14, p. 3422-3427Article in journal (Refereed)
    Abstract [en]

    We have studied a wide range of transition metals to find potential carbon nanotube (CNT) catalysts for chemical vapor deposition (CVD) production. The adhesion strengths between a CNT and a metal cluster were calculated using first principle density functional theory (DFT) for all 1st, 2nd and 3rd row transition metals. We have developed the criterion that the metal-carbon adhesion strength per bond must fulfill a Goldilocks principle for catalyzing CNT growth and used it to identify, besides the well known catalysts Fe, Co and Ni, a number of other potential catalysts, namely Y, Zr, Rh, Pd, La, Ce and Pt. Our results are consistent with previous experiments performed either in a carbon arc discharge environment or by a CVD-process with regard to CNT catalyst activity.

  • 8.
    Sjöström, Oskar
    et al.
    Linköping University, Department of Computer and Information Science, Software and Systems.
    Ko, Soon Heum
    Linköping University, National Supercomputer Centre (NSC).
    Dastgeer, Usman
    Linköping University, Department of Computer and Information Science, Software and Systems.
    Li, Lu
    Linköping University, Department of Computer and Information Science, Software and Systems.
    Kessler, Christoph
    Linköping University, Department of Computer and Information Science, Software and Systems. Linköping University, Faculty of Science & Engineering.
    Portable Parallelization of the EDGE CFD Application for GPU-based Systems using the SkePU Skeleton Programming Library2016In: Parallel Computing: On the Road to Exascale / [ed] Gerhard R. Joubert, Hugh Leather, Mark Parsons, Frans Peters, Mark Sawyer, IOS Press, 2016, p. 135-144Chapter in book (Refereed)
    Abstract [en]

    EDGE is a complex application for computational fluid dynamics used e.g. for aerodynamic simulations in avionics industry. In this work we present the portable, high-level parallelization of EDGE for execution on multicore CPU and GPU based systems by using the multi-backend skeleton programming library SkePU. We first expose the challenges of applying portable high-level parallelization to a complex scientific application for a heterogeneous (GPU-based) system using (SkePU) skeletons and discuss the encountered flexibility problems that usually do not show up in skeleton toy programs. We then identify and implement necessary improvements in SkePU to become applicable for applications containing computations on complex data structures and with irregular data access. In particular, we improve the MapArray skeleton and provide a new MultiVector container for operand data that can be used with unstructured grid data structures. Although there is no SkePU skeleton specifically dedicated to handling computations on unstructured grids and its data structures, we still obtain portable speedup of EDGE with both multicore CPU and GPU execution by using the improved MapArray skeleton of SkePU.

  • 9.
    Xia, Chao
    et al.
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials.
    Tal, Alexey
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering. Natl Univ Sci and Technol MISIS, Russia.
    Johansson, Leif
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Olovsson, Weine
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering. Linköping University, National Supercomputer Centre (NSC).
    Abrikosov, Igor
    Linköping University, Department of Physics, Chemistry and Biology, Theoretical Physics. Linköping University, Faculty of Science & Engineering.
    Virojanadara, Chariya
    Linköping University, Department of Physics, Chemistry and Biology, Semiconductor Materials. Linköping University, Faculty of Science & Engineering.
    Effects of rhenium on graphene grown on SiC(0001)2018In: Journal of Electron Spectroscopy and Related Phenomena, ISSN 0368-2048, E-ISSN 1873-2526, Vol. 222, p. 117-121Article in journal (Refereed)
    Abstract [en]

    We study the effects of Rhenium (Re) deposited on epitaxial monolayer graphene grown on SiC(0001) and after subsequent annealing at different temperatures, by performing high resolution photoelectron spectroscopy (PES) and angle resolved photoelectron spectroscopy (ARPES). The graphene-Re system is found to be thermally stable. While no intercalation or chemical reaction of the Re is detected after deposition and subsequent annealing up to 1200 degrees C, a gradual decrease in the binding energy of the Re 4f doublet is observed. We propose that a larger mobility of the Re atoms with increasing annealing temperature and hopping of Re atoms between different defective sites on the graphene sample could induce this decrease of Re 4f binding energy. This is corroborated by first principles density functional theory (DFT) calculations of the Re core-level binding energy shift. No change in the doping or splitting of the initial monolayer graphene electronic band structure is observed after Re deposition and annealing up to 1200 degrees C, only a broadening of the bands. (C) 2017 Elsevier B.V. All rights reserved.

    The full text will be freely available from 2019-08-07 00:01
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