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2.
  • Gilbert, F., et al. (author)
  • Sediment reworking by the burrowing polychaete Hediste diversicolor modulated by environmental and biological factors across the temperate North Atlantic. A tribute to Gaston Desrosiers
  • 2021
  • In: Journal of Experimental Marine Biology and Ecology. - : Elsevier BV. - 0022-0981. ; 541
  • Journal article (peer-reviewed)abstract
    • Particle mixing and irrigation of the seabed by benthic fauna (bioturbation) have major impacts on ecosystem functions such as remineralization of organic matter and sediment-water exchange. As a tribute to Prof. Gaston Desrosiers by the Nereis Park association, eighteen laboratories carried out a collaborative experiment to acquire a global snapshot of particle reworking by the polychaete Hediste diversicolor at 16 sites surrounding the Northern Atlantic. Organisms and soft sediments were collected during May - July at different geographical locations and, using a common laboratory protocol, particulate fluorescent tracers (`luminophores') were used to quantify particle transport over a 10-day period. Particle mixing was quantified using the maximum penetration depth of tracers (MPD), particle diffusive coefficients (D-b), and non-local transport coefficients (r). Non-local coefficients (reflecting centimeter scale transport steps) ranged from 0.4 to 15 yr(-1), and were not correlated across sites with any measured biological (biomass, biovolume) or environmental parameters (temperature, grain size, organic matter). Maximum penetration depths (MPD) averaged similar to 10.7 cm (6.5-14.5 cm), and were similar to the global average bioturbation depth inferred from short-lived radiochemical tracers. MPD was also not correlated with measures of size (individual biomass), but increased with grain size and decreased with temperature. Bio-diffusion (D-b) correlated inversely with individual biomass (size) and directly with temperature over the environmental range (Q(10) similar to 1.7; 5-21 degrees C). The transport data were comparable in magnitude to rates reported for localized H. diversicolor populations of similar size, and confirmed some but not all correlations between sediment reworking and biological and environmental variables found in previous studies. The results imply that measures of particle reworking activities of a species from a single location can be generally extrapolated to different populations at similar conditions.
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3.
  • Gonze, X., et al. (author)
  • Recent developments in the ABINIT software package
  • 2016
  • In: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 205, s. 106-131
  • Journal article (peer-reviewed)abstract
    • ABINIT is a package whose main program allows one to find the total energy, charge density, electronic structure and many other properties of systems made of electrons and nuclei, (molecules and periodic solids) within Density Functional Theory (DFT), Many-Body Perturbation Theory (GW approximation and Bethe-Salpeter equation) and Dynamical Mean Field Theory (DMFT). ABINIT also allows to optimize the geometry according to the DFT forces and stresses, to perform molecular dynamics simulations using these forces, and to generate dynamical matrices, Born effective charges and dielectric tensors. The present paper aims to describe the new capabilities of ABINIT that have been developed since 2009. It covers both physical and technical developments inside the ABINIT code, as well as developments provided within the ABINIT package. The developments are described with relevant references, input variables, tests and tutorials. Program summary: . Program title: ABINIT. . Catalogue identifier: AEEU_v2_0. . Program summary URL: . http://cpc.cs.qub.ac.uk/summaries/AEEU_v2_0.html . . Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. . Licensing provisions: GNU General Public License, version 3. . No. of lines in distributed program, including test data, etc.: 4845789. . No. of bytes in distributed program, including test data, etc.: 71340403. . Distribution format: tar.gz. . Programming language: Fortran2003, PERL scripts, Python scripts. . Classification: 7.3, 7.8. . External routines: (all optional) BigDFT [2], ETSF_IO [3], libxc [4], NetCDF [5], MPI [6], Wannier90 [7], FFTW [8]. . Catalogue identifier of previous version: AEEU_v1_0. . Journal reference of previous version: Comput. Phys. Comm. 180 (2009) 2582. . Does the new version supersede the previous version?: Yes. The abinit-7.10.5 version is now the up to date stable version of ABINIT. . Nature of problem: . This package has the purpose of computing accurately material and nanostructure properties: electronic structure, bond lengths, bond angles, primitive cell size, cohesive energy, dielectric properties, vibrational properties, elastic properties, optical properties, magnetic properties, non-linear couplings, electronic and vibrational life-times, and others. . Solution method: . Software application based on Density Functional Theory, Many-Body Perturbation Theory and Dynamical Mean Field Theory, pseudopotentials, with plane waves or wavelets as basis functions. . Reasons for new version: . Since 2009, the abinit-5.7.4 version of the code has considerably evolved and is not yet up to date. The abinit- 7.10.5 version contains new physical and technical features that allow electronic structure calculations impossible to carry out in the previous versions. . Summary of revisions: . •new physical features: quantum effects for the nuclei treated by the Path-integral Molecular Dynamics; finding transition states using image dynamics (NEB or string methods); two component DFT for electron-positron annihilation; linear response in a Projector Augmented-Wave approach -PAW-, electron-phonon interactions and temperature dependence of the gap; Bethe Salpeter Equation -BSE-; Dynamical Mean Field Theory (DMFT).•new technical features: development of a PAW approach for a wavelet basis; parallelisation of the code on more than 10,000 processors; new build system.•new features in the ABINIT package: tests; test farm; new tutorials; new pseudopotentials and PAW atomic data tables; GUI and postprocessing tools like the AbiPy and APPA libraries. . Running time: . It is difficult to answer to the question as the use of ABINIT is very large. On one hand, ABINIT can run on 10,000 processors for hours to perform quantum molecular dynamics on large systems. On the other hand, tutorials for students can be performed on a laptop within a few minutes. . References: . 1 http://www.gnu.org/copyleft/gpl.txt 2 http://bigdft.org 3 http://www.etsf.eu/fileformats 4 http://www.tddft.org/programs/octopus/wiki/index.php/Libxc 5 http://www.unidata.ucar.edu/software/netcdf 6 https://en.wikipedia.org/wiki/Message_Passing_Interface 7 http://www.wannier.org 8M. Frigo and S.G. Johnson, Proceedings of the IEEE, 93, 216-231 (2005). . .
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  • Biurrun, Idoia, et al. (author)
  • Benchmarking plant diversity of Palaearctic grasslands and other open habitats
  • 2021
  • In: Journal of Vegetation Science. - Oxford : John Wiley & Sons. - 1100-9233 .- 1654-1103. ; 32:4
  • Journal article (peer-reviewed)abstract
    • Journal of Vegetation Science published by John Wiley & Sons Ltd on behalf of International Association for Vegetation Science.Aims: Understanding fine-grain diversity patterns across large spatial extents is fundamental for macroecological research and biodiversity conservation. Using the GrassPlot database, we provide benchmarks of fine-grain richness values of Palaearctic open habitats for vascular plants, bryophytes, lichens and complete vegetation (i.e., the sum of the former three groups). Location: Palaearctic biogeographic realm. Methods: We used 126,524 plots of eight standard grain sizes from the GrassPlot database: 0.0001, 0.001, 0.01, 0.1, 1, 10, 100 and 1,000 m2 and calculated the mean richness and standard deviations, as well as maximum, minimum, median, and first and third quartiles for each combination of grain size, taxonomic group, biome, region, vegetation type and phytosociological class. Results: Patterns of plant diversity in vegetation types and biomes differ across grain sizes and taxonomic groups. Overall, secondary (mostly semi-natural) grasslands and natural grasslands are the richest vegetation type. The open-access file ”GrassPlot Diversity Benchmarks” and the web tool “GrassPlot Diversity Explorer” are now available online (https://edgg.org/databases/GrasslandDiversityExplorer) and provide more insights into species richness patterns in the Palaearctic open habitats. Conclusions: The GrassPlot Diversity Benchmarks provide high-quality data on species richness in open habitat types across the Palaearctic. These benchmark data can be used in vegetation ecology, macroecology, biodiversity conservation and data quality checking. While the amount of data in the underlying GrassPlot database and their spatial coverage are smaller than in other extensive vegetation-plot databases, species recordings in GrassPlot are on average more complete, making it a valuable complementary data source in macroecology. © 2021 The Authors.
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6.
  • Dengler, Juergen, et al. (author)
  • GrassPlot - a database of multi-scale plant diversity in Palaearctic grasslands
  • 2018
  • In: Phytocoenologia. - : Schweizerbart. - 0340-269X. ; 48:3, s. 331-347
  • Journal article (peer-reviewed)abstract
    • GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). GrassPlot collects plot records (releves) from grasslands and other open habitats of the Palaearctic biogeographic realm. It focuses on precisely delimited plots of eight standard grain sizes (0.0001; 0.001;... 1,000 m(2)) and on nested-plot series with at least four different grain sizes. The usage of GrassPlot is regulated through Bylaws that intend to balance the interests of data contributors and data users. The current version (v. 1.00) contains data for approximately 170,000 plots of different sizes and 2,800 nested-plot series. The key components are richness data and metadata. However, most included datasets also encompass compositional data. About 14,000 plots have near-complete records of terricolous bryophytes and lichens in addition to vascular plants. At present, GrassPlot contains data from 36 countries throughout the Palaearctic, spread across elevational gradients and major grassland types. GrassPlot with its multi-scale and multi-taxon focus complements the larger international vegetationplot databases, such as the European Vegetation Archive (EVA) and the global database " sPlot". Its main aim is to facilitate studies on the scale-and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. GrassPlot is a dynamic database and will expand through new data collection coordinated by the elected Governing Board. We invite researchers with suitable data to join GrassPlot. Researchers with project ideas addressable with GrassPlot data are welcome to submit proposals to the Governing Board.
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7.
  • El, Goresy A, et al. (author)
  • An ultradense polymorph of rutile with seven-coordinated titanium from the Ries crater
  • 2001
  • In: SCIENCE. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075. ; 293:5534, s. 1467-1470
  • Journal article (peer-reviewed)abstract
    • We report the discovery of an ultradense post-rutile polymorph of titanium dioxide in shocked gneisses of the Ries crater in Germany. The microscopic diagnostic feature is intense blue internal reflections in crossed polarizers in reflected light. X-ray d
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8.
  • Gagliardini, O., et al. (author)
  • Capabilities and performance of Elmer/Ice, a new-generation ice sheet model
  • 2013
  • In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 6:4, s. 1299-1318
  • Journal article (peer-reviewed)abstract
    • The Fourth IPCC Assessment Report concluded that ice sheet flow models, in their current state, were unable to provide accurate forecast for the increase of polar ice sheet discharge and the associated contribution to sea level rise. Since then, the glaciological community has undertaken a huge effort to develop and improve a new generation of ice flow models, and as a result a significant number of new ice sheet models have emerged. Among them is the parallel finite-element model Elmer/Ice, based on the open-source multi-physics code Elmer. It was one of the first full-Stokes models used to make projections for the evolution of the whole Greenland ice sheet for the coming two centuries. Originally developed to solve local ice flow problems of high mechanical and physical complexity, Elmer/Ice has today reached the maturity to solve larger-scale problems, earning the status of an ice sheet model. Here, we summarise almost 10 yr of development performed by different groups. Elmer/Ice solves the full-Stokes equations, for isotropic but also anisotropic ice rheology, resolves the grounding line dynamics as a contact problem, and contains various basal friction laws. Derived fields, like the age of the ice, the strain rate or stress, can also be computed. Elmer/Ice includes two recently proposed inverse methods to infer badly known parameters. Elmer is a highly parallelised code thanks to recent developments and the implementation of a block preconditioned solver for the Stokes system. In this paper, all these components are presented in detail, as well as the numerical performance of the Stokes solver and developments planned for the future.
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9.
  • Gillet, P, et al. (author)
  • Natural NaAlSi3O8-hollandite in the shocked Sixiangkou meteorite
  • 2000
  • In: SCIENCE. - : AMER ASSOC ADVANCEMENT SCIENCE. - 0036-8075. ; 287:5458, s. 1633-1636
  • Journal article (peer-reviewed)abstract
    • The hollandite high-pressure polymorph of plagioclase has been identified in shock-induced melt veins of the Sixiangkou 16 chondrite. It is intimately intergrown with feldspathic glass within grains previously thought to be "maskelynite." The crystallogra
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10.
  • Govaerts, S., et al. (author)
  • Lessons learned from the development of the role ple framework
  • 2015
  • In: Responsive Open Learning Environments: Outcomes of Research from the Role Project. - Cham : Springer. - 9783319023991 ; , s. 185-217
  • Book chapter (other academic/artistic)abstract
    • Within the ROLE European research project, an interoperability framework has been developed to support self-regulated learning and to enable learners and teachers to create personal learning environments (PLEs). This framework enables learners to assemble tools, services and resources together to create their own custom learning environment. This chapter discusses the overall architecture, the specific components of this architecture and the platforms in which we have integrated the ROLE framework. Additionally, we share the lessons learned from the design and development. Furthermore, we discuss our experience with the ROLE development infrastructure and our collaboration within the ROLE development team and with several open-source projects.
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  • Result 1-10 of 15
Type of publication
journal article (13)
conference paper (1)
book chapter (1)
Type of content
peer-reviewed (12)
other academic/artistic (3)
Author/Editor
Gillet, P (3)
Sjoberg, J (2)
Decock, J. (2)
Chen, M (2)
De Frenne, Pieter (2)
Diekmann, Martin (2)
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FALORNI, A (2)
Lewensohn, R. (2)
Viktorsson, K. (2)
Bjorkholm, M (2)
Prentice, Honor C (2)
Dubrovinsky, L. (2)
Landgren, O (2)
Pakeman, Robin J. (2)
Pielech, Remigiusz (2)
Boch, Steffen (2)
Patel, C. (2)
Jentsch, Anke (2)
Wang, Yun (2)
Bruun, Hans Henrik (2)
Coucke, W (2)
Vanneste, S (2)
Couturier, E (2)
Becker, Thomas (2)
Hajek, Michal (2)
Natcheva, Rayna (2)
Bergamini, Ariel (2)
Stenke, L (2)
Biurrun, Idoia (2)
Dembicz, Iwona (2)
Gillet, François (2)
Kozub, Łukasz (2)
Marcenò, Corrado (2)
Reitalu, Triin (2)
Guarino, Riccardo (2)
Axmanová, Irena (2)
Bartha, Sándor (2)
Conradi, Timo (2)
Filibeck, Goffredo (2)
Jiménez-Alfaro, Borj ... (2)
Kuzemko, Anna (2)
Molnár, Zsolt (2)
Roleček, Jan (2)
Sutcliffe, Laura M. ... (2)
Terzi, Massimo (2)
Winkler, Manuela (2)
Aćić, Svetlana (2)
Akasaka, Munemitsu (2)
Apostolova, Iva (2)
Baumann, Esther (2)
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University
Karolinska Institutet (6)
Uppsala University (5)
Lund University (5)
University of Gothenburg (1)
Royal Institute of Technology (1)
Halmstad University (1)
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University of Gävle (1)
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Language
English (15)
Research subject (UKÄ/SCB)
Natural sciences (5)
Medical and Health Sciences (2)
Engineering and Technology (1)

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