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  • Articles  (29)
  • Geosciences  (20)
  • Computer Science  (7)
  • Energy, Environment Protection, Nuclear Power Engineering  (3)
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  • Articles  (29)
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  • 1
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    Combinatorics of chromosomal rearrangements based on synteny blocks and synteny packs (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-17
    Description: The reconstruction of the history of rearrangements and the reconstruction of ancestral genomes are some of the challenges of bioinformatics today. Many algorithms already exist, treating one or the other question but none treating both. These reconstructions are interdependent and we argue on the interest of treating both problems in parallel to lead to a richer and more complete output. We also argue on the importance of redefining several steps of these algorithms to improve both reconstructions: the identification of synteny blocks has to be as precise as possible, and the treatment of multiple genomes has to be based on pairwise comparisons to ensure the most detailed reconstructions. In this article, we highlight novel solutions to these points and focus on the need of explicitly treating overlapping, included, duplicated and unsigned synteny blocks. To do so, we introduce the new notion of synteny pack , which is a representation of local hypothetical intermediate ancestral genomes. We discuss a number of examples on yeast genomes to illustrate the importance of such a definition.
    Print ISSN: 0955-792X
    Electronic ISSN: 1465-363X
    Topics: Computer Science , Mathematics
    Published by Oxford University Press
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  • 2
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    catena-Poly[[(tetrahydrofuran-κO)potassium]-μ-(η5:η5)-2,3,4,5-tetramethyl-1-n-pentylcyclopentadienyl] (2013)
    Wiley-Blackwell
    Details
    Publication Date: 2013-05-10
    Description: The title compound, [K(C 14 H 23 )(C 4 H 8 O)] n , comprises zigzag chains of alternating bridging 2,3,4,5-tetramethyl-1- n -pentylcyclopentadienyl ligands and potassium ions, with an ancillary tetrahydrofuran ligand in the coordination environment of potassium. The coordination polymer strands so formed extend by 2 1 screw symmetry in the b -axis direction. The chemically modified cyclopentadienyl ligand, with a tethered n -pentyl group, was synthesized from 2,3,4,5-tetramethylcyclopent-2-enone by a Grignard reaction.
    Print ISSN: 0108-2701
    Electronic ISSN: 1600-5759
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley-Blackwell on behalf of International Union of Crystallography (IUCr).
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  • 3
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    Iron-Based Metal–Organic Frameworks MIL-88B and NH2-MIL-88B: High Quality Microwave Synthesis and Solvent-Induced Lattice “Breathing” (2013)
    American Chemical Society (ACS)
    Details
    Publication Date: 2013-04-26
    Description: Crystal Growth & Design DOI: 10.1021/cg301738p
    Print ISSN: 1528-7483
    Electronic ISSN: 1528-7505
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Chemical Society (ACS)
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  • 4
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    Axisymmetric circulation driven by marginal heating in ice-covered lakes (2015)
    Wiley-Blackwell
    Details
    Publication Date: 2015-04-01
    Description: Below the temperature of maximum density (TMD) in freshwater lakes, heating at the lateral margins produces gravity currents along the bottom slope, akin to katabatic winds in the atmosphere and currents on continental shelves. We describe axisymmetric basin-scale circulation driven by heat flux at the shorelines in polar Lake Kilpisjärvi. A dense underflow originating near the shore converges towards the lake center, where it produces warm upwelling and return flow across the bulk of lake water column. The return flow, being subject to Coriolis force, creates a lake-wide anticyclonic gyre with velocities of 2-4 cm s -1 . While warm underflows are common on ice-covered lakes, the key finding is the basin-scale anticyclonic gyre with warm upwelling in the core. This circulation mechanism provides a key to understanding transport processes in (semi-) enclosed basins subject to negative buoyancy flux due to heating (or cooling at temperatures above TMD) at their lateral boundaries.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley-Blackwell on behalf of American Geophysical Union (AGU).
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  • 5
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    Equation of state of pyrite to 80 GPa and 2400 K (2016)
    Mineralogical Society of America
    Details
    Publication Date: 2016-05-03
    Description: The high-cosmic abundance of sulfur is not reflected in the terrestrial crust, implying it is either sequestered in the Earth’s interior or was volatilized during accretion. As it has widely been suggested that sulfur could be one of the contributing light elements leading to the density deficit of Earth’s core, a robust thermal equation of state of iron sulfide is useful for understanding the evolution and properties of Earth’s interior. We performed X-ray diffraction measurements on FeS 2 achieving pressures from 15 to 80 GPa and temperatures up to 2400 K using laser-heated diamond-anvil cells. No phase transitions were observed in the pyrite structure over the pressure and temperature ranges investigated. Combining our new P-V-T data with previously published room-temperature compression and thermochemical data, we fit a Debye temperature of 624(14) K and determined a Mie-Grüneisen equation of state for pyrite having bulk modulus K T = 141.2(18) GPa, pressure derivative K ' T = 5.56(24), Grüneisen parameter 0 = 1.41, anharmonic coefficient A 2 = 2.53(27) x 10 –3 J/(K 2 ·mol), and q = 2.06(27). These findings are compared to previously published equation of state parameters for pyrite from static compression, shock compression, and ab initio studies. This revised equation of state for pyrite is consistent with an outer core density deficit satisfied by 11.4(10) wt% sulfur, yet matching the bulk sound speed of PREM requires an outer core composition of 4.8(19) wt% S. This discrepancy suggests that sulfur alone cannot satisfy both seismological constraints simultaneously and cannot be the only light element within Earth’s core, and so the sulfur content needed to satisfy density constraints using our FeS 2 equation of state should be considered an upper bound for sulfur in the Earth’s core.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
    Published by Mineralogical Society of America
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  • 6
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    Localized shear in the deep lithosphere beneath the San Andreas fault system (2014)
    Geological Society of America (GSA)
    In: Geology
    Details
    Publication Date: 2014-03-15
    Description: Seismic images of the base of the lithosphere across the San Andreas fault system (California, USA) yield new constraints on the distribution of deformation in the deep lithosphere beneath this strike-slip plate boundary. We show that conversions of shear to compressional waves (Sp) across the base of the lithosphere are systematically weaker on the western side of the plate boundary, indicating that the drop in seismic shear-wave velocity from lithosphere to asthenosphere is either smaller or occurs over a larger depth range. In central and northern California, the lithosphere-asthenosphere boundary changes character across a distance of 〈50 km, and does so directly beneath the San Andreas fault along its simple central segment, and beneath the Calaveras–Green Valley–Bartlett Springs faults to the north. Given the absolute velocities of the North America and Pacific plates, and low viscosities inferred for the asthenosphere, these results indicate the juxtaposition of mantle lithospheres with different properties across these faults. The spatial correlation between the central San Andreas fault and the laterally abrupt change in the velocity structure of the deepest mantle lithosphere points to the accommodation of relative plate motion on a narrow shear zone (〈50 km in width), and a rheology that enables strain localization throughout the thickness of the lithosphere.
    Print ISSN: 0091-7613
    Electronic ISSN: 1943-2682
    Topics: Geosciences
    Published by Geological Society of America (GSA)
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  • 7
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    Equations of state in the Fe–FeSi system at high pressures and temperatures (2014)
    Wiley-Blackwell
    Details
    Publication Date: 2014-03-16
    Description: Earth's core is an iron-rich alloy containing several weight percent of light element(s), possibly including silicon. Therefore the high pressure-temperature equations of state of iron–silicon alloys can provide understanding of the properties of Earth's core. We performed X-ray diffraction experiments using laser-heated diamond anvil cells to achieve simultaneous high pressures and temperatures, up to ~200 GPa for Fe–9wt%Si alloy and ~145 GPa for stoichiometric FeSi. We determined equations of state of the D0 3 , hcp + B2, and hcp phases of Fe–9Si, and the B20 and B2 phases of FeSi. We also calculated equations of state of Fe, Fe 11 Si, Fe 5 Si, Fe 3 Si, and FeSi using ab initio methods, finding that iron and silicon atoms have similar volumes at high pressures. By comparing our experimentally-determined equations of state to the observed core density deficit, we find that the maximum amount of silicon in the outer core is ~11 wt%, while the maximum amount in the inner core is 6–8 wt%, for a purely Fe–Si–Ni core. Bulk sound speeds predicted from our equations of state also match those of the inner and outer core for similar ranges of compositions. We find a compositional contrast between the inner and outer core of 3.5–5.6 wt% silicon, depending on the seismological model used. Theoretical and experimental equations of state agree at high pressures. We find a good match to the observed density, density profile, and sound speed of the Earth's core, suggesting that silicon is a viable candidate for the dominant light element.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley-Blackwell on behalf of American Geophysical Union (AGU).
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  • 8
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    Phase transition and metallization of FeO at high pressures and temperatures (2011)
    Wiley-Blackwell
    Details
    Publication Date: 2011-12-16
    Description: Wüstite, Fe1-xO, is an important component in the mineralogy of Earth's lower mantle and may also be a component of the core. Therefore its high pressure-temperature behavior, including its electronic structure, is essential to understanding the nature and evolution of Earth's deep interior. We performed X-ray diffraction and radiometric measurements on wüstite in a laser-heated diamond anvil cell, finding an insulator-metal transition at high pressures and temperatures. Our data show a negative slope for this apparently isostructural phase boundary, which is characterized by a volume decrease and emissivity increase. The metallic phase of FeO is stable at conditions of the lower mantle and core, which has implications for the high P-T character of Fe-O bonds, magnetic field propagation, and lower mantle conductivity.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley-Blackwell on behalf of American Geophysical Union (AGU).
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  • 9
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    The Impact of Sea-level Rise on Snowy Plovers in Florida: Integrating Geomorphological, Habitat, and Metapopulation Models (2011)
    Wiley-Blackwell
    Details
    Publication Date: 2011-07-10
    Description: Sea-level rise is a projected consequence of global climate change that will result in complex changes in coastal ecosystems. These changes will cause transitions among coastal habitat types, which will be compounded by human-made barriers to the gradual inland migration of these habitat types. The effect of these changes on the future viability of coastal species will depend on the habitat requirements and population dynamics of these species. Thus, realistic assessments of the impact of sea-level rise (SLR) require linking geomorphological models with habitat and population models. In this study, we implemented a framework that allows this linkage, and demonstrated its feasibility to assess the effect of SLR on the viability of the Snowy Plover population in Florida. The results indicate that SLR will cause a decline in suitable habitat and carrying capacity for this species, and an increase in the risk of its extinction and decline. The model projected that the population size will decline faster than the area of habitat or carrying capacity, demonstrating the necessity of incorporating population dynamics in assessing the impacts of SLR on coastal species. The results were most sensitive to uncertainties in survival rate and fecundity, and suggested that future studies on this species should focus on the average and variability of these demographic rates and their dependence on population density. The effect of SLR on this species’ viability was qualitatively similar with most alternative models that used the extreme values of each uncertain parameter, indicating that the results are robust to uncertainties in the model.
    Print ISSN: 1354-1013
    Electronic ISSN: 1365-2486
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Geography
    Published by Wiley-Blackwell
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  • 10
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    Coherent two-dimensional nanoscopy (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-08-13
    Description: We introduce a spectroscopic method that determines nonlinear quantum mechanical response functions beyond the optical diffraction limit and allows direct imaging of nanoscale coherence. In established coherent two-dimensional (2D) spectroscopy, four-wave-mixing responses are measured using three ingoing waves and one outgoing wave; thus, the method is diffraction-limited in spatial resolution. In coherent 2D nanoscopy, we use four ingoing waves and detect the final state via photoemission electron microscopy, which has 50-nanometer spatial resolution. We recorded local nanospectra from a corrugated silver surface and observed subwavelength 2D line shape variations. Plasmonic phase coherence of localized excitations persisted for about 100 femtoseconds and exhibited coherent beats. The observations are best explained by a model in which coupled oscillators lead to Fano-like resonances in the hybridized dark- and bright-mode response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aeschlimann, Martin -- Brixner, Tobias -- Fischer, Alexander -- Kramer, Christian -- Melchior, Pascal -- Pfeiffer, Walter -- Schneider, Christian -- Struber, Christian -- Tuchscherer, Philip -- Voronine, Dmitri V -- New York, N.Y. -- Science. 2011 Sep 23;333(6050):1723-6. doi: 10.1126/science.1209206. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Fachbereich Physik and Research Center OPTIMAS, Technische Universitat Kaiserslautern, Erwin-Schrodinger-Str. 46, 67663 Kaiserslautern, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835982" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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