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  • Oxford University Press  (114,882)
  • American Institute of Physics (AIP)  (88,036)
  • Copernicus  (52,346)
  • American Association of Petroleum Geologists (AAPG)
  • 2010-2014  (189,258)
  • 2000-2004  (66,361)
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  • 1
    Publication Date: 2014-10-14
    Description: The composition and abundance of algal pigments provide information on characteristics of a phytoplankton community in respect to its photoacclimation, overall biomass, and taxonomic composition. Particularly, these pigments play a major role in photoprotection and in the light-driven part of photosynthesis. Most phytoplankton pigments can be measured by High Performance Liquid Chromatography (HPLC) techniques to filtered water samples. This method, like others when water samples have to be analysed in the laboratory, is time consuming and therefore only a limited number of data points can be obtained. In order to receive information on phytoplankton pigment composition with a higher temporal and spatial resolution, we have developed a method to assess pigment concentrations from continuous optical measurements. The method applies an Empirical Orthogonal Function (EOF) analysis to remote sensing reflectance data derived from ship-based hyper-spectral underwater radiometric and from multispectral satellite data (using the MERIS Polymer product developed by Steinmetz et al., 2011) measured in the Eastern Tropical Atlantic. Subsequently we developed statistically linear models with measured (collocated) pigment concentrations as the response variable and EOF loadings as predictor variables. The model results, show that surface concentrations of a suite of pigments and pigment groups can be well predicted from the ship-based reflectance measurements, even when only a multi-spectral resolution is chosen (i.e. eight bands similar to those used by MERIS). Based on the MERIS reflectance data, concentrations of total and monovinyl chlorophyll a and the groups of photoprotective and photosynthetic carotenoids can be predicted with high quality. The fitted statistical model constructed on the satellite reflectance data as input was applied to one month of MERIS Polymer data to predict the concentration of those pigment groups for the whole Eastern Tropical Atlantic area. Bootstrapping explorations of cross-validation error indicate that the method can produce reliable predictions with relatively small data sets (e.g., 〈 50 collocated values of reflectance and pigment concentration). The method allows for the derivation of time series from continuous reflectance data of various pigment groups at various regions, which can be used to study variability and change of phytoplankton composition and photo-physiology.
    Repository Name: EPIC Alfred Wegener Institut
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  • 2
    Publication Date: 2019-07-17
    Description: Sea ice thickness information is important for sea ice modelling and ship operations. Here a method to detect the thickness of sea ice up to 50 cm during the freeze-up season based on high incidence angle observations of the Soil Moisture and Ocean Salinity (SMOS) satellite working at 1.4 GHz is suggested. By comparison of thermodynamic ice growth data with SMOS brightness temperatures, a high correlation to intensity and an anticorrelation to the difference between vertically and horizontally polarised brightness temperatures at incidence angles between 40 and 50° are found and used to develop an empirical retrieval algorithm sensitive to thin sea ice up to 50 cm thickness. The algorithm shows high correlation with ice thickness data from airborne measurements and reasonable ice thickness patterns for the Arctic freeze-up period.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
    Publication Date: 2014-06-02
    Description: Following the launch of ESA's Soil Moisture and Ocean Salinity (SMOS) mission, it has been shown that brightness temperatures at a low microwave frequency of 1.4 GHz (L-band) are sensitive to sea ice properties. In the first demonstration study, sea ice thickness up to 50 cm has been derived using a semi-empirical algorithm with constant tie-points. Here, we introduce a novel iterative retrieval algorithm that is based on a thermodynamic sea ice model and a three-layer radiative transfer model, which explicitly takes variations of ice temperature and ice salinity into account. In addition, ice thickness variations within the SMOS spatial resolution are considered through a statistical thickness distribution function derived from high-resolution ice thickness measurements from NASA's Operation IceBridge campaign. This new algorithm has been used for the continuous operational production of a SMOS-based sea ice thickness data set from 2010 on. The data set is compared to and validated with estimates from assimilation systems, remote sensing data, and airborne electromagnetic sounding data. The comparisons show that the new retrieval algorithm has a considerably better agreement with the validation data and delivers a more realistic Arctic-wide ice thickness distribution than the algorithm used in the previous study (Kaleschke et al., 2012).
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
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    Copernicus
    In:  EPIC3The Cryosphere Discussions, Copernicus, 8(1), pp. 919-951, ISSN: 1994-0440
    Publication Date: 2019-07-16
    Description: The ice shelf caverns around Antarctica are sources of cold and fresh water which contributes to the formation of Antarctic bottom water and thus to the ventilation of the deep basins of the World Ocean. While a realistic simulation of the cavern circulation requires high resolution, because of the complicated bottom topography and ice shelf morphology, the physics of melting and freezing at the ice shelf base is relatively simple. We have developed an analytically solvable box model of the cavern thermohaline state, using the formulation of melting and freezing as in Olbers and Hellmer (2010). There is high resolution along the cavern's path of the overturning circulation whereas the cross-path resolution is fairly coarse. The circulation in the cavern is prescribed and used as a tuning parameter to constrain the solution by attempting to match observed ranges for outflow temperature and salinity at the ice shelf front as well as of the mean basal melt rate. The method, tested for six Antarctic ice shelves, can be used for a quick estimate of melt/freeze rates and the overturning rate in particular caverns, given the temperature and salinity of the inflow and the above mentioned constrains for outflow and melting. In turn, the model can also be used for testing the compatibility of remotely sensed basal mass loss with observed cavern inflow characteristics.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev
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  • 5
    Publication Date: 2015-03-19
    Description: The Surface Ocean CO2 Atlas (SOCAT), an activity of the international marine carbon research community, provides access to synthesis and gridded fCO2 (fugacity of carbon dioxide) products for the surface oceans. Version 2 of SOCAT is an update of the previous release (version 1) with more data (increased from 6.3 million to 10.1 million surface water fCO2 values) and extended data coverage (from 1968–2007 to 1968–2011). The quality control criteria, while identical in both versions, have been applied more strictly in version 2 than in version 1. The SOCAT website (http://www.socat.info/) has links to quality control comments, metadata, individual data set files, and synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longerterm variation, as well as initialisation or validation of ocean carbon models and coupled climate-carbon models.
    Repository Name: EPIC Alfred Wegener Institut
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  • 6
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    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(1), pp. 419-432, ISSN: 1991-9603
    Publication Date: 2019-07-17
    Description: In a feasibility study, the potential of proxy data for the temperature and salinity during the Last Glacial Maximum (LGM, about 19 000 to 23 000 years before present) in constraining the strength of the Atlantic meridional overturning circulation (AMOC) with a general ocean circulation model was explored. The proxy data were simulated by drawing data from four different model simulations at the ocean sediment core locations of the Multiproxy Approach for the Reconstruction of the Glacial Ocean surface (MARGO) project, and perturbing these data with realistic noise estimates. The results suggest that our method has the potential to provide estimates of the past strength of the AMOC even from sparse data, but in general, paleo-sea-surface temperature data without additional prior knowledge about the ocean state during the LGM is not adequate to constrain the model. On the one hand, additional data in the deep-ocean and salinity data are shown to be highly important in estimating the LGM circulation. On the other hand, increasing the amount of surface data alone does not appear to be enough for better estimates. Finally, better initial guesses to start the state estimation procedure would greatly improve the performance of the method. Indeed, with a sufficiently good first guess, just the sea-surface temperature data from the MARGO project promise to be sufficient for reliable estimates of the strength of the AMOC.
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
    Repository Name: Woods Hole Open Access Server
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  • 8
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    Copernicus
    In:  EPIC3Geoscientific Model Development, Copernicus, 7(5), pp. 2003-2013, ISSN: 1991-9603
    Publication Date: 2016-12-09
    Description: We present first results from a coupled model setup, consisting of the state-of-the-art ice sheet model RIMBAY (Revised Ice Model Based on frAnk pattYn), and the community earth system model COSMOS. We show that special care has to be provided in order to ensure physical distributions of the forcings as well as numeric stability of the involved models. We demonstrate that a suitable statistical downscaling is crucial for ice sheet stability, especially for southern Greenland where surface temperatures are close to the melting point. The downscaling of net snow accumulation is based on an empirical relationship between surface slope and rainfall. The simulated ice sheet does not show dramatic loss of ice volume for pre-industrial conditions and is comparable with present-day ice orography. A sensitivity study with high CO2 level is used to demonstrate the effects of dynamic ice sheets onto climate compared to the standard setup with prescribed ice sheets.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
    Repository Name: Woods Hole Open Access Server
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  • 12
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2014-12-13
    Description: Current earthquake early warning (EEW) systems lack the ability to appropriately handle multiple concurrent earthquakes, which led to many false alarms during the 2011 Tohoku earthquake sequence in Japan. This paper uses a Bayesian probabilistic approach to handle multiple concurrent events for EEW. We implement the theory using a two-step algorithm. First, an efficient approximate Bayesian model class selection scheme is used to estimate the number of concurrent events. Then, the Rao-Blackwellized Importance Sampling method with a sequential proposal probability density function is used to estimate the earthquake parameters, that is hypocentre location, origin time, magnitude and local seismic intensity. A real data example based on 2 months data (2011 March 9–April 30) around the time of the 2011 M 9 Tohoku earthquake is studied to verify the proposed algorithm. Our algorithm results in over 90 per cent reduction in the number of incorrect warnings compared to the existing EEW system operating in Japan.
    Keywords: Seismology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 14
    Publication Date: 2014-12-13
    Description: A Lagrangian advection scheme with shape matrix (LASM) for solving advection problems Geoscientific Model Development, 7, 2951-2968, 2014 Author(s): L. Dong, B. Wang, and L. Liu A new Lagrangian advection scheme with shape matrix (LASM) is proposed to take advantage of the extreme low numerical diffusion of the Lagrangian methods. The tracer is discretized into finite parcels, which move along the downstream trajectories. Different from other Lagrangian schemes, the parcel shape is simulated explicitly by a linear transformation matrix. By doing so, the aliasing error in the Lagrangian schemes is largely reduced without introducing substantial interparcel mixing in the pure advection stage, because the flow information will be respected when remapping tracer density onto the fixed model grids. An adaptive interparcel mixing algorithm is constructed to ensure the validity of the linear approximation of the parcel shape, where the mixing is only triggered when it is necessary and resembles the physical mixing. The total tracer mass on the parcels is conserved exactly. The new scheme is validated by using several test cases.
    Print ISSN: 1991-959X
    Electronic ISSN: 1991-9603
    Topics: Geosciences
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  • 15
    Publication Date: 2014-12-13
    Description: Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 16
    Publication Date: 2014-12-13
    Description: Technical Note: Reducing the spin-up time of integrated surface water–groundwater models Hydrology and Earth System Sciences, 18, 5169-5179, 2014 Author(s): H. Ajami, J. P. Evans, M. F. McCabe, and S. Stisen One of the main challenges in the application of coupled or integrated hydrologic models is specifying a catchment's initial conditions in terms of soil moisture and depth-to-water table (DTWT) distributions. One approach to reducing uncertainty in model initialization is to run the model recursively using either a single year or multiple years of forcing data until the system equilibrates with respect to state and diagnostic variables. However, such "spin-up" approaches often require many years of simulations, making them computationally intensive. In this study, a new hybrid approach was developed to reduce the computational burden of the spin-up procedure by using a combination of model simulations and an empirical DTWT function. The methodology is examined across two distinct catchments located in a temperate region of Denmark and a semi-arid region of Australia. Our results illustrate that the hybrid approach reduced the spin-up period required for an integrated groundwater–surface water–land surface model (ParFlow.CLM) by up to 50%. To generalize results to different climate and catchment conditions, we outline a methodology that is applicable to other coupled or integrated modeling frameworks when initialization from an equilibrium state is required.
    Print ISSN: 1027-5606
    Electronic ISSN: 1607-7938
    Topics: Geography , Geosciences
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  • 17
    Publication Date: 2014-12-13
    Description: Extending periodic eddy covariance latent heat fluxes through tree sapflow measurements to estimate long-term total evaporation in a peat swamp forest Hydrology and Earth System Sciences Discussions, 11, 13607-13661, 2014 Author(s): A. D. Clulow, C. S. Everson, M. G. Mengistu, J. S. Price, A. Nickless, and G. P. W. Jewitt A combination of measurement and modelling was used to find a pragmatic solution to estimate the annual total evaporation (ET) from the rare and indigenous Nkazana Peat Swamp Forest (PSF) on the east coast of Southern Africa to improve the water balance estimates within the area. Total evaporation was measured during three window periods (between seven and nine days each) using an eddy covariance (EC) system on a telescopic mast above the forest canopy. Sapflow of an understory and an emergent tree was measured using a low maintenance heat pulse velocity system for an entire hydrological year (October 2009 to September 2010). An empirical model was derived, describing the relationship between the observed ET of the Nkazana PSF measured during two of the window periods ( R 2 = 0.92 and 0.90) which, overlapped with sapflow measurements, thereby providing hourly estimates of predicted ET of the Nkazana PSF for a year, totalling 1125 mm (while rainfall was 650 mm). In building the empirical model, it was found that including the understory tree sapflow provided no benefit to the model performance. In addition, the observed emergent tree sapflow relationship with observed ET between the two field campaigns was consistent and could be represented by a single empirical model ( R 2 = 0.90; RMSE = 0.08 mm). During the window periods of EC measurement, no single meteorological variable was found to describe the Nkazana PSF ET satisfactorily. However, in terms of evaporation models, the hourly FAO56 Penman–Monteith equation best described the observed ET from EC during the August 2009 ( R 2 = 0.75), November 2009 ( R 2 = 0.85) and March 2010 ( R 2 = 0.76) field campaigns, compared to the Priestley–Taylor model ( R 2 = 0.54, 0.74 and 0.62 during the respective field campaigns). From the empirical model of ET and the FAO56 Penman–Monteith equation, a monthly crop factor ( K c ) was derived for the Nkazana PSF providing a method of estimating long-term swamp forest ET from meteorological data. The monthly crop factor indicated two distinct periods. From February to May, it was between 1.2 and 1.4 compared with June to January, when the crop factor was 0.8 to 1.0. The derived monthly K c values were verified as accurate (to one significant digit) using historical data measured at the same site, also using EC, from a~previous study. The measurements provided insights into the microclimate within a subtropical peat swamp forest and the contrasting sapflow of emergent and understory trees. They showed that expensive, high maintenance equipment can be used during manageable window periods in conjunction with low maintenance systems, dedicated to individual trees, to derive a model to estimate long-term ET over remote heterogeneous forests. In addition, the contrast in ET and rainfall emphasises the reliance of the Nkazana PSF on groundwater.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
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  • 18
    Publication Date: 2014-12-12
    Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 19
    Publication Date: 2014-12-13
    Description: Charge generation in a typical intermediate connector, composed of “n-type doped layer/transition metal oxide (TMO)/hole transporting layer (HTL),” of a tandem organic light-emitting device (OLED) has recently been found to arise from charge transfer at the TMO/HTL interfaces. In this paper, we investigate the effect of hole injection barriers from intermediate connectors on the performance of tandem OLEDs. The hole injection barriers are caused by the offset of the highest occupied molecular orbital (HOMO) energy levels between HTLs contained in the intermediate connector and the top electroluminescence (EL) unit. We also find that although charge generation can occur at the interfaces between the TMO and a wide variety of HTLs of different HOMO values, an increase in the hole injection barrier however limits the electroluminescence efficiency of the top EL units. In the case of large hole injection barriers, significant charge accumulation in the HTLs makes the intermediate connector lose its functionality gradually over operating time, and limits device stability.
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  • 20
    Publication Date: 2014-12-09
    Description: Spin-dependent transport properties in CoFe/MgO/n + -Si junctions were investigated by Hanle effect measurements and inelastic electron tunneling (IET) spectroscopy. The CoFe/MgO/n + -Si junctions examined in this study exhibited two different Hanle curves. In the low bias region, broad Hanle signals were mainly observed; in the high bias region, narrow Hanle signals were mainly observed. The d 2 I / dV 2 - V curves (which correspond to IET spectra) contain several peaks originating from phonon modes and other peaks originating from electron trap states. At the bias voltage where electron trap states are observed, Δ d 2 I / dV 2 depends on the magnetic field and the full width at half-maximum of the Δ d 2 I / dV 2 – H curves corresponds to that of the broad Hanle signals. These results indicate that electron trap states are located in the low energy region and cause a decrease in spin lifetime.
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  • 21
    Publication Date: 2014-12-09
    Description: We elucidate a strong room temperature stimulated emission (SE) of In 0.17 Ga 0.83 N epilayer grown by molecular beam epitaxy under the subpicosecond pulse excitation. The SE peak at 428 nm emerges on the higher energy side of the spontaneous emission in photoluminescence spectra when the excitation density exceeds the threshold of ∼3.68 mJ/cm 2 . Nondegenerate transient differential reflectivity measurements show that a multi-stage carrier thermalization from excited states to localized edge states and stimulated emission dominate the decay processes of photogenerated carriers under various excitation densities. Our results indicate that the existence of phonon bottleneck effect could result in a slow thermalization process in the InGaN material even under the condition of stimulated emission.
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  • 22
    Publication Date: 2014-12-09
    Description: The relationship between carrier concentration and donor atomic concentration has been determined in n -type Ge films doped with P. The samples were carefully engineered to minimize non-active dopant incorporation by using specially designed P(SiH 3 ) 3 and P(GeH 3 ) 3 hydride precursors. The in situ nature of the doping and the growth at low temperatures, facilitated by the Ge 3 H 8 and Ge 4 H 10 Ge sources, promote the creation of ultra-low resistivity films with flat doping profiles that help reduce the errors in the concentration measurements. The results show that Ge deviates strongly from the incomplete ionization expected when the donor atomic concentration exceeds N d  = 10 17  cm −3 , at which the energy separation between the donor and Fermi levels ceases to be much larger than the thermal energy. Instead, essentially full ionization is seen even at the highest doping levels beyond the solubility limit of P in Ge. The results can be explained using a model developed for silicon by Altermatt and coworkers, provided the relevant model parameter is properly scaled. The findings confirm that donor solubility and/or defect formation, not incomplete ionization, are the major factors limiting the achievement of very high carrier concentrations in n -type Ge. The commercially viable chemistry approach applied here enables fabrication of supersaturated and fully ionized prototypes with potential for broad applications in group-IV semiconductor technologies.
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  • 23
    Publication Date: 2014-12-09
    Description: We developed a T-gate technology based on selective wet etching yielding 200 nm wide T-gate structures used for fabrication of High Electron Mobility Transistors (HEMT). Major advantages of our process are the use of only standard photolithographic process and the ability to generate T-gate stacks. A HEMT fabricated on AlGaN/GaN/sapphire with gate length L g  = 200 nm and double-stacked T-gates exhibits 60 GHz cutoff frequency showing ten-fold improvement compared to 6 GHz for the same device with 2  μ m gate length. HEMTs with a double-level-T-gate (DLTG) structure exhibit up to 35% improvement of f max value compared to a single T-gate device. This indicates a significant reduction of skin effect losses in DLTG structure compared to its standard T-gate counterpart. These results agree with the theoretical predictions.
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  • 24
    Publication Date: 2014-12-12
    Description: This investigation analyzes the effect of vortex wakes on the Lagrangian displacement of particles induced by the passage of an obstacle in a two-dimensional incompressible and inviscid fluid. In addition to the trajectories of individual particles, we also study their drift and the corresponding total drift areas in the Föppl and Kirchhoff potential flow models. Our findings, which are obtained numerically and in some regimes are also supported by asymptotic analysis, are compared to the wakeless potential flow which serves as a reference. We show that in the presence of the Föppl vortex wake, some of the particles follow more complicated trajectories featuring a second loop. The appearance of an additional stagnation point in the Föppl flow is identified as a source of this effect. It is also demonstrated that, while the total drift area increases with the size of the wake for large vortex strengths, it is actually decreased for small circulation values. On the other hand, the Kirchhoff flow model is shown to have an unbounded total drift area. By providing a systematic account of the wake effects on the drift, the results of this study will allow for more accurate modeling of hydrodynamic stirring.
    Print ISSN: 1070-6631
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  • 25
    Publication Date: 2014-12-09
    Description: The magnetic configuration of Mn 2 NiAl ribbon has been investigated. In contrast to Ni 2 MnAl, the compound Mn 2 NiAl with considerable disorder does exhibit ferromagnetism and, due to exchange interaction competition, both ferromagnetic and antiferromagnetic moment orientations can coexist between nearest neighbor Mn atoms. This is unexpected in Heusler alloys. Regarding the mechanism of the martensitic transformation in Mn 50 Ni 50− x Al x , it is found that increasing the Al content results in an unusual change in the lattice constant, a decrease of the transformation entropy change, and enhancement of the calculated electron localization. These results indicate that the p-d covalent hybridization between Mn (or Ni) and Al atoms gradually increases at the expense of the d-d hybridization between Ni and Mn atoms. This leads to an increased stability of the austenite phase and a decrease of the martensitic transformation temperature. For 11 ≤  x  ≤ 14, Mn 50 Ni 50− x Al x ferromagnetic shape memory alloys are obtained.
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  • 26
    Publication Date: 2014-12-09
    Description: Electrowetting (EW) has applications including displays, microactuation, miniaturized chemistry, adaptive optics, and energy harvesting—understanding the physics of EW junctions is of key importance. Here, the roles of semiconductor space-charge and electric double layer in continuous EW at an electrolyte-insulator-semiconductor junction are considered. A model is formulated in terms of experimental parameters—applied voltage, zero-bias wetting contact angle, semiconductor type and doping, insulator thickness and dielectric constant, and electrolyte concentration and dielectric constant. The model predicts, and experiments indicate, that the EW behavior is diminished for low concentration solutions (∼1–10 nM) and lowly doped silicon (10 14 –10 15  cm −3 ).
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  • 27
    Publication Date: 2014-12-12
    Description: The dynamics of the magnetic relaxation process during the sustainment of spheromak configurations at different helicity injection rates is studied. The three-dimensional activity is recovered using time-dependent resistive magnetohydrodynamic simulations. A cylindrical flux conserver with concentric electrodes is used to model configurations driven by a magnetized coaxial gun. Magnetic helicity is injected by tangential boundary flows. Different regimes of sustainment are identified and characterized in terms of the safety factor profile. The spatial and temporal behavior of fluctuations is described. The dynamo action is shown to be in close agreement with existing experimental data. These results are relevant to the design and operation of helicity injected devices, as well as to basic understanding of the plasma relaxation mechanism in quasi-steady state.
    Print ISSN: 1070-664X
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  • 28
    Publication Date: 2014-12-12
    Description: The present experiments were performed on the PF-1000 plasma focus device at a current of 2 MA with the deuterium injected from the gas-puff placed in the axis of the anode face. The XUV frames showed, in contrast with the interferograms, the fine structure: filaments and spots up to 1 mm diameter. In the deuterium filling, the short filaments are registered mainly in the region of the internal plasmoidal structures and their number correlates with the intensity of neutron production. The longer filamentary structure was recorded close to the anode after the constriction decay. The long curve-like filaments with spots were registered in the big bubble formed after the pinch phase in the head of the umbrella shape of the plasma sheath. Filaments can indicate the filamentary structure of the current in the pinch. Together with the filaments, small compact balls a few mm in diameter were registered by both interferometry and XUV frame pictures. They emerge out of the dense column and their life-time can be greater than hundreds of ns.
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  • 29
    Publication Date: 2014-12-12
    Description: The radiation pressure acceleration of protons in the interaction of Gaussian laser pulses and surface modulated targets is examined by multi-dimensional particle-in-cell simulations. It is shown that strong longitudinal quasi-static magnetic field is generated on the modulated surface of the target, which significantly enhances the transverse diffusion of electrons. This is beneficial for suppressing the transverse Rayleigh-Taylor instability. Finally, the surface of the accelerated proton beams becomes smoother than that in the case of the planar target, and a final mono-energetic proton beam is obtained by using the surface modulated target.
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  • 30
    Publication Date: 2014-12-09
    Description: We have studied the impact dynamics of non-Newtonian droplets containing poly-(ethylene oxide) (PEO) by using a high speed camera. To get a deeper insight into the droplet-substrate interaction on droplet impact behavior, both the bare droplet and the liquid marbles have been investigated. The usually observed anti-rebound phenomenon caused by the PEO additives can be rejuvenated by enwrapment of droplets with nanoparticles. The presence of PEO in bare droplets greatly enhances the contact line friction and leads to irreversible impalement of the surface structure. Whereas for liquid marbles, the nanoparticle shell on the droplet surface inhibits the impalement. Our results clearly demonstrate that it is the droplet-substrate friction rather than the bulk rheological properties of the liquid that plays the essential role in the anti-rebound effect.
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  • 31
    Publication Date: 2014-12-09
    Description: Stratospheric ozone depletion from future nitrous oxide increases Atmospheric Chemistry and Physics, 14, 12967-12982, 2014 Author(s): W. Wang, W. Tian, S. Dhomse, F. Xie, J. Shu, and J. Austin We have investigated the impact of the assumed nitrous oxide (N 2 O) increases on stratospheric chemistry and dynamics using a series of idealized simulations with a coupled chemistry-climate model (CCM). In a future cooler stratosphere the net yield of NO y from N 2 O is shown to decrease in a reference run following the IPCC A1B scenario, but NO y can still be significantly increased by extra increases of N 2 O over 2001–2050. Over the last decade of simulations, 50% increases in N 2 O result in a maximal 6% reduction in ozone mixing ratios in the middle stratosphere at around 10 hPa and an average 2% decrease in the total ozone column (TCO) compared with the control run. This enhanced destruction could cause an ozone decline in the first half of this century in the middle stratosphere around 10 hPa, while global TCO still shows an increase at the same time. The results from a multiple linear regression analysis and sensitivity simulations with different forcings show that the chemical effect of N 2 O increases dominates the N 2 O-induced ozone depletion in the stratosphere, while the dynamical and radiative effects of N 2 O increases are overall insignificant. The analysis of the results reveals that the ozone depleting potential of N 2 O varies with the time period and is influenced by the environmental conditions. For example, carbon dioxide (CO 2 ) increases can strongly offset the ozone depletion effect of N 2 O.
    Print ISSN: 1680-7316
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  • 32
    Publication Date: 2014-12-09
    Description: Corrigendum to "Air-sea exchange and gas-particle partitioning of polycyclic aromatic hydrocarbons in the Mediterranean" published in Atmos. Chem. Phys., 14, 8905–8915, 2014 Atmospheric Chemistry and Physics, 14, 12965-12965, 2014 Author(s): M. D. Mulder, A. Heil, P. Kukučka, J. Klánová, J. Kuta, R. Prokeš, F. Sprovieri, and G. Lammel No abstract available.
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  • 33
    Publication Date: 2014-12-09
    Description: Mechanistic study of secondary organic aerosol components formed from nucleophilic addition reactions of methacrylic acid epoxide Atmospheric Chemistry and Physics, 14, 12951-12964, 2014 Author(s): A. W. Birdsall, C. R. Miner, L. E. Mael, and M. J. Elrod Recently, methacrylic acid epoxide (MAE) has been proposed as a precursor to an important class of isoprene-derived compounds found in secondary organic aerosol (SOA): 2-methylglyceric acid (2-MG) and a set of oligomers, nitric acid esters, and sulfuric acid esters related to 2-MG. However, the specific chemical mechanisms by which MAE could form these compounds have not been previously studied with experimental methods. In order to determine the relevance of these processes to atmospheric aerosol, MAE and 2-MG have been synthesized and a series of bulk solution-phase experiments aimed at studying the reactivity of MAE using nuclear magnetic resonance (NMR) spectroscopy have been performed. The present results indicate that the acid-catalyzed MAE reaction is more than 600 times slower than a similar reaction of an important isoprene-derived epoxide, but is still expected to be kinetically feasible in the atmosphere on more acidic SOA. The specific mechanism by which MAE leads to oligomers was identified, and the reactions of MAE with a number of atmospherically relevant nucleophiles were also investigated. Because the nucleophilic strengths of water, sulfate, alcohols (including 2-MG), and acids (including MAE and 2-MG) in their reactions with MAE were found to be of similar magnitudes, it is expected that a diverse variety of MAE + nucleophile product species may be formed on ambient SOA. Thus, the results indicate that epoxide chain reaction oligomerization will be limited by the presence of high concentrations of non-epoxide nucleophiles (such as water); this finding is consistent with previous environmental chamber investigations of the relative humidity dependence of 2-MG-derived oligomerization processes and suggests that extensive oligomerization may not be likely on ambient SOA because of other competitive MAE reaction mechanisms.
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  • 34
    Publication Date: 2014-12-09
    Description: Megacity emission plume characteristics in summer and winter investigated by mobile aerosol and trace gas measurements: the Paris metropolitan area Atmospheric Chemistry and Physics, 14, 12931-12950, 2014 Author(s): S.-L. von der Weiden-Reinmüller, F. Drewnick, Q. J. Zhang, F. Freutel, M. Beekmann, and S. Borrmann For the investigation of megacity emission plume characteristics mobile aerosol and trace gas measurements were carried out in the greater Paris region in July 2009 and January–February 2010 within the EU FP7 MEGAPOLI project (Megacities: Emissions, urban, regional and Global Atmospheric POLlution and climate effects, and Integrated tools for assessment and mitigation). The deployed instruments measured physical and chemical properties of sub-micron aerosol particles, gas phase constituents of relevance for urban air pollution studies and meteorological parameters. The emission plume was identified based on fresh pollutant (e.g., particle-bound polycyclic aromatic hydrocarbons, black carbon, CO 2 and NO x ) concentration changes in combination with wind direction data. The classification into megacity influenced and background air masses allowed a characterization of the emission plume during summer and winter environmental conditions. On average, a clear increase of fresh pollutant concentrations in plume compared to background air masses was found for both seasons. For example, an average increase of 190% (+ 8.8 ng m −3 ) in summer and of 130% (+ 18.1 ng m −3 ) in winter was found for particle-bound polycyclic aromatic hydrocarbons in plume air masses. The aerosol particle size distribution in plume air masses was influenced by nucleation and growth due to coagulation and condensation in summer, while in winter only the latter process (i.e., particle growth) seemed to be initiated by urban pollution. The observed distribution of fresh pollutants in the emission plume – its cross sectional Gaussian-like profile and the exponential decrease of pollutant concentrations with increasing distance to the megacity – are in agreement with model results. Differences between model and measurements were found for plume center location, plume width and axial plume extent. In general, dilution was identified as the dominant process determining the axial variations within the Paris emission plume. For in-depth analysis of transformation processes occurring in the advected plume, simultaneous measurements at a suburban measurement site and a stationary site outside the metropolitan area using the mobile laboratory have proven to be most useful. Organic aerosol oxidation was observed in summer, while in winter transformation processes seemed to occur at a slower rate.
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  • 35
    Publication Date: 2014-12-09
    Description: A regional CO 2 observing system simulation experiment for the ASCENDS satellite mission Atmospheric Chemistry and Physics, 14, 12897-12914, 2014 Author(s): J. S. Wang, S. R. Kawa, J. Eluszkiewicz, D. F. Baker, M. Mountain, J. Henderson, T. Nehrkorn, and T. S. Zaccheo Top–down estimates of the spatiotemporal variations in emissions and uptake of CO 2 will benefit from the increasing measurement density brought by recent and future additions to the suite of in situ and remote CO 2 measurement platforms. In particular, the planned NASA Active Sensing of CO 2 Emissions over Nights, Days, and Seasons (ASCENDS) satellite mission will provide greater coverage in cloudy regions, at high latitudes, and at night than passive satellite systems, as well as high precision and accuracy. In a novel approach to quantifying the ability of satellite column measurements to constrain CO 2 fluxes, we use a portable library of footprints (surface influence functions) generated by the Stochastic Time-Inverted Lagrangian Transport (STILT) model in combination with the Weather Research and Forecasting (WRF) model in a regional Bayesian synthesis inversion. The regional Lagrangian particle dispersion model framework is well suited to make use of ASCENDS observations to constrain weekly fluxes in North America at a high resolution, in this case at 1° latitude × 1° longitude. We consider random measurement errors only, modeled as a function of the mission and instrument design specifications along with realistic atmospheric and surface conditions. We find that the ASCENDS observations could potentially reduce flux uncertainties substantially at biome and finer scales. At the grid scale and weekly resolution, the largest uncertainty reductions, on the order of 50%, occur where and when there is good coverage by observations with low measurement errors and the a priori uncertainties are large. Uncertainty reductions are smaller for a 1.57 μm candidate wavelength than for a 2.05 μm wavelength, and are smaller for the higher of the two measurement error levels that we consider (1.0 ppm vs. 0.5 ppm clear-sky error at Railroad Valley, Nevada). Uncertainty reductions at the annual biome scale range from ~40% to ~75% across our four instrument design cases and from ~65% to ~85% for the continent as a whole. Tests suggest that the quantitative results are moderately sensitive to assumptions regarding a priori uncertainties and boundary conditions. The a posteriori flux uncertainties we obtain, ranging from 0.01 to 0.06 Pg C yr −1 across the biomes, would meet requirements for improved understanding of long-term carbon sinks suggested by a previous study.
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  • 36
    Publication Date: 2014-12-09
    Description: Estimating regional fluxes of CO 2 and CH 4 using space-borne observations of XCH 4 : XCO 2 Atmospheric Chemistry and Physics, 14, 12883-12895, 2014 Author(s): A. Fraser, P. I. Palmer, L. Feng, H. Bösch, R. Parker, E. J. Dlugokencky, P. B. Krummel, and R. L. Langenfelds We use the GEOS-Chem global 3-D atmospheric chemistry transport model to interpret XCH 4 :XCO 2 column ratios retrieved from the Japanese Greenhouse Gases Observing Satellite (GOSAT). The advantage of these data over CO 2 and CH 4 columns retrieved independently using a full physics optimal estimation algorithm is that they are less prone to scattering-related regional biases. We show that the model is able to reproduce observed global and regional spatial (mean bias =0.7%) and temporal variations (global r 2 =0.92) of this ratio with a model bias 〈 2.5%. We also show that these variations are driven by emissions of CO 2 and CH 4 that are typically 6 months out of phase, which may reduce the sensitivity of the ratio to changes in either gas. To simultaneously estimate fluxes of CO 2 and CH 4 we use a maximum likelihood estimation approach. We use two approaches to resolve independent flux estimates of these two gases using GOSAT observations of XCH 4 :XCO 2 : (1) the a priori error covariance between CO 2 and CH 4 describing common source from biomass burning; and (2) also fitting independent surface atmospheric measurements of CH 4 and CO 2 mole fraction that provide additional constraints, improving the effectiveness of the observed GOSAT ratio to constrain flux estimates. We demonstrate the impact of these two approaches using numerical experiments. A posteriori flux estimates inferred using only the GOSAT ratios and taking advantage of the error covariance due to biomass burning are not consistent with the true fluxes in our experiments, as the inversion system cannot judge which species' fluxes to adjust. This reflects the weak dependence of XCH 4 :XCO 2 on biomass burning. We find that adding the surface data effectively provides an "anchor" to the inversion that dramatically improves the ability of the GOSAT ratios to infer both CH 4 and CO 2 fluxes. We show that the regional flux estimates inferred from GOSAT XCH 4 :XCO 2 ratios together with the surface mole fraction data during 2010 are typically consistent with or better than the corresponding values inferred from fitting XCH 4 or the full-physics XCO 2 data products, as judged by a posteriori uncertainties. We show that the fluxes inferred from the ratio measurements perform best over regions where there is a large seasonal cycle such as Tropical South America, for which we report a small but significant annual source of CO 2 compared to a small annual sink inferred from the XCO 2 data. We argue that given that the ratio measurements are less compromised by systematic error than the full physics data products, the resulting a~posteriori estimates and uncertainties provide a more faithful description of the truth. Based on our analysis we also argue that by using the ratios we may be reaching the current limits on the precision of these observed space-based data.
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  • 37
    Publication Date: 2014-12-13
    Description: Long-term variability of storm surge frequency in the Venice Lagoon: an update thanks to eighteenth century sea level observations Natural Hazards and Earth System Sciences Discussions, 2, 7465-7486, 2014 Author(s): F. Raicich Sea level observations made in the Venice Lagoon between 1751 and 1792 have been recovered, consisting of two time series of daily data on high and low waters at Venice and Chioggia. From comparisons with modern observations the quality of the 18th century data appears to be good enough to allow a useful analysis. A composite time series of daily mean sea level is obtained by merging the 18th century data and 1872–2004 observations at Venice Punta della Salute. The absence of reliable information on vertical references prevents the connection of the two 18th century time series with each other and with modern observations. However, daily sea level anomalies relative to the mean sea level enable to recognize storm surge events, that appear to occur more frequently in the second half of the 18th century than in the late 19th and 20th centuries, particularly during the 1751–1769 period. The record-breaking storm surge of 4 November 1966 turns out to be a remarkable event also in comparison with the events extracted from the 18th century time series. Further work is required to fill the gap between the old and modern observations.
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
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  • 38
    Publication Date: 2014-12-13
    Description: Ground-penetrating radar observations for estimating the vertical displacement of rotational landslides Natural Hazards and Earth System Sciences Discussions, 2, 7487-7506, 2014 Author(s): C. Lissak, O. Maquaire, J.-P. Malet, F. Lavigne, C. Virmoux, C. Gomez, and R. Davidson The objective of this paper is to demonstrate the applicability of Ground Penetrating Radar (GPR) for monitoring the displacement of slow-moving landslides. GPR data is used to estimate the vertical movement of rotational slides in combination with other surveying techniques. The experimental site is located along the Normandy coast (North East France) here several rotational landslides are continuously affected by a seasonal kinematic pattern (low displacement rates of 0.01 to 0.10 m yr −1 ) and periodically by major acceleration events (high displacement of 1.0 to 7.0 m per event).
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
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  • 39
    Publication Date: 2014-12-13
    Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.
    Print ISSN: 0035-8711
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  • 40
    Publication Date: 2014-12-13
    Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.
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  • 41
    Publication Date: 2014-12-13
    Description: Global representation of tropical cyclone-induced ocean thermal changes using Argo data – Part 2: Estimating air–sea heat fluxes and ocean heat content changes Ocean Science Discussions, 11, 2907-2937, 2014 Author(s): L. Cheng, J. Zhu, and R. L. Sriver We use Argo temperature data to examine changes in ocean heat content (OHC) and air–sea heat fluxes induced by tropical cyclones (TC)s on a global scale. A footprint technique that analyzes the vertical structure of cross-track thermal responses along all storm tracks during the period 2004–2012 is utilized (see part I). We find that TCs are responsible for 1.87 PW (11.05 W m −2 when averaging over the global ocean basin) of heat transfer annually from the global ocean to the atmosphere during storm passage (0–3 days) on a global scale. Of this total, 1.05 ± 0.20 PW (4.80 ± 0.85 W m −2 ) is caused by Tropical storms/Tropical depressions (TS/TD) and 0.82 ± 0.21 PW (6.25 ± 1.5 W m −2 ) is caused by hurricanes. Our findings indicate that ocean heat loss by TCs may be a substantial missing piece of the global ocean heat budget. Net changes in OHC after storm passage is estimated by analyzing the temperature anomalies during wake recovery following storm events (4–20 days after storm passage) relative to pre-storm conditions. Results indicate the global ocean experiences a 0.75 ± 0.25 PW (5.98 ± 2.1W m −2 ) net heat gain annually for hurricanes. In contrast, under TS/TD conditions, ocean experiences 0.41 ± 0.21 PW (1.90 ± 0.96 W m −2 ) net ocean heat loss, suggesting the overall oceanic thermal response is particularly sensitive to the intensity of the event. The net ocean heat uptake caused by all storms is 0.34 PW.
    Print ISSN: 1812-0806
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  • 42
    Publication Date: 2014-12-13
    Description: The dependence of divertor asymmetry and scrape-off layer (SOL) flow on heating power has been investigated in the Experimental Advanced Superconducting Tokamak (EAST). Divertor plasma exhibits an outboard-enhanced in-out asymmetry in heat flux in lower single null configuration for in reversed (ion ∇ B drift direction toward the upper X-point) field directions. Upper single null exhibits an inboard-favored asymmetry in low heating power condition, while exhibits an outboard-favored asymmetry when increasing the heating power. Double null has the strongest in-out asymmetry in heat flux, favoring the outer divertor. The in-out asymmetry ratios of q t , out / q t , in and P out / P total increase with the power across the separatrix P loss , which is probably induced by the enhanced radial particle transport due to a large pressure gradient. The characteristics of the measured SOL parallel flow under various discharge conditions are consistent with the Pfirsch-Schlüter (PS) flow with the parallel Mach number M ∥ decreasing with the line averaged density but increasing with P loss , in the same direction as the PS flow. The contributions of both poloidal E × B drift and parallel flow on poloidal particle transport in SOL on EAST are also assessed.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
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  • 43
    facet.materialart.
    Unknown
    American Institute of Physics (AIP)
    Publication Date: 2014-12-13
    Description: Magnetic islands have been implemented in the gyrokinetic toroidal code to study the effects of the islands on microturbulence. The pressure profile flattening is verified in the simulation with the islands. Simulations of ion temperature gradient instability find that different toroidal modes are linearly coupled together and that toroidal spectra become broader when the island width increases. The real frequencies and growth rates of different toroidal modes approach each other with the averaged value independent of the island width. The linear mode structures are enhanced at the island separatrices and weakened at the island centers, consistent with the flattening of the pressure profile inside the islands.
    Print ISSN: 1070-664X
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  • 44
    Publication Date: 2014-12-13
    Description: The slow motion of a circular cylinder in a plane Poiseuille flow in a microchannel is analyzed for a wide range of cylinder radii and positions across the channel. The cylinder translates parallel to the channel walls and rotates about its axis. The Stokes approximation is used and the problem is solved analytically using the Papkovich-Fadle eigenfunction expansion and the least-squares method. The stream function and the pressure distribution of the flow field are obtained as results. The force and moment exerted on the cylinder, and the pressure change far from the cylinder, are calculated and shown as functions of the size and location of the cylinder. The results confirm some reciprocal relations exactly. In particular, the translational and rotational velocities of the drifting cylinder in the existing Poiseuille flow are determined. The induced pressure change, when the cylinder drifts in the Poiseuille flow, is also calculated. Some typical streamline patterns, depending on the size and location of the cylinder, are shown and discussed. When the cylinder translates and/or rotates in the channel blocked at infinity, a series of Moffatt eddies appears far from the cylinder in the channel, as expected.
    Print ISSN: 1070-6631
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  • 45
    facet.materialart.
    Unknown
    American Institute of Physics (AIP)
    Publication Date: 2014-12-13
    Description: Interactions between capillary and elastic effects are relevant to a variety of applications from micro- and nano-scale manufacturing to biological systems. In this work, we investigate capillary flows in flexible, millimeter-scale cylindrical elastic tubes. We demonstrate that surface tension can cause sufficiently flexible tubes to collapse and coalesce spontaneously through non-axisymmetric buckling, and develop criteria for the initial deformation and complete collapse of a circular tube. Experimental results for capillary rise and evaporation of a liquid in a flexible tube are presented, and several regimes are seen for the equilibrium state of a flexible tube deforming under capillary pressure. Deformations of the tube walls are measured in different regimes and compared with a shell theory model. Analysis and experimental results show that despite the complex and non-axisymmetric deformed shapes of cylindrical structures, the elastocapillary length used in previous literature for flat plates and sheets can be used to predict the behavior of flexible tubes.
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  • 46
    Publication Date: 2014-12-13
    Description: A study is presented for the oblique propagation of ion acoustic cnoidal waves in a magnetized plasma consisting of cold ions and two temperature superthermal electrons modelled by kappa-type distributions. Using the reductive perturbation method, the nonlinear Korteweg de-Vries equation is derived, which further gives the solutions with a special type of cnoidal elliptical functions. Both compressive and rarefactive structures are found for these cnoidal waves. Nonlinear periodic cnoidal waves are explained in terms of plasma parameters depicting the Sagdeev potential and the phase curves. It is found that the density ratio of hot electrons to ions μ significantly modifies compressive/refractive wave structures. Furthermore, the combined effects of superthermality of cold and hot electrons κ c , κ h , cold to hot electron temperature ratio σ , angle of propagation and ion cyclotron frequency ω ci have been studied in detail to analyze the height and width of compressive/refractive cnoidal waves. The findings in the present study could have important implications in understanding the physics of electrostatic wave structures in the Saturn's magnetosphere where two temperature superthermal electrons are present.
    Print ISSN: 1070-664X
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  • 47
    Publication Date: 2014-12-13
    Description: A smart monitoring system for superconducting cable test is proposed with an adaptive current control of a superconducting transformer secondary. The design, based on Fuzzy Gain Scheduling, allows the controller parameters to adapt continuously, and finely, to the working variations arising from transformer nonlinear dynamics. The control system is integrated in a fully digital control loop, with all the related benefits, i.e., high noise rejection, ease of implementation/modification, and so on. In particular, an accurate model of the system, controlled by a Fuzzy Gain Scheduler of the superconducting transformer, was achieved by an experimental campaign through the working domain at several current ramp rates. The model performance was characterized by simulation, under all the main operating conditions, in order to guide the controller design. Finally, the proposed monitoring system was experimentally validated at European Organization for Nuclear Research (CERN) in comparison to the state-of-the-art control system [P. Arpaia, L. Bottura, G. Montenero, and S. Le Naour, “Performance improvement of a measurement station for superconducting cable test,” Rev. Sci. Instrum.83, 095111 (2012)] of the Facility for the Research on Superconducting Cables, achieving a significant performance improvement: a reduction in the system overshoot by 50%, with a related attenuation of the corresponding dynamic residual error (both absolute and RMS) up to 52%.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 48
    Publication Date: 2014-12-13
    Description: This paper presents a method which uses the characteristics of the etch pits induced in a polyallyl-diglycol-carbonate (PADC) detector of the CR-39/PM-355 type to estimate particle energy. This method is based on the data provided by a semiautomatic system that selects tracks according to two parameters, crater diameters, and mean gray level values. In this paper we used the results of the calibration measurements that were obtained in our laboratory in the period 2000–2014. Combining the information on the two parameters it is possible to determine unambiguously the incident projectile energy values. The paper presents the results of an attempt to estimate the energy resolution of the method when analyzing the tracks produced in the CR-39/PM-355 detector by energetic ions such as alpha particles, protons, and deuterons. We discuss the energy resolution of the measurement of light charged particle energy which is based on the parameters (crater diameter and mean gray level value) of tracks induced in solid state nuclear track detectors of the PADC type.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 49
    Publication Date: 2014-12-13
    Description: In this work, an automated apparatus for driving single electrostatic probes and acquiring the plasma-related data has been designed and fabricated. The voltage range of the present system is ±110 V with an adjustable voltage step as low as 3 mV. Voltage and current measurements are carried out with high resolution and high accuracy circuits, both based on 16 bit analog-to-digital converters. The code embedded in a micro-controller, schedules the operation of the device and transfers the experimental data to a personal computer. The modular design of the system makes possible its modification and thus increases its adaptability to different plasma setups. Finally, the reliable operation of the entire device is confirmed by tests in Electron Cyclotron Resonance plasma.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 50
    Publication Date: 2014-12-16
    Description: For magnon spintronic applications, the detailed knowledge of spin wave (SW) beam dispersion, transmission (reflection) of SWs passing through (reflected from) interfaces, or borders or the scattering of SWs by inhomogeneities is crucial. These wave properties are decisive factors on the usefulness of a particular device. Here, we demonstrate, using micromagnetic simulations supported by an analytical model, that the Goos-Hänchen (GH) shift exists for SW reflecting from thin film edge and that with the effect becomes observable. We show that this effect will exist for a broad range of frequencies in the dipole-exchange range, with the magnetization degree of pinning at the film edge as the crucial parameter, whatever its nature. Moreover, we have also found that the GH effect can be accompanied or even dominating by a bending of the SW beam due to the inhomogeneity of the internal magnetic field. This inhomogeneity, created by demagnetizing field taking place at the film edge, causes gradual change of SWs refractive index. The refraction of the SW beams by the non-uniformity of the magnetic field enables the exploration of graded index magnonics and metamaterial properties for the transmission and processing of information at nanoscale.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
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  • 51
    Publication Date: 2014-12-16
    Description: As a non-magnetic heavy metal is attached to a ferromagnet, a vertically flowing heat-driven spin current is converted to a transverse electric voltage, which is known as the longitudinal spin Seebeck effect (SSE). If the ferromagnet is a metal, this voltage is also accompanied by voltages from two other sources, i.e., the anomalous Nernst effect in both the ferromagnet and the proximity-induced ferromagnetic boundary layer. By properly identifying and carefully separating those different effects, we find that in this pure spin current circuit the additional spin current drawn by the heavy metal generates another significant voltage by the ferromagnetic metal itself which should be present in all relevant experiments.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
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  • 52
    Publication Date: 2014-12-16
    Description: We introduce a confocal shift-interferometer based on optical fibers. The presented spectroscopy allows measuring coherence maps of luminescent samples with a high spatial resolution even at cryogenic temperatures. We apply the spectroscopy onto electrostatically trapped, dipolar excitons in a semiconductor double quantum well. We find that the measured spatial coherence length of the excitonic emission coincides with the point spread function of the confocal setup. The results are consistent with a temporal coherence of the excitonic emission down to temperatures of 250 mK.
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    Electronic ISSN: 1077-3118
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  • 53
    Publication Date: 2014-12-16
    Description: We demonstrate enhanced hydrogen generation rates at high pH using colloidal cadmium sulphide nanorods decorated with Pt nanoparticles. We introduce a simplified procedure for the decoration and subsequent hydrogen generation, reducing both the number of working steps and the materials costs. Different Pt precursor concentrations were tested to reveal the optimal conditions for the efficient hydrogen evolution. A sharp increase in hydrogen evolution rates was measured at pH 13 and above, a condition at which the surface charge transfer was efficiently mediated by the formation of hydroxyl radicals and further consumption by the sacrificial triethanolamine hole scavenger.
    Electronic ISSN: 2166-532X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 54
    Publication Date: 2014-12-16
    Description: Spatial gaps between grains and other grains, substrates, or electrodes in organic electronic devices are one of the causes of the reduction in the electrical characteristics. In this study, we demonstrate that cold isostatic pressing (CIP) is an effective method to crush the gaps and enhance the electrical characteristics. CIP of metal-free phthalocyanine (H 2 PC) films induced a decrease in the film thickness by 34%–40% because of the gap crush. The connection of smaller grains into a larger grain and planarization of the film surface were also observed in the CIP film. The crystal axes of the H 2 PC crystallites were rearranged from the a-axis to the c-axis of the α-phase crystal structure in a direction perpendicular to the substrate by CIP, indicating favorable hole injection and transport in this direction because of a better overlap of π orbitals. Thermally stimulated current measurements showed that deep hole traps disappeared and the total hole-trap density decreased after CIP. These CIP-induced changes of the film thicknesses, crystal axes and the hole traps lead to a marked increase in the hole mobility of the H 2 PC films from 2.0 × 10 −7 to 4.0 × 10 −4 cm 2 /V s by 2000 times in the perpendicular direction. We believe that these findings are important for unveiling the underlying carrier injection and transport mechanisms of organic films and for enhancing the performance of future organic electronic devices.
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  • 55
    Publication Date: 2014-12-16
    Description: Anomalous Hall effect (AHE) based ferromagnetic resonance (FMR) measurements were carried out on perpendicularly magnetized Co/Pt multilayer single dots of 0.4–3  μ m in diameter. The resonance behavior was measured by detecting the decrease of perpendicular magnetization component due to magnetization precession. Resonance behavior was observed as a clear decrease of Hall voltages, and the obtained resonance fields were consistent with the results of vector-network-analyzer FMR. Spin-waves with cylindrical symmetry became significant by decreasing the dot diameter, and quantized multiple resonances were observed in the dot of 0.4 μm in diameter. The AHE based FMR proposed here is a powerful method to approach magnetization dynamics including spin waves and non-linear behavior excited in a finite nanostructure.
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  • 56
    Publication Date: 2014-12-16
    Description: Development and field testing of a rapid and ultra-stable atmospheric carbon dioxide spectrometer Atmospheric Measurement Techniques, 7, 4445-4453, 2014 Author(s): B. Xiang, D. D. Nelson, J. B. McManus, M. S. Zahniser, R. A. Wehr, and S. C. Wofsy We present field test results for a new spectroscopic instrument to measure atmospheric carbon dioxide (CO 2 ) with high precision (0.02 μmol mol −1 , or ppm at 1 Hz) and demonstrate high stability (within 0.1 ppm over more than 8 months), without the need for hourly, daily, or even monthly calibration against high-pressure gas cylinders. The technical novelty of this instrument (ABsolute Carbon dioxide, ABC) is the spectral null method using an internal quartz reference cell with known CO 2 column density. Compared to a previously described prototype, the field instrument has better stability and benefits from more precise thermal control of the optics and more accurate pressure measurements in the sample cell (at the mTorr level). The instrument has been deployed at a long-term ecological research site (the Harvard Forest, USA), where it has measured for 8 months without on-site calibration and with minimal maintenance, showing drift bounds of less than 0.1 ppm. Field measurements agree well with those of a commercially available cavity ring-down CO 2 instrument (Picarro G2301) run with a standard calibration protocol. This field test demonstrates that ABC is capable of performing high-accuracy, unattended, continuous field measurements with minimal use of reference gas cylinders.
    Print ISSN: 1867-1381
    Electronic ISSN: 1867-8548
    Topics: Geosciences
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  • 57
    Publication Date: 2014-12-16
    Description: Meteorological factors controlling low-level continental pollutant outflow across a coast Atmospheric Chemistry and Physics, 14, 13295-13312, 2014 Author(s): D. L. Peake, H. F. Dacre, J. Methven, and O. Coceal Coastal outflow describes the horizontal advection of pollutants from the continental boundary layer (BL) across a coastline. The outflow can ventilate polluted continental BLs and thus regulate air quality in highly populated coastal regions. This paper investigates the factors controlling coastal outflow and quantifies their importance as a ventilation mechanism. Tracers in the Met Office Unified Model (MetUM) are used to examine the magnitude and variability of coastal outflow over the eastern United States during summer 2004. Over the 4 week period examined, ventilation of tracer from the continental BL via coastal outflow occurs with the same magnitude as vertical ventilation via convection and advection. The relative importance of tracer decay rate, cross-coastal advection rate, and a parameter based on the relative continental and marine BL heights on coastal outflow is assessed by reducing the problem to a time-dependent box model. The ratio of the advection rate and decay rate is a dimensionless parameter which determines whether tracers are long-lived or short-lived. Long- and short-lived tracers exhibit different behaviours with respect to coastal outflow. Short-lived tracers exhibit large diurnal variability in coastal outflow but long-lived tracers do not. For short-lived tracers, increasing the advection rate increases the diurnally averaged magnitude of coastal outflow, but this has the opposite effect for very long-lived tracers. By using the box-model solutions to interpret the MetUM simulations, a land width is determined which represents the distance inland over which emissions contribute significantly to coastal outflow. A land width of between 100 and 400 km is found to be representative for a tracer with a lifetime of 24 h.
    Print ISSN: 1680-7316
    Electronic ISSN: 1680-7324
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  • 58
    Publication Date: 2014-12-14
    Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 59
    Publication Date: 2014-12-16
    Description: Continental Portuguese Territory Flood Susceptibility Index – contribution for a vulnerability index Natural Hazards and Earth System Sciences Discussions, 2, 7521-7552, 2014 Author(s): R. Jacinto, N. Grosso, E. Reis, L. Dias, F. D. Santos, and P. Garrett This work defines a national flood susceptibility index for the Portuguese continental territory, by proposing the aggregation of different variables which represent natural conditions for permeability, runoff and accumulation. This index is part of the national vulnerability index developed in the scope of Flood Maps in Climate Change Scenarios (CIRAC) project, supported by the Portuguese Association of Insurers (APS). This approach expands on previous works by trying to bridge the gap between different floods mechanisms (e.g. progressive and flash floods) occurring at different spatial scales in the Portuguese territory through: (a) selecting homogeneously processed datasets, (b) aggregating their values to better translate the spatially continuous and cumulative influence in floods at multiple spatial scales. Results show a good ability to capture, in the higher susceptibility classes, different flood types: progressive floods and flash floods. Lower values are usually related to: mountainous areas, low water accumulation potential and more permeable soils. Validation with independent flood datasets confirmed these index characteristics, although some overestimation can be seen in the southern region of Alentejo where, due to a dense hydrographic network and an overall low slope, floods are not as frequent as a result of lower precipitation mean values. Future work will focus on: (i) including extreme precipitation datasets to represent the triggering factor, (ii) improving representation of smaller and stepper basins, (iii) optimizing variable weight definition process, (iii) developing more robust independent flood validation datasets.
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
    Published by Copernicus
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  • 60
    Publication Date: 2014-12-16
    Description: Simple, affordable and sustainable borehole observatories for complex monitoring objectives Geoscientific Instrumentation, Methods and Data Systems Discussions, 4, 653-681, 2014 Author(s): A. Kopf, T. Freudenthal, V. Ratmeyer, M. Bergenthal, M. Lange, T. Fleischmann, S. Hammerschmidt, C. Seiter, and G. Wefer Seafloor drill rigs are remotely operated systems that provide a cost effective means to recover sedimentary records of the upper sub-seafloor deposits. Recent increases in their payload included downhole logging tools or autoclave coring systems. We here report on another milestone in using seafloor rigs: the development and installation of shallow borehole observatories. Three different systems have been developed for the MARUM-MeBo seafloor drill, which is operated by MARUM, University of Bremen, Germany. A simple design, the MeBoPLUG, separates the inner borehole from the overlying ocean by using o-ring seals at the conical threads of the drill pipe. The systems are self-contained and include data loggers, batteries, thermistors and a differential pressure sensor. A second design, the so-called MeBoCORK, is more sophisticated and also hosts an acoustic modem for data transfer and, if desired, fluid sampling capability using osmotic pumps. Of these MeBoCORKs, two systems have to be distinguished: the CORK-A (A = autonomous) can be installed by the MeBo alone and monitors pressure and temperature inside and above the borehole (the latter for reference). The CORK-B (B = bottom) has a higher payload and can additionally be equipped with geochemical, biological or other physical components. Owing to its larger size, it is installed by ROV and utilises a hotstab connection in the upper portion of the drill string. Either design relies on a hotstab connection from beneath which coiled tubing with a conical drop weight is lowered to couple to the formation. These tubes are fluid-saturated and either serve to transmit pore pressure signals or collect pore water in the osmo-sampler. The third design, the MeBoPUPPI ( P op- U p P ore P ressure I nstrument), is similar to the MeBoCORK-A and monitors pore pressure and temperature in a self-contained manner. Instead of transferring data upon command using an acoustic modem, the MeBoPUPPI contains a pop-up telemetry with Iridium link. After a predefined period, the data unit with satellite link is released, ascends to the sea surface, and remains there for up to two weeks while sending the long-term data sets to shore. In summer 2012, two MeBoPLUGs, one MeBoCORK-A and one MeBoCORK-B were installed with MeBo on German RV Sonne in the Nankai Trough area, Japan. We have successfully downloaded data from the CORKs, attesting that coupling to the formation worked and pressure records were elevated relative to the seafloor reference. In the near future, we will further deploy the first two MeBoPUPPIs. Recovery of all monitoring systems by ROV is planned for 2016.
    Electronic ISSN: 2193-0872
    Topics: Geosciences
    Published by Copernicus
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  • 61
    Publication Date: 2014-12-16
    Description: Dye tracing for investigating flow and transport properties of hydrocarbon-polluted Rabots glaciär, Kebnekaise, Sweden Hydrology and Earth System Sciences Discussions, 11, 13711-13744, 2014 Author(s): C. C. Clason, C. Coch, J. Jarsjö, K. Brugger, P. Jansson, and G. Rosqvist Over 11 000 L of hydrocarbon pollution was deposited on the surface of Rabots glaciär on the Kebnekaise Massif, northern Sweden, following the crash of a Royal Norwegian Air Force aircraft in March 2012. An environmental monitoring programme was subsequently commissioned, including water, snow and ice sampling. The scientific programme further included a series of dye tracing experiments during the 2013 melt season, conducted to investigate flow pathways for pollutants through the glacier hydrological system, and to gain new insight to the internal hydrological system of Rabots glaciär. Results of dye tracing reveal a degree of homogeneity in the topology of the drainage system throughout July and August, with an increase in efficiency as the season progresses, as reflected by decreasing temporary storage and dispersivity. Early onset of melting likely led to formation of an efficient, discrete drainage system early in the melt season, subject to decreasing sinuosity and braiding as the season progressed. Analysis of turbidity-discharge hysteresis further supports the formation of discrete, efficient drainage, with clockwise diurnal hysteresis suggesting easy mobilisation of readily-available sediments in channels. Dye injection immediately downstream of the pollution source zone revealed prolonged storage of dye followed by fast, efficient release. Twinned with a low dye recovery, and supported by sporadic detection of hydrocarbons in the proglacial river, we suggest that meltwater, and thus pollutants in solution, may be released periodically from this zone of the glacier hydrological system. The here identified dynamics of dye storage, dispersion and breakthrough indicate that the ultimate fate and permanence of pollutants in the glacier system is likely to be governed by storage of pollutants in the firn layer and ice mass, or within the internal hydrological system, where it may refreeze. This shows that future studies on the fate of hydrocarbons in pristine, glaciated mountain environments should address the extent to which pollutants in solution act like water molecules or whether they are more susceptible to, for example, refreezing into the surrounding ice, becoming stuck in micro-fractures and pore spaces, or sorption onto subglacial sediments.
    Print ISSN: 1812-2108
    Electronic ISSN: 1812-2116
    Topics: Geography , Geosciences
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  • 62
    Publication Date: 2014-12-16
    Description: We introduce a method for generating rational extensions of time-dependent potentials, such that the associated Schrödinger equation admits solutions in terms of exceptional orthogonal polynomials. Our method is applicable to position-dependent Schrödinger equations, as well as to their conventional counterparts for constant mass.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
    Topics: Mathematics , Physics
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  • 63
    facet.materialart.
    Unknown
    American Institute of Physics (AIP)
    Publication Date: 2014-12-16
    Description: In this paper, we prove the existence of the Stark-Wannier quantum resonances for one-dimensional Schrödinger operators with smooth periodic potential and small external homogeneous electric field. Such a result extends the existence result previously obtained in the case of periodic potentials with a finite number of open gaps.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
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  • 64
    Publication Date: 2014-12-16
    Description: We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the closed and two in the open conformations. Even though the proteins belong to the same fold, the model distinguishes the properties of these proteins in a way which is consistent with experiments. For instance, the thermophilic proteins are more stable thermodynamically than their mesophilic and cryophilic homologues, which we observe both in the magnitude of thermal fluctuations near the native state and in the kinetics of thermal unfolding. The level of stability correlates with the average coordination number for amino acid contacts and with the degree of structural compactness. The pattern of positional fluctuations along the sequence in the closed conformation is different than in the open conformation, including within the active site. The modes of correlated and anticorrelated movements of pairs of amino acids forming the active site are very different in the open and closed conformations. Taken together, our results show that the precise location of amino acid contacts in the native structure appears to be a critical element in explaining the similarities and differences in the thermodynamic properties, local flexibility, and collective motions of the different forms of the enzyme.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
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  • 65
    Publication Date: 2014-12-16
    Description: We give an algorithm which produces a unique element of the Clifford group on n qubits ( C n ) from an integer 0 ≤ i 〈 C n (the number of elements in the group). The algorithm involves O ( n 3 ) operations and provides, in addition to a canonical mapping from the integers to group elements g , a factorization of g into a sequence of at most 4 n symplectic transvections. The algorithm can be used to efficiently select random elements of C n which are often useful in quantum information theory and quantum computation. We also give an algorithm for the inverse map, indexing a group element in time O ( n 3 ).
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
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  • 66
    Publication Date: 2014-12-16
    Print ISSN: 0022-2488
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  • 67
    Publication Date: 2014-12-16
    Description: We present laboratory experimental results demonstrating that librational forcing of an ellipsoidal container of water can produce intense motions through the mechanism of a libration driven elliptical instability (LDEI). These libration studies are conducted using an ellipsoidal acrylic container filled with water. A particle image velocimetry method is used to measure the 2D velocity field in the equatorial plane over hundreds libration cycles for a fixed Ekman number, E = 2 × 10 −5 . In doing so, we recover the libration induced base flow and a time averaged zonal flow. Further, we show that LDEI in non-axisymmetric container geometries is capable of driving both intermittent and saturated turbulent motions in the bulk fluid. Additionally, we measure the growth rate and amplitude of the LDEI induced excited flow in a fully ellipsoidal container at more extreme parameters than previously studied [Noir et al. , “Experimental study of libration-driven flows in nonaxisymmetric containers,” Phys. Earth Planet. Inter. 204-205 , 1 (2012); Cébron et al. , Phys. Fluids 24 , 061703, “Libration driven elliptical instability,” (2012)]. Excitation of bulk filling turbulence by librational forcing provides a mechanism for transferring rotational energy into turbulent fluid motion and thus can play an important role in the thermal evolution, interior dynamics, and magneto-hydrodynamics of librating bodies, as appear to be common in solar system settings [e.g., Comstock and Bills, “A solar system survey of forced librations in longitude,” J. Geophys. Res. Planets 108 , 1 (2003)].
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
    Topics: Physics
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  • 68
    Publication Date: 2014-12-16
    Description: We numerically study the displacement flow of two iso-viscous Newtonian fluids in an inclined two-dimensional channel, formed by two parallel plates. The results are complementary to our previous studies on displacement flows in pipes and channels. The heavier displacing fluid moves the lighter displaced fluid in the downward direction. Three dimensionless groups largely describe these flows: the densimetric Froude number ( Fr ), the Reynolds number ( Re ), and the duct inclination (β). As a first order approximation, we are able to classify different flow regimes phenomenologically in a two-dimensional ( Fr ; Re cosβ/ Fr )-plane and provide leading order expressions for the transitions between different regimes. The stabilizing and/or de-stabilizing effects of the imposed mean flow on buoyant exchange flows (zero imposed velocity) are described for a broad range of dimensionless parameters.
    Print ISSN: 1070-6631
    Electronic ISSN: 1089-7666
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  • 69
    Publication Date: 2014-12-16
    Description: Compressible granular materials are involved in many applications, some of them being related to energetic porous media. Gas permeation effects are important during their compaction stage, as well as their eventual chemical decomposition. Also, many situations involve porous media separated from pure fluids through two-phase interfaces. It is thus important to develop theoretical and numerical formulations to deal with granular materials in the presence of both two-phase interfaces and gas permeation effects. Similar topic was addressed for fluid mixtures and interfaces with the Discrete Equations Method (DEM) [R. Abgrall and R. Saurel, “Discrete equations for physical and numerical compressible multiphase mixtures,” J. Comput. Phys. 186 (2), 361-396 (2003)] but it seemed impossible to extend this approach to granular media as intergranular stress [K. K. Kuo, V. Yang, and B. B. Moore, “Intragranular stress, particle-wall friction and speed of sound in granular propellant beds,” J. Ballist. 4 (1), 697-730 (1980)] and associated configuration energy [J. B. Bdzil, R. Menikoff, S. F. Son, A. K. Kapila, and D. S. Stewart, “Two-phase modeling of deflagration-to-detonation transition in granular materials: A critical examination of modeling issues,” Phys. Fluids 11 , 378 (1999)] were present with significant effects. An approach to deal with fluid-porous media interfaces was derived in Saurel et al. [“Modelling dynamic and irreversible powder compaction,” J. Fluid Mech. 664 , 348-396 (2010)] but its validity was restricted to weak velocity disequilibrium only. Thanks to a deeper analysis, the DEM is successfully extended to granular media modelling in the present paper. It results in an enhanced version of the Baer and Nunziato [“A two-phase mixture theory for the deflagration-to-detonation transition (DDT) in reactive granular materials,” Int. J. Multiphase Flow 12 (6), 861-889 (1986)] model as symmetry of the formulation is now preserved. Several computational examples are shown to validate and illustrate method’s capabilities.
    Print ISSN: 1070-6631
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  • 70
    Publication Date: 2014-12-16
    Description: We perform a theoretical and numerical study of the Coulomb-driven electroconvection flow of a dielectric liquid between two coaxial cylinders. The specific case, where the inner to outer diameter ratio is 0.5, is analyzed. A strong unipolar injection of ions either from the inner or outer cylinder is considered to introduce free charge carriers into the system. A finite volume method is used to solve all governing equations including Navier-Stokes equations and a simplified set of Maxwell’s equations. The flow is characterized by a subcritical bifurcation in the finite amplitude regime. A linear stability criterion and a nonlinear one that correspond to the onset and stop of the flow motion, respectively, are linked with a hysteresis loop. In addition, we also explore the behavior of the system for higher values of the stability parameter. For inner injection, we observe a transition between the patterns made of 7 and 8 cells, before an oscillatory regime is attained. Such a transition leads to a second finite amplitude stability criterion. A simple modal analysis reveals that the competition of different modes is at the origin of this behavior. The charge density, as well as velocity field distributions is provided to help understand the bifurcation behavior.
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  • 71
    Publication Date: 2014-12-16
    Description: We report on the production of metal ions of magnesium and zinc in the beam plasma formed by a forevacuum-pressure electron source. Magnesium and zinc vapor were generated by electron beam evaporation from a crucible and subsequently ionized by electron impact from the e-beam itself. Both gaseous and metallic plasmas were separately produced and characterized using a modified RGA-100 quadrupole mass-spectrometer. The fractional composition of metal isotopes in the plasma corresponds to their fractional natural abundance.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
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  • 72
    Publication Date: 2014-12-16
    Description: To better understand the role of residual electrons in the repeatability of an atmospheric pressure plasma plume, the characteristics of a helium plasma jet from the 1st, 2nd,… until the repeatable discharge pulse are investigated for the first time. It's found that the longest plasma plume is achieved in the 1st discharge pulse. The length of the plasma plume becomes shorter and shorter and reaches a constant value in the 3rd discharge pulse and keeps the same for the following pulses. The dynamics of the 1st discharge pulse show that the plasma bullet appears random in nature. Two photomultiplier tubes are used to distinguish the two potential factors that could result in the stochastic dynamics of the plasma bullet, i.e., stochastic ignition of the plasma and the stochastic propagation velocity. The results show that the stochastic propagation velocity occurs only in the 1st and the 2nd discharge pulses, while the stochastic ignition of the plasma presents until the 100th pulse. The dynamics of the plasma propagation become repeatable after about 100 pulses. Detail analysis shows that the repeatability of plasma bullet is due to the residual electrons density. The residual electron density of 10 9  cm −3 or higher is needed for repeatable discharges mode.
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  • 73
    Publication Date: 2014-12-16
    Description: We present a full two-fluid magnetohydrodynamic (MHD) description for a completely ionized hydrogen plasma, retaining the effects of the Hall current, electron pressure, and electron inertia. According to this description, each plasma species introduces a new spatial scale: the ion inertial length λ i and the electron inertial length λ e , which are not present in the traditional MHD description. In the present paper, we seek for possible changes in the energy power spectrum in fully developed turbulent regimes, using numerical simulations of the two-fluid equations in two-and-a-half dimensions. We have been able to reproduce different scaling laws in different spectral ranges, as it has been observed in the solar wind for the magnetic energy spectrum. At the smallest wavenumbers where plain MHD is valid, we obtain an inertial range following a Kolmogorov k −5∕3 law. For intermediate wavenumbers such that λ i − 1 ≪ k ≪ λ e − 1 , the spectrum is modified to a k −7∕3 power-law, as has also been obtained for Hall-MHD neglecting electron inertia terms. When electron inertia is retained, a new spectral region given by k 〉 λ e − 1 arises. The power spectrum for magnetic energy in this region is given by a k −11∕3 power law. Finally, when the terms of electron inertia are retained, we study the self-consistent electric field. Our results are discussed and compared with those obtained in the solar wind observations and previous simulations.
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  • 74
    Publication Date: 2014-12-16
    Description: A novel mechanism of collisionless heating in large planar arrays of small inductive coils operated at radio frequencies is presented. In contrast to the well-known case of non-local heating related to the transversal conductivity, when the electrons move perpendicular to the planar coil, we investigate the problem of electrons moving in a plane parallel to the coils. Two types of periodic structures are studied. Resonance velocities where heating is efficient are calculated analytically by solving the Vlasov equation. Certain scaling parameters are identified. The concept is further investigated by a single particle simulation based on the ergodic principle and combined with a Monte Carlo code allowing for collisions with Argon atoms. Resonances, energy exchange, and distribution functions are obtained. The analytical results are confirmed by the numerical simulation. Pressure and electric field dependences are studied. Stochastic heating is found to be most efficient when the electron mean free path exceeds the size of a single coil cell. Then the mean energy increases approximately exponentially with the electric field amplitude.
    Print ISSN: 1070-664X
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  • 75
    Publication Date: 2014-12-16
    Description: A pulsed slow-positron beam generated by an electron linear accelerator was directly used for positron annihilation lifetime spectroscopy without any positron storage devices. A waveform digitizer was introduced to simultaneously capture multiple gamma-ray signals originating from positron annihilation events during a single accelerator pulse. The positron pulse was chopped and bunched with the chopper signals also sent to the waveform digitizer. Time differences between the annihilation gamma-ray and chopper peaks were calculated and accumulated as lifetime spectra in a computer. The developed technique indicated that positron annihilation lifetime spectroscopy can be performed in a 20 μ s time window at a pulse repetition rate synchronous with the linear accelerator. Lifetime spectra of a Kapton sheet and a thermally grown SiO 2 layer on Si were successfully measured. Synchronization of positron lifetime measurements with pulsed ion irradiation was demonstrated by this technique.
    Print ISSN: 0034-6748
    Electronic ISSN: 1089-7623
    Topics: Electrical Engineering, Measurement and Control Technology , Physics
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  • 76
    Publication Date: 2014-12-17
    Description: Surface nuclear magnetic resonance (surface-NMR) is a promising technique for exploring shallow subsurface aquifer structures. Surface-NMR can be applied in environments that are characterized as a 1-D layered Earth. The technique utilizes a single loop and is referred to as magnetic resonance sounding. The technique referred to as magnetic resonance tomography (MRT) allows complex 2-D aquifer structures to be explored. Currently, MRT requires multiple loops and a roll along measurement scheme, which causes long survey time. We propose a loop layout using an elongated transmitter and an in-loop receiver arrays (ETRA) to conduct a 2-D survey with just one measurement. We present a comprehensive comparison between the new layout and the common approaches based on sensitivity and resolution analyses and show synthetic and field data. The results show that ETRA generates subsurface images at sufficient resolution with significantly lower survey times than other loop layouts.
    Keywords: Geomagnetism, Rock Magnetism and Palaeomagnetism
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 77
    Publication Date: 2014-12-17
    Description: Measurements of ground deformation can be used to identify and interpret geophysical processes occurring at volcanoes. Most studies rely on a single geodetic technique, or fit a geophysical model to the results of multiple geodetic techniques. Here we present a methodology that combines GPS, Total Station measurements and InSAR into a single reference frame to produce an integrated 3-D geodetic velocity surface without any prior geophysical assumptions. The methodology consists of five steps: design of the network, acquisition and processing of the data, spatial integration of the measurements, time series computation and finally the integration of spatial and temporal measurements. The most significant improvements of this method are (1) the reduction of the required field time, (2) the unambiguous detection of outliers, (3) an increased measurement accuracy and (4) the construction of a 3-D geodetic velocity field. We apply this methodology to ongoing motion on Arenal's western flank. Integration of multiple measurement techniques at Arenal volcano revealed a deformation field that is more complex than that described by individual geodetic techniques, yet remains consistent with previous studies. This approach can be applied to volcano monitoring worldwide and has the potential to be extended to incorporate other geodetic techniques and to study transient deformation.
    Keywords: Gravity, Geodesy and Tides
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 78
    Publication Date: 2014-12-16
    Description: Air temperature variability over three glaciers in the Ortles-Cevedale (Italian Alps): effects of glacier disintegration, intercomparison of calculation methods, and impacts on mass balance modeling The Cryosphere Discussions, 8, 6147-6192, 2014 Author(s): L. Carturan, F. Cazorzi, F. De Blasi, and G. Dalla Fontana Glacier mass balance models rely on accurate spatial calculation of input data, in particular air temperature. Lower temperatures (the so-called glacier cooling effect), and lower temperature variability (the so-called glacier damping effect) generally occur over glaciers, compared to ambient conditions. These effects, which depend on the geometric characteristics of glaciers and display a high spatial and temporal variability, have been mostly investigated on medium- to large-size glaciers so far, while observations on smaller ice bodies are scarce. Using a dataset from 8 on-glacier and 4 off-glacier weather stations, collected in summer 2010 and 2011, we analyzed the air temperature variability and wind regime over three different glaciers in the Ortles-Cevedale. The magnitude of the cooling effect and the occurrence of katabatic boundary layer (KBL) processes showed remarkable differences among the three ice bodies, suggesting the likely existence of important reinforcing mechanisms during glacier decay and disintegration. None of the methods proposed in the literature for calculating on-glacier temperature from off-glacier data fully reproduced our observations. Among them, the more physically-based procedure of Greuell and Böhm (1998) provided the best overall results where the KBL prevail, but it was not effective elsewhere (i.e. on smaller ice bodies and close to the glacier margins). The accuracy of air temperature estimations strongly impacted the results from a mass balance model which was applied to the three investigated glaciers. Most importantly, even small temperature deviations caused distortions in parameter calibration, thus compromising the model generalizability.
    Print ISSN: 1994-0432
    Electronic ISSN: 1994-0440
    Topics: Geography , Geosciences
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  • 79
    Publication Date: 2014-12-17
    Description: Structured metal surfaces could support spoof surface plasmon polaritons (SPPs), the dispersion of which is determined by the cutoff condition of guided modes in the nanostructures. We show that we can achieve split spoof SPPs by breaking the degeneracy of guided helical modes in concentric nanostructures via the classic analogue of the Zeeman effect. This split effect is shown to be observable from the spectra of enhanced electromagnetic transmission. Spin-sensitive enhanced electromagnetic transmission and the associated characteristics of field are investigated. Transmission branches versus parallel wavevector can be satisfactorily fitted by using the dispersion of spoof SPPs.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
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  • 80
    Publication Date: 2014-12-17
    Description: Light-induced degradation (LID) is a deleterious effect in crystalline silicon, which is considered to originate from recombination-active boron-oxygen complexes and/or copper-related defects. Although LID in both cases appears as a fast initial decay followed by a second slower degradation, we show that the time constant of copper-related degradation increases with increasing boron concentration in contrast to boron-oxygen LID. Temperature-dependent analysis reveals that the defect formation is limited by copper diffusion. Finally, interface defect density measurements confirm that copper-related LID is dominated by recombination in the wafer bulk.
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  • 81
    Publication Date: 2014-12-17
    Description: In this paper, we report the existence of intervalence charge transfer (IVCT) luminescence in Yb-doped fluorite-type crystals associated with Yb 2+ –Yb 3+ mixed valence pairs. By means of embedded cluster, wave function theory ab initio calculations, we show that the widely studied, very broad band, anomalous emission of Yb 2+ -doped CaF 2 and SrF 2 , usually associated with impurity-trapped excitons, is, rather, an IVCT luminescence associated with Yb 2+ –Yb 3+ mixed valence pairs. The IVCT luminescence is very efficiently excited by a two-photon upconversion mechanism where each photon provokes the same strong 4 f 14 –1 A 1g → 4 f 13 ( 2 F 7/2 )5 de g –1 T 1u absorption in the Yb 2+ part of the pair: the first one, from the pair ground state; the second one, from an excited state of the pair whose Yb 3+ moiety is in the higher 4 f 13 ( 2 F 5/2 ) multiplet. The Yb 2+ –Yb 3+ → Yb 3+ –Yb 2+ IVCT emission consists of an Yb 2+ 5 de g → Yb 3+ 4 f 7/2 charge transfer accompanied by a 4 f 7/2 → 4 f 5/2 deexcitation within the Yb 2+ 4 f 13 subshell: [ 2 F 5/2 5 de g , 2 F 7/2 ] → [ 2 F 7/2 ,4 f 14 ]. The IVCT vertical transition leaves the oxidized and reduced moieties of the pair after electron transfer very far from their equilibrium structures; this explains the unexpectedly large band width of the emission band and its low peak energy, because the large reorganization energies are subtracted from the normal emission. The IVCT energy diagrams resulting from the quantum mechanical calculations explain the different luminescent properties of Yb-doped CaF 2 , SrF 2 , BaF 2 , and SrCl 2 : the presence of IVCT luminescence in Yb-doped CaF 2 and SrF 2 ; its coexistence with regular 5 d -4 f emission in SrF 2 ; its absence in BaF 2 and SrCl 2 ; the quenching of all emissions in BaF 2 ; and the presence of additional 5 d –4 f emissions in SrCl 2 which are absent in SrF 2 . They also allow to interpret and reproduce recent experiments on transient photoluminescence enhancement in Yb 2+ -doped CaF 2 and SrF 2 , the appearance of Yb 2+ 4 f –5 d absorption bands in the excitation spectra of the IR Yb 3+ emission in partly reduced CaF 2 :Yb 3+ samples, and to identify the broadband observed in the excitation spectrum of the so far called anomalous emission of SrF 2 :Yb 2+ as an IVCT absorption, which corresponds to an Yb 2+ 4 f 5/2 → Yb 3+ 4 f 7/2 electron transfer.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 82
    Publication Date: 2014-12-17
    Description: A classical limit of quantum dynamics can be defined by compensation of the quantum potential in the time-dependent Schrödinger equation. The quantum potential is a non-local quantity, defined in the trajectory-based form of the Schrödinger equation, due to Madelung, de Broglie, and Bohm, which formally generates the quantum-mechanical features in dynamics. Selective inclusion of the quantum potential for the degrees of freedom deemed “quantum,” defines a hybrid quantum/classical dynamics, appropriate for molecular systems comprised of light and heavy nuclei. The wavefunction is associated with all of the nuclei, and the Ehrenfest, or mean-field, averaging of the force acting on the classical degrees of freedom, typical of the mixed quantum/classical methods, is avoided. The hybrid approach is used to examine evolution of light/heavy systems in the harmonic and double-well potentials, using conventional grid-based and approximate quantum-trajectory time propagation. The approximate quantum force is defined on spatial domains, which removes unphysical coupling of the wavefunction fragments corresponding to distinct classical channels or configurations. The quantum potential, associated with the quantum particle, generates forces acting on both quantum and classical particles to describe the backreaction.
    Print ISSN: 0021-9606
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    Topics: Chemistry and Pharmacology , Physics
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  • 83
    Publication Date: 2014-12-17
    Description: In the present work, we redefine and generalize the action principle for dissipative systems proposed by Riewe by fixing the mathematical inconsistencies present in the original approach. In order to formulate a quadratic Lagrangian for non-conservative systems, the Lagrangian functions proposed depend on mixed integer order and fractional order derivatives. As examples, we formulate a quadratic Lagrangian for a particle under a frictional force proportional to the velocity and to the classical problem of an accelerated point charge.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
    Topics: Mathematics , Physics
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  • 84
    Publication Date: 2014-12-17
    Description: We consider a very natural generalization of quantum theory by letting the dimension of the Bloch ball be not necessarily three. We analyze bipartite state spaces where each of the components has a d -dimensional Euclidean ball as state space. In addition to this, we impose two very natural assumptions: the continuity and reversibility of dynamics and the possibility of characterizing bipartite states by local measurements. We classify all these bipartite state spaces and prove that, except for the quantum two-qubit state space, none of them contains entangled states. Equivalently, in any of these non-quantum theories, interacting dynamics is impossible. This result reveals that “existence of entanglement” is the requirement with minimal logical content which singles out quantum theory from our family of theories.
    Print ISSN: 0022-2488
    Electronic ISSN: 1089-7658
    Topics: Mathematics , Physics
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  • 85
    Publication Date: 2014-12-17
    Description: A covariant algorithm for deriving the conserved quantities for natural Hamiltonian systems is combined with the non-relativistic framework of Eisenhart, and of Duval, in which the classical trajectories arise as geodesics in a higher dimensional space-time, realized by Brinkmann manifolds. Conserved quantities which are polynomial in the momenta can be built using time-dependent conformal Killing tensors with flux. The latter are associated with terms proportional to the Hamiltonian in the lower dimensional theory and with spectrum generating algebras for higher dimensional quantities of order 1 and 2 in the momenta. Illustrations of the general theory include the Runge-Lenz vector for planetary motion with a time-dependent gravitational constant G ( t ), motion in a time-dependent electromagnetic field of a certain form, quantum dots, the Hénon-Heiles and Holt systems, respectively, providing us with Killing tensors of rank that ranges from one to six.
    Print ISSN: 0022-2488
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    Topics: Mathematics , Physics
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  • 86
    Publication Date: 2014-12-17
    Description: We demonstrate both theoretically and experimentally that the microwave-shielding effectiveness of a double-layer metallic mesh with a submillimeter period can be improved by increasing the separation between the two mesh layers (without affecting transmittance). This double-layer mesh consists of two layers of square aluminum mesh separated by a quartz-glass substrate. By increasing the substrate's optical thickness from zero to λ / 4   of the shielding band's upper frequency, the shielding of the double-layer mesh improves considerably, owing to the increased reflectivity of the double-layer mesh with increasing separation in the low-frequency band. A Ku-band shielding effectiveness of over 32 dB is observed for the double-layer mesh with a normalized visible transmittance greater than 91%. It is found that the electromagnetic shielding effectiveness is enhanced by over 7 dB (80.0% energy attenuation) across the Ku-band, compared with that of a single-layer mesh, while the optical transmittances are almost identical for both tested structures. Such an enhancement permits the design of high-transparency optical elements with stronger microwave shielding that can be achieved using single-layer metallic mesh.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
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  • 87
    Publication Date: 2014-12-17
    Description: This letter performed polarized microscopic laser Raman scattering spectroscopy on the curved edges of transferred epitaxial graphene on SiO 2 /Si. The intensity ratio between the parallel and perpendicular polarized D band is evolved, providing a spectroscopy-based technique to probe the atomic-scale edge structures in graphene. A detailed analysis procedure for non-ideal disordered curved edges of graphene is developed combining the atomic-scale zigzag and armchair edge structures along with some point defects. These results could provide valuable information of the realistic edges of graphene at the atomic-scale that can strongly influence the performance of graphene-based nanodevices.
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  • 88
    Publication Date: 2014-12-17
    Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
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  • 89
    Publication Date: 2014-12-17
    Description: In this paper, we explore the effects of electrostatic parametric amplification on a high quality factor (Q 〉 100 000) encapsulated disk resonator gyroscope (DRG), fabricated in 〈100〉 silicon. The DRG was operated in the n = 2 degenerate wineglass mode at 235 kHz, and electrostatically tuned so that the frequency split between the two degenerate modes was less than 100 mHz. A parametric pump at twice the resonant frequency is applied to the sense axis of the DRG, resulting in a maximum scale factor of 156.6  μ V/(°/s), an 8.8× improvement over the non-amplified performance. When operated with a parametric gain of 5.4, a minimum angle random walk of 0.034°/√h and bias instability of 1.15°/h are achieved, representing an improvement by a factor of 4.3× and 1.5×, respectively.
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  • 90
    Publication Date: 2014-12-17
    Description: We propose a control element for a Josephson spin valve. It is a complex Josephson device containing ferromagnetic (F) layer in the weak-link area consisting of two regions, representing 0 and π Josephson junctions, respectively. The valve's state is defined by mutual orientations of the F-layer magnetization vector and boundary line between 0 and π sections of the device. We consider possible implementation of the control element by introduction of a thin normal metal layer in a part of the device area. By means of theoretical simulations, we study properties of the valve's structure as well as its operation, revealing such advantages as simplicity of control, high characteristic frequency, and good legibility of the basic states.
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    Electronic ISSN: 1077-3118
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  • 91
    Publication Date: 2014-12-17
    Description: Thin films of the lead-free ferroelectric Na 0.5 Bi 0.5 TiO 3 grown on thin-film Pt electrodes supported by SrTiO 3 substrates have a complex microstructure consisting of crystalline grains with three distinct major crystallographic orientations. The piezoelectric response measured in spatially separated sub-micron grains using time-resolved synchrotron x-ray microdiffraction is highly inhomogeneous even among grains sharing the same major orientation. The piezoelectric coefficient d 33 varies by nearly a factor of two in a series of areas sharing the 〈001〉 orientation. The piezoelectric inhomogeneity is linked to the peculiar microstructure of the film, arising from local variations in the stress imposed by surrounding grains with different crystallographic orientations and differing directions of the ferroelectric remnant polarization. A systematic nonlinearity of the piezoelectric strain is observed in applied electric fields with small magnitudes in all regions, consistent with the coexistence of domains of differing polarization direction at zero applied electric field.
    Print ISSN: 0003-6951
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  • 92
    Publication Date: 2014-12-17
    Description: The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species 〉15 kb and the remaining 〉10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.
    Keywords: Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 93
    Publication Date: 2014-12-17
    Description: The efficacy and the mutation spectrum of genome editing methods can vary substantially depending on the targeted sequence. A simple, quick assay to accurately characterize and quantify the induced mutations is therefore needed. Here we present TIDE, a method for this purpose that requires only a pair of PCR reactions and two standard capillary sequencing runs. The sequence traces are then analyzed by a specially developed decomposition algorithm that identifies the major induced mutations in the projected editing site and accurately determines their frequency in a cell population. This method is cost-effective and quick, and it provides much more detailed information than current enzyme-based assays. An interactive web tool for automated decomposition of the sequence traces is available. TIDE greatly facilitates the testing and rational design of genome editing strategies.
    Keywords: Targeted gene modification
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 94
    Publication Date: 2014-12-17
    Description: NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients ( r 2 ) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization.
    Keywords: Nucleic acid structure, Protein-nucleic acid interaction
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 95
    Publication Date: 2014-12-17
    Description: Bicyclic oxazaphospholidine monomers were used to prepare a series of phosphorothioate (PS)-modified gapmer antisense oligonucleotides (ASOs) with control of the chirality of each of the PS linkages within the 10-base gap. The stereoselectivity was determined to be 98% for each coupling. The objective of this work was to study how PS chirality influences biophysical and biological properties of the ASO including binding affinity ( T m ), nuclease stability, activity in vitro and in vivo , RNase H activation and cleavage patterns (both human and E. coli ) in a gapmer context. Compounds that had nine or more Sp-linkages in the gap were found to be poorly active in vitro , while compounds with uniform Rp-gaps exhibited activity very similar to that of the stereo-random parent ASOs. Conversely, when tested in vivo , the full Rp-gap compound was found to be quickly metabolized resulting in low activity. A total of 31 ASOs were prepared with control of the PS chirally of each linkage within the gap in an attempt to identify favorable Rp/Sp positions. We conclude that a mix of Rp and Sp is required to achieve a balance between good activity and nuclease stability.
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 96
    Publication Date: 2014-12-17
    Description: In an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. DNA modification is an important epigenetic factor that can regulate phenotypic heterogeneity. The single molecule real-time (SMRT) sequencing technology provides a unique platform for detecting a wide range of DNA modifications, including N6-methyladenine (6-mA), N4-methylcytosine (4-mC) and 5-methylcytosine (5-mC). Here we present qDNAmod, a novel bioinformatic tool for genome-wide quantitative profiling of intercellular heterogeneity of DNA modification from SMRT sequencing data. It is capable of estimating proportion of isogenic haploid cells, in which the same loci of the genome are differentially modified. We tested the reliability of qDNAmod with the SMRT sequencing data of Streptococcus pneumoniae strain ST556. qDNAmod detected extensive intercellular heterogeneity of DNA methylation (6-mA) in a clonal population of ST556. Subsequent biochemical analyses revealed that the recognition sequences of two type I restriction–modification (R-M) systems are responsible for the intercellular heterogeneity of DNA methylation initially identified by qDNAmod. qDNAmod thus represents a valuable tool for studying intercellular phenotypic heterogeneity from genome-wide DNA modification.
    Keywords: Nucleic acid modification, Computational Methods
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    Topics: Biology
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  • 97
    Publication Date: 2014-12-17
    Description: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the ‘enhanceosome’ versus the ‘TF collective’ model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair—E-box and GATA, and in two previously unknown motif-pairs with constrained spacing—Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the ‘enhanceosome’ model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
    Keywords: Computational Methods
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  • 98
    Publication Date: 2014-12-17
    Description: In silico tools have been developed to predict variants that may have an impact on pre-mRNA splicing. The major limitation of the application of these tools to basic research and clinical practice is the difficulty in interpreting the output. Most tools only predict potential splice sites given a DNA sequence without measuring splicing signal changes caused by a variant. Another limitation is the lack of large-scale evaluation studies of these tools. We compared eight in silico tools on 2959 single nucleotide variants within splicing consensus regions (scSNVs) using receiver operating characteristic analysis. The Position Weight Matrix model and MaxEntScan outperformed other methods. Two ensemble learning methods, adaptive boosting and random forests, were used to construct models that take advantage of individual methods. Both models further improved prediction, with outputs of directly interpretable prediction scores. We applied our ensemble scores to scSNVs from the Catalogue of Somatic Mutations in Cancer database. Analysis showed that predicted splice-altering scSNVs are enriched in recurrent scSNVs and known cancer genes. We pre-computed our ensemble scores for all potential scSNVs across the human genome, providing a whole genome level resource for identifying splice-altering scSNVs discovered from large-scale sequencing studies.
    Keywords: RNA characterisation and manipulation, Computational Methods
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  • 99
    Publication Date: 2014-12-17
    Description: In mammals, RNA interference is primarily a post-transcriptional mechanism. Evidence has accumulated for additional role in transcriptional gene silencing (TGS) but the question for a good paradigm for small interfering antigene RNA (agRNA)-induced chromatin modification remains unanswered. Here, we show that SETDB1, a histone H3-lysine 9 (H3K9)-specific methyltransferase, cooperates with Argonaute-2 (AGO2) and plays an essential role in agRNA-induced TGS. The androgen receptor ( AR ) gene was transcriptionally silenced by agRNA targeted to its promoter, and we show that this repression was mitigated by knockdown of SETDB1 or AGO2 . Chromatin immunoprecipitation demonstrated that agRNA-driven AGO2 was first targeted to the AR promoter, followed by SETDB1. SIN3A and HDAC1/2, the components of the SIN3-HDAC complex, immunoprecipitated with SETDB1, and localized at the agRNA-targeted promoter. Agreeing with the presence of SETDB1, trimethyl-H3K9 was enriched in the AR promoter. Both EZH2 and trimethyl-H3K27 were also present in the targeted locus; accordingly, EZH2 immunoprecipitated with SETDB1. DNA methylation level was not significantly changed, suggesting the absence of de novo methylating activity in agRNA-induced AR promoter. Our results demonstrate that SETDB1, together with AGO2, plays an essential role in TGS through recruiting chromatin remodeler and/or other modifiers, consequently creating a repressive chromatin milieu at the targeted promoter.
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  • 100
    Publication Date: 2014-12-17
    Description: LEF/TCFs direct the final step in Wnt/β-catenin signalling by recruiting β-catenin to genes for activation of transcription. Ancient, non-vertebrate TCFs contain two DNA binding domains, a High Mobility Group box for recognition of the Wnt Response Element (WRE; 5'-CTTTGWWS-3') and the C-clamp domain for recognition of the GC-rich Helper motif (5'-RCCGCC-3'). Two vertebrate TCFs (TCF-1/TCF7 and TCF-4/TCF7L2) use the C-clamp as an alternatively spliced domain to regulate cell-cycle progression, but how the C-clamp influences TCF binding and activity genome-wide is not known. Here, we used a doxycycline inducible system with ChIP-seq to assess how the C-clamp influences human TCF1 binding genome-wide. Metabolic pulse-labeling of nascent RNA with 4'Thiouridine was used with RNA-seq to connect binding to the Wnt transcriptome. We find that the C-clamp enables targeting to a greater number of gene loci for stronger occupancy and transcription regulation. The C-clamp uses Helper sites concurrently with WREs for gene targeting, but it also targets TCF1 to sites that do not have readily identifiable canonical WREs. The coupled ChIP-seq/4'Thiouridine-seq analysis identified new Wnt target genes, including additional regulators of cell proliferation. Thus, C-clamp containing isoforms of TCFs are potent transcriptional regulators with an expanded transcriptome directed by C-clamp-Helper site interactions.
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    Topics: Biology
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