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  • Oxford University Press  (139,906)
  • American Institute of Physics (AIP)  (107,702)
  • 2015-2019  (109,926)
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  • 1
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    Oxford University Press
    Publication Date: 2024-03-23
    Description: "With so much media and political criticism of their shortcomings and failures, it is easy to overlook the fact that many governments work pretty well much of the time. Great Policy Successes turns the spotlight on instances of public policy that are remarkably successful. It develops a framework for identifying and assessing policy successes, paying attention not just to their programmatic outcomes but also to the quality of the processes by which policies are designed and delivered, the level of support and legitimacy they attain, and the extent to which successful performance endures over time. The bulk of the book is then devoted to 15 detailed case studies of striking policy successes from around the world, including Singapore's public health system, Copenhagen and Melbourne's rise from stilted backwaters to the highly liveable and dynamic urban centres they are today, Brazil's Bolsa Familia poverty relief scheme, the US's GI Bill, and Germany's breakthrough labour market reforms of the 2000s. Each case is set in context, its main actors are introduced, key events and decisions are described, the assessment framework is applied to gauge the nature and level of its success, key contributing factors to success are identified, and potential lessons and future challenges are identified. Purposefully avoiding the kind of heavy theorizing that characterizes many accounts of public policy processes, each case is written in an accessible and narrative style ideally suited for classroom use in conjunction with mainstream textbooks on public policy design, implementation, and evaluation.
    Keywords: public policy ; policy evaluation ; government ; governance ; social policy ; health policy ; economic policy ; thema EDItEUR::J Society and Social Sciences::JP Politics and government
    Language: English
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  • 2
    Publication Date: 2021-06-21
    Description: We present the analysis of rotational and translational ground motions from earthquakes recorded during October–November 2016, in association with the Central Italy seismic sequence. We use co-located measurements of the vertical ground rotation rate from a large ring laser gyroscope and the three components of ground velocity from a broad-band seismometer. Both instruments are positioned in a deep underground environment, within the Gran Sasso National Laboratories of the Istituto Nazionale di Fisica Nucleare. We collected dozens of events spanning the 3.5–5.9 magnitude range and epicentral distances between 30 and 70 km. This data set constitutes an unprecedented observation of the vertical rotational motions associated with an intense seismic sequence at local distance. Under the plane-wave approximation we process the data set in order to get an experimental estimation of the events backazimuth. Peak values of rotation rate (PRR) and horizontal acceleration (PGA) are markedly correlated, according to a scaling constant which is consistent with previous measurements from different earthquake sequences. We used a prediction model in use for Italy to calculate the expected PGA at the recording site, obtaining consequently predictions for PRR. Within the modelling uncertainties, predicted rotations are consistent with the observed ones, suggesting the possibility of establishing specific attenuation models for ground rotations, like the scaling of peak velocity and peak acceleration in empirical ground-motion prediction relationships. In a second step, after identifying the direction of the incoming wavefield, we extract phase-velocity data using the spectral ratio of the translational and rotational components. This analysis is performed over time windows associated with the P-coda, S-coda and Lg phase. Results are consistent with independent estimates of shear wave velocities in the shallow crust of the Central Apennines
    Description: Published
    Description: 705-715
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Rotational seismology ; Surface waves and free oscillations ; Wave propagation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 208(1), pp. 449-467, ISSN: 1365-246X
    Publication Date: 2016-12-03
    Description: The Mozambique Ridge, a prominent basement high in the southwestern Indian Ocean, consists of four major geomorphological segments associated with numerous phases of volcanic activity in the Lower Cretaceous. The nature and origin of the Mozambique Ridge have been intensely debated with one hypothesis suggesting a Large Igneous Province origin. High-resolution seismic reflection data reveal a large number of extrusion centres with a random distribution throughout the southern Mozambique Ridge and the nearby Transkei Rise. Intra-basement reflections emerge from the extrusion centres and are interpreted to represent massive lava flow sequences. Such lava flow sequences are characteristic of eruptions leading to the formation of continental and oceanic flood basalt provinces, hence supporting a Large Igneous Province origin of the Mozambique Ridge. We observe evidence for widespread post-sedimentary magmatic activity that we correlate with a southward propagation of the East African Rift System. Based on our volumetric analysis of the southern Mozambique Ridge we infer a rapid sequential emplacement between ~131 Ma and ~125 Ma, which is similar to the short formation periods of other Large Igneous Provinces like the Agulhas Plateau.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2018-11-09
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 6
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-04-28
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 7
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    Oxford University Press
    In:  EPIC3Marine Plankton, Marine Plankton, Oxford University Press, 704 p., ISBN: 9780199233267
    Publication Date: 2017-05-11
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 8
    Publication Date: 2017-04-04
    Description: The mineralogy of thermometamorphic granites is relatively simple, making it possible to track the spatial distribution of chemical and mineralogical variations in these rocks and investigate the processes that underpin these metamorphic reactions.We have undertaken a detailed investigation of metagranites from the contact aureole that fringes a quartz diorite intrusion of Late Permian age, emplaced into Carboniferous peraluminous granites of the Gennargentu Igneous Complex (Sardinia, Italy). New data are presented including the petrography of metagranites within a 500 m zone adjacent to the quartz diorite intrusion, the compositions of minerals and bulk-rocks, and the oxygen isotope compositions of separated minerals. We have used these data to assess the mobility of elements, expressed as oxide, in the aureole, and the physical conditions of fluid-assisted thermometamorphism. Modal variations and the oscillatory zoning of plagioclase demonstrate that the shallow (P 200MPa) quartz diorite intrusion was emplaced through a number of magmatic injections.The border zone of the quartz diorite intrusion presents evidence of two main processes: hybridization between andesite and rhyolite magmas and volatile saturation of the mingled magma. Modal differences in the contact zone with respect to the protolith (i.e. peraluminous granite), variations in mineral composition, temperature constraints and K2O, Na2O, SiO2 and Al2O3 indicate that a relatively large volume of the host granite (up to 400 m from the contact) was metasomatized by high-temperature (650^3508C) fluids derived from the mingled zone of the quartz diorite intrusion. In detail, the metasomatic K2O-rich fluid reacted with albite to form K-feldspar, and triggered the recrystallization of quartz and plagioclase to higher calcium concentrations. The progressive increase in the MgO/(MgOþFeO) of chlorite closer to the contact indicates that this phase also recrystallized. The iron released during chlorite recrystallization was buffered by hematite formation in the pores of metasomatic K-feldspar. The Gennargentu metagranites provide evidence that metasomatic fluids can play a major role in driving metamorphic reactions in contact aureoles. For instance, the expected increase of Ca in plagioclase owing to thermal equilibration was not achieved in the high-T zone of the aureole because of fluid-assisted removal of cations.We conclude that caution should be taken when interpreting the processes that underpin contact metamorphism in terms of thermally driven, ionic diffusion alone, because the role of fluids may be significant, if not overwhelming, in the domains closest to the magmatic source.
    Description: Published
    Description: 839-859
    Description: 3V. Dinamiche e scenari eruttivi
    Description: JCR Journal
    Description: restricted
    Keywords: contact metamorphism ; metasomatism ; red metagranites ; oxygen isotopes ; Gennargentu Igneous Complex ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 9
    Publication Date: 2017-04-04
    Description: We reply to the comments of De Natale and Pino (2013) on the paper “Are the source models of the M 7.1 1908 Messina Straits earthquake reliable? Insights from a novel inversion and sensitivity analysis of levelling data” by Aloisi et al. (2012). We entirely reject their speculative comments and confirm our viewpoint about the impossibility of discriminating between the two oppositely dipping fault models on the basis of the levelling data alone; we state again that their role as a keystone for modellers is untenable. The comment of De Natale and Pino (2013) are welcomed insofar they give us the possibility to improve our previous analysis, and to criticize the mainstream hypothesis favoring to a low-angle East dipping fault in the Sicilian side of the Messina Straits as responsible of the 1908 destructive earthquake.
    Description: Published
    Description: 1403–1409
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Transient deformation ; Earthquake dynamics ; Earthquake source observations ; 04. Solid Earth::04.03. Geodesy::04.03.01. Crustal deformations ; 04. Solid Earth::04.06. Seismology::04.06.01. Earthquake faults: properties and evolution ; 04. Solid Earth::04.06. Seismology::04.06.03. Earthquake source and dynamics ; 04. Solid Earth::04.06. Seismology::04.06.04. Ground motion
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 10
    Publication Date: 2017-04-04
    Description: In order to exploit radon profiles for geophysical purposes and also to estimate its entry indoors, it is necessary to study its transport through porous soils. The great number of involved parameters and processes affecting the emanation of radon from the soil grains and its transport in the source medium has led to many theoretical and/or laboratory studies. The authors report the first results of a laboratory study carried out at the Radioactivity Laboratory of the Department of Physics and Astronomy (University of Catania) by means of a facility for measuring radon concentrations in the sample pores at various depths under well-defined and controlled conditions of physical parameters. In particular, radon concentration vertical profiles extracted in low-moisture samples for different advective fluxes and temperatures were compared with expected concentrations, according to a three-phase transport model developed by Andersen (Risø National Laboratory, Denmark), showing, in general, a good agreement between measurements and model calculations.
    Description: Published
    Description: 575-581
    Description: 4V. Vulcani e ambiente
    Description: JCR Journal
    Description: reserved
    Keywords: Radon ; profile ; geophysic ; porous ; 01. Atmosphere::01.01. Atmosphere::01.01.05. Radiation
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 11
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    Oxford University Press
    Publication Date: 2017-04-04
    Description: We provide an updated present-day stress map for the Italian territory. Following the World Stress Map (WSM) Project guidelines, we list the different stress indicators, explaining the criteria used to select data. We discuss the data, which will also be included in the 2016 release of the WSM, highlighting the areas for which we have added stress information. Our map displays the minimum horizontal stress orientations inferred from crustal stress indicators down to 40 km depth using data of A–C quality, updated for earthquakes until December 2015. We have completely reviewed all data, and the data set now contains 855 entries, in contrast to the previous 715. The number of data with A–C quality of 630 corresponds to an increase of 26 per cent relative to the previous data set. In particular, the new data set contains the results of the analysis of borehole breakouts, critically reviewed data from earthquake focal mechanisms, data concerning active faults, formal inversions of focal mechanisms of seismic sequences or of restricted areas and one stress determination from overcoring. The new data set defines the stress field in areas not well covered by the previous data: the region north to the Po Plain and the central Adriatic sea, both characterized by a thrust- and strike-faulting regime, the northern Sicilian belt with a prevailing normal-faulting regime, and the Ionian sea with a strike-slip regime.
    Description: Published
    Description: 1525-1531
    Description: 2T. Tettonica attiva
    Description: JCR Journal
    Description: restricted
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Crustal structure ; Europe ; 04. Solid Earth::04.07. Tectonophysics::04.07.05. Stress
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 12
    Publication Date: 2018-09-20
    Description: The relationships between trachytes and peralkaline rhyolites (i.e. pantellerites and comendites), which occur in many continental rift systems, oceanic islands and continental intraplate settings, is unclear. To fill this gap, we have performed phase equilibrium experiments on two representative metaluminous trachytes from Pantelleria to determine both their pre-eruptive equilibration conditions (pressure, temperature, H2O content and redox state) and liquid lines of descent. Experiments were performed in the temperature range 750–950 C, pressure 0 5–1 5 kbar and fluid saturation conditions with XH2O [¼H2O/(H2OþCO2)] ranging between zero and unity. Redox conditions were fixed below the nickel–nickel oxide buffer (NNO). The results show that at 950 C and melt water contents (H2Omelt) close to saturation, trachytes are at liquidus conditions at all pressures. Clinopyroxene is the liquidus phase, being followed by iron-rich olivine and alkali feldspar. Comparison of experimental and natural phases (abundances and compositions) yields the following pre-eruptive conditions: P¼160 5 kbar, T¼925625 C, H2Omelt¼261wt %, and fO2 between NNO– 0 5 and NNO– 2. A decrease in temperature from 950 C to 750 C, as well as of H2Omelt, promotes a massive crystallization of alkali feldspar to over 80 wt %. Iron-bearing minerals show gradual iron enrichment when T and fO2 decrease, trending towards the compositions of the phenocrysts of natural pantellerites. Despite the metaluminous character of the bulk-rock compositions, residual glasses obtained after 80 wt % crystallization evolve toward comenditic compositions, owing to profuse alkali feldspar crystallization, which decreases the Al2O3 of the melt, leading to a consequent increase in the peralkalinity index [PI¼molar (Na2OþK2O)/Al2O3]. This is the first experimental demonstration that peralkaline felsic derivatives can be produced by low-pressure fractional crystallization of metaluminous mafic magmas. Our results show that the pantelleritic magmas of basalt–trachyte–rhyolite igneous suites require at least 95 wt % of parental basalt crystallization, consistent with trace element evidence. Redox conditions, through their effect on Fe–Ti oxide stabilities, control the final iron content of the evolving melt.
    Description: Published
    Description: 559- 588
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: JCR Journal
    Keywords: peralkaline silicic magmatism ; Pantelleria ; Green Tuff ; petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 13
    Publication Date: 2019-03-13
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2015. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: Mud volcanoes are geological systems often characterized by elevated fluid pressures at depth deviating from hydrostatic conditions. This near-critical state makes mud volcanoes particularly sensitive to external forcing induced by natural or man-made perturbations. We used the Nirano mud volcanic field as a natural laboratory to test pre- and post-seismic effects generated by distant earthquakes.We first characterized the subsurface structure of the Nirano mud volcanic field with a geoelectrical study. Next, we deployed a broad-band seismic station in the area to understand the typical seismic signal generated by the mud volcano. Seismic records show a background noise below 2 s, sometimes interrupted by pulses of drumbeatlike high-frequency signals lasting from several minutes to hours. To date this is the first observation of drumbeat signal observed in mud volcanoes. In 2013 June we recorded a M4.7 earthquake, that occurred approximately 60 km far from our seismic station. According to empirical estimations the Nirano mud volcanic field should not have been affected by the M4.7 earthquake. Yet, before the seismic event we recorded an increasing amplitude of the signal in the 10–20 Hz frequency band. The signal emerged approximately two hours before the earthquake and lasted for about three hours. Our statistical analysis suggests the presence of a possible precursory signal about 10 min before the earthquake.
    Description: Published
    Description: 907–917
    Description: 7A. Geofisica per il monitoraggio ambientale
    Description: JCR Journal
    Keywords: Tomography ; Gas and hydrate systems ; Earthquake interaction, forecasting, and prediction ; Seismicity and tectonics ; Volcano seismology ; Mud volcanism
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 14
    Publication Date: 2017-04-04
    Description: Although there are many methods for investigating tectonic structures, many faults remain hidden, and they can endanger the life and property of people living along them. The slopes of volcanoes are covered with such hidden faults, near which strong earthquakes and gas releases can appear. Revealing hidden faults can therefore contribute significantly to the protection of people living in volcanic areas. In the study, seven different techniques were used for making measurements of in-soil radon concentrations in order to search for hidden faults on the SE flank of the Mt. Etna volcano. These reported methods had previously been proved to be useful tools for investigating fault structures. The main aim of the experiment presented here was to evaluate the usability of these methods in the geological conditions of the Mt. Etna region, and to find the best place for continual radon monitoring using a permanent station in the near future.
    Description: Published
    Description: 70-73
    Description: 5V. Sorveglianza vulcanica ed emergenze
    Description: JCR Journal
    Description: restricted
    Keywords: Mt. Etna ; soil gas ; hidden faults ; radon ; 04. Solid Earth::04.02. Exploration geophysics::04.02.01. Geochemical exploration
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 15
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    Oxford University Press
    In:  EPIC3The Natural History of Crustacea, Physiology (Vol. 4), New York, Oxford University Press, 35 p., pp. 285-319, ISBN: 9780199832415
    Publication Date: 2015-03-23
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 37(3), pp. 584-595, ISSN: 0142-7873
    Publication Date: 2015-08-22
    Description: Plankton fractions from a saline lake in Argentina were studied using a combined trophic marker approach. A strong seasonality of biomarkers was characteristic for the different fractions, particularly the variations in the 18:4(n 2 3) and 20:4(n 2 3) fatty acids and the d13C values. The primary production in the lake was mainly driven by diatoms, reflected by the close relation of d13C, chlorophyll a and diatom fatty acid markers. The combined approach of d13C and 20:4(n 2 3) enabled processes in the lipid metabolism of the copepod Boeckella poopoensis to be inferred. The polyunsaturated fatty acid 22:6(n 2 3) and the d15N separated the trophic levels in this food web with copepods at higher trophic level. Nutritional stress and omnivory of B. poopoensis partially explained the d15N variations in mesozooplankton. The d15N signature was probably driven by cyanobacteria in the microplankton and by microbial processes in the nanoplankton fraction. Warmer temperatures may favour the saturation of microalgae fatty acids and the abundance of plankton groups richer in saturated fatty acids. The tendency to unsaturation in mesozooplankton at colder temperatures was probably influenced by diet and metabolic requirements. Future temperature increase and eutrophication-like processes may increase the importance of cyanobacterial and bacterial markers under climate change scenarios.
    Repository Name: EPIC Alfred Wegener Institut
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  • 17
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    Oxford University Press
    In:  EPIC3ICES Journal of Marine Science, Oxford University Press, 73, pp. 772-782, ISSN: 1054-3139
    Publication Date: 2016-11-30
    Description: Global warming and ocean acidification are among the most important stressors for aquatic ecosystems in the future. To investigate their direct and indirect effects on a near-natural plankton community, a multiple-stressor approach is needed. Hence, we set up mesocosms in a full-factorial design to study the effects of both warming and high CO2 on a Baltic Sea autumn plankton community, concentrating on the impacts on microzooplankton (MZP). MZP abundance, biomass, and species composition were analysed over the course of the experiment. We observed that warming led to a reduced time-lag between the phytoplankton bloom and an MZP biomass maximum. MZP showed a significantly higher growth rate and an earlier biomass peak in the warm treatments while the biomass maximum was not affected. Increased pCO2 did not result in any significant effects on MZP biomass, growth rate, or species composition irrespective of the temperature, nor did we observe any significant interactions between CO2 and temperature. We attribute this to the high tolerance of this estuarine plankton community to fluctuations in pCO2, often resulting in CO2 concentrations higher than the predicted end-of-century concentration for open oceans. In contrast, warming can be expected to directly affect MZP and strengthen its coupling with phytoplankton by enhancing its grazing pressure.
    Repository Name: EPIC Alfred Wegener Institut
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  • 18
    Publication Date: 2022-05-25
    Description: Author Posting. © Crown Copyright, 2015. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 204 (2016): 1-20, doi:10.1093/gji/ggv416.
    Description: The Canada Basin and the southern Alpha-Mendeleev ridge complex underlie a significant proportion of the Arctic Ocean, but the geology of this undrilled and mostly ice-covered frontier is poorly known. New information is encoded in seismic wide-angle reflections and refractions recorded with expendable sonobuoys between 2007 and 2011. Velocity–depth samples within the sedimentary succession are extracted from published analyses for 142 of these records obtained at irregularly spaced stations across an area of 1.9E + 06 km2. The samples are modelled at regional, subregional and station-specific scales using an exponential function of inverse velocity versus depth with regionally representative parameters determined through numerical regression. With this approach, smooth, non-oscillatory velocity–depth profiles can be generated for any desired location in the study area, even where the measurement density is low. Practical application is demonstrated with a map of sedimentary thickness, derived from seismic reflection horizons interpreted in the time domain and depth converted using the velocity–depth profiles for each seismic trace. A thickness of 12–13 km is present beneath both the upper Mackenzie fan and the middle slope off of Alaska, but the sedimentary prism thins more gradually outboard of the latter region. Mapping of the observed-to-predicted velocities reveals coherent geospatial trends associated with five subregions: the Mackenzie fan; the continental slopes beyond the Mackenzie fan; the abyssal plain; the southwestern Canada Basin; and, the Alpha-Mendeleev magnetic domain. Comparison of the subregional velocity–depth models with published borehole data, and interpretation of the station-specific best-fitting model parameters, suggests that sandstone is not a predominant lithology in any of the five subregions. However, the bulk sand-to-shale ratio likely increases towards the Mackenzie fan, and the model for this subregion compares favourably with borehole data for Miocene turbidites in the eastern Gulf of Mexico. The station-specific results also indicate that Quaternary sediments coarsen towards the Beaufort-Mackenzie and Banks Island margins in a manner that is consistent with the variable history of Laurentide Ice Sheet advance documented for these margins. Lithological factors do not fully account for the elevated velocity–depth trends that are associated with the southwestern Canada Basin and the Alpha-Mendeleev magnetic domain. Accelerated porosity reduction due to elevated palaeo-heat flow is inferred for these regions, which may be related to the underlying crustal types or possibly volcanic intrusion of the sedimentary succession. Beyond exploring the variation of an important physical property in the Arctic Ocean basin, this study provides comparative reference for global studies of seismic velocity, burial history, sedimentary compaction, seismic inversion and overpressure prediction, particularly in mudrock-dominated successions.
    Keywords: Numerical approximations and analysis ; Spatial analysis ; Controlled source seismology ; Acoustic properties ; Sedimentary basin processes ; Large igneous provinces ; Crustal structure ; Arctic region
    Repository Name: Woods Hole Open Access Server
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  • 19
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    Oxford University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author, 2015. 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 203 (2015): 893-895, doi:10.1093/gji/ggv324.
    Description: The statistics of directional data on a sphere can be modelled either using the Fisher distribution that is conditioned on the magnitude being unity, in which case the sample space is confined to the unit sphere, or using the latitude–longitude marginal distribution derived from a trivariate Gaussian model that places no constraint on the magnitude. These two distributions are derived from first principles and compared. The Fisher distribution more closely approximates the uniform distribution on a sphere for a given small value of the concentration parameter, while the latitude–longitude marginal distribution is always slightly larger than the Fisher distribution at small off-axis angles for large values of the concentration parameter. Asymptotic analysis shows that the two distributions only become equivalent in the limit of large concentration parameter and very small off-axis angle.
    Keywords: Numerical approximations and analysis ; Probability distributions ; Marine magnetics and palaeomagnetics
    Repository Name: Woods Hole Open Access Server
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  • 20
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 7 (2015): 3207-3225, doi:10.1093/gbe/evv210.
    Description: High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes—generically known as restriction site associated DNA sequencing (RAD-seq)—is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for nonmodel species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting “neutral” elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced representation data are available (including transcriptomes and neutral RAD-seq data sets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
    Description: This research was supported by the Office of Ocean Exploration and Research of the National Oceanic and Atmospheric Administration (NA09OAR4320129 to T.S.); the Division of Ocean Sciences of the National Science Foundation (OCE-1131620 to T.S.); the Astrobiology Science and Technology for Exploring Planets program of the National Aeronautics and Space Administration (NNX09AB76G to T.S.); and the Academic Programs Office (Ocean Ventures Fund to S.H.), the Ocean Exploration Institute (Fellowship support to T.M.S.), and the Ocean Life Institute of the Woods Hole Oceanographic Institution (internal grant to T.M.S. and S.H.).
    Keywords: RAD-seq ; Reduced representation sequencing ; PredRAD ; Experimental design ; Genome size prediction ; Restriction recognition sequence probability
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/vnd.ms-excel
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  • 21
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.
    Description: The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.
    Description: This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14).
    Keywords: RNA editing ; ADAR ; Evolution ; Coral
    Repository Name: Woods Hole Open Access Server
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  • 22
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 6 (2018): coy049, doi:10.1093/conphys/coy049.
    Description: Male baleen whales have long been suspected to have annual cycles in testosterone, but due to difficulty in collecting endocrine samples, little direct evidence exists to confirm this hypothesis. Potential influences of stress or adrenal stress hormones (cortisol, corticosterone) on male reproduction have also been difficult to study. Baleen has recently been shown to accumulate steroid hormones during growth, such that a single baleen plate contains a continuous, multi-year retrospective record of the whale’s endocrine history. As a preliminary investigation into potential testosterone cyclicity in male whales and influences of stress, we determined patterns in immunoreactive testosterone, two glucocorticoids (cortisol and corticosterone), and stable-isotope (SI) ratios, across the full length of baleen plates from a bowhead whale (Balaena mysticetus), a North Atlantic right whale (Eubalaena glacialis) and a blue whale (Balaenoptera musculus), all adult males. Baleen was subsampled at 2 cm (bowhead, right) or 1 cm (blue) intervals and hormones were extracted from baleen powder with methanol, followed by quantification of all three hormones using enzyme immunoassays validated for baleen extract of these species. Baleen of all three males contained regularly spaced peaks in testosterone content, with number and spacing of testosterone peaks corresponding well to SI data and to species-specific estimates of annual baleen growth rate. Cortisol and corticosterone exhibited some peaks that co-occurred with testosterone peaks, while other glucocorticoid peaks occurred independent of testosterone peaks. The right whale had unusually high glucocorticoids during a period with a known entanglement in fishing gear and a possible disease episode; in the subsequent year, testosterone was unusually low. Further study of baleen testosterone patterns in male whales could help clarify conservation- and management-related questions such as age of sexual maturity, location and season of breeding, and the potential effect of anthropogenic and natural stressors on male testosterone cycles.
    Description: This work was supported by (1) the Arizona Board of Regents Technology Research Initiative Fund; (2) the Center for Bioengineering Innovation at Northern Arizona University; (3) the Greenland Institute of Natural Resources; (4) the Woods Hole Oceanographic Institution Ocean Life Institute and (5) Fisheries and Ocean Canada’s (DFO) Priorities and Partnership Strategic Initiatives Fund and Oceans Protection Plan.
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  • 23
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2015. 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 203 (2015): 1-21, doi:10.1093/gji/ggv251.
    Description: We examine along-axis variations in melt content of the axial magma lens (AML) beneath the fast-spreading East Pacific Rise (EPR) using an amplitude variation with angle of incidence (AVA) crossplotting method applied to multichannel seismic data acquired in 2008. The AVA crossplotting method, which has been developed for and, so far, applied for hydrocarbon prospection in sediments, is for the first time applied to a hardrock environment. We focus our analysis on 2-D data collected along the EPR axis from 9°29.8′N to 9°58.4′N, a region which encompasses the sites of two well-documented submarine volcanic eruptions (1991–1992 and 2005–2006). AVA crossplotting is performed for a ∼53 km length of the EPR spanning nine individual AML segments (ranging in length from ∼3.2 to 8.5 km) previously identified from the geometry of the AML and disruptions in continuity. Our detailed analyses conducted at 62.5 m interval show that within most of the analysed segments melt content varies at spatial scales much smaller (a few hundred of metres) than the length of the fine-scale AML segments, suggesting high heterogeneity in melt concentration. At the time of our survey, about 2 yr after the eruption, our results indicate that the three AML segments that directly underlie the 2005–2006 lava flow are on average mostly molten. However, detailed analysis at finer-scale intervals for these three segments reveals AML pockets (from 〉62.5 to 812.5 m long) with a low melt fraction. The longest such mushy section is centred beneath the main eruption site at ∼9°50.4′N, possibly reflecting a region of primary melt drainage during the 2005–2006 event. The complex geometry of fluid flow pathways within the crust above the AML and the different response times of fluid flow and venting to eruption and magma reservoir replenishment may contribute to the poor spatial correlation between incidence of hydrothermal vents and presence of highly molten AML. The presented results are an important step forward in our ability to resolve small-scale characteristics of the AML and recommend the AVA crossplotting as a tool for examining mid-ocean ridge magma-systems elsewhere.
    Description: This research was supported by NSF awards OCE0327872 to J.C.M. and S.M.C., OCE-0327885 to J.P.C., and OCE0624401 to M.R.N.
    Keywords: Mid-ocean ridge processes ; Submarine tectonics and volcanism ; Crustal structure ; Physics of magma and magma bodies
    Repository Name: Woods Hole Open Access Server
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  • 24
    Publication Date: 2022-05-25
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 44 (2016): e157, doi:10.1093/nar/gkw738.
    Description: Site-directed RNA editing (SDRE) is a strategy to precisely alter genetic information within mRNAs. By linking the catalytic domain of the RNA editing enzyme ADAR to an antisense guide RNA, specific adenosines can be converted to inosines, biological mimics for guanosine. Previously, we showed that a genetically encoded iteration of SDRE could target adenosines expressed in human cells, but not efficiently. Here we developed a reporter assay to quantify editing, and used it to improve our strategy. By enhancing the linkage between ADAR's catalytic domain and the guide RNA, and by introducing a mutation in the catalytic domain, the efficiency of converting a UAG premature termination codon (PTC) to tryptophan (UGG) was improved from ∼11% to ∼70%. Other PTCs were edited, but less efficiently. Numerous off-target edits were identified in the targeted mRNA, but not in randomly selected endogenous messages. Off-target edits could be eliminated by reducing the amount of guide RNA with a reduction in on-target editing. The catalytic rate of SDRE was compared with those for human ADARs on various substrates and found to be within an order of magnitude of most. These data underscore the promise of site-directed RNA editing as a therapeutic or experimental tool.
    Description: National Institutes of Health [1R0111223855, 1R01NS64259]; Cystic Fibrosis Foundation Therapeutics [Rosent14XXO]; Infrastructural support was provided by the National Institutes of Health [NIGMS 1P20GM103642, NIMHD 8G12-MD007600]; National Science Foundation [DBI 0115825, DBI 1337284]; Department of Defense [52680-RT-ISP].
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  • 25
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 208 (2017): 1026-1042, doi:10.1093/gji/ggw435.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the subseafloor conductivity that is assumed to be isotropic. The deep water (ocean layer electrically much thicker than the overburden) seafloor EM response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a half-space, or a stronger and faster response. For an ocean whose electrical thickness is comparable to or much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. These transitions can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire subseafloor resistivity structure with the sea surface. A stronger and faster response occurs when guided energy flow is dominant, while a weaker and slower response occurs when the air interaction is dominant. However, at intermediate offsets for some models, the air interaction can partially or fully reverse the direction of energy flux in the reservoir layer toward rather than away from the source, resulting in a stronger and slower response. The Fréchet derivatives are dominated by preferential sensitivity to the reservoir layer conductivity for all water depths except at high frequencies, but also display a shift with offset from the galvanic to the inductive mode in the underburden and overburden due to the interplay of guided energy flow and the air interaction. This means that the sensitivity to the horizontal conductivity is almost as strong as to the vertical component in the shallow parts of the subsurface, and in fact is stronger than the vertical sensitivity deeper down. However, the sensitivity to horizontal conductivity is still weak compared to the vertical component within thin resistive regions. The horizontal sensitivity is gradually decreased when the water becomes deep. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Keywords: Electrical properties ; Marine electromagnetics
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  • 26
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioscience 67 (2017): 760–768, doi:10.1093/biosci/bix059.
    Description: As the sampling frequency and resolution of Earth observation imagery increase, there are growing opportunities for novel applications in population monitoring. New methods are required to apply established analytical approaches to data collected from new observation platforms (e.g., satellites and unmanned aerial vehicles). Here, we present a method that estimates regional seasonal abundances for an understudied and growing population of gray seals (Halichoerus grypus) in southeastern Massachusetts, using opportunistic observations in Google Earth imagery. Abundance estimates are derived from digital aerial survey counts by adapting established correction-based analyses with telemetry behavioral observation to quantify survey biases. The result is a first regional understanding of gray seal abundance in the northeast US through opportunistic Earth observation imagery and repurposed animal telemetry data. As species observation data from Earth observation imagery become more ubiquitous, such methods provide a robust, adaptable, and cost-effective solution to monitoring animal colonies and understanding species abundances.
    Description: We would like to thank generous support from International Fund for Animal Welfare, the Bureau of Ocean Energy, and the Oak Foundation for funding support for the telemetry devices.
    Keywords: Abundance estimation ; Gray seals (Halichoerus grypus) ; Cape Cod ; Remote sensing ; Earth observation
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  • 27
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Environmental Epigenetics 4 (2018): dvy005, doi:10.1093/eep/dvy005.
    Description: There is growing evidence that environmental toxicants can affect various physiological processes by altering DNA methylation patterns. However, very little is known about the impact of toxicant-induced DNA methylation changes on gene expression patterns. The objective of this study was to determine the genome-wide changes in DNA methylation concomitant with altered gene expression patterns in response to 3, 3’, 4, 4’, 5-pentachlorobiphenyl (PCB126) exposure. We used PCB126 as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. Adult zebrafish were exposed to 10 nM PCB126 for 24 h (water-borne exposure) and brain and liver tissues were sampled at 7 days post-exposure in order to capture both primary and secondary changes in DNA methylation and gene expression. We used enhanced Reduced Representation Bisulfite Sequencing and RNAseq to quantify DNA methylation and gene expression, respectively. Enhanced reduced representation bisulfite sequencing analysis revealed 573 and 481 differentially methylated regions in the liver and brain, respectively. Most of the differentially methylated regions are located more than 10 kilobases upstream of transcriptional start sites of the nearest neighboring genes. Gene Ontology analysis of these genes showed that they belong to diverse physiological pathways including development, metabolic processes and regeneration. RNAseq results revealed differential expression of genes related to xenobiotic metabolism, oxidative stress and energy metabolism in response to polychlorinated biphenyl exposure. There was very little correlation between differentially methylated regions and differentially expressed genes suggesting that the relationship between methylation and gene expression is dynamic and complex, involving multiple layers of regulation.
    Description: This work was supported by the National Institute of Health Outstanding New Environmental Scientist Award to NA (NIH R01ES024915) and Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) grant P01ES021923 and National Science Foundation Grant OCE-1314642 to M. Hahn, J. Stegeman, NA and SK].
    Repository Name: Woods Hole Open Access Server
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  • 28
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 1072–1087, doi:10.1093/gji/ggy203.
    Description: An earthquake rupture process can be kinematically described by rupture velocity, duration and spatial extent. These key kinematic source parameters provide important constraints on earthquake physics and rupture dynamics. In particular, core questions in earthquake science can be addressed once these properties of small earthquakes are well resolved. However, these parameters of small earthquakes are poorly understood, often limited by available data sets and methodologies. The Incorporated Research Institutions for Seismology Community Wavefield Experiment in Oklahoma deployed ∼350 three-component nodal stations within 40 km2 for a month, offering an unprecedented opportunity to test new methodologies for resolving small earthquake finite source properties in high resolution. In this study, we demonstrate the power of the nodal data set to resolve the variations in the seismic wavefield over the focal sphere due to the finite source attributes of an M2 earthquake within the array. The dense coverage allows us to tightly constrain rupture area using the second moment method even for such a small earthquake. The M2 earthquake was a strike-slip event and unilaterally propagated towards the surface at 90 per cent local S-wave speed (2.93 km s−1). The earthquake lasted ∼0.019 s and ruptured Lc ∼70 m and Wc ∼45 m. With the resolved rupture area, the stress-drop of the earthquake is estimated as 7.3 MPa for Mw 2.3. We demonstrate that the maximum and minimum bounds on rupture area are within a factor of two, much lower than typical stress-drop uncertainty, despite a suboptimal station distribution. The rupture properties suggest that there is little difference between the M2 Oklahoma earthquake and typical large earthquakes. The new three-component nodal systems have great potential for improving the resolution of studies of earthquake source properties.
    Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. JM was partially supported by SCEC grant #17177 at Woods Hole Oceanographic Institution. This research was supported by the Southern California Earthquake Center (Contribution No. 8014). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038.
    Keywords: Inverse theory ; Waveform inversion ; Body waves ; Earthquake dynamics ; Earthquake source observations ; Seismic instruments
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  • 29
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 942–958, doi:10.1093/gji/ggy316.
    Description: Surface waves recorded by global arrays have proven useful for locating tectonic earthquakes and in detecting slip events depleted in high frequency, such as glacial quakes. We develop a novel method using an aggregation of small- to continental-scale arrays to detect and locate seismic sources with Rayleigh waves at 20–50 s period. The proposed method is a hybrid approach including first dividing a large aperture aggregate array into Delaunay triangular subarrays for beamforming, and then using the resolved surface wave propagation directions and arrival times from the subarrays as data to formulate an inverse problem to locate the seismic sources and their origin times. The approach harnesses surface wave coherence and maximizes resolution of detections by combining measurements from stations spanning the whole U.S. continent. We tested the method with earthquakes, glacial quakes and landslides. The results show that the method can effectively resolve earthquakes as small as ∼M3 and exotic slip events in Greenland. We find that the resolution of the locations is non-uniform with respect to azimuth, and decays with increasing distance between the source and the array when no calibration events are available. The approach has a few advantages: the method is insensitive to seismic event type, it does not require a velocity model to locate seismic sources, and it is computationally efficient. The method can be adapted to real-time applications and can help in identifying new classes of seismic sources.
    Description: WF is currently supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Weston Howland Jr. Postdoctoral Scholarship. This work was supported by National Science Foundation grant EAR-1358520 at Scripps Institution of Oceanography, UC San Diego.
    Repository Name: Woods Hole Open Access Server
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  • 30
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 211 (2017): 1046–1061, doi:10.1093/gji/ggx360.
    Description: In recent years, marine controlled source electromagnetics (CSEM) has found increasing use in hydrocarbon exploration due to its ability to detect thin resistive zones beneath the seafloor. It is the purpose of this paper to evaluate the physics of CSEM for an ocean whose electrical thickness is comparable to or much thinner than that of the overburden using the in-line configuration through examination of the elliptically-polarized seafloor electric field, the time-averaged energy flow depicted by the real part of the complex Poynting vector, energy dissipation through Joule heating and the Fréchet derivatives of the seafloor field with respect to the sub-seafloor conductivity that is assumed to be transversely anisotropic, with a vertical-to-horizontal resistivity ratio of 3:1. For an ocean whose electrical thickness is comparable to that of the overburden, the seafloor electromagnetic response for a model containing a resistive reservoir layer has a greater amplitude and reduced phase as a function of offset compared to that for a halfspace, or a stronger and faster response, and displays little to no evidence for the air interaction. For an ocean whose electrical thickness is much smaller than that of the overburden, the electric field displays a greater amplitude and reduced phase at small offsets, shifting to a stronger amplitude and increased phase at intermediate offsets, and a weaker amplitude and enhanced phase at long offsets, or a stronger and faster response that first changes to stronger and slower, and then transitions to weaker and slower. By comparison to the isotropic case with the same horizontal conductivity, transverse anisotropy stretches the Poynting vector and the electric field response from a thin resistive layer to much longer offsets. These phenomena can be understood by visualizing the energy flow throughout the structure caused by the competing influences of the dipole source and guided energy flow in the reservoir layer, and the air interaction caused by coupling of the entire sub-seafloor resistivity structure with the sea surface. The Fréchet derivatives are dominated by preferential sensitivity to the vertical conductivity in the reservoir layer and overburden at short offsets. The horizontal conductivity Fréchet derivatives are weaker than to comparable to the vertical derivatives at long offsets in the substrate. This means that the sensitivity to the horizontal conductivity is present in the shallow parts of the subsurface. In the presence of transverse anisotropy, it is necessary to go to higher frequencies to sense the horizontal conductivity in the overburden as compared to an isotropic model with the same horizontal conductivity. These observations in part explain the success of shallow towed CSEM using only measurements of the in-line component of the electric field.
    Description: This work was supported at WHOI by an Independent Research and Development award, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
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  • 31
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 214 (2018): 2224–2235, doi:10.1093/gji/ggy201.
    Description: The key kinematic earthquake source parameters: rupture velocity, duration and area, shed light on earthquake dynamics, provide direct constraints on stress drop, and have implications for seismic hazard. However, for moderate and small earthquakes, these parameters are usually poorly constrained due to limitations of the standard analysis methods. Numerical experiments by Kaneko and Shearer demonstrated that standard spectral fitting techniques can lead to roughly one order of magnitude variation in stress-drop estimates that do not reflect the actual rupture properties even for simple crack models. We utilize these models to explore an alternative approach where we estimate the rupture area directly. For the suite of models, the area averaged static stress drop is nearly constant for models with the same underlying friction law, yet corner-frequency-based stress-drop estimates vary by a factor of 5–10 even for noise-free data. Alternatively, we simulated inversions for the rupture area as parametrized by the second moments of the slip distribution. A natural estimate for the rupture area derived from the second moments is A = πLcWc, where Lc and Wc are the characteristic rupture length and width. This definition yields estimates of stress drop that vary by only 10 per cent between the models but are slightly larger than the true area averaged values. We simulate inversions for the second moments for the various models and find that the area can be estimated well when there are at least 15 available measurements of apparent duration at a variety of take-off angles. The improvement compared to azimuthally averaged corner-frequency-based approaches results from the second moments accounting for directivity and removing the assumption of a circular rupture area, both of which bias the standard approach. We also develop a new method that determines the minimum and maximum values of rupture area that are consistent with a particular data set at the 95 per cent confidence level. For the Kaneko and Shearer models with 20+ randomly distributed observations and ∼10 per cent noise levels, we find that the maximum and minimum bounds on rupture area typically vary by a factor of two and that the minimum stress drop is often more tightly constrained than the maximum.
    Description: This work was supported by USGS NEHRP Award G17AP00029. The research was supported by the Southern California Earthquake Center (SCEC; Contribution No. 8013). SCEC is funded by NSF Cooperative Agreement EAR-1033462 and USGS Cooperative Agreement G12AC20038. YK was supported by both public funding from the Government of New Zealand and the Royal Society of New Zealand’s Rutherford Discovery Fellowship.
    Keywords: Earthquake dynamics ; Earthquake source observations ; Body waves
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  • 32
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    Oxford University Press
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 713–735, doi:10.1093/gji/ggy313.
    Description: Gas flux in volcanic conduits is often associated with long-period oscillations known as seismic tremor (Lesage et al.; Nadeau et al.). In this study, we revisit and extend the ‘magma wagging’and ‘whirling’models for seismic tremor, in order to explore the effects of gas flux on the motion of a magma column surrounded by a permeable vesicular annulus (Jellinek & Bercovici; Bercovici et al.; Liao et al.). We find that gas flux flowing through the annulus leads to a Bernoulli effect, which causes waves on the magma column to become unstable and grow. Specifically, the Bernoulli effects are associated with torques and forces acting on the magma column, increasing its angular momentum and energy. As the displacement of the magma column becomes large due to the Bernoulli effect, frictional drag on the conduit wall decelerates the motions of the column, restoring them to small amplitude. Together, the Bernoulli effect and the damping effect contribute to a self-sustained wagging-and-whirling mechanism that help explain the longevity of long-period seismic tremor.
    Description: This work was supported by National Science Foundation grants EAR-1344538 and EAR-1645057
    Keywords: Physics of magma and magma bodies ; Volcano seismology ; Volcanic gases
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  • 33
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2018. 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 215 (2018): 460–473, doi:10.1093/gji/ggy152.
    Description: In this work, we present a new methodology to predict grain-size distributions from geophysical data. Specifically, electric conductivity and magnetic susceptibility of seafloor sediments recovered from electromagnetic profiling data are used to predict grain-size distributions along shelf-wide survey lines. Field data from the NW Iberian shelf are investigated and reveal a strong relation between the electromagnetic properties and grain-size distribution. The here presented workflow combines unsupervised and supervised machine-learning techniques. Non-negative matrix factorization is used to determine grain-size end-members from sediment surface samples. Four end-members were found, which well represent the variety of sediments in the study area. A radial basis function network modified for prediction of compositional data is then used to estimate the abundances of these end-members from the electromagnetic properties. The end-members together with their predicted abundances are finally back transformed to grain-size distributions. A minimum spatial variation constraint is implemented in the training of the network to avoid overfitting and to respect the spatial distribution of sediment patterns. The predicted models are tested via leave-one-out cross-validation revealing high prediction accuracy with coefficients of determination (R2) between 0.76 and 0.89. The predicted grain-size distributions represent the well-known sediment facies and patterns on the NW Iberian shelf and provide new insights into their distribution, transition and dynamics. This study suggests that electromagnetic benthic profiling in combination with machine learning techniques is a powerful tool to estimate grain-size distribution of marine sediments.
    Description: This work was funded through DFG Research Center/Cluster of Excellence ‘The Ocean in the Earth System’ and was part of MARUM Research Area SD
    Keywords: Neural networks ; Fuzzy logic ; Statistical methods ; Electrical properties ; Magnetic properties ; Marine electromagnetics ; Controlled source electromagnetics (CSEM)
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  • 34
    Publication Date: 2021-11-09
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2019. Published by Oxford University Press on behalf of the Royal Astronomical Society. All rights reserved. Uploaded in accordance with the publisher's self-archiving policy.
    Description: The Amatrice–Norcia–Visso sequence is characterized by complex behaviour that is somewhat atypical of main-shock–aftershock sequences, as there were multiple large main shocks that continued for months. In this study we focus on the Amatrice sequence (main shock 2016 August 24, Mw = 5.97) to evaluate the apparent stress values and magnitude-dependent scaling in order to improve our knowledge of processes that control small and large earthquakes within this active region of Italy. Apparent stress is proportional to the ratio of radiated seismic energy and seismic moment, and as such, these stress parameters play an important role in hazard prediction as they have a strong effect on the observed and predicted ground shaking. We analyse 83 events of the sequence from 2016 August 24 to October 16, within a radius of 20 km from the main shock and with an Mw ranging between 5.97 and 2.72. Taking advantage of the averaging nature of coda waves, we analyse coda-envelope-based spectral ratios between neighbouring event pairs.We use equations proposed byWalter et al. to consider stable, low-frequency and high-frequency spectral ratio levelswhich provide measures of the corner frequency and apparent stress ratios of the events within the sequence. The results demonstrate non-self-similar behaviour within the sequence, suggesting a change in dynamics between the largest events and the smaller aftershocks. The apparent stress and corner frequency estimates are compared to those obtained by Malagnini and Munaf`o who utilized hundreds of direct S-wave spectral ratio measurements to obtain their results. Although our analysis is based only on 83 events, our results are in very good agreement, demonstrating once more that the use of coda waves is very stable and provides lower variance measures than those using direct waves. A comparison with recent Central Apennines source scaling models derived from various seismic sequences (1997–1998 Colfiorito, 2002 San Giuliano di Puglia, 2009 L’Aquila) shows that the Amatrice sequence source scaling in this study is well represented by the models proposed by Pacor et al. and Malagnini and Mayeda.
    Description: Published
    Description: 446-455
    Description: 3T. Sorgente sismica
    Description: JCR Journal
    Keywords: Coda waves; Earthquake dynamics; Earthquake source observations; Amatrice ; earthquake stress parameters
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 35
    Publication Date: 2022-05-26
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bioinformatics 31 (2015): 1872-1874, doi:10.1093/bioinformatics/btv045.
    Description: The association of organisms to their environments is a key issue in exploring biodiversity patterns. This knowledge has traditionally been scattered, but textual descriptions of taxa and their habitats are now being consolidated in centralized resources. However, structured annotations are needed to facilitate large-scale analyses. Therefore, we developed ENVIRONMENTS, a fast dictionary-based tagger capable of identifying Environment Ontology (ENVO) terms in text. We evaluate the accuracy of the tagger on a new manually curated corpus of 600 Encyclopedia of Life (EOL) species pages. We use the tagger to associate taxa with environments by tagging EOL text content monthly, and integrate the results into the EOL to disseminate them to a broad audience of users.
    Description: The Encyclopedia Of Life Rubenstein Fellows Program [CRDF EOL-33066-13/E33066], the LifeWatchGreece Research Infrastructure [384676-94/GSRT/ NSRF(C&E)] and the Novo Nordisk Foundation Center for Protein Research [NNF14CC0001].
    Repository Name: Woods Hole Open Access Server
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  • 36
    Publication Date: 2022-06-20
    Description: A major uncertainty in determining the mass balance of the Antarctic ice sheet from measurements of satellite gravimetry, and to a lesser extent satellite altimetry, is the poorly known correction for the ongoing deformation of the solid Earth caused by glacial isostatic adjustment (GIA). Although much progress has been made in consistently modeling the ice-sheet evolution throughout the last glacial cycle, as well as the induced bedrock deformation caused by these load changes, forward models of GIA remain ambiguous due to the lack of observational constraints on the ice sheet's past extent and thickness and mantle rheology beneath the continent. As an alternative to forward-modeling GIA, we estimate GIA from multiple space-geodetic observations: Gravity Recovery and Climate Experiment (GRACE), Envisat/ICESat and Global Positioning System (GPS). Making use of the different sensitivities of the respective satellite observations to current and past surface-mass (ice mass) change and solid Earth processes, we estimate GIA based on viscoelastic response functions to disc load forcing. We calculate and distribute the viscoelastic response functions according to estimates of the variability of lithosphere thickness and mantle viscosity in Antarctica. We compare our GIA estimate with published GIA corrections and evaluate its impact in determining the ice-mass balance in Antarctica from GRACE and satellite altimetry. Particular focus is applied to the Amundsen Sea Sector in West Antarctica, where uplift rates of several centimetres per year have been measured by GPS. We show that most of this uplift is caused by the rapid viscoelastic response to recent ice-load changes, enabled by the presence of a low-viscosity upper mantle in West Antarctica. This paper presents the second and final contributions summarizing the work carried out within a European Space Agency funded study, REGINA (www.regina-science.eu).
    Repository Name: EPIC Alfred Wegener Institut
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  • 37
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 1822-1837, doi: 10.1093/gji/ggz253.
    Description: Joint inversion of multiple electromagnetic data sets, such as controlled source electromagnetic and magnetotelluric data, has the potential to significantly reduce uncertainty in the inverted electrical resistivity when the two data sets contain complementary information about the subsurface. However, evaluating quantitatively the model uncertainty reduction is made difficult by the fact that conventional inversion methods—using gradients and model regularization—typically produce just one model, with no associated estimate of model parameter uncertainty. Bayesian inverse methods can provide quantitative estimates of inverted model parameter uncertainty by generating an ensemble of models, sampled proportional to data fit. The resulting posterior distribution represents a combination of a priori assumptions about the model parameters and information contained in field data. Bayesian inversion is therefore able to quantify the impact of jointly inverting multiple data sets by using the statistical information contained in the posterior distribution. We illustrate, for synthetic data generated from a simple 1-D model, the shape of parameter space compatible with controlled source electromagnetic and magnetotelluric data, separately and jointly. We also demonstrate that when data sets contain complementary information about the model, the region of parameter space compatible with the joint data set is less than or equal to the intersection of the regions compatible with the individual data sets. We adapt a trans-dimensional Markov chain Monte Carlo algorithm for jointly inverting multiple electromagnetic data sets for 1-D earth models and apply it to surface-towed controlled source electromagnetic and magnetotelluric data collected offshore New Jersey, USA, to evaluate the extent of a low salinity aquifer within the continental shelf. Our inversion results identify a region of high resistivity of varying depth and thickness in the upper 500 m of the continental shelf, corroborating results from a previous study that used regularized, gradient-based inversion methods. We evaluate the joint model parameter uncertainty in comparison to the uncertainty obtained from the individual data sets and demonstrate quantitatively that joint inversion offers reduced uncertainty. In addition, we show how the Bayesian model ensemble can subsequently be used to derive uncertainty estimates of pore water salinity within the low salinity aquifer.
    Description: We gratefully acknowledge funding support from National Science Foundation grants 1458392 and 1459035. We thank the captain and crew of the R.V. Marcus G. Langseth for a successful cruise and the Marine EM Lab at Scripps Institution of Oceanography for providing the instrumentation. We also thank Chris Armerding, Marah Dahn, John Desanto, Jimmy Elsenbeck, Matt Folsom, Keiichi Ishizu, Jeff Pepin, Charlotte Wiman and Georgie Zelenak for participating in the cruise. We gratefully acknowledge Alberto Malinverno for the idea to use a Monte Carlo scheme to estimate the distribution of pore fluid salinity, and William Menke for many constructive conversations and suggestions.
    Keywords: Controlled source electromagnetics (CSEM) ; Joint inversion ; Magnetotellurics ; Statistical methods ; Marine electromagnetics ; Probability distributions
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  • 38
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2122-2135, doi: 10.1093/gji/ggz272.
    Description: We have conducted the first passive Ocean Bottom Seismograph (OBS) experiment near the Challenger Deep at the southernmost Mariana subduction zone by deploying and recovering an array of 6 broad-band OBSs during December 2016–June 2017. The obtained passive-source seismic records provide the first-ever near-field seismic observations in the southernmost Mariana subduction zone. We first correct clock errors of the OBS recordings based on both teleseismic waveforms and ambient noise cross-correlation. We then perform matched filter earthquake detection using 53 template events in the catalogue of the US Geological Survey and find 〉7000 local earthquakes during the 6-month OBS deployment period. Results of the two independent approaches show that the maximum clock drifting was ∼2 s on one instrument (OBS PA01), while the rest of OBS waveforms had negligible time drifting. After timing correction, we locate the detected earthquakes using a newly refined local velocity model that was derived from a companion active source experiment in the same region. In total, 2004 earthquakes are located with relatively high resolution. Furthermore, we calibrate the magnitudes of the detected earthquakes by measuring the relative amplitudes to their nearest relocated templates on all OBSs and acquire a high-resolution local earthquake catalogue. The magnitudes of earthquakes in our new catalogue range from 1.1 to 5.6. The earthquakes span over the Southwest Mariana rift, the megathrust interface, forearc and outer-rise regions. While most earthquakes are shallow, depths of the slab earthquakes increase from ∼100 to ∼240 km from west to east towards Guam. We also delineate the subducting interface from seismicity distribution and find an increasing trend in dip angles from west to east. The observed along-strike variation in slab dip angles and its downdip extents provide new constraints on geodynamic processes of the southernmost Mariana subduction zone.
    Description: We express our appreciation to the science parties and crew members of the R/V Shiyan 3 for deployment and collection of the OBS instruments during the Mariana expeditions. This study is supported by the Hong Kong Research Grant Council Grants (No. 14313816), Faculty of Science at CUHK, Chinese Academy of Sciences (No. Y4SL021001, QYZDY-SSW-DQC005, 133244KYSB20180029), the National Natural Science Foundation of China (No. 41890813, 91628301, 41676042, U1701641, 41576041, 91858207 and U1606401), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100). Generic Mapping Tools (Wessel & Smith 1991) and PSSAC (developed by Prof Lupei Zhu) are used for data analysis and figure preparation in this study. Constructive comments from Dr Lidong Bie and two anonymous reviewers are helpful in improving the manuscript.
    Keywords: Seismicity and tectonics ; Dynamics: seismotectonics ; Subduction zone processes
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  • 39
    Publication Date: 2022-05-26
    Description: Author Posting. © Oxford University Press, 2016. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 205 (2016): 728-743, doi:10.1093/gji/ggw044.
    Description: While elasticity is a defining characteristic of the Earth's lithosphere, it is often ignored in numerical models of long-term tectonic processes in favour of a simpler viscoplastic description. Here we assess the consequences of this assumption on a well-studied geodynamic problem: the growth of normal faults at an extensional plate boundary. We conduct 2-D numerical simulations of extension in elastoplastic and viscoplastic layers using a finite difference, particle-in-cell numerical approach. Our models simulate a range of faulted layer thicknesses and extension rates, allowing us to quantify the role of elasticity on three key observables: fault-induced topography, fault rotation, and fault life span. In agreement with earlier studies, simulations carried out in elastoplastic layers produce rate-independent lithospheric flexure accompanied by rapid fault rotation and an inverse relationship between fault life span and faulted layer thickness. By contrast, models carried out with a viscoplastic lithosphere produce results that may qualitatively resemble the elastoplastic case, but depend strongly on the product of extension rate and layer viscosity U × ηL. When this product is high, fault growth initially generates little deformation of the footwall and hanging wall blocks, resulting in unrealistic, rigid block-offset in topography across the fault. This configuration progressively transitions into a regime where topographic decay associated with flexure is fully accommodated within the numerical domain. In addition, high U × ηL favours the sequential growth of multiple short-offset faults as opposed to a large-offset detachment. We interpret these results by comparing them to an analytical model for the fault-induced flexure of a thin viscous plate. The key to understanding the viscoplastic model results lies in the rate-dependence of the flexural wavelength of a viscous plate, and the strain rate dependence of the force increase associated with footwall and hanging wall bending. This behaviour produces unrealistic deformation patterns that can hinder the geological relevance of long-term rifting models that assume a viscoplastic rheology.
    Description: This work was supported by NSF grants OCE-11-54238 (JAO, MDB), EAR-10-10432 (MDB) and OCE-11-55098 (GI), as well as a WHOI Deep Exploration Institute grant and start-up support from the University of Idaho (EM).
    Keywords: Mid-ocean ridge processes ; Continental tectonics: extensional ; Lithospheric flexure ; Mechanics, theory, and modelling
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  • 40
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 4 (2016): cow014, doi:10.1093/conphys/cow014.
    Description: Reproduction of mysticete whales is difficult to monitor, and basic parameters, such as pregnancy rate and inter-calving interval, remain unknown for many populations. We hypothesized that baleen plates (keratinous strips that grow downward from the palate of mysticete whales) might record previous pregnancies, in the form of high-progesterone regions in the sections of baleen that grew while the whale was pregnant. To test this hypothesis, longitudinal baleen progesterone profiles from two adult female North Atlantic right whales (Eubalaena glacialis) that died as a result of ship strike were compared with dates of known pregnancies inferred from calf sightings and post-mortem data. We sampled a full-length baleen plate from each female at 4 cm intervals from base (newest baleen) to tip (oldest baleen), each interval representing ∼60 days of baleen growth, with high-progesterone areas then sampled at 2 or 1 cm intervals. Pulverized baleen powder was assayed for progesterone using enzyme immunoassay. The date of growth of each sampling location on the baleen plate was estimated based on the distance from the base of the plate and baleen growth rates derived from annual cycles of stable isotope ratios. Baleen progesterone profiles from both whales showed dramatic elevations (two orders of magnitude higher than baseline) in areas corresponding to known pregnancies. Baleen hormone analysis shows great potential for estimation of recent reproductive history, inter-calving interval and general reproductive biology in this species and, possibly, in other mysticete whales.
    Description: This work was supported by the Eppley Foundation for Research, the National Oceanographic and Atmospheric Administration Marine Mammal Health and Stranding Program and the Woods Hole Oceanographic Institution Ocean Life Institute.
    Keywords: Baleen ; Cetacea ; Marine mammals ; Pregnancy ; Progesterone ; Reproduction
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  • 41
    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 7 (2015): 457-464, doi:10.1093/gbe/evu289.
    Description: The uptake and transport of vitamin B12 (cobalamin; Cbl) in mammals involves a refined system with three evolutionarily related transporters: transcobalamin 1 (Tcn1), transcobalamin 2 (Tcn2), and the gastric intrinsic factor (Gif). Teleosts have a single documented binder with intermediate features to the human counterparts. Consequently, it has been proposed that the expansion of Cbl binders occurred after the separation of Actinopterygians. Here, we demonstrate that the diversification of this gene family took place earlier in gnathostome ancestry. Our data indicates the presence of single copy orthologs of the Sarcopterygii/Tetrapoda duplicates Tcn1 and Gif, and Tcn2, in Chondrichthyes. In addition, a highly divergent Cbl binder was found in the Elasmobranchii. We unveil a complex scenario forged by genome, tandem duplications and lineage-specific gene loss. Our findings suggest that from an ancestral transporter, exhibiting large spectrum and high affinity binding, highly specific Cbl transporters emerged through gene duplication and mutations at the binding pocket.
    Description: This work was funded by the Fundação para a Ciência e a Tecnologia (FCT) project PEst-C/MAR/LA0015/2013. PhD grant SFRH/BD/84238/2012 awarded to M.L-.M. Postdoctoral grant SFRH/BPD/72519/2010 awarded to R.R.
    Keywords: Cobalamin transport ; Genome duplications ; Gnathostomes
    Repository Name: Woods Hole Open Access Server
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  • 42
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2016. 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 205 (2016): 785-795, doi:10.1093/gji/ggw036.
    Description: An L-configured, three-component short period seismic array was deployed on the Ross Ice Shelf, Antarctica during November 2014. Polarization analysis of ambient noise data from these stations shows linearly polarized waves for frequency bands between 0.2 and 2 Hz. A spectral peak at about 1.6 Hz is interpreted as the resonance frequency of the water column and is used to estimate the water layer thickness below the ice shelf. The frequency band from 4 to 18 Hz is dominated by Rayleigh and Love waves propagating from the north that, based on daily temporal variations, we conclude were generated by field camp activity. Frequency–slowness plots were calculated using beamforming. Resulting Love and Rayleigh wave dispersion curves were inverted for the shear wave velocity profile within the firn and ice to ∼150 m depth. The derived density profile allows estimation of the pore close-off depth and the firn–air content thickness. Separate inversions of Rayleigh and Love wave dispersion curves give different shear wave velocity profiles within the firn. We attribute this difference to an effective anisotropy due to fine layering. The layered structure of firn, ice, water and the seafloor results in a characteristic dispersion curve below 7 Hz. Forward modelling the observed Rayleigh wave dispersion curves using representative firn, ice, water and sediment structures indicates that Rayleigh waves are observed when wavelengths are long enough to span the distance from the ice shelf surface to the seafloor. The forward modelling shows that analysis of seismic data from an ice shelf provides the possibility of resolving ice shelf thickness, water column thickness and the physical properties of the ice shelf and underlying seafloor using passive-source seismic data.
    Description: PDB, AD and PG were supported by NSF Grant PLR 1246151. RAS was supported by NSF Grant PLR-1246416. DAW, RA and AN were supported under NSF Grants PLR-1142518, 1141916 and 1142126, respectively. PDB also received support from the California Department of Parks and Recreation, Division of Boating and Waterways under contract 11-106-107.
    Keywords: Glaciology ; Surface waves and free oscillations ; Seismic anisotropy ; Antarctica
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  • 43
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in ICES Journal of Marine Science 76(4), (2010): 781-786, doi:10.1093/icesjms/fsy194.
    Description: Whales are federally protected by the Marine Mammal Protection Act; endangered species, such as the North Atlantic right whale, receive additional protection under the Endangered Species Act. However, their regulations have failed to satisfy conservation and animal welfare concerns. From 1990 to 2011 the North Atlantic right whale (Eubalaena glacialis, NARW) population grew at a mean of 2.8% annually. However, population trends reversed since 2011; the species is in decline, with only ∼100 reproductively active females remaining. This failure is driven by vessel collisions and increasingly fatal and serious entanglement in fixed fishing gear, whose rope strength has increased substantially. Chronic entanglement, drag, and associated morbidity have been linked to poor fecundity. Genuine solutions involve designating areas to be avoided and speed restrictions for ships and removing fishing trap ropes from the water column. A trap fishing closure for NARW habitat in the Cape Cod Bay (U.S.) area has been in place seasonally since 2015. 2017 mortalities in Eastern Canada elicited substantive management changes whereby the 2018 presence of NARW in active trap fishing areas resulted in an effective closure. To avoid these costly closures, the traditional trap fishery model of rope end lines attached to surface marker buoys has to be modified so that traps are marked virtually, and retrieved with gear that does not remain in the water column except during trap retrieval. Consumer demand for genuinely whale-safe products will augment and encourage the necessary regulatory changes so that trap fisheries conserve target and nontarget species.
    Description: I thank Mark Baumgartner, Scott Kraus, Tim Werner, Amy Knowlton, Heather Pettis, Scott Landry, Stormy Mayo, Fred Penney, and Beth Casoni for discussions on this topic and Natalie Renier for drawing Figures 5 and 6. Funding was provided by the Woods Hole Oceanographic Institution Independent Research and Development Program.
    Description: 2020-01-10
    Keywords: end line ; entanglement ; large whale ; rope removal ; trap
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  • 44
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International, 219(1), (2019): 464-478, doi:10.1093/gji/ggz315.
    Description: The electromagnetic (EM) field generated by ocean tidal flow is readily detectable in both satellite magnetic field data, and in ocean-bottom measurements of electric and magnetic fields. The availability of accurate charts of tidal currents, constrained by assimilation of modern satellite altimetry data, opens the possibility of using tidal EM fields as a source to image mantle electrical resistivity beneath the ocean basins, as highlighted by the recent success in defining the globally averaged lithosphere–asthenosphere boundary (LAB) with satellite data. In fact, seafloor EM data would be expected to provide better constraints on the structure of resistive oceanic lithosphere, since the toroidal magnetic mode, which can constrain resistive features, is a significant component of the tidal EM field within the ocean, but is absent above the surface (in particular in satellite data). Here we consider this issue in more detail, using a combination of simplified theoretical analysis and 1-D and 3-D numerical modelling to provide a thorough discussion of the sensitivity of satellite and seafloor data to subsurface electrical structure. As part of this effort, and as a step toward 3-D inversion of seafloor tidal data, we have developed a new flexible 3-D spherical-coordinate finite difference scheme for both global and regional scale modelling, with higher resolution models nested in larger scale solutions. We use the new 3-D model, together with Monte Carlo simulations of errors in tidal current estimates, to provide a quantitative assessment of errors in the computed tidal EM signal caused by uncertainty in the tidal source. Over the open ocean this component of error is below 0.01 nT in Bz at satellite height and 0.05 nT in Bx on the seafloor, well below typical signal levels. However, as coastlines are approached error levels can increase substantially. Both analytical and 3-D modelling demonstrate that the seafloor magnetic field is most sensitive to the lithospheric resistance (the product of resistivity and thickness), and is more weakly influenced (primarily in the phase) by resistivity of the underlying asthenosphere. Satellite data, which contain only the poloidal magnetic mode, are more sensitive to the conductive asthenosphere, but have little sensitivity to lithospheric resistance. For both seafloor and satellite data’s changes due to plausible variations in Earth parameters are well above error levels associated with source uncertainty, at least in the ocean interior. Although the 3-D modelling results are qualitatively consistent with theoretical analysis, the presence of coastlines and bathymetric variations generates a complex response, confirming that quantitative interpretation of ocean tidal EM fields will require a 3-D treatment. As an illustration of the nested 3-D scheme, seafloor data at five magnetic and seven electric stations in the northeastern Pacific (41○N, 165○W) are fit with trial-and-error forward modelling of a local domain. The simulation results indicate that the lithospheric resistance is roughly 7 × 108 Ωm2. The phase of the seafloor data in this region are inconsistent with a sharp transition between the resistive lithosphere and conductive asthenosphere.
    Description: This work has been supported by National Natural Science Foundation of China grants 41804072 and 41574104, and NSF grant EAR-1447109. Special thanks to Dr Benjamin Murphy who provided the conductivity-depth profile for 1-D earth model, Dr Min Ding who provided valuable discussion about the oceanic lithosphere and Dr Jeffery Love who provided comments on the stylistics of the manuscript.
    Keywords: Composition and structure of the mantle ; Pacific Ocean ; Electromagnetic theory ; Geomagnetic induction ; Satellite magnetics
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  • 45
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.
    Description: Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.
    Description: This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.).
    Keywords: Population genomics ; Genome sequence ; Comparative genomics ; Adaptation ; Genetic diversity
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  • 46
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 5 (2017): cox061, doi:10.1093/conphys/cox061.
    Description: Recent studies have demonstrated that some hormones are present in baleen powder from bowhead (Balaena mysticetus) and North Atlantic right (Eubalaena glacialis) whales. To test the potential generalizability of this technique for studies of stress and reproduction in large whales, we sought to determine whether all major classes of steroid and thyroid hormones are detectable in baleen, and whether these hormones are detectable in other mysticetes. Powdered baleen samples were recovered from single specimens of North Atlantic right, bowhead, blue (Balaenoptera [B.]musculus), sei (B. borealis), minke (B. acutorostrata), fin (B. physalus), humpback (Megaptera novaeangliae) and gray (Eschrichtius robustus) whales. Hormones were extracted with a methanol vortex method, after which we tested all species with commercial enzyme immunoassays (EIAs, Arbor Assays) for progesterone, testosterone, 17β-estradiol, cortisol, corticosterone, aldosterone, thyroxine and tri-iodothyronine, representing a wide array of steroid and thyroid hormones of interest for whale physiology research. In total, 64 parallelism tests (8 species × 8 hormones) were evaluated to verify good binding affinity of the assay antibodies to hormones in baleen. We also tested assay accuracy, although available sample volume limited this test to progesterone, testosterone and cortisol. All tested hormones were detectable in baleen powder of all species, and all assays passed parallelism and accuracy tests. Although only single individuals were tested, the consistent detectability of all hormones in all species indicates that baleen hormone analysis is likely applicable to a broad range of mysticetes, and that the EIA kits tested here perform well with baleen extract. Quantification of hormones in baleen may be a suitable technique with which to explore questions that have historically been difficult to address in large whales, including pregnancy and inter-calving interval, age of sexual maturation, timing and duration of seasonal reproductive cycles, adrenal physiology and metabolic rate.
    Description: This work was supported by (1) the Center for Bioengineering Innovation at Northern Arizona University and (2) the New England Aquarium.
    Keywords: Baleen ; Cetaceans ; Hormones ; Marine mammals ; Reproduction ; Stress
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  • 47
    Publication Date: 2022-05-26
    Description: Author Posting. © Author(s), 2017. This article is posted here by permission of Oxford University Press for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 212 (2018): 1429–1449, doi:10.1093/gji/ggx488.
    Description: We conducted detailed analyses of a global array of trenches, revealing systematic intra- and intertrench variations in plate bending characteristics. The intratrench variations of the Manila and Mariana Trenches were analysed in detail as end-member cases of the relatively young (16–36 Ma) and old (140–160 Ma) subducting plates, respectively. Meanwhile, the intertrench variability was investigated for a global array of additional trenches including the Philippine, Kuril, Japan, Izu-Bonin, Aleutian, Tonga-Kermadec, Middle America, Peru, Chile, Sumatra and Java Trenches. Results of the analysis show that the trench relief (W0) and width (X0) of all systems are controlled primarily by the faulting-reduced elastic thickness near the trench axis (Tme) and affected only slightly by the initial unfaulted thickness (TMe) of the incoming plate. The reduction in Te has caused significant deepening and narrowing of trench valleys. For the cases of relatively young or old plates, the plate age could be a dominant factor in controlling the trench bending shape, regardless the variations in axial loadings. Our calculations also show that the axial loading and stresses of old subducting plates can vary significantly along the trench axis. In contrast, the young subducting plates show much smaller values and variations in axial loading and stresses.
    Description: This work was supported by Chinese Academy of Sciences Grants (Y4SL021001, QYZDY-SSW-DQC005, YZ201325 and YZ201534), National Natural Science Foundation of China Grants (91628301, U1606401, 41376063 and 41706056) and HKSAR Research Grant Council Grants (24601515, 14313816).
    Keywords: Lithospheric flexure ; Subduction zone processes
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  • 48
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aslan, C., Beckman, N. G., Rogers, H. S., Bronstein, J., Zurell, D., Hartig, F., Shea, K., Pejchar, L., Neubert, M., Poulsen, J., HilleRisLambers, J., Miriti, M., Loiselle, B., Effiom, E., Zambrano, J., Schupp, G., Pufal, G., Johnson, J., Bullock, J. M., Brodie, J., Bruna, E., Cantrell, R. S., Decker, R., Fricke, E., Gurski, K., Hastings, A., Kogan, O., Razafindratsima, O., Sandor, M., Schreiber, S., Snell, R., Strickland, C., & Zhou, Y. Employing plant functional groups to advance seed dispersal ecology and conservation. AoB Plants, 11(2), (2019):plz006, doi:10.1093/aobpla/plz006.
    Description: Seed dispersal enables plants to reach hospitable germination sites and escape natural enemies. Understanding when and how much seed dispersal matters to plant fitness is critical for understanding plant population and community dynamics. At the same time, the complexity of factors that determine if a seed will be successfully dispersed and subsequently develop into a reproductive plant is daunting. Quantifying all factors that may influence seed dispersal effectiveness for any potential seed-vector relationship would require an unrealistically large amount of time, materials and financial resources. On the other hand, being able to make dispersal predictions is critical for predicting whether single species and entire ecosystems will be resilient to global change. Building on current frameworks, we here posit that seed dispersal ecology should adopt plant functional groups as analytical units to reduce this complexity to manageable levels. Functional groups can be used to distinguish, for their constituent species, whether it matters (i) if seeds are dispersed, (ii) into what context they are dispersed and (iii) what vectors disperse them. To avoid overgeneralization, we propose that the utility of these functional groups may be assessed by generating predictions based on the groups and then testing those predictions against species-specific data. We suggest that data collection and analysis can then be guided by robust functional group definitions. Generalizing across similar species in this way could help us to better understand the population and community dynamics of plants and tackle the complexity of seed dispersal as well as its disruption.
    Description: Ideas for this manuscript initiated during the Seed Dispersal Workshop held in May 2016 at the Socio-Environmental Synthesis Center in Annapolis, MD and supported by the US National Science Foundation Grant DEB-1548194 to N.G.B. and the National Socio‐Environmental Synthesis Center under the US National Science Foundation Grant DBI‐1052875. D.Z. received funding from the Swiss National Science Foundation (SNF, grant: PZ00P3_168136/1) and from the German Science Foundation (DFG, grant: ZU 361/1- 1). Contributions by the authors C.A. led the development of the concepts, writing, and revising of the manuscript with input from N.G.B. and H.S.R. All authors contributed to the development of concepts and are listed in order of contribution and alphabetical order within each level of contribution.
    Keywords: dependency ; directed dispersal ; dispersal vectors ; generalization ; mutualism ; seed dispersal effectiveness
    Repository Name: Woods Hole Open Access Server
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Alexander, H., Johnson, L. K., & Brown, C. T.. Keeping it light: (re)analyzing community-wide datasets without major infrastructure. Gigascience, 8(2),(2019): giy159, doi:10.1093/gigascience/giy159.
    Description: DNA sequencing technology has revolutionized the field of biology, shifting biology from a data-limited to data-rich state. Central to the interpretation of sequencing data are the computational tools and approaches that convert raw data into biologically meaningful information. Both the tools and the generation of data are actively evolving, yet the practice of re-analysis of previously generated data with new tools is not commonplace. Re-analysis of existing data provides an affordable means of generating new information and will likely become more routine within biology, yet necessitates a new set of considerations for best practices and resource development. Here, we discuss several practices that we believe to be broadly applicable when re-analyzing data, especially when done by small research groups.
    Description: Funding was provided by the Gordon and Betty Moore Foundation (award GBMF4551 to C.T.B.).
    Keywords: reproducibility ; data reuse ; open data
    Repository Name: Woods Hole Open Access Server
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  • 50
    Publication Date: 2022-05-26
    Description: © International Council for the Exploration of the Sea, 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ICES Journal of Marine Science 73 (2016): 1839-1850, doi: 10.1093/icesjms/fsw086.
    Description: For terrestrial and marine benthic ecologists, landscape ecology provides a framework to address issues of complexity, patchiness, and scale—providing theory and context for ecosystem based management in a changing climate. Marine pelagic ecosystems are likewise changing in response to warming, changing chemistry, and resource exploitation. However, unlike spatial landscapes that migrate slowly with time, pelagic seascapes are embedded in a turbulent, advective ocean. Adaptations from landscape ecology to marine pelagic ecosystem management must consider the nature and scale of biophysical interactions associated with organisms ranging from microbes to whales, a hierarchical organization shaped by physical processes, and our limited capacity to observe and monitor these phenomena across global oceans. High frequency, multiscale, and synoptic characterization of the 4-D variability of seascapes are now available through improved classification methods, a maturing array of satellite remote sensing products, advances in autonomous sampling of multiple levels of biological complexity, and emergence of observational networks. Merging of oceanographic and ecological paradigms will be necessary to observe, manage, and conserve species embedded in a dynamic seascape mosaic, where the boundaries, extent, and location of features change with time.
    Description: This work was supported by NASA grant NNX14AP62A “National Marine Sanctuaries as Sentinel Sites for a Demonstration Marine Biodiversity Observation Network (MBON)” funded under the National Ocean Partnership Program (NOPP RFP NOAA-NOS-IOOS-2014-2003803 in partnership between NOAA, BOEM, and NASA), the NOAA Integrated Ocean Observing System (IOOS) Program Office, and the LenFest Ocean Program.
    Keywords: Biodiversity ; Conservation ; Landscape ; Ocean observations ; Pelagic ; Phytoplankton ; Seascape
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  • 51
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2022-05-26
    Description: Author Posting. © The Authors, 2019. 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 218(3), (2019): 2165-2178, doi: 10.1093/gji/ggz280.
    Description: A multitaper estimator is proposed that accommodates time-series containing gaps without using any form of interpolation. In contrast with prior missing-data multitaper estimators that force standard Slepian sequences to be zero at gaps, the proposed missing-data Slepian sequences are defined only where data are present. The missing-data Slepian sequences are frequency independent, as are the eigenvalues that define the energy concentration within the resolution bandwidth, when the process bandwidth is [−1/2,1/2) for unit sampling and the sampling scheme comprises integer multiples of unity. As a consequence, one need only compute the ensuing missing-data Slepian sequences for a given sampling scheme once, and then the spectrum at an arbitrary set of frequencies can be computed using them. It is also shown that the resulting missing-data multitaper estimator can incorporate all of the optimality features (i.e. adaptive-weighting, F-test and reshaping) of the standard multitaper estimator, and can be applied to bivariate or multivariate situations in similar ways. Performance of the missing-data multitaper estimator is illustrated using length of day, seafloor pressure and Nile River low stand time-series.
    Description: The length of day utilized in Section 3 are available from http://hpiers.obspm.fr. The pressure data used in Section 4 are available from https://doi.org/10.1029/2018JC014586. A Matlab function MDmwps.m to compute missing-data power spectra is available from the Mathworks file exchange website. The author thanks Jeff Park and editor F.J. Simons for thorough reviews. This work was supported by an Internal Research and Development award at WHOI, and by the Walter A. and Hope Noyes Smith Chair for Excellence in Oceanography.
    Keywords: Fourier analysis ; Numerical approximations and analysis ; Statistical methods ; Time-series analysis
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, L. K., Alexander, H., & Brown, C. T. Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes. Gigascience, 8(4), (2019): giy158, doi: 10.1093/gigascience/giy158.
    Description: Background: De novo transcriptome assemblies are required prior to analyzing RNA sequencing data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, the effects of using different workflows, or “pipelines,” on the resulting assemblies are poorly understood. Here, a pipeline was programmatically automated and used to assemble and annotate raw transcriptomic short-read data collected as part of the Marine Microbial Eukaryotic Transcriptome Sequencing Project. The resulting transcriptome assemblies were evaluated and compared against assemblies that were previously generated with a different pipeline developed by the National Center for Genome Research. Results: New transcriptome assemblies contained the majority of previous contigs as well as new content. On average, 7.8% of the annotated contigs in the new assemblies were novel gene names not found in the previous assemblies. Taxonomic trends were observed in the assembly metrics. Assemblies from the Dinoflagellata showed a higher number of contigs and unique k-mers than transcriptomes from other phyla, while assemblies from Ciliophora had a lower percentage of open reading frames compared to other phyla. Conclusions: Given current bioinformatics approaches, there is no single “best” reference transcriptome for a particular set of raw data. As the optimum transcriptome is a moving target, improving (or not) with new tools and approaches, automated and programmable pipelines are invaluable for managing the computationally intensive tasks required for re-processing large sets of samples with revised pipelines and ensuring a common evaluation workflow is applied to all samples. Thus, re-assembling existing data with new tools using automated and programmable pipelines may yield more accurate identification of taxon-specific trends across samples in addition to novel and useful products for the community.
    Description: Funding was provided by the Gordon and Betty Moore Foundation under award number GBMF4551 to C.T.B. Jetstream cloud platform was used with XSEDE allocation TG-BIO160028 [66, 67].
    Keywords: marine microbial eukaryote ; transcriptome assembly ; automated pipeline ; re-analysis
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  • 53
    Publication Date: 2024-04-05
    Description: Secondary microseismic noise is generated by non-linear interactions between ocean waves at the ocean surface. We present here the theory for computing the site effect of the ocean layer upon body waves generated by noise sources distributed along the ocean surface. By defining the wavefield as the superposition of plane waves, we show that the ocean site effect can be described as the constructive interference of multiply reflected P waves in the ocean that are then converted to either P or SV waves at the ocean–crust interface. We observe that the site effect varies strongly with period and ocean depth, although in a different way for body waves than for Rayleigh waves. We also show that the ocean site effect is stronger for P waves than for S waves. We validate our computation by comparing the theoretical noise body wave sources with the sources inferred from beamforming analysis of the three seismogram components recorded by the Southern California Seismic Network. We use rotated traces for the beamforming analysis, and we show that we clearly detect P waves generated by ocean gravity wave interactions along the track of typhoon Ioke (2006 September). We do not detect the corresponding SV waves, and we demonstrate that this is because their amplitude is too weak.
    Description: Published
    Description: 1096-1106
    Description: 1T. Geodinamica e interno della Terra
    Description: JCR Journal
    Description: restricted
    Keywords: Body waves ; Site effects ; Theoretical Seismology ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    The Journal of Chemical Physics 111 (1999), S. 3820-3831 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we apply the recently developed state-specific multireference coupled-cluster and perturbation theories to calculate electrical properties such as dipole moment and static polarizability using perturbed orbitals in finite fields. The theories are built on complete active space reference functions, and are designed to treat quasidegeneracy of varying degrees while bypassing the intruder problem. Numerical results are presented for the model systems H4 with trapezoidal geometry and the lowest two singlet states of CH2. Both the systems require a multireference formulation due to quasidegeneracy. In the field-free situation, the former encounters intruders at an intermediate trapezoidal geometry in the traditional treatment using effective Hamiltonians, while the latter shows a pronounced multireference character in the two singlet states. This affects the response properties in the presence of a perturbing field. A comparison with the full CI results in the same basis indicates the efficacy of the state-specific methods in wide ranges of geometries, even when the traditional effective Hamiltonian based methods fail due to intruders. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3812-3819 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A compact basis set is constructed for the water dimer by focusing directly on an optimal description of the counterpoise-corrected interaction energy (ΔE) rather than on the total energy of the fragments. The optimization criterion is that the basis set should be of uniform accuracy, i.e., the truncation error in ΔE due to the basis set incompleteness should be the same for all symmetry types at all sites. Aiming at a truncation error of 10 μhartree per symmetry at the SCF+MP2 (self-consistent field+Møller–Plesset second-order) frozen core level the resulting interaction optimized basis set comprises 249 functions. The composition of this IO249 set is O/5s3p4d3f2g1h, H(donor)/2s4p1d, H(else)/2s3p, bond function set/3s3p2d1f. An all-electron variant, IO275, is described as well. A recipe to obtain interaction optimized sets for other systems is given. The set IO249 yields a ΔE(fc) value at the Feller–Frisch geometry of −4.87 kcal/mol. Of the many orbital-based calculations that have been reported for this system only Schütz' 1046-function calculation [J. Chem. Phys. 107, 4597 (1997)] was more accurate. The small size of the interaction optimized sets opens the possibility for high-accuracy SCF+MP2 work on larger systems than have been accessible before. It also brings higher-level correlated treatments within reach. An Appendix summarizes two additivity rules which allow the ΔE for a larger basis set to be estimated to very high accuracy from the results of smaller basis sets. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3832-3836 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper we present Z-vector formalism for the Fock space multireference coupled cluster framework. We present detailed equations describing the derivative effective Hamiltonian, where the response amplitudes of the highest Fock sector are eliminated. We discuss the conditions and approximations under which the formalism is possible. We also discuss the implications and comparison with the similar formalism in the single reference framework. The computational advantages and feasibility are also commented upon in this paper. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3837-3845 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Ten low-lying electronic states of Fe(II) porphine, 5A1g, 5Eg, 5B2g, 3A2g, 3B2g, 3Eg(A), 3Eg(B), 1A1g, 1B2g, and 1Eg states, are studied with multiconfigurational second-order perturbation (CASPT2) calculations with complete active space self-consistent field (CASSCF) reference functions with larger active space and basis sets. The enlargement of active space and basis sets has no influence on the conclusion of a previous multireference Møller–Plesset perturbation (MRMP) study. The present CASPT2 calculation concludes that the 5A1g state is the ground state. A relativistic correction has been performed by the relativistic scheme of eliminating small components (RESC). For energetics, no significant contribution from the relativistic correction was found. The relative energies and orbital energies are not changed appreciably by the introduction of a relativistic correction. The present result does not agree with all the spectroscopic observations, but is consistent with a magnetic moment study. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3846-3854 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The two-body interaction energies of the cyclic (C3h) and noncyclic (C2) trimers at the basis set limit (15.55 and 16.55 kJ/mol) were estimated by means of second-order Møller–Plesset perturbation theory including terms linear in the interelectronic distance (MP2-R12 approach). Coupled cluster calculations with single and double substitutions and with noniterative triple excitations [CCSD(T)] were carried out to correct the MP2-R12 two-body interaction energies for the effect of higher excitations, and also for the evaluation of the three-body interaction energies. The calculated bonding energies of the trimers using this model calculation (16.82 and 17.20 kJ/mol) suggest that the two isomers are nearly isoenergetic. The three-body terms are small (only of the order of 1 kJ/mol), stabilizing the cyclic trimer, but destabilizing the noncyclic trimer. © 1999 American Institute of Physics.
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  • 59
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    The Journal of Chemical Physics 111 (1999), S. 3855-3861 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The structure and the relative stability of the ethanol dimer and the cyclic ethanol trimer were studied using density functional theory methods. The geometries of the different dimers and trimers were optimized at the B3LYP/6-311+G(d,p) level of theory, while the final energies were obtained at the B3LYP/6-311+G(3df,2p) level. Four different (ethanol)2 complexes were found to be local minima of the potential energy surface, the global minimum being that in which both monomers exhibit a trans conformation. The hydrogen bond (HB) in ethanol dimer is slightly stronger than in methanol dimer, reflecting the enhanced intrinsic basicity of ethanol with regards to methanol. The OH donor stretch appears redshifted by 161 cm−1, while the redshifting undergone by the OH acceptor stretch is negligibly small. The relative stability of the trimers is a function of the number of monomers with a gauche conformation, the global minimum being that in which the three monomers have a trans conformation. As for water and methanol trimers, the three HBs in the cyclic ethanol trimer are not strictly equivalent. Consistently, the redshiftings of the OH stretching frequencies are different. Cooperative effects are sizably large, as reflected in the O(centered ellipsis)O distances, the elongation of the OH donor groups, the charge density at the bond critical points, the frequency shiftings of the OH stretches, and the additivity interaction energy. The most significant features of the vibrational spectra of the monomers, the dimers, and the trimers in the 800–1200 cm−1 region are reasonably well reproduced by our calculations.© 1999 American Institute of Physics.
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  • 60
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    The Journal of Chemical Physics 111 (1999), S. 3862-3873 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new potential energy surface for the lowest 3A″ electronic state of the O(3P)+HCl system is presented. This surface is based on electronic energies calculated at the multireference configuration interaction level of theory with the Davidson correction (MR-CI+Q) using the Dunning cc-pVTZ one-electron basis sets. The ab initio energies thus obtained are scaled using the scaled external correlation (SEC) method of Brown and Truhlar. The SEC-scaled energies are fitted to a simple analytical expression to yield a potential energy surface which correlates the reactants O(3P)+HCl(1Σ+) to the products OH(2Π)+Cl(2P). The reaction barrier on this surface lies at an O–H–Cl angle of 131.4° at an energy of 9.78 kcal/mol above the asymptotic O+HCl minimum. This barrier is 1.3 kcal/mol higher than that on the potential energy surface obtained by Koizumi, Schatz, and Gordon (KSG) [J. Chem. Phys. 95, 6421 (1991)] and 1.1 kcal/mol lower than the S2 surface of Ramachandran, Senekowitsch, and Wyatt (RSW) [J. Mol. Struct. (Theochem) 454, 307 (1998)]. The dynamics of the reaction O(3P)+HCl(v=2; j=1,6,9)→OH(v′,j′)+Cl on this potential surface is studied using quasi-classical trajectory (QCT) propagation and the results are compared to the experimental observations of Zhang et al. [R. Zhang, W. J. van der Zande, M. J. Bronikowski, and R. N. Zare, J. Chem. Phys. 94, 2704 (1991)]. The broad distribution of collision energies in the experiment is modeled by computing weighted averages of the quantities of interest with the weighting factor at each collision energy determined by the collision energy distribution. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2103-2108 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The vapor–liquid coexistence densities for water near the critical point were determined using a polarizable ab initio based model and grand canonical Monte Carlo simulations combined with the histogram reweighting technique. The predictions of the model used, which is found to give good agreement with experimental data at ambient conditions, are far below the experimental critical temperature and density. The saturation pressure is also overestimated. The source of this discrepancy may be related to the high pressure that the model exhibits even for liquid water. Since there is no fitting to experimental data, it is possible to refine the potential in a systematic way. In particular, an improvement in the sampling of the ab initio calculation for the repulsive part of the intermolecular potential is suggested in order to obtain better agreement with experiment at high temperatures and pressures. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2143-2150 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A model to investigate a gel-to-zeolite transformation as a possible growth mechanism through association and rearrangements of extended precursor structures is developed and solved via continuum time lattice Monte Carlo simulations. The model is used to study the morphology of zeolite L nanocrystals grown from an initial amorphous microporous precursor gel. The model considers gel dissolution to release growth precursor extended structures, precursor migration, precursor–precursor association, precursor incorporation into zeolite nanoparticles, and zeolite dissolution. It is shown that the gel-to-zeolite transformation can occur when dissolved precursor migration is slow compared to precursor incorporation and zeolite dissolution. Under these conditions, the initial gel microstructure (intraparticle porosity) has a significant effect on the zeolite morphology and on the crystallization kinetics. This transformation proceeds in two stages: A zeolitic framework forms initially without long-range order, followed by slow rearrangement of building units into nanocrystalline particles with possible defects. Finally different growth modes are identified as a function of microkinetic parameters and gel morphology. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2157-2163 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The electronic structure of tris(8-hydroxyquinoline) aluminum (Alq3) has been studied in the pristine molecular solid state as well as upon interaction (doping) with potassium and lithium. We discuss the results of a joint theoretical and experimental investigation, based on a combination of x-ray and ultraviolet photoelectron spectroscopies with quantum-chemical calculations at the density functional theory level. Upon doping, each electron transferred from an alkali metal atom is stored on one of the three ligands of the Alq3 molecule, resulting in a new spectral feature (peak) in the valence band that evolves uniformly when going from a doping level of one to three metal atoms per Alq3 molecule. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2151-2156 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A fluid with an interaction potential consisting of a hard core and an attractive Yukawa tail is considered. The strength of the attraction is taken to depend both on density and temperature in order to take into account the state dependence of the effective interaction suggested by the analysis of structural data of several colloidal suspensions, in particular microemulsions of AOT reverse micelles. The thermodynamics of this fluid is investigated starting from the inverse temperature expansion of the free energy in the mean spherical approximation. The temperature and density dependence of the interaction is incorporated in consistent expressions for the pressure, isothermal compressibility, and chemical potential. The phase diagram predicted by this method is in agreement with experimental data on AOT reverse micelles analyzed in the effective one component approach. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2176-2180 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The size-dependent melting temperature and the size-dependent melting entropy of organic nanocrystals are predicted by use of our simple model being free of any adjustable parameter. The model predictions for the size-dependent melting temperature and the size-dependent melting entropy are supported by the experimental results on benzene, chlorobenzene, heptane, and naphthalene nanocrystals. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2169-2175 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The O2 adsorption on Ag(111) single crystal in the range of 300–500 K has been studied by XPS, ADXPS, and TPD. At room temperature, the O1s line observed at 530.0 eV goes down to 528.2 eV when the sample is heated to 420 K. The comparison of XPS and TPD data indicates that both lines can be assigned to chemisorbed atomic oxygen. The depth concentration profiles calculated on the basis of the angular-dependent XPS data show that the line at 530.0 eV is responsible for oxygen adsorbed at the surface, as opposed to that at 528.2 eV which is assigned to oxygen between the top and second silver layers. The formation of surface silver oxide is concluded in the latter case. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2181-2189 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report the results of self-consistent quantum Monte Carlo simulations of the structure of the liquid-vapor interface of the alloy Sn0.09Ga0.81. Our calculations are in very good agreement with the experimental results reported by Lei, Huang and Rice [J. Chem. Phys. 107, 4051 (1997)]. In particular, our calculations confirm the experimentally inferred existence of a partial second layer of Sn below the complete outermost layer of Sn in the stratified liquid-vapor interface of this alloy. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3929-3939 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In this paper, we present detailed quantum treatment of the semirigid vibrating rotor target (SVRT) model for reaction dynamics involving polyatomic molecules. In the SVRT model, the reacting (target) molecule is treated as a semirigid vibrating rotor which can be considered as a three-dimensional generalization of the diatomic molecule. This model provides a realistic framework to treat reaction dynamics of polyatomic systems. Using the SVRT model, it becomes computationally practical to carry out quantitatively accurate quantum dynamics calculation for a variety of dynamics problems in which the reacting molecule is a polyatomic or complex molecule. In this work, specific theoretical treatment and mathematical formulation of the SVRT model are presented for three general classes of reaction systems: (1) reaction of an atom with a polyatomic molecule (atom–polyatom reaction), (2) reaction between two polyatomic molecules (polyatom–polyatom reaction), and (3) polyatomic reaction with a rigid surface (polyatom–surface reaction). Since the number of dynamical degrees of freedom in the SVRT model for the above three classes of dynamical problems is limited, accurate quantum (both ab initio and dynamical) calculations are possible for many reactions of practical chemical interest. In this paper, a time-dependent wave packet approach is employed to implement the SVRT model for dynamics calculation of polyatomic reactions. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3919-3928 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: A pulsed molecular beam cavity Fourier transform microwave spectrometer was used to measure pure rotational spectra of nine isotopomers of Ne2–N2O, and of three isotopomers of the Ar2–N2O van der Waals trimer. For Ne2–N2O, these are 20Ne20Ne–14N14N16O, 20Ne22Ne–14N14N16O, 22Ne22Ne–14N14N16O, 20Ne20Ne–15N14N16O, 20Ne22Ne–15N14N16O, 22Ne22Ne–15N14N16O, 20Ne20Ne–14N15N16O, 20Ne22Ne–14N15N16O, and 22Ne22Ne–14N15N16O. Those for Ar2–N2O are 40Ar40Ar–14N14N16O, 40Ar40Ar–15N14N16O, and 40Ar40Ar–14N15N16O. The spectra were measured in the frequency range between 3 and 18 GHz. Both a- and c-type transitions were measured for all Ne2–N2O isotopomers. In the case of the mixed, 20Ne22Ne containing, isotopomers a small b-dipole moment occurs and two b-type transitions were measured. In the spectra of Ar2–N2O only b- and c-type transitions were measured. Rotational and centrifugal distortion constants were determined for all the isotopomers of each complex. The spectral analyses show that Ne2–N2O is a highly asymmetric prolate rotor (κ=−0.158 for 20Ne20Ne–14N14N16O) while Ar2–N2O is a highly asymmetric oblate rotor (κ=0.285 for 40Ar40Ar–14N14N16O). Both trimers were found to have distorted tetrahedral structures with the rare gases tilted towards the O atom of the N2O subunit. Nuclear quadrupole hyperfine structures due to both terminal and central 14N nuclei were observed and analyzed to give the nuclear quadrupole coupling constants, χaa(1), χbb(1) and χaa(2), χbb(2). The resulting spectroscopic constants were utilized to derive ground state effective structures, ground state average structures, and partial substitution structures. Harmonic force field analyses were performed for each complex using the obtained quartic centrifugal distortion constants. The results of the spectroscopic analyses are discussed in the light of possible three-body nonadditive interactions. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3940-3945 
    ISSN: 1089-7690
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    Topics: Physics , Chemistry and Pharmacology
    Notes: Photodissociation of the H2S molecule at 157.6 nm was studied experimentally using the Rydberg tagging technique. Translational energy distributions of the H-atom product from the H2S photodissociation were measured, and the SH(X 2Π)+H(2S) channel was found to be the dominant dissociation process. Spin-orbit and rovibrational state distributions were also obtained for the SH product, which was found to be both vibrationally and rotationally excited. An intriguing bimodal rotational distribution in the lowest two vibrational states, v=0 and 1, has been clearly observed for the SH product, indicating that there are two distinctive dissociation mechanisms involved in the photodissociation of H2S at 157 nm excitation. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2242-2254 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The reactions of HOCl with HCl on water clusters have been theoretically investigated. Ab initio calculations indicate that hydrogen bond and cooperative effect play an essential role in the reactions; that the reaction barrier of HOCl with cyclic (H2O)n.HCl cluster is the least at n=3 and that the ionization of HCl and HOCl on ice surfaces may not be complete but partly at very low temperatures. Two cases a and b of the model reactions are considered for detailed analysis. On the surface of ice, the barrier energies are about 4 and 6 kcal/mol for cases a and b, respectively, at the MP2//HF/6-31G(d) level, which is close to an experimental estimation. This study suggests a similar previously reported mechanism that the heterogeneous reaction of HOCl with HCl on ice is catalyzed at the stratospheric conditions through structure catalysis and hydration that enhances ion character of species. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2235-2241 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: A newly developed "interrupted creep" experiment has been used to study the physical aging of a low molecular weight polystyrene, Tg∼69 °C. The results of the new experiment are compared to those obtained from traditional "periodic creep" experiments. The interrupted creep experiment provides information about the viscosity, the recoverable creep compliance and the steady-state compliance, Js, during aging. Low molecular weight polystyrene was chosen because it exhibits a steady-state compliance that is a strong function of temperature. Aging was conducted at three temperatures, 68.2, 65.7 and 61.0 °C, using both down-jump and up-jump experiments. The behavior observed in the new experiments mirrors the behavior observed in the traditional experiments. In addition, the new experiments allow the first ever determination of how Js evolves during aging. The change of Js with aging time was calculated using the relationship between the shift factors, obtained from the recoverable creep compliance data, and the average relaxation times, obtained from the viscosity. The advantage of the new experiment is that it provides both the short-time recoverable creep compliance information and the long-time viscous flow. By combining these contributions to the creep compliance in a simple additive fashion, one can obtain a more complete picture of how the material is behaving during aging. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 2259-2269 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The effect of a patterned surface on the phase separation kinetics of a thin polymer film has been investigated using the Cahn–Hilliard–Cook model in three dimensions with the addition of a short range surface potential. We have observed pattern-induced spinodal waves perpendicular to the surface creating "checkerboard"-like composition fluctuations for a wide range of patterns used in this study. The number of such layers strongly depends on the magnitude of the thermal noise. For sufficiently thin films, where the film thickness is smaller than the spinodal wavelength, spinodal decomposition can be arrested if the surface potential and the characteristic size of the pattern are chosen accordingly, enabling the transfer of surface patterns to the film material. The kinetic pathways through which the equilibrium states are reached delicately depend on the particular pattern, its size, and the film thickness. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4013-4024 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: Exact and approximate quantum mechanical calculations of reaction probabilities and cumulative reaction probabilities have been carried out for the F+H2 reaction on the ab initio adiabatic potential energy surfaces by Stark and Werner (SW) and by Hartke, Stark, and Werner (HSW), the latter including spin–orbit corrections in the entrance channel. These data have been employed to obtain thermal rate constants for the title reaction in the temperature range 200–700 K. The exact and approximate results have been compared with experimental determinations and previous theoretical predictions. In particular, the reaction probabilities obtained on the HSW surface are found to be in very good agreement with recent calculations by Alexander et al. [J. Chem. Phys. 109, 5710 (1998)] based on the exact treatment of spin–orbit and Coriolis coupling for this system. However, the rate constants calculated on the HSW PES are systematically lower than the experimental values, which indicates that the height of the adiabatic potential energy surface is too high. Furthermore, an estimate of cross sections from the reaction probabilities calculated by Alexander et al. shows that the contribution to the low temperature rate constants from spin–orbit excited F(2P1/2) atoms through nonadiabatic channels is very small and, thus, nonadiabatic effects are not sufficient to bring the calculated rate constants to a better agreement with the experimental measurements. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4068-4076 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The rate coefficients of reactions that occur on potential energy surfaces without a barrier often exhibit a negative temperature dependence at low temperatures. Generally, this behavior is modeled with either the Harcourt–Essen equation, k(T)=AT−m, or a "negative" activation energy, k(T)=ATm exp{ΔE/kBT}. Neither of these expressions is consistent with the Wigner threshold law. The general expression k(T)=(1+T/TW)−m∑l=0∞Al(1+T/TW)−l(T/TW)l is proposed where the relative angular momentum of the reacting species is l, TW and m are independent parameters to be extracted from the data, and the amplitude of each partial wave is Al. This expression may be approximated by k(T)=A0(1+T/TW)−m exp[(T/TW)/(1+T/TW)]. For CN+O2→ NCO+O and CO+NO the above expression reproduces the rate data, the branching ratio to the CO+NO channel, and the reactive cross section for the NCO+O channel. The rate coefficient for the NCO+O channel is given by k(cm3 s−1)=1.79×10−10(+T/21.7)−1.38{exp[(T/21.7)/(1+T/21.7)]−1}+4.62×10−12 exp[(T/21.7)/(1+T/21.7)] while for CO+NO we obtain k(cm3 s−1)=1.79×10−10(1+T/21.7)−1.38. An analytic form of the C–O bonding potential and the electric dipole–quadrupole interaction is used to show that the quantum threshold region extends up to 7 K. These results demonstrate the need of a complete quantum treatment for reactions that proceed on potential surfaces without a barrier. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4077-4086 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The first optical investigation of the spectra of diatomic PdC has revealed that the ground state has Ω=0+, with a bond length of r0=1.712 Å. The Hund's case (a) nature of this state could not be unambiguously determined from the experimental data, but dispersed fluorescence studies to be reported in a separate publication, in combination with a comparison to theoretical calculations, demonstrate that it is the 2δ4 12σ2, 1Σ0++ state, which undergoes spin–orbit mixing with a low-lying 2δ4 12σ1 6π1, 3Π0+ state. An excited 3Σ+ state with re=1.754±0.003 Å (r0=1.758±0.002 Å) and ΔG1/2=794 cm−1 is found at T0=17 867 cm−1. Although only the Ω=1 component of this state is directly observed, the large hyperfine splitting of this state for the 105Pd 12C isotopomer implies that an unpaired electron occupies an orbital that is primarily of 5s character on Pd. Comparison to ab initio calculations identifies this state as 2δ4 12σ1 13σ1, 3Σ1+. To higher wavenumbers a number of transitions to states with Ω=0+ have been observed and rotationally analyzed. Two groups of these have been organized into band systems, despite the clear presence of homogeneous perturbations between states with Ω=0+ in the region between 22 000 and 26 000 cm−1. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4087-4100 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: An intramolecular theory of the unusual mass-independent isotope effect for ozone formation and dissociation is described. The experiments include the enrichment factor, its dependence on the ambient pressure, the ratio of the formation rates of symmetric and asymmetric ozone isotopomers, the enrichment of ozone formed from heavily enriched oxygen isotopes, the comparison of that enrichment to that when the heavy isotopes are present in trace amounts, the isotopic exchange rate constant, and the large mass-dependent effect when individual rate constants are measured, in contrast with the mass-independent effect observed for scrambled mixtures. To explain the results it is suggested that apart from the usual symmetry number ratio of a factor of 2, the asymmetric ozone isotopomers have a larger density of reactive (coupled) quantum states, compared with that for the symmetric isotopomers (about 10%), due to being more "RRKM-like" (Rice–Ramsperger–Kessel–Marcus): Symmetry restricts the number of intramolecular resonances and coupling terms in the Hamiltonian which are responsible for making the motion increasingly chaotic and, thereby, increasingly statistical. As a result the behavior occurs regardless of whether the nuclei are bosons (16O, 18O) or fermions (17O). Two alternative mechanisms are also considered, one invoking excited electronic states and the other invoking symmetry control in the entrance channel. Arguments against each are given. An expression is given relating the mass-independent rates of the scrambled systems to the mass-dependent rates of the unscrambled ones, and the role played by a partitioning term in the latter is described. Different definitions for the enrichment factor for heavily enriched isotopic systems are also considered. In the present paper attention is focused on setting up theoretical expressions and discussing relationships. They provide a basis for future detailed calculations. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4300-4309 
    ISSN: 1089-7690
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    Topics: Physics , Chemistry and Pharmacology
    Notes: Thermodynamic and structural properties of an asymmetric electrolyte containing macroions with 60 elementary charges and monovalent counterions in aqueous solution at different concentrations have been studied by means of Monte Carlo (MC) simulations and molecular dynamics (MD) employing two different short-range potentials. The long-range Coulombic interactions were handled by using Ewald summation and the MC simulations were accelerated by a cluster-move technique, which was found to be two orders of magnitude more efficient for this system than the standard MC method. An effective repulsion was found to operate between the macroions at all concentrations. The electrostatic screening of the macroion repulsion by the counterions was stronger in the hard-sphere model as compared to a soft-sphere model. The origin of this difference arises primarily from the deeper macroion–ion potential in the former model. The results of the hard-sphere model have been compared with different more approximate theories such as the cell model solved by MC simulations, the cell model solved by the Poisson–Boltzmann (PB) equation, and the Derjaguin–Landau–Vervey–Overbeek (DLVO) theory. We have found that the cell model solved by MC simulations and combined with a charge renormalization approach is superior to the other simplified approaches and its predictions are in excellent agreement with the exact simulation results. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 4334-4342 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: We present calculations of the anisotropy of the tension of interfaces separating an isotropic phase rich in a flexible polymer from a nematic phase rich in a semiflexible polymer. We find that the interfacial tension is always lower when the director is parallel to the plane of the interface than when it is perpendicular. The ratio of the tension in the perpendicular to parallel case can be quite large, of order 5 or so, depending on the strength of the nematic interactions. We also find that the interfacial width is always lower in the parallel case even though the tension is lower; this is because the orientational density prefers parallel alignment of chains at the interface. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1501-1510 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: We compute the melting curve of n-octane using Molecular Dynamics simulations with a realistic all-atom molecular model. Thermodynamic integration methods are used to calculate the free energy of the system in both the crystalline solid and isotropic liquid phases. The Gibbs–Duhem integration procedure is used to calculate the melting curve, starting with an initial point obtained from the free energy calculations. The calculations yield quantitatively accurate results: in the pressure range of 0–100 MPa, the calculated melting curve deviates by only 3 K from the experimental curve. This deviation falls just within the range of uncertainty of the calculations. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1511-1519 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: We develop the average Hamiltonian theory of a class of symmetrical radio-frequency pulse sequences in the NMR of rotating solids. Theorems are presented which allow one to predict the elimination of many average Hamiltonian terms, without detailed calculation. These results are applied to the problem of heteronuclear decoupling in the presence of rapid magic angle spinning. We present sequences which minimize the number of heteronuclear terms at the same time as recoupling the homonuclear interactions of the irradiated spins. The performance of the new sequences is tested on 13C labeled calcium formate. Experimental measurements of double-quantum 1H excitation indicate a relationship between good heteronuclear decoupling of the observed spin species and efficient recoupling of the irradiated spin species. The heteronuclear decoupling performance of the new sequences is significantly better than that obtained with an unmodulated radio-frequency field. The decoupling performance is improved further by breaking the pulse sequence symmetry in a controlled fashion. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3349-3356 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: We revisit the far from equilibrium escape problem across a fluctuating potential barrier that is driven by asymmetric, unbiased dichotomous noise. Our closed analytical solution for arbitrary noise strengths reveals new aspects of the so-called "resonant-activation" effect and leads to interesting implications regarding far from equilibrium or externally controlled chemical reaction processes. Specifically, a genuine asymmetry-induced variant of resonant activation within the constant intensity scaling scheme is discovered, and a new possibility to manipulate reaction rates and yields, as well as the balance between reactants and products, is put forward. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3357-3364 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The performance of current density functionals is analyzed in detail for the electric field gradients (EFG) of hydrogen chloride and copper chloride by comparison with ab initio methods and available experimental data. The range of density functionals applied shows good agreement with coupled cluster H and Cl field gradients for HCl, as has been demonstrated previously for other main-group element containing compounds. However, the performance of most density functionals is very poor for the Cu EFG in CuCl (EFG for Cu -0.44 a.u. at the coupled-cluster singles and doubles with perturbative triples [CCSD(T)] level, compared to, e.g., +0.54 a.u. at the B-LYP level). Only the "half-and-half" hybrid functionals give field gradients with the correct sign. The reason for the poor performance of the density functional theory is analyzed in detail comparing density functional with ab initio total electronic densities ρ(r). Due to the conservation of the number of particles, a change in the valence part of the electron density can lead to changes in the core part of the density. Errors in valence electronic properties like the dipole moment and in core properties like the Cu and Cl EFGs may therefore be connected. In fact the errors in both properties show a distinct linear relationship, indicating that if the dipole moment is correctly described by density functionals, the Cu and Cl EFGs may be accurate as well. Furthermore, at the atomic level, electric field gradients are described with reasonable accuracy by current density functionals as calculations for the Cu 2P excited state and the Cu2+ 2D ground state show. A comparison between the different density functionals shows that the incorrect behavior of the electronic density appears to be mainly due to defects in the exchange part of the functional.© 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1580-1586 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: Theoretical expressions for the ultrasonically induced birefringence of liquids are obtained in the frame work of de Gennes' phenomenological theory. The intensity and frequency dependence of ultrasonically induced birefringence in the isotropic phase of p-n-pentyl p′-cyanobiphenyl (5CB) was measured in order to examine the usefulness of birefringence measurements for investigating dynamical properties liquids. The observed birefringence was proportional to the square root of ultrasonic intensity. The birefringence divided by the square root of ultrasonic intensity increases with increasing frequency and appears to saturate when the ultrasonic frequency approaches the relaxation frequency of molecular reorientation. The observed values of birefringence were reproduced satisfactorily by the expression derived in this paper. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1592-1594 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The noisy dynamic behavior of a surface catalytic reaction model to describe the oxidation of carbon monoxide is investigated when the control parameter is perturbed by external noise near a supercritical Hopf bifurcation point. Noise induced coherent oscillation (NICO) is observed and the NICO strength goes through two maxima with the increment of the noise intensity D from zero, characteristic of the occurrence of stochastic multiresonance without external signal. The frequency of the NICO also increases with the increment of D. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1595-1607 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The structural, dynamical, and electronic properties of solid HBr at high pressure are investigated using the ab initio constant pressure molecular dynamics method. A detailed analysis of the orientational distribution, and the reorientational and vibrational dynamics of the disordered phase I at ambient temperature showed that this phase can be described as a rotator phase with fluctuating hydrogen bonds up to pressures well over 10 GPa. We predict that the disorder at higher densities leads to cooperative proton-transfer dynamics. The approach to hydrogen-bond symmetrization is studied in phase I and the high pressure ordered phase III. The simulation results for phase III also indicate that this phase develops dielectric instabilities at high density. At pressures over 40 GPa we observe spontaneous formation of H2 with rearrangement of the Br lattice from fcc to hcp. The chemical reactivity is rationalized in terms of the electronic structure under conditions of near symmetrical hydrogen bonding. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1608-1614 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The effect of attractive interactions on the behavior of polymers between surfaces is studied using Monte Carlo simulations. The molecules are modeled as fused sphere freely rotating chains with fixed bond lengths and bond angles; wall–fluid and fluid–fluid site–site interaction potentials are of the hard sphere plus Yukawa form. For athermal chains the density at the surface (relative to the bulk) is depleted at low densities and enhanced at high densities. The introduction of a fluid–fluid attraction causes a reduction of site density at the surface, and an introduction of a wall–fluid attraction causes an enhancement of site density at the surface, compared to when these interactions are absent. When the wall–fluid and fluid–fluid attractions are of comparable strength, however, the depletion mechanism due to the fluid–fluid attraction dominates. The center of mass profiles show the same trends as the site density profiles. Near the surface, the parallel and the perpendicular components of chain dimensions are different, which is explained in terms of a reorientation of chains. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 1615-1627 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The dynamical properties of an oscillating tip–cantilever system are now widely used in the field of scanning force microscopy. The aim of the present work is to get analytical expressions describing the nonlinear dynamical properties of the oscillator in noncontact and intermittent contact situations in the tapping mode. Three situations are investigated: the pure attractive interaction, the pure repulsive interaction, and a mixing of the two. The analytical solutions obtained allow general trends to be extracted: the noncontact and the intermittent contact show a very discriminate variation of the phase. Therefore the measurement of the phase becomes a simple way to identify whether or not the tip touches the surface during the oscillating period. It is also found that the key parameter governing the structure of the dynamical properties is the product of the quality factor by a reduced stiffness. In the attractive regime, the reduced stiffness is the ratio of an attractive effective stiffness and the cantilever one. In the repulsive regime, the reduced stiffness is the ratio between the contact stiffness and the cantilever one. The quality factor plays an important role. For large values of the quality factor; it is predicted that a pure topography can be obtained whatever the value of the contact stiffness. For a smaller quality factor, the oscillator becomes more sensitive to change of the local mechanical properties. As a direct consequence, varying the quality factor, for example with a vacuum chamber, would be a very interesting way to investigate soft materials either to access topographic information or nanomechanical properties. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3468-3478 
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    Topics: Physics , Chemistry and Pharmacology
    Notes: Inner shell electron energy spectroscopy (ISEELS) was used to study HBS, HBO, and H3B3O3, reactive, transient species generated in situ. The reaction of H2S with crystalline boron in a quartz tube was used to produce thioborine (HBS) at ∼1100 °C, and borine (HBO) at ∼1200 °C. The reaction of H2O vapor with crystalline boron in a quartz tube at ∼1200 °C was used to produce boroxine (H3B3O3). These species were identified from their inner shell excitation spectra and mass spectrometry. The B 1s, S 2s, and S 2p ISEEL spectra of HBS, and the B 1s and O 1s spectra of HBO and H3B3O3 are reported and analyzed with the help of GSCF3 ab initio calculations. A reaction scheme is proposed for the generation of HBO from the reaction of H2S and boron in a heated quartz tube. © 1999 American Institute of Physics.
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    The Journal of Chemical Physics 111 (1999), S. 3494-3497 
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    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Transitions into the doubly excited Na2 1 3Σg− state have been analyzed using near-dissociation expansions (NDE) to represent the vibrational energies and inertial rotational constants, while the centrifugal distortion constants were held fixed at "mechanically consistent" values calculated from the Rydberg–Klein–Rees (RKR) potential implied by those G(v) and Bv functions. The input data cover the range v=0 to 57 and N up to 47, and the fit yields vD=61.41(±0.10) and D0=3385.70(±0.2) cm−1. © 1999 American Institute of Physics.
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  • 91
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    The Journal of Chemical Physics 111 (1999), S. 3508-3516 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Time-independent quantum scattering calculations have been performed to study the H+CH4→H2+CH3 reaction, using the analytic potential-energy surface developed by Jordan and Gilbert. A rotating bond umbrella (RBU) approximation with the implementation of a guided spectral transform subspace iteration technique has been applied together with a log-derivative method in hyperspherical coordinates. A single sector hyperspherical projection method was used to apply the boundary conditions to extract the S matrix at a large hyperradius. The results show that the H+CH4→H2+CH3 reaction occurs via a direct mechanism. The tunneling effect is pronounced, while there is little recrossing. Vibrational excitation of the C–H stretch and/or the H–CH3 bending modes of CH4 significantly enhance the reactivity. Exciting the umbrella mode of CH4 also enhance the reactivity, although less efficiently. The calculated thermal rate constants are larger than the experimental ones. However, good agreement has been obtained by including a barrier height correction of the potential function to make it agree with ab initio results. Finally, vibrational and rotational distributions of the reaction products are discussed in detail. © 1999 American Institute of Physics.
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  • 92
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    The Journal of Chemical Physics 111 (1999), S. 3517-3525 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report experiments that investigate the influence of long-range attractive forces on collisional energy loss from highly vibrationally excited molecules. State-resolved studies of energy transfer from highly vibrationally excited pyridine (μ=2.2 D) to water (μ=1.8 D) in a low-pressure environment at 298 K have been performed using high-resolution transient absorption spectroscopy of water at λ(approximate)2.7 μm. Pyridine in its ground electronic state with 37 900 cm−1 of vibrational energy was prepared by absorption of pulsed ultraviolet light (λ=266 nm) to the S1 state, followed by rapid internal conversion to the S0 state. Collisions between vibrationally excited pyridine and water that result in rotational and translational excitation of the ground vibrationless state of H2O (000) were investigated by monitoring the populations of individual rotational states of H2O (000) at short times following pyridine excitation. The infrared probe of water was the highly allowed asymmetric stretching (000→001) transition. The nascent distribution of rotationally excited H2O (000) states is well described by a thermal distribution with a rotational temperature of Trot=770±80 K. Doppler-broadened transient linewidth measurements yield the velocity distributions of the recoiling H2O (000) molecules that correspond to center-of-mass translational temperatures of Ttrans∼515 K for all water rotational states investigated. Additionally, rate constants for energy gain in individual water states were determined, yielding an integrated rate constant of k2int=1.1×10−11 cm3 mol−1 s−1 for the appearance of H2O (000) with Erot=1000–2000 cm−1. These results are compared with previous relaxation studies of excited pyrazine (μ=0 D) with water and of excited pyridine with CO2 (μ=0 D), and the influence of electrostatic attraction on the relaxation dynamics is discussed. © 1999 American Institute of Physics.
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  • 93
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study theoretically the generation of coherent, anharmonic phonon-polariton responses through impulsive stimulated Raman scattering with intense, crossed ultrafast excitation pulses. We find that the refractive index appears modulated at the stimulated scattering wave vector and the corresponding phonon-polariton frequency, and, due to anharmonicity, at stimulated scattering wave vector overtones and their corresponding frequencies. A realistic model of the soft lattice vibrational mode of the ferroelectric crystal lithium tantalate is considered in detail. Specific predictions for the magnitudes of different wave vector overtone contributions to the lattice displacement are made compared to experimental observations of anharmonic lattice responses. © 1999 American Institute of Physics.
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  • 94
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    The Journal of Chemical Physics 111 (1999), S. 3548-3558 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Highly monochromatized electrons (with energy distributions of less than 30 meV FWHM) are used in a crossed beam experiments to investigate electron attachment to oxygen clusters (O2)n at electron energies from approximately zero eV up to several eV. At energies close to zero the attachment cross section for the reaction (O2)n+e→(O2)m− (for m=1, 2, and 3) rises strongly with decreasing electron energy compatible with s-wave electron capture to (O2)n. Peaks in the oxygen attachment cross sections present at higher energies ((approximate)80 meV, 193 meV, 302 meV) can be ascribed to vibrational levels of the anion populated by attachment of an electron to a single oxygen molecule within the target cluster via a direct Franck–Condon transition from the ground vibrational state v=0 to a vibrational excited state v′=7,8,9,... of the anion produced. The vibrational structures observed here for the first time can be quantitatively accounted for by model calculations using a microscopic model to examine the attachment of an electron to an oxygen molecule inside a cluster. This involves (i) molecular dynamics simulations to calculate the structure of neutral clusters prior to the attachment process and (ii) calculation of the solvation energy of an oxygen anion in the cluster from the electrostatic polarization of the molecules of the cluster. The occurrence of this polarization energy at the surface of larger clusters explains the appearance of an s-wave capturing cross section at 0 eV and the slightly smaller spacings (compared to the monomer case) between the peaks at finite energy, as observed experimentally. The relative transition probabilities from the ground state of the neutral oxygen molecule to the different vibrational levels of the anion are obtained by calculating the corresponding Franck–Condon factors thereby resulting in a reasonable theoretical fit to the observed yields of negatively charged oxygen molecules and clusters. © 1999 American Institute of Physics.
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  • 95
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    The Journal of Chemical Physics 111 (1999), S. 3581-3589 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Umbrella sampling Monte Carlo simulations are used to calculate free energy barriers to homogeneous liquid–vapor nucleation in the superheated Lennard-Jones fluid. The calculated free energy barriers decrease with increased superheating and vanish at the spinodal curve. A statistical geometric analysis reveals the existence of two types of voids: Small interstitial cavities, which are present even in the equilibrium liquid, and much larger cavities that develop as the system climbs the nucleation free energy barrier. The geometric analysis also shows that the average cavity size within the superheated liquid is a function of density but not of temperature. The critical nucleus for the liquid–vapor transition is found to be a large system-spanning cavity that grows as the free energy barrier is traversed. The weblike cavity is nonspherical at all superheatings studied here, suggesting a phenomenological picture quite different from that of classical nucleation theory. © 1999 American Institute of Physics.
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  • 96
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    The Journal of Chemical Physics 111 (1999), S. 3612-3615 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: High-resolution Stark effect measurements on the S1←S0(ππ*) origin of cis-free base isobacteriochlorin in single crystals of n-octane at 5 K are reported. The spectral splittings of the band at 15 822 cm−1 are linearly dependent on the applied electric field. The change in dipole moment (Δμ) was found to be 1.32 D and is parallel to the crystal's b-axis. This band blueshifted as the polarity of the solvents at room temperature was increased, which implies that Δμ is negative. To rationalize the large magnitudes and opposite signs of the cis and trans tautomers' Δμ values, we propose a simple valence-bond model based on ionic resonance structures. © 1999 American Institute of Physics.
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  • 97
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    The Journal of Chemical Physics 111 (1999), S. 1784-1785 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The relative mixing coefficients of the zero-order 1B1(n,0,0) vibrational levels present in the hybrid 1A2–1B1 wave functions are estimated according to the observed Franck–Condon patterns in dispersed fluorescence spectra. Non-Condon effects and spin–orbit coupling have been ignored in the treatment. The data cover nearly 50 cold vibronic bands in the 32 895–34 040 cm−1 region in addition to 9 vibronic bands in the 32 185–32 559 cm−1 region. © 1999 American Institute of Physics.
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  • 98
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    The Journal of Chemical Physics 111 (1999), S. 3668-3674 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We study the drift mobility of a molecular polaron in the presence of an external applied field and Coulomb traps. The model is based on one previously developed for geminate recombination of photogenerated charge carriers. It is shown that the unusual combination of Poole–Frenkel-like field dependence and non-Arrhenius temperature dependence of the mobility, measured experimentally in molecular films, is well reproduced by this model. Our key result is that this nearly universal experimental behavior of the mobility arises from competition between rates of polaron trapping and release from a very low density of Coulomb traps. © 1999 American Institute of Physics.
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  • 99
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    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 111 (1999), S. 3675-3678 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: It is known that the presence of cations like Ca++ or Pb++ in the water subphase alters the pressure-area isotherms for fatty acid monolayers. The corresponding lattice constant changes have been studied using x-ray diffraction. Reflection-absorption spectroscopy has been used to probe the chemical composition of the film. We report on the first measurements of the time evolution of the shear viscosity of arachidic acid monolayers in the presence of Ca++ ions in the subphase. We find that the introduction of Ca++ ions to the water subphase results in an increase of the film's viscosity by at least three orders of magnitude. This increase occurs in three distinct stages. First, there is a rapid change in the viscosity of up to one order of magnitude. This is followed by two periods, with very different time constants, of a relatively slow increase in the viscosity over the next 10 or more hours. The corresponding time constants for this rise decrease as either the subphase pH or Ca++ concentration is increased. © 1999 American Institute of Physics.
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  • 100
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    The Journal of Chemical Physics 111 (1999), S. 3679-3695 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: In the interaction of low energy F2 with Si(100) at 250 K, a dissociative chemisorption mechanism called atom abstraction is identified in which only one of the F atoms is adsorbed while the other F atom is scattered into the gas phase. The dynamics of atom abstraction are characterized via time-of-flight measurements of the scattered F atoms. The F atoms are translationally hyperthermal but only carry a small fraction (∼3%) of the tremendous exothermicity of the reaction. The angular distribution of F atoms is unusually broad for the product of an exothermic reaction. These results suggest an "attractive" interaction potential between F2 and the Si dangling bond with a transition state that is not constrained geometrically. These results are in disagreement with the results of theoretical investigations implying that the available potential energy surfaces are inadequate to describe the dynamics of this gas–surface interaction. In addition to single atom abstraction, two atom adsorption, a mechanism analogous to classic dissociative chemisorption in which both F atoms are adsorbed onto the surface, is also observed. The absolute probability of the three scattering channels (single atom abstraction, two atom adsorption, and unreactive scattering) for an incident F2 are determined as a function of F2 exposure. The fluorine coverage is determined by integrating the reaction probabilities over F2 exposure, and the reaction probabilities are recast as a function of fluorine coverage. Two atom adsorption is the dominant channel [P2=0.83±0.03(95%, N=9)] in the limit of zero coverage and decays monotonically to zero. Single atom abstraction is the minor channel (P1=0.13±0.03) at low coverage but increases to a maximum (P1=0.35±0.08) at about 0.5 monolayer (ML) coverage before decaying to zero. The reaction ceases at 0.94±0.11(95%, N=9) ML. Thermal desorption and helium diffraction confirm that the dangling bonds are the abstraction and adsorption sites. No Si lattice bonds are broken, in contrast to speculation by other investigators that the reaction exothermicity causes lattice disorder. © 1999 American Institute of Physics.
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