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  • Wiley-Blackwell  (136,307)
  • American Institute of Physics (AIP)  (81,592)
  • Blackwell Publishing Ltd  (69,647)
  • Oxford University Press  (67,792)
  • 2020-2023  (49)
  • 1995-1999  (154,153)
  • 1985-1989  (136,126)
  • 1975-1979  (65,010)
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  • 1
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    3-D attenuation image of fluid storage and tectonic interactions across the Pollino fault network (2022)
    Oxford University Press
    Details
    Publication Date: 2022-03-07
    Description: The Pollino range is a region of slow deformation where earthquakes generally nucleate on low-angle normal faults. Recent studies have mapped fault structures and identified fluid related dynamics responsible for historical and recent seismicity in the area. Here, we apply the coda-normalization method at multiple frequencies and scales to image the 3-D P-wave attenuation (QP) properties of its slowly deforming fault network. The wide-scale average attenuation properties of the Pollino range are typical for a stable continental block, with a dependence of QP on frequency of Q−1 P = (0.0011   0.0008) f (0.36 0.32). Using only waveforms comprised in the area of seismic swarms, the dependence of attenuation on frequency increases [Q−1 P = (0.0373   0.0011) f (−0.59 0.01)], as expected when targeting seismically active faults. A shallow very-low-attenuation anomaly (max depth of 4–5 km) caps the seismicity recorded within the western cluster 1 of the Pollino seismic sequence (2012, maximum magnitude Mw = 5.1). High-attenuation volumes below this anomaly are likely related to fluid storage and comprise the western and northern portions of cluster 1 and the Mercure basin. These anomalies are constrained to the NW by a sharp low-attenuation interface, corresponding to the transition towards the eastern unit of the Apennine Platform under the Lauria mountains. The low-seismicity volume between cluster 1 and cluster 2 (maximum magnitude Mw = 4.3, east of the primary) shows diffuse low-to-average attenuation features. There is no clear indication of fluid-filled pathways between the two clusters resolvable at our resolution. In this volume, the attenuation values are anyway lower than in recognized low-attenuation blocks, like the Lauria Mountain and Pollino Range. As the volume develops in a region marked at surface by small-scale cross-faulting, it suggests no actual barrier between clusters, more likely a system of small locked fault patches that can break in the future. Our model loses resolution at depth, but it can still resolve a 5-to-15-km-deep high-attenuation anomaly that underlies the Castrovillari basin. This anomaly is an ideal deep source for the SE-to-NW migration of historical seismicity. Our novel deep structural maps support the hypothesis that the Pollino sequence has been caused by a mechanism of deep and lateral fluid-induced migration.
    Description: Natural Environment Research Council (NERC) Centre for Doctoral Training (CDT) in Oil and Gas. University of Aberdeen.
    Description: Published
    Description: 536–547
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: body waves ; seismic attenuation ; seismic tomography ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland) (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-28
    Description: Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a relocation strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide on horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area.
    Description: Published
    Description: 1244–1257
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations (2022)
    Oxford University Press
    Details
    Publication Date: 2022-11-10
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Sassenhagen, I., Erdner, D., Lougheed, B., Richlen, M., & SjÖqvist, C. Estimating genotypic richness and proportion of identical multi-locus genotypes in aquatic microalgal populations. Journal of Plankton Research, 44(4), (2022): 559-572, https://doi.org/10.1093/plankt/fbac034.
    Description: The majority of microalgal species reproduce asexually, yet population genetic studies rarely find identical multi-locus genotypes (MLG) in microalgal blooms. Instead, population genetic studies identify large genotypic diversity in most microalgal species. This paradox of frequent asexual reproduction but low number of identical genotypes hampers interpretations of microalgal genotypic diversity. We present a computer model for estimating, for the first time, the number of distinct MLGs by simulating microalgal population composition after defined exponential growth periods. The simulations highlighted the effects of initial genotypic diversity, sample size and intraspecific differences in growth rates on the probability of isolating identical genotypes. We estimated the genotypic richness for five natural microalgal species with available high-resolution population genetic data and monitoring-based growth rates, indicating 500 000 to 2 000 000 distinct genotypes for species with few observed clonal replicates (〈5%). Furthermore, our simulations indicated high variability in genotypic richness over time and among microalgal species. Genotypic richness was also strongly impacted by intraspecific variability in growth rates. The probability of finding identical MLGs and sampling a representative fraction of genotypes decreased noticeably with smaller sample sizes, challenging the detection of differences in genotypic diversity with typical isolate numbers in the field.
    Description: This work was supported by the Olle Engkvist foundation [200-0564 to I.S.]; the Swedish Research Council (Vetenskapsrådet) [2018-04992 to B.C.L.]; the Academy of Finland [321609 to C.S.]; the National Science Foundation [NSF OCE-1841811 to D.L.E. and M.L.R.]; and the National Institute of Environmental Health [NIEHS P01ES028949 to M.L.R.].
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-24
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Page, H. N., Bahr, K. D., Cyronak, T., Jewett, E. B., Johnson, M. D., & McCoy, S. J. Responses of benthic calcifying algae to ocean acidification differ between laboratory and field settings. Ices Journal of Marine Science, 79(1), (2022): 1–11, https://doi.org/10.1093/icesjms/fsab232.
    Description: Accurately predicting the effects of ocean and coastal acidification on marine ecosystems requires understanding how responses scale from laboratory experiments to the natural world. Using benthic calcifying macroalgae as a model system, we performed a semi-quantitative synthesis to compare directional responses between laboratory experiments and field studies. Variability in ecological, spatial, and temporal scales across studies, and the disparity in the number of responses documented in laboratory and field settings, make direct comparisons difficult. Despite these differences, some responses, including community-level measurements, were consistent across laboratory and field studies. However, there were also mismatches in the directionality of many responses with more negative acidification impacts reported in laboratory experiments. Recommendations to improve our ability to scale responses include: (i) developing novel approaches to allow measurements of the same responses in laboratory and field settings, and (ii) researching understudied calcifying benthic macroalgal species and responses. Incorporating these guidelines into research programs will yield data more suitable for robust meta-analyses and will facilitate the development of ecosystem models that incorporate proper scaling of organismal responses to in situ acidification. This, in turn, will allow for more accurate predictions of future changes in ecosystem health and function in a rapidly changing natural climate.
    Description: We would like to thank the Ocean Carbon and Biogeochemistry Program for organizing the fourth U.S. Ocean Acidification Principal Investigators meeting, which is where this synthesis was conceived. HNP was a postdoctoral research fellow at Mote Marine Laboratory. MDJ is a postdoctoral scholar at Woods Hole Oceanographic Institution. SJM is a Norma J. Lang early career fellow of the Phycological Society of America.
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Spectral elements numerical simulation of the 2009 L’Aquila earthquake on a detailed reconstructed domain (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: In this paper we simulate the earthquake that hit the city of L'Aquila on the 6th of April 2009 using SPEED (SPectral Elements in Elastodynamics with Discontinuous Galerkin), an open-source code able to simulate the propagation of seismic waves in complex three-dimensional (3D) domains. Our model includes an accurate 3D recon- struction of the Quaternary deposits, according to the most up-to-date data obtained from the Microzonation studies in Central Italy and a detailed model of the topography incorporated using a newly developed tool (May et al. 2021). The sensitivity of our results with respect to dfferent kinematic seismic sources is inves- tigated. The results obtained are in good agreement with the recordings at the available seismic stations at epicentral distances within a range of 20km. Finally, a blind source prediction scenario application shows a reasonably good agreement between simulations and recordings can be obtained by simulating stochastic rupture realizations with basic input data. These results, although limited to nine simulated scenarios, demonstrate that it is possible to obtain a satisfactory reconstruction of a ground shaking scenario employing a stochastic source constrained on a limited amount of ex-ante information. A similar approach can be used to model future and past earthquakes for which little or no information is typically available, with potential relevant implications for seismic risk assessment.
    Description: Published
    Description: 29–49
    Description: 3T. Fisica dei terremoti e Sorgente Sismica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Environmental effects and seismogenic source characterization of the December 2020 earthquake sequence near Petrinja, Croatia (2022)
    Oxford University Press
    Details
    Publication Date: 2022-06-22
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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: On 29 December 2020, a shallow earthquake of magnitude Mw 6.4 struck northern Croatia, near the town of Petrinja, more than 24 hours after a strong foreshock (Ml 5). We formed a reconnaissance team of European geologists and engineers, from Croatia, Slovenia, France, Italy and Greece, rapidly deployed in the field to map the evidence of coseismic environmental effects. In the epicentral area, we recognized surface deformation, such as tectonic breaks along the earthquake source at the surface, liquefaction features (scattered in the fluvial plains of Kupa, Glina and Sava rivers), and slope failures, both caused by strong motion. Thanks to this concerted, collective and meticulous work, we were able to document and map a clear and unambiguous coseismic surface rupture associated with the main shock. The surface rupture appears discontinuous, consisting of multi-kilometer en échelon right stepping sections, along a NW-SE striking fault that we call the Petrinja-Pokupsko Fault (PPKF). The observed deformation features, in terms of kinematics and trace alignments, are consistent with slip on a right lateral fault, in agreement with the focal solution of the main shock. We found mole tracks, displacement on faults affecting natural features (e. g. drainage channels), scarplets, and more frequently breaks of anthropogenic markers (roads, fences). The surface rupture is observed over a length of ∼13 km from end-to-end, with a maximum displacement of 38 cm, and an average displacement of ∼10 cm. Moreover, the liquefaction extends over an area of nearly 600 km² around the epicenter. Typology of liquefaction features include sand blows, lateral spreading phenomenon along the road and river embankments, as well as sand ejecta of different grain size and matrix. Development of large and long fissures along the fluvial landforms, current or ancient, with massive ejections of sediments is pervasive. These features are sometimes accompanied by small horizontal displacements. Finally, the environmental effects of the earthquake appear to be reasonably consistent with the usual scaling relationships, in particular the surface faulting. This rupture of the ground occurred on or near traces of a fault that shows clear evidence of Quaternary activity. Further and detailed studies will be carried out to characterize this source and related faults in terms of future large earthquakes potential, for their integration into seismic hazard models.
    Description: Published
    Description: 1394–1418
    Description: 2T. Deformazione crostale attiva
    Description: JCR Journal
    Keywords: Seismicity and tectonics ; Earthquake hazards ; Coseismic effects ; M6.4 Petrinja earthquake (Croatia)
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 7
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    Moho depths for Antarctica Region by the inversion of ground-based gravity data (2022)
    Oxford University Press
    Details
    Publication Date: 2022-09-01
    Description: In the last years the scientific literature has been enriched with new models of the Moho depth in the Antarctica Continent derived by the seismic reflection technique and refraction profiles, receiver functions and seismic surface waves, but also by gravimetric observations over the continent. In particular, the gravity satellite missions of the last two decades have provided data in this remote region of the Earth and have allowed the investigation of the crust properties. Meanwhile, other important contributions in this direction has been given by the fourth International Polar Year (IPY, 2007–2008) which started seismographic and geodetic networks of unprecedented duration and scale, including airborne gravimetry over largely unexplored Antarctic frontiers. In this study, a new model for the Antarctica Moho depths is proposed. This new estimation is based on no satellite gravity measures, thanks to the availability of the gravity database ANTGG2015, that collects gravity data from ground-base, airborne and shipborne campaigns. In this new estimate of the Moho depths the contribution of the gravity measures has been maximized reducing any correction of the gravity measures and avoiding constraints of the solution to seismological observations and to geological evidence. With this approach a pure gravimetric solution has been determined. The model obtained is pretty in agreement with other Moho models and thanks to the use of independent data it can be exploited also for cross-validating different Moho depths solutions.
    Description: Published
    Description: 1404–1420
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Antarctica ; Moho ; Gravity inversion ; Collocation ; ANTGG2015
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
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    Distribution of oceanic crust in the Enderby Basin offshore East Antarctica (2022)
    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 231, pp. 1959-1981
    Details
    Publication Date: 2022-09-16
    Description: Seismic reflection and refraction data were collected in 2007 and 2012 to reveal the crustal fabric on a single long composite profile offshore Prydz Bay, East Antarctica. A P-wave velocity model provides insights on the crustal fabric, and a gravity-constrained density model is used to describe the crustal and mantle structure. The models show that a 230-km- wide continent–ocean transition separates stretched continental from oceanic crust along our profile. While the oceanic crust close to the continent–ocean boundary is just 3.5–5 km thick, its thickness increases northwards towards the Southern Kerguelen Plateau to 12 km. This change is accompanied by thickening of a lower crustal layer with high P-wave velocities of up to 7.5 km s–1, marking intrusive rocks emplaced beneath the mid-ocean ridge under increasing influence of the Kerguelen plume. Joint interpretations of our crustal model, seismic reflection data and magnetic data sets constrain the age and extent of oceanic crust in the research area. Oceanic crust is shown to continue to around 160 km farther south than has been interpreted in previous data, with profound implications for plate kinematic models of the region. Finally, by combining our findings with a regional magnetic data compilation and regional seismic reflection data we propose a larger extent of oceanic crust in the Enderby Basin than previously known.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
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    TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Tassia, M. G., David, K. T., Townsend, J. P., & Halanych, K. M. TIAMMAt: leveraging biodiversity to revise protein domain models, evidence from innate immunity. Molecular Biology and Evolution, 38(12), (2021): 5806–5818, https://doi.org/10.1093/molbev/msab258.
    Description: Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR’s NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt’s flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.
    Description: This work was supported by The National Science Foundation (Grant No. IOS—1755377 to K.M.H., Rita Graze, and Elizabeth Hiltbold Schwartz), and K.T.D. was supported by The National Science Foundation’s Graduate Research Fellowship Program.
    Keywords: Protein evolution ; Domain annotation ; Animal evolution ; Innate immunity
    Repository Name: Woods Hole Open Access Server
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  • 10
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    Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Shoshan, Y., Liscovitch-Brauer, N., Rosenthal, J. J. C., & Eisenberg, E. Adaptive proteome diversification by nonsynonymous A-to-I RNA editing in coleoid cephalopods. Molecular Biology and Evolution, 38(9), (2021): 3775–3788, https://doi.org/10.1093/molbev/msab154.
    Description: RNA editing by the ADAR enzymes converts selected adenosines into inosines, biological mimics for guanosines. By doing so, it alters protein-coding sequences, resulting in novel protein products that diversify the proteome beyond its genomic blueprint. Recoding is exceptionally abundant in the neural tissues of coleoid cephalopods (octopuses, squids, and cuttlefishes), with an over-representation of nonsynonymous edits suggesting positive selection. However, the extent to which proteome diversification by recoding provides an adaptive advantage is not known. It was recently suggested that the role of evolutionarily conserved edits is to compensate for harmful genomic substitutions, and that there is no added value in having an editable codon as compared with a restoration of the preferred genomic allele. Here, we show that this hypothesis fails to explain the evolutionary dynamics of recoding sites in coleoids. Instead, our results indicate that a large fraction of the shared, strongly recoded, sites in coleoids have been selected for proteome diversification, meaning that the fitness of an editable A is higher than an uneditable A or a genomically encoded G.
    Description: This research was supported by a grants from the United States–Israel Binational Science Foundation (BSF), Jerusalem, Israel (BSF2017262 to J.J.C.R. and E.E.), the Israel Science Foundation (3371/20 to E.E.) and the National Science Foundation (IOS 1827509 and 1557748 to J.J.C.R).
    Keywords: RNA editing ; Adaptation ; Evolution
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  • 11
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    Interspecific differences in the flow regimes and drag of North Pacific skate egg cases (2022)
    Oxford University Press
    Details
    Publication Date: 2022-10-12
    Description: Author Posting. © The Author(s), 2022. 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 Integrative & Comparative Biology 62(3), (2022): 805-816, https://doi.org/10.1093/icb/icac108.
    Description: Skates are a diverse group of dorso-ventrally compressed cartilaginous fish found primarily in high-latitude seas. These slow-growing oviparous fish deposit their fertilized eggs into cases, which then rest on the seafloor. Developing skates remain in their cases for 1–4 years after they are deposited, meaning the abiotic characteristics of the deposition sites, such as current and substrate type, must interact with the capsule in a way to promote long residency. Egg cases are morphologically variable and can be identified to species. Both the gross morphology and the microstructures of the egg case interact with substrate to determine how well a case stays in place on a current-swept seafloor. Our study investigated the egg case hydrodynamics of eight North Pacific skate species to understand how their morphology affects their ability to stay in place. We used a flume to measure maximum current velocity, or “break-away velocity,” each egg case could withstand before being swept off the substrate and a tilt table to measure the coefficient of static friction between each case and the substrate. We also used the programing software R to calculate theoretical drag on the egg cases of each species. For all flume trials, we found the morphology of egg cases and their orientation to flow to be significantly correlated with break-away velocity. In certain species, the morphology of the egg case was correlated with flow rate required to dislodge a case from the substrate in addition to the drag experienced in both the theoretical and flume experiments. These results effectively measure how well the egg cases of different species remain stationary in a similar habitat. Parsing out attachment biases and discrepancies in flow regimes of egg cases allows us to identify where we are likely to find other elusive species nursery sites. These results will aid predictive models for locating new nursery habitats and protective policies for avoiding the destruction of these nursery sites.
    Description: This work was supported by the NSF-REU and FHL Blinks-Beacon for funding JNE. And the Stephen and Ruth Wainwright Endowed Fellowship, BEACON and Hoag Awards, Robert T. Paine Experimental and Field Ecology Award, FHL Award, FHL Marine Science Fund, FHL Student Fund (Kohn), Patricia L. Dudley Endowment for funding KCH.
    Description: 2023-07-04
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  • 12
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    Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Wiley, D. N., Silva, T. L., Robuck, A. R., Richardson, D. E., Glancy, S. G., Clancey, E., Giandonato, T., Solow, A. R., Thompson, M. A., Hong, P., Baumann, H., Kaufman, L., & Llopiz, J. K. Sensitivity of sand lance to shifting prey and hydrography indicates forthcoming change to the northeast US shelf forage fish complex. Ices Journal of Marine Science, 78(3), (2021): 1023–1037, https://doi.org/10.1093/icesjms/fsaa251.
    Description: Northern sand lance (Ammodytes dubius) and Atlantic herring (Clupea harengus) represent the dominant lipid-rich forage fish species throughout the Northeast US shelf and are critical prey for numerous top predators. However, unlike Atlantic herring, there is little research on sand lance or information about drivers of their abundance. We use intra-annual measurements of sand lance diet, growth, and condition to explain annual variability in sand lance abundance on the Northeast US Shelf. Our observations indicate that northern sand lance feed, grow, and accumulate lipids in the late winter through summer, predominantly consuming the copepod Calanus finmarchicus. Sand lance then cease feeding, utilize lipids, and begin gonad development in the fall. We show that the abundance of C. finmarchicus influences sand lance parental condition and recruitment. Atlantic herring can mute this effect through intra-guild predation. Hydrography further impacts sand lance abundance as increases in warm slope water decrease overwinter survival of reproductive adults. The predicted changes to these drivers indicate that sand lance will no longer be able to fill the role of lipid-rich forage during times of low Atlantic herring abundance—changing the Northeast US shelf forage fish complex by the end of the century.
    Description: Research was funded by the Bureau of Ocean Energy Management (IA agreement M17PG0019; DNW, LK, HB, and JKL), including a subaward via the National Marine Sanctuary Foundation (18-11-B-203). Additional support came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project No. R/O-57; JKL, HB, and DNW) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE 1655686; JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship programme. ARR was funded by an NOAA Nancy Foster Scholarship.
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  • 13
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    Inspecting the Reliability of Geochemical Facies Identified for the Waterworks' Capture Zone in Germany (2022)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-09-27
    Description: Little research attention has been given to validating clusters obtained from the groundwater geochemistry of the waterworks' capture zone with a prevailing lake‐groundwater exchange. To address this knowledge gap, we proposed a new scheme whereby Gaussian finite mixture modeling (GFMM) and Spike‐and‐Slab Bayesian (SSB) algorithms were utilized to cluster the groundwater geochemistry while quantifying the probability of the resulting cluster membership against each other. We applied GFMM and SSB to 13 geochemical parameters collected during different sampling periods at 13 observation points across the Barnim Highlands plateau located in the northeast of Berlin, Germany; this included 10 observation wells, two lakes, and a gallery of drinking production wells. The cluster analysis of GFMM yielded nine clusters, either with a probability ≥0.8, while the SSB produced three hierarchical clusters with a probability of cluster membership varying from 〈0.2 to 〉0.8. The findings demonstrated that the clustering results of GFMM were in good agreement with the classification as per the principal component analysis and Piper diagram. By superimposing the parameter clustering onto the observation clustering, we could identify discrepancies that exist among the parameters of a certain cluster. This enables the identification of different factors that may control the geochemistry of a certain cluster, although parameters of that cluster share a strong similarity. The GFMM results have shown that from 2002, there has been active groundwater inflow from the lakes towards the capture zone. This means that it is necessary to adopt appropriate measures to reverse the inflow towards the lakes.
    Description: Article impact statement: The probability of cluster membership quantified using an algorithm should be validated against another probabilistic‐based classifier.
    Description: Federal Ministry of Education and Research http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.9 ; ddc:551.49
    Language: English
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  • 14
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    Application of mixed‐effects modelling and rule‐based models to explain copper variation in soil profiles of southern Germany (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-10-01
    Description: Copper (Cu) is an essential element for plants and microorganisms and at larger concentrations a toxic pollutant. A number of factors controlling Cu dynamics have been reported, but information on quantitative relationships is scarce. We aimed to (i) quantitatively describe and predict soil Cu concentrations (CuAR) in aqua regia considering site‐specific effects and effects of pH, soil organic carbon (SOC) and cation exchange capacity (CEC), and (ii) study the suitability of mixed‐effects modelling and rule‐based models for the analysis of long‐term soil monitoring data. Thirteen uncontaminated long‐term monitoring soil profiles in southern Germany were analysed. Since there was no measurable trend of increasing CuAR concentrations with time in the respective depth ranges of the sites, data from different sampling dates were combined and horizon‐specific regression analyses including model simplifications were carried out for 10 horizons. Fixed‐ and mixed‐effects models with the site as a random effect were useful for the different horizons and significant contributions (either of main effects or interactions) of SOC, CEC and pH were present for 9, 8 and 7 horizons, respectively. Horizon‐specific rule‐based cubist models described the CuAR data similarly well. Validations of cubist models and mixed‐effects models for the CuAR concentrations in A horizons were successful for the given population after random splitting into calibration and validation samples, but not after independent validations with random splitting according to sites. Overall, site, CEC, SOC and pH provide important information for a description of CuAR concentrations using the different regression approaches. Highlights: Information on quantitative relationships for factors controlling Cu dynamics is scarce. Site, CEC, SOC and pH provide important information for a description of Cu concentrations. Validations of cubist models and mixed‐effects models for A horizons were successful for a closed population of sites.
    Description: Bavarian State Ministry of the Environment and Consumer Protection http://dx.doi.org/10.13039/501100010219
    Description: Ministry of Agriculture and Environment Mecklenburg‐Western Pomerania
    Keywords: ddc:631.4
    Language: English
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  • 15
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    Millimetre scale aeration of the rhizosphere and drilosphere (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-10-04
    Description: Soil aeration is a critical factor for oxygen‐limited subsoil processes, as transport by diffusion and advection is restricted by the long distance to the free atmosphere. Oxygen transport into the soil matrix is highly dependent on its connectivity to larger pore channels like earthworm and root colonised biopores. Here we hypothesize that the soil matrix around biopores represents different connectivity depending on biopore genesis and actual coloniser. We analysed the soil pore system of undisturbed soil core samples around biopores generated or colonised by roots and earthworms and compared them with the pore system of soil, not in the immediacy of a biopore. Oxygen partial pressure profiles and gas relative diffusion was measured in the rhizosphere and drilosphere from the biopore wall into the bulk soil with microelectrodes. The measurements were linked with structural features such as porosity and connectivity obtained from X‐ray tomography and image analysis. Aeration was enhanced in the soil matrix surrounding biopores in comparison to the bulk soil, shown by higher oxygen concentrations and higher relative diffusion coefficients. Biopores colonised by roots presented more connected lateral pores than earthworm colonised ones, which resulted in enhanced aeration of the rhizosphere compared to the drilosphere. This has influenced biotic processes (microbial turnover/mineralization or root respiration) at biopore interfaces and highlights the importance of microstructural features for soil processes and their dependency on the biopore's coloniser.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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  • 16
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    An alternative method to evaluate earthquake detection from synthetic Wood–Anderson seismograms: an application in Italy (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-26
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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: Defining the regional variability of minimum magnitude for earthquake detection is crucial for planning seismic networks. Knowing the earthquake detection magnitude values is fundamental for the optimal location of new stations and to select the priority for reactivating the stations of a seismic network in case of a breakdown. In general, the assessment of earthquake detection is performed by analysing seismic noise with spectral or more sophisticated methods. Further, to simulate amplitude values at the recording sites, spectral methods require knowledge of several geophysical parameters including rock density, S-wave velocity, corner frequency, quality factor, site specific decay parameter and so on, as well as a velocity model for the Earth's interior. The simulation results are generally expressed in terms of Mw and therefore a further conversion must be done to obtain the values of local magnitude (ML), which is the parameter commonly used for moderate and small earthquakes in seismic catalogues. Here, the relationship utilized by a seismic network to determine ML is directly applied to obtain the expected amplitude [in mm, as if it were recorded by a Wood–Anderson (WA) seismometer] at the recording site, without any additional assumptions. The station detection estimates are obtained by simply considering the ratio of the expected amplitude with respect to the background noise, also measured in mm. The seismic noise level for the station is estimated starting from four waveforms (each signal lasting 1 min) sampled at various times of the day for a period of one week. The proposed method is tested on Italian seismic events occurring in 2019 by using the locations of 16.879 earthquakes recorded by 374 stations. The first results indicate that by evaluating the station noise level with 5-s windows, a representative sample of the variability in expected noise level is generated for every station, even if only 4 min of signal per day over a week of recordings is used. The method was applied to define the detection level of the Italian National Seismic Network (RSN). The RSN detection level represents a reference for the definition and application of guidelines in the field of monitoring of subsurface industrial activities in Italy. The proposed approach can be successfully applied to define the current performance of a local seismic network (managed by private companies) and to estimate the expected further improvements, requested to fulfil the guidelines with the installation of new seismic stations. This method has been tested in Italy and can be reproduced wherever the local magnitude ML, based on synthetic WA records, is used.
    Description: Published
    Description: 1283–1297
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Time-series analysis ; Earthquake ground motions ; Seismic noise ; Induced seismicity ; 04.06. Seismology ; 05.04. Instrumentation and techniques of general interest
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches (2022)
    Oxford University Press
    Details
    Publication Date: 2022-08-19
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Aoki, L. R., Brisbin, M. M., Hounshell, A. G., Kincaid, D. W., Larson, E., Sansom, B. J., Shogren, A. J., Smith, R. S., & Sullivan-Stack, J. Preparing aquatic research for an extreme future: call for improved definitions and responsive, multidisciplinary approaches. Bioscience, 72(6), (2022): 508-520, https://doi.org/10.1093/biosci/biac020.
    Description: Extreme events have increased in frequency globally, with a simultaneous surge in scientific interest about their ecological responses, particularly in sensitive freshwater, coastal, and marine ecosystems. We synthesized observational studies of extreme events in these aquatic ecosystems, finding that many studies do not use consistent definitions of extreme events. Furthermore, many studies do not capture ecological responses across the full spatial scale of the events. In contrast, sampling often extends across longer temporal scales than the event itself, highlighting the usefulness of long-term monitoring. Many ecological studies of extreme events measure biological responses but exclude chemical and physical responses, underscoring the need for integrative and multidisciplinary approaches. To advance extreme event research, we suggest prioritizing pre- and postevent data collection, including leveraging long-term monitoring; making intersite and cross-scale comparisons; adopting novel empirical and statistical approaches; and developing funding streams to support flexible and responsive data collection.
    Repository Name: Woods Hole Open Access Server
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  • 18
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    Response of subsoil organic matter contents and physical properties to long‐term, high‐rate farmyard manure application (2022)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-07-26
    Description: Application of farmyard manure (FYM) is common practice to improve physical and chemical properties of arable soil and crop yields. However, studies on effects of FYM application mainly focussed on topsoils, whereas subsoils have rarely been addressed so far. We, therefore, investigated the effects of 36‐year FYM application with different rates of annual organic carbon (OC) addition (0, 469, 938 and 1875 g C m−2 a−1) on OC contents of a Chernozem in 0–30 cm (topsoil) and 35–45 cm (subsoil) depth. We also investigated its effects on soil structure and hydraulic properties in subsoil. X‐ray computed tomography was used to analyse the response of the subsoil macropore system (≥19 μm) and the distribution of particulate organic matter (POM) to different FYM applications, which were related to contents in total OC (TOC) and water‐extractable OC (WEOC). We show that FYM‐C application of 469 g C m−2 a−1 caused increases in TOC and WEOC contents only in the topsoil, whereas rates of ≥938 g C m−2 a−1 were necessary for TOC enrichment also in the subsoil. At this depth, the subdivision of TOC into different OC sources shows that most of the increase was due to fresh POM, likely by the stimulation of root growth and bioturbation. The increase in subsoil TOC went along with increases in macroporosity and macropore connectivity. We neither observed increases in plant‐available water capacity nor in unsaturated hydraulic conductivity. In conclusion, only very high application of FYM over long periods can increase OC content of subsoil at our study site, but this increase is largely based on fresh, easily degradable POM and likely accompanied by high C losses when considering the discrepancy between OC addition rate by FYM and TOC response in soil. Highlights A new image processing procedure to distinguish fresh and decomposed POM. The increase of subsoil C stock based to a large extend on fresh, labile POM. Potential of arable subsoils for long‐term C storage by large FYM application rates is limited. The increase in TOC has no effect on hydraulic properties of the subsoil.
    Description: Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659
    Keywords: ddc:631.4
    Language: English
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  • 19
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    Environmental drivers and trends in forage fish occupancy of the Northeast US shelf (2022)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Suca, J. J., Deroba, J. J., Richardson, D. E., Ji, R., & Llopiz, J. K. Environmental drivers and trends in forage fish occupancy of the Northeast US shelf. Ices Journal of Marine Science, 78(10), (2021): 3687–3708, https://doi.org/10.1093/icesjms/fsab214.
    Description: The Northeast US shelf ecosystem is undergoing unprecedented changes due to long-term warming trends and shifts in regional hydrography leading to changes in community composition. However, it remains uncertain how shelf occupancy by the region's dominant, offshore small pelagic fishes, also known as forage fishes, has changed throughout the late 20th and early 21st centuries. Here, we use species distribution models to estimate the change in shelf occupancy, mean weighted latitude, and mean weighted depth of six forage fishes on the Northeast US shelf, and whether those trends were linked to coincident hydrographic conditions. Our results suggest that observed shelf occupancy is increasing or unchanging for most species in both spring and fall, linked both to gear shifts and increasing bottom temperature and salinity. Exceptions include decreases to observed shelf occupancy by sand lance and decreases to Atlantic herring's inferred habitat suitability in the fall. Our work shows that changes in shelf occupancy and inferred habitat suitability have varying coherence, indicating complex mechanisms behind observed shelf occupancy for many species. Future work and management can use these results to better isolate the aspects of forage fish life histories that are important for determining their occupancy of the Northeast US shelf.
    Description: Funding came from the National Oceanic and Atmospheric Administration Woods Hole Sea Grant Program (NA18OAR4170104, Project number R/O-57; RJ and JKL) and a National Science Foundation Long-term Ecological Research grant for the Northeast US Shelf Ecosystem (OCE1655686; RJ and JKL). JJS was funded by the National Science Foundation Graduate Research Fellowship program.
    Repository Name: Woods Hole Open Access Server
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  • 20
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    How to Find Aquifer Statistics Utilizing Pumping Tests? Two Field Studies Using welltestpy (2021)
    Blackwell Publishing Ltd | Malden, US
    Details
    Publication Date: 2022-04-01
    Description: We present a workflow to estimate geostatistical aquifer parameters from pumping test data using the Python package welltestpy. The procedure of pumping test analysis is exemplified for two data sets from the Horkheimer Insel site and from the Lauswiesen site, Germany. The analysis is based on a semi‐analytical drawdown solution from the upscaling approach Radial Coarse Graining, which enables to infer log‐transmissivity variance and horizontal correlation length, beside mean transmissivity, and storativity, from pumping test data. We estimate these parameters of aquifer heterogeneity from type‐curve analysis and determine their sensitivity. This procedure, implemented in welltestpy, is a template for analyzing any pumping test. It goes beyond the possibilities of standard methods, for example, based on Theis' equation, which are limited to mean transmissivity and storativity. A sensitivity study showed the impact of observation well positions on the parameter estimation quality. The insights of this study help to optimize future test setups for geostatistical aquifer analysis and provides guidance for investigating pumping tests with regard to aquifer statistics using the open‐source software package welltestpy.
    Description: Article impact statement: We present a workflow to infer parameters of subsurface heterogeneity from pumping test data exemplified at two sites using welltestpy.
    Description: German Federal Environmental Foundation (DBU) http://dx.doi.org/10.13039/100007636
    Keywords: ddc:551.49
    Language: English
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  • 21
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    Importance of sources of variability, scales and experimental design: A case study about the effects of biochar and slurry application on soil properties in agricultural silty loam soils (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: In designed experiments, different sources of variability and an adequate scale of measurement need to be considered, but not all approaches in common usage are equally valid. In order to elucidate the importance of sources of variability and choice of scale, we conducted an experiment where the effects of biochar and slurry applications on soil properties related to soil fertility were studied for different designs: (a) for a field‐scale sampling design with either a model soil (without natural variability) as an internal control or with composited soils, (b) for a design with a focus on amendment variabilities, and (c) for three individual field‐scale designs with true field replication and a combined analysis representative of the population of loess‐derived soils. Three silty loam sites in Germany were sampled and the soil macroaggregates were crushed. For each design, six treatments (0, 0.15 and 0.30 g slurry‐N kg−1 with and without 30 g biochar kg−1) were applied before incubating the units under constant soil moisture conditions for 78 days. CO2 fluxes were monitored and soils were analysed for macroaggregate yields and associated organic carbon (C). Mixed‐effects models were used to describe the effects. For all soil properties, results for the loess sites differed with respect to significant contributions of fixed effects for at least one site, suggesting the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils to be made and showed that site:slurry:biochar and site:slurry interactions were not negligible for macroaggregate yields. The use of a model soil as an internal control enabled observation of variabilities other than those related to soils or amendments. Experiments incorporating natural variability in soils or amendments resulted in partially different outcomes, indicating the need to include all important sources of variability. Highlights Effects of biochar and slurry applications were studied for different designs and mixed‐effects models were used to describe the effects. Including an internal control allowed observation of, e.g., methodological and analytical variabilities. The results suggested the need for a general inclusion of different sites. Analysis using a multilevel model allowed generalizations for loess soils. The results indicated the need to include all important sources of variability.
    Keywords: ddc:631.4
    Language: English
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  • 22
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    Do tree species affect decadal changes in soil organic carbon and total nitrogen stocks in Danish common garden experiments? (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-04-01
    Description: Temperate forest soils are often considered as an important sink for atmospheric carbon (C), thereby buffering anthropogenic CO2 emissions. However, the effect of tree species composition on the magnitude of this sink is unclear. We resampled a tree species common garden experiment (six sites) a decade after initial sampling to evaluate whether forest floor (FF) and topsoil organic carbon (Corg) and total nitrogen (Nt) stocks changed in dependence of tree species (Norway spruce—Picea abies L., European beech—Fagus sylvatica L., pedunculate oak—Quercus robur L., sycamore maple—Acer pseudoplatanus L., European ash—Fraxinus excelsior L. and small‐leaved lime—Tilia cordata L.). Two groups of species were identified in terms of Corg and Nt distribution: (1) Spruce with high Corg and Nt stocks in the FF developed as a mor humus layer which tended to have smaller Corg and Nt stocks and a wider Corg:Nt ratio in the mineral topsoil, and (2) the broadleaved species, of which ash and maple distinguished most clearly from spruce by very low Corg and Nt stocks in the FF developed as mull humus layer, had greater Corg and Nt stocks, and narrow Corg:Nt ratios in the mineral topsoil. Over 11 years, FF Corg and Nt stocks increased most under spruce, while small decreases in bulk mineral soil (esp. in 0–15 cm and 0–30 cm depth) Corg and Nt stocks dominated irrespective of species. Observed decadal changes were associated with site‐related and tree species‐mediated soil properties in a way that hinted towards short‐term accumulation and mineralisation dynamics of easily available organic substances. We found no indication for Corg stabilisation. However, results indicated increasing Nt stabilisation with increasing biomass of burrowing earthworms, which were highest under ash, lime and maple and lowest under spruce. Highlights We studied if tree species differences in topsoil Corg and Nt stocks substantiate after a decade. The study is unique in its repeated soil sampling in a multisite common garden experiment. Forest floors increased under spruce, but topsoil stocks decreased irrespective of species. Changes were of short‐term nature. Nitrogen was most stable under arbuscular mycorrhizal species.
    Description: Deutsche Forschungsgemeinschaff (DFG)
    Keywords: ddc:551.9 ; ddc:631.41
    Language: English
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  • 23
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    Natural Radioactivity of the Crystalline Basement Rocks of the Peloritani Mountains (North-Eastern Sicily, Italy): Measurements and Radiological Hazard (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-02
    Description: Crystalline rocks can produce dangerous radiation levels on the basis of their content in radioisotopes. Here, we report radiological data from 10 metamorphic and igneous rock samples collected from the crystalline basement of the Peloritani Mountains (southern Italy). In order to evaluate the radiological properties of these rocks, the gamma radiation and the radon emanation have been measured. Moreover, since some of these rocks are employed as building materials, we assess the potential hazard for population connected to their use. Gamma spectroscopy was used to measure the 226Ra, 232Th and 40K activity concentration, whereas the radon emanation was investigated by using a RAD 7 detector. The results show 226Ra, 232Th and 40K activity concentration values ranging from (17 ± 4) to (56 ± 8) Bq kg-1, (14 ± 3) to (77 ± 14) Bq kg-1 and (167 ± 84) to (1760 ± 242) Bq kg-1, respectively. Values of the annual effective dose equivalent outdoor range from 0.035 to 0.152 mSv y-1, whereas the gamma index is in the range of 0.22-0.98. The 222Rn emanation coefficient and the 222Rn surface exhalation rate vary from (0.63 ± 0.3) to (8.27 ± 1.6)% and from (0.12 ± 0.03) to (2.75 ± 0.17) Bq m-2 h-1, respectively. The indoor radon derived from the building use of these rocks induces an approximate contribution to the annual effective dose ranging from 8 to 176 μSv y-1. All the obtained results suggest that the crystalline rocks from the Peloritani Mountains are not harmful for the residential population, even though they induce annual effective doses due to terrestrial gamma radiation above the worldwide average values. Moreover, their use as building materials does not produce significant health hazards connected to the indoor radon exposure.
    Description: Published
    Description: 452–464
    Description: 6A. Geochimica per l'ambiente e geologia medica
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Transfer learning: Improving neural network based prediction of earthquake ground shaking for an area with insufficient training data (2021)
    Oxford University Press
    Details
    Publication Date: 2022-03-16
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. 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: In a recent study (Jozinovi\'c et al, 2020) we showed that convolutional neural networks (CNNs) applied to network seismic traces can be used for rapid prediction of earthquake peak ground motion intensity measures (IMs) at distant stations using only recordings from stations near the epicenter. The predictions are made without any previous knowledge concerning the earthquake location and magnitude. This approach differs from the standard procedure adopted by earthquake early warning systems (EEWSs) that rely on location and magnitude information. In the previous study, we used 10 s, raw, multistation waveforms for the 2016 earthquake sequence in central Italy for 915 events (CI dataset). The CI dataset has a large number of spatially concentrated earthquakes and a dense station network. In this work, we applied the CNN model to an area around the VIRGO gravitational waves observatory sited near Pisa, Italy. In our initial application of the technique, we used a dataset consisting of 266 earthquakes recorded by 39 stations. We found that the CNN model trained using this smaller dataset performed worse compared to the results presented in the original study by Jozinovi\'c et al. (2020). To counter the lack of data, we adopted transfer learning (TL) using two approaches: first, by using a pre-trained model built on the CI dataset and, next, by using a pre-trained model built on a different (seismological) problem that has a larger dataset available for training. We show that the use of TL improves the results in terms of outliers, bias, and variability of the residuals between predicted and true IMs values. We also demonstrate that adding knowledge of station positions as an additional layer in the neural network improves the results. The possible use for EEW is demonstrated by the times for the warnings that would be received at the station PII.
    Description: RISE (Union's Horizon 2020 research and innovation programme, grant agreement No.821115)
    Description: Published
    Description: 704–718
    Description: 5T. Sismologia, geofisica e geologia per l'ingegneria sismica
    Description: JCR Journal
    Keywords: Physics - Geophysics; Physics - Geophysics ; machine learning ; ground motion prediction ; seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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    Azimuthal anisotropy from Eikonal Tomography: example from ambient-noise measurements in the AlpArray network (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-24
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2021. 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: Ambient-noise records from the AlpArray network are used to measure Rayleigh wave phase velocities between more than 150,000 station pairs. From these, azimuthally anisotropic phase-velocity maps are obtained by applying the Eikonal tomography method. Several synthetic tests are shown to study the bias in the Ψ2 anisotropy. There are two main groups of bias, the first one caused by interference between refracted/reflected waves and the appearance of secondary wavefronts that affect the phase travel-time measurements. This bias can be reduced if the amplitude field can be estimated correctly. Another source of error is related to the incomplete reconstruction of the travel-time field that is only sparsely sampled due to the receiver locations. Both types of bias scale with the magnitude of the velocity heterogeneities. Most affected by the spurious Ψ2 anisotropy are areas inside and at the border of low-velocity zones. In the isotropic velocity distribution, most of the bias cancels out if the azimuthal coverage is good. Despite the lack of resolution in many parts of the surveyed area, we identify a number of anisotropic structures that are robust: in the central Alps, we find a layered anisotropic structure, arc-parallel at midcrustal depths and arc-perpendicular in the lower crust. In contrast, in the eastern Alps, the pattern is more consistently E-W oriented which we relate to the eastward extrusion. The northern Alpine forleand exhibits a preferential anisotropic orientation that is similar to SKS observations in the lowermost crust and uppermost mantle.
    Description: German Science Foundation (SPP-2017, Project Ha 2403/21-1); Swiss National Science Foundation SINERGIA Project CRSII2-154434/1 (Swiss-AlpArray); Progetto Pianeta Dinamico, finanziamento MUR-INGV, Task S2 – 2021
    Description: Published
    Description: 151–170
    Description: 1T. Struttura della Terra
    Description: JCR Journal
    Keywords: Seismic anisotropy ; Seismic interferometry ; Seismic tomography ; Wave propagation ; Continental tectonics: compressional ; 04.01. Earth Interior ; 04.06. Seismology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 26
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    The focal mechanism of the 7 September 1920, Mw 6.5 earthquake: insights into the seismotectonics of the Lunigiana–Garfagnana area, Tuscany, Italy (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-15
    Description: This article has been accepted for publication in Geophysical Journal International ©: The Authors 2022. 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: To understand the seismotectonics and the seismic hazard of the study sector of the Northern Apennines (Italy), one of the most important earthquakes of magnitude Mw = 6.5 which struck the Lunigiana and Garfagnana areas (Tuscany) on 7 September 1920 should be studied. Given the early instrumental epoch of the event, neither geometric and kinematic information on the fault-source nor its fault-plane solution were available. Both areas were candidates for hosting the source fault and there was uncertainty between a normal fault with Apenninic direction or an anti-Apenninic strike-slip. We retrieved 11 focal parameters (including the fault-plane solution) of the 1920 earthquake. Only macroseismic intensity information (from 499 inhabited centres) through the KF-NGA inversion technique was used. This technique uses a Kinematic model of the earthquake source and speeds up the calculation by a Genetic Algorithm with Niching. The result is a pure dip-slip focal solution. The intrinsic ambiguities of the KF-NGA method (±180° on the rake angle; choice of the fault plane between the two nodal planes) were solved with field and seismotectonic evidence. The earthquake was generated by a normal fault (rake angle = 265° ± 8°) with an Apennine direction (114° ± 5°) and dipping 38° ± 6° towards SW. The likely candidate for hosting the source-fault in 1920 is the Compione-Comano fault that borders the NE edge of the Lunigiana graben. The KF-NGA algorithm proved to be invaluable for studying the kinematics of early instrumental earthquakes and allowed us to uniquely individuate, for the first time ever, the seismogenic source of the 1920 earthquake. Our findings have implications in hazard computation and seismotectonic contexts.
    Description: Published
    Description: 1465–1477
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: Inverse theory ; Body waves ; Earthquake source observations ; Seismicity and tectonics ; Dynamics: seismotectonics ; Fractures, faults, and high strain deformation zones ; 04.06. Seismology
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  • 27
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    Intraplate Basalt Alkalinity Modulated by a Lithospheric Mantle Filter at the Dunedin Volcano (New Zealand) (2021)
    Oxford University Press
    Details
    Publication Date: 2021-12-22
    Description: Systematic variations in the crystal cargo and whole-rock isotopic compositions of mantle-derived basalts in the intraplate Dunedin Volcano (New Zealand) indicate the influence of a complex mantle-to-crust polybaric plumbing system. Basaltic rocks define a compositional spectrum from low-alkali basalts through mid-alkali basalts to high-alkali basalts. High-alkali basalts display clinopyroxene crystals with sector (hourglass) and oscillatory zoning (Mg#61–82) as well as Fe-rich green cores (Mg#43–69), whereas low-alkali basalts are characterized by clinopyroxenes with unzoned overgrowths (Mg#69–83) on resorbed mafic cores (Mg#78–88), coexisting with reversely zoned plagioclase crystals (An43–68 to An60–84 from core to rim). Complex magma dynamics are indicated by distinctive compositional variations in clinopyroxene phenocrysts, with Cr-rich zones (Mg#74–87) indicating continuous recharge by more mafic magmas. Crystallization of olivine, clinopyroxene and titanomagnetite occurred within a polybaric plumbing system extending from upper mantle to mid-crustal depths (485–1059 MPa and 1147–1286°C), whereas crystallization of plagioclase with subordinate clinopyroxene and titanomagnetite proceeded towards shallower crustal levels. The compositions of high-alkali basalts and mid-alkali basalts resemble those of ocean island basalts and are characterized by FOZO-HIMU isotopic signatures (87Sr/86Sri = 0.70277–0.70315, 143Nd/144Ndi = 0.51286–0.51294 and 206Pb/204Pb = 19.348–20.265), whereas low-alkali basalts have lower incompatible element abundances and isotopic compositions trending towards EMII (87Sr/86Sri = 0.70327–70397, 143Nd/144Ndi = 0.51282–0.51286 and 206Pb/204Pb = 19.278–19.793). High- and mid-alkali basalt magmas mostly crystallized in the lower crust, whereas low-alkali basalt magma recorded deeper upper mantle clinopyroxene crystallization before eruption. The variable alkaline character and isotope composition may result from interaction of low-alkaline melts derived from the asthenosphere with melts derived from lithospheric mantle, possibly initiated by asthenospheric melt percolation. The transition to more alkaline compositions was induced by variable degrees of melting of metasomatic lithologies in the lithospheric mantle, leading to eruption of predominantly small-volume, high-alkali magmas at the periphery of the volcano. Moreover, the lithosphere imposed a filtering effect on the alkalinity of these intraplate magmas. As a consequence, the eruption of low-alkali basalts with greater asthenospheric input was concentrated at the centre of the volcano, where the plumbing system was more developed.
    Description: Published
    Description: egab062
    Description: 2V. Struttura e sistema di alimentazione dei vulcani
    Description: 3V. Proprietà chimico-fisiche dei magmi e dei prodotti vulcanici
    Description: 4V. Processi pre-eruttivi
    Description: JCR Journal
    Keywords: alkali basalts ; Dunedin Volcano ; thermobarometry ; primary magma ; lithospheric mantle filter ; Igneous Petrology ; Thermobarometry ; Mantle melting and metasomatism ; Magmatic plumbing systems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 28
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    Characterizing the culturable surface microbiomes of diverse marine animals (2021)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keller, A. G., Apprill, A., Lebaron, P., Robbins, J., Romano, T. A., Overton, E., Rong, Y., Yuan, R., Pollara, S., & Whalen, K. E. Characterizing the culturable surface microbiomes of diverse marine animals. FEMS Microbiology Ecology, 97(4), (2021): fiab040, https://doi.org/10.1093/femsec/fiab040.
    Description: Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.
    Description: Funding was provided by the National Science Foundation (Biological Oceanography) award #1657808 and National Institutes of Health grants 1R21-AI119311–01 to K. E. Whalen, as well as funding from the Koshland Integrated Natural Science Center and Green Fund at Haverford College. This constitutes scientific manuscript #298 from the Sea Research Foundation.
    Keywords: Bacteria ; SSU rRNA ; Coral ; Whale ; Microbiome ; Skin
    Repository Name: Woods Hole Open Access Server
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  • 29
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    On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172 (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: Author Posting. © Oxford University Press, 2021. This article is posted here by permission of [publisher] for personal use, not for redistribution. The definitive version was published in Lund, S., Acton, G., Clement, B., Okada, M., & Keigwin, L. On the relationship between palaeomagnetic secular variation and excursions-records from MIS 8-ODP leg 172. Geophysical Journal International, 225(2), (2021): 1129-1141, https://doi.org/10.1093/gji/ggaa564.
    Description: Palaeomagnetic secular variation (PSV) and excursion data obtained across MIS 8 (243–300 ka) from the western North Atlantic Ocean ODP (Ocean Drilling Program) sites 1060–1063 show composite high-resolution PSV records (both directions and relative palaeointensity) developed for each site and intercompared. Two methods of chronostratigraphy allow us to date these records. First, we used published results that compared the calcium carbonate records of ODP Leg 172 sediments and tuned them with Milankovich cyclicity. We also compared our palaeointensity records with the PISO-1500 global palaeointensity record that was dated with oxygen isotope stratigraphy. We prefer the PISO-1500 record to date our cores. Two excursions are preserved in our PSV records—Excursions 8α and 9α. Our revised age estimates for both excursions are 8α (236.7–239.8 ka) and 9α (283.7–286.9 ka). We have compared shipboard measurements of the two excursions with u-channel measurements of selected excursion intervals. Excursion 8α is interpreted as a ‘Class II’ excursion (local reversal) with in-phase inclination and declination changes; Excursion 9α is a ‘Class I’ excursion with 90° out-of-phase inclination and declination changes. Averaged directions (after removal of true excursional directions) and relative palaeointensity in 3 and 9 ka overlapping intervals show significant PSV directional variability over 104 yr timescales that is regionally correlatable among the four sites. A notable pattern of angular dispersion variability involves most time spent with low (∼10°) dispersion, with three shorter intervals of high (∼25°) dispersion. The relative palaeointensity variability also shows significant variability over 104 yr timescales with three notable intervals of low palaeointensity in all four records and a direct correspondence between the three low-palaeointensity intervals and the three intervals of high angular dispersion. The two magnetic field excursions occur in two of the three low-palaeointensity/high-dispersion intervals. This suggests that the geomagnetic field operates in two states between reversals, one with regular to high palaeointensity and low directional variability and one with low palaeointensity and significantly higher directional variability and excursions.
    Keywords: Geomagnetic excursions ; Palaeointensity ; Palaeomagnetic secular variation
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  • 30
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    Urban pluvial flood adaptation: Results of a household survey across four German municipalities (2021)
    Blackwell Publishing Ltd | Oxford, UK
    Details
    Publication Date: 2022-09-30
    Description: In recent years, German cities were heavily impacted by pluvial flooding and related damage is projected to increase due to climate change and urbanisation. It is important to ask how to improve urban pluvial flood risk management. To understand the current state of property level adaptation, a survey was conducted in four municipalities that had recently been impacted by pluvial flooding. A hybrid framework based on the Protection Motivation Theory (PMT) and the Protection Action Decision Model (PADM) was used to investigate drivers of adaptive behaviour through both descriptive and regression analyses. Descriptive statistics revealed that participants tended to instal more low‐ and medium‐cost measures than high‐cost measures. Regression analyses showed that coping appraisal increased protection motivation, but that the adaptive behaviour also depends on framing factors, particularly homeownership. We further found that, while threat appraisal solely affects protection motivation and responsibility appraisal affects solely maladaptive thinking, coping appraisal affects both. Our results indicate that PMT is a solid starting point to study adaptive behaviours in the context of pluvial flooding, but we need to go beyond that by, for instance, considering factors of the PADM, such as responsibility, ownership, or respondent age, to fully understand this complex decision‐making process.
    Description: Bundesministerium für Bildung und Forschung http://dx.doi.org/10.13039/501100002347
    Keywords: ddc:551.489 ; ddc:363.34
    Language: English
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  • 31
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    Developmental exposure to domoic acid disrupts startle response behavior and circuitry in zebrafish (2021)
    Oxford University Press
    Details
    Publication Date: 2022-06-07
    Description: Author Posting. © The Author(s), 2021. 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 Toxicological Sciences 182(20), (2021): 310-326, https://doi.org/10.1093/toxsci/kfab066.
    Description: Harmful algal blooms produce potent neurotoxins that accumulate in seafood and are hazardous to human health. Developmental exposure to the harmful algal bloom toxin, domoic acid (DomA), has behavioral consequences well into adulthood, but the cellular and molecular mechanisms of DomA developmental neurotoxicity are largely unknown. To assess these, we exposed zebrafish embryos to DomA during the previously identified window of susceptibility and used the well-known startle response circuit as a tool to identify specific neuronal components that are targeted by exposure to DomA. Exposure to DomA reduced startle responsiveness to both auditory/vibrational and electrical stimuli, and even at the highest stimulus intensities tested, led to a dramatic reduction of one type of startle (short-latency c-starts). Furthermore, DomA-exposed larvae had altered kinematics for both types of startle responses tested, exhibiting shallower bend angles and slower maximal angular velocities. Using vital dye staining, immunolabeling, and live imaging of transgenic lines, we determined that although the sensory inputs were intact, the reticulospinal neurons required for short-latency c-starts were absent in most DomA-exposed larvae. Furthermore, axon tracing revealed that DomA-treated larvae also showed significantly reduced primary motor neuron axon collaterals. Overall, these results show that developmental exposure to DomA targets large reticulospinal neurons and motor neuron axon collaterals, resulting in measurable deficits in startle behavior. They further provide a framework for using the startle response circuit to identify specific neural populations disrupted by toxins or toxicants and to link these disruptions to functional consequences for neural circuit function and behavior.
    Description: This research was supported by a WHOI Von Damm and Ocean Ridge Initiative Fellowships to J.M.P. and the Woods Hole Center for Oceans and Human Health (NIH: P01ES021923 and P01ES028938; NSF: OCE-1314642 and OCE-1840381).
    Description: 2022-06-07
    Keywords: domoic acid ; harmful algal blooms ; harmful algal bloom toxins ; developmental toxicity ; startle response ; escape response ; startle circuit
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 32
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    Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bowen, J. L., Giblin, A. E., Murphy, A. E., Bulseco, A. N., Deegan, L. A., Johnson, D. S., Nelson, J. A., Mozdzer, T. J., & Sullivan, H. L. Not all nitrogen is created equal: differential effects of nitrate and ammonium enrichment in coastal wetlands. Bioscience, 70(12), (2020): 1108-1119, doi:10.1093/biosci/biaa140.
    Description: Excess reactive nitrogen (N) flows from agricultural, suburban, and urban systems to coasts, where it causes eutrophication. Coastal wetlands take up some of this N, thereby ameliorating the impacts on nearshore waters. Although the consequences of N on coastal wetlands have been extensively studied, the effect of the specific form of N is not often considered. Both oxidized N forms (nitrate, NO3−) and reduced forms (ammonium, NH4+) can relieve nutrient limitation and increase primary production. However, unlike NH4+, NO3− can also be used as an electron acceptor for microbial respiration. We present results demonstrating that, in salt marshes, microbes use NO3− to support organic matter decomposition and primary production is less stimulated than when enriched with reduced N. Understanding how different forms of N mediate the balance between primary production and decomposition is essential for managing coastal wetlands as N enrichment and sea level rise continue to assail our coasts.
    Description: This work was supported by the following funding sources: National Science Foundation (NSF) grant no. DEB 1902712 to LAD, JLB, DSJ, and TJM; NSF grant no. DEB 1902695 to AEG; NSF grant no. DEB 1902704 to JAN; NSF grant no. DEB 1354214 to TJM; NSF grant no. DEB 1350491 to JLB; NSF grant no. OCE 1637630 to AEG and LAD; and additional funding from the Dorr Foundation, the Department of the Interior Northeast Climate Science Center (grant no. DOI G12AC00001), and a Bullard Fellowship (Harvard University) to LAD and from the National Academies of Science, Medicine, and Engineering Gulf Research Program to JAN. Resources purchased with funds from the NSF Biological Field Stations and Marine Laboratories program (grant no. DBI 1722553, to Northeastern University) were used to generate the data for the manuscript. Initial conversations on the effects of nutrient enrichment in marshes with Scott Warren and Bruce Peterson were critical in informing the work described in the manuscript. Sam Kelsey and Jane Tucker contributed to much of the N cycling biogeochemistry; Caitlin Bauer, Frankie Leach, Paige Weber, Emily Geoghegan and Sophie Drew assisted with field work; and Joe Vineis assisted with metagenomic analysis. This is contribution 3941 from the Virginia Institute of Marine Science. The data were compiled from multiple published sources. Links to published data can be found here: https://pie-lter.ecosystems.mbl.edu/data. The sequence data used to derive figure 6 are publicly available on the MG-RAST website under project number mgp84173.
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  • 33
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    Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirschberger, C., Sleight, V. A., Criswell, K. E., Clark, S. J., & Gillis, J. A. Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw. Molecular Biology and Evolution, (2021): msab123, https://doi.org/10.1093/molbev/msab123
    Description: The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral patterning mechanisms within the developing mandibular, hyoid and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralising BMP and endothelin signalling pathways and their effectors, the joint markers nkx3.2 and gdf5 and pro-chondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, while differences in notch signalling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the dorsoventral axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.
    Description: This work was supported by a Biotechnology and Biological Sciences Research Council Doctoral Training Partnership studentship to CH, by a Wolfson College Junior Research Fellowship and MBL Whitman Early Career Fellowship to VAS, and by a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377) and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) to JAG.
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  • 34
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    The challenges of detecting and attributing ocean acidification impacts on marine ecosystems (2021)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Doo, S. S., Kealoha, A., Andersson, A., Cohen, A. L., Hicks, T. L., Johnson, Z., I., Long, M. H., McElhany, P., Mollica, N., Shamberger, K. E. F., Silbiger, N. J., Takeshita, Y., & Busch, D. S. The challenges of detecting and attributing ocean acidification impacts on marine ecosystems. ICES Journal of Marine Science, 77(7-8), (2020): 2411-2422, https://doi.org/10.1093/icesjms/fsaa094.
    Description: A substantial body of research now exists demonstrating sensitivities of marine organisms to ocean acidification (OA) in laboratory settings. However, corresponding in situ observations of marine species or ecosystem changes that can be unequivocally attributed to anthropogenic OA are limited. Challenges remain in detecting and attributing OA effects in nature, in part because multiple environmental changes are co-occurring with OA, all of which have the potential to influence marine ecosystem responses. Furthermore, the change in ocean pH since the industrial revolution is small relative to the natural variability within many systems, making it difficult to detect, and in some cases, has yet to cross physiological thresholds. The small number of studies that clearly document OA impacts in nature cannot be interpreted as a lack of larger-scale attributable impacts at the present time or in the future but highlights the need for innovative research approaches and analyses. We summarize the general findings in four relatively well-studied marine groups (seagrasses, pteropods, oysters, and coral reefs) and integrate overarching themes to highlight the challenges involved in detecting and attributing the effects of OA in natural environments. We then discuss four potential strategies to better evaluate and attribute OA impacts on species and ecosystems. First, we highlight the need for work quantifying the anthropogenic input of CO2 in coastal and open-ocean waters to understand how this increase in CO2 interacts with other physical and chemical factors to drive organismal conditions. Second, understanding OA-induced changes in population-level demography, potentially increased sensitivities in certain life stages, and how these effects scale to ecosystem-level processes (e.g. community metabolism) will improve our ability to attribute impacts to OA among co-varying parameters. Third, there is a great need to understand the potential modulation of OA impacts through the interplay of ecology and evolution (eco–evo dynamics). Lastly, further research efforts designed to detect, quantify, and project the effects of OA on marine organisms and ecosystems utilizing a comparative approach with long-term data sets will also provide critical information for informing the management of marine ecosystems.
    Description: SSD was funded by NSF OCE (grant # 1415268). DSB and PM were supported by the NOAA Ocean Acidification Program and Northwest Fisheries Science Center, MHL was supported by NSF OCE (grant # 1633951), ZIJ was supported by NSF OCE (grant # 1416665) and DOE EERE (grant #DE-EE008518), NJS was supported by NSF OCE (grant # 1924281), ALC was supported by NSF OCE (grant # 1737311), and AA was supported by NSF OCE (grant # 1416518). KEFS, AK, and TLH were supported by Texas A&M University. This is CSUN Marine Biology contribution (# 306).
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  • 35
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    Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Carroll, E. L., Ott, P. H., McMillan, L. F., Galletti Vernazzani, B., Neveceralova, P., Vermeulen, E., Gaggiotti, O. E., Andriolo, A., Baker, C. S., Bamford, C., Best, P., Cabrera, E., Calderan, S., Chirife, A., Fewster, R. M., Flores, P. A. C., Frasier, T., Freitas, T. R. O., Groch, K., Hulva, P., Kennedy, A., Leaper, R., Leslie, M. S., Moore, M., Oliveira, L., Seger, J., Stepien, E. N., Valenzuela, L. O., Zerbini, A., & Jackson, J. A. Genetic diversity and connectivity of southern right whales (Eubalaena australis) found in the Brazil and Chile-Peru wintering grounds and the South Georgia (Islas Georgias del Sur) feeding ground. Journal of Heredity, 111(3), (2020): 263-276, doi:10.1093/jhered/esaa010.
    Description: As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile–Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile–Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile–Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile–Peru.
    Description: This work was supported by the EU BEST 2.0 medium grant 1594 and UK DARWIN PLUS grant 057 and additional funding from the World Wildlife Fund GB107301. The collection of the Chile–Peru sample was supported by the Global Greengrants Fund and the Pacific Whale Foundation. The collection of the Brazilian samples was supported through grants by the Brazilian National Research Council to Paulo H. Ott (CNPq proc. n° 144064/98-7) and Paulo A.C. Flores (CNPq proc. n° 146609/1999-9) and with support from the World Wildlife Fund (WWF-Brazil). The collection of the South African samples was supported by the Global Greengrants Fund, the Pacific Whale Foundation and Charles University Grant Agency (1140217). E.L.C. was partially supported by a Rutherford Discovery Fellowship from the Royal Society of New Zealand. This study forms part of the Ecosystems component of the British Antarctic Survey Polar Sciences for Planet Earth Programme, funded by the Natural Environment Research Council.
    Keywords: population structure ; connectivity ; migration ; gene flow
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  • 36
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    Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Johnson, W. M., Alexander, H., Bier, R. L., Miller, D. R., Muscarella, M. E., Pitz, K. J., & Smith, H. Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? FEMS Microbiology Ecology, (2020): fiaa115, doi: 10.1093/femsec/fiaa115.
    Description: Auxotrophy, or an organism's requirement for an exogenous source of an organic molecule, is widespread throughout species and ecosystems. Auxotrophy can result in obligate interactions between organisms, influencing ecosystem structure and community composition. We explore how auxotrophy-induced interactions between aquatic microorganisms affect microbial community structure and stability. While some studies have documented auxotrophy in aquatic microorganisms, these studies are not widespread, and we therefore do not know the full extent of auxotrophic interactions in aquatic environments. Current theoretical and experimental work suggests that auxotrophy links microbial community members through a complex web of metabolic dependencies. We discuss the proposed ways in which auxotrophy may enhance or undermine the stability of aquatic microbial communities, highlighting areas where our limited understanding of these interactions prevents us from being able to predict the ecological implications of auxotrophy. Finally, we examine an example of auxotrophy in harmful algal blooms to place this often theoretical discussion in a field context where auxotrophy may have implications for the development and robustness of algal bloom communities. We seek to draw attention to the relationship between auxotrophy and community stability in an effort to encourage further field and theoretical work that explores the underlying principles of microbial interactions.
    Description: This work was supported by the National Science Foundation [OCE-1356192].
    Keywords: Auxotrophy ; Microbial community stability ; Microbial interactions ; Aquatic
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  • 37
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    The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wang, P., Huang, C., Lin, J., Jian, Z., Sun, Z., & Zhao, M. The South China Sea is not a mini-Atlantic: plate-edge rifting vs intra-plate rifting. National Science Review, 6(5), (2019): 902-913, doi:10.1093/nsr/nwz135.
    Description: The South China Sea, as ‘a non-volcanic passive margin basin’ in the Pacific, has often been considered as a small-scale analogue of the Atlantic. The recent ocean drilling in the northern South China Sea margin found, however, that the Iberian model of non-volcanic rifted margin from the Atlantic does not apply to the South China Sea. In this paper, we review a variety of rifted basins and propose to discriminate two types of rifting basins: plate-edge type such as the South China Sea and intra-plate type like the Atlantic. They not only differ from each other in structure, formation process, lifespan and geographic size, but also occur at different stages of the Wilson cycle. The intra-plate rifting occurred in the Mesozoic and gave rise to large oceans, whereas the plate-edge rifting took place mainly in the mid-Cenozoic, with three-quarters of the basins concentrated in the Western Pacific. As a member of the Western Pacific system of marginal seas, the South China Sea should be studied not in isolation on its origin and evolution, but in a systematic context to include also its neighboring counterparts.
    Description: This work was supported by the National Natural Science Foundation of China as a part of the ‘South China Sea Deep’ Project (91128000).
    Keywords: Rifting ; Marginal basin ; Passive margin ; South China Sea ; Western Pacific ; Subduction
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  • 38
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    A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses (2020)
    Oxford University Press
    Details
    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 Lasek-Nesselquist, E., & Johnson, M. D. A phylogenomic approach to clarifying the relationship of Mesodinium within the Ciliophora: a case study in the complexity of mixed-species transcriptome analyses. Genome Biology and Evolution, 11(11), (2019): 3218–3232, doi:10.1093/gbe/evz233.
    Description: Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium—M. rubrum, M. major, and M. chamaeleon—being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination—particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate—requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
    Description: We thank David Beaudoin and Holly V. Moeller for their assistance in collecting cells and extracting RNA. We thank the Josephine Bay Paul Center for Comparative Molecular Biology and Evolution at the Marine Biological Laboratory for the generous use of their servers. This work was supported in part by a National Science Foundation grant to both authors (IOS 1354773).
    Keywords: Mesodinium ; Litostomatea ; ciliate phylogenomics ; mixed-species transcriptomes ; sequence contamination
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  • 39
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    Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis (2020)
    Oxford University Press
    Details
    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 Xu, X., Li, G., Li, C., Zhang, J., Wang, Q., Simmons, D. K., Chen, X., Wijesena, N., Zhu, W., Wang, Z., Wang, Z., Ju, B., Ci, W., Lu, X., Yu, D., Wang, Q., Aluru, N., Oliveri, P., Zhang, Y. E., Martindale, M. Q., & Liu, J. Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis. National Science Review, 6(5), (2019):993-1003, doi:10.1093/nsr/nwz064.
    Description: Major evolutionary transitions are enigmas, and the most notable enigma is between invertebrates and vertebrates, with numerous spectacular innovations. To search for the molecular connections involved, we asked whether global epigenetic changes may offer a clue by surveying the inheritance and reprogramming of parental DNA methylation across metazoans. We focused on gametes and early embryos, where the methylomes are known to evolve divergently between fish and mammals. Here, we find that methylome reprogramming during embryogenesis occurs neither in pre-bilaterians such as cnidarians nor in protostomes such as insects, but clearly presents in deuterostomes such as echinoderms and invertebrate chordates, and then becomes more evident in vertebrates. Functional association analysis suggests that DNA methylation reprogramming is associated with development, reproduction and adaptive immunity for vertebrates, but not for invertebrates. Interestingly, the single HOX cluster of invertebrates maintains unmethylated status in all stages examined. In contrast, the multiple HOX clusters show dramatic dynamics of DNA methylation during vertebrate embryogenesis. Notably, the methylation dynamics of HOX clusters are associated with their spatiotemporal expression in mammals. Our study reveals that DNA methylation reprogramming has evolved dramatically during animal evolution, especially after the evolutionary transitions from invertebrates to vertebrates, and then to mammals.
    Description: This work was supported by the National Key Research and Development Program of China (2018YFC1003303), the Strategic Priority Research Program of the CAS (XDB13040200), the National Natural Science Foundation of China (91519306, 31425015), the Youth Innovation Promotion Association of the CAS and the Key Research Program of Frontier Sciences, CAS (QYZDY-SSW-SMC016).
    Keywords: DNA methylation ; evolution ; development ; reprogramming
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    Spatially regulated editing of genetic information within a neuron (2020)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Vallecillo-Viejo, I. C., Liscovitch-Brauer, N., Diaz Quiroz, J. F., Montiel-Gonzalez, Maria F., Nemes, Sonya E., Rangan, K. J., Levinson, S. R., Eisenberg, E., & Rosenthal, J. J. C. Spatially regulated editing of genetic information within a neuron. Nucleic Acids Research, (2020): gkaa172, doi: 10.1093/nar/gkaa172.
    Description: In eukaryotic cells, with the exception of the specialized genomes of mitochondria and plastids, all genetic information is sequestered within the nucleus. This arrangement imposes constraints on how the information can be tailored for different cellular regions, particularly in cells with complex morphologies like neurons. Although messenger RNAs (mRNAs), and the proteins that they encode, can be differentially sorted between cellular regions, the information itself does not change. RNA editing by adenosine deamination can alter the genome’s blueprint by recoding mRNAs; however, this process too is thought to be restricted to the nucleus. In this work, we show that ADAR2 (adenosine deaminase that acts on RNA), an RNA editing enzyme, is expressed outside of the nucleus in squid neurons. Furthermore, purified axoplasm exhibits adenosine-to-inosine activity and can specifically edit adenosines in a known substrate. Finally, a transcriptome-wide analysis of RNA editing reveals that tens of thousands of editing sites (〉70% of all sites) are edited more extensively in the squid giant axon than in its cell bodies. These results indicate that within a neuron RNA editing can recode genetic information in a region-specific manner.
    Description: National Science Foundation (NSF) [IOS1557748 to J.R.]; United States–Israel Binational Science Foundation [BSF2013094 to J.R. and E.E.]; The Grass Foundation grant in support of the Doryteuthis pealeii Genome Project, and a gift by Mr. Edward Owens. Funding for open access charge: United States–Israel Binational Science Foundation [BSF2013094].
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
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    Advancing an interdisciplinary framework to study seed dispersal ecology (2020)
    Oxford University Press
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beckman, N. G., Asian, C. E., Rogers, H. S., Kogan, O., Bronstein, J. L., Bullock, J. M., Hartig, F., HilleRisLambers, J., Zhou, Y., Zurell, D., Brodie, J. F., Bruna, E. M., Cantrell, R. S., Decker, R. R., Efiom, E., Fricke, E. C., Gurski, K., Hastings, A., Johnson, J. S., Loiselle, B. A., Miriti, M. N., Neubert, M. G., Pejchar, L., Poulsen, J. R., Pufal, G., Razafindratsima, O. H., Sandor, M. E., Shea, K., Schreiber, S., Schupp, E. W., Snell, R. S., Strickland, C., & Zambrano, J. Advancing an interdisciplinary framework to study seed dispersal ecology. Aob Plants, 12(2), (2020): plz048, doi:10.1093/aobpla/plz048.
    Description: Although dispersal is generally viewed as a crucial determinant for the fitness of any organism, our understanding of its role in the persistence and spread of plant populations remains incomplete. Generalizing and predicting dispersal processes are challenging due to context dependence of seed dispersal, environmental heterogeneity and interdependent processes occurring over multiple spatial and temporal scales. Current population models often use simple phenomenological descriptions of dispersal processes, limiting their ability to examine the role of population persistence and spread, especially under global change. To move seed dispersal ecology forward, we need to evaluate the impact of any single seed dispersal event within the full spatial and temporal context of a plant’s life history and environmental variability that ultimately influences a population’s ability to persist and spread. In this perspective, we provide guidance on integrating empirical and theoretical approaches that account for the context dependency of seed dispersal to improve our ability to generalize and predict the consequences of dispersal, and its anthropogenic alteration, across systems. We synthesize suitable theoretical frameworks for this work and discuss concepts, approaches and available data from diverse subdisciplines to help operationalize concepts, highlight recent breakthroughs across research areas and discuss ongoing challenges and open questions. We address knowledge gaps in the movement ecology of seeds and the integration of dispersal and demography that could benefit from such a synthesis. With an interdisciplinary perspective, we will be able to better understand how global change will impact seed dispersal processes, and potential cascading effects on plant population persistence, spread and biodiversity.
    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).
    Keywords: Analytical models ; demography ; global change ; individual-based models ; long-distance seed dispersal ; population models ; seed dispersal
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    PCB126 exposure revealed alterations in m6A RNA modifications in transcripts associated with AHR activation (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2020. 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 Toxicological Sciences (2020): kfaa158, doi:10.1093/toxsci/kfaa158.
    Description: Chemical modifications of proteins, DNA, and RNA moieties play critical roles in regulating gene expression. Emerging evidence suggests the RNA modifications (epitranscriptomics) have substantive roles in basic biological processes. One of the most common modifications in mRNA and noncoding RNAs is N6-methyladenosine (m6A). In a subset of mRNAs, m6A sites are preferentially enriched near stop codons, in 3′ UTRs, and within exons, suggesting an important role in the regulation of mRNA processing and function including alternative splicing and gene expression. Very little is known about the effect of environmental chemical exposure on m6A modifications. As many of the commonly occurring environmental contaminants alter gene expression profiles and have detrimental effects on physiological processes, it is important to understand the effects of exposure on this important layer of gene regulation. Hence, the objective of this study was to characterize the acute effects of developmental exposure to PCB126, an environmentally relevant dioxin-like PCB, on m6A methylation patterns. We exposed zebrafish embryos to PCB126 for 6 h starting from 72 h post fertilization and profiled m6A RNA using methylated RNA immunoprecipitation followed by sequencing (MeRIP-seq). Our analysis revealed 117 and 217 m6A peaks in the DMSO and PCB126 samples (false discovery rate 5%), respectively. The majority of the peaks were preferentially located around the 3′ UTR and stop codons. Statistical analysis revealed 15 m6A marked transcripts to be differentially methylated by PCB126 exposure. These include transcripts that are known to be activated by AHR agonists (eg, ahrra, tiparp, nfe2l2b) as well as others that are important for normal development (vgf, cebpd, sned1). These results suggest that environmental chemicals such as dioxin-like PCBs could affect developmental gene expression patterns by altering m6A levels. Further studies are necessary to understand the functional consequences of exposure-associated alterations in m6A levels.
    Description: National Institute of Health National Institute of Environmental Health Sciences Outstanding New Environmental Scientist (NIH R01ES024915 to N.A.); Woods Hole Center for Oceans and Human Health [National Institutes of Health (NIH) (Grant P01ES028938); National Science Foundation (Grant OCE-1840381) to M. E. Hahn, J. J. Stegeman, N.A., and S.K.].
    Description: 2021-10-16
    Keywords: dioxin-like PCBs ; development ; zebrafish ; epitranscriptomics ; m6A ; MeRIP
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    Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases (2020)
    Oxford University Press
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lamb, D. C., Hargrove, T. Y., Zhao, B., Wawrzak, Z., Goldstone, J. V., Nes, W. D., Kelly, S. L., Waterman, M. R., Stegeman, J. J., & Lepesheva, G. I. Concerning P450 evolution: structural analyses support bacterial origin of sterol 14α-demethylases. Molecular Biology and Evolution, (2020): msaa260, doi:10.1093/molbev/msaa260.
    Description: Sterol biosynthesis, primarily associated with eukaryotic kingdoms of life, occurs as an abbreviated pathway in the bacterium Methylococcus capsulatus. Sterol 14α-demethylation is an essential step in this pathway and is catalyzed by cytochrome P450 51 (CYP51). In M. capsulatus, the enzyme consists of the P450 domain naturally fused to a ferredoxin domain at the C-terminus (CYP51fx). The structure of M. capsulatus CYP51fx was solved to 2.7 Å resolution and is the first structure of a bacterial sterol biosynthetic enzyme. The structure contained one P450 molecule per asymmetric unit with no electron density seen for ferredoxin. We connect this with the requirement of P450 substrate binding in order to activate productive ferredoxin binding. Further, the structure of the P450 domain with bound detergent (which replaced the substrate upon crystallization) was solved to 2.4 Å resolution. Comparison of these two structures to the CYP51s from human, fungi, and protozoa reveals strict conservation of the overall protein architecture. However, the structure of an “orphan” P450 from nonsterol-producing Mycobacterium tuberculosis that also has CYP51 activity reveals marked differences, suggesting that loss of function in vivo might have led to alterations in the structural constraints. Our results are consistent with the idea that eukaryotic and bacterial CYP51s evolved from a common cenancestor and that early eukaryotes may have recruited CYP51 from a bacterial source. The idea is supported by bioinformatic analysis, revealing the presence of CYP51 genes in 〉1,000 bacteria from nine different phyla, 〉50 of them being natural CYP51fx fusion proteins.
    Description: The study was supported by National Institutes of Health (Grant No. R01 GM067871 to G.I.L.) and by a UK-USA Fulbright Scholarship and the Royal Society (to D.C.L.).
    Keywords: sterol biosynthesis ; evolution ; cytochrome P450 ; CYP51 redox partner ; crystallography
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    Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies (2020)
    Oxford University Press
    Details
    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 Zemeckis, D. R., Dean, M. J., DeAngelis, A. I., Van Parijs, S. M., Hoffman, W. S., Baumgartner, M. F., Hatch, L. T., Cadrin, S. X., & McGuire, C. H. Identifying the distribution of Atlantic cod spawning using multiple fixed and glider-mounted acoustic technologies. ICES Journal of Marine Science, 76(6), (2019): 1610-1625, doi: 10.1093/icesjms/fsz064.
    Description: Effective fishery management measures to protect fish spawning aggregations require reliable information on the spatio-temporal distribution of spawning. Spawning closures have been part of a suite of fishery management actions to rebuild the Gulf of Maine stock of Atlantic cod (Gadus morhua), but difficulties remain with managing rebuilding. The objective of this study was to identify the spatial and temporal distribution of cod spawning during winter in Massachusetts Bay to improve our understanding of cod spawning dynamics and inform fisheries management. Spawning was investigated in collaboration with commercial fishermen during three winter spawning seasons (October 2013–March 2016) using acoustic telemetry and passive acoustic monitoring equipment deployed in fixed-station arrays and mounted on mobile autonomous gliders. Tagged cod exhibited spawning site fidelity and spawning primarily occurred from early November through January with a mid-December peak and some inter-annual variability. The spatial distribution of spawning was generally consistent among years with multiple hotspots in areas 〉50 m depth. Current closures encompass most of spawning, but important areas are recommended for potential modifications. Utilizing multiple complementary technologies and deployment strategies in collaboration with commercial fishermen enabled a comprehensive description of spawning and provides a valuable model for future studies.
    Description: Year 1 was jointly funded by The Nature Conservancy and Massachusetts Division of Marine Fisheries. The remainder of this research was funded through the 2013–2014 NOAA Saltonstall Kennedy grant program (Award No. NA14NMF4270027) with additional support from the Nature Conservancy and Cabot Family Charitable Foundation.
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (2020)
    Oxford University Press
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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 Dong, E., Zhang, Y., Song, Z., Zhang, T., Cai, C., & Fang, N. X. Physical modeling and validation of porpoises' directional emission via hybrid metamaterials. National Science Review, 6(5), (2019): 921-928, doi:10.1093/nsr/nwz085.
    Description: In wave physics and engineering, directional emission sets a fundamental limitation on conventional simple sources as their sizes should be sufficiently larger than their wavelength. Artificial metamaterial and animal biosonar both show potential in overcoming this limitation. Existing metamaterials arranged in periodic microstructures face great challenges in realizing complex and multiphase biosonar structures. Here, we proposed a physical directional emission model to bridge the gap between porpoises’ biosonar and artificial metamaterial. Inspired by the anatomical and physical properties of the porpoise's biosonar transmission system, we fabricated a hybrid metamaterial system composed of multiple composite structures. We validated that the hybrid metamaterial significantly increased directivity and main lobe energy over a broad bandwidth both numerically and experimentally. The device displayed efficiency in detecting underwater target and suppressing false target jamming. The metamaterial-based physical model may be helpful to achieve the physical mechanisms of porpoise biosonar detection and has diverse applications in underwater acoustic sensing, ultrasound scanning, and medical ultrasonography.
    Description: E.D., Y.Z., Z.S., T.Z. and C.C. acknowledge the financial support in part by the National Key Research and Development Program of China (2018YFC1407504), the National Natural Science Foundation of China (41676023, 41276040 and 41422604). N.X.F. acknowledges the support from the MIT Energy Initiative grant. Z.S. thanks the China Scholarship Council for the financial support of his oversea study in Woods Hole Oceanographic Institution.
    Keywords: porpoise's physical model ; metamaterials ; biosonar ; directional emission
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (2020)
    Oxford University Press
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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 Lin, J., Xu, Y., Sun, Z., & Zhou, Z. Mantle upwelling beneath the South China Sea and links to surrounding subduction systems. National Science Review, 6(5), (2019): 877-881, doi:10.1093/nsr/nwz123.
    Description: The evolution of the South China Sea (SCS) is directly linked to the complex subduction systems of the surrounding Pacific, Philippine Sea and Indo-Australian Plates (Fig. 1a). Major advances in the last several years are providing new insights into the SCS-mantle dynamics, through regional seismic imaging of the upper mantle [1,2], unprecedented IODP drilling expeditions (349/367/368/368X) [3–5] that obtained the oceanic basement basalt samples for the first time, geochemical analyses of the SCS-mantle source compositions [6–8] and geodynamic modeling [9,10]. Furthermore, new geological mapping, seismic imaging [11,12] and IODP drilling [13,14] have revealed evidence for significantly greater magma production at the northern SCS rifted margin, in comparison to the magma-poor end-member of the Atlantic rifted margins. This paper provides a new perspective of the SCS-mantle dynamics inspired by new observations and geodynamic modeling. We first highlight new geophysical evidence for a broad region of low-seismic-velocity anomalies in the upper mantle beneath the northern SCS, abundant magmatism during continental breakup and post-seafloor spreading, and geochemical evidence for recycled oceanic components beneath the SCS. We then present new models of layered flows in the mantle beneath the SCS, revealing two modes of plate- and subduction-driven mantle upwelling, including (i) narrow centers of mantle upwelling at shallow depths induced by divergent plate motion at seafloor-spreading centers and (ii) broad zones of mantle upwelling as a result of subduction-induced mantle-return flows at greater depths. These new observations and geodynamic studies suggest strong links between mantle upwelling beneath the SCS and surrounding subducting plates.
    Description: This work was supported by the National Natural Science Foundation of China (41890813, 91628301, U1606401, 41976066, 91858207 and 41706056), the Chinese Academy of Sciences (Y4SL021001, QYZDY-SSW-DQC005 and 133244KYSB20180029), the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou, GML2019ZD0205), the National Key R&D Program of China (2018YFC0309800 and 2018YFC0310100), the State Oceanic Administration (GASI-GEOGE-02) and China Ocean Mineral Resources R&D Association (DY135-S2–1-04).
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    The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling (2020)
    Oxford University Press
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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 Sun, Z., Lin, J., Qiu, N., Jian, Z., Wang, P., Pang, X., Zheng, J., & Zhu, B. The role of magmatism in the thinning and breakup of the South China Sea continental margin: Special Topic: the South China Sea Ocean Drilling. National Science Review, 6(5), (2019): 871-876, doi:10.1093/nsr/nwz116.
    Description: Magmatism plays a key role in the process of continental margin breakup and ocean formation. Even in the extremely magma-poor Iberia and Newfoundland margin, studies of field outcrops have shown that syn-rift magmatism had participated in rifting from a very early stage and contributed directly to the rifting process. The final transition from exhumed continental mantle to the ocean formation is also triggered by the accumulation and eruption of magma [1]. Therefore, Atlantic-type passive continental margins are classified into two end-members: magma-poor (non-volcanic) and magma-rich (volcanic). The differences between them lie in whether a large amount of intrusive and extrusive magmatism from the mantle plume/hotspot is involved in the syn-rift and breakup stages. A magma-rich margin [2] should include the following characteristics: (i) a high-velocity lower crust (HVLC) caused by syn-rift mafic magma underplating; (ii) continental crust intruded by abundant sills and dikes; (iii) a large volume of seaward-dipping reflectors (SDRs) caused by flood basalt eruption or tuffs. All other margins are classified as magma-poor margins.
    Description: We thank the research team project of Guangdong Natural Science Foundation (2017A030312002), IODP-China and South China Sea Deep Project (91628301) and K.C. Wong Education Foundation (GJTD-2018-13) for providing support for the research. This research was also supported by the China National Science and Technology Major Project (2016ZX05026–003), the joint foundation of the National Natural Science Foundation of China and Guangdong province (U1301233), as well as the National Natural Science Foundation of China (41576070 and 41890813).
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    Large Diversity in Nitrogen- and Sulfur-Containing Compatible Solute Profiles in Polar and Temperate Diatoms (2020)
    Oxford University Press
    In:  Integrative and Comparative Biology, 60 (6). pp. 1401-1413.
    Details
    Publication Date: 2022-01-07
    Description: Intense bottom-ice algal blooms, often dominated by diatoms, are an important source of food for grazers, organic matter for export during sea ice melt, and dissolved organic carbon. Sea-ice diatoms have a number of adaptations, including accumulation of compatible solutes, that allows them to inhabit this highly variable environment characterized by extremes in temperature, salinity, and light. In addition to protecting them from extreme conditions, these compounds present a labile, nutrient-rich source of organic matter, and include precursors to climate active compounds (e.g., dimethyl sulfide [DMS]), which are likely regulated with environmental change. Here, intracellular concentrations of 45 metabolites were quantified in three sea-ice diatom species and were compared to two temperate diatom species, with a focus on compatible solutes and free amino acid pools. There was a large diversity of metabolite concentrations between diatoms with no clear pattern identifiable for sea-ice species. Concentrations of some compatible solutes (isethionic acid, homarine) approached 1 M in the sea-ice diatoms, Fragilariopsis cylindrus and Navicula cf. perminuta, but not in the larger sea-ice diatom, Nitzschia lecointei or in the temperate diatom species. The differential use of compatible solutes in sea-ice diatoms suggests different adaptive strategies and highlights which small organic compounds may be important in polar biogeochemical cycles.
    Type: Article , PeerReviewed
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    Determination of diffusion in polycrystalline platinum thin films (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4902-4907 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Grain boundary diffusion of titanium through platinum thin films has been carried out in the temperature range from 200 to 600 °C. Five different platinum/titanium bilayer thicknesses, from 35 to 800 Å Pt, were annealed in 5% O2/95% N2. The accumulation of titanium at the platinum surface layer was measured by x-ray photoelectron spectroscopy (XPS) to determine the grain boundary diffusion coefficient (Db). Diffusivity values were calculated based on two different analysis methods assuming type C kinetics. For Pt layers thicker than 200 Å, the activation energy (Qb) for titanium diffusion was found to be 118±15 kJ/mol (1.22±0.16 eV). For Pt layers thinner than 200 Å, there was a thickness dependence on the diffusion kinetics, resulting in activation energies as low as 20±4 kJ/mol (0.21±0.04 eV). XPS results gave no evidence for any Pt-Ti alloy formation in these layers. The suppression of alloy formation may be attributed to the presence of oxygen at the Pt/Ti interface during layer deposition. The quantitative analysis of titanium interdiffusion in platinum provides valuable information regarding Pt/Ti surface concentrations in thin-film chemical sensors, and for understanding changes in operational characteristics of platinum electrodes. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371458
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    Tensile testing of AlCu thin films on polyimide foils (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4922-4929 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Mechanical properties of sputtered AlCu(0.5 wt %) thin films, 0.2–2.0 μm thick, were determined by tensile testing. For comparison, tensile tests were also performed on bulk samples of the same composition. The films were deposited on thin polyimide foils. They were characterized with respect to the surface, microstructure, residual stress, and concentration of copper and oxygen. Stress-strain curves of the films were obtained by separating the force working on the polyimide foil from that working on the metal-polyimide compound. Young's modulus of the films almost corresponded to the bulk value. Films with a thickness 〉1.5 μm broke by formation of macrocracks while thinner films showed formation of microcracks. The Hall–Petch model, additional strengthening by small grain size, and the role of grain boundary sliding for crack formation are discussed. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371461
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    Effect of pre-amorphization of polycrystalline silicon on agglomeration of TiSi2 in subquarter micron Si lines (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4943-4948 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We investigated the effect of C49-to-C54 conversion behavior on the agglomeration of Ti-silicide fabricated on subquarter micron polycrystalline Si lines by comparing pre-amorphized samples with conventional ones. Pre-amorphization of polycrystalline Si enhances the C49-to-C54 transformation on subquarter micron linewidths, however, it results in the early development of macroscopic grooves during the second rapid thermal annealing. From these results, we suggest the existence of an extra thermal budget during the second rapid thermal annealing of the pre-amorphized samples, which deteriorates the thermal stability of the C54-TiSi2 featured line. It is also shown that C49-to-C54 transformation on a 0.2 μm linewidth in the conventional samples has two kinds of competing factors when postannealing is added. One is the tendency of C54 transformation and the other is agglomeration of C49-TiSi2 grains. During high temperature annealing (〉850 °C), C49-TiSi2 has been agglomerated by a thinning mechanism instead of transformation into the C54 phase. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371523
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    Space charge effects in carrier escape from single quantum well structures (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5109-5115 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Recently published data on the variation with applied bias and temperature of steady-state photoluminescence and photoconductivity from a series of GaAs/AlGaAs single quantum well p-i-n structures are subjected to detailed theoretical analysis, using phenomenological variables introduced in connection with these results. The data are interpreted as revealing the presence in the well of a space charge, which causes band bending and hence indirectly modifies carrier escape lifetimes. It is shown that the thermionic escape of holes can affect the electron tunneling escape lifetime so that the latter displays a thermal activation energy which is quantitatively similar to the hole well depth. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371487
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    Transient electroluminescence of polymer light emitting diodes using electrical pulses (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5116-5130 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Detailed experimental and theoretical analysis of the pulsed excitation of polymer light emitting diodes is presented. We find a set of universal transient features for a variety of device configurations (different polymers/cathodes) which can be reproduced using our phenomenological numerical model. We find that the temporal evolution of the electroluminescence in response to a step voltage pulse is characterized by: (i) a delay followed by; (ii) a fast initial rise at turn-on followed by; (iii) a slow rise (slower by at least one order of magnitude). The large mobility mismatch between holes and electrons in conjugated polymers allows us to separately time resolve the motion of holes and electrons. We suggest a method for extracting mobility values that takes into account the possible field-induced broadening of carrier fronts, and which is found to be compatible with mobilities determined from constant wave measurements. By using appropriate device configurations it is possible to determine the mobilities of both holes and electrons from a single device. Mobilities for holes and electrons are extracted for a poly(p-phenylenevinylene) copolymer and poly(di-octyl fluorene). © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371488
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    Structure and magnetization of arrays of electrodeposited Co wires in anodic alumina (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5141-5145 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We have produced arrays of Co nanowires in anodic porous alumina filters by means of electrodeposition. The structure and magnetization behavior of the wires was investigated with nuclear magnetic resonance (NMR) and magnetization measurements. NMR shows that the wires consist of a mixture of fcc and hcp texture with the (0001) texture of the hcp fraction oriented preferentially perpendicular to the wires. The magnetization direction is determined by a competition of demagnetizing fields and dipole–dipole fields and can be tuned parallel or perpendicular to the wires by changing the length of the wires. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371490
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    Effect of Fe doping in La1−xSrxMnO3 (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5164-5168 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The effects of Fe doping on the magnetic, transport, and magnetoresistance properties are studied for La0.7Sr0.3Mn1−yFeyO3 (y=0–0.18) and La1−xSrxMn0.88Fe0.12O3 (x=0.1–0.50). For increasing y, a peak in the thermal dependence of the resistivity appears and develops at the temperature TPl lower than TC, while the another peak near TC becomes smaller and then disappears. At 78 K the La1−xSrxMn0.88Fe0.12O3 oxides are insulators for x〈0.2 and x〉0.5 and only the lower-temperature metal–insulator transition peak appears for 0.25〈x〈0.45. With increase of x from 0.25, TPl increases, becomes maximum at x=0.4 and then decreases. The temperature dependence of resistivity for the doped samples is quite different from that of the undoped La1−xSrxMnO3 series. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371494
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    Abnormal junction leakage characteristics in titanium-capped cobalt disilicide (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5293-5295 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Abnormal junction leakage characteristics in titanium-capped cobalt disilicide were investigated. The cobalt silicide n+-p junctions, fabricated with different capping layers, were characterized by current–voltage measurements and transmission electron microscopy. The reverse junction leakage currents of Ti-capped 13.5-nm-thick cobalt disilicide (CT) are higher than those of TiN-capped samples. The activation energy of CT at temperatures below 80 °C is 0.41 eV, and its dominant leakage mechanism is consistent with phonon-assisted tunneling. Transmission electron microscopy analysis indicates the existence of island phases and precipitates located at the silicide/Si interface, which are titanium disilicide and CoxTi1−xSi2 phases, as evidenced by energy dispersive spectroscopy. As a result, for the case of CT, the reasons for higher junction leakage currents and their field dependence appear to be the result of the diffusion of Ti atoms into CoSi2 grain boundaries and the resulting formation of TiSi2 and CoxTi1−xSi2 phases, which gives rise to a rougher silicide interface and a close spacing between silicide and the junction. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371513
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    A noninvasive rf probe for the study of ionization and dissociation processes in technological plasmas (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4100-4106 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A swept frequency absorbance plasma diagnostic technique for measurement of self-resonance frequency, intrinsic plasma-tool distributed capacitance, radiative energy loss, and effective plasma capacitance is described. The ex situ probe measures the plasma properties independently of all contributions from the plasma-tool and transmission line connection to the rf supply. The technique employs a swept frequency source and a balanced equal ratio arm bridge to measure the frequency response of the plasma tool after the plasma has been extinguished under plasma conjugate matching conditions. The resonant frequency of the combination of capacitances due to plasma-tool geometry (intrinsic capacitance, Ci) and the matching network (Cm) exhibits a shift from the excitation frequency (13.56 MHz) that is dependent on the effective plasma capacitance. Resonance frequency shift data are given for He, Ne, Ar, O2, N2, and N2O as a function of both pressure (0.02–0.8 mbar) and incident power (50 and 100 W). This technique allows the differentiation between dissociation and ionization processes within the plasma through a simple noninvasive rf measurement. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371334
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    Charge distribution function of plasma dust particles with secondary electron emission (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4118-4123 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The charge distribution function (CDF) of dust particles in low temperature plasmas is obtained as a function of both negative and positive discrete charges Z=(minus-plus)1,(minus-plus)2;,..., and various plasma parameters. Positively charged grains can be formed when secondary electron emission, that is, ionization of the grains by electron impact, is sufficiently important to change their charge. An expression for the CDF is derived from steady-state master equations for the densities of monodispersed, negatively or positively charged dust particles, with Z=(minus-plus)1,(minus-plus)2,... discrete elementary charges and radius R, taking into account single and double elementary charge changes in collisions of the particle with plasma electrons or ions. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371336
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    Role of Ar2+ and Ar2+ ions in a direct current argon glow discharge: A numerical description (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4124-4133 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A two-dimensional model has been developed for calculating the behavior of Ar2+ and Ar2+ ions in a direct current argon glow discharge, by the use of balance equations describing the various production and loss processes for these species, as well as their transport by diffusion and migration. These balance equations are coupled to the equations for the Ar+ ions and electrons and solved simultaneously with Poisson's equation, to obtain a self-consistent description of the charged particles behavior and the electrical characteristics in the glow discharge. Moreover, this model is combined with the other models that we have developed previously for the Ar atoms in various excited levels and the Cu atomic and ionic species, to obtain an overall description of the direct current argon glow discharge. The model is applied to typical conditions used for glow discharge mass spectrometry (pressure of 50–100 Pa, voltage of 600–1400 V, and current of 0.4–15 mA). Typical calculation results include the densities and fluxes of these ionic species, as well as the relative contributions of their production and loss processes. The Ar2+ ions are almost exclusively formed by two-electron ionization from Ar0 atoms, and they become primarily lost by diffusion and subsequent recombination at the cell walls. The Ar2+ ions are mainly created by Hornbeck–Molnar and metastable-metastable associative ionization, whereas atom to molecule conversion seems to play only a minor role at the discharge conditions under study. Loss of these Ar2+ ions is caused primarily by diffusion and recombination at the cell walls, but dissociative recombination in the plasma plays also a significant role. We found that the ratios of Ar2+/Ar+ and Ar2+/Ar+ ion densities and fluxes were in the order of 1%–10%, which is in good agreement with experimental observations. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371337
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    Sensitivity of near-edge x-ray absorption fine structure spectroscopy to ion beam damage in diamond films (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4192-4198 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: In the present work, we study the sensitivity of the near-edge x-ray absorption fine structure (NEXAFS) spectroscopy to ion induced defects in polycrystalline diamond films. The ion bombardment of hydrogenated films is performed using 30 keV Xe+ ions at room temperature for doses ranging from 2×1013 ions/cm2, producing local point defects, to 2×1015 ions/cm2, which results in almost complete amorphization of the diamond surface. Auger electron spectroscopy measurements are not sensitive to the modifications induced by the lowest implantation dose. Whereas partial electron yield (PEY) NEXAFS measurements, applied in surface and bulk-sensitive modes, using 35, 15, and 8 eV secondary electrons, respectively, reveals the formation of a defective structure and gradual deterioration of diamond in the near-surface region. From PEY NEXAFS spectra measured using 15 eV secondary electrons, the position of C(1s) binding energy is measured. The x-ray photoelectron spectra of the samples were measured using an incident photon energy of 450 eV. It is found that the C(1s) binding energy in the implanted samples has a positive shift of 0.6–1 eV, which is indicative of transformation of diamond to disordered carbon. The high sensitivity of NEXAFS spectroscopy to point defects induced by the low dose ion implantation was reflected by a sharp reduction in the intensity of the diamond core exciton peak and by the appearance of a new spectral feature in the pre-edge region, below the C(1s)−π* transition. Analysis of the NEXAFS spectra of ion implanted films is performed on the basis of the electronic structure of diamond. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371346
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    Nematic polar anchoring strength measured by electric field techniques (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4199-4213 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We analyze the high-electric-field technique designed by Yokoyama and van Sprang [J. Appl. Phys. 57, 4520 (1985)] to determine the polar anchoring coefficient W of a nematic liquid crystal-solid substrate. The technique implies simultaneous measurement of the optical phase retardation and capacitance as functions of the applied voltage well above the threshold of the Frederiks transition. We develop a generalized model that allows for the determination of W for tilted director orientation. Furthermore, the model results in a new high-field technique, (referred to as the RV technique), based on the measurement of retardation versus applied voltage. W is determined from a simple linear fit over a well-specified voltage window. No capacitance measurements are needed to determine W when the dielectric constants of the liquid crystal are known. We analyze the validity of the Yokoyama–van Sprang (YvS) and RV techniques and show that experimental data in real cells often do not follow the theoretical curves. The reason is that the director distribution is inhomogeneous in the plane of the bounding plates, while the theory assumes that the director is not distorted in this plane. This discrepancy can greatly modify the fitted value of 1/W, and even change its sign, thus making the determination of W meaningless. We suggest a protocol that allows one to check if the cell can be used to measure W by the YvS or RV techniques. The protocol establishes new criteria that were absent in the original YvS procedure. The results are compared with other data on W, obtained by a threshold-field technique for the same nematic-substrate pair. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371347
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    Gettering of Cu by microcavities in bonded/ion-cut silicon-on-insulator and separation by implantation of oxygen (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4214-4219 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Microcavities formed by H+ and He+ implantation and subsequent annealing are effective gettering sites for transition metal impurities in silicon. However, gettering in silicon-on-insulator (SOI) materials is quite different from that in silicon. In this work, we investigate the gettering of Cu to these microcavities in silicon, separation by implantation of oxygen (SIMOX) and bonded/ion-cut SOI wafers. Our data indicate that He+ implantation in the high dose regime (0.2–1×1017 cm−2) creates a wide band of microcavities near the projected range without causing blistering on the sample surface. On the other hand, the implantation dose of H+ needed for stable microcavity formation is relatively narrow (3–4×1016 cm−2), and this value is related to the projected range. The different behavior of H and He in silicon is discussed and He implantation is more desirable with regard to impurity gettering. Cu is implanted into the surface region of the Si and SOI samples, followed by annealing at 700 and 1000 °C. Our results indicate that the microcavities can effectively getter a high dose of Cu (2.5×1015 cm−2) at 700 °C in bulk Si wafer, but higher temperature annealing is needed for the effective gettering in SIMOX. Gettering of Cu by the intrinsic defects at or beneath the buried oxide interface of the SIMOX is observed at 700 °C, but no trapped impurities are observed after 1000 °C annealing in the samples in the presence of microcavities. Almost all of the 1×1014 cm−2 Cu implanted into the Si overlayer of the bonded/ion-cut SOI diffuse through the thermally grown oxide layer and are captured by the cavities in the substrate after annealing at 1000 °C. © 1999 American Institute of Physics.
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    Viscoelastic crack healing and adhesion (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4232-4241 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Closing cracks in viscoelastic materials are analyzed using a cohesive zone model. The analysis is relevant to the bonding of surfaces of viscoelastic materials, and in particular to the Johnson–Kendall–Roberts (JKR) experiment. A crack bonding theory due to Schapery is extended to include the case of the standard linear solid material, and some consequences of this material's finite long time compliance are illustrated. The stress field behind a steadily closing crack in a standard linear solid is also investigated in detail. Finally, a method for applying Schapery's crack bonding theory to the analysis of a JKR-type experiment involving viscoelastic cylinders is given explicitly. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371351
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    Investigation of nanostructures in ordinary Portland cement through positron annihilation lifetime spectroscopy (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4225-4231 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Early hydration (up to four weeks) of five ordinary Portland cement pastes with different water-to-cement ratios (0.3, 0.4, 0.5, 0.6, and 1.0 wt) was investigated through positron annihilation lifetime spectroscopy. Measurements were performed at four different hydration times (1 day and 1, 2, and 4 weeks) and compared with results obtained from thermogravimetric analyses. Deconvolution of positron spectra allowed us to separate orthopositronium annihilations in the evacuated gel pores from those in the pores containing water, and therefore, to monitor the pores' evolution with aging time. It is found that the concentration of gel pores increases with aging time, as well as by increasing the content of water in the paste; on the other hand, the typical sizes of the pores do not show significant variations, either with aging time or with the water-to-cement ratio.© 1999 American Institute of Physics.
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    High-speed spin-polarized intersubband lasers (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4734-4739 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Spin-polarized intersubband lasers based on optically pumped type-II antimonide quantum wells in a magnetic field are proposed. Complete discretization of the electron energy spectrum is predicted to extend the electron lifetime considerably. Continuous-wave room-temperature operation is projected for both interband and intersubband pumping configurations lasing at λ=16–24 μm. Furthermore, the parasitic capacitances associated with electrical injection are eliminated, and the large differential gain and fast intrinsic time scale should give modulation bandwidths in excess of 100 GHz. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371437
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    Ion behavior and gas mixing in electron cyclotron resonance plasmas as sources of highly charged ions (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4772-4779 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This article deals with ion behavior in small open-ended magnetic devices, the electron cyclotron resonance ion sources (ECRIS) that were developed for multicharged ion production. The ECRIS are basically ECR-heated plasma confinement machines with hot electrons and cold ions. The main parameters of the ion population in ECRIS plasmas are successively analyzed: temperature, collisions, losses, confinement times, followed by the gas mixing effect, a specific technique to improve the performance as an ion source. A series of experiments is described for the systematic analysis of this effect. It is experimentally shown that high charge state optimization by gas mixing results from an ion confinement time improvement due to ion cooling, and relies on a compromise between three criteria, ion losses, mass effect, and ionization rates. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371442
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    Effect of a magnetic field on the plasma plume from Hall thrusters (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4786-4791 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: An axial profile of the quasineutral plasma jet exhaust from a Hall thruster is studied. The plasma jet expansion is modeled using the sourceless steady-state hydrodynamic equations. It is considered that the plasma jet has a conical shape with a half angle of about 40°. The magnetic field surrounding the Hall thruster exit is included in the calculation. It is found that a magnetic field may significantly affect the axial profile of the plasma potential. For instance, in the case of zero magnetic field, the plasma potential is about −10 V at 1 m from the thruster exit, while in the case of a 0.1 T magnetic field, the plasma has a potential of about +25 V. Results predicted by the model are found to be in good agreement with experimental data for three different Hall thruster designs. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371444
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    Indium-modified growth kinetics of cubic and hexagonal GaN in molecular beam epitaxy (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4322-4325 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The kinetics changes in the growth of GaN induced by the presence of In segregated on the surface have been investigated in situ by using reflection high energy electron diffraction intensity oscillations. Two types of surfaces have been studied, namely, Ga-polar (0001) wurtzite, and (001) zinc blende. It has been found that In influenced both Ga and N surface kinetics, leading to a change in the growth rate associated with a change in the amount of Ga and N effectively available for the GaN growth. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371364
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    Investigation of nitric oxide and Ar annealed SiO2/SiC interfaces by x-ray photoelectron spectroscopy (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4316-4321 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Silicon dioxide (SiO2)/silicon carbide (SiC) structures annealed in nitric oxide (NO) and argon gas ambiences were investigated using x-ray photoelectron spectroscopy (XPS). The XPS depth profile analysis shows a nitrogen pileup of 1.6 at. % close to the NO annealed SiO2/SiC interface. The results of Si 2p, C 1s, O 1s, and N 1s core-level spectra are presented in detail to demonstrate significant differences between NO and Ar annealed samples. A SiO2/SiC interface with complex intermediate oxide/carbon states is found in the case of the Ar annealed sample, while the NO annealed SiO2/SiC interface is free of these compounds. The Si 2p spectrum of the Ar annealed sample is much broader than that of the NO annealed sample and can be fitted with three peaks compared with the two peaks in the NO annealed sample, indicating a more complex interface in the Ar annealed sample. Also the O 1s spectrum of the NO annealed samples is narrow and symmetrical and can be fitted with only one peak whereas that of the Ar annealed sample is broad and asymmetrical and is fitted with two peaks. It is evident that the Ar annealed sample contains some structural defects at the interface, which have been removed from the interface by NO annealing as shown by O 1s spectra. The C 1s spectra at the interface reveal the subtle difference between NO and Ar annealed samples. An additional peak representing the interface oxide/carbon species is observed in the Ar annealed sample. At the interface, the N 1s spectrum is symmetrical and can be fitted with one peak, representing the strong Si(Triple Bond)N bond. However, the N 1s and C 1s XPS spectra acquired in the bulk of the dielectric showed not only the Si(Triple Bond)N bond but also a trace amount of the N–C bond. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371363
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    Nondestructive evaluation of channel carrier concentration in modulation-doped InAlAs/InGaAs field-effect transistor structures by room-temperature photoluminescence (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4333-4340 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The sheet carrier concentration (Ns) of channel layers in modulation-doped InAlAs/InGaAs heterostructure field-effect transistor (HFET) structures with n+InGaAs contact layers has been successfully and nondestructively determined using the room-temperature photoluminescence (PL) method. It is found that the spectral energy width between the maximum position of the main PL peak around 0.8 eV and the half-maximum position on the higher energy side has a good positive linear correlation with the Ns of the channel measured by the van der Pauw method. The scattering of the data is less than ±3×1011 cm−2. The determination of Ns is effective even if the HFET structures have not only n+InGaAs contact layers but also layers for InAlAs Schottky level-shift diodes. From a comparison with low-temperature PL spectra, the main PL peak is attributed to the e2h transition in the quantum well of the channel. It is considered that the slope of the peak stretches further to the high energy as the Fermi energy in the channel become higher, i.e., as the Ns becomes larger. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371366
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    Photoluminescence and Zeeman effect in chromium-doped 4H and 6H SiC (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4348-4353 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Photoluminescence (PL) and Zeeman effect measurements in near-infrared luminescence bands in Cr-doped 4H and 6H SiC are presented. The PL spectrum consists of two no-phonon lines (NPLs) at 1.1583 and 1.1898 eV in 4H SiC and three NPLs at 1.1556, 1.1797, and 1.1886 eV in 6H SiC. The observed Zeeman splittings and temperature dependence studies reveal the spin triplet of the ground state and the orbital doublet structure of the excited state of the Cr-related center. All the triplets have almost isotropic g values close to 2 with trigonal symmetry and small zero-field splitting values D. In contrast, the effective g values of the excited state of the center are very anisotropic with g(parallel) in the range of 0.22–0.64 and g⊥=0 for different NPLs in both polytypes. Based on the Zeeman results, the PL is attributed to the internal transition 1E(D)→3A2(F) within the d shell of a substitutional, neutral chromium (Cr4+) in the 3d2 electronic configuration. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371368
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    Synchrotron characterization of deep depletion epitaxial GaAs detectors (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4341-4347 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We report the results of a series of synchrotron characterizations of two epitaxial GaAs detectors of active areas 2.22 mm2 and thicknesses 40 and 400 μm. In spite of an order of magnitude difference in depletion depths, the detectors were found to have comparable performances at ∼−40 °C, with energy resolutions of ∼1 keV full width at half maximum (FWHM) at 7 keV rising to ∼2 keV FWHM at 200 keV and noise floors in the range of 1–1.5 keV. At the lower energies, the energy resolution was dominated by leakage current and electromagnetic pickup. At the highest energies, however, the measured resolutions appear to approach the expected Fano limit; e.g., ∼950 eV at 200 keV. Both detectors were remarkably linear, with average rms nonlinearities of 0.2% over the energy range of 10–60 keV. By raster scanning the active areas with 20×20 μm2 monoenergetic photon beams, it was found that the nonuniformity in the spatial response of both detectors was less than 1% and independent of energy. The material used to fabricate the detector is extremely pure. For example, low temperature photoluminescence measurements indicate that the density of the As antisite defect (EL2) is of the order of 1012 cm−3, which is ∼2–3 orders of magnitude lower than that generally reported. This indirect measurement of material purity is confirmed by Monte Carlo simulations of the detector x-ray response, which show that in order to reproduce the observed energy-loss spectra, electron and hole trapping cross-section/density products must be (very-much-less-than)1 cm−1. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371367
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    Optical characterizations of CuInSe2 epitaxial layers grown by molecular beam epitaxy (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4354-4359 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: CuInSe2 (CIS) films with Cu/In ratios of γ=0.82–1.79 have been grown on a GaAs (001) substrate by molecular beam epitaxy. Piezoelectric photoacoustic (PPA) measurements were carried out from liquid helium to room temperature to investigate nonradiative carrier recombination processes in comparison with photoluminescence (PL) measurements which directly detected radiative carrier recombination processes. Three PPA signal peaks which corresponded to band gap energies of the CIS (AB and C bands) and the GaAs substrate, were clearly obtained between liquid helium and room temperatures. A free-exciton emission line was observed up to 200 K in the PL spectra. Two additional peaks on intrinsic defects which are Cu vacancy (VCu) and interstitial In (Ini) were observed in the In-rich CIS samples. The PPA measurements were useful in investigating the defect levels and the band gap energy in the CIS/GaAs thin films. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371369
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    Electroabsorption studies on quasi-three-dimensional and quasi-two-dimensional excitons in (Zn,Cd)Se/Zn(S,Se) structures (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4360-4364 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The electro-optical properties of (Zn,Cd)Se/Zn(S,Se) quantum well structures grown on GaAs substrates have been studied with differential electroabsorption spectroscopy at room temperature and compared to model calculations. (Zn,Cd)Se wells of 20, 10, and 4×5 nm are investigated, corresponding to well widths of four, two, and one times the exciton Bohr radius in this material system, respectively. We observe the quantum confined Stark effect for the 4×5 nm sample and find a Stark shift of 18 meV in the heavy-hole exciton peak for an electric field change from 82 to 175 kV/cm. In contrast, the 10 nm sample shows a rather weak and more Franz–Keldysh-like signal. We show that the 20-nm-thick quantum-well sample behaves like bulk material, i.e., the electro-absorption signal is well described by Franz–Keldysh oscillations. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371370
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    Interaction between guided optical waves and magnetostatic waves in bismuth-doped yttrium–iron–garnet waveguide under inclined magnetic fields (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4365-4368 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The noncollinear interaction between guided optical waves and magnetostatic waves under inclined bias magnetic field is studied in detail. The diffraction efficiency (DE) and the mode-conversion efficiency (MCE) of guided optical waves with magnetostatic forward volume waves in the bismuth-doped yttrium–iron–garnet (Bi-doped YIG) waveguide are calculated numerically. The calculation results indicate that the DE and the MCE are different in physical conception and the DE is not equal to the MCE in magnitude under inclined bias magnetic field. The DE may be greatly increased by using an appropriately inclined bias magnetic field, which has been experimentally confirmed in a pure YIG waveguide. By using an inclined bias magnetic field and the Bi-doped YIG waveguide, under the phase-matching conditions, the maximum DE can come up to 79.5% or more. © 1999 American Institute of Physics.
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    Raman study of the topology of InAs/GaAs self-assembled quantum dots (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4387-4389 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The topology of self-assembled InAs/GaAs quantum dots was studied by resonant Raman scattering caused by the interface modes localized near the edges of the dots. Evidences were found that on both sides of the InAs layer containing the dots, their topologies show some resemblances. In addition, in the multilayered systems the evidence of the coalescence of the dots (which form vertical columns) in neighbor layers separated by the distance smaller than 25 monolayers was obtained. © 1999 American Institute of Physics.
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    Giant magnetic viscosity in SmCo5−xCux alloys (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5157-5163 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Hysteresis loops in SmCo5−xCux as-cast and annealed magnets (1〈x≤3) were measured at room temperature using a pulsed-field magnetometer and a static vibrating sample magnetometer. At field sweeps between 2 and 17 (GA/m)/s a giant—in this field range nearly constant—magnetic viscosity Sv was obtained. The viscosity is approximately proportional to the Cu concentration and to the coercive field. A heat treatment at 1273 K for three weeks changes the microstructure and enhances strongly the intensity and the time dependence of the coercivity. The decay of the inverse of the coercive field Hc with time follows a simple ln(t) relation between 10−5 and 10 s. Data analysis allows a density of stacking faults N to be extracted for each sample. Sv (and Hc) increases with N which increases with x. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371493
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    Angular dependence of exchange anisotropy in Ni81Fe19/CrMnPtx bilayers (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5169-5174 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We have investigated the unidirectional exchange anisotropy between a ferromagnetic (FM) Ni81Fe19 film and a disordered antiferromagnetic (AF) CrMnPtx (x=3, 6, or 9) film. The angular dependence of the exchange coupling in these FM/AF bilayers has been measured. We show that the complex angular dependence of this exchange coupling can be understood by a simple Stoner–Wohlfarth model involving only a uniaxial anisotropy and a unidirectional exchange coupling. Numerical results are in excellent agreement with the experimental data. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371495
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    1/f noise in n-channel metal-oxide-semiconductor field-effect transistors under different hot-carrier stresses (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5203-5206 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Degradation mechanisms contributing to increased 1/f noise of n-channel metaloxide-semiconductor field-effect transistors (n-MOSFETs) after different hot-carrier stresses are investigated. It is demonstrated that for any hot-carrier stress, the stress-induced enhancement of 1/f noise is mainly attributed to increased carrier-number fluctuation arising from created oxide traps, while enhanced surface-mobility fluctuation associated with electron trapping at preexisting and generated fast interface states and near-interface oxide traps is also responsible under maximum substrate- and gate-current stresses. Besides thermal-oxide n-MOSFETs, nitrided-oxide devices are also used to further support the above analysis. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371501
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    Double-barrier THz source based on electrical excitation of electrons and holes (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5215-5231 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A detailed dynamical analysis of an all solid-state THz source is given. This is based on the polarization-induced autonomous oscillation in resonant tunneling heterostructure with staggered band-gap alignment. The physical model consists of the following processes: (a) Generation by Zener tunneling of holes trapped in the barrier and electrons drifting in the depletion layer of the drain, whose rate decreases with the polarization between the barrier and quantum well. (b) Stimulated generation of barrier-well polarization. (c) Nonradiative decay of barrier-well polarization through barrier-hole recombination and quantum-well electron discharge. It is shown that a limit cycle oscillation of the barrier-well polarization and trapped-hole charge in the barrier can occur which induce THz oscillations in the resonant tunneling current across the device. The time-averaged results agree with the measured current–voltage characteristic of AlGaSb/InAs/AlGaSb staggered band-gap double-barrier structure. In particular, the measured smaller current offset at forward bias compared to that of reverse bias in the current–voltage hysteresis loop is predicted by our physical model and limit cycle analysis. Thus, we have experimental evidence indicating the correctness of our approach and the promising potential of this device as a novel all solid-state THz source. © 1999 American Institute of Physics.
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    Van der Waals and capacitive forces in atomic force microscopies (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5245-5248 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: In this article we show that in the atomic force microscopy experiments performed on a metallic surface, there is always a long range electrostatic force in addition to the van der Waals forces. This capacitive force is due to the contact potential between the tip and the surface and exists even without external applied potential. We have calculated this capacitive force for a real geometry of the tip–sample system and compared it to the van der Waals force calculated for the same geometry. We conclude that the electrostatic force is always dominant for a tip–surface distance larger than half of the tip radius of curvature. © 1999 American Institute of Physics.
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    URL: http://dx.doi.org/10.1063/1.371506
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    Adsorption site determination of light elements on heavy substrates by low-energy ion channeling (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5256-5262 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Ion channeling in the low-keV energy range is demonstrated by means of the technique of time-of-flight scattering and recoiling spectrometry. The predictions of the Lindhard string model of ion channeling are compared with the experimental findings. Qualitative agreement was obtained between the experimentally measured critical angles and the predictions of the model. The technique of low-energy ion channeling is shown to be capable of quantitatively probing the positions of light elements on heavy substrates with analysis by simple geometrical constructs. Classical ion trajectory simulations using the scattering and recoiling imaging code were used to observe the details of the ion trajectories. Quantitative analysis of the Pt(111)-(1×1)-H surface using 5 keV Ne+ shows that the hydrogen atoms preferentially populate the threefold fcc sites with a height of 0.9±0.1 Å above the first-layer Pt atoms and a corresponding Pt–H bond length of 1.9±0.1 Å. © 1999 American Institute of Physics.
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    Effect of annealing on Ge-doped SiO2 thin films (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5270-5273 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Thermal annealing effects on optical and structural properties of Ge-doped SiO2 thin films prepared by the chemical vapor deposition and flame hydrolysis deposition methods were investigated. The thin film prepared by the former method showed inhomogeneous Ge distribution, and Ge oxygen-deficient centers were observed. When it was thermally annealed at temperatures higher than 800 °C, the Ge distribution became uniform. The concentration of oxygen deficient centers was found to decrease with the thermal annealing in an O2 atmosphere, while it increased with the thermal annealing at 1000 °C in N2. This suggests that improvement of the film quality can be achieved by thermal annealing. On the other hand, neither inhomogeneity of Ge distribution nor the appearance of oxygen deficient centers was observed in the film prepared by the latter method, and its film quality was scarcely affected by the thermal annealing. © 1999 American Institute of Physics.
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    Numerical and experimental studies on synthesis of ultrafine nanosize powders of AlN by ion beam evaporation (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5279-5285 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Synthesis of ultrafine nanosize powders by ion beam evaporation (IBE) has been studied numerically and experimentally. Theoretical models have been developed, which involve such physical processes as beam-target interaction, plasma expansion, and the synthesis of powders. The macroscopic properties of the ultrafine powders have been predicted. As an application of our models, the macroscopic properties of AlN powders synthesized by IBE with an AlN target have been predicted. The energy density, pulse width, and spot size of the ion beam are 20 J/cm2, 70 ns, and 1 cm2, respectively. The main results have shown that the particle size distribution is log normal and that 70% of all particles exist between 20 and 40 nm. The average diameter and the specific surface area are ∼30 nm and ∼50 m2/g, respectively. Experimentally, the ultrafine AlN powders have been successfully synthesized by IBE, which has been verified by x-ray diffraction and transmission electron diffraction. Furthermore, particle size distributions have been obtained by transmission electron microscopy. The experimental results are found to be in a reasonable agreement with the numerical studies. © 1999 American Institute of Physics.
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    Response to "Comment on ‘Monte Carlo simulation of the laser-induced plasma plume expansion under vacuum: Comparison with experiments' " [J. Appl. Phys. 86, 4709 (1999)] (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4711-4712 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: This response recalls the bases of the Monte Carlo methods of gas flow simulations. Basic points and explicit parameters used in both the DSMC method and the method of random trajectories are underlined. Some clarifications are made on the confusion made by the author of the comment on this subject. The justification of the validity of the method is recalled, as already made in the original article. © 1999 American Institute of Physics.
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    Broad band p-Ge optical amplifier of terahertz radiation (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3512-3515 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A solid state broad band amplifier of terahertz radiation (1.5–4 THz), based on intersubband transitions of hot holes in p-Ge is demonstrated. The gain is investigated as a function of applied magnetic and electric fields by transmission measurements using a laser system with two p-Ge active crystals, when one operates as an oscillator and one as an amplifier. A peak gain higher than usually reported for p-Ge lasers has been achieved using time separated excitation of the oscillator and amplifier. Distinct differences in gain dependence on applied fields are noted between low- and high-frequency modes of p-Ge laser operation. © 1999 American Institute of Physics.
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    Lasers in dense gases pumped by low-energy electron beams (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3525-3529 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The use of low-energy ((approximate)15 keV) electron beams for pumping laser systems in dense gases with high specific power deposition is described. Thin (300 nm) SiNx ceramic foils used as entrance window in a transverse geometry for the electron beam allows pressure differentials of several atmospheres with low percentage energy loss in transmission. The 1.73 μm XeI (5d[3/2]1–6p[5/2]2) infrared laser was used for a first demonstration of this concept. The laser operated between 130 and 650 mbar. A threshold pumping power of 5.3 W and a maximum output power of 6 mW were observed. The system can be scaled to high pumping power ((approximate)MW/cm3) and short wavelength. © 1999 American Institute of Physics.
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    Growth of particles in cluster-size range in low pressure and low power SiH4 rf discharges (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3543-3549 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Growth processes of particles in a cluster-size range below a few nm in size in low pressure and low power SiH4 rf discharges are studied using the new method, in which the threshold photoemission method is coupled with the microwave interferometry, for measurements of their size and density. The density of particles is above 1010 cm−3 and much exceeds that of positive ions, the result of which shows that most of them are neutral. The particles grow mainly around the plasma/sheath boundary near the powered electrode and their size growth rate is 3.4–4.4 nm/s, being much higher than a film growth rate of 0.064–0.12 nm/s. These features strongly indicate that their growth is due to deposition of polymerized species, originated from short lifetime SiH2 radicals, on them, while coagulation between particles becomes appreciable after a time when their density reaches about 1011 cm−3. Moreover, the pulse modulation of rf discharge is found to be effective in reducing the density of cluster-size particles. The reduction can be explained by a model taking account of diffusion of the polymerized species through the radical production region, where the particles nucleate and grow. © 1999 American Institute of Physics.
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    Molybdenum substitutional doping and its effects on phase transition properties in single crystalline vanadium dioxide thin film (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 5311-5313 
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    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Molybdenum (Mo) doped vanadium dioxide thin films were synthesized using a Mo striped vanadium (V) target during pulsed laser ablation process. The film structure was characterized by high resolution x-ray diffraction, x-ray rocking curve and Rutherford backscattering/channeling measurements. The results show that the full width at half magnitude of the x-ray rocking curve is as narrow as 0.0074°, comparable to that of the (0001) sapphire substrate, 0.0042°, in this study. The ratio of the aligned-to-random backscattered yield reaches 5%, implying that the growth is that of the single crystalline epitaxy. The result of angular scans for both V and Mo atomic channelings reveals that Mo atoms successfully take sites of the V sublattice as a substitutional dopant. It has been noted that the degradation of the phase transition properties of the film upon doping is closely related to the conductivity in the semiconductor phase. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371519
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    Simulation of the dynamics of twisted nematic devices including flow (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4091-4095 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We have modeled the switching behavior of a twisted nematic cell using the one-dimensional Ericksen–Leslie equations of nematodynamics. We compare the modeling results with experimental data on transmission versus time. Excellent agreement between experiment and model is achieved at all voltages and viewing angles. To achieve this agreement, only two viscosity parameters are required; these are combinations of the Leslie viscosity coefficients, namely, α3−α2 (the rotational viscosity) and α4+α5. A fast and stable adaptive numerical algorithm, based on an effective viscosity parameter, is developed for solving the equations of motion. The viscosity parameters obtained from fitting the flow experiments are in good agreement with those obtained from dynamic light-scattering measurements. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371333
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  • 92
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    Transparent stacked organic light emitting devices. II. Device performance and applications to displays (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4076-4084 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Vertical stacking of organic light emitting devices (OLEDs) that emit the three primary colors is shown to be a means for achieving efficient and bright full-color displays. In Paper I, we addressed stacked OLED (SOLED) design and fabrication principles to optimize emission colors, operating voltage, and efficiency. Here, we present results on two different (metal-containing and metal-free cathode) SOLED structures that exhibit performance suitable for many full-color display applications. The operating voltages at 10 mA/cm2 (corresponding to video display brightnesses) are 6.8, 8.5, and 12.1 V for the red (R), green (G), and blue (B) elements of the metal-containing SOLED, respectively. The respective subpixel luminous efficiencies are 0.53, 1.44, and 1.52 cd/A, and the Commission Internationale de L'Éclairage (CIE) chromaticity coordinates are (0.72, 0.28), (0.42, 0.56), and (0.20, 0.22). In the high transparency metal-free SOLED, an insulating layer was inserted between the two upper subpixels to allow for independent grounding of all color emitters in the stack. At operating voltages of 12–14 V, video display brightnesses were achieved with luminous efficiencies of 0.35, 1.36, and 1.05 cd/A for the R, G, and B subpixels, respectively. The respective CIE coordinates for R, G, and B emissions are (0.72, 0.28), (0.26, 0.63), and (0.17, 0.28) in the normal viewing direction, shifting inperceptibly as the viewing angle is increased to as large as 60°. Finally, we discuss addressing schemes of SOLED displays, and compare them with other strategies for achieving full-color, OLED-based displays. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371428
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  • 93
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    Fast polarization switching with memory effect in a vertical cavity surface emitting laser subject to modulated optical injection (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4096-4099 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The polarization state of a vertical cavity surface emitting laser (VCSEL) output was driven by means of optical injection from another VCSEL. The bistability inherent to polarization locking allowed us to generate a memory effect. The control parameter was the modulated bias current of the maser laser and effects were shown to exist at frequencies up to 1 GHz. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371429
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  • 94
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    High-frequency modulation of an electron beam produced by a plasma cathode (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4107-4117 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We present a detailed study of the recently discovered modulation at frequencies of hundreds of MHz of an electron beam produced by a plasma cathode. The plasma cathode consists of a ferroelectric disk sample [BaTiO3 or Pb(Zr, Ti)O3] that is placed in a cylindrical metal box having an output window covered by a grid. The plasma is prepared by an incomplete discharge that was ignited by a few kV driving pulse applied across the ferroelectric disk. It was shown that the current modulation appears only when the driving pulse is applied to the front gridded electrode of the ferroelectric sample and the solid rear electrode is grounded. The modulation spectrum is quite narrow (≤3%), with harmonics at frequencies up to a few GHz. The basic frequency of modulation was found to be dependent on the length of the feed cable to the sample. Investigation of the plasma and the beam modulation properties and their dependence on the experimental parameters is presented. The results indicate the formation of a plasma at the vicinity of the front electrode of the ferroelectric sample during the modulation. The results are discussed within the frame of electrons oscillating in the potential well created by the positively charged plasma having feedback coupling with the input cable. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371335
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  • 95
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    Room-temperature vacancy migration in crystalline Si from an ion-implanted surface layer (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4861-4864 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Migration of vacancies in crystalline, n-type silicon at room temperature from Ge+-implanted (150 keV, 5×109–1×1011 cm−2) surface layers was studied by tracing the presence of P–V pairs (E centers) in the underlying layer using deep level transient spectroscopy (DLTS). Under the conditions we have examined, the vacancies migrate to a maximum depth of about 1 μm and at least one vacancy per implanted Ge ion migrates into the silicon crystal. The annealing of the E centers is accompanied, in an almost one-to-one fashion, by the appearance of a new DLTS line corresponding to a level at EC−Et(approximate)0.15 eV that has donor character. It is argued that the center associated with this line is most probably the P2–V complex; it anneals at about 550 K. A lower limit of the RT-diffusion coefficient of the doubly charged, negative vacancy is estimated to be 4×10−11 cm2/s. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371453
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  • 96
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    Site selectively excited luminescence and energy transfer of X1-Y2SiO5:Eu at nanometric scale (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3751-3757 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Two different types of structure called X1 and X2 are existing in Y2SiO5 at normal conditions. In X1 type, Y3+ ions occupy two sites where they are surrounded respectively by nine and seven oxygen ions, while in X2 structure, only six and seven oxygen ions are involved. Nanometric scale X1-Y2SiO5 crystals were prepared by sol-gel method with particle size around 50 nm. Site selective excitation at low temperature has shown four different luminescent centers. Two of them belong to Eu3+ embedded in X1-Y2SiO5, the other two are attributed to Y2O3:Eu phase and to a particular site on the surface. The occurrence of the latter site may be related to the nanometric size of the sample. A pronounced excitation energy transfer from site 2 to site 1 was also observed on excitation spectra. The energy transfer rate increases rapidly with increasing Eu3+ concentration and for x=0.7 in Y2−xSiO5:Eux, no fluorescence takes place in site 2 at 15 K. The lifetimes of the 5D0 levels of Eu3+ in the two sites were measured as a function of Eu3+ concentration. The results have shown that the lifetime of the 5D0 level of Eu3+ in site 2 decreases with increasing Eu3+ concentration. The energy transfer rate dependence upon temperature was studied in detail and compared to a theoretical simulation. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371246
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  • 97
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    Quantized current jumps in silicon photoconductors at room temperature (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3787-3791 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We report on the observation of quantized jumps due to single-carrier trapping and detrapping at defect states in silicon photoconductors of 103 μm3 in volume. A specifically designed electrical test structure in a low-doped (2×1014 cm−3) silicon crystal was fabricated. It consists in four substrate resistances connected in a Wheatstone bridge. After the exposure to light, the bridge offset voltage recovers its equilibrium value with steps of 5–10 μV, corresponding to the emission or capture of a single carrier. Such structures also display random telegraph signals in the dark, with steps of similar amplitude. This behavior is observed with structures processed on Czochralski-grown substrates and not with those processed on float-zone substrates. Simple calculations based on quantized free carrier concentration variations corroborate the above measurements. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371288
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  • 98
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    Linear electroabsorption in semi-insulating GaAs/AlGaAs asymmetric double quantum wells (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3822-3825 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: Electroabsorption has been investigated in semi-insulating asymmetric GaAs/AlGaAs double quantum wells presenting high linear Stark responses, adequate for photorefractive applications. We have used the envelope function approximation to calculate the linear Stark shifts of the energy levels and select a suitable structure for the experimental study. The experimental data indicate that the response to the applied field critically depends on a complicated interplay of effects that compete or cooperate to suppress or enhance the electroabsorption. For positive field polarity, the competing contributions of the overlapping e1–hh1 and e1–hh2 transitions partially cancel the electroabsorption despite large linear Stark shifts. On the other hand, small negative fields induce large electroabsorption because the Stark shifts of the two transitions have opposite signs. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371293
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  • 99
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    Simulation studies of persistent photoconductivity and filamentary conduction in opposed contact semi-insulating GaAs high power switches (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 3833-3843 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A self-consistent, two-dimensional, time-dependent, drift-diffusion model is developed to simulate the response of high power photoconductive switches. Effects of spatial inhomogeneities associated with the contact barrier potential are incorporated and shown to foster filamentation. Results of the dark current match the available experiment data. Persistent photoconductivity is shown to arise at a high bias even under the conditions of spatial uniformity. Filamentary currents require an inherent spatial inhomogeneity, and are more likely to occur for low optical excitation. Under strong uniform illumination, the spatial nonuniformities were quenched as a result of a polarization-induced collapse in the internal fields. However, strong electric fields resulting at the contacts create a bipolar plasma, and hence, a virtual "double injection." © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371295
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  • 100
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    Effect of an electric field on the exciton linewidth due to scattering of excitons by ionized impurities in semiconducting quantum well structures (1999)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 86 (1999), S. 4477-4482 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: We have calculated the effect of an electric field applied along the direction of carrier confinement on the exciton linewidth due to the scattering of excitons by ionized impurities in semiconducting quantum well structures. The contributions to the linewidth due to the elastic and inelastic scattering of the excitons by the ionized impurities have both been taken into account. Both these contributions to the linewidth are found to increase with the applied electric field except for the narrowest wells. However, the linewidth is found to initially decrease with increasing well width for all electric fields and then increase again with increasing well widths for finite electric field for the case where the exciton is scattered elastically. The minimum in the linewidth as a function of well width shifts to smaller well widths with increasing electric field. In the absence of an electric field, the linewidth continues to decrease with increasing well width. When the exciton is ionized as a result of the scattering, the linewidth increases with well width for all nonzero electric fields. However, in the absence of the electric field, the linewidth decreases with increasing well width. This reflects the effect of decreasing confinement on the scattering by ionized impurities. In the case of elastic scattering of the exciton by the ionized impurities, the linewidth has a maximum as a function of the exciton energy with the maximum shifting to lower energies as the well width decreases. For scattering which results in the ionization of the exciton, there is a threshold in the linewidth as a function of the exciton's center of mass energy with the threshold being larger for smaller well widths. The contribution to the linewidth due to elastic scattering of the exciton is many orders of magnitude larger than that due to scattering in which the exciton is ionized. © 1999 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.371390
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