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  • American Institute of Physics  (37,419)
  • American Institute of Physics (AIP)  (31,708)
  • Oxford University Press  (23,335)
  • International Union of Crystallography (IUCr)
  • 2020-2023  (41)
  • 1985-1989  (98,671)
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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
    Repository Name: Woods Hole Open Access Server
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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
    Repository Name: Woods Hole Open Access Server
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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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    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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  • 14
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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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  • 15
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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.
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  • 16
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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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  • 17
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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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  • 18
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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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  • 19
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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
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 20
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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
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  • 21
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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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  • 22
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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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  • 23
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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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  • 24
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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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  • 25
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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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    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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    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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    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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    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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    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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    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
    Repository Name: Woods Hole Open Access Server
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  • 36
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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
    Repository Name: Woods Hole Open Access Server
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  • 37
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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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  • 38
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    Physical modeling and validation of porpoises' directional emission via hybrid metamaterials (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 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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  • 39
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    Mantle upwelling beneath the South China Sea and links to surrounding subduction systems (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 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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  • 40
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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
    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 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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  • 41
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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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  • 42
    Electronic Resource
    Electronic Resource
    Anisotropic intermolecular potentials. III. Rare-gas–hydrogen bromide systems (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4455-4461 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Intermolecular potentials for Ar and Kr interacting with HBr are obtained by least-squares fitting of potential parameters to data obtained from the molecular-beam microwave spectra of the Ar–HBr and Kr–HBr van der Waals complexes. The equilibrium geometry is linear Rg–H–Br in each case, but there are substantial secondary minima at the linear Rg–Br–H geometries; for Ar–HBr, the secondary minimum is only about 5 cm−1 shallower than the primary minimum. This potential feature is found to explain the anomalous H/D isotope effects in centrifugal distortion constants that have been observed for the Rg–HBr complexes. It is predicted that Ar–HBr will have a very low-energy bending state, only 11 cm−1 above the ground state, arising from the secondary minimum.
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    URL: http://dx.doi.org/10.1063/1.456782
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  • 43
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    Electronic Resource
    Excited rovibronic level dependence of the magnetic quenching of slow fluorescence of pyrazine vapor (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4477-4484 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Excited rotational level dependence of the external magnetic field effects both on intensity and on decay of fluorescence of pyrazine vapor has been carefully examined for the zero-point vibrational level in S1 with a field strength of 0–170 G. The magnetic quenching of the slow fluorescence becomes more effective with increasing rotational quantum number J' of the excited level, and the field strength at which the amount of fluorescence quenching becomes one-half of the total amount of quenching at the saturated fields is roughly proportional to (2J'+1)−1. The magnetic quenching is also found to depend on K' of the excited level. The rotational level dependence of the magnetic quenching of the slow fluorescence is related to a difference in the number of the triplet levels coupled to the optically excited singlet rovibronic level, based on the spin decoupling mechanism of the singlet–triplet mixed level.
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    URL: http://dx.doi.org/10.1063/1.456785
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  • 44
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    Electronic Resource
    Observation of collision-induced-dipole absorption bands in strontium–rare-gas mixtures. II. Bands involving high-lying states (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4499-4503 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We have observed many collision-induced-dipole (CID) absorption bands arising from the transitions between quasimolecular ground and high-lying (n≤10) states in the strontium–rare-gas systems. For each absorption band, we have measured the energy shift of the absorption peak from the energy of the correlating atomic forbidden transition and the effective oscillator strength per unit perturber density fCID/Np. The shift is roughly proportional to the electron scattering length L0 for each rare-gas atom, whereas the fCID/Np is roughly proportional to L20. The shift decreases in general as the principal quantum number n increases, and increases as one goes from the s state to the d state, and to the degenerate manifold state with l≥3. These general features of the shift and fCID/Np are consistent with the predictions by a simple Fermi-potential model, suggesting the important role of the interaction between a Rydberg electron and a rare-gas atom in the CID absorption processes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456788
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  • 45
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    Electronic Resource
    Detection of the silylene ν2 band by infrared diode laser kinetic spectroscopy (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4582-4586 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ν2 band of the silylene SiH2 molecule in X˜ 1 A1 was observed for the first time in the gas phase by using infrared diode laser kinetic spectroscopy. Silylene molecules were generated by the photolysis of phenylsilane at 193 nm. The observed spectrum was analyzed to determine the rotational and centrifugal distortion constants in the ground and v2 =1 states and the band origin ν0 =998.6241(3) cm−1 with one standard deviation in parentheses. The significance of the derived parameters is discussed in detail.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456746
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  • 46
    Electronic Resource
    Electronic Resource
    Dissociation dynamics of the d 1Πg and C 3Πg v=0–2 vibrational states in O2 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4597-4602 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using translational spectroscopy we have studied the d 1Πg and C 3 Πg Rydberg states of O2 . The dissociation of the vibrational levels v=0–2 to all energetically accessible dissociation limits has been followed. The dissociation pathways directly reflect the predissociation mechanisms involved. For the d 1 Πg Rydberg state competition between predissociation by a 3 Πg valence state, due to singlet–triplet mixing, and by a 1 Πg valence state has been observed. Using the Fermi golden rule the observed vibrationally dependent competition is reproduced, corroborating the positions of the lower 1 Πg and 3 Πg valence state curves and yielding various coupling strengths.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456749
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  • 47
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    Electronic Resource
    Quantum state-resolved study of pure rotational excitation of CO2 by hot atoms (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4636-4642 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Rotationally inelastic scattering of carbon dioxide by translationally hot H, D, and Cl atoms was studied by time-resolved diode laser absorption. The high J rotational distribution falls off quite rapidly between J=60 and J=80. D atom collisions have roughly twice the excitation cross section versus H atom collisions, with the H*/D* ratio decreasing with increasing J. These results are consistent with a constraint on the total reagent orbital angular momentum available for rotational excitation. Transient Doppler profiles measured immediately after hot atom/CO2 collisions indicate that CO2 molecules excited to high J levels have a larger recoil velocity than molecules excited to lower J levels. This result is consistent with predictions based on a simple model which treats the CO2 potential as a hard shell ellipsoid.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456753
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  • 48
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    Electronic Resource
    Diffusion-controlled reactions. I. Molecular dynamics simulation of a noncontinuum model (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4643-4650 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The molecular dynamics simulation method is extended to study a model of diffusion-controlled reactions. This allows a molecular description of solvent at an equal footing of reactants. Nondiffusional dynamic behavior of reactive molecules is found at short times. It enhances the rate of reactive encounter in comparison to the prediction of Smoluchowski theory. The model studied in this work can be regarded as a theoretical prototype of fluorescence quenching. In this context it is shown that the nondiffusional dynamics is mainly responsible for the discrepancy between Stern–Volmer plots measured in a continuous excitation experiment or obtained by integrating the time resolved fluorescence intensity. The other aspects such as the long-time behavior of survival probability, solvent effect as well as competing effect from finite concentration of one reactive species are also studied in some detail.
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  • 49
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    Electronic Resource
    The reactions of iron clusters with water (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4714-4727 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reactions of neutral iron clusters Fe7–27 with water are studied in a laser-vaporization cluster source coupled to a continuous-flow reactor. Reaction products are detected via laser ionization and time-of-flight mass spectrometry. The reactions of room-temperature clusters with H2O show adsorbate decomposition and hydrogen desorption, as do the reactions with D2O at elevated temperatures. The room-temperature reaction with D2O appears not to involve any decomposition, and is at equilibrium under the conditions of these experiments. The dependence of reaction extent on D2O pressure yields equilibrium constants for the addition of the first and second D2O molecules. The analysis is complicated by the presence of two-photon ionization processes that are treated quantitatively with a rate-equation model. This treatment also yields estimates for cluster photoabsorption cross sections, which are found to be approximately linear in cluster size, having a magnitude of 2.3×10−17 cm2 per iron atom. From the derived equilibrium constants and estimated adsorption entropies, approximate D2O–cluster binding energies are determined. They range from 0.42 to 0.59 eV, and their dependence on cluster size shows a remarkable similarity to the dependence of the rate constants for reaction of iron clusters with H2. The implications of this similarity are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.456760
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  • 50
    Electronic Resource
    Electronic Resource
    Relativistic effect on total energies for determination of correlation energies of atoms from their experimental total energies (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4738-4744 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Relativistic effect Erel upon the total electronic energy of an atom is discussed with particular reference to obtaining the nonrelativistic total energy Eexact from the experimental total energy. Numerical values of this effect obtained by various authors by different nonempirical methods are compared for neutral atoms of rare-gas elements. It is shown that methods either of a Hartree–Fock-type or of a Dirac–Hartree–Fock-type give much the same Erel value for He through Ar. It is pointed out that Erel calculated with Hartree–Fock wave functions is not adequate for use in obtaining Eexact from the experimental total energy and that the Erel value calculated with wave functions including electron correlation should work well, although an actual demonstration can be done only for two-electron systems for lack of data. A semiempirical formula is therefore proposed, which is useful for least-squares fit of experimental total energies of isoelectronic series of atoms to extract nonrelativistic total energies along with the relativistic effect. From nonrelativistic energies thus derived, semiempirical values of correlation energies of atoms are obtained. The results thus obtained are in reasonable agreement with correlation energies derived by Clementi along somewhat different lines. The power series expansion in Z of the fitted formula for the He series shows that numerical values of expansion coefficients agree reasonably well with the corresponding values obtained by accurate relativistic and nonrelativistic Z expansion-type calculations.
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    URL: http://dx.doi.org/10.1063/1.456763
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  • 51
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    Electronic Resource
    On the electronic structure and spectrum of CuF2 and CuCl2 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4785-4792 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ground and low-lying states of CuF2 and CuCl2 have been studied using the single and doubles configuration interaction (SDCI) and coupled pair functional (CPF) methods in a large Gaussian basis set including up to g-type functions. The results include a determination of the bond distances for all the ligand field states (the three states with one hole in the 3d shell) and charge transfer (CT) states, and force constants for the ligand field states. Overall the SDCI (with or without the Davidson correction for higher excitations) and CPF results are in good agreement. The CPF results, which we believe to be the most accurate, can be summarized as follows. The computed value for the asymmetric stretching frequency in the 2Σ+g ground state of CuF2 is 740 cm−1, compared to the experimental value of 765 cm−1. The d–d transition energies for CuF2 are 2500 and 10 800 cm−1. The two lowest charge transfer states are at 31 200 and 33 900 cm−1, respectively. CuCl2 has been found to have a ground state which is an almost equal mixture of 2Σ+g and 2Πg when an estimate of the spin–orbit interaction is included. Three d–d transitions are found: 1600 cm−1 ( J=1/2), 7500 cm−1 (J=3/2), and 9700 cm−1 (J=5/2). The lowest charge transfer states have been computed to lie at 16 700 and 19 600 cm−1. Two bands have been found in the gas-phase spectrum of CuCl2 at 9000 and 19 000 cm−1, in good agreement with the present results. The computed f value for the CT band is 0.017, to be compared to the experimental value of 0.014.
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    Dissociation energy of the molecule AlBr from equilibrium measurements (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4909-4911 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dissociation equilibrium AlBr=Al+Br was studied by effusion beam mass spectrometry over the range 1970 to 2260 K and the dissociation energy D00(AlBr) was derived as 4.41±0.06 eV. This value is in general agreement with other fragmentary thermochemical results, but it is lower than a value derived from a short extrapolation of vibrational levels in the excited 1π state, doubtless because of a potential maximum of about 0.22 eV in that state. A Birge–Sponer extrapolation of the ground state vibrational levels, when corrected for degree of ionicity, yields a D00 value in close accord with the experimental result, but an electrostatic model calculation falls short by 0.45 eV.
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    A new scheme for determination of the carrier mobility and main-chain conformation of an electroactive polymer chain by transient electric birefringence (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4920-4925 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new scheme of experimental criterion is proposed for estimating the carrier mobility and main-chain conformation of an electroactive polymer chain by the technique of transient electric birefringence (TEB). The rise response Δnr (t) and the decay response Δnd (t) in the TEB satisfy in the Kerr regime (i) Δnr (t)=Δnst -Δnd (t) for a polymer molecule of arbitrary conformation with an induced dipole moment alone arising from carriers highly mobile along the main chain, (ii) Δnr (t)=Δnst -(3/2)Δnd (t/3)+(1/2)Δnd (t) for a rodlike polymer molecule with a permanent dipole moment alone originating from carriers with low mobility, and (iii) Δnr(t)=Δnst-2Δnd (t/2)+Δnd (t) for a random-coiled polymer with a permanent dipole moment alone due to low-mobility carriers, where Δnst =limt→∞ Δnr(t) . Then, comparison of the TEB rise and decay responses gives us information on the carrier mobility and main-chain conformation. This criterion is valid also for polydispersed polymer samples. By applying the criterion to the exemplifying data of the TEB responses for soluble urethane-substituted polydiacetylenes, it is found that the polydiacetylene molecules take a random-coil conformation with a permanent dipole moment in a good solvent, while in a poor solvent the carrier mobility depends crucially on the solvent condition.
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    Imaging of spatial pattern formation in an oscillatory surface reaction by scanning photoemission microscopy (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4942-4948 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The rate of catalytic carbon monoxide oxidation on a Pt(100) single crystal surface under isothermal, low-pressure conditions exhibits for certain ranges of parameters (O2 and CO partial pressures, temperature) sustained temporal oscillations whose mechanism had been explored in previous work. Coupling between reaction and diffusion leads to spatial pattern formation as manifested by patches with different work function on the intrinsically homogeneous surface. Imaging is performed by means of the novel technique of scanning photoemission microscopy. Typically, nuclei with dimensions of a few microns, as determined by the instrumental resolution, are formed spontaneously and expand with sharp fronts and velocities of about 0.5 mm/min (at 480 K) up to sizes ≥1 mm. Waves with even more extended fronts propagating with somewhat higher velocities across the sample surface are responsible for the occurrence of large amplitude temporal oscillations of the integral reaction rate.
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    The bonding of acetonitrile and CH2CN on Ag(110) determined by near edge x-ray absorption fine structure: Evidence for π-donor bonding and azimuthal ordering (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4338-4345 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Carbon K edge near edge x-ray absorption fine structure (NEXAFS) spectra of adsorbed acetonitrile and reactive intermediates derived therefrom on Ag(110) were studied in order to determine their orientation and bonding to the surface. For both the multilayer and the adsorbed monolayer there is excellent agreement between the spectra of the adsorbed acetonitrile and the gas phase species. For the multilayer coverage the orientation of the acetonitrile molecules is not completely random; the molecules prefer an orientation with their bond axes closer to parallel than perpendicular to the surface. At monolayer coverage acetonitrile bound to the surface is unrehybridized. It is bound with its linear molecular skeleton parallel to the surface and randomly oriented azimuthally. Annealing molecular CH3 CN to 325 K in the presence of coadsorbed atomic oxygen produces a linear CH2 CN surface intermediate, the molecular axis of which is parallel to the surface and perpendicular to the close-packed direction. The C–C and C–N bond lengths are essentially unperturbed from their values in gas phase CH3 CN. Bonding appears to occur between the methylene carbon and the metal, as expected. A broadening of the π* resonance for transition into the π* orbital perpendicular to the surface is interpreted in terms of π-donor bonding.
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    Attenuated total reflectance infrared spectra of strongly absorbing anisotropic crystals: Orthorhombic Na2[Fe(CN)5NO]⋅2H2O (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4265-4272 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Attenuated total reflectance (ATR) from principal faces of orthorhombic (and higher symmetry) crystals in spectral regions including strongly polar optic modes is considered. A detailed, quantitative comparison between experimental and calculated ATR infrared (IR) spectra of orthorhombic sodium nitroprusside dihydrate (SNP), Na2[Fe(CN)5NO]⋅2H2O, single crystals in the 500–3800 cm−1 region is presented. Calculated ATR spectra are generated employing the dielectric tensor of SNP obtained from Kramers–Kronig analysis of external reflectance data. The dependence of intensities, profiles, and locations of bands in the spectra upon the relative refractive index of the sample against the ATR prism and the polarization state of the reflected IR beam will be discussed. Both theoretical and experimental evidence of the coupling of the TM-polarized evanescent wave with strong in-plane-polarized optic modes at about their LO frequencies will be given with reference to the case of the strong NO stretching mode of SNP. Finally, the computed and experimental ATR results in SNP single crystals will be critically compared with powder ATR data and reported polarized IR transmittance spectra of SNP single crystals plates.
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    X-ray diffraction study of liquid n-butane at 140 and 267 K (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4299-4306 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: X-ray diffraction data for liquid n-butane near the triple and boiling points are presented. The data are analyzed using scattering factors for −CH3 and −CH2 groups which permits extraction of structure and distribution functions for carbon sites. An intramolecular carbon–carbon distance at approximately 3.1 A(ring) is assigned to a short end-to-end distance in a near-gauche conformation, which is in agreement with the electron diffraction results for gaseous n-butane. The intermolecular pair distribution functions show a large difference in the liquid structure for the low and high temperature states, similar to that found in liquid propane.
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    Kinetics of the thermal desorption of indium from GaAs(100) (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4330-4337 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: We report studies of the kinetics of thermal desorption of In from Ga-stabilized GaAs(100) in ultrahigh vacuum. The relative coverage of In was monitored by x-ray photoelectron spectroscopy (XPS), while the substrate temperature was accurately measured using infrared laser interferometric thermometry. The In was deposited on GaAs by dosing, at room temperature, to saturated monolayer coverage with trimethylindium, yielding In ∼2×1014 cm−2. Subsequent heating to 400 °C desorbs all hydrocarbon species without affecting the In coverage. Further heating leads to first-order desorption of In, as confirmed by exponential decay of In(3d 5/2) XPS signal in isothermal desorption experiments at 473 and 503 °C. From temperature programmed desorption studies through the range 450 to 530 °C, differentiation of the In coverage vs time yielded desorption rates from which Arrhenius parameters were extracted. The unit-weighted average values of the preexponential factor and the desorption energy, obtained from three experiments with heating rates from 0.6 to 3.2 °C/min, are: log10A(s−1)=12.2±0.5 and Ed=53.5±1.2 kcal/mol, where the uncertainties are 1σ sample standard deviations. The Arrhenius parameters of desorption of In from Ga-stabilized GaAs(100) are found to be similar to those of vaporization of pure In. This is consistent with the known tendency of In to form islands on GaAs surfaces, but could also reflect the similarity of the local environments of an In atom adsorbed on an In island and an In atom adsorbed on a Ga-terminated surface. The observed first-order kinetics and the constancy of the In(3d 5/2) XPS signal up to the temperature where desorption occurs indicates that if islands are formed they are small (〈10 A(ring) diameter) at the low coverage used here.
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    Quasielastic light scattering studies of swollen and stretched polymer gels (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4360-4368 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Cooperative diffusion D of polyacrylamide gels in water was investigated by quasielastic light scattering both under the isotropically swollen state and under the uniaxially stretched and swollen state. The concentration (Ce) dependence of D for the isotropic gels having equilibrium degrees of swelling was measured by systematically changing crosslinking density of gels. The results yielded D=(3.4±0.5)×10−6 C0.76±0.03e cm2/s, in accord with a scaling prediction. For each of the gels prepared and having a given Ce, the uniaxial stretching was applied, and the values D were investigated as a function of extension ratio α and direction β with respect to the stretching direction. The results gave D (α,Ce)=(3.4±0.5)×10−6 αx Cye cm2/s, where x=2/3 for β=0° and −1/4 for β=90°, and y=0.76, independent of α and β. The results clearly indicate that upon increasing α, D increases and decreases, respectively, in the direction parallel and perpendicular to the stretching direction, implying suppression and enhancement of the concentration fluctuations as a result of the network being stiffened and softened in the respective directions.
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    Leading concentration correction to polymer dynamic self-structure factor (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4387-4400 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The discrete chain representation of multiple scattering theory of the concentration dependence of the hydrodynamics of polymer solutions is applied to the calculation of the leading concentration correction to the dynamic structure factor S(k,t) and its first and second cumulants of individual labeled Gaussian chains in theta solutions at nonzero concentrations. Contributions are separated into those from overall translational and internal chain motions as well as couplings between different internal modes and between translation and internal modes, coupling that are introduced by interchain hydrodynamic interactions. The separate contributions are analyzed as a function of k and of t in order to isolate regions where certain contributions are dominant. As expected, short times and larger k tend to favor contributions from internal chain dynamics, while longer times and smaller k make concentration dependent translational effects predominate. Computations for shorter chains are extrapolated to provide the asymptotic long chain behavior.
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    Symmetry breaking in HCl and DCl dimers: A direct near-infrared measurement of interconversion tunneling rates (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4418-4419 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The interconversion tunneling frequencies for (HCl)2 and (DCl)2 are obtained from near-infrared absorption spectra of the H(D)Cl stretching transitions, to spectroscopic precision for the mixed 35Cl–37Cl dimers. A phenomenological model of the interconversion process explains several experimental observations, and provides good estimates of the splittings expected for the 35Cl–35Cl and 37Cl–37Cl species.
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    Comment on "A theoretical study of the dissociation energy of BH using quadratic configuration interaction'' (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 4425-4426 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The dissociation energy of boron hydride has been calculated ab initio using a very accurate theoretical model, with an expected accuracy of ±0.2 kcal mol−1. The values of 85.7 and 82.4 kcal mol−1 for De and D0, respectively, confirm the conclusion of Curtiss and Pople [J. Chem. Phys. 90, 2522 (1989)], that the predissociation limit of 82.6±0.4 kcal mol−1 might be close to the actual dissociation energy, and that an earlier proposed De of 78.9 kcal mol−1 is in error.
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    Ultrafast vibrational dynamics of a photoexcited metalloporphyrin (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3525-3531 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ultrafast photodynamics of four-coordinate nickel(II) porphyrins in noncoordinating solvents has been studied using femtosecond time resolved optical spectroscopy. Unambiguous evidence has been found for the formation of a metastable metal (d,d) excited state in less than 350 fs following excitation of the macrocycle. However, the transient absorption spectrum of this ligand-field electronic excited state continues to evolve and reaches the steady-state form only after about 20 ps. This spectral behavior and the attendant complex kinetics can be modeled phenomenologically in terms of a broad distribution of the (d,d) excited states evolving to a narrower distribution. The dynamics are associated with vibrational relaxation. Intramolecular and intermolecular contributions to this process are considered.
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    The Fourier grid Hamiltonian method for bound state eigenvalues and eigenfunctions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3571-3576 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new method for the calculation of bound state eigenvalues and eigenfunctions of the Schrödinger equation is presented. The Fourier grid Hamiltonian method is derived from the discrete Fourier transform algorithm. Its implementation and use is extremely simple, requiring the evaluation of the potential only at certain grid points and yielding directly the amplitude of the eigenfunctions at the same grid points.
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    Treatment of rotational isomers in free energy calculations. II. Molecular dynamics simulation study of 18-crown-6 in aqueous solution as an example of systems with large numbers of rotational isomeric states (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3631-3637 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The evaluation of free energy differences using the perturbation method or thermodynamic integration method requires special caution if multiple rotational isomeric states may exist in the system under investigation. In this article a recently suggested procedure to properly treat rotational isomeric states is illustrated with a molecular dynamics simulation of an aqueous solution of uncomplexed 18-crown-6 crown ether, as an example of a system in which large numbers of isomeric states may exist. By using very long molecular dynamics simulations, thermodynamic perturbation methods and symmetry arguments, the free energy of host organization into the conformation required to form the complex with K+ is estimated to be 2.6 kJ mol−1. It has also been found that the lowest energy conformations of 18-crown-6 in vacuo do not necessarily correspond to the most populated conformations in aqueous solution.
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    The structure of liquid 1,2-dichloroethane by neutron diffraction. II. Pulsed neutron and isotope difference studies (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3689-3699 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Pulsed neutron diffraction measurements have been made on liquid 1,2-dichloroethane-d4 (DCE). The wide momentum-transfer range (∼0.3–50 A(ring)−1) available has been used to further refine previously measured molecular structure parameters as well as to test the validity of the inelasticity corrections applied. A measurement using chlorine isotopes on a steady (reactor) source served to partially separate the chlorine–chlorine and the chlorine–carbon plus chlorine–deuterium correlations. The isotopic difference curves were then analyzed and the relevant features of the distribution of internal dihedral angles [P(τ)] obtained by adequate inversion of the experimental difference–functions. The intermolecular pair correlation function was then derived and both sets of functions (from pulsed and steady sources) are compared and tentatively assigned.
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    Brownian dynamics study of the end-to-end distribution function of star and linear polymers in different regimes (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3721-3723 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Brownian dynamics computer simulations are used to investigate the shape of the mean-squared end-to-end distance distribution function in the three regimes: (1) excluded volume; (2) θ; (3) collapsed. It is found that Mazur's function fits regime (1), that the Gaussian function fits regime (2), and that neither of these appear to describe the collapsed state. The implications of these results to theories of ring formation during polymerization is pointed out.
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    An ab initio semirigid bender calculation of the rotation and trans-tunneling spectra of (HF)2 and (DF)2 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5154-5159 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Using a purely ab initio minimum energy path for the trans-tunneling motion in the HF dimer, the energy levels for the K-type rotation and trans-tunneling motion for (HF)2 and (DF)2 are calculated with a one-dimensional semirigid bender Hamiltonian and no adjustable parameters. The transition moments for rotation-tunneling transitions are calculated, using our ab initio value for the dipole moment of an isolated HF molecule, and we also calculate B¯ values. The energy levels we obtain are in close agreement with experiment; for example, the K=0 tunneling splitting in (HF)2 is calculated as 0.65 cm−1 compared to the experimental value of 0.658 69 cm−1. As well as showing that our ab initio minimum energy path is very good, the calculation demonstrates that the semirigid bender formalism is able to account quantitatively for the unusual K dependence of the rotational energies resulting from the quasilinear behavior, and that the trans-tunneling motion is separable from the other degrees of freedom. We use the results to predict the locations, and transition moments, of the ΔK=0 and ±1 subbands in the tunneling spectra of (HF)2 and (DF)2, many of which have not yet been observed.
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    Infrared spectroscopy of carbo-ions. V. Classical vs nonclassical structure of protonated acetylene C2H+3 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5139-5153 
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    ISSN: 1089-7690
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    Topics: Physics , Chemistry and Pharmacology
    Notes: The problem of classical vs nonclassical structure of protonated acetylene (vinyl cation) C2H+3 has been studied using high resolution infrared spectroscopy. The spectrum has been observed in the 3.2 μm region in air-cooled and water-cooled plasmas using C2H2:H2:He mixtures and in liquid nitrogen-cooled plasmas using CH4:H2:He mixtures. The difference frequency spectrometer with the velocity modulation method has been used to conduct the Doppler-limited, high sensitivity spectroscopy.The observed vibration–rotation pattern with the band origin at 3142.2 cm−1 has been identified as due to the antisymmetric CH stretching ν6 band of the C2H+3 ion with the nonclassical (bridged) structure. The observed spectral pattern was anomalous, but definitive assignments could be made for a part of the spectrum using the ground state combination differences which fit to the usual asymmetric rotor pattern. The discrimination between the classical and nonclassical structures is based on the observed spectral intensity pattern due to spin statistical weights. Agreement of vibrational band patterns and the rotational constants with ab initio values gives supporting evidence. The anomaly of the spectrum is at least partly ascribed to the small energy difference between the classical and nonclassical structures and possible rearrangement between them, the idea used by organic chemists over the years in wet chemistry. Systematic splittings with the intensity ratio of 2:1 have been noticed in some parts of the spectrum indicating that the protons tunnel between the apex and the two end equilibrium positions of the bridged structure. Using a simplified internal rotation model proposed by Hougen, the barrier height of the tunneling has been estimated. Chemical kinetics in plasmas related to C2H+3 is also discussed.We conclude that (1) the nonclassical structure is lower in energy than the classical structure, and (2) the apex proton and the two end protons exchange their positions with a measurable time scale.
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    Phonon wings in inelastic neutron scattering spectroscopy: The harmonic approximation (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5164-5169 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The inelastic neutron scattering (INS) spectra of some ammonium halides and ammonium nitrate are analyzed in terms of the internal vibrations of the NH+4 ion convoluted with multiphonon lattice modes up to the eighth term. Due to the low mass of this ion, most of the intensity of the internal-mode region of the INS spectra is in the "phonon wings,'' differences between the salts in this spectral region being mainly due to differences in their lattice-mode spectra. Refinement of the lattice Debye–Waller factor is included in the profile refinement of interatomic force constants.
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    A new determination of the dissociation energy of acetylene (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5160-5163 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new upper bound for the dissociation energy of acetylene, D00(HCC–H) =529.89(±0.01) kJ/mol, has been determined by Stark anticrossing spectroscopy. The zero-pressure extrapolated (unimolecular) decay rates of levels of S1 (A˜ 1Au) v'3=2 and 3 (quanta of the trans-bending vibration) increase upon application of an electric field of 113 kV/cm. We attribute this increase in molecular decay rate to predissociation rather than any other Stark-induced nonradiative or radiative phenomenon. The lowest level (v'3 =2, J'=2, K'=1) from which we have observed an increase in decay rate (i.e., predissociation) has an internal energy of 44 295.65 cm−1 relative to v=0, J=0 of S0 (X˜ 1∑+g). This corresponds to a value about 24 kJ/mol lower then the consensus upper bound result from four different recent experimental determinations (including one of ours) as well as current ab initio results. The new value agrees, however, with earlier work and with recent modeling studies of acetylene pyrolysis kinetics.
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    Photoelectron spectra of the alkali metal cluster anions: Na−n=2–5, K−n=2–7, Rb−n=2–3, and Cs−n=2–3 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3792-3793 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
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    URL: http://dx.doi.org/10.1063/1.456861
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    Divalent manganese in tetragonal sites of Cs2NaYCl6 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2776-2778 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Electron paramagnetic resonance (EPR) studies performed at room tempertaure in Mn2+ doped Cs2NaYCl6 single crystals (elpasolite) showed that the Mn2+ ion occupies a tetragonal symmetry site in the cubic crystalline lattice. In contrast with previous results on elpasolite, where trivalent rare earth impurities occupy Oh sites, and divalent europium impurities occupy trigonal sites, this work reports, the first evidence of an impurity in a tetragonal symmetry site in this host with principal axes along 〈100〉 crystallographic directions. The unusually large total splitting of the EPR spectrum (∼10 000×10−4 cm−1) is discussed in order to establish a tentative model for the site.
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    Rigorous bounds to molecular electron repulsion and electrostatic potential integrals (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3596-3602 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Novel rigorous upper and lower bounds, at primitive level, to general electron-repulsion integrals (ERIs) involving Gaussian basis sets have been derived and interconnections with the earlier works in the literature are brought out. New optimal strategies for a preemptive elimination of insignificant ERIs at atom and contraction levels are discussed and tested, resulting in a significant reduction in CPU time. Similar analysis is carried out for the computation of the molecular electrostatic potential for the first time in the literature, leading to a marked savings in computer time.
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    Multiphoton ionization of O2 X 3Σ−g, a 1Δg, and b 1Σ+g via the two-photon resonant nsσg, ndσg, and ndπg Rydberg levels (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5185-5200 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Multiphoton ionization spectra have been obtained and analyzed for excitation in the 215–360 nm region from the X 3Σ−g, a 1Δg, and b 1Σ+g states of O2. The 0–0 band of the C 1Πg state is reported for the first time. Measurements of other vibrational bands terminating in the C 3Πg and d 1Πg states are in good agreement with determinations by other groups. Several vibrational levels (v'=0–5) of the 3dπg Rydberg complex have been assigned on the basis of (1) an analysis of the spin–orbit couplings between the (Λ,S) basis-set states, (2) spectral simulation, and (3) the behavior of the states when the excitation radiation is changed from linear to circular polarization.
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    Rotational populations in OD formed in the reaction O(1D)+D2 investigated by infrared rotational absorption spectroscopy (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5201-5207 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Diode laser transient absorption/gain spectroscopy is used to monitor time-dependent populations of high rotational levels in OD (v=0) produced in the reaction of O(1D)+D2. Pure rotational transitions on species with large dipole moments offer good sensitivity, full state resolution and μs time resolution in the present apparatus. Measured nascent populations of OD in the four highest rotational levels thermodynamically accessible in this reaction are in reasonable agreement with the reported results of earlier laser-induced-fluorescence measurements, in which corrections for transition moments and predissociation introduce increasing uncertainties at high rotational levels. The relaxation kinetics of the highest rotational levels are not hopelessly complex, and evidence is presented for strong, but not complete propensity for conservation of Λ doublet symmetry during rotational relaxation.
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    A surface constrained all-atom solvent model for effective simulations of polar solutions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3647-3661 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A consistent simulation of ionic or strongly polar solutes in polar solvents presents a major challenge from both fundamental and practical aspects. The frequently used method of periodic boundary conditions (PBC) does not correctly take into account the symmetry of the solute field. Instead of using PBC, it is natural to model this type of system as a sphere (with the solute at the origin), but the boundary conditions to be used in such a model are not obvious. Early calculations performed with our surface constrained soft sphere dipoles (SCSSD) model indicated that the dipoles near the surface of the sphere will show unusual orientational preferences (they will overpolarize) unless a corrective force is included in the model, and thus we implemented polarization constraints in this spherical model of polar solutions. More recent approaches that treated the surface with stochastic dynamics, but did not take into account the surface polarization effects, were also found to exhibit these nonphysical orientational preferences. The present work develops a surface constrained all-atom solvent (SCAAS) model in order to consistently treat the surface polarization effects in all-atom molecular dynamics simulations. The SCAAS model, which was presented in a preliminary way in previous works, introduces surface constraints as boundary conditions in order to make the necessarily finite system behave as if it was part of an infinite system. The performance of the model with regard to various properties of bulk water is examined by comparing its results to those obtained by PBC simulations. The results obtained from SCAAS models of different sizes are found to be similar to each other and to the corresponding PBC results. The performance of the model in simulations of solvated ions is emphasized and a comparison of the results obtained with spheres of different sizes demonstrates that the model does not possess significant size dependence. This indicates that the model can be used with a relatively small number of solvent molecules for convergent simulation of structure, energetics, and dynamics of polar solutions. The much simpler fixedcenter Langevin dipoles (FCLD) model is also examined and found to provide a powerful tool for estimating solvation free energies. Finally, a preliminary study of the dielectric properties of the SCAAS model is reported and the potential of this model for exploring the correct implementation of the solvent reaction field is discussed.
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    Shift of first-order phase transitions in thin films due to boundary fields: A computer simulation (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3700-3706 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The first-order phase transition of the ferromagnetic Ising model driven by the magnetic field at temperatures below criticality is studied by Monte Carlo methods for a two-dimensional thin film geometry, L×M with two free boundaries of length M(very-much-greater-than)L, at which boundary fields act. This model study is relevant, in particular, for phase transitions in monolayers adsorbed at stepped surfaces. While in the bulk geometry (L→∞) this transition occurs for zero field in the present model, with the system "jumping'' from a state with uniformly positive magnetization to a state with uniformly negative magnetization, in the thin film geometry the transition occurs at a critical field H*∼L−1, and the two states between which the transition occurs are characterized by strongly nonuniform magnetization profiles across the film. These findings are in agreement with the scaling theory of Fisher and Nakanishi.
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    A stability condition for the Hartree–Fock solution of the infinite one-dimensional system (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3724-3728 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A simplified stability condition for the Hartree–Fock (HF) solution giving the self-consistent field crystal orbitals (SCF-CO) of the infinite one-dimensional system is derived. Since the present formulation, particularly for the systems having nearly or entirely degenerated highest occupied and the lowest unoccupied COs, contains only two physical parameters, that is, the density of states and the Coulomb repulsion integrals both at the Fermi level, it is tractable to examine the stability of the HF solutions of such polymers as well as the ordinary molecular systems. An example of its application to metallic trans-type polyacetylene is also shown.
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    Distributed electronic relaxation and nonexponential fluorescence in polymers: Reversibility in donor–excimer pairs—A perturbation theory treatment (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3744-3761 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: An ensemble of distributed donor molecules that undergoes rotational transitions into a discrete excimer state has been analyzed, in an attempt to model distributed electronic relaxation and nonexponential fluorescence of aromatic polymers in presence of rotational sampling processes. In case of irreversible trapping, the donor survival function has been formulated in terms of the one-sided Laplace transform and specified for a modified Gaussian distribution to yield a closed-form expression for the donor decay. The formalism permits a time-dependent rate function to be derived that makes possible the construction of the excimer excitation function by means of the convolution theorem. In case of reversible constraints, a generalized treatment based upon time-dependent transition and transform matrices has been given which applies a perturbation technique for approximately solving the system of nonautonomous differential equations in the time domain. In the limit of weak coupling, the method develops approximate Mth order expressions (M=2,4,6, and 8) to the fluorescence response functions of donor and excimer. The perturbational solutions are well behaved up to relatively long time scales and they prove useful for providing the typical nonexponential time behavior of such a system affected by dispersion and dissociation. The physical restriction of this mathematical analysis (weak reversibility) has been addressed and the implications of distributed event times in future analyses of polymer fluorescence have been discussed.
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    Vibrational spectra and potential energy surface for the ring bending and ring twisting of 5,6-dihydro-2H-thiopyran (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2771-2775 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: 5,6-Dihydro-2H-thiopyran, CH2CH2CH=CHCH2S, has been synthesized and its far-infrared and Raman spectra recorded. Two series of sharp bands were observed originating from 139 and 235 cm−1 in the infrared spectrum for the out-of-plane ring-bending and the ring-twisting vibrations, respectively. A detailed energy level diagram including numerous excited states was determined for the two coupled vibrations. The two-dimensional potential energy surface, which satisfactorily fits more than two dozen observed transitions, was calculated to be V=2.431×104 x41 −0.383×104x21 +2.258×104x42 −1.966×104 x22 +1.026×105x21 x22 , where x1 is the ring-bending coordinate and x2 is the ring-twisting coordinate. The minimum energy on the potential surface corresponds to a twisting angle of 37.8° (the half-chair conformation). The lowest energy bent (boat) conformation corresponds to a saddle point 4130 cm−1 above the twisted conformation on the potential energy surface. The results are compared to analogous molecules and to molecular mechanics calculations.
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    Vacuum ultraviolet absorption spectra of thiirane and thietane (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2808-2813 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Photoabsorption cross sections of thiirane and thietane vapors have been studied in the 110–240 nm region using synchrotron radiation. A number of peaks from thiirane and thietane are arranged into four and five Rydberg series, respectively, converging to the first ionization potential. Many Rydberg peaks from both molecules are observed to possess vibronic structures. The vibrational progressions from thiirane are assigned to the CH2 wagging (ν4) and CS symmetry stretching (ν5) modes. For thietane, the CH2 wagging (ν5) and CS symmetry stretching (ν7) modes of the excited states are found to be active. Molecular geometries and vibrational frequencies for the excited states are discussed on the basis of ab initio calculations.
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    Close-coupling and coupled states calculation of low energy He–CH4 and Ne–CH4 collisions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2840-2847 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Exact close-coupling calculations are used to evaluate the effectiveness of the coupled states approximation in the interpretation of low energy, noble gas methane collisions. The effect of the higher order angle dependent terms of the potential on the inelastic rotational transition was investigated. Calculations using only open channel basis functions were clearly different from converged calculations, but the differences were small enough to be negligible in comparison with experiment. It was shown that open channel coupled states calculations are of sufficient accuracy to evaluate the agreement of the potential model with experiment. The use of the coupled states approximation does not fully account for discrepancies between theory and experiment observed earlier.
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    Examination of a generalized model for radiationless energy transfer in dyes. Comparisons of theory and experiments (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2892-2897 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A modified general model for radiationless energy transfer is examined. The model does not rely on selection criteria and is intended to apply over the range of diffusion and resonance energy transfer parameters normally encountered in quenching experiments. Experimental data is compared with theoretical predictions and found to confirm the model's validity for a wide range of physical conditions.
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    Photodissociation kinetics of aluminum cluster ions: Determination of cluster dissociation energies (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2912-2921 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The photodissociation of aluminum clusters, Al+n (n=7–17), has been studied over a broad energy range (1.88–6.99 eV). Measurements of the lifetimes of the photoexcited clusters are described. Dissociation energies have been determined by comparing the measured lifetimes with the predictions of a simple RRKM model. The dissociation energies show an overall increase with cluster size, but there are substantial oscillations around n=7–8 and n=13–15. Cluster cohesive energies are derived from these results and from previous measurements of the dissociation energies of the smaller clusters. The cohesive energies of the larger clusters (n〉6) are in good agreement with the predictions of a simple model based on the bulk cohesive energy and the cluster surface energy. However, the cohesive energies are substantially larger than the results of recent ab initio calculations. The photodissociation spectrum of Al+8 has been measured and shows a broad absorption feature with a maximum ∼470 nm.
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    Microwave spectroscopic detection of dichlorosilylene SiCl2 in the ground state (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2102-2107 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The microwave spectrum of dichlorosilylene SiCl2 has been observed to characterize this molecule of chemical interest. The molecule was generated by the thermal reaction between silicon powder and tetrachlorosilane at about 1000 °C. The rotational constants and the centrifugal distortion constants were determined for the three isotopic species Si35Cl2, Si35Cl37Cl, and Si37Cl2. The nuclear quadrupole coupling constants were determined from triplet hyperfine splittings observed for several transitions. The asymmetry of the Cl nuclear quadrupole coupling tensor was found to be very large and was accounted for by π electron backdonation from Cl to Si.
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    Isoelectronic analogs of molecular nitrogen: Tightly bound multiply charged species (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 2971-2979 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The structures and stabilities of N2 and its 15 possible first-row isoelectronic analogs (CO, BF, BeNe, NO+, CF+, BNe+, O2+2, NF2+, CNe2+, OF3+, NNe3+, ONe4+, F4+2, FNe5+, and Ne6+2) have been examined using ab initio molecular orbital theory. Equilibrium structures have been obtained at a variety of levels of theory including MP3/6-311G(d) and ST4CCD/6-311+G(2df ) and dissociation energies determined at the MP4/6-311+G(3d2f ) level. Full potential energy curves for dissociation, including dissociation barriers, have been obtained at the CASSCF/6-311G(d) level. Spectroscopic constants have also been determined at this level. For the neutral and monocation analogs of N2, the calculated equilibrium geometries, dissociation energies, and spectroscopic constants are in good agreement with the experimental values. The dication analogs of N2, namely O2+2, NF2+, and CNe2+, are all found to be kinetically stable species lying in deep potential wells. In particular, the hitherto unobserved NF2+ dication is predicted to have a short equilibrium bond length (1.102 A(ring)) and a large barrier (445 kJ mol−1) to dissociation to N++F+. Thus NF2+ should be experimentally accessible in the gas phase. The (experimentally known) O2+2 dication is predicted to contain the shortest bond between any two heavy atoms, our best estimate of the bond length being 1.052 A(ring). The first excited state (A 3Σ+u) of O2+2 is predicted to be unbound, and observed metastable decomposition processes are reinterpreted in terms of the ground-state (X 1Σ+g) potential surface. In agreement with previous theoretical studies, we find that CNe2+ is a kinetically stable species, albeit with a relatively long C–Ne bond length. The OF3+ trication is calculated to have a relatively short bond but lies in a well of depth only 23 kJ mol−1. The potential energy curves of the other highly charged species are found to be purely repulsive.
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    Comparison of complete model space quasidegenerate many-body perturbation theory for LiH with multireference coupled cluster method (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3002-3011 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The relative efficacy of using low order trucations with large reference space vs high order methods with small reference space is tested by comparing quasidegenerate many-body perturbation theory (QDMBPT) calculations of potential curves for the five lowest electronic states of LiH with the multireference coupled cluster calculations of Ben-Shlomo and Kaldor [J. Chem. Phys. 89, 956 (1988)]. The infinite order coupled cluster calculations use two configurational reference spaces involving the 2σ, 3σ, and 1π orbitals, while the QDMBPT computations are truncated at either second or third orders and employ the full active reference space formed either from the 2σ, 3σ, and 1π or from the 2σ, 3σ, 4σ, and 1π orbitals. This gives us the opportunity of testing the dependence of QDMBPT computations on the size of reference space, the available freedom in choosing valence orbitals and orbital energies, and the order of truncation. Second order, four valence orbital space QDMBPT calculations provide good agreement with the repulsive portion of the coupled cluster potentials, but yield a separated atom limit that is too high and that therefore distorts the remainder of the potential. Third order improves the separated atom limit considerably, providing good agreement with the coupled cluster calculations. The "full chemical'' five orbital reference space, on the other hand, yields very good agreement with coupled cluster potentials when using only the simpler second order QDMBPT calculations, and third order corrections in this case are very small but generally improve agreement with coupled cluster potentials. The five orbital reference space calculations are quite insensitive to a wide range of different choices of valence orbitals and orbital energies, demonstrating a robustness to the QDMBPT formalism used.
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    Fluids of dipolar hard ellipsoids: Structural properties and isotropic–nematic phase transitions (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 3045-3055 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The hypernetted-chain (HNC) approximation is solved for fluids of dipolar hard ellipsoids and the structural, thermodynamic, and dielectric properties of the isotropic phase are discussed in some detail. Both prolate and oblate particles are considered and the isotropic–nematic transition is investigated using density functional theory (DFT). For fluids of prolate particles dipolar forces are found to have a significant effect upon the isotropic–nematic transition which occurs at lower densities as the dipole moment is increased. For the oblate case the dipolar interactions have only a very small, if any, influence upon the isotropic–nematic transition density. For both prolate and oblate particles the present HNC/DFT calculations do not predict ferroelectric nematic phases.
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    Observation of the ν3 fundamental bands of HOSi+ and DOSi+ (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5313-5315 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The ν3 (O–Si stretch) fundamental bands of the HOSi+ and DOSi+ molecular ions in the 9 μm region have been detected for the first time, using a tunable infrared diode laser spectrometer and a hollow cathode discharge cell. Analysis of the results yielded accurate values for the molecular rotational and centrifugal distortion parameters, as well as for the band origins, which are 1127.009 cm−1 for HOSi+ and 1103.112 cm−1 for DOSi+ . The ground vibrational state parameters are in excellent agreement with those determined from the ν1 bands of the two isotopes.
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    Fragmentation of N2 in the inner-shell to Rydberg-orbital excited states (K)−1(nl)1 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5324-5328 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Fragment ions from N2 in the states of (K)−1(nl)1 have been measured at 54.7° with respect to the polarization direction of the incident photon by using a time-of-flight (TOF) mass spectrometer. Simulation fitting calculation to the measured TOF spectra gave distributions of the kinetic energy for these ions. Ion yield spectra observed showed that no singly charged molecular ion was produced from the states of (K)−1(nl)1 in contrast to that of (K)−1(1πg)1. These results are discussed in connection to the dissociation pathway of N2 in these states.
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    Dissociation of O2 induced by selective K-shell excitation (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5329-5334 
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    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Dissociation of O2 stimulated by soft x-ray absorption has been studied by using a monochromatized synchrotron radiation and a time-of-flight mass spectrometer. The parent molecular ion O+2 was formed only at 531 eV (excitation of 1s→1πg), and a fragment ion O+ had the highest intensity in all the energies giving core–hole states. The measured time-of-flight spectra were reproduced by a simulation calculation, which provided kinetic energy distributions of O+ and O++. The dissociation pathways from the core–hole states of O2 were discussed using the obtained kinetic energy distribution and ion intensity ratios as well as Auger electron spectra in the literature.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457581
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  • 93
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    Rotationally inelastic collisions of a molecule in a 1Δ electronic state: NH(a 1Δ) (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5316-5323 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The general theory for inelastic scattering of molecules 1Δ electronic states is outlined and applied to the specific case of 1Δ states arising from a π2 electron occupancy, e.g., NH(a 1Δ). Integral cross sections for rotational transitions out of the lowest rotational level (J=2) of NH(a 1Δ) v=0 are reported for several targets. A pulsed beam of rotationally cold NH(a 1Δ) was produced by 193 nm photolysis of a dilute mixture of hydrazoic acid in nitrogen seed gas at the tip of a nozzle. The target beam was also prepared as a pulsed supersonic beam. The final rotational state distribution was measured in the collision zone by laser fluorescence excitation. The state-to-state cross sections were found to decrease significantly with increasing final rotational quantum number J'. The magnitude of the J=2→J'=3 cross sections were compared for the different targets. Isotopic scrambling in NH(a 1Δ)–D2 collisions was also searched for but not observed.
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    URL: http://dx.doi.org/10.1063/1.457579
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  • 94
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    The yield of metastable atoms through dissociative recombination of O+2 ions with electrons (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5335-5342 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The yield of metastable oxygen atoms through dissociative recombination of O+2 ions with electrons has been studied using a plasma flow tube experiment. For O+2 with high vibrational excitation (around v=9) it was found that half of the oxygen atoms are formed on the O(1D) state and that the branching ratio toward O(1S) is large (∼0.4). Using Xe+ instead of Ar+ as precursor ions, it was shown that the O(1S) yield is much less for ions with low vibrational excitation. However, the present experimental results are not compatible with the extremely low theoretical value of this yield which was reported recently for O+2 (v=0).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457582
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  • 95
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    Quenching and vibrational energy transfer in the B 2Π state of the NS molecule (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5343-5351 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Quenching and vibrational energy transfer in the B2Π state of the NS free radical have been studied using temporally and spectrally resolved laser-induced fluorescence in a low-pressure discharge flow reactor. The collision partners were He, Ar, H2, N2, O2, SF6, CO2, and N2O. Total removal cross sections show an oscillatory behavior with v' in the range of unperturbed levels, v'=4–7, for all colliders studied save O2 where a nearly monotonic increase is seen. Vibrational transfer occurs for H2 and the polyatomics; the rates vary little with v'. Δv=2 transfer occurs with the polyatomic colliders for v'=5. Fluorescence decay traces from the perturbed v'=3 and 8 levels differ from the unperturbed levels and from each other. v'=3 is perturbed by quartets and shows "gateway'' level behavior whereas v'=8 is perturbed by a doublet and shows efficient interelectronic transfer for all rotational levels.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457665
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  • 96
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    Theoretical state-to-state cross sections for collisions of N+2(v)+Ar. II. Results at higher energies (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5359-5364 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: State-to-state charge–transfer cross sections have been computed for N+2(X;v=0,1,2) +Ar at 12 collision energies between 1.2 and 320 eV. A classical path method is used, whereby the vibronic degrees of freedom are treated quantum mechanically as the system moves along a classical trajectory. The calculations use the potential energy surfaces computed by Archirel and Levy. Comparison is made with experimental results for this system, including the recent work from Ng's laboratory. In most cases the agreement is quite good. There is, however, a significant difference in the charge–transfer branching ratios to produce Ar+(2P3/2) or Ar+(2P1/2) products. Possible explanations of the discrepancy are discussed. As expected, the cross sections obey the Franck–Condon principle at energies above 200 eV.
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    URL: http://dx.doi.org/10.1063/1.457584
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  • 97
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    Second virial coefficients for O2 and N2 mixtures with rare gases: A computational assessment (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5352-5358 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Second virial coefficients as function of temperature are computed for the title molecular systems interacting with He, Ne, and Ar. The relevant anisotropic forces are obtained via accurate potential functions tested earlier through the analysis of several, different properties of the various systems. The relevant quantum corrections are also computed, in addition to the classical results, and their effects analyzed vis à vis the available experimental data. The influence of such corrections on the very low-T behavior of the virial coefficients and on the determination of the Boyle temperatures is also shown and discussed. All examined potential functions are found to yield B(T) values in rather good accord with experiments, in spite of their marked differences in anisotropic behavior and in the shape of their potential well regions.
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    URL: http://dx.doi.org/10.1063/1.457583
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  • 98
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    Crossed molecular beam study of the reaction O(3P)+C2H2 (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5365-5373 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The reaction between ground state atomic oxygen and acetylene was studied using the crossed molecular beam method with an average collision energy of 6 kcal/mol. The two major primary reaction channels are (a) formation of CH2 and CO and (b) formation of HCCO and H. Product angular distributions and time-of-flight spectra were measured and the translational energy release was determined for each channel. The reaction proceeds primarily on the triplet surface through a long-lived intermediate. For both channels the translational energy distributions were found to peak at about 30% of the total available energy, indicating the existence of an exit channel barrier in each case. The branching ratio between channel (a) and (b) was found to be 1.4±0.5.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457585
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  • 99
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    Temperature effect on nascent rotational state distribution of product MgH in reaction of Mg(3s3p1P1)+H2→MgH+H (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5387-5391 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A pump-and-probe technique is utilized to yield a population distribution over the rotational quantum states of the nascent product MgH in the reaction of Mg(1P1) and H2. The resulting normalized profile of the MgH bimodal distribution at 693 K coincides with that at 733 K, as well as with the results obtained at 380 K by Breckenridge and co-workers. This temperature dependence demonstrates that the bimodality actually results from the insertive reaction alone. This conclusion is consistent with the isotopic effect.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.457587
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  • 100
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    Oscillations in methylamine decomposition on Pt, Rh, and Ir: Experiments and models (1989)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 91 (1989), S. 5374-5386 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Oscillations with large amplitudes (〉500 K), high frequencies (〉8 Hz), and good reproducibility are observed in methylamine decomposition on electrically heated Pt, Rh, and Ir wires at pressures of 0.25–8.0 Torr and temperatures between 900 and 1500 K. The major reaction involves formation of HCN which is endothermic by 37 kcal/mol, so that the reaction strongly cools the wire, which counteracts resistive heating. A photodiode array was used to monitor spatial and temporal oscillations with resolutions of 1 mm and 30 Hz, respectively. On Pt, the frequency increased with increasing pressure and with decreasing wire diameter, while amplitude was a weak function of these parameters. On Ir, oscillations were more complex with regions of the wire often oscillating independently and more variability between experiments. However, the overall behavior resembles that on Pt. On Rh, frequencies were much lower (〈0.03 Hz), oscillations occurred over a smaller temperature range and halves of the wire frequently oscillated out of phase with each other. Oscillatory behavior of methylamine decomposition on Pt was modeled by a simple lumped model which gives semiquantitative agreement with observations. The model assumes a simple unimolecular reaction with CH3NH2 adsorption blocked at low temperatures by formation of a strongly adsorbed CN which is known to be very stable on Pt (Ed (approximately-equal-to)50 kcal/mol). Calculated frequencies, pressure dependencies, amplitudes, and temperature range of oscillations agree quite well with experiments using reasonable values for adsorption and reaction rate parameters, and wire geometry and properties.
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    URL: http://dx.doi.org/10.1063/1.457586
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