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  • American Physical Society (APS)  (75,161)
  • International Union of Crystallography (IUCr)
  • National Academy of Sciences
  • 2015-2019  (110,808)
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  • 1
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    Nitrate is an important nitrogen source for Arctic tundra plants (2018)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 3398-3403, doi:10.1073/pnas.1715382115.
    Description: Plant nitrogen (N) use is a key component of the N cycle in terrestrial ecosystems. The supply of N to plants affects community species composition and ecosystem processes such as photosynthesis and carbon (C) accumulation. However, the availabilities and relative importance of different N forms to plants are not well understood. While nitrate (NO3−) is a major N form used by plants worldwide, it is discounted as a N source for Arctic tundra plants because of extremely low NO3− concentrations in Arctic tundra soils, undetectable soil nitrification, and plant-tissue NO3− that is typically below detection limits. Here we reexamine NO3− use by tundra plants using a sensitive denitrifier method to analyze plant-tissue NO3−. Soil-derived NO3− was detected in tundra plant tissues, and tundra plants took up soil NO3− at comparable rates to plants from relatively NO3−-rich ecosystems in other biomes. Nitrate assimilation determined by 15N enrichments of leaf NO3− relative to soil NO3− accounted for 4 to 52% (as estimated by a Bayesian isotope-mixing model) of species-specific total leaf N of Alaskan tundra plants. Our finding that in situ soil NO3− availability for tundra plants is high has important implications for Arctic ecosystems, not only in determining species compositions, but also in determining the loss of N from soils via leaching and denitrification. Plant N uptake and soil N losses can strongly influence C uptake and accumulation in tundra soils. Accordingly, this evidence of NO3− availability in tundra soils is crucial for predicting C storage in tundra.
    Description: his study was supported by the Kyoto University Foundation, the Sumitomo Foundation, Program for Next Generation World-Leading Researcher (Grant GS008) and Grant-in-Aid for Scientific Research (KAKENHI Grants 26252020, 26550004, 17H06297, and P09316) from the Japan Society for Promotion of Science, the National Natural Science Foundation of China (Grants 41730855, 41522301, and 41473081), the National Key Research and Development Program of China (Grants 2016YFA0600802 and 2017YFC0210101), and the 11th Recruitment Program of Global Experts (the Thousand Talents Plan) for Young Professionals granted by the central budget of China.
    Keywords: Arctic tundra plants ; Nitrogen dynamics ; Plant nitrate ; Soil nitrate ; Stable isotopes
    Repository Name: Woods Hole Open Access Server
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  • 2
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    Primary productivity below the seafloor at deep-sea hot springs (2018)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 6756–6761, doi:10.1073/pnas.1804351115.
    Description: The existence of a chemosynthetic subseafloor biosphere was immediately recognized when deep-sea hot springs were discovered in 1977. However, quantifying how much new carbon is fixed in this environment has remained elusive. In this study, we incubated natural subseafloor communities under in situ pressure/temperature and measured their chemosynthetic growth efficiency and metabolic rates. Combining these data with fluid flux and in situ chemical measurements, we derived empirical constraints on chemosynthetic activity in the natural environment. Our study shows subseafloor microorganisms are highly productive (up to 1.4 Tg C produced yearly), fast-growing (turning over every 17–41 hours), and physiologically diverse. These estimates place deep-sea hot springs in a quantitative framework and allow us to assess their importance for global biogeochemical cycles.
    Description: This research was funded by a grant of the Dimensions of Biodiversity program of the US National Science Foundation (NSF-OCE-1136727 to S.M.S. and J.S.S.). Funding for J.M. was further provided by doctoral fellowships from the Natural Sciences and Engineering Research Council of Canada (PGSD3-430487-2013, PGSM-405117-2011) and the National Aeronautics and Space Administration Earth Systems Science Fellowship (PLANET14F-0075), an award from the Canadian Meteorological and Oceanographic Society, and the WHOI Academic Programs Office.
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  • 3
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    River-discharge effects on United States Atlantic and Gulf coast sea-level changes (2018)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences.of the United States of America 115 (2018): 7729-7734, doi:10.1073/pnas.1805428115.
    Description: Identifying physical processes responsible for historical coastal sea-level changes is important for anticipating future impacts. Recent studies sought to understand the drivers of interannual to multidecadal sea-level changes on the United States Atlantic and Gulf coasts. Ocean dynamics, terrestrial water storage, vertical land motion, and melting of land ice were highlighted as important mechanisms of sea-level change along this densely populated coast on these time scales. While known to exert an important control on coastal ocean circulation, variable river discharge has been absent from recent discussions of drivers of sea-level change. We update calculations from the 1970s, comparing annual river-discharge and coastal sea-level data along the Gulf of Maine, Mid-Atlantic Bight, South Atlantic Bight, and Gulf of Mexico during 1910–2017. We show that river-discharge and sea-level changes are significantly correlated (p〈0.01), such that sea level rises between 0.01 and 0.08 cm for a 1 km3 annual river-discharge increase, depending on region. We formulate a theory that describes the relation between river-discharge and halosteric sea-level changes (i.e., changes in sea level related to salinity) as a function of river discharge, Earth’s rotation, and density stratification. This theory correctly predicts the order of observed increment sea-level change per unit river-discharge anomaly, suggesting a causal relation. Our results have implications for remote sensing, climate modeling, interpreting Common Era proxy sea-level reconstructions, and projecting coastal flood risk.
    Description: C.G.P. and R.M.P. acknowledge support from NASA Contract NNH16CT01C (which also supported C.M.L.), NASA Jet Propulsion Laboratory Subcontract 1569246, and National Science Foundation Award 1558966. C.G.P. also acknowledges support from The Investment in Science Fund at Woods Hole Oceanographic Institution. A.C.K. and S.E.E. acknowledge NSF Awards OCE-1458921 and OCE-1458903, respectively.
    Keywords: Coastal sea level ; Coastal river plumes ; Coastal flood risk ; Climate modeling ; Physical oceanography
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  • 4
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    Different iron storage strategies among bloom-forming diatoms (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115(52), (2018): E12275-E12284. doi: 10.1073/pnas.1805243115.
    Description: Diatoms are prominent eukaryotic phytoplankton despite being limited by the micronutrient iron in vast expanses of the ocean. As iron inputs are often sporadic, diatoms have evolved mechanisms such as the ability to store iron that enable them to bloom when iron is resupplied and then persist when low iron levels are reinstated. Two iron storage mechanisms have been previously described: the protein ferritin and vacuolar storage. To investigate the ecological role of these mechanisms among diatoms, iron addition and removal incubations were conducted using natural phytoplankton communities from varying iron environments. We show that among the predominant diatoms, Pseudo-nitzschia were favored by iron removal and displayed unique ferritin expression consistent with a long-term storage function. Meanwhile, Chaetoceros and Thalassiosira gene expression aligned with vacuolar storage mechanisms. Pseudo-nitzschia also showed exceptionally high iron storage under steady-state high and low iron conditions, as well as following iron resupply to iron-limited cells. We propose that bloom-forming diatoms use different iron storage mechanisms and that ferritin utilization may provide an advantage in areas of prolonged iron limitation with pulsed iron inputs. As iron distributions and availability change, this speculated ferritin-linked advantage may result in shifts in diatom community composition that can alter marine ecosystems and biogeochemical cycles.
    Description: We thank the captain and crew of the R/V Melville and the CCGS J. P. Tully as well as the participants of the IRNBRU (MV1405) cruise for the California-based data, particularly K. Ellis [University of North Carolina (UNC)], T. Coale (University of California, San Diego), F. Kuzminov (Rutgers), H. McNair [University of California, Santa Barbara (UCSB)], and J. Jones (UCSB). W. Burns (UNC), S. Haines (UNC), and S. Bargu (Louisiana State University) assisted with sample processing and analysis. This work was funded by the National Science Foundation Grants OCE-1334935 (to A.M.), OCE-1334632 (to B.S.T.), OCE-1333929 (to K.T.), OCE-1334387 (to M.A.B.), OCE-1259776 (to K.W.B), and DGE-1650116 (Graduate Research Fellowship to R.H.L).
    Description: 2019-06-11
    Keywords: phytoplankton ; iron limitation ; Pseudo-nitzschia ; ferritin ; metatranscriptomics
    Repository Name: Woods Hole Open Access Server
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  • 5
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    Elesclomol restores mitochondrial function in genetic models of copper deficiency (2018)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2018. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 115 (2018): 8161-8166, doi:10.1073/pnas.1806296115.
    Description: Copper is an essential cofactor of cytochrome c oxidase (CcO), the terminal enzyme of the mitochondrial respiratory chain. Inherited loss-of-function mutations in several genes encoding proteins required for copper delivery to CcO result in diminished CcO activity and severe pathologic conditions in affected infants. Copper supplementation restores CcO function in patient cells with mutations in two of these genes, COA6 and SCO2, suggesting a potential therapeutic approach. However, direct copper supplementation has not been therapeutically effective in human patients, underscoring the need to identify highly efficient copper transporting pharmacological agents. By using a candidate-based approach, we identified an investigational anticancer drug, elesclomol (ES), that rescues respiratory defects of COA6-deficient yeast cells by increasing mitochondrial copper content and restoring CcO activity. ES also rescues respiratory defects in other yeast mutants of copper metabolism, suggesting a broader applicability. Low nanomolar concentrations of ES reinstate copper-containing subunits of CcO in a zebrafish model of copper deficiency and in a series of copper-deficient mammalian cells, including those derived from a patient with SCO2 mutations. These findings reveal that ES can restore intracellular copper homeostasis by mimicking the function of missing transporters and chaperones of copper, and may have potential in treating human disorders of copper metabolism.
    Description: This work was supported by National Institutes of Health Awards R01GM111672 (to V.M.G.), R01 DK110195 (to B.-E.K.), and DK 44464 (to J.D.G.); Welch Foundation Grant A-1810 (to V.M.G.); and Canadian Institutes of Health Research Operating Grant MOP 133562 (to S.C.L.).
    Keywords: Copper ; Mitochondria ; Elesclomol ; Cytochrome c oxidase
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  • 6
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    A kleptoplastidic dinoflagellate and the tipping point between transient and fully integrated plastid endosymbiosis (2019)
    National Academy of Sciences
    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 Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17934-17942, doi:10.1073/pnas.1910121116.
    Description: Plastid endosymbiosis has been a major force in the evolution of eukaryotic cellular complexity, but how endosymbionts are integrated is still poorly understood at a mechanistic level. Dinoflagellates, an ecologically important protist lineage, represent a unique model to study this process because dinoflagellate plastids have repeatedly been reduced, lost, and replaced by new plastids, leading to a spectrum of ages and integration levels. Here we describe deep-transcriptomic analyses of the Antarctic Ross Sea dinoflagellate (RSD), which harbors long-term but temporary kleptoplasts stolen from haptophyte prey, and is closely related to dinoflagellates with fully integrated plastids derived from different haptophytes. In some members of this lineage, called the Kareniaceae, their tertiary haptophyte plastids have crossed a tipping point to stable integration, but RSD has not, and may therefore reveal the order of events leading up to endosymbiotic integration. We show that RSD has retained its ancestral secondary plastid and has partitioned functions between this plastid and the kleptoplast. It has also obtained genes for kleptoplast-targeted proteins via horizontal gene transfer (HGT) that are not derived from the kleptoplast lineage. Importantly, many of these HGTs are also found in the related species with fully integrated plastids, which provides direct evidence that genetic integration preceded organelle fixation. Finally, we find that expression of kleptoplast-targeted genes is unaffected by environmental parameters, unlike prey-encoded homologs, suggesting that kleptoplast-targeted HGTs have adapted to posttranscriptional regulation mechanisms of the host.
    Description: We are grateful to Martin Kolisko and Fabien Burki for helpful discussion about and comments on the phylogenetic analysis; and Filip Husnik and Vittorio Boscaro for valuable comments on the manuscript. This work was supported by a grant from the National Science Foundation to R.J.G. and P.J.K. (PLR-1341362) and from the Natural Sciences and Engineering Research Council of Canada to P.J.K. (RGPIN-2014-03994).
    Description: 2020-02-19
    Keywords: plastid endosymbiosis ; kleptoplasty ; dinoflagellates ; plastid integration
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  • 7
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    NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica (2019)
    National Academy of Sciences
    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 Diaz, J. M., Plummer, S., Hansel, C. M., Andeer, P. F., Saito, M. A., & McIlvin, M. R. NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica. Proceedings of the National Academy of Sciences of the United States of America, 116 (33), (2019): 16448-16453, doi: 10.1073/pnas.1821233116.
    Description: Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.
    Description: This work was supported by a postdoctoral fellowship from the Ford Foundation (to J.M.D.), the National Science Foundation (NSF) under grants OCE 1225801 (to J.M.D.) and OCE 1246174 (to C.M.H.), a Junior Faculty Seed Grant from the University of Georgia Research Foundation (to J.M.D.), and a National Science Foundation Graduate Research Fellowship (to S.P.). The FIRe was purchased through a NSF equipment improvement grant (1624593).The authors thank Melissa Soule for assistance with LC/MS/MS analysis of peptide samples.
    Keywords: Reactive oxygen species ; Photosynthesis ; Oxidative stress ; Biogeochemistry
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  • 8
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    Rapid mixing and exchange of deep-ocean waters in an abyssal boundary current. (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(27), (2019): 13233-13238, doi: 10.1073/pnas.1904087116.
    Description: The overturning circulation of the global ocean is critically shaped by deep-ocean mixing, which transforms cold waters sinking at high latitudes into warmer, shallower waters. The effectiveness of mixing in driving this transformation is jointly set by two factors: the intensity of turbulence near topography and the rate at which well-mixed boundary waters are exchanged with the stratified ocean interior. Here, we use innovative observations of a major branch of the overturning circulation—an abyssal boundary current in the Southern Ocean—to identify a previously undocumented mixing mechanism, by which deep-ocean waters are efficiently laundered through intensified near-boundary turbulence and boundary–interior exchange. The linchpin of the mechanism is the generation of submesoscale dynamical instabilities by the flow of deep-ocean waters along a steep topographic boundary. As the conditions conducive to this mode of mixing are common to many abyssal boundary currents, our findings highlight an imperative for its representation in models of oceanic overturning.
    Description: The DynOPO project is supported by the UK Natural Environment Research Council (grants NE/K013181/1 and NE/K012843/1) and the US National Science Foundation (grants OCE-1536453 and OCE-1536779). A.C.N.G. acknowledges the support of the Royal Society and the Wolfson Foundation. S.L. acknowledges the support of award NA14OAR4320106 from the National Oceanic and Atmospheric Administration, US Department of Commerce. The statements, findings, conclusions, and recommendations are those of the authors, and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, or the US Department of Commerce. We are grateful to the scientific party, crew, and technicians on the RRS James Clark Ross for their hard work during data collection.
    Description: 2019-12-18
    Keywords: Ocean mixing ; Overturning circulation ; Submesoscale instabilities ; Turbulence
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  • 9
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    Causes of ice age intensification across the Mid-Pleistocene Transition (2017)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 114 (2017): 13114-13119, doi: 10.1073/pnas.1702143114.
    Description: During the Mid-Pleistocene Transition (MPT; 1,200–800 kya), Earth’s orbitally paced ice age cycles intensified, lengthened from ∼40,000 (∼40 ky) to ∼100 ky, and became distinctly asymmetrical. Testing hypotheses that implicate changing atmospheric CO2 levels as a driver of the MPT has proven difficult with available observations. Here, we use orbitally resolved, boron isotope CO2 data to show that the glacial to interglacial CO2 difference increased from ∼43 to ∼75 μatm across the MPT, mainly because of lower glacial CO2 levels. Through carbon cycle modeling, we attribute this decline primarily to the initiation of substantive dust-borne iron fertilization of the Southern Ocean during peak glacial stages. We also observe a twofold steepening of the relationship between sea level and CO2-related climate forcing that is suggestive of a change in the dynamics that govern ice sheet stability, such as that expected from the removal of subglacial regolith or interhemispheric ice sheet phase-locking. We argue that neither ice sheet dynamics nor CO2 change in isolation can explain the MPT. Instead, we infer that the MPT was initiated by a change in ice sheet dynamics and that longer and deeper post-MPT ice ages were sustained by carbon cycle feedbacks related to dust fertilization of the Southern Ocean as a consequence of larger ice sheets.
    Description: Research was supported by National Environmental Research Council (NERC) Studentship NE/I528626/1 (to T.B.C.); NERC Grant NE/P011381/1 (to T.B.C., M.P.H., G.L.F., E.J.R., and P.A.W.); NERC Fellowships NE/K00901X/1 (to M.P.H.), NE/I006346/1 (to G.L.F. and R.D.P), and NE/H006273/1 (to R.D.P.); Royal Society Wolfson Awards (to G.L.F. and P.A.W.); Australian Research Council Laureate Fellowship FL1201000050 (to E.J.R.); Swiss National Science Foundation Grant PP00P2-144811 (to S.L.J.); ETH Research Grant ETH-04 11-1 (to S.L.J.); European Research Council Consolidator Grant (ERC CoG) Grant 617462 (to H.P.); and NERC UK IODP Grant NE/F00141X/1 (to P.A.W.).
    Keywords: Boron isotopes ; MPT ; Geochemistry ; Carbon dioxide ; Paleoclimate
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  • 10
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    On the occurrence of cytochrome P450 in viruses (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(25), (2019):12343-12352, doi:10.1073/pnas.1901080116.
    Description: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 Å. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.
    Description: We thank Dr. David Nes (Texas Tech University) for providing sterols and Dr. Matthieu Legendre and Dr. Chantal Abergel (CNRS, Marseille) for access to the P. celtis sequences. Drs. Irina Arkhipova, Mark Hahn, Judith Luborsky, and Ann Bucklin commented on the manuscript. The research was supported by a USA-UK Fulbright Scholarship and a Royal Society grant (to D.C.L.), the Boston University Superfund Research Program [NIH Grant 5P42ES007381 (to J.J.S. and J.V.G.) and NIH Grant 5U41HG003345 (to J.V.G.)], the European Regional Development Fund and Welsh Government Project BEACON (S.L.K.), the Woods Hole Center for Oceans and Human Health [NIH Grant P01ES021923 and National Science Foundation Grant OCE-1314642 (to J.J.S.)], and NIH Grant R01GM53753 (to T.L.P.).
    Description: 2019-12-05
    Keywords: cytochrome P450 ; virus ; evolution ; domains of life ; redox partner
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  • 11
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    Mesoscale eddies release pelagic sharks from thermal constraints to foraging in the ocean twilight zone (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17187-17192, doi:10.1073/pnas.1903067116.
    Description: Mesoscale eddies are critical components of the ocean’s “internal weather” system. Mixing and stirring by eddies exerts significant control on biogeochemical fluxes in the open ocean, and eddies may trap distinctive plankton communities that remain coherent for months and can be transported hundreds to thousands of kilometers. Debate regarding how and why predators use fronts and eddies, for example as a migratory cue, enhanced forage opportunities, or preferred thermal habitat, has been ongoing since the 1950s. The influence of eddies on the behavior of large pelagic fishes, however, remains largely unexplored. Here, we reconstruct movements of a pelagic predator, the blue shark (Prionace glauca), in the Gulf Stream region using electronic tags, earth-observing satellites, and data-assimilating ocean forecasting models. Based on 〉2,000 tracking days and nearly 500,000 high-resolution time series measurements collected by 15 instrumented individuals, we show that blue sharks seek out the interiors of anticyclonic eddies where they dive deep while foraging. Our observations counter the existing paradigm that anticyclonic eddies are unproductive ocean “deserts” and suggest anomalously warm temperatures in these features connect surface-oriented predators to the most abundant fish community on the planet in the mesopelagic. These results also shed light on the ecosystem services provided by mesopelagic prey. Careful consideration will be needed before biomass extraction from the ocean twilight zone to avoid interrupting a key link between planktonic production and top predators. Moreover, robust associations between targeted fish species and oceanographic features increase the prospects for effective dynamic ocean management.
    Description: We thank D. McGillicuddy, G. Lawson, and G. Flierl for helpful discussions while developing this work and 2 anonymous reviewers whose feedback significantly improved the manuscript. We also thank C. Fischer and the OCEARCH team for their support of this research. This work was funded by awards to C.D.B. from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology; the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution; and the National Aeronatics and Space Administration (NASA) Earth and Space Science Fellowship. C.D.B. and P.G. acknowledge support from the NASA New Investigator Program Award 80NSSC18K0757, and P.G. acknowledges support from NSF Award OCE-1558809. This research is partially supported by funding to S.R.T. as part of the Audacious Project, a collaborative endeavor, housed at TED. We thank donors to the Woods Hole Oceanographic Institution (WHOI) ProjectWHOI crowdfunding campaign: The Secret Lives of Sharks. Computational support was provided by the Amazon Web Services Cloud Credits for Research program. Funding for the development of HYCOM has been provided by the National Ocean Partnership Program and the Office of Naval Research.
    Description: 2020-02-06
    Keywords: remote sensing ; oceanographic model ; satellite telemetry ; marine predator ; mesopelagic
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  • 12
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    A productivity collapse to end earth's great oxidation (2019)
    National Academy of Sciences
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    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (35), (2019): 17207-17212, doi:10.1073/pnas.1900325116.
    Description: It has been hypothesized that the overall size of—or efficiency of carbon export from—the biosphere decreased at the end of the Great Oxidation Event (GOE) (ca. 2,400 to 2,050 Ma). However, the timing, tempo, and trigger for this decrease remain poorly constrained. Here we test this hypothesis by studying the isotope geochemistry of sulfate minerals from the Belcher Group, in subarctic Canada. Using insights from sulfur and barium isotope measurements, combined with radiometric ages from bracketing strata, we infer that the sulfate minerals studied here record ambient sulfate in the immediate aftermath of the GOE (ca. 2,018 Ma). These sulfate minerals captured negative triple-oxygen isotope anomalies as low as ∼ −0.8‰. Such negative values occurring shortly after the GOE require a rapid reduction in primary productivity of 〉80%, although even larger reductions are plausible. Given that these data imply a collapse in primary productivity rather than export efficiency, the trigger for this shift in the Earth system must reflect a change in the availability of nutrients, such as phosphorus. Cumulatively, these data highlight that Earth’s GOE is a tale of feast and famine: A geologically unprecedented reduction in the size of the biosphere occurred across the end-GOE transition.
    Description: Olivia M. J. Dagnaud assisted during fieldwork. S. V. Lalonde and E. A. Sperling provided helpful comments on an early version of the manuscript. We thank N. J. Planavsky and an anonymous reviewer for their constructive feedback. M.S.W.H. was supported by an NSERC PGS-D and student research grants from National Geographic, the APS Lewis and Clark Fund, Northern Science Training Program, McGill University Graduate Research Enhancement and Travel Awards, Geological Society of America, Mineralogical Association of Canada, and Stanford University. P.W.C. acknowledges support from the University of Colorado Boulder, the Agouron Institute Geobiology postdoctoral Fellowship program, a Natural Sciences and Engineering Council of Canada Postgraduate Scholarship–Doctoral Program scholarship, and the NSTP. Y.P. was supported by the Strategic Priority Research Program of CAS (XDB26000000). T.J.H. thanks Maureen E. Auro for laboratory assistance and the NSF for supporting isotope research in the NIRVANA Labs.
    Description: 2020-02-12
    Keywords: Proterozoic ; primary productivity ; Great Oxidation Event ; triple-oxygen isotopes ; nutrient limitation
    Repository Name: Woods Hole Open Access Server
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  • 13
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    Sustained wood burial in the Bengal Fan over the last 19 My (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116(45), (2019): 22518-22525, doi:10.1073/pnas.1913714116.
    Description: The Ganges–Brahmaputra (G-B) River system transports over a billion tons of sediment every year from the Himalayan Mountains to the Bay of Bengal and has built the world’s largest active sedimentary deposit, the Bengal Fan. High sedimentation rates drive exceptional organic matter preservation that represents a long-term sink for atmospheric CO2. While much attention has been paid to organic-rich fine sediments, coarse sediments have generally been overlooked as a locus of organic carbon (OC) burial. However, International Ocean Discovery Program Expedition 354 recently discovered abundant woody debris (millimeter- to centimeter-sized fragments) preserved within the coarse sediment layers of turbidite beds recovered from 6 marine drill sites along a transect across the Bengal Fan (∼8°N, ∼3,700-m water depth) with recovery spanning 19 My. Analysis of bulk wood and lignin finds mostly lowland origins of wood delivered episodically. In the last 5 My, export included C4 plants, implying that coarse woody, lowland export continued after C4 grassland expansion, albeit in reduced amounts. Substantial export of coarse woody debris in the last 1 My included one wood-rich deposit (∼0.05 Ma) that encompassed coniferous wood transported from the headwaters. In coarse layers, we found on average 0.16 weight % OC, which is half the typical biospheric OC content of sediments exported by the modern G-B Rivers. Wood burial estimates are hampered by poor drilling recovery of sands. However, high-magnitude, low-frequency wood export events are shown to be a key mechanism for C burial in turbidites.
    Description: This work was funded by National Science Foundation Grants OCE-1401217 and COL-T354A55 to S.J.F. and OCE-1400805 to V.G. Graduate student participation in the project received support from University of Southern California Provost’s Fellowship to H.L. Samples were provided by the International Ocean Discovery Program. We are grateful for the efforts of the Expedition 354 Science Party, Carl Johnson, and Zongguang Liu. C.F.-L. and A.G. were supported by IODP-France. We thank Colin Osborne and Maria Vorontsova for helpful discussions.
    Description: 2020-04-21
    Keywords: carbon cycle ; wood ; lignin ; Himalaya ; Bengal Fan
    Repository Name: Woods Hole Open Access Server
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  • 14
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    Abiotic methane synthesis and serpentinization in olivine-hosted fluid inclusions (2019)
    National Academy of Sciences
    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 Proceedings of the National Academy of Sciences.of the United States of America 116(36), (2019): 17666-17672. doi:10.1073/pnas.1907871116.
    Description: The conditions of methane (CH4) formation in olivine-hosted secondary fluid inclusions and their prevalence in peridotite and gabbroic rocks from a wide range of geological settings were assessed using confocal Raman spectroscopy, optical and scanning electron microscopy, electron microprobe analysis, and thermodynamic modeling. Detailed examination of 160 samples from ultraslow- to fast-spreading midocean ridges, subduction zones, and ophiolites revealed that hydrogen (H2) and CH4 formation linked to serpentinization within olivine-hosted secondary fluid inclusions is a widespread process. Fluid inclusion contents are dominated by serpentine, brucite, and magnetite, as well as CH4(g) and H2(g) in varying proportions, consistent with serpentinization under strongly reducing, closed-system conditions. Thermodynamic constraints indicate that aqueous fluids entering the upper mantle or lower oceanic crust are trapped in olivine as secondary fluid inclusions at temperatures higher than ∼400 °C. When temperatures decrease below ∼340 °C, serpentinization of olivine lining the walls of the fluid inclusions leads to a near-quantitative consumption of trapped liquid H2O. The generation of molecular H2 through precipitation of Fe(III)-rich daughter minerals results in conditions that are conducive to the reduction of inorganic carbon and the formation of CH4. Once formed, CH4(g) and H2(g) can be stored over geological timescales until extracted by dissolution or fracturing of the olivine host. Fluid inclusions represent a widespread and significant source of abiotic CH4 and H2 in submarine and subaerial vent systems on Earth, and possibly elsewhere in the solar system.
    Description: We are indebted to J. Eckert for his support with FE-EMPA; to K. Aquinho and E. Codillo for providing samples from Zambales; to K. Aquinho for Raman analysis of some of the samples from Zambales and Mt. Dent; to H. Dick for providing access to his thin section collection; to the curators of the IODP core repositories for providing access to Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) samples; and to the captains and crews of the many cruises without whom the collection of these samples would not have been possible. Reviews by Peter Kelemen and an anonymous referee greatly improved this manuscript. This study is supported with funds provided by the National Science Foundation (NSF-OCE Award 1634032 to F.K. and J.S.S.).
    Description: 2020-02-19
    Keywords: Abiotic methane ; Fluid inclusions ; Serpentinization ; Methane seeps ; Carbon cycling
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  • 15
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    Complete arsenic-based respiratory cycle in the marine microbial communities of pelagic oxygen-deficient zones. (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © The Author(s), 2019. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 116(20), (2019):9925-9930, doi:10.1073/pnas.1818349116.
    Description: Microbial capacity to metabolize arsenic is ancient, arising in response to its pervasive presence in the environment, which was largely in the form of As(III) in the early anoxic ocean. Many biological arsenic transformations are aimed at mitigating toxicity; however, some microorganisms can respire compounds of this redox-sensitive element to reap energetic gains. In several modern anoxic marine systems concentrations of As(V) are higher relative to As(III) than what would be expected from the thermodynamic equilibrium, but the mechanism for this discrepancy has remained unknown. Here we present evidence of a complete respiratory arsenic cycle, consisting of dissimilatory As(V) reduction and chemoautotrophic As(III) oxidation, in the pelagic ocean. We identified the presence of genes encoding both subunits of the respiratory arsenite oxidase AioA and the dissimilatory arsenate reductase ArrA in the Eastern Tropical North Pacific (ETNP) oxygen-deficient zone (ODZ). The presence of the dissimilatory arsenate reductase gene arrA was enriched on large particles (〉30 um), similar to the forward bacterial dsrA gene of sulfate-reducing bacteria, which is involved in the cryptic cycling of sulfur in ODZs. Arsenic respiratory genes were expressed in metatranscriptomic libraries from the ETNP and the Eastern Tropical South Pacific (ETSP) ODZ, indicating arsenotrophy is a metabolic pathway actively utilized in anoxic marine water columns. Together these results suggest arsenic-based metabolisms support organic matter production and impact nitrogen biogeochemical cycling in modern oceans. In early anoxic oceans, especially during periods of high marine arsenic concentrations, they may have played a much larger role.
    Description: We thank John Baross and Rika Anderson for helpful discussions and feedback on this project. We also thank the chief scientists of the research cruise, Al Devol and Bess Ward, as well as the captain and crew of the R/V Thomas G. Thompson. This work was supported through a NASA Earth and Space Sciences Graduate Research Fellowship to J.K.S. and National Science Foundation Grant OCE-1138368 (to G.R.).
    Description: 2019-10-29
    Keywords: Oxygen deficient zones ; Arsenic ; Chemoautotrophy ; Dissimilatory arsenate reduction ; Marine metagenome
    Repository Name: Woods Hole Open Access Server
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  • 16
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    Decadal trends in the ocean carbon sink (2019)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-26
    Description: Author Posting. © National Academy of Sciences, 2019. This article is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 116 (24), (2019):11646-11651, doi:10.1073/pnas.1900371116.
    Description: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from pCO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.
    Description: We thank Rebecca Wright and Erik Buitenhuis at University of East Anglia, Norwich, for providing updated runs from the NEMO-PlankTOM5 model. T.D. was supported by NSF Grant OCE-1658392. C.L.Q. thanks the UK Natural Environment Research Council for supporting the SONATA Project (Grant NE/P021417/1). P.L. was supported by the Max Planck Society for the Advancement of Science. J.H. was supported under Helmholtz Young Investigator Group Marine Carbon and Ecosystem Feedbacks in the Earth System (MarESys) Grant VH-NG-1301. S.B. and R.S. were supported by the H2020 project CRESCENDO “Coordinated Research in Earth Systems and Climate: Experiments, Knowledge, Dissemination and Outreach,” which received funding from the European Union’s Horizon 2020 research and innovation program under Grant No 641816. SOCAT is an international effort, endorsed by the International Ocean Carbon Coordination Project, the Surface Ocean-Lower Atmosphere Study, and the Integrated Marine Biosphere Research program, to deliver a uniformly quality-controlled surface ocean CO2 database. The many researchers and funding agencies responsible for the collection of data and quality control are thanked for their contributions to SOCAT.
    Description: 2019-11-28
    Keywords: Carbon dioxide ; Ocean carbon sink ; Terrestrial carbon sink ; Climate variability ; Carbon budget
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  • 17
    Electronic Resource
    Electronic Resource
    K-edge anomalous scattering in rubidium hydrogen tartrate (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 18-20 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Anomalous X-ray scattering terms for Rb+ near the K-edge measured in diffraction experiments with synchrotron radiation range up to 4.71 (6) for f′′ and down to −9.80 (11) for f′, in agreement with values derived from the absorption spectrum.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S002188988901023X
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  • 18
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    X-ray reflectivity of bent perfect crystals in Bragg and Laue geometry (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 35-42 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The X-ray reflectivity of bent perfect crystals is calculated from a model where the crystal is approximated by a stack of perfect-crystal lamellae which have a gradually changing orientation. A computer program is developed for calculation of the reflectivity of the composite crystal from the dynamical theory of diffraction. An approximate solution is also given where an analytical formula for the reflectivity of a non-absorbing lamella is used and the effects of absorption are calculated separately. Typically, in the Bragg case, the reflectivity curve has a steep edge and an exponentially falling slope, while in the Laue case the curve is almost rectangular if the absorption is not too large. The width of the curve is inversely proportional to the bending radius in both cases. Reflectivity curves were measured for the 111 and 400 reflections of Si with Mo Kα1 radiation. The agreement with analytical and computer calculations is good, particularly at small bending radii where the kinematical limit is approached.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889010800
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  • 19
    Electronic Resource
    Electronic Resource
    A fast high-accuracy lattice-parameter comparator (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 63-69 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method of measuring differences in lattice spacing with an accuracy of 1 part in 108 in a period as short as two minutes is described. The method uses one source of copper radiation and a triple-axis arrangement. Two of these axes are double-leaf silicon springs in monolithic crystal assemblies which achieve the high stability required by such measurements. Samples are easily changed and sequences of measurements are performed entirely under computer control. The method is demonstrated by a comparison of the lattice spacings of four samples which reveals differences of up to 60 parts in 108 between silicon crystals of different origins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889011623
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  • 20
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    Radiographic test of sample arrangement in synchrotron radiation (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 77-78 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889011635
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  • 21
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    Electronic Resource
    An elastically bent silicon crystal as a monochromator for thermal neutrons (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 105-110 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Some experimental results are presented for an elastically bent perfect silicon crystal in a strongly asymmetric diffraction geometry as a neutron monochromator. The use of this unconventional geometry of the monochromator appears to be suitable for a wide (several centimetres) incident polychromatic beam, when, thanks to the spatial condensation of the diffracted neutrons (Fankuchen effect), a high monochromatic beam density may be obtained. Furthermore, when using focusing in real and in momentum space by adjusting an optimum bending radius, the intensity diffracted by a sample may be comparable even with the best mosaic monochromators such as highly oriented pyrolytic graphite (PG). A comparison is demonstrated on the rocking curves of a strongly mosaic Ni–Al(020) crystal obtained with the monochromatic beam from bent Si(111), Si(400) and from PG(002), Cu(220) mosaic monochromators.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889012975
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  • 22
    Electronic Resource
    Electronic Resource
    Easy derivation of the formula relating the fluctuations of a binary system to the X-ray scattering intensity extrapolated to s = 0 (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 134-135 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Bhatia & Thornton [Phys. Rev. B. (1970), 2, 3004–3012] have derived the formula that relates the scattering intensity of a binary system to the Fourier transform of the local number density and concentration. For the intensity at the limit of zero scattering angle, the same formula can be derived by a much simpler process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889012331
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  • 23
    Electronic Resource
    Electronic Resource
    SGROUP – a program for determination of possible space groups from structure-factor listings (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 142-143 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889010423
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  • 24
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    New Commercial Products (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 144-146 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890099897
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  • 25
    Electronic Resource
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    Laue film integration and deconvolution of spatially overlapping reflections (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 169-174 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Single-crystal synchrotron-radiation Laue photographs of protein crystals and viruses are densely populated and a considerable amount of spatial overlapping of spots often occurs on the films. An integration procedure which enables the efficient deconvolution of these spots in order to obtain their integrated intensity has been developed and implemented. Some results are given for glycogen phosphorylase b and tomato bushy stunt virus. A comparative study of reflections overlapped on one exposure and separated on another, taken from the same crystal at a longer crystal-to-film distance, gives merging statistics comparable to those from the treatment of spatially separated spots only. In all cases the majority of the spatially overlapped data is made available for subsequent analyses.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890000346
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  • 26
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    Electronic Resource
    Absolute polarity of α-lithium iodate (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 211-212 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Previous reports by Rosenzweig & Morosin [Acta Cryst. (1966). 20, 758–761], Liminga & Abrahams [J. Appl. Cryst. (1976). 9, 42–47] and Svensson, Albertsson, Liminga, Kvick & Abrahams [J. Chem. Phys. (1983). 78, 7343–7352], that the more steeply pointed ends of α-LiIO3 crystals grown from aqueous solution with 3 ≤ pH ≤ 7 have the apex of each pyramidal IO−3 ion pointing toward the direction which develops a positive polarity (d33 〉 0) under tensile stress applied along the polar hexagonal axis, have been confirmed contrary to the conclusion of Yang Hua-guang, Zhang Dao-fan, Chen Wan-chun & Li Yin-yuan [J. Appl. Cryst.(1989). 22, 144–149]. The error leading to the latter conclusion is identified.
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  • 27
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    Electronic Resource
    Crystallographers (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 223-223 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890004046
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  • 28
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    Electronic Resource
    EDAUTOCAL – a program to calibrate EDXRD detector systems (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 222-223 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890001716
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  • 29
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    Extreme asymmetric X-ray Bragg reflection of semiconductor heterostructures near the edge of total external reflection (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 228-233 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Synchrotron radiation has been used to measure the rocking curves from a (GaIn)(AsP) single layer grown on an InP (100)-oriented substrate. For angles of incidence ΦB = (ΘB − φ) ≤ 0.7° measured at the Bragg angle ΘB (φ is the angle between the diffracting lattice plane and the surface), the rocking curve (RC) is very strongly influenced by total external reflection (TER). This causes a decrease in the full width at half-maximum (FWHM) and an asymmetrical shape for the RC for small ΦB. Both of these effects are due to the Bragg-angle shift from the actual incident angle Φ which is not considered in the conventional dynamical theory. In this paper the essential influence of TER on any thin-layer rocking curve is investigated using a numerical solution of the extended dynamical theory. The pattern can be interpreted up to ΦB ≥ ΘC (ΘC is the angle of TER) by semiempirical incorporation of the results of the extended theory with the coupling formalism of Barrels, Hornstra & Lobeek [Acta Cryst. (1986). A42, 539–545].
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    URL: http://dx.doi.org/10.1107/S0021889890001704
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  • 30
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    Study of ferroelastic domains in HTMA crystals at the ferroelectric–ferroelastic transition (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 277-281 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The ferroelectric ferroelastic phase transitions of tetramethylammonium tetrachlorozincate (HTMA) were observed by standard X-ray topography and by synchrotron topography. Observation of the phase boundary is possible in the latter case. The different kinds of domain walls observed in the ferroelastic phase cast doubts on the commonly assumed symmetry group of this phase.
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  • 31
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    Convolutional approach to the normalization of intensity scattered by polycrystalline substances (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 180-185 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A theory is presented describing convolutional properties of the reduced intensity distribution (intensity divided by the square of the atomic factor and multiplied by the scattering-vector length). The approximation used, verified on model data, leads to a relation between the effect of the multiple running average routine applied to reduced intensity and both normalization constant and local atomic density in the neighbourhood of any given atom. This enables an estimate of the normalization constant and the local density to be made with a high degree of accuracy. The effect of the choice of adjustable parameters in the running average routine is discussed. The procedure to calculate the interference function in the presence of an unknown background varying slowly with the scattering vector is presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S002188989000036X
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  • 32
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    An omega-scan artifact observed in Nicolet P3F diffractometers (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 212-214 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: This paper describes an instrumental artifact which has been observed in three Nicolet P3F diffractometers. In cases where the peaks are very sharp in ω, the artifact causes azimuthal or ψ scans to appear very noisy and to show a complex periodic variation of intensity with ψ. These intensity variations are reproducible. A simple correction is described which, when applied to the data, dramatically improves the appearance of these aberrant ψ scans. This correction is not limited to ψ scans and should improve the quality of all data collected on the machine.
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    URL: http://dx.doi.org/10.1107/S0021889889014329
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  • 33
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    A procedure for the generation of the symmetry of the multiple implication function from the crystal symmetry (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 225-227 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A computer-oriented procedure for the generation of the symmetry of the multiple implication function has been developed. The symmetry of the multiple implication function, referred to its own conventional unit cell, is tabulated for all space groups.
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    Auto-indexing of oscillation images (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 253-257 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method is presented which indexes spots recorded on single oscillation images without any a priori knowledge of cell parameters. The strategy is similar to that used in four-circle diffractometry and the method works in a fully automatic manner. It is applicable to multiple oscillation images or multiple stills. A complementary method is also described to obtain orientation angles for the case where cell parameters have already been determined.
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    A high-resolution Weissenberg camera for X-ray synchrotron radiation (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 351-354 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A photographic Weissenberg camera has been constructed which can be mounted on the 2θ arm of a four-circle diffractometer. At a distance of 0.5 m from the sample the 2θ resolution for a 100 μm crystal is 0.2 mrad (0.01°), allowing a high-resolution mapping of reciprocal space at a synchrotron source in an efficient way. As sample experimental results, a study is presented of the streak system around the 111 reflection of a perfect germanium crystal and the detection of a minute phase transformation in a single-powder grain of a high-Tc superconductor.
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    Improvements to the Chebyshev expansion of attenuation correction factors for cylindrical samples (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 378-386 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The accuracy of the Chebyshev expansion coefficients used for the calculation of attenuation correction factors for cylindrical samples has been improved. An increased order of expansion allows the method to be useful over a greater range of attenuation. It is shown that many of these coefficients are exactly zero, others are rational numbers, and others are rational fractions of π−1 The assumptions of Sears [J. Appl. Cryst. (1984), 17, 226–230] in his asymptotic expression of the attenuation correction factor are also examined.
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    High-pressure single-crystal study on AlPO4 with synchrotron radiation (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 397-400 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A single-crystal study on AlPO4 was performed at 2.90 (7) GPa with synchrotron radiation using a diamond-anvil cell with a beryllium gasket. For the data collection the radiation wavelength of only 0.54 Å, was chosen to minimize the absorption of X-rays in the pressure cell. The diffracted intensity was high enough to measure even weak reflections with sufficient counting statistics. The refined structural parameters are in good agreement with those determined from data collected with a conventional X-ray tube.
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    Structural study of Cd(S,Se) doped glasses. High-resolution transmission electron microscopy (HRTEM) assisted by image processing (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 418-423 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: High-resolution transmission electron microscopy (HRTEM) was used for examining Cd(S,Se) nanocrystals grown in silicate glasses commercially available as optical filters. The lattice images of the nanocrystals were numerated and submitted to filtering through Fourier transformation in order to sweep off the background signal originating mainly from glass. Optical filters from several firms were examined. The nanocrystals have been identified with Cd(S,Se) compounds crystallized in the wurzite structure, as in bulk material. The lattice images indicate crystallites having the shape of hexagonal prisms a little elongated along the c axis. The distribution of grain size differs according to the filter: the smallest size being about 1.5 nm (threshold for detection), the largest size varies from 7 to 10 nm, the average size sa, from 3–4 to 5–6 nm and the characteristic size sc from 5–6 to 7–8 nm (sc is the size of grains occupying the main part of the crystallized volume).
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    Silicon photodiode detector for small-angle X-ray scattering (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 430-432 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A photodiode X-ray detector was built to measure small-angle X-ray scattering (SAXS) at a synchrotron-radiation source in conjunction with a double-crystal diffractometer SAXS camera at photon energies between 5 and 11 keV. The photodiode detector response in this energy range is linear at photon counting rates up to 1012 photons s−1 and thus it was not necessary to attenuate the monochromatic X-ray beam with calibrated foils. SAXS data taken with a scintillation counter and the photodiode detector are compared, demonstrating marked improvement in counting statistics, rate of data acquisition and signal-to-noise ratio.
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    Sub-nanosecond X-ray powder diffraction (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 441-443 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The X-rays emitted from a laser-produced plasma have been used to obtain powder diffraction patterns with exposures of less than a nanosecond. The X-rays were produced by focusing approximately 50 J of 0.53 μm laser light in a 600 ps (FWHM) pulse to a tight (1̃00 μm diameter) spot on a solid titanium target. The spectral brightness of the resonance line of the helium-like titanium thus produced was sufficient to record diffraction from LiF powder in a single exposure using the Seemann–Bohlin geometry. These results indicate that time-resolved measurements of the lattice parameters of polycrystalline materials can be made with sub-nanosecond temporal resolution.
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    New Commercial Products (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 446-446 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
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    A position-sensitive detector system for the measurement of diffuse X-ray scattering (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 476-484 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The use of a one-dimensional position-sensitive detector for diffuse X-ray scattering measurements is described. Calibration procedures for scattering angle and intensity measurements are discussed. Some nonuniformities have been found in the counting efficiency as a function of distance along the detector. A procedure is described for measuring the diffuse scattering in a section of reciprocal space.
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    Short-range-order determination in quenched NbC0.73 by elastic diffuse neutron scattering (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 497-508 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The elastic diffuse neutron scattering of an NbC0.73 single-crystal has been measured at room temperature on two different spectrometers, the four-circle D10 at the HFR–ILL (Grenoble), and the two-axis G44 with time-of-flight analysis at the Laboratoire Léon Brillouin (Saclay). The data were treated either by Fourier transformations or by least-squares fit. The short-range-order parameters and the interatomic static displacements obtained by the various experiments and/or data treatment are in good agreement: carbon vacancies tend to be third neighbours in the f.c.c. metalloid sublattice and metal atoms relax away from the vacancy first neighbours by 0̃.05 Å. It is shown that the treatment of diffuse scattering data limited to two reciprocal planes [(001) and (1{\bar 1}0)] gives satisfactory results.
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    Electron-density distribution from X-ray powder data by use of profile fits and the maximum-entropy method (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 526-534 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Following the profile decomposition of CeO2 X-ray powder data into individual structure factors, the maximum-entropy method (MEM) has been used to obtain an electron-density-distribution map. In the profile decomposition process, it is impossible to avoid the problems of overlapping peaks which have the same magnitude of reciprocal vectors, such as d*(511) and d*(333), for a cubic crystal, or very severely overlapping reflections. The formalism to treat such overlapping reflections in the MEM analysis is to introduce combined structure factors. The maximum value of the scattering vector, 4π(sinθ)/λ, which was used in the present analysis is small (about 7.8 Å−1) but the resulting electron-density-distribution map is of a high quality and much superior to the conventional map. As a consequence, the ionic charge of Ce and O ions can be obtained with reasonable accuracy from the MEM density map. Furthermore, the map reveals the existence of electrons around the supposedly vacant site surrounded by eight O atoms, which is probably related to the high ionic conductivity of this substance.
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    SYMABS – an interactive program for checking systematic absences caused by lattice centering, glide planes and screw axes (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 558-558 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Prices of Acta Crystallographica and Journal of Applied Crystallography (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 560-560 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    The rôle of phase in diffuse diffraction patterns and its effect on real-space structure (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 18-29 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A previously described method of synthesizing a real-space distribution of scattering points which will give rise to virtually any required diffraction pattern has been investigated from the point of view of trying to establish the rôle that the phase of individual modulations plays in determining the real-space structure. For an object involving continuous random variables, the choice of phase cannot affect the diffracted intensity and phases can be chosen freely. Although such variation of phases does not affect the diffracted intensity, the real-space amplitudes are no longer normally distributed and the structures will in general contain non-zero multisite correlations. For an object involving binary variables (such as site occupancy), it is shown that the phases of individual elementary volumes of reciprocal space not only contain information about multisite correlations, but also contain the information that the object is binary. It is also shown that the information concerning multisite correlations can be, at least partially, transferred to an object giving a different diffraction pattern by using a known set of phases with a different set of amplitudes.
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    Absolute structures: is your diffractometer right-handed? (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 63-63 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Establishment of absolute structures requires measurement of Bijvoet differences with a right-handed set of axes. There can be pitfalls in the satisfaction of this requirement, and a very simple method of assessing this hand is described.
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    Restrained refinement and results analysis for incommensurate crystal structures (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 66-70 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Restraint equations suitable for incommensurate (IC) structure refinement by least squares are defined. Other quantities used in the final results analysis are reviewed. The main purpose of such a restrained refinement is to prevent high local variations of stereochemical parameters (e.g. bond lengths and/or angles), leaving the corresponding average values to be refined. The method is a natural generalization of that commonly used for commensurate structures and in some cases does not require user-supplied parameters.
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    New Commercial Products (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 78-78 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Accurate determination of the deviation from coincidence orientation for grain boundaries in hexagonal materials (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 96-101 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Accurate measurement of the deviation from coincidence orientation for grain boundaries allows the intergranular dislocation structure to be predicted. For hexagonal symmetry, the deviation may generally be split into two components: a pure rotation and a deformation. This rotation may be determined directly by measuring the displacement of rational common zone axes across the grain boundary plane, independently of any coincidence site lattice (CSL). The precision on the elements of the rotation – axis and angle – depends strongly on the sharpness of the Kikuchi lines. For deformed and annealed magnesium, a precision of 10° on the axis position and of 0.2° on the rotation angle has been obtained.
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    XENVIEW - an interactive program to display and analyze electronic area detector data (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 196-196 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    A standardless method of quantitative mineral analysis using X-ray and chemical data (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 197-202 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: A complex standardless mineral-analysis method is described which determines both the concentrations and the chemistry of minerals in a batch of m ≤ w + t suitable rock samples, where w and t are the numbers of crystalline and amorphous minerals, respectively. The method is based on data from X-ray diffractometry and the bulk chemistry of the samples. Analytical examples are given. The problem of the accuracy of the analysis is discussed.
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    High-resolution small-angle X-ray scattering camera for anomalous scattering (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 30-37 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The design and operation of a new small-angle X-ray scattering instrument, optimized for high throughput at a synchrotron source, high angular and wavelength resolution, large sample cross-sectional area, accurate energy tuning, excellent signal-to-noise ratio and harmonic rejection are presented. The principles of design and implementation are given, as are the details of primary calibration of absolute intensity and experimental desmearing. The instrument has been tested for application to anomalous-scattering measurements near the chromium K edge. Preliminary results on samples of a heat-treated steel are presented as a demonstration of the capability of this experiment to separate the microstructure evolution as a function of temperature of a chromium-rich precipitate from the thermal behavior of other precipitates in the steel.
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    A multimode high-angular-resolution powder diffractometer (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 61-63 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: A new powder diffractometer has been designed which can be used for various experimental geometries such as the long-arm Bragg–Brentano method, Guinier method and parallel-beam method. The X-ray source, goniometer and scintillation counter are placed on rails so that the source-to-monochromator, monochromator-to-sample and sample-to-counter distances can be changed arbitrarily. A FWHM of 0.07° for the Kα1 peak of the silicon 111 reflection was obtained by lengthening the counter arm in the Bragg-Brentano method. Rather high angular resolution was achieved by the Guinier and parallel-beam methods for organic samples having poor crystallinity and low absorption.
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    Monteregian treasures by J. A. Mandarino and V. Anderson (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 266-266 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Structure determination of magnesium boron nitride, Mg3BN3, from X-ray powder diffraction data (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 286-292 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The crystal structure of magnesium boron nitride in the low-pressure phase, Mg3BN3(L), has been solved ab initio from X-ray powder data. The cell is hexagonal (space group P63/mmc, Z = 2) with a = 3.54453 (4), c = 16.03536 (30) Å. Initial positional parameters for the Mg atoms were obtained from Patterson functions generated by 50 integrated intensities derived from a whole-powder pattern decomposition. The remaining atoms were located by trial-and-error model building, followed by Rietveld refinements (Rwp = 8.5%). The structure can be described as consisting of ABB′BACC′CA... layers perpendicular to the c axis with linear N=B=N molecular anions at position A, Mg2+ at positions B and C and Mg2+ with three coordinating N atoms at positions B′ and C′, although Mg3BN3(L) is not a layer compound. A very similar structure has also been obtained by applying standard direct methods to the same intensity data. A high-quality electron-density map has been calculated from the structure factor data using the maximum-entropy method.
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    Strain field due to a slip band near a grain boundary in an Fe-6at.% Si bicrystal. I. Elastic strain of a slip band meeting the free surface (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 316-323 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Measurements of lattice distortion due to a slip band were carried out and compared with the theoretically estimated values. A simple model of a single-slip system with uniformly distributed dislocations in a narrow planar slip band was adopted. It was shown that both the effect of all dislocations in the slip band and the surface relaxation must be taken into account.
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    Determination of the direction of the propagation vector for incommensurate structures from neutron powder diffraction patterns (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 365-368 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method is presented for indexing the powder diffraction lines from incommensurate structures by a systematic search of reciprocal space, choosing a propagation vector length derived from a satellite reflection in the powder diagram. An interactive computer program gives a graphical display of the direction of the propagation vector which gives the best fit to the pattern.
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    Diffractometer devices controlled by a personal computer (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 190-193 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: The application of single-board microcomputers as programmable interfaces simplifies the construction of complex diffractometer control units. The amount of hardware components of the control units is reduced and the structure of the circuits is easy to survey. These intelligent multipurpose single-board microcomputers unburden the personal computer and simplify the development of the diffractometer measuring program. The presented solution is based on an Atari 1040 STF. The concept, however, can be applied to any type of personal computer.
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    C3DCON: a stereo 3D electron-density cage contouring and atomic structure plotting program (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 193-195 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A Fortran computer program is described which performs three-dimensional electron-density cage contouring together with atomic structure model display on a Tektronix-4100 command graphics terminal hosted to a VAX/VMS computer. The program also supports ball-and-stick visualization of the model, on-line manipulation of the display and convenient hard-copy output. Such a program is useful in a research environment where an expensive graphics workstation is not readily available and hard copies of publication quality are often desired.
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    URL: http://dx.doi.org/10.1107/S002188989000989X
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    Geometrical principles of the monolithic X-ray magnifier (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 212-221 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The principles of the monolithic X-ray magnifier based on two successive asymmetric non-coplanar diffractions from the same crystal are analyzed from the geometrical point of view. The conditions of the distortion-free two-dimensional pattern magnification are formulated by means of matrix formalism. The general solution of the problem of determination of the crystal surface planes satisfying the conditions of distortion-free magnification is derived in the closed form. The calculation is performed on the basis of the kinematical theory of diffraction. It is shown that the number of solutions is infinite for any given pair of diffraction vectors and magnification. General properties of the solution are illustrated by some examples. The effect of the refraction of X-rays on the pattern distortion is estimated. The results suggest that the refractive index correction has a negligible influence on the distortion of the magnified pattern. The results presented enable us to prepare monolithic X-ray magnifiers or demagnifiers that can be used in various fields of X-ray optics, especially in X-ray topography and X-ray lithography.
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    URL: http://dx.doi.org/10.1107/S0021889890014285
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    High-symmetry triple junctions in polycrystalline silicon (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 232-238 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Triple junctions in polycrystalline silicon for solar cell applications have been studied by TEM (transmission electron microscopy). The typical characteristic of these junctions is the existence of high-symmetry interfaces, i.e. twins of different order. Whenever the triple junction contains two such interfaces, the intersection axis is a CSL (coincidence site lattice) symmetry axis. In this case the mutual relation of the grain boundaries of the triple junctions is revealed by symmetry rules, since the boundaries are described by symmetry elements of the corresponding CSL which do not belong to the symmetry group of the parent lattice. Therefore, the different variant orientations of these CSL symmetry elements, implied by the symmetry of the lattice, are used for the study of triple junctions. A junction is geometrically characterized by the point-group-symmetry properties. The observations concern symmetrically different triple junctions of the same type of macroscopically stable grain boundaries and faceted and microfaceted interfaces. It is shown that in silicon the thermodynamically favored twins are combined by specific symmetry rules. The results are discussed in accordance with the possible growth mechanisms.
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    Experimental verification of the triple isotopic substitution method in small-angle neutron scattering (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 243-254 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The theoretical predictions of the triple isotopic substitution (TIS) method in small-angle neutron scattering have been confirmed experimentally. A unique advantage of the method, namely the possibility to make part of a complex particle `invisible' in normal (H2O) buffer, is demonstrated. Particle association, the addition of `small' molecules (such as glycerol) or `large' molecules (such as pyruvate kinase) in the solutions under study have been shown not to influence the difference scattering curve obtained. The possibility of extracting normalized interparticle interference functions from the TIS data is discussed. This enables the detection of the presence of aggregates (e.g. dimers) in the solution, even in cases where the molar mass of a particle and/or its concentration are unknown. A simple internal test is suggested which checks whether or not sufficient conditions for the applicability of the method are fulfilled.
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    New Commercial Products (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 264-264 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889891099831
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    Experimental strategies in Laue crystallography (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 267-277 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The efficiency of data collection using the Laue technique varies with the wavelength range, the crystal symmetry, the orientation of the crystal in the X-ray beam, the crystal-to-film distance and the acceptance angle of the detector. By optimizing these parameters and by taking advantage of the diffraction symmetry represented by the Laue class, it is often possible to collect a nearly complete data set in one or two exposures. This paper discusses general strategies for data collection and presents results from a computer survey to find optimal crystal orientations for the eleven Laue classes.
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    Modelling of Bragg intensity profiles. 2. Allowance for thermal diffuse scattering (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 293-297 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method for empirical determination of TDS (thermal diffuse scattering) corrections in X-ray structure analysis is developed. Thermal diffuse scattering is introduced into the model suggested earlier [Chulichkov et al. (1987). Sov. Phys. Crystallogr. 32, 649–653; Laktionov, Chulichkov, Chulichkova, Fetisov, Pyt'ev & Aslanov (1989). J. Appl. Cryst. 22, 315–320] for measuring the Bragg reflection intensity profile with a four-circle diffractometer. The improved model in combination with the mathematical reduction method enables the extraction of TDS and background intensity values from the experimental intensity profile. Thus the problem of TDS correction in crystal structure refinement is solved without knowledge of the sample's elasticity constants. The comparison of TDS corrections obtained by this method with those calculated from elasticity constants for hexamethylenetetramine, C6H2N4, and sulfur, S8, crystals shows good agreement.
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    Strain field due to a slip band near a grain boundary in an Fe-6at.% Si bicrystal. II. Interpretation of double-crystal topographs (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 324-330 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The lattice distortion due to the head of the slip band at the grain boundary is measured by double-crystal topography. The head of the slip band is approximated by a macrodislocation situated at the grain boundary. To interpret the topographs, the relaxation due to the free surface is included. The Burgers vectors of macrodislocations, i.e. the number of accumulated dislocations, are found.
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    Powder Diffraction Program Information 1990 Program List (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 369-402 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889891003473
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    Protein crystal growth in the presence of poly(vinylidene difluoride) membrane (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 406-408 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889891001644
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    Time-resolved phenomena in cements, clays and porous rocks (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 624-634 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Small-angle neutron scattering (SANS) provides a powerful tool in the non-destructive characterization of statistically representative microstructures in technologically important disordered materials. While qualitative microstructural models must be provided by other methods such as transmission electron microscopy (TEM), SANS quantifies the microstructural parameters and can characterize scale-invariant (fractal) disordered materials such as cements, clays and porous rocks. H2O/D2O contrast-variation methods have proved particularly useful for investigating the accessibility of different parts of the pore structure and in differentiating between pore-volume access (measured by other methods) and pore-surface accessibility (likely to control sorption and leaching processes). This paper describes SANS studies of disordered porous materials, particularly the hydration of cement and the real-time permeation of water in clay minerals. Other microstructural effects are also considered.
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    Grazing-incidence X-ray scattering study of the microstructure of tungsten–carbon films (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 638-644 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The microstructure of a coating deposited onto a tungsten carbide layer by cathodic sputtering assisted by chemical vapour deposition (CVD) has been analysed by small-angle scattering of X-rays (SAXS) with a conventional laboratory set-up specially adapted for grazing incidence. Anomalous-scattering measurements have also been performed at LURE, the French synchrotron-radiation facility at Orsay with the aim of characterizing the structure of phases present in the coating. SAXS results reveal the existence of very small precipitates; the size of these precipitates determined from the use of the Guinier approximation is about 16 Å, the correlation length deduced from the position of the peak in the small-angle scattering pattern is about 36 Å. The value of the experimental integrated intensity and the variation of the observed intensities with photon energy lead to the conclusion that these nanocrystals are highly enriched in tungsten and embedded in a carbon-based matrix having a weak electronic density. Electron diffraction results support the assumption of the presence of β-WC1 − x, an unstable high-temperature phase. Furthermore, the low electronic density of the matrix is in agreement with face-centred-cubic carbon recently proposed in the literature.
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    Small-angle X-ray scattering study of lamellar microdomains in a block copolymer (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 679-684 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Lamellar microdomains formed in the solvent-cast films of a poly[styrene-block-(ethylene-alt-propylene)] (SEP) diblock polymer were studied by small-angle X-ray scattering (SAXS). The SAXS profiles, displaying a series of peculiar scattering maxima which cannot be ascribed to the higher-order diffraction maxima from a regular lamellar spacing, were analyzed based on a model of the one-dimensional paracrystal with a preferential orientation. The results suggest that these maxima are due to higher-order scattering maxima from single lamellar microdomains. The maxima suggest that the relative standard deviation for the distribution of the polystyrene lamellar size is much smaller than that of the lamellar spacing, giving rise to a situation in which the oscillation of the particle factor with scattering vector h persists up to high h values while that of the lattice factor damps to unity at low h values. The SAXS result was interpreted as being due to a bending distortion of the polystyrene lamella with a smaller thickness and a narrower thickness distribution than those of the poly(ethylene-alt-propylene) lamella. A study by transmission electron microscopy tends to support this result.
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    URL: http://dx.doi.org/10.1107/S0021889890012109
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    Small-angle neutron scattering from colloidal dispersions (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 436-443 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A survey is given of recent work on the use of small-angle neutron scattering to examine colloidal dispersions. Particular attention is given to the determination of particle size and polydispersity, the determination of particle morphology and the behaviour of concentrated colloidal dispersions, both at rest and under the influence of an applied shear field.
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    Profile analysis application in the modelling of multiwave diffraction (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 910-912 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The results of intensity profile analysis of Bragg reflections are used for the calculation of the reflectivity Q(Δθij, σij) = W(Δθij, σij)(|F|2Lp)ij in the energy transfer equation for multiwave X-ray diffraction in crystals. The diffraction profiles in the profile analysis are fitted by different analytical functions and the fitting results are used for modelling the multiwave diffraction. The results of modelling multiwave diffraction in Si and V3Si crystals with different grades of perfection demonstrate that the method suggested here is sensitive to the content of defects in crystals and can be used not only for simultaneous reflection correction in X-ray structure analysis but also for estimation of single-crystal perfection.
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    Dependence of the diffraction angle on the surface microstructure of a steel sample (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 928-930 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: While the deviations from linearity of ε−sin2ψ curves in the case of two welded hot-rolled C40 steel bars were being studied, this paper was prompted by the observation that, at ψ = 0°, the diffraction angle 2θ depends on φ, the inclination angle of the diffraction plane with respect to an arbitrarily chosen reference plane attached to the specimen. This result is unexpected and cannot be explained by bulk structural or microstructural factors. A surface effect is offered as a possible explanation.
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    MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 946-950 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The MOLSCRIPT program produces plots of protein structures using several different kinds of representations. Schematic drawings, simple wire models, ball-and-stick models, CPK models and text labels can be mixed freely. The schematic drawings are shaded to improve the illusion of three dimensionality. A number of parameters affecting various aspects of the objects drawn can be changed by the user. The output from the program is in PostScript format.
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    Closed-cycle helium cryostat mount for the Huber 511.1 diffractometer circle (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 961-962 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Modifications to the high-stability mounting device for the closed-cycle helium cryostat as developed by Henriksen, Larsen & Rasmussen [J. Appl. Cryst. (1986). 19, 390–394] are described. They allow use of the cryostat on the smaller Huber 511.1 diffractometer circle with a smaller source-to-sample distance and reduced blind and collision zones.
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    THGROUP – a program for determination of possible trigonal and hexagonal space groups from structure-factor listings (1991)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 24 (1991), S. 972-973 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
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    Treatment of SANS data from hot stretched polystyrene chains (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 1-5 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: The small-angle neutron scattering technique is applied to a hot stretched 5% perdeuterated polystyrene sample in order to investigate the residual macromolecular orientation at various length scales. The observed orientation is left over after fast quenching (in ice water) of the hot stretched sample. Previous investigations focused on how much polymer chains follow the external stretching. It is found that, even when macromolecules follow the external stretching affinely on the average, they do not deform uniformly. Moreover, over the time scale of the temperature quench, small chain portions relax more rapidly than large ones.
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    Measurement of anisotropic diffuse scattering with synchrotron radiation (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 21-25 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: Anisotropic diffuse scattering of the one-dimensional conductor K-hollandite has been measured at a synchrotron source and compared with measurements with a rotating anode. The intensity gain of more than one order of magnitude and the ability to adjust the wavelength provide the counting statistics in a few hours that are necessary for a quantitative analysis of diffuse phenomena. The main advantage of a synchrotron source is the high resolution throughout reciprocal space (low and high Q). Thus, commensurate/incommensurate positions of diffuse layers may be distinguished, weak diffuse maxima become detectable and small peak shifts of diffuse modulations clearly visible. Correlation functions may be determined directly from the diffuse profiles without tedious resolution corrections. These features are essential for a dedicated instrument at a storage ring.
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    MINREF – a new computer program for neutron refinement of incommensurate multiphase nuclear and magnetic structures (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 73-76 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: A new computer program MINREF has been developed for the refinement of neutron powder diffraction patterns as well as single-crystal data corresponding to incommensurate structures. The program is written in VAX Fortran 77 and is of modular construction. The program allows user-desired modifications and permits in the present version simultaneous refinement of the structures of three phases: one commensurate and two incommensurate.
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    Crystallographers (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 78-78 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Correction for absorption and beam inhomogeneity in X-ray single-crystal diffractometry: method of analytical integration (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 94-98 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Notes: A computational method of absorption correction in X-ray diffractometry for single crystals in the shape of convex polyhedra bathed in an inhomogeneous and in a homogeneous X-ray beam is suggested. An absorption correction is calculated for each reflection of the data set using the measured coordinates of the specimen vertices and the experimentally measured intensity distribution in the primary beam. The program ABSCOR is written in Fortran and may be readily adopted to any four-circle diffractometer and data format. The results of the method described for crystals of different dimensions and different absorption coefficients are given. It is shown that beam inhomogeneity strongly influences the reflection intensity of large non-isometric crystals.
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    N-beam interactions examined with the help of the computer programs PSIINT and PSILAM (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 99-104 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Two computer programs – one for calculation and graphical representation of the azimuthal angle ψ of all possible multiple reflections versus the wavelength λ (PSILAM) and one for the simulation of the Umweganregung-intensity variation during rotation of the crystal about the scattering vector of a `forbidden' or very weak reflection (PSIINT) – have been developed on the basis of the program UMWEG [Rossmanith (1985). Z. Kristallogr. 171, 253–254; (1986). Acta Cryst. A42, 344–348] with emphasis on suitability for inexpensive hardware. Examples of the excellent agreement between measurements and calculations and of the necessity of the combined application of both programs are given.
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    XTL-SIZE: a computer program for crystal-size-distribution calculation from X-ray diffraction line broadening (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 136-137 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A computer program has been written for the determination of crystal-size distribution in a direction perpendicular to an (hkl) crystal plane, from a digitized XRD peak. It implements an information theory approach devised by Guérin, Alvarez, Rebollo Neira, Plastino & Bonetto [Acta Cryst. (1986), A42, 30–35] and Alvarez, Bonetto, Guérin, Plastino & Rebollo Neira [Powder Diffr. (1987), 2, 220–224]. The program has a fully automated operation mode and owing to the very restricted amount of input data this program is specially suited to users with a limited knowledge of crystal-size-determination methods.
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    Crystallographers (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 144-144 
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    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
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    Calculation of the lattice deformation at the phase transitions of [Fe(ptz)6](BF4)2 from powder diffraction patterns (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 151-160 
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    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The thermal and light-induced high-spin (HS: 5T2g) low-spin (LS: 1A1g) transitions of [Fe(ptz)6](BF4)2 (ptz = 1-propyltetrazole) are investigated by X-ray powder diffractometry in the range between ambient temperature and 1̃5 K. The anisotropic lattice deformation caused by variation of the HS fraction and by temperature change was calculated directly from the differences in peak positions of the powder diagrams measured at different temperatures. An analytical expression for the dependence of peak shifts and splittings on the deformation tensor elements was derived. The differences of the lattice deformations accompanying the thermal and light-induced spin transitions are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889014020
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    A small 50 K cooling device for a quarter-circle Eulerian cradle diffractometer (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 175-179 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A one-stage He refrigerator (Displex CS1003) has been modified and installed on a quarter-circle Eulerian cradle of 250 mm diameter (AED Siemens) and has been operated down to 50 K. The mechanical interface, which can easily be mounted, is described as well as some alignment problems. The device is suitable for any Eulerian cradle 250 mm or larger. Structure redeterminations of two organic compounds were carried out at 52 K. R values of 2.2 and 3.6% were obtained and proved the quality of this set up.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890000358
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  • 90
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    CONEXN – a procedure to generate ideal groups for stereochemically restrained refinement of protein models (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 218-221 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A procedure has been developed to incorporate stereo-chemical restraints information for new groups into the dictionary of ideal groups used by the program PROTIN which prepares the input file needed by the reciprocal-space least-squares refinement program PROLSQ. It requires the availability of Cartesian coordinates for the group to be added to the dictionary, usually obtained from crystallographic analysis of crystals of the compound. If no such information is available these coordinates can be generated by an ancillary program, MOLBLD, which makes use of specified bond lengths, bond angles and dihedral angles to produce the required coordinates. The program is written in standard Fortran 77 and has been used in the refinement of several structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889889014378
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  • 91
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    New Commercial Products (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 223-224 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890099885
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  • 92
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    Factors affecting data reproducibility on an area detector (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 234-240 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The reproducibility of data collected on a Seimens/ Nicolet area detector has been tested with respect to crystal orientation, X-ray collimation and scaling procedure. In addition, a comparison between area detector data and diffractometer data was made in order to determine the accuracy of the area detector data. The reproducibility of the area detector data, although acceptable, is somewhat affected by crystal orientation (shape effect) and appears to be insensitive to X-ray collimation, contrary to what would be expected. The scaling procedures used in the tests were XENGEN [Howard, Gilliland, Finzel, Poulos, Ohlendorf & Salemme (1987). J. Appl. Cryst. 20, 383–387] (one, two and three parameters), FBSCALE [Weissman (1982). In Computational Crystallography, edited by D. Sayre, pp. 56–63. Oxford: Clarendon Press] and SIMPLAD [Takusagawa (1987). J. Appl. Cryst. 20, 243–245]. It was found that, although these procedures do an adequate job of scaling area detector data, none can totally correct for crystal-shape effects. From our experience, XENGEN multi-parameter or SIMPLAD scaling on data sets having low redundancy must be used with care. When compared to diffractometer data, area detector data scaled by any of the above procedures is in good agreement, with merging R-factors (on F) in the range 3.45 to 4.55%. A plot of 〈Fad〉 versus 〈Fd〉 shows a straight line with slope of 1(3)%. No saturation problems were observed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890001881
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  • 93
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    Time-resolved neutron diffraction analyses of hydrothermal syntheses using a novel autoclave cell (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 258-262 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An autoclave cell has been designed for performing time-resolved neutron diffraction analyses of the dynamic processes occurring during hydrothermal syntheses under hostile (corrosive and explosive) conditions: such conditions include those of hot NaOH/NaOD solutions and pressurized steam. The cell is also capable of measuring differential pressures and accurate sample temperatures as required for the study of reactions which are temperature sensitive. The cell is described and examples of its successful use are given illustrating the synthesis of basic zeolites and a layered calcium silicate hydrate. This technique has considerable potential for studying a variety of synthesis processes of industrial importance, such as in the production of catalysts and the hydration of cements.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890002473
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  • 94
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    Simultaneous peak-shift correction in the least-squares determination of unit-cell parameters of a sample with standard reference material (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 282-285 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A straightforward method for the systematic peak-shift correction using the standard reference material is proposed for the least-squares determination of unit-cell parameters. It requires no pre-determined angle-calibration curve, and the peak-shift correction can be applied simultaneously during the least squares. The procedure, programmed with Fortran 77 statements, has been tested with powder diffractometer data of an α-SiO2 + Si mixture. Advantages of the procedure are: (i) all reflection data from both sample and standard reference material contribute to determining the angle-dependent calibration curve, and (ii) one reflection from the standard reference material suffices for the correction of systematic errors.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890001996
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  • 95
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    Optical transforms of disordered systems containing symmetry-related scattering sites (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 303-314 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A previously described method of synthesizing a real-space distribution of scattering points which will give rise to virtually any required diffraction pattern has been extended to include the possibility of multiple symmetry-related sites per unit cell. The distribution may be used in the form of an optical diffraction screen to give an immediate visual check on both the real-space and reciprocal-space distributions. The method has been applied successfully to two examples which exhibit strong diffuse X-ray scattering effects: a molecular crystal sample, 1,3-dibromo-2,5-diethyl-4,6-dimethylbenzene (BEMB2), in which disorder occurs because the molecule can take up two different orientations in any given molecular site, and a mineral mullite, Al2(Al2 + 2xSi2 − 2x)O10 − x⊗x, where disorder diffuse scattering occurs as a result of the oxygen vacancies ⊗ and the accompanying cation displacements.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S002188989000379X
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  • 96
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    An automatic diffraction data collection system with an imaging plate (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 334-339 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: An automatic diffraction data collection system with an imaging plate has been developed for protein crystallography. The system works in a similar way to the conventional rotation camera method, but in full online mode. After exposure to the X-ray beam, the imaging plate (100 mm radius) rotates whilst a reading head scans across the plate to measure the stimulated luminescence in a record-player-like manner. During the next period of exposure, the image taken immediately before is processed in parallel. The system has been tested using both peptide and protein crystals and has been proven to work successfully.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890004009
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  • 97
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    TEXCAM – an interpretation aid for cylindrical texture camera X-ray diffraction patterns (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 347-348 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: TEXCAM is an interactive program designed for IBM PC/XT/AT or compatible personal computers. It constructs schematic simulations which represent diffraction patterns produced by the texture camera. The program can be used to produce patterns from samples which are both polycrystalline and epitaxic in nature. Patterns from polycrystalline samples containing uniaxial texture may also be calculated. An installation program facilitates scaling of the on-screen image allowing texture camera films to be directly superimposed upon the simulation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890004265
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  • 98
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    The rotation rate field and geometry of orientation space (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 374-377 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: This paper contains information about the Riemannian structure of orientation space which is necessary for the analysis of the rotation rate field, which in turn describes some aspects of the plastic deformation of textured polycrystalline materials. The components of the metric tensor and the connection coefficients in the coordinates used in quantitative texture analysis are given. The relation between the vector components at symmetrically equivalent points and the relation between the frequently used vectors of infinitesimal rotations are presented. The solution of the continuity equation is given for the case of a constant rotation rate field during the deformation process.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S002188989000512X
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  • 99
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    Mounting of crystals for macromolecular crystallography in a free-standing thin film (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 387-391 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A method for mounting single crystals in macromolecular crystallographic studies is described in which the crystal is suspended in a thin film. The film is formed from a mixture of the crystallization buffer and a hydrophilic viscous material, confined within a thin-wire loop by surface tension. Compared with conventional crystal mounting methods, this method greatly simplifies and speeds the mounting procedure, is well suited to shock freezing and to optical monitoring of the crystals, deforms fragile crystals less and gives a lower and more uniform background in the X-ray diffraction patterns.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889890005568
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  • 100
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    A robust alternative to η refinement for assessing the hand of chiral compounds (1990)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 23 (1990), S. 406-411 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: Assessment of the hand of chiral molecular compounds by least-squares refinement of a chirality parameter with all reflections is not statistically robust and can lead to incorrect answers due to a single, unnoticed, gross intensity-measurement error. An alternative is described in which the most easily observable Bijvoet differences are derived from the solved structure and remeasured at slow speed and possibly longer wavelength. Errors due to absorption, multiple reflections and anisotropic extinction can be cancelled out in the measurement for the sense of Bijvoet pairs with the proper experimental technique. An estimate of the probability of having derived the wrong hand, based exclusively on the number of remeasurements and the number of contradictions, and therefore insensitive to individual measurement errors, is developed. With this estimate, determination of the hand of compounds with oxygen as the heaviest scatterer is statistically unambiguous with Cu Kα intensity data, and feasible even with Mo Kα data. Consequently, the method can be applied to Cu Kα data for molecules with carbon as the heaviest scatterer. This approach has been automated as the utility BIVOET in the NRCVAX system of programs.
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    URL: http://dx.doi.org/10.1107/S0021889890005775
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