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  • Other Sources  (75)
  • Cambridge University Press  (38)
  • 5 Abbey Square, Chester, Cheshire CH1 2HU, England  (37)
  • 2020-2022  (39)
  • 1990-1994  (35)
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  • 1
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 2
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 3
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Description: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 4
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Description: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 5
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Description: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 6
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Description: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 7
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 8
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-03
    Description: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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  • 9
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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  • 10
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    Crystal structure of a calcium(II)–pyrroloquinoline quinone (PQQ) complex outside a protein environment (2021)
    5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-04-14
    Description: Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium‐ and lanthanide‐dependent alcohol dehydrogenases, and has been known for over 30 years. Crystal structures of Ca–MDH enzymes (MDH is methanol dehydrogenase) have been known for some time; however, crystal structures of PQQ with biorelevant metal ions have been lacking in the literature for decades. We report here the first crystal structure analysis of a Ca–PQQ complex outside the protein environment, namely, poly[[undecaaquabis(μ‐4,5‐dioxo‐4,5‐dihydro‐1H‐pyrrolo[2,3‐f]quinoline‐2,7,9‐tricarboxylato)tricalcium(II)] dihydrate], {[Ca3(C14H3N2O8)2(H2O)11]·2H2O}n. The complex crystallized as Ca3PQQ2·13H2O with Ca2+ in three different positions and PQQ3−, including an extensive hydrogen‐bond network. Similarities and differences to the recently reported structure with biorelevant europium (Eu2PQQ2) are discussed.
    Description: Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium‐ and lanthanide‐dependent alcohol dehydrogenases. The crystal structure of a Ca–PQQ complex (Ca3PQQ2·13H2O) is reported for the first time outside a protein environment. image
    Description: research
    Keywords: 548 ; pyrroloquinoline quinone ; calcium ; PQQ ; methanol dehydrogenase ; crystal structure ; FID-GEO-DE-7
    Language: English
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  • 11
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Description: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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  • 12
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Description: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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  • 13
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Description: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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  • 14
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Description: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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  • 15
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-17
    Description: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 16
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Description: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Keywords: 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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  • 17
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-02
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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  • 18
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-06
    Description: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Description: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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  • 19
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Description: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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  • 20
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Description: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Keywords: 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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  • 21
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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  • 22
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Description: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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  • 23
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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  • 24
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-27
    Description: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 25
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-20
    Description: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Description: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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  • 26
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Description: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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  • 27
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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  • 28
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-05
    Description: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Description: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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  • 29
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-30
    Description: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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  • 30
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Description: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Description: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-26
    Description: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Description: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-07-01
    Description: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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  • 38
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    THE INTCAL20 NORTHERN HEMISPHERE RADIOCARBON AGE CALIBRATION CURVE (0–55 CAL kBP) (2020)
    Department of Geosciences, University of Arizona | Cambridge University Press
    In:  Radiocarbon, 62 (4). pp. 725-757.
    Details
    Publication Date: 2021-01-08
    Description: Radiocarbon (14C) ages cannot provide absolutely dated chronologies for archaeological or paleoenvironmental studies directly but must be converted to calendar age equivalents using a calibration curve compensating for fluctuations in atmospheric 14C concentration. Although calibration curves are constructed from independently dated archives, they invariably require revision as new data become available and our understanding of the Earth system improves. In this volume the international 14C calibration curves for both the Northern and Southern Hemispheres, as well as for the ocean surface layer, have been updated to include a wealth of new data and extended to 55,000 cal BP. Based on tree rings, IntCal20 now extends as a fully atmospheric record to ca. 13,900 cal BP. For the older part of the timescale, IntCal20 comprises statistically integrated evidence from floating tree-ring chronologies, lacustrine and marine sediments, speleothems, and corals. We utilized improved evaluation of the timescales and location variable 14C offsets from the atmosphere (reservoir age, dead carbon fraction) for each dataset. New statistical methods have refined the structure of the calibration curves while maintaining a robust treatment of uncertainties in the 14C ages, the calendar ages and other corrections. The inclusion of modeled marine reservoir ages derived from a three-dimensional ocean circulation model has allowed us to apply more appropriate reservoir corrections to the marine 14C data rather than the previous use of constant regional offsets from the atmosphere. Here we provide an overview of the new and revised datasets and the associated methods used for the construction of the IntCal20 curve and explore potential regional offsets for tree-ring data. We discuss the main differences with respect to the previous calibration curve, IntCal13, and some of the implications for archaeology and geosciences ranging from the recent past to the time of the extinction of the Neanderthals.
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  • 39
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    Marine20—The Marine Radiocarbon Age Calibration Curve (0–55,000 cal BP) (2020)
    Department of Geosciences, University of Arizona | Cambridge University Press
    In:  Radiocarbon, 62 (4). pp. 779-820.
    Details
    Publication Date: 2021-01-08
    Description: The concentration of radiocarbon (14C) differs between ocean and atmosphere. Radiocarbon determinations from samples which obtained their 14C in the marine environment therefore need a marine-specific calibration curve and cannot be calibrated directly against the atmospheric-based IntCal20 curve. This paper presents Marine20, an update to the internationally agreed marine radiocarbon age calibration curve that provides a non-polar global-average marine record of radiocarbon from 0–55 cal kBP and serves as a baseline for regional oceanic variation. Marine20 is intended for calibration of marine radiocarbon samples from non-polar regions; it is not suitable for calibration in polar regions where variability in sea ice extent, ocean upwelling and air-sea gas exchange may have caused larger changes to concentrations of marine radiocarbon. The Marine20 curve is based upon 500 simulations with an ocean/atmosphere/biosphere box-model of the global carbon cycle that has been forced by posterior realizations of our Northern Hemispheric atmospheric IntCal20 14C curve and reconstructed changes in CO2 obtained from ice core data. These forcings enable us to incorporate carbon cycle dynamics and temporal changes in the atmospheric 14C level. The box-model simulations of the global-average marine radiocarbon reservoir age are similar to those of a more complex three-dimensional ocean general circulation model. However, simplicity and speed of the box model allow us to use a Monte Carlo approach to rigorously propagate the uncertainty in both the historic concentration of atmospheric 14C and other key parameters of the carbon cycle through to our final Marine20 calibration curve. This robust propagation of uncertainty is fundamental to providing reliable precision for the radiocarbon age calibration of marine based samples. We make a first step towards deconvolving the contributions of different processes to the total uncertainty; discuss the main differences of Marine20 from the previous age calibration curve Marine13; and identify the limitations of our approach together with key areas for further work. The updated values for ΔR, the regional marine radiocarbon reservoir age corrections required to calibrate against Marine20, can be found at the data base http://calib.org/marine/.
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  • 40
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    Squid diet of emperor penguins (Aptenodytes forsteri) in the eastern Weddell Sea, Antarctica during late summer (1994)
    Cambridge University Press
    In:  Antarctic Science, 6 (02). pp. 241-247.
    Details
    Publication Date: 2019-01-15
    Description: The data presented provides new information on the distribution of Antarctic squids and on the summer diet of the emperor penguins. The diet of 58 adult emperor penguins (Aptenodytes forsteri) on the fast ice of the Drescher Inlet, Vestkapp Ice Shelf (72°52′S, 19°25′W) in the eastern Weddell Sea was investigated. Prey consisted principally of squid, fish, krill, amphipods and isopods. Squids were identified by the lower beaks and allometric equations were used to estimate the squid biomass represented. Beaks occurred in 93% of the stomach samples. Each sample contained a mean of 27 beaks (range 1–206). Ninety-two percent of the squids could be identified by the lower beaks and belonged to four families (Onychoteuthidae, Psychroteuthidae, Neoteuthidae and Gonatidae). The most abundant squid was Psychroteuthis glacialis which occurred in 52 samples with lower rostral lengths (LRL) ranging from 1.4–7.2 mm. Forty-five samples contained Alluroteuthis antarcticus (LRL range 1.8–5.8 mm), 17 Kondakovia longimana (LRL range 4–12.1 mm), and four Gonatus antarcticus (LRL range 4.1–6.1 mm). In terms of biomass K. longimana was the most important species taken by the penguins comprising 50% of total estimated squid wet mass (245348 g) in 1990 and 48% in 1992 (154873 g). However, if only fresh beaks were considered for estimations of squid consumption, i.e. beaks that have been accumulated for not longer than 5–6 days in the stomachs, squid diet was of minor importance. Then total squid wet mass accounted for only 4809 g in 1990 and 5445 g in 1992 which implies that one penguin took c.30 g squid d−1 with P. glacialis and A. antarcticus being the most important by mass. The prey composition suggests that emperor penguins take squid at the steep slope regions of the eastern Weddell Sea.
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  • 41
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    Reproductive biology of Todaropsis eblanae (Cephalopoda: Ommastrephidae) in Scottish waters (1994)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 74 (02). pp. 367-382.
    Details
    Publication Date: 2020-07-16
    Description: During a study based on catches taken in the northern North Sea by selected Scottish fishing boats during 1985–1992, large numbers of the normally rare short-fin squid, Todaropsis eblanae (Cephalopoda: Ommastrephidae), were recorded in 1987 and 1990. Our findings, supported by data obtained from plankton/young fish surveys in 1988 and 1989, suggest that in northern waters Todaropsis eblanae generally mates and spawns during late summer and early autumn (June-November). Successful hatching events appear to occur during October-March, producing juvenile (stage I) squid in the early part of the year (January-June). Estimations of maximum male reproductive output and female fecundity were up to 130 spermatophores and ~28,000 eggs per individual, respectively.
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  • 42
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    Morphology and function of the mandibular muscles in some coleoid cephalopods (1994)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 74 . pp. 801-822.
    Details
    Publication Date: 2021-01-19
    Description: The functional morphology of the buccal mass of 23 species of cephalopod (Octopoda, 4 species; Teuthoidea, 17; Sepioidea, 2) was investigated by gross dissection, histology and observations on fresh preparations. Cephalopod beaks lack a joint or articulation point. The jaws slide and rotate around an area rather than a fixed point. During closing the superior mandibular muscle (SMM) provides the force of a bite and the largest movement vector, whilst the inferior mandibular muscle (IMM) acts to retract the upper beak, causing shearing action. Dorsal portions of the lateral mandibular muscles (LMM) flex the upper beak walls outwards, probably to accomodate the backwards sweep of the radula and buccal palps during closing. To open the beaks, the ventral portions to the lateral mandibular muscles pull the rear lateral walls of the two beaks towards each other, moving the lower beak back relative to the upper. The buccal mass weighs more in decapods (0.65-4.34% of body weight) than octopods (0.49-0.77%). The weight difference is mainly accounted for by the size of the superior mandibular muscle. Beak shape and muscle volume are related. Increasing the size of the upper beak hood and lateral wall area results in larger SMM and LMM respectively Increasing hood size in the lower beak increases IMM size, and altering the angle by which the wings meet the lateral wall changes the volume of the SMM and LMM. To accomodate the decapod pointed upper rostrum, the lateral walls of the lower beak have shortened in length, whilst increasing in breadth and surface relief to maintain the area available for muscle insertion. In species with a lateral wall ridge or fold (e.g. Onychoteuthis) this may mark the insertion point of the LMM.
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  • 43
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    Arm autotomy and arm branching pattern as anti-predatory adaptations in stalked and stalkless crinoids (1994)
    Cambridge University Press
    In:  Paleobiology, 20 (1). pp. 27-39.
    Details
    Publication Date: 2021-02-22
    Description: Arm autotomy was induced in a living specimen of Metacrinus rotundus (Echinodermata: Crinoidea). An arm was autotomized at a ligamentary articulation known as a cryptosyzygy, following incision by scissors distal to the break point. Although sessile stalked crinoids cannot entirely escape from a predatory attack by arm autotomy and they do not have an active defense, arm autotomy at cryptosyzygies reduces damage and arm loss by effective distribution, and by minimizing trauma and facilitating subsequent regeneration. The paradigmatic distribution of cryptosyzygies in which arm loss is set at a minimum, compared with the actual distribution, shows that these two patterns are similar and that actual specimens successfully reduce arm loss by the effective distribution of cryptosyzygies. The crinoid branching pattern also affects arm loss, and two different paradigms are discussed: anti-predatory and harvesting. Arm branching patterns of various isocrinids have tended toward the anti-predatory configuration from the Jurassic to the Recent, suggesting that the isocrinids have coped with increased predation. Shallow-water comatulids generally adopt the anti-predatory paradigm in their branching pattern, whereas many deep-water, stalked crinoids adopt a harvesting paradigm, reflecting that shallow-water comatulids receive more predatory attacks than do deep-water crinoids.
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  • 44
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    Unbounded Quantum Diffusion and Fractal Spectra (1994)
    Cambridge University Press
    In:  Unbounded Quantum Diffusion and Fractal Spectra | Quantum Chaos: Between Order and Disorder
    Details
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/bookPart
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    CITATION PIK
  • 45
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    Fracture of Brittle Solids (1993)
    Cambridge University Press
    In:  Cambridge, Cambridge University Press, vol. 34, no. 22, pp. 65-70, (ISBN 0-691-12183-4, 2005 (481 pp. + CD-ROM))
    Details
    Publication Date: 1993
    Keywords: Textbook of geophysics ; Textbook of geology ; Rock mechanics ; Physical properties of rocks ; Fracture
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    BIBLIOGRAPHY SEISMOLOGY
  • 46
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    Food of striped dolphin, Stenella coeruleoalba, in the Ligurian Sea (1993)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 73 (03). p. 571.
    Details
    Publication Date: 2020-07-16
    Description: The stomachsof 23 striped dolphins (Stenella coeruleoalba Meyen, 1833, Cetacea), stranded along the Ligurian coast (western Mediterranean Sea), contained 32 species of cephalopods, crustaceans and fishes, totalling an estimated 2,723 prey specimens representing about 36 kg in weight. Cephalopods and bony fishes were equally important in the diet (50%). Todarodes sagittatus (34.5%) and Micromesistius poutassou (25.9%) were found to be the most important food species. Other species belonging to six cephalopod families, three crustacean families and nine bony fish families, contributed to the diet with variable numbers, weights, and occurrences, demonstrating the opportunistic character of striped dolphin feeding.
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  • 47
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    Age, growth and maturation of the loliginid squids Alloteuthis africana and A. Subulata on the west African shelf (1993)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 73 (04). p. 949.
    Details
    Publication Date: 2020-07-16
    Description: Samples of two loliginid squids Alloteuthis africana and A. subulata were collected from the continental shelf off the west Sahara in August-September 1987. Statoliths were taken from 124 specimens and processed using statolith ageing techniques. Statoliths of both species were very similar in shape. In the ground statolith, growth increments were examined and grouped into four growth zones distinguished mainly by the width of the increments. Age of adult mature males of both species did not exceed eight months, that of females six months. Alloteuthis africana grew faster than A. subulata in weight and, particularly, in length. At age 180 d the mantle of A. africana was twice as long and the body weight 1·2–1·5 times as large. Both species matured over a wide range of sizes and ages (from 120 to 180 d). The life span of A. africana and A. subulata hatching between January and May on the west Saharan shelf is about six months, much shorter than that of A. subulata in its northern temperate range.
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  • 48
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    Statolith Microstructure and Maximum age of Loligo Gahi (Myopsida: Loliginidae) on the Patagonian Shelf (1993)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 73 (04). p. 979.
    Details
    Publication Date: 2020-07-16
    Description: Statoliths of Loligo gahi were sampled in the fishery region 45–47°S on the Patagonian shelf during September 1989. Peculiarities of the growth zones in the ground statoliths of adults are described. Maximum age of large maturing and mature females (130–160 mm of mantle length, ML) was estimated to be 325–345 d, that of large mature males (250–290 mm ML) ranged from 360 to 396 d. The squid Loligo gahi d'Orbigny, 1835, occurs in temperate shelf and upper slope waters of the Atlantic and Pacific coasts of South America and is caught commercially by the international fleet in the southern part of the Patagonian shelf within the Falkland Islands Interim Conservation Zone (FICZ) (Roper et al., 1984; Csirke, 1987). Occasionally, dense shoals of L. gahi appear in the fishery region 45–47°S off the Exclusive Economic Zone of Argentina (EEZA) and have been caught in significant numbers by trawlers at depths of 120–150 m in September-October (Chesheva, 1990). Loligo gahi is a medium sized loliginid; in Falkland waters males attain 350 mm ML, females 210 mm ML (Hatfield, 1991), while in the fishery region 45–47°S maximum size is 260 mm and 160 mm, respectively (Chesheva, 1990). Patterson (1988) revealed two Falkland spawning stocks of L. gahi of unclear status, spring-spawners and autumn-spawners (austral seasons) and pointed out that the life span of squid of each stock lasted ~1 y. Recently Hatfield (1991) used statoliths to elucidate Patterson's (1988) estimations of age and growth of Falkland stocks of L. gahi and confirmed the 1-y duration of L. gahi's life span.
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  • 49
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    Preparation and characterization of highly pure fractions of outer membrane, cytoplasmic and intracytoplasmic membranes from Ectothiorhodospira mobilis (1993)
    Cambridge University Press
    In:  Journal of General Microbiology, 139 (1). pp. 111-117.
    Details
    Publication Date: 2020-07-24
    Description: Outer membrane (OM), cytoplasmic membrane (CM) and intracytoplasmic membranes (ICM) from the halophilic phototrophic purple sulphur bacterium Ectothiorhodospira mobilis 9903 were purified and characterized. The three membrane fractions were significantly different in regard to protein profiles on SDS-PAGE, and to the composition of amino acids, fatty acids and lipids. The presence of lipoproteins, the occurrence of lyso-phosphatidyl-ethanolamine and an increased content of saturated and short-chain fatty acids are characteristic properties of the OM. CM and ICM fractions are different on the basis of buoyant density, of protein profiles and amino acid composition, and due to the presence of succinate dehydrogenase activity in CM. In addition, CM and ICM showed significant differences in pigment content and absorption spectra.
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  • 50
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    Breeding habitats of emperor penguins in the western Ross Sea (1993)
    Cambridge University Press
    In:  Antarctic Science, 5 (2). pp. 143-148.
    Details
    Publication Date: 2021-06-17
    Description: Within the Western Ross Sea, there are six emperor penguin colonies of widely different size that occur exclusively on sea ice. In 1990 a survey of all six sites, two by close overflights and four from the ground, showed that the breeding habitats were highly variable. The most important physical characteristics of these habitats appear to be stable fast ice, nearby open water, access to fresh snow, and shelter from the wind.
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  • 51
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    Flow direction and groundmass shear zones in dykes, Shimane Peninsula, Japan (1993)
    Cambridge University Press
    In:  Geological Magazine, 130 (01). p. 117.
    Details
    Publication Date: 2020-07-31
    Description: The groundmass of andesitic dykes at Sezaki, southwest Japan, has trachytic texture and contains microscopic shear zones. The shear zones comprise a conjugate pair formed by flattening of the solidifying dyke rock, probably caused by the magma pressure of the still molten part of the dyke. This pressure shortened the solidifying rock perpendicular to the dyke margins and caused it to extrude parallel to the magma flow direction. The groundmass shears indicate that locally the magma flowed 60° upward in the dykes. It is concluded that while groundmass shears are a useful indicator of flow direction in dykes, phenocryst alignment in dykes is strongly influenced by magma-pressure flattening and thus may be a poor indicator of flow direction.
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  • 52
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    Fractals and Chaos in Geology and Geophysics (1992)
    Cambridge University Press
    In:  Cambridge, Cambridge University Press, vol. 271, no. ALEX(01)-FR-77-01, AFTAC Contract F08606-76-C-0025, pp. 329, (ISBN: 0-08-043649-8)
    Details
    Publication Date: 1992
    Keywords: FractureT ; Chaotic behaviour ; Handbook of geophysics ; Handbook of geology
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    BIBLIOGRAPHY SEISMOLOGY
  • 53
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    Europe's lithosphere - seismic structure (1992)
    Cambridge University Press
    In:  A Continent Revealed - the European Geotraverse, Cambridge, Cambridge University Press, vol. 37, pp. 33-69, (ISBN 0080419208)
    Details
    Publication Date: 1992
    Keywords: Deep seismic sounding (espec. cont. crust) ; Review article ; Earth model, also for more shallow analyses ! ; European Geotraverse ; CRUST ; earth mantle ; Muller
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  • 54
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    Age and growth estimation of the European squid, Loligo vulgaris, based on statolith microstructure (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (02). p. 271.
    Details
    Publication Date: 2020-07-16
    Description: Age and growth were estimated in the European squid, Loligo vulgaris, by examining growth increments in the statoliths of 203 specimens collected from off the French Mediterranean coast. Length and increment data were analyzed assuming that the increments were formed daily. The relationships between age and length showed that: growth rate varied considerably among individuals; growth was double exponential; the squids grew on average to 240 mm ML at 240 d from hatching, with a maximum of 350 mm at 240 d; the life span is probably about one year.
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  • 55
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    Loss of meal antigenicity during digestion in Sepia officinalis (Cephalopoda: Sepioidea) (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (03). p. 543.
    Details
    Publication Date: 2020-07-16
    Description: Some of the limits to the use of serology to identify prey species in the digestive tracts of cephalopods have been evaluated. Cuttlefish, Sepia officinalis, were given meals of krill slurry (Euphausia superba). Protein extracts of contents from four regions of the digestive tract, stomach, caecum, digestive gland and intestine, were tested for prey antigenicity. Digestion times (loss of antigenicity) ranged from 1 to 8 h depending on sampling site. Stomach and caecum emptied rapidly, but meal antigenicity persisted longer in the digestive gland. The Sepia experiments provide a basis for interpretation of results from natural predation by cephalopods).
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  • 56
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    Production of soma and gonad in maturing female Illex argentinus (Mollusca: Cephalopoda) (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (02). pp. 281-291.
    Details
    Publication Date: 2020-07-16
    Description: Samples of female lllex argentinus were taken from the catch of a Japanese squid jigging vessel on the Patagonian Shelf during March 1986. Morphometrics of the somatic and reproductive organ systems and the histological structure of the mantle in relation to maturation were examined. The data suggest that growth and maturation occur simultaneously during most of the time that lllex argentinus females are on the feeding grounds. In a squid of a ‘standard’ mantle length the whole body mass increases relative to mantle length during maturation and growth of the reproductive organs. This is accompanied by a small but significant decrease in the relative mass of the mantle, head and viscera whilst the mass of the digestive gland remains constant. Although mantle mass of a ‘standard’ female squid decreases relative to mantle length with maturity this is not associated with degeneration of the mantle muscles. Energy and nutrient resources for maturation are apparently derived from the squid's food, not from reserves, and during the course of maturation there is an increasing shift of emphasis from somatic growth to production of gonad and accessory reproductive organs.
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  • 57
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    Timing of spawning and recruitment in Loligo forbesi (Cephalopoda: Loliginidae) in Scottish waters (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (02). pp. 301-311.
    Details
    Publication Date: 2020-07-16
    Description: The timing of spawning and recruitment in the squid Loligo forbesi in Scottish waters is described on the basis of data from three sources: monthly samples of squid caught by commercial trawls (1986–1988), egg masses found by fishermen (1987–1991), and statistical data on animals caught by research trawls (1978–1987). Spawning females were present in samples from December to June, with peak spawning occurring in March. Most records of egg masses were from these months, but eggs were also found in August and September. These results suggest that there is an extended spawning season. Small squid (≤100 mm dorsal mantle length) were rarely present in commercial samples, but were recorded in research samples almost all year round. Thus there appears to be more or less continuous recruitment into the catchable population. The results of the present study are consistent with published data from other parts of the geographic range in that there is a regular seasonal peak in spawning, and spawning adults disappear from the population in summer. Further interpretation of the life-cycle of this species is not justified on the basis of current knowledge, and more information is needed on migrations, geographical variation, and lifespan in Loligo forbesi.
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  • 58
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    Cephalopods from the stomachs of a Risso's dolphin (Grampus griseus) from the Mediterranean (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (04). p. 861.
    Details
    Publication Date: 2020-07-16
    Description: Cephalopod remains from the stomachs of a Risso's dolphin (Grampus griseus Cuvier, 1812, Cetacea) entangled in a fishing net off the Ligurian coast (central Mediterranean Sea) include squids Ancistroteuthis lichtensteini, Histioteuthis bonnellii, H. reversa and Todarodes sagittatus and the sepiolid Heteroteuthis dispar. All these cephalopods live in oceanic water including water over the steep continental slope where Risso's dolphin is frequently sighted. Histioteuthis reversa contributed 78% of the cephalopods by number, 81% of the wet weight and 73% of the dry weight and calorific value. The total calorific value of the cephalopods represented by lower beaks was 17,300 kj.
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  • 59
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    Feeding spectrum of squid Sthenoteuthis oualaniensis (Oegopsida) in the eastern Pacific (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (04). p. 849.
    Details
    Publication Date: 2020-07-16
    Description: The stomach contents of 235 specimens of the squid Sthenoteuthis oualaniensis (4·3–36·5 cm mantle length, ML) were examined. A detailed list of 60 species of prey, comprising young and adult squid, is given together with their frequency of occurrence and proportional contribution. The size and number of each food item was investigated. Three ontogenetic size-groups of S. oualaniensis were distinguished: I, fry and young (4–10 cm ML), micronektonic epipelagic plankton-eaters; II, transient critical size group (10–15 cm ML), converting from feeding on planktonic crustaceans and fish larvae to myctophid fishes; III, medium-sized (adult) nyctoepipelagic nektonic predators (15–36·5 cm ML), feeding primarily on myctophids and secondarily on squid. Myctophids (genera Symbolophorus, Myctophum and Hygophum) were the most abundant prey in the diet of adult S. oualaniensis from different parts of its distribution.
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  • 60
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    Production of soma and gonad in maturing male Illex argentinus (Mollusca: Cephalopoda) (1992)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 72 (02). p. 293.
    Details
    Publication Date: 2020-07-16
    Description: Samples of male Illex argentinus were taken from the catch of a Japanese squid jigging vessel on the Patagonian Shelf during March 1986 and an analysis was carried out on the morphometrics of the somatic and reproductive organ systems in relation to maturation. The data show that growth and maturation occurred simultaneously during most of the time that Illex argentinus males were on the feeding grounds over the southern Patagonian Shelf. In a squid of a ‘standard’ mantle length the whole body mass increased relative to mantle length during maturation and this could be attributed to the increase in mass of the reproductive and accessory reproductive organs. During maturation the mantle and digestive gland mass showed no significant change relative to mantle length. The mass of the head increased and the mass of the viscera decreased relative to mantle length. In male Illex argentinus, as in the female, the energy and nutrient resources for maturation are derived from the squid's food and during the course of maturation there is an increasing shift of emphasis from somatic growth to production of gonad and accessory reproductive organs. The proportional investment of body mass in reproductive and accessory reproductive organs predicted for a fully mature male Illex argentinus was less than half that of the female.
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  • 61
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    The Pennatulid Kophobelemnon stelliferum (Cnidaria: Octocorallia) in the Porcupine Seabight (north-east Atlantic Ocean) (1992)
    Cambridge University Press
    In:  Journal of The Marine Biological Association of The United Kingdom, 72 (2). pp. 417-434.
    Details
    Publication Date: 2020-07-17
    Description: The upper bathyal sea-pen Kophobelemnon stelliferum extends to depths of about 1600 m in the Porcupine Seabight, to the south-west of Ireland, but is rare below about 1150 m. Photographic data suggest that the species attains numerical abundances of more than 2 m−2and a wet weight biomass of at least 4 g m−2. The highest densities, however, do not necessarily correspond to the highest biomass values since there is a clear depth-related change in population structure. The largest sea-pens are restricted to the deeper parts of the bathymetric range of the species. There is also a marked change in the growth form at a total colony length of about 250 mm, with larger colonies having relatively more polyps than smaller ones. The sexes are separate in Kophobelemnon stelliferum and the sex ratio of colonies is about 1:1. The maximum oocyte diameter is about 800 μm, but there is no evidence of seasonal reproduction by this pennatulid in the Porcupine Seabight.
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  • 62
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    The butterfly squid Stoloteuthis leucoptera in the Mediterranean (1991)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 71 (01). p. 47.
    Details
    Publication Date: 2020-07-16
    Description: The presence of Stoloteuthis leucoptera in the Mediterranean is recorded on the basis of three specimens, including an adult male, caught by IKMT and by commercial otter-trawl in the Ligurian Sea. The hypothesis of a recent immigration is discussed. The list of Mediterranean cephalopods (Mangold Wirz, 1963; Torchio, 1968; Bello, 1986; Mangold & Boletzsky, 1987) includes the Sepiolidae of the subfamily Heteroteuthinae, whose members are supposed to be pelagic throughout their life cycle. Mangold Wirz (1963) recognizes in the Mediterranean fauna the unique species Heteroteuthis dispar, the other authors include H. atlantis Voss, which Voss himself (1955) reported at Messina. To this group may now be added Stoloteuthis leucoptera (Verrill, 1878) a species until now recorded in limited Atlantic areas. Verrill (1881) wrote “This species is an exceedingly beautiful one, when living, owing to the elegance and brilliancy of its colours and the gracefulness of its movements. In swimming it moves its fins in a manner analogous to the motion of the wings of a butterfly.”
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  • 63
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    Biostratigraphical correlation of the Campanian–Maastrichtian boundary: Lägerdorf–Hemmoor (northwestern Germany), DSDP Sites 548A, 549 and 551 (eastern North Atlantic) with palaeobiogeographical and palaeoceanographical implications (1991)
    Cambridge University Press
    In:  Geological Magazine, 128 (5). pp. 479-503.
    Details
    Publication Date: 2020-07-31
    Description: A correlation of the Campanian–Maastrichtian boundary is attempted using foraminiferal and nannoplankton data from two areas: the eastern North Atlantic and northwestern Germany. The Boreal benthic and Tethyan planktonic foraminiferal zonation schemes are applied to Site 548A, where both foraminiferal groups occur frequently. A direct comparison of both biozonations reveals that the base of the Maastrichtian, according to planktonic foraminifers, has to be placed in the Upper Campanian of the Boreal benthic foraminiferal biozonation, which concurs with the nannoplankton results. The Tethyan Middle and Upper Maastrichtian are probably equivalent to the Upper Maastrichtian in the Boreal sense. The bases of the Maastrichtian substages are thus diachronous between the Boreal and Tethyan realms. Palaeotemperatures (which were estimated using the oxygen isotopic composition of the Goban Spur chalks) indicate, in combination with palaeowind directions, that the faunal and floral distribution pattern recorded is the result of a stable, warm water outflow from the northwest European epicontinental seas through the Channel area to the Celtic Shelf sea and Goban Spur. This mechanism appears to have been a dominant separating factor of the Boreal and Tethyan bioprovinces on the western European Shelf.
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  • 64
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    Comparative locomotor activity patterns in the portunid crabs Liocarcinus holsatus and L. depurator (1991)
    Cambridge University Press
    In:  Journal of The Marine Biological Association of The United Kingdom, 71 (1). pp. 1-10.
    Details
    Publication Date: 2020-07-17
    Description: The free-running locomotor activity rhythms of freshly-captured swimming crabs Liocarcinus holsatus and L. depurator have been studied in constant conditions in the laboratory. L. holsatus captured in the intertidal zone of sandy beaches showed strong circatidal activity rhythms with maximum activity at high tide. L. holsatus captured in the sublittoral zone had a clear tendency to show circadian activity rhythms with highest activity during day-time hours. L. depurator occurred only sublittorally and showed circadian activity patterns with highest activity during the night. Exposure to hydrostatic pressure cycles of tidal amplitude and periodicity, entrained strong circatidal activity rhythms in previously arhythmic L. holsatus. This activity pattern also showed a marked circadian component. Exposure to the same regime entrained a circadian rhythm, but not a circatidal rhythm in L. depurator. In the sublittoral zone L. depurator is active mainly during the night, whereas L. holsatus, is active mainly during the day. This may constitute a behavioural mechanism for minimizing competitive interactions between these two sympatric crabs
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  • 65
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    The Asian snow cover - monsoon - ENSO connection (1991)
    Cambridge University Press
    In:  In: Teleconnections Linking Worldwide Climate Anomalies. , ed. by Glantz, M. H. Cambridge University Press, Cambridge, UK, pp. 191-226. ISBN 978-0521364751
    Details
    Publication Date: 2019-08-07
    Type: Book chapter , NonPeerReviewed
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  • 66
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    Chaotic Dynamics: An Introduction (1990)
    Cambridge University Press
    In:  Cambridge, Cambridge University Press, vol. 3, pp. 6322, (ISBN 0-521-79203-7)
    Details
    Publication Date: 1990
    Keywords: Textbook of physics ; Chaotic behaviour ; FractureT
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  • 67
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    Sandeels in the diets of seals: application of novel and conventional methods of analysis to faeces from seals in the Moray Firth area of Scotland (1990)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 70 (04). pp. 829-840.
    Details
    Publication Date: 2020-07-16
    Description: Serological methods for prey identification have been applied to detection of residues ofsandeel (Ammodytidae) protein in faeces of common seals (Phoca vitulina) and grey seals(Halichoerus grypus) from the Moray Firth, north-east Scotland. Antisera raised to muscleprotein from Ammodytes marinus were evaluated by testing their reactions with proteinextracts made from a range of North Sea fish species and protein residues in in vitro digestates,seal digestive tracts and seal faeces. It was concluded that, using fused rocketimmuno-electrophoresis, linkage of precipitin peaks from unknown samples with peaksfrom standard sandeel extract was a reliable indicator of the presence of sandeel in theunknown sample. Seasonal variation in the incidence of sandeels in common seal diet in theMoray Firth was examined by identifying otoliths, bones, and proteins, and all threemethods indicated that sandeels occurred in the majority of samples tested in the summer,but were less important during the winter. Proteins were detected in fewer samples thanotoliths, particularly in February and March. Possible reasons for this difference arediscussed. Serological identification of sandeel proteins is potentially applicable to dietarystudies on all marine predators.
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  • 68
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    Some observations on the behaviour of adult squids, Loligo forbesi, in captivity (1990)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 70 (02). p. 459.
    Details
    Publication Date: 2020-07-16
    Description: Thirty-four adult individuals of Loligo forbesi (males and females with dorsal mantle lengths from 27–77 cm) were observed in captivity in a 3 m diameter closed sea-water system on Faial Island, Azores. Squids were caught by jigging and were fed with horse mackerel (Trachurus picturatus) and chub mackerel (Scomber japonicus), either alive or dead. The maximum survival was 73 days. Feeding behaviour was dependent upon both the size of prey and its state of preservation;e.g. the squid would eat the head of small fish (〈 about 15 cm), reject the head of medium-sized fish (about 15–35 cm) and would eat only the dorsal part of a big fish (〉 about 35 cm) or a fish poorly preserved. Seventeen chromatic, 9 postural and 6 movement components of body patterns were observed and described. Conspecific interactions considered to be aggression and dominance were observed among males; no such interactions occurred when one male and two females were kept together. Body patterns in relation to relaxation, stress, shock, feeding, locomotion and aggression are also described.
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  • 69
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    The role of bacterial mats in phosphate mineralization with particular reference to the Monterey Formation (1990)
    Cambridge University Press
    In:  In: Phosphate Deposits of the World Vol. 3: Neogene to modern phosphorites. , ed. by Burnett, W. C. and Riggs, S. R. Cambridge University Press, Camridge, England, pp. 300-311.
    Details
    Publication Date: 2020-05-04
    Description: Organic-rich shales sampled from the aples Beach section of the Monterey Formation. Califomia. contain authigenic phosphorite phases which apparently formed within bacterial mat laminations. Light and scanning electron microscope observations show that the fossilized remains ofthese mats are similar to communities of filamentous sulfur-oxidizing bacteria found today at slope-depth, sediment, oxic anoxic interfaces. The crystal size and habits ofthe phosphatic minerals resemble contemporaf) prec1pitates in contact with pore water solutions. Mineralogical and chemical analyses ofthe most phosphatic layers show that some are a nearly pure carbonate fluorapatite (or francolite). These la)ers are lightly colored and are sandwiched between black siliceous muds with 〈0.2% CaCOJ . and organic carbon contents that excecd 25%. In othcr phosphatic intcrvals of thc Naplcs Beach section. ca leite is a major diluent oflight and dark layers. The C:P ratio of a single modern bacterial mat sample shows that these benthic communities are more enriched in phosphorus than planktonic organic matter. Thus, the generally believed premise that authigenic phosphorite formation results from organic matter diagenesis in near-surface anoxic sediments is hcre modified by the contention that such transformations are more highly favored in sediments supporting massive microbial communities.
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  • 70
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    The impact of photoperiodicity on hatching of Loligo vulgaris and Loligo forbesi (1990)
    Cambridge University Press
    In:  Journal of the Marine Biological Association of the United Kingdom, 70 . pp. 597-610.
    Details
    Publication Date: 2020-11-16
    Description: The influence of photoperiodicity on hatching of Loligo forbesi and Loligo vulgaris embryos was investigated under different experimental light-dark (LD) conditions. The transition from light to dark stimulated hatching and functions as a "Zeitgeber" or synchronizer. Independent of the timing and duration of the dark period most embryos hatched soon after termination of the light period. Embyros which had developed in constant light, showed no hatching rhythm at all. If these embryos were exposed to a dark shock most embryos hatched soon after the onset of darkness. A twilight shock, in which the light was reduced by 50% (i.e. 50 µE s -1m-²), could not simulate hatching. Embryos which were kept from stage X on in an artifically controlled LD cycle, preferentially hatch in a period which coincides with the period at which darkness usually occured when placed in constant illumination from stage XX onwards.
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  • 71
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    Photoreception in squid (1990)
    Cambridge University Press
    In:  In: Light and life in the sea. , ed. by Herring, P. J. Cambridge University Press, Cambridge, pp. 199-207. ISBN 0-521-39207-1
    Details
    Publication Date: 2021-05-04
    Description: Light absorbed by the photoreceptor membranes of the retina is transformed by a series of biochemical steps into changes in receptor potential. The visual pigment, rhodopsin, and associated enzymes which relay the visual signal belong to a widespread family of receptorenzyme complexes which transmit sensory, hormonal and neurotransmitter signals into cells. In the invertebrate visual system, rhodopsin activates enzymes which increase cytoplasmic calcium. The highly specialised and structurally ordered photoreceptors of the squid retina provide a favourable system for studying the mechanisms of these enzyme pathways.
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  • 72
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    Emperor penguin colony at Cape Washington, Antarctica (1990)
    Cambridge University Press
    In:  Polar Record, 26 (157). pp. 103-108.
    Details
    Publication Date: 2021-06-23
    Description: This article describes the natural history of a large colony of emperor penguins Aptenodytes for steri , its size, dispersal pattern of chicks, and associations with other bird and mammal species. A mid-season count of 19,364 chicks indicated that about 20–25,000 breeding pairs had been present in June and July. The colony was fragmented into several sub-groups which showed different mean sizes of chicks and survival to fledging. Other species observed included leopard seals Hydrurga leptonyx , the only major predators, which preyed heavily on both adults and fledging chicks. Fledgelings left the colony over a period of about 10 days; departure was an active process in which the chicks walked to the ice edge and dispersed in groups, swimming consistently southward. At this time they were still in about 60% down and weighed about 10 kg, having lost some 30% of the heaviest mass achieved during parental feeding.
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  • 73
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    Properties and history of the central eastern Arctic sea floor (1990)
    Cambridge University Press
    In:  Polar Record, 26 (156). pp. 1-6.
    Details
    Publication Date: 2021-11-18
    Description: The deep eastern Arctic basin between the Lomonosov Ridge and the Eurasian continental margin differs from other ocean basins in the very slow spreading of its floor and unusual depositional environment under perennial sea-ice cover. The recent expedition ARK IV/3 of RV Polar stern for the first time made geoscientific investigations from the northern margin of the Barents Sea north to the Nansen-Gakkel Ridge. Much deeper than most other mid-ocean ridges, this ridge is poorly-surveyed, but has a central valley which in places is deeper than 5.5 km, 1–1.5 km below the basin floors on either side. Heat flow in the central part of the valley is very rapid; both basement rocks and overlying sediments showed unexpectedly the influence of intense and long-term hydrothermal activity. The sediments on the northern and southern flanks of the ridge are slightly calcareous pelagic mud layers alternating with carbonate-free horizons, where up to 40% of the sedimentary section is soft mud clasts. Similar mud aggregates were observed on the surface of the multi-year sea ice, appearing to represent a special type of sediment transport by sea ice in the Transpolar Drift. In contrast to the western Arctic, Fram Strait and the Norwegian-Greenland Sea, gravel is rarely found in sediment cores. Recovered cores indicate that icebergs and sea ice carrying coarse sediment seldom rafted detritus to the study area during the last approximately 300,000 years.
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  • 74
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    Forsterite dissolution in superheated basaltic, andesitic and rhyolitic melts (1990)
    Cambridge University Press
    Details
    Publication Date: 2023-11-16
    Description: Dissolution rates of small forsterite spheres in superheated melts of basalt, andesite and rhyolite composition have been measured at 1300°C, atmospheric pressure. The rate is constant (83 µm hr−1) in the basalt, regardless of run duration. In the andesite the initial dissolution rate is 200µm hr−1, followed by a decrease to a constant value of 16µmhr−1 in 2–3 hours. Dissolution rate in the rhyolite decreases from an initial value of 1.7 to 〈0.1 µmhr−1 over 280 hours and never reaches a constant rate. Once the rate of dissolution has become constant, the film of contaminated melt that forms in melt about a crystal does not thicken with time, indicating attainment of a steady-state condition. Steady state is attributed to natural convection arising from the difference in density between the film of contaminated melt surrounding a crystal and that beyond. The density difference is approximately 2% of the density of the rock melt.
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  • 75
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    The motion of a spherical liquid drop at high Reynolds number (1968)
    Cambridge University Press
    In:  Journal of Fluid Mechanics, 32 (2). pp. 367-391.
    Details
    Publication Date: 2020-03-11
    Description: The steady motion of a liquid drop in another liquid of comparable density and viscosity is studied theoretically. Both inside and outside the drop, the Reynolds number is taken to be large enough for boundary-layer theory to hold, but small enough for surface tension to keep the drop nearly spherical. Surface-active impurities are assumed absent. We investigate the boundary layers associated with the inviscid first approximation to the flow, which is shown to be Hill's spherical vortex inside, and potential flow outside. The boundary layers are shown to perturb the velocity field only slightly at high Reynolds numbers, and to obey linear equations which are used to find first and second approximations to the drag coefficient and the rate of internal circulation.
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