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  • Periodicals Archive Online (PAO)  (190,459)
  • Annual Reviews
  • International Union of Crystallography
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  • 1
    Journal cover
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    Annual Reviews
    Online: 2017 –
    Publisher: Annual Reviews
    Description: What is known? What isn’t known? Knowable Magazine, the digital publication from Annual Reviews, seeks to make that knowledge accessible to all. Knowable Magazine explores the real-world significance of scholarly work through a journalistic lens. We report on the current state of play across a wide variety of fields — from agriculture to high-energy physics; biochemistry to water security; the origins of the universe to psychology. Review articles written by leading scholars from the 50 Annual Reviews journals serve as springboards for stories in Knowable Magazine. Through in-depth features, explainers, articles, essays, interviews, infographics, slideshows, and comics, Knowable Magazine presents insights from research to a broader audience. The content is published under a CC BY-ND copyright license, and the Annual Reviews journal articles featured in Knowable Magazine are free to all for a limited period. Knowable Magazine content is thoroughly researched, reported, edited, copy-edited and fact-checked. Review articles in Annual Review journals provide ideas, but editorial decisions and reporting decisions are made by the magazine staff, guided by what will best inform and intrigue readers.
    Electronic ISSN: 2575-4459
    Topics: Natural Sciences in General
    Keywords: Allgemeine Naturwissenschaften ; Forschung
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  • 2
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    Annual Reviews
    Online: 1.1967 – 50.2016
    Online: 1.1967 – 50.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4197
    Electronic ISSN: 1545-2948
    Topics: Biology
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  • 3
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    Annual Reviews
    Online: 1973 – 1996
    Publisher: Annual Reviews
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 4
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    Annual Reviews
    Online: 1.1950 – 67.2016
    Online: 1.1950 – 67.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-426X
    Electronic ISSN: 1545-1593
    Topics: Chemistry and Pharmacology , Physics
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  • 5
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    Annual Reviews
    Online: 1.1952 –
    Online: 1.1952 –
    Formerly as: Annual Review of Nuclear Science  (1952–1977)
    Publisher: Annual Reviews
    Print ISSN: 0066-4243 , 0163-8998
    Electronic ISSN: 1545-4134
    Topics: Physics
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  • 6
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    Annual Reviews
    Online: 1.1961 – 56.2016
    Online: 1.1961 – 56.2016
    Formerly as: Annual Review of Pharmacology  (1961–1975)
    Publisher: Annual Reviews
    Print ISSN: 0066-4251 , 0362-1642
    Electronic ISSN: 1545-4304
    Topics: Chemistry and Pharmacology , Medicine
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  • 7
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    Annual Reviews
    Online: 1.2017 –
    Publisher: Annual Reviews
    Electronic ISSN: 2472-3428
    Topics: Biology , Medicine
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  • 8
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    Annual Reviews
    Online: 1.1985 – 32.2016
    Online: 1.1985 – 32.2016
    Formerly as: Annual Review of Cell Biology  (1985–1994)
    Publisher: Annual Reviews
    Print ISSN: 0743-4634 , 1081-0706
    Electronic ISSN: 1530-8995
    Topics: Biology , Medicine
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  • 9
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    Annual Reviews
    Online: 1.1969 – 48.2016
    Online: 1.1969 – 48.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4189
    Electronic ISSN: 1545-4479
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 10
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    Annual Reviews
    Online: 1.1939 – 78.2016
    Online: 1.1939 – 78.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4278
    Electronic ISSN: 1545-1585
    Topics: Biology , Medicine
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  • 11
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    Annual Reviews
    Online: 1.2008 – 9.2016
    Online: 1.2008 – 9.2016
    Publisher: Annual Reviews
    Print ISSN: 1936-1327
    Electronic ISSN: 1936-1335
    Topics: Chemistry and Pharmacology
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  • 12
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    Annual Reviews
    Online: 1.1963 – 54.2016
    Online: 1.1963 – 54.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 13
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    Annual Reviews | JSTOR
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews , JSTOR
    Print ISSN: 1941-1367
    Electronic ISSN: 1941-1375
    Topics: Economics
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  • 14
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    Annual Reviews
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews
    Print ISSN: 1941-1340
    Electronic ISSN: 1941-1359
    Topics: Economics
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  • 15
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    Annual Reviews
    Online: 1.1963 – 54.2016
    Online: 1.1963 – 54.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4286
    Electronic ISSN: 1545-2107
    Topics: Biology , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 16
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    Annual Reviews
    Online: 1.2014 – 3.2016
    Online: 1.2014 – 3.2016
    Publisher: Annual Reviews
    Print ISSN: 2326-8298
    Electronic ISSN: 2326-831X
    Topics: Mathematics
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  • 17
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    Annual Reviews
    Online: 1.2010 – 7.2016
    Online: 1.2010 – 7.2016
    Publisher: Annual Reviews
    Print ISSN: 1947-5454
    Electronic ISSN: 1947-5462
    Topics: Physics
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  • 18
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    Annual Reviews
    Online: 1.1972 – 45.2016
    Online: 1.1972 – 45.2016
    Publisher: Annual Reviews
    Print ISSN: 0084-6570
    Electronic ISSN: 1545-4290
    Topics: Biology , Ethnic Sciences
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  • 19
    Formerly as: Annual Review of Biophysics and Biomolecular Structure ; Annual Review of Biophysics and Biophysical Chemistry ; Annual Review of Biophysics and Bioengineering  (1972–2007)
    Publisher: Annual Reviews
    Print ISSN: 0084-6589 , 0883-9182 , 1056-8700 , 1936-122X
    Electronic ISSN: 1545-4266 , 1936-1238
    Topics: Biology , Physics
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  • 20
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    Annual Reviews
    Online: 1.1947 – 70.2016
    Online: 1.1947 – 70.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4227
    Electronic ISSN: 1545-3251
    Topics: Biology
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  • 21
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    Annual Reviews
    Online: 1.1981 – 36.2016
    Online: 1.1981 – 36.2016
    Publisher: Annual Reviews
    Print ISSN: 0199-9885
    Electronic ISSN: 1545-4312
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 22
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    Annual Reviews
    Online: 1.2013 – 4.2016
    Online: 1.2013 – 4.2016
    Publisher: Annual Reviews
    Print ISSN: 2165-8102
    Electronic ISSN: 2165-8110
    Topics: Biology
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  • 23
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    Annual Reviews
    Online: 1.1999 – 18.2016
    Online: 1.1999 – 18.2016
    Online: 1.2021 –
    Publisher: Annual Reviews
    Print ISSN: 1523-9829
    Electronic ISSN: 1545-4274
    Topics: Medicine , Technology
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  • 24
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    Annual Reviews
    Online: 1.1986 – 4.1990
    Online: 1.1986 – 4.1990
    Publisher: Annual Reviews
    Print ISSN: 8756-7016
    Electronic ISSN: 8756-7016
    Topics: Computer Science
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  • 25
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    Annual Reviews
    Online: 1.2000 –
    Online: 1.2021 –
    Publisher: Annual Reviews
    Print ISSN: 1527-8204
    Electronic ISSN: 1545-293X
    Topics: Biology
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  • 26
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    Annual Reviews | JSTOR
    Online: 1.2009 – 5.2013
    Publisher: Annual Reviews , JSTOR
    Print ISSN: 1941-1383
    Electronic ISSN: 1941-1391
    Topics: Economics
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  • 27
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    Annual Reviews
    Online: 1.1956 – 61.2016
    Online: 1.1956 – 61.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4170
    Electronic ISSN: 1545-4487
    Topics: Biology
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  • 28
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    Annual Reviews
    Online: 1.1983 – 34.2016
    Online: 1.1983 – 34.2016
    Publisher: Annual Reviews
    Print ISSN: 0732-0582
    Electronic ISSN: 1545-3278
    Topics: Biology , Medicine
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  • 29
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    Annual Reviews
    Online: 1.1971 – 46.2016
    Online: 1.1971 – 46.2016
    Formerly as: Annual Review of Materials Science  (1971–2000)
    Publisher: Annual Reviews
    Print ISSN: 0084-6600 , 1531-7331
    Electronic ISSN: 1545-4118
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 30
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    Annual Reviews
    Online: 1963 – 1995
    Publisher: Annual Reviews
    Print ISSN: 0066-4146
    Electronic ISSN: 1545-4282
    Topics: Physics
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  • 31
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    Annual Reviews
    Online: 1.1932 – 85.2016
    Online: 1.1932 – 85.2016
    Publisher: Annual Reviews
    Print ISSN: 0066-4154
    Electronic ISSN: 1545-4509
    Topics: Biology , Chemistry and Pharmacology
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  • 32
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    Annual Reviews
    Online: 1.1970 – 47.2016
    Online: 1.1970 – 47.2016
    Formerly as: Annual Review of Ecology and Systematics  (1970–2002)
    Publisher: Annual Reviews
    Print ISSN: 0066-4162 , 1543-592X
    Electronic ISSN: 1545-2069
    Topics: Biology
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  • 33
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    Annual Reviews
    Online: 1.1950 – 67.2016
    Online: 1.1950 – 67.2016
    Formerly as: Annual Review of Plant Physiology and Plant Molecular Biology ; Annual Review of Plant Physiology  (1950–2001)
    Publisher: Annual Reviews
    Print ISSN: 0066-4294 , 1040-2519 , 1543-5008
    Electronic ISSN: 1545-2123
    Topics: Biology
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  • 34
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    Annual Reviews
    Online: 1.1973 –
    Print: 8.1980 – 46.2018 (Location: A17, Kompaktmagazin, 5/6-7)
    Publisher: Annual Reviews
    Print ISSN: 0084-6597
    Electronic ISSN: 1545-4495
    Topics: Geosciences , Physics
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  • 35
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    Annual Reviews
    Online: 1.1976 –
    Online: 1.1976 –
    Formerly as: Annual Review of Energy and the Environment ; Annual Review of Energy  (1976–2002)
    Publisher: Annual Reviews
    Print ISSN: 0362-1626 , 1056-3466 , 1543-5938
    Electronic ISSN: 1545-2050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
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  • 36
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    Annual Reviews
    Online: 1.2009 – 8.2016
    Online: 1.2009 – 8.2016
    Publisher: Annual Reviews
    Print ISSN: 1941-1405
    Electronic ISSN: 1941-0611
    Topics: Biology , Geosciences
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  • 37
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    Annual Reviews
    Online: 1.1978 – 39.2016
    Online: 1.1978 – 39.2016
    Publisher: Annual Reviews
    Print ISSN: 0147-006X
    Electronic ISSN: 1545-4126
    Topics: Biology , Medicine
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  • 38
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    International Union of Crystallography
    Online: 1(1).2016 –
    Publisher: International Union of Crystallography
    Electronic ISSN: 2414-3146
    Topics: Geosciences , Physics
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  • 39
    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
    Type: article
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  • 40
    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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  • 41
    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
    Type: article
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  • 42
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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
    Type: article
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  • 43
    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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  • 44
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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
    Type: article
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  • 45
    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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  • 46
    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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  • 47
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 48
    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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  • 49
    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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  • 50
    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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  • 51
    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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  • 52
    facet.materialart.
    Unknown
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 53
    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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  • 54
    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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  • 55
    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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  • 56
    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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  • 57
    facet.materialart.
    Unknown
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 58
    facet.materialart.
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 59
    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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  • 60
    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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  • 61
    facet.materialart.
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 62
    facet.materialart.
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 63
    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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  • 64
    facet.materialart.
    Unknown
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 65
    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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  • 66
    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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  • 67
    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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  • 68
    facet.materialart.
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 69
    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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  • 70
    Publication Date: 2019-07-17
    Description: The public health, tourism, fisheries, and ecosystem impacts from harmful algal blooms (HABs) have all increased over the past few decades. This has led to heightened scientific and regulatory attention, and the development of many new technologies and approaches for research and management. This, in turn, is leading to significant paradigm shifts with regard to, e.g.,our interpretation of the phytoplankton species concept (strain variation), the dogma of their apparent cosmopolitanism, the role of bacteria and zooplankton grazing in HABs, and our approaches to investigating the ecological and genetic basis for the production of toxins and allelochemicals. Increasingly,eutrophication and climate change are viewed andmanaged as multifactorial environmental stressors that will further challenge managers of coastal resources and those responsible for protecting human health. Here we review HABscience with an eye toward new concepts and approaches,emphasizing, where possible, the unexpected yet promising new directions that research has taken in this diverse field.
    Repository Name: EPIC Alfred Wegener Institut
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  • 71
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Publication Date: 2022-04-07
    Description: Incoherent diffractive imaging (IDI) promises structural analysis with atomic resolution based on intensity interferometry of pulsed X‐ray fluorescence emission. However, its experimental realization is still pending and a comprehensive theory of contrast formation has not been established to date. Explicit expressions are derived for the equal‐pulse two‐point intensity correlations, as the principal measured quantity of IDI, with full control of the prefactors, based on a simple model of stochastic fluorescence emission. The model considers the photon detection statistics, the finite temporal coherence of the individual emissions, as well as the geometry of the scattering volume. The implications are interpreted in view of the most relevant quantities, including the fluorescence lifetime, the excitation pulse, as well as the extent of the scattering volume and pixel size. Importantly, the spatiotemporal overlap between any two emissions in the sample can be identified as a crucial factor limiting the contrast and its dependency on the sample size can be derived. The paper gives rigorous estimates for the optimum sample size, the maximum photon yield and the expected signal‐to‐noise ratio under optimal conditions. Based on these estimates, the feasibility of IDI experiments for plausible experimental parameters is discussed. It is shown in particular that the mean number of photons per detector pixel which can be achieved with X‐ray fluorescence is severely limited and as a consequence imposes restrictive constraints on possible applications.
    Description: Starting from a simple model of stochastic fluorescence emission, a theory is derived of contrast formation and signal‐to‐noise ratio for incoherent diffractive imaging; its feasibility for plausible experimental parameters is discussed. image
    Keywords: ddc:548
    Language: English
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  • 72
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Publication Date: 2022-03-24
    Description: The Inorganic Crystal Structure Database (ICSD) is the world's largest database of fully evaluated and published crystal structure data, mostly obtained from experimental results. However, the purely experimental approach is no longer the only route to discover new compounds and structures. In the past few decades, numerous computational methods for simulating and predicting structures of inorganic solids have emerged, creating large numbers of theoretical crystal data. In order to take account of these new developments the scope of the ICSD was extended in 2017 to include theoretical structures which are published in peer‐reviewed journals. Each theoretical structure has been carefully evaluated, and the resulting CIF has been extended and standardized. Furthermore, a first classification of theoretical data in the ICSD is presented, including additional categories used for comparison of experimental and theoretical information.
    Description: The article discusses how theoretical crystal data are supplementing experimental data for simulation and prediction of structures of inorganic solids in the Inorganic Crystal Structure Database.
    Keywords: ddc:548
    Language: English
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  • 73
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2003. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Environment and Resources 28 (2003): 521-558, doi:10.1146/annurev.energy.28.011503.163443.
    Description: Agriculture and industrial development have led to inadvertent changes in the natural carbon cycle. As a consequence, concentrations of carbon dioxide and other greenhouse gases have increased in the atmosphere and may lead to changes in climate. The current challenge facing society is to develop options for future management of the carbon cycle. A variety of approaches has been suggested: direct reduction of emissions, deliberate manipulation of the natural carbon cycle to enhance sequestration, and capture and isolation of carbon from fossil fuel use. Policy development to date has laid out some of the general principles to which carbon management should adhere. These are summarized as: how much carbon is stored, by what means, and for how long. To successfully manage carbon for climate purposes requires increased understanding of carbon cycle dynamics and improvement in the scientific capabilities available for measurement as well as for policy needs. The specific needs for scientific information to underpin carbon cycle management decisions are not yet broadly known. A stronger dialogue between decision makers and scientists must be developed to foster improved application of scientific knowledge to decisions. This review focuses on the current knowledge of the carbon cycle, carbon measurement capabilities (with an emphasis on the continental scale) and the relevance of carbon cycle science to carbon sequestration goals.
    Description: The National Center for Atmospheric Research is supported by the National Science Foundation.
    Keywords: Carbon sequestration ; Measurement techniques ; Climate ; Kyoto protocol
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 74
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    Annual Reviews
    Publication Date: 2022-05-25
    Description: Author Posting. © Annual Reviews, 2006. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Fluid Mechanics 38 (2006): 395-425, doi:10.1146/annurev.fluid.38.050304.092129.
    Description: Over the past four decades, the combination of in situ and remote sensing observations has demonstrated that long nonlinear internal solitary-like waves are ubiquitous features of coastal oceans. The following provides an overview of the properties of steady internal solitary waves and the transient processes of wave generation and evolution, primarily from the point of view of weakly nonlinear theory, of which the Korteweg-de Vries equation is the most frequently used example. However, the oceanographically important processes of wave instability and breaking, generally inaccessible with these models, are also discussed. Furthermore, observations often show strongly nonlinear waves whose properties can only be explained with fully nonlinear models.
    Description: KRH acknowledges support from NSF and ONR and an Independent Study Award from the Woods Hole Oceanographic Institution. WKM acknowledges support from NSF and ONR, which has made his work in this area possible, in close collaboration with former graduate students at Scripps Institution of Oceanography and MIT.
    Keywords: Solitary waves ; Nonlinear waves ; Stratified flow ; Physical Oceanography
    Repository Name: Woods Hole Open Access Server
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  • 75
    Publication Date: 2022-05-25
    Description: First published online as a Review in Advance on October 24, 2005. (Some corrections may occur before final publication online and in print)
    Description: Author Posting. © Annual Reviews, 2005. This article is posted here by permission of Annual Reviews for personal use, not for redistribution. The definitive version was published in Annual Review of Physiology 68 (2006): 22.1-22.29, doi:10.1146/annurev.physiol.68.040104.105418.
    Description: Superfast muscles of vertebrates power sound production. The fastest, the swimbladder muscle of toadfish, generates mechanical power at frequencies in excess of 200 Hz. To operate at these frequencies, the speed of relaxation has had to increase approximately 50-fold. This increase is accomplished by modifications of three kinetic traits: (a) a fast calcium transient due to extremely high concentration of sarcoplasmic reticulum (SR)-Ca2+ pumps and parvalbumin, (b) fast off-rate of Ca2+ from troponin C due to an alteration in troponin, and (c) fast cross-bridge detachment rate constant (g, 50 times faster than that in rabbit fast-twitch muscle) due to an alteration in myosin. Although these three modifications permit swimbladder muscle to generate mechanical work at high frequencies (where locomotor muscles cannot), it comes with a cost: The high g causes a large reduction in attached force-generating cross-bridges, making the swimbladder incapable of powering low-frequency locomotory movements. Hence the locomotory and sound-producing muscles have mutually exclusive designs.
    Description: This work was made possible by support from NIH grants AR38404 and AR46125 as well as the University of Pennsylvania Research Foundation.
    Keywords: Parvalbumin ; Ca2+ release ; Ca2+ uptake ; Cross-bridges ; Adaptation ; Sound production ; Whitman Center
    Repository Name: Woods Hole Open Access Server
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  • 76
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 77
    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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  • 78
    Publication Date: 2017-04-04
    Description: A series of computed microtomography experiments are reported which were performed by using a third-generation synchrotron radiation source on volcanic rocks from various active hazardous volcanoes in Italy and other volcanic areas in the world. The applied technique allowed the internal structure of the investigated material to be accurately imaged at the micrometre scale and three-dimensional views of the investigated samples to be produced as well as three-dimensional quantitative measurements of textural features. The geometry of the vesicle (gas-filled void) network in volcanic products of both basaltic and trachytic compositions were particularly focused on, as vesicle textures are directly linked to the dynamics of volcano degassing. This investigation provided novel insights into modes of gas exsolution, transport and loss in magmas that were not recognized in previous studies using solely conventional two-dimensional imaging techniques. The results of this study are important to understanding the behaviour of volcanoes and can be combined with other geosciences disciplines to forecast their future activity.
    Description: Published
    Description: 215-221
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: high-resolution three-dimensional imaging ; X-ray computed microtomography ; volcanic eruptions ; volcanic rock textures ; 04. Solid Earth::04.08. Volcanology::04.08.05. Volcanic rocks ; 04. Solid Earth::04.08. Volcanology::04.08.07. Instruments and techniques
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 79
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    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    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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  • 80
    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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  • 81
    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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  • 82
    Publication Date: 2022-06-24
    Description: Scientific tasks aimed at decoding and characterizing complex systems and processes at high pressures set new challenges for modern X‐ray diffraction instrumentation in terms of X‐ray flux, focal spot size and sample positioning. Presented here are new developments at the Extreme Conditions beamline (P02.2, PETRA III, DESY, Germany) that enable considerable improvements in data collection at very high pressures and small scattering volumes. In particular, the focusing of the X‐ray beam to the sub‐micrometer level is described, and control of the aberrations of the focusing compound refractive lenses is made possible with the implementation of a correcting phase plate. This device provides a significant enhancement of the signal‐to‐noise ratio by conditioning the beam shape profile at the focal spot. A new sample alignment system with a small sphere of confusion enables single‐crystal data collection from grains of micrometer to sub‐micrometer dimensions subjected to pressures as high as 200 GPa. The combination of the technical development of the optical path and the sample alignment system contributes to research and gives benefits on various levels, including rapid and accurate diffraction mapping of samples with sub‐micrometer resolution at multimegabar pressures.
    Description: Facing the challenges of X‐ray diffraction from tiny samples subjected to multimegabar pressures, instrumentation developments are presented that enable, among other studies, single‐crystal data collection from micrometer‐ to sub‐micrometer‐sized grains. The developments are based on a sub‐micrometer beam capability employing compound refractive lenses operating with a phase correcting plate and a precise motorization solution.
    Keywords: ddc:548
    Language: English
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  • 83
    Publication Date: 2022-10-27
    Description: This paper is not subject to U.S. copyright. The definitive version was published in Sherwood, C. R., van Dongeren, A., Doyle, J., Hegermiller, C. A., Hsu, T.-J., Kalra, T. S., Olabarrieta, M., Penko, A. M., Rafati, Y., Roelvink, D., van der Lugt, M., Veeramony, J., & Warner, J. C. Modeling the morphodynamics of coastal responses to extreme events: what shape are we in? Annual Review of Marine Science, 14, (2022): 457–492, https://doi.org/10.1146/annurev-marine-032221-090215.
    Description: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these models simulate morphodynamics across the Sallenger storm-impact scale, including swash,collision, overwash, and inundation. Models are becoming both wider (as more processes are added) and deeper (as detailed physics replaces earlier parameterizations). Algorithms for wave-induced flows and sediment transport under shoaling waves are among the recent developments. Community and open-source models have become the norm. Observations of initial conditions (topography, land cover, and sediment characteristics) have become more detailed, and improvements in tropical cyclone and wave models provide forcing (winds, waves, surge, and upland flow) that is better resolved and more accurate, yielding commensurate improvements in model skill. We foresee that future storm-impact models will increasingly resolve individual waves, apply data assimilation, and be used in ensemble modeling modes to predict uncertainties.
    Description: All authors except D.R. were partially supported by the IFMSIP project, funded by US Office of Naval Research grant PE 0601153N under contracts N00014-17-1-2459 (Deltares), N00014-18-1-2785 (University of Delaware), N0001419WX00733 (US Naval Research Laboratory, Monterey), N0001418WX01447 (US Naval Research Laboratory, Stennis Space Center), and N0001418IP00016 (US Geological Survey). C.R.S., C.A.H., T.S.K., and J.C.W. were supported by the US Geological Survey Coastal/Marine Hazards and Resources Program. A.v.D. and M.v.d.L. were supported by the Deltares Strategic Research project Quantifying Flood Hazards and Impacts. M.O. acknowledges support from National Science Foundation project OCE-1554892.
    Keywords: Coastal morphodynamics ; Extreme storms ; Coastal modeling ; Sandy coasts ; Waves ; Sediment transport
    Repository Name: Woods Hole Open Access Server
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  • 84
    Publication Date: 2022-10-04
    Description: The small‐angle neutron scattering data of nanostructured magnetic samples contain information regarding their chemical and magnetic properties. Often, the first step to access characteristic magnetic and structural length scales is a model‐free investigation. However, due to measurement uncertainties and a restricted q range, a direct Fourier transform usually fails and results in ambiguous distributions. To circumvent these problems, different methods have been introduced to derive regularized, more stable correlation functions, with the indirect Fourier transform being the most prominent approach. Here, the indirect Fourier transform is compared with the singular value decomposition and an iterative algorithm. These approaches are used to determine the correlation function from magnetic small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles; it is shown that with all three methods, in principle, the same correlation function can be derived. Each method has certain advantages and disadvantages, and thus the recommendation is to combine these three approaches to obtain robust results.
    Description: Three different approaches are compared for determination of the correlation function from the small‐angle neutron scattering data of a powder sample of iron oxide nanoparticles.
    Keywords: ddc:548
    Language: English
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  • 85
    Publication Date: 2022-06-16
    Description: A method of ab initio crystal structure determination from powder diffraction data for organic and metal–organic compounds, which does not require prior indexing of the powder pattern, has been developed. Only a reasonable molecular geometry is required, needing knowledge of neither unit‐cell parameters nor space group. The structures are solved from scratch by a global fit to the powder data using the new program FIDEL‐GO (`FIt with DEviating Lattice parameters ‐ Global Optimization'). FIDEL‐GO uses a similarity measure based on cross‐correlation functions, which allows the comparison of simulated and experimental powder data even if the unit‐cell parameters deviate strongly. The optimization starts from large sets of random structures in various space groups. The unit‐cell parameters, molecular position and orientation, and selected internal degrees of freedom are fitted simultaneously to the powder pattern. The optimization proceeds in an elaborate multi‐step procedure with built‐in clustering of duplicate structures and iterative adaptation of parameter ranges. The best structures are selected for an automatic Rietveld refinement. Finally, a user‐controlled Rietveld refinement is performed. The procedure aims for the analysis of a wide range of `problematic' powder patterns, in particular powders of low crystallinity. The method can also be used for the clustering and screening of a large number of possible structure candidates and other application scenarios. Examples are presented for structure determination from unindexed powder data of the previously unknown structures of the nanocrystalline phases of 4,11‐difluoro‐, 2,9‐dichloro‐ and 2,9‐dichloro‐6,13‐dihydro‐quinacridone, which were solved from powder patterns with 14–20 peaks only, and of the coordination polymer dichloro‐bis(pyridine‐N)copper(II).
    Description: A new method for the structure determination of molecular crystals from unindexed powder data has been developed and successfully applied. The method performs a global optimization using pattern comparison based on cross‐correlation functions.
    Keywords: ddc:548
    Language: English
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  • 86
    Publication Date: 2022-12-06
    Description: The nuclear and magnetic structures of Mn3Fe2Si3 are investigated in the temperature range from 20 to 300 K. The magnetic properties of Mn3Fe2Si3 were measured on a single crystal. The compound undergoes a paramagnetic to antiferromagnetic transition at TN2 ≃ 120 K and an antiferromagnetic to antiferromagnetic transition at TN1 ≃ 69 K. A similar sequence of magnetic phase transitions is found for the parent compound Mn5Si3 upon temperature variation, but the field‐driven transition observed in Mn5Si3 is not found in Mn3Fe2Si3, resulting in a strongly reduced magnetocaloric effect. Structurally, the hexagonal symmetry found for both compounds under ambient conditions is preserved in Mn3Fe2Si3 through both magnetic transitions, indicating that the crystal structure is only weakly affected by the magnetic phase transition, in contrast to Mn5Si3 where both transitions distort the nuclear structure. Both compounds feature a collinear high‐temperature magnetic phase AF2 and transfer into a non‐collinear phase AF1 at low temperature. While one of the distinct crystallographic sites remains disordered in the AF2 phase in the parent compound, the magnetic structure in the AF2 phase involves all magnetic atoms in Mn3Fe2Si3. These observations imply that the distinct sites occupied by the magnetic atoms play an important role in the magnetocaloric behaviour of the family.
    Description: The nuclear and magnetic structures of Mn3Fe2Si3 are determined and the magnetic properties are compared with those of the parent compound Mn5Si3. The results imply that the distinct magnetic sites play an important role in the magnetocaloric behaviour of the family. image
    Keywords: ddc:548 ; magnetocaloric effect ; magnetic structure ; neutron diffraction ; synchrotron diffraction ; site dependence
    Language: English
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  • 87
    Publication Date: 2022-05-26
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Annual Review of Marine Science 9 (2017): 173-203, doi:10.1146/annurev-marine-010816-060733.
    Description: The events that followed the Tohoku earthquake and tsunami on March 11, 2011, included the loss of power and overheating at the Fukushima Daiichi nuclear power plants, which led to extensive releases of radioactive gases, volatiles, and liquids, particularly to the coastal ocean. The fate of these radionuclides depends in large part on their oceanic geochemistry, physical processes, and biological uptake. Whereas radioactivity on land can be resampled and its distribution mapped, releases to the marine environment are harder to characterize owing to variability in ocean currents and the general challenges of sampling at sea. Five years later, it is appropriate to review what happened in terms of the sources, transport, and fate of these radionuclides in the ocean. In addition to the oceanic behavior of these contaminants, this review considers the potential health effects and societal impacts.
    Description: K.B. was supported in part by the Gordon and Betty Moore Foundation and the Deerbrook Charitable Trust. P.M. was supported in part by the Generalitat de Catalunya through MERS (grant 2014 SGR 1356), the European Commission 7th Framework COMET-FRAME project (grant agreement 604974), and the Ministerio de Economía y Competitividad of Spain (project CTM2011-15152-E). S.C. was supported in part by the French program Investissement d'Avenir run by the National Research Agency (AMORAD project, grant ANR-11-RSNR-0002). D.O. was supported in part by the Center for Environmental Radioactivity (NFR Centers of Excellence grant 223268/F50). J.N.S. was supported in part by the Marine Environmental Observation, Prediction, and Response Network.
    Keywords: Cesium ; Caesium ; North Pacific ; Radioactivity ; Japan
    Repository Name: Woods Hole Open Access Server
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  • 88
    Publication Date: 2023-01-15
    Description: A Guinier camera equipped with an imaging plate is used to investigate and eliminate the sources of instrumental errors affecting the quality of the obtained scanned Guinier data. A program with a graphical user interface is presented which converts the data of the scanned images into different standard file formats for powder X‐ray patterns containing intensities, their standard deviations and the diffraction angles. The program also allows for manual and automatic correction of the 2gθ scale against a known reference material. It is shown using LaB6 that the exported X‐ray diffraction patterns provide a 2gθ scale reproducible enough to allow for averaging diffractograms obtained from different exposures of the imaging plate for the same sample. As shown on a mixture of NaCl and sodalite, the quality of the produced data is sufficient for Rietveld refinement. The software including source code is made available under a free software license.
    Description: A program for the digitization of Guinier powder diffraction images is described, which works with images from both optical and laser scanners. Thus, processing of data from storage‐phosphor‐based imaging plates and Ag‐based photographic films is possible.
    Keywords: ddc:548 ; IPreader software ; Guinier cameras ; imaging plates (IPs) ; diffraction pattern conversion into data columns ; powder X‐ray diffraction ; data processing ; Guinier method
    Language: English
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  • 89
    Publication Date: 2023-07-04
    Description: The recent diversification of macromolecular crystallographic experiments including the use of pink beams, convergent electron diffraction and serial snapshot crystallography has shown the limitations of using the Laue equations for diffraction prediction. This article gives a computationally efficient way of calculating approximate crystal diffraction patterns given varying distributions of the incoming beam, crystal shapes and other potentially hidden parameters. This approach models each pixel of a diffraction pattern and improves data processing of integrated peak intensities by enabling the correction of partially recorded reflections. The fundamental idea is to express the distributions as weighted sums of Gaussian functions. The approach is demonstrated on serial femtosecond crystallography data sets, showing a significant decrease in the required number of patterns to refine a structure to a given error.
    Description: Reflection position, size and shape prediction and partiality estimation of crystal diffraction by integrating using a Gaussian basis are described.
    Keywords: ddc:548 ; partiality estimation ; diffraction prediction ; merging ; serial snapshot crystallography
    Language: English
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  • 90
    Publication Date: 2023-07-04
    Description: Magnetic small‐angle neutron scattering (SANS) is ideally suited to providing direct reciprocal‐space information on long‐wavelength magnetic modulations, such as helicoids, solitons, merons or skyrmions. SANS of such structures in thin films or micro‐structured bulk materials is strongly limited by the tiny scattering volume vis a vis the prohibitively high background scattering by the substrate and support structures. Considering near‐surface scattering just above the critical angle of reflection, where unwanted signal contributions due to substrate or support structures become very small, it is established that the scattering patterns of the helical, conical, skyrmion lattice and fluctuation‐disordered phases in a polished bulk sample of MnSi are equivalent for conventional transmission and near‐surface SANS geometries. This motivates the prediction of a complete repository of scattering patterns expected for thin films in the near‐surface SANS geometry for each orientation of the magnetic order with respect to the scattering plane.
    Description: Near‐surface SANS is discussed for its potential as a probe of long‐wavelength magnetic modulations in specimens with reduced sample dimensions.
    Keywords: ddc:548 ; small‐angle neutron scattering ; near‐surface SANS ; magnetism ; non‐collinear magnetism ; thin films ; skyrmions ; MnSi
    Language: English
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  • 91
    Publication Date: 2023-10-24
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Complex functional materials play a crucial role in a broad range of energy‐related applications and in general for materials science. Revealing the structural mechanisms is challenging due to highly correlated coexisting phases and microstructures, especially for 〈italic〉in situ〈/italic〉 or 〈italic〉operando〈/italic〉 investigations. Since the grain sizes influence the properties, these microstructural features further complicate investigations at synchrotrons due to the limitations of illuminated sample volumes. In this study, it is demonstrated that such complex functional materials with highly correlated coexisting phases can be investigated under 〈italic〉in situ〈/italic〉 conditions with neutron diffraction. For large grain sizes, these experiments are valuable methods to reveal the structural mechanisms. For an example of 〈italic〉in situ〈/italic〉 experiments on barium titanate with an applied electric field, details of the electric‐field‐induced phase transformation depending on grain size and frequency are revealed. The results uncover the strain mechanisms in barium titanate and elucidate the complex interplay of stresses in relation to grain sizes as well as domain‐wall densities and mobilities.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉This work reports 〈italic〉in situ〈/italic〉 neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain‐size‐dependent strain mechanisms and shows the competitiveness of neutron diffraction with high‐resolution synchrotron diffraction.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2vb5054:jcr2vb5054-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:550.724 ; ddc:548 ; neutron diffraction ; in situ ; applied electric fields ; barium titanate ; strain mechanisms ; grain sizes ; complex functional materials ; microstructures ; coexisting phases
    Language: English
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  • 92
    Publication Date: 2023-12-04
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉A way has been developed to measure the unit‐cell parameters of a single crystal just from an energy scan with X‐rays, even when the exact energy of the X‐rays is not well defined due to an error in the pitch angle of the monochromator. The precision of this measurement reaches 〈italic〉da〈/italic〉/〈italic〉a〈/italic〉 ∼ 1 × 10〈sup〉−5〈/sup〉. The method is based on the analysis of diffraction losses of the beam, transmitted through a single crystal (the so‐called `glitch effect'). This method can be easily applied to any transmissive X‐ray optical element made of single crystals (for example, X‐ray lenses). The only requirements are the possibility to change the energy of the generated X‐ray beam and some intensity monitor to measure the transmitted intensity. The method is agnostic to the error in the monochromator tuning and it can even be used for determination of the absolute pitch (or 2gθ) angle of the monochromator. Applying the same method to a crystal with well known lattice parameters allows determination of the exact cell parameters of the monochromator at any energy.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉Diffraction losses (glitches) at certain energies of the X‐ray beam, transmitted through a single crystal, can be used for lattice parameters determination as well as for calibrating the monochromator (absolute pitch angle and the unit‐cell parameter).〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005775:jsy2ay5590:jsy2ay5590-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; X‐ray glitches ; diffraction losses ; unit‐cell parameter ; single‐crystal X‐ray optics ; monochromator calibration
    Language: English
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  • 93
    Publication Date: 2023-09-12
    Description: Two data evaluation concepts for X‐ray stress analysis based on energy‐dispersive diffraction on polycrystalline materials with cubic crystal structure, almost random crystallographic texture and strong single‐crystal elastic anisotropy are subjected to comparative assessment. The aim is the study of the residual stress state in hard‐to‐reach measurement points, for which the sin2ψ method is not applicable due to beam shadowing at larger sample tilting. This makes the approaches attractive for stress analysis in engineering parts with complex shapes, for example. Both approaches are based on the assumption of a biaxial stress state within the irradiated sample volume. They exploit in different ways the elastic anisotropy of individual crystallites acting at the microscopic scale and the anisotropy imposed on the material by the near‐surface stress state at the macroscopic scale. They therefore complement each other, in terms of both their preconditions and their results. The first approach is based on the evaluation of strain differences, which makes it less sensitive to variations in the strain‐free lattice parameter a0. Since it assumes a homogeneous stress state within the irradiated sample volume, it provides an average value of the in‐plane stresses. The second approach exploits the sensitivity of the lattice strain to changes in a0. Consequently, it assumes a homogeneous chemical composition but provides a stress profile within the information depth. Experimental examples from different fields in materials science, namely shot peening of austenitic steel and in situ stress analysis during welding, are presented to demonstrate the suitability of the proposed methods.
    Description: The single‐crystal elastic anisotropy and the anisotropy of the near‐surface (residual) stress state of polycrystalline materials with random texture are exploited in energy‐dispersive X‐ray stress analysis to study samples under constrained measurement conditions.
    Keywords: ddc:548 ; X‐ray stress analysis ; energy‐dispersive diffraction ; polycrystalline materials ; single‐crystal elastic anisotropy
    Language: English
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  • 94
    Publication Date: 2023-07-20
    Description: A pseudosymmetric description of the crystal lattice derived from a single wide‐angle Kikuchi pattern can have several causes. The small size (〈15%) of the sector covered by an electron backscatter diffraction pattern, the limited precision of the projection centre position and the Kikuchi band definition are crucial. Inherent pseudosymmetries of the crystal lattice and/or structure also pose a challenge in the analysis of Kikuchi patterns. To eliminate experimental errors as much as possible, simulated Kikuchi patterns of 350 phases have been analysed using the software CALM [Nolze et al. (2021). J. Appl. Cryst.54, 1012–1022] in order to estimate the frequency of and reasons for pseudosymmetric crystal lattice descriptions. Misinterpretations occur in particular when the atomic scattering factors of non‐equivalent positions are too similar and reciprocal‐lattice points are systematically missing. As an example, a pseudosymmetry prediction depending on the elements involved is discussed for binary AB compounds with B1 and B2 structure types. However, since this is impossible for more complicated phases, this approach cannot be directly applied to compounds of arbitrary composition and structure.
    Description: Distinguishing between actual and apparent pseudosymmetry in electron backscatter diffraction patterns is nearly impossible, even for simulated patterns. However, the resulting lattice is always a superlattice as long as the signal is not a superposition of multiple patterns.
    Keywords: ddc:548 ; Bravais lattices ; pseudosymmetry ; lattice point density ; ordered/disordered structures ; lattice distortion ; electron backscatter diffraction ; backscattered Kikuchi diffraction patterns ; lattice parameters ; Funk transform
    Language: English
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  • 95
    Publication Date: 2023-07-21
    Description: Finite size effects in partial pair distribution functions generate artefacts in the scattering structure factor and scattering intensity. It is shown how they can be overcome using a binned version of the Debye scattering equation. Accordingly, reverse Monte Carlo simulations are used for very small nanoparticles of LaFeO3 with diameters below 10 nm to simultaneously analyse X‐ray scattering data and extended X‐ray absorption fine structure spectra at the La K and Fe K edges. The structural information obtained is consistent regarding local structure and long‐range order.
    Description: Computing scattering intensity using the Debye scattering equation after binning interatomic distances avoids finite size artefacts and is efficient enough for simultaneous refinement of scattering data and extended X‐ray absorption spectra by reverse Monte Carlo simulations.
    Keywords: ddc:548 ; extended X‐ray absorption fine structure ; EXAFS ; wide‐angle X‐ray scattering ; WAXS ; reverse Monte Carlo ; RMC ; nanocrystals ; LaFeO3
    Language: English
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  • 96
    Publication Date: 2023-07-21
    Description: A band width determination using the first derivative of the band profile systematically underestimates the true Bragg angle. Corrections are proposed to compensate for the resulting offset Δa/a of the mean lattice parameters derived from as many Kikuchi band widths as possible. For dynamically simulated Kikuchi patterns, Δa/a can reach up to 8% for phases with a high mean atomic number Z, whereas for much more common low‐Z materials the offset decreases linearly. A predicted offset Δa/a = f(Z) is therefore proposed, which also includes the unit‐cell volume and thus takes into account the packing density of the scatterers in the material. Since Z is not always available for unknown phases, its substitution by Zmax, i.e. the atomic number of the heaviest element in the compound, is still acceptable for an approximate correction. For simulated Kikuchi patterns the offset‐corrected lattice parameter deviation is Δa/a 〈 1.5%. The lattice parameter ratios, and the angles α, β and γ between the basis vectors, are not affected at all.
    Description: Automatically determined band widths in simulated backscatter Kikuchi patterns exhibit differences from the double Bragg angles that correlate with the scatterer density. Corrections are proposed to compensate for this.
    Keywords: ddc:548 ; mean atomic number ; Kikuchi patterns ; lattice parameters ; automated Bragg angle determination ; lattice parameter determination ; dynamical theory of electron diffraction ; electron backscatter diffraction ; Funk transform
    Language: English
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  • 97
    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The high‐intensity time‐of‐flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world‐wide 〈sup〉3〈/sup〉He crisis in 2009, the authors promptly initiated the development of 〈sup〉3〈/sup〉He‐free detector alternatives that are tailor‐made for the requirements of large‐area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular‐ and wavelength‐dependent data from the POWTEX detector, unfortunately damaged by a 50〈italic〉g〈/italic〉 shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the 〈italic〉PowderReduceP2D〈/italic〉 algorithm implemented in 〈italic〉Mantid〈/italic〉 [Arnold 〈italic〉et al.〈/italic〉 (2014). 〈italic〉Nucl. Instrum. Methods Phys. Res. A〈/italic〉, 〈bold〉764〈/bold〉, 156–166]. The final part of the data treatment chain, namely a novel multi‐dimensional refinement using a modified version of the 〈italic〉GSAS‐II〈/italic〉 software suite [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?aj5212"〉Toby & Von Dreele (2013). 〈italic〉J. Appl. Cryst.〈/italic〉〈bold〉46〈/bold〉, 544–549〈/ext-link〉], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of 〈italic〉GSAS‐II〈/italic〉. This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly‐user sample, BaZn(NCN)〈sub〉2〈/sub〉. Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi‐dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the 〈italic〉a〈/italic〉 and 〈italic〉b〈/italic〉 lattice parameters of BaZn(NCN)〈sub〉2〈/sub〉 crystallizing in 〈italic〉Pbca〈/italic〉 as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, 〈italic〉e.g.〈/italic〉 the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large‐area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The first real‐world neutron diffraction data have been collected with one of the POWTEX detectors (FRM II, Garching, Germany) mounted for testing at the Spallation Neutron Source (Oak Ridge National Laboratory, USA). They allow for angular‐ and wavelength‐dispersive Rietveld refinement using a modified version of 〈italic〉GSAS‐II〈/italic〉.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:16005767:jcr2tu5033:jcr2tu5033-fig-0001"〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; neutron detectors ; POWGEN beamline ; POWTEX detector ; DREAM beamline ; time‐of‐flight diffraction ; angular‐dispersive refinement ; wavelength‐dispersive refinement ; powder diffraction ; Rietveld refinement ; multi‐dimensional refinement
    Language: English
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  • 98
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    Unknown
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Publication Date: 2023-07-21
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉The paper by Gopalan [〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327〈/ext-link〉] presented an enumeration of the 41 physical quantity types in non‐relativistic physics, in arbitrary dimensions, based on the formalism of Clifford algebra. Gopalan considered three antisymmetries: spatial inversion, 〈overline〉1〈/overline〉, time reversal, 1′, and wedge reversion, 1〈sup〉†〈/sup〉. A consideration of the set of all seven antisymmetries (〈overline〉1〈/overline〉, 1′, 1〈sup〉†〈/sup〉, 1′〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉〈sup〉†〈/sup〉, 〈overline〉1〈/overline〉′, 〈overline〉1〈/overline〉′〈sup〉†〈/sup〉) leads to an extension of the results obtained by Gopalan. It is shown that there are 51 types of physical quantities with distinct symmetry properties in total.〈/p〉
    Description: 〈p xmlns:mml="http://www.w3.org/1998/Math/MathML" xml:lang="en"〉It is shown that there are 51 types of physical quantities in arbitrary dimensions with distinct transformations by wedge reversion symmetry. In the paper by 〈ext-link ext-link-type="uri" xlink:href="http://scripts.iucr.org/cgi-bin/paper?ib5086"〉Gopalan [(2020). 〈italic〉Acta Cryst.〈/italic〉 A〈bold〉76〈/bold〉, 318–327]〈/ext-link〉 only 41 types were enumerated.〈boxed-text position="anchor" content-type="graphic" xml:lang="en"〉〈graphic position="anchor" id="jats-graphic-1" xlink:href="urn:x-wiley:20532733:aya2ib5117:aya2ib5117-fig-0001"〉 〈alt-text〉image〈/alt-text〉 〈/graphic〉〈/boxed-text〉〈/p〉
    Keywords: ddc:548 ; multivectors ; wedge reversion ; antisymmetry ; Clifford algebra
    Language: English
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  • 99
    Publication Date: 2023-07-19
    Description: The derivation of a crystal structure and its phase‐specific parameters from a single wide‐angle backscattered Kikuchi diffraction pattern requires reliable extraction of the Bragg angles. By means of the first derivative of the lattice profile, an attempt is made to determine fully automatically and reproducibly the band widths in simulated Kikuchi patterns. Even under such ideal conditions (projection centre, wavelength and lattice plane traces are perfectly known), this leads to a lattice parameter distribution whose mean shows a linear offset that correlates with the mean atomic number Z of the pattern‐forming phase. The consideration of as many Kikuchi bands as possible reduces the errors that typically occur if only a single band is analysed. On the other hand, the width of the resulting distribution is such that higher image resolution of diffraction patterns, employing longer wavelengths to produce wider bands or the use of higher interference orders is less advantageous than commonly assumed.
    Description: The lattice parameters of more than 350 phases have been determined from simulated backscatter Kikuchi patterns. The deviations correlating with the mean atomic number correspond to those observed previously for experimental electron backscatter diffraction patterns.
    Keywords: ddc:548 ; Bragg angles ; Kikuchi bands ; Kikuchi patterns ; first derivative ; lattice parameters ; lattice parameter determination ; Bravais lattice type ; electron backscatter diffraction ; Radon transform
    Language: English
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  • 100
    Publication Date: 2023-07-19
    Description: Serial crystallography experiments produce massive amounts of experimental data. Yet in spite of these large‐scale data sets, only a small percentage of the data are useful for downstream analysis. Thus, it is essential to differentiate reliably between acceptable data (hits) and unacceptable data (misses). To this end, a novel pipeline is proposed to categorize the data, which extracts features from the images, summarizes these features with the `bag of visual words' method and then classifies the images using machine learning. In addition, a novel study of various feature extractors and machine learning classifiers is presented, with the aim of finding the best feature extractor and machine learning classifier for serial crystallography data. The study reveals that the oriented FAST and rotated BRIEF (ORB) feature extractor with a multilayer perceptron classifier gives the best results. Finally, the ORB feature extractor with multilayer perceptron is evaluated on various data sets including both synthetic and experimental data, demonstrating superior performance compared with other feature extractors and classifiers.
    Description: A machine learning method for distinguishing good and bad images in serial crystallography is presented. To reduce the computational cost, this uses the oriented FAST and rotated BRIEF feature extraction method from computer vision to detect image features, followed by a multilayer perceptron (neural network) to classify the images.
    Keywords: ddc:548 ; serial crystallography ; data reduction ; machine learning ; feature extraction
    Language: English
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