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Open-access and free articles in Acta Crystallographica Section D: Biological Crystallography




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From space group to space groupoid: the partial symmetry of low-temperature E-vanillyl oxime

The phase transition of E-vanillyl oxime {1-[(E)-(hydroxyimino)methyl]-4-hydroxy-3-methoxybenzene, C8H9NO3} has been analysed by single-crystal and powder X-ray diffraction. The high-temperature (HT) phase (P21/a, Z' = 1) transforms into the low-temperature (LT) phase (threefold superstructure, Poverline{1}, Z' = 6) at ca 190 K. The point operations lost on cooling, {m[010], 2[010]}, are retained as twin operations and constitute the twin law. The screw rotations and glide reflections are retained in the LT phase as partial operations acting on a subset of Euclidean space {b E}^3. The full symmetry of the LT phase, including partial operations, is described by a disconnected space groupoid which is built of three connected components.




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Structure variations within RSi2 and R2TSi3 silicides. Part I. Structure overview

Here, structural parameters of various structure reports on RSi2 and R2TSi3 compounds [where R is an alkaline earth metal, a rare earth metal (i.e. an element of the Sc group or a lathanide), or an actinide and T is a transition metal] are summarized. The parameters comprising composition, lattice parameters a and c, ratio c/a, formula unit per unit cell and structure type are tabulated. The relationships between the underlying structure types are presented within a group–subgroup scheme (Bärnighausen diagram). Additionally, unexpectedly missing compounds within the R2TSi3 compounds were examined with density functional theory and compounds that are promising candidates for synthesis are listed. Furthermore, a correlation was detected between the orthorhombic AlB2-like lattices of, for example, Ca2AgSi3 and the divalence of R and the monovalence of T. Finally, a potential tetragonal structure with ordered Si/T sites is proposed.




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Shack–Hartmann wavefront sensors based on 2D refractive lens arrays and super-resolution multi-contrast X-ray imaging

Different approaches of 2D lens arrays as Shack–Hartmann sensors for hard X-rays are compared. For the first time, a combination of Shack–Hartmann sensors for hard X-rays (SHSX) with a super-resolution imaging approach to perform multi-contrast imaging is demonstrated. A diamond lens is employed as a well known test object. The interleaving approach has great potential to overcome the 2D lens array limitation given by the two-photon polymerization lithography. Finally, the radiation damage induced by continuous exposure of an SHSX prototype with a white beam was studied showing a good performance of several hours. The shape modification and influence in the final image quality are presented.




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Laser-induced metastable mixed phase of AuNi nanoparticles: a coherent X-ray diffraction imaging study

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.




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Quantifying redox heterogeneity in single-crystalline LiCoO2 cathode particles

Active cathode particles are fundamental architectural units for the composite electrode of Li-ion batteries. The microstructure of the particles has a profound impact on their behavior and, consequently, on the cell-level electrochemical performance. LiCoO2 (LCO, a dominant cathode material) is often in the form of well-shaped particles, a few micrometres in size, with good crystallinity. In contrast to secondary particles (an agglomeration of many fine primary grains), which are the other common form of battery particles populated with structural and chemical defects, it is often anticipated that good particle crystallinity leads to superior mechanical robustness and suppressed charge heterogeneity. Yet, sub-particle level charge inhomogeneity in LCO particles has been widely reported in the literature, posing a frontier challenge in this field. Herein, this topic is revisited and it is demonstrated that X-ray absorption spectra on single-crystalline particles with highly anisotropic lattice structures are sensitive to the polarization configuration of the incident X-rays, causing some degree of ambiguity in analyzing the local spectroscopic fingerprint. To tackle this issue, a methodology is developed that extracts the white-line peak energy in the X-ray absorption near-edge structure spectra as a key data attribute for representing the local state of charge in the LCO crystal. This method demonstrates significantly improved accuracy and reveals the mesoscale chemical complexity in LCO particles with better fidelity. In addition to the implications on the importance of particle engineering for LCO cathodes, the method developed herein also has significant impact on spectro-microscopic studies of single-crystalline materials at synchrotron facilities, which is broadly applicable to a wide range of scientific disciplines well beyond battery research.




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Synchrotron X-ray diffraction investigation of the surface condition of artefacts from King Henry VIII's warship the Mary Rose

Synchrotron X-ray diffraction (XRD) measured on the XMaS beamline at the ESRF was used to characterize the alloy composition and crystalline surface corrosion of three copper alloy Tudor artefacts recovered from the undersea wreck of King Henry VIII's warship the Mary Rose. The XRD method adopted has a dynamic range ∼1:105 and allows reflections <0.002% of the height of major reflections in the pattern to be discerned above the background without smoothing. Laboratory XRD, scanning electron microscopy–energy dispersive spectroscopy, synchrotron X-ray fluorescence and X-ray excited optical luminescence–X-ray near-edge absorption structure were used as supporting techniques, and the combination revealed structural and compositional features of importance to both archaeology and conservation. The artefacts were brass links believed to be fragments of chainmail and were excavated from the seabed during 1981 and 1982. Their condition reflects very different treatment just after recovery, viz. complete cleaning and conservation, chemical corrosion inhibition and chloride removal only, and distilled water soaking only (to remove the chlorides). The brass composition has been determined for all three at least in the top 7 µm or so as Cu(73%)Zn(27%) from the lattice constant. Measurement of the peak widths showed significant differences in the crystallite size and microstrain between the three samples. All of the links are found to be almost chloride-free with the main corrosion products being spertiniite, sphalerite, zincite, covellite and chalcocite. The balance of corrosion products between the links reflects the conservation treatment applied to one and points to different corrosion environments for the other two.




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Solid/liquid-interface-dependent synthesis and immobilization of copper-based particles nucleated by X-ray-radiolysis-induced photochemical reaction




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Forthcoming article in Journal of Synchrotron Radiation




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Comment on the article The nanodiffraction problem




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Response to Zbigniew Kaszkur's comment on the article The nanodiffraction problem




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Quantifying nanoparticles in clays and soils with a small-angle X-ray scattering method

Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3–10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and α-aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.




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Local orientational order in self-assembled nanoparticle films: the role of ligand composition and salt

An X-ray cross-correlation study of the impact of ligand composition and salt content on the self-assembly of soft-shell nanoparticles is presented, indicating symmetry-selective formation of order.




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sasPDF: pair distribution function analysis of nanoparticle assemblies from small-angle scattering data

The sasPDF method, an extension of the atomic pair distribution function (PDF) analysis to the small-angle scattering (SAS) regime, is presented. The method is applied to characterize the structure of nanoparticle assemblies with different levels of structural order.




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Forthcoming article in Journal of Applied Crystallography




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Structure variations within RSi2 and R2Si3 silicides. Part II. Structure driving factors

Most articles dealing with R2TSi3 compounds are only interested in one specific composite or in a series of composites with varying T elements while keeping R fixed (or vice versa). The present work gives an overview of the complete range of 2:1:3 silicides, similar those of Hoffmann & Pöttgen (2001) and Pan et al. (2013). In contrast to the work of Hoffmann & Pöttgen (2001), reasons for formation of the different symmetries and superstructures are discussed. Here, crystallographic properties are in[the] focus, whereas physical and magnetic properties are omitted because those are given by Pan et al. (2013). READS LIKE AN ABSTRACT, please re-write and remove references if possible. Should be two sentences max.




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Forthcoming article in Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials




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Open-access and free articles in Acta Crystallographica Section F: Structural Biology and Crystallization Communications




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In face of crisis, National Zoo to start captive population of Virginia big-eared bats

The National Zoo has been awarded a grant from the U.S. Fish and Wildlife Service to establish a captive population of the Virginia big-eared bat at the National Zoo’s Conservation & Research Center near Front Royal, Va. Only 15,000 Virginia big-eared bats remain living in caves in West Virginia, Virginia, Kentucky and North Carolina, and these are threatened by the white-nose syndrome.

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Astronomers Find Super-Earth Using Amateur, Off-the-Shelf Technology

The newfound world, GJ1214b, is about 6.5 times as massive as the Earth. Its host star, GJ1214, is a small, red type M star about one-fifth the size of the Sun. GJ1214b orbits its star once every 38 hours at a distance of only 1.3 million miles. Astronomers estimate the planet's temperature to be about 400 degrees Fahrenheit. Although warm as an oven, it is still cooler than any other known transiting planet because it orbits a very dim star.

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Strawberry dart frogs bred at National Zoo for first time in Zoo’s history

For the first time in its history, the National Zoo has bred strawberry dart frogs (Oophaga pumilio), which are known primarily for their vibrant colors and poisonous skin. These frogs also stand out among others because of their dedication to their young as they undergo metamorphosis from egg to tadpole to frog.

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Double Black-Hole Mystery: Dance Partners or Breakup Survivors?

Smithsonian astronomers have just discovered a rare example of a galaxy that appears to have a pair of giant black holes. Now they are trying to determine if those black holes are partners tied together by gravity, or if one of the two has been kicked out in a cosmic breakup.

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Net survey: For quarter century, scientists have been counting creatures traveling Chesapeake Bay tributary

More than 25 years ago, researchers at the Smithsonian Environmental Research Center's Fish and Invertebrate Ecology Lab began taking weekley surveys of the species that make their way in and out of Muddy Creek.

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Super sensitive telescope will detect “killer” asteroids and comets on collision course with Earth

This innovative facility will be at the front line of Earth defense by searching for "killer" asteroids and comets. It will map large portions of the sky nightly, making it an efficient sleuth for not just asteroids but also supernovae and other variable objects.

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NSRC to receive $25 million Investing in Innovation grant from U.S. Department of Education

The funding will allow the National Science Resources Center to validate its LASER (Leadership Assistance for Science Education Reform) Model. LASER, a systemic approach to reform, is a set of processes and strategies designed to help state, district and school leadership teams effectively implement and sustain
high-quality science education for elementary, middle and secondary school students.

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Great Sichuan earthquake of 2008 had little impact on of China’s wild takins

Data from a recent study of wild takins in the high-altitude forests of the Tangjiahe National Nature Reserve in southeast China has shown that the […]

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Earth’s highest coastal mountain range moved 1,367 miles in 170 million years

Using the ancient magnetic field recorded in these rocks, a Smithsonian research group revealed Santa Marta’s 2,200-kilometer journey from northern Peru to its modern position on the Caribbean coast of Colombia during the past 170 million years.

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Kepler spacecraft used by Smithsonian astronomers to find other earths

The Kepler spacecraft was launched in March of 2009 to study extrasolar planets. One of its major goals is the detection of terrestrial planets in habitable zones.

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A Halloween roundup featuring recent articles on spiders, bats and rats

A roundup of recent articles featuring spiders, bats and rats....

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National Zoo and partners first to breed critically endangered tree frog

Although the La Loma tree frog, Hyloscirtus colymba, is notoriously difficult to care for in captivity, the Panama Amphibian Rescue and Conservation Project is the first to successfully breed this species.

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Super-earth has an atmosphere, but is it steamy or gassy?

The extrasolar planet GJ 1214b has a radius of about 2.7 times that of the Earth and is about 6.5 times as massive putting it squarely into the class of exoplanets known as super-Earths.

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Giant impact may explain origin of Martian moons Phobos and Deimos

The Martian moons, Phobos and Deimos, may have been the result of a giant impact that sent rocks and debris into orbit around Mars, instead of asteroids that were captured by the planet’s gravity as previously thought.

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A St. Partick’s Day treat for the Zoo’s red-ruffed lemur

The National Zoological Park’s 23-year-old male red-ruffed lemur, Joven, enjoys a tasty St. Patrick’s Day frozen treat made of apples, pears, cucumbers, honeydew and diluted […]

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Artist’s recreation of 7- to 6-million-year-old early human unveiled in Hall of Human Origins

Meet Sahelanthropus tchadensis. This newly unveiled bust by artist John Gurche is now on view in the the Hall of Human Origins at the Smithsonian's National Museum of Natural History.

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Bone fragment is only Ice Age artwork from America to show a “proboscidean”

Researchers from the Smithsonian Institution and the University of Florida have announced the discovery of a bone fragment, approximately 13,000 years old, in Florida with an incised image of a mammoth or mastodon.

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Smithsonian Conservation Biology Institute and George Mason University expand partnership

Scientists and educators from the Smithsonian Conservation Biology Institute and George Mason University broke ground June 29 on a green-design conservation complex that embodies the concept of the living classroom.

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Stellar eclipse gives glimpse of exoplanet: New data reveals a ‘super-Earth’ next door, astronomically speaking

The far-out planet, named 55 Cancri e, is twice as big as Earth and nearly nine times more massive. It is most likely composed of rocky material, similar to Earth, supplemented with light elements such as water and hydrogen gas. Scientists estimate the planet’s surface is much hotter than ours: close to 2,700 degrees Celsius.

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Earthquake causes minor damage to Smithsonian natural history collections

The 5.8-magnitude earthquake that shook the eastern United States on the afternoon of Tuesday, Aug. 23, caused minor damage to some of the Smithsonian's natural history collections. All public Smithsonian museums are open and have been determined safe for visitors and staff.

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Newly discovered supermassive black holes are just 160 million light years from Earth

Astronomers using NASA's Chandra X-ray Observatory discovered the first pair of supermassive black holes in a spiral galaxy similar to the Milky Way. Approximately 160 million light years from Earth, the pair is the nearest known such phenomenon.

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Location matters: For invasive aquatic species, it’s better to start upstream

These green crabs have been doing a number on native shellfish. They eat a lot of clams. And they're a very cosmopolitan species—they've now spread all over, to places as far afield as the West Coast of the U.S. and South Africa.

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Infrared survey reveals fewer near-Earth asteroids than previously thought

New observations by NASA's Wide-field Infrared Survey Explorer, or WISE, show there are significantly fewer near-Earth asteroids in the mid-size range than previously thought.

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Two closely related bee species discovered far apart in Panama and northern Colombia

Our studies of the genetic relationships between these bees tells us that they originated in the Amazon about 22 million years ago and that they moved north into Central America before 3 million years ago.

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Two Earth-sized planets discovered orbiting a distant Sun-like star

Astronomers using NASA's Kepler mission have detected two Earth-sized planets orbiting a distant star. This discovery marks a milestone in the hunt for alien worlds, since it brings scientists one step closer to their ultimate goal of finding a twin Earth.

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Rising seas, development are altering prehistoric artifacts in the Chesapeake’s tidal zone

As a coastal archaeologist and expert in prehistoric and historic settlement sites in the Chesapeake Bay region, Darrin Lowery of the Smithsonian’s National Museum of Natural History and University of Deleware, is carefully watching the effects of coastal erosion and rising sea levels on coastal archaeological sites.

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Earthworms to blame for decline of Ovenbirds in northern Midwest forests, study reveals

A recent decline in Ovenbirds (Seiurus aurocapilla), a ground-nesting migratory songbird, in forests in the northern Midwest United States is being linked by scientists to a seemingly unlikely culprit: earthworms.

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Heart disease study to benefit lowland gorillas at the National Zoo

The same device used to detect early warning signs of heart disease in humans will now benefit two male sub-adult gorillas at the Smithsonian’s National Zoo.

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Steady diet of binary star partners makes black holes grow “supermassive”

A new study by astrophysicists at the University of Utah and the Smithsonian Astrophysical Observatory in Cambridge, Mass., has found a new explanation for the growth of supermassive black holes: they repeatedly capture and swallow single stars from pairs of stars that get too close.

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Smithsonian astronomers and colleagues to photograph black hole at our galaxy’s heart

Smithsonian astronomers have joined their colleagues from other observatories in a daring new venture: to photograph the giant black hole at the heart of our Milky Way galaxy.

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Alien Earths may have formed in Universe earlier than expected

New research by a team of astronomers found that planets smaller than Neptune are located around a wide variety of stars, including those with fewer heavy elements than the Sun.

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