A versatile, compact heater designed at National Synchrotron Light Source-II for in situ X-ray nano-imaging in a full-field transmission X-ray microscope is presented. Heater design for nano-imaging is challenging, combining tight spatial constraints with stringent design requirements for the temperature range and stability. Finite-element modeling and analytical calculations were used to determine the heater design parameters. Performance tests demonstrated reliable and stable performance, including maintaining the exterior casing close to room temperature while the heater is operating at above 1100°C, a homogenous heating zone and small temperature fluctuations. Two scientific experiments are presented to demonstrate the heater capabilities: (i) in situ 3D nano-tomography including a study of metal dealloying in a liquid molten salt extreme environment, and (ii) a study of pore formation in icosahedral quasicrystals. The progression of structural changes in both studies were clearly resolved in 3D, showing that the new heater enables powerful capabilities to directly visualize and quantify 3D morphological evolution of materials under real conditions by X-ray nano-imaging at elevated temperature during synthesis, fabrication and operation processes. This heater design concept can be applied to other applications where a precise, compact heater design is required.

A Thomson scattering X-ray source can provide quasi-monochromatic, continuously energy-tunable, polarization-controllable and high-brightness X-rays, which makes it an excellent tool for X-ray fluorescence computed tomography (XFCT). In this paper, we examined the suppression of Compton scattering background in XFCT using the linearly polarized X-rays and the implementation feasibility of linearly polarized XFCT based on this type of light source, concerning the influence of phantom attenuation and the sampling strategy, its advantage over K-edge subtraction computed tomography (CT), the imaging time, and the potential pulse pile-up effect by Monte Carlo simulations. A fan beam and pinhole collimator geometry were adopted in the simulation and the phantom was a polymethyl methacrylate cylinder inside which were gadolinium (Gd)-loaded water solutions with Gd concentrations ranging from 0.2 to 4.0 wt%. Compared with the case of vertical polarization, Compton scattering was suppressed by about 1.6 times using horizontal polarization. An accurate image of the Gd-containing phantom was successfully reconstructed with both spatial and quantitative identification, and good linearity between the reconstructed value and the Gd concentration was verified. When the attenuation effect cannot be neglected, one full cycle (360°) sampling and the attenuation correction became necessary. Compared with the results of K-edge subtraction CT, the contrast-to-noise ratio values of XFCT were improved by 2.03 and 1.04 times at low Gd concentrations of 0.2 and 0.5 wt%, respectively. When the flux of a Thomson scattering light source reaches 1013 photons s−1, it is possible to finish the data acquisition of XFCT at the minute or second level without introducing pulse pile-up effects.

A dedicated X-ray imaging detector for 200 keV high-energy X-ray microtomography was developed to realize high-efficiency high-resolution imaging while keeping the field of view wide.

A complete method of comprehensive and quantitative evaluation of through-silicon via reliability using a highly sensitive phase-contrast X-ray microtomography was established. Quantitative characterizations include 3D local morphology and overall consistency of statistics.

A method for reconstructing the three-dimensional grain structure from data collected with a recently introduced laboratory-based X-ray diffraction contrast tomography system is presented. Diffraction contrast patterns are recorded in Laue-focusing geometry. The diffraction geometry exposes shape information within recorded diffraction spots. In order to yield the three-dimensional crystallographic microstructure, diffraction spots are extracted and fed into a reconstruction scheme. The scheme successively traverses and refines solution space until a reasonable reconstruction is reached. This unique reconstruction approach produces results efficiently and fast for well suited samples.

The neutron powder diffractometer POWGEN at the Spallation Neutron Source has recently (2017–2018) undergone an upgrade which resulted in an increased detector complement along with a full overhaul of the structural design of the instrument. The current instrument has a solid angular coverage of 1.2 steradians and maintains the original third-generation concept, providing a single-histogram data set over a wide d-spacing range and high resolution to access large unit cells, detailed structural refinements and in situ/operando measurements.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

Molybdenum oxides and sulfides on various low-cost high-surface-area supports are excellent catalysts for several industrially relevant reactions. The surface layer structure of these materials is, however, difficult to characterize due to small and disordered MoOx domains. Here, it is shown how X-ray total scattering can be applied to gain insights into the structure through differential pair distribution function (d-PDF) analysis, where the scattering signal from the support material is subtracted to obtain structural information on the supported structure. MoOx catalysts supported on alumina nanoparticles and on zeolites are investigated, and it is shown that the structure of the hydrated molybdenum oxide layer is closely related to that of disordered and polydisperse polyoxometalates. By analysing the PDFs with a large number of automatically generated cluster structures, which are constructed in an iterative manner from known polyoxometalate clusters, information is derived on the structural motifs in supported MoOx.

An online knowledge base on the alternate conformations adopted by main-chain and side-chain atoms in protein structures solved by X-ray crystallography is described.

New developments in the program CrystalCMP are presented, and the program is tested on a large number of crystal structures extracted from the Cambridge Structural Database.

The principles of using the Laue-analyzer as an X-ray optical element for separating two characteristic lines of an X-ray tube are presented.

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (dmin ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) applied through DiSCaMB software library in the structure refinement against X-ray diffraction data largely improves the X—H bond lengths and make them comparable to the averaged neutron bond lengths.

A recent survey of the bottom-dwelling animals of the Chesapeake has revealed that communities of even these relatively hardy organisms are under stress. Many regions of the bay are becoming inhospitable to bottom-dwelling animals because of a lack of oxygen—a condition known as “hypoxia.”

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Snowflake Study through Photomicrography, 1890 Wilson A. Bentley became fascinated with the crystalline structure of individual snowflakes on his parent’s Vermont farm. By adapting a […]

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Viewed from inside the SOMATOM Emotion 6CT scanner used at the Smithsonian’s National Museum of Natural History, the skeleton and internal organs of this well-preserved […]

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Food is scarce in the deep, dark regions of the ocean where barbeled dragonfishes and their relatives dwell. Known as the Stomiidae, some of these […]

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David Guerit, Pauline Marie, Anne Morel, Justine Maurin, Christel Verollet, Brigitte Raynaud-Messina, Serge Urbach, and Anne Blangy

Among hematopoietic cells, osteoclasts (Oc) and immature dendritic cells (Dc) are closely related myeloid cells with distinct functions; Oc participate skeleton maintenance while Dc sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during Oc and Dc differentiation. We provide global proteomic and transcriptomic analyses of primary mouse Oc and Dc, based on original SILAC and RNAseq data. We established specific signatures for Oc and Dc including genes and proteins of unknown functions. In particular, we showed that Oc and Dc have the same α and β tubulin isotypes repertoire but that Oc express much more β tubulin isotype Tubb6. In both mouse and human Oc, we demonstrate that elevated expression of Tubb6 in Oc is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hindered Oc resorption activity. Overall, we highlight here potential new regulators of Oc and Dc biology and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.

Björn Eismann, Teresa G. Krieger, Jürgen Beneke, Ruben Bulkescher, Lukas Adam, Holger Erfle, Carl Herrmann, Roland Eils, and Christian Conrad

3D cell cultures enable the in vitro study of dynamic biological processes such as the cell cycle, but their use in high-throughput screens remains impractical with conventional fluorescent microscopy. Here, we present a screening workflow for the automated evaluation of mitotic phenotypes in 3D cell cultures by light-sheet microscopy. After sample preparation by a liquid handling robot, cell spheroids are imaged for 24 hours in toto with a dual-view inverted selective plane illumination microscope (diSPIM) with a much improved signal-to-noise ratio, higher imaging speed, isotropic resolution and reduced light exposure compared to a spinning disc confocal microscope. A dedicated high-content image processing pipeline implements convolutional neural network based phenotype classification. We illustrate the potential of our approach by siRNA knock-down and epigenetic modification of 28 mitotic target genes for assessing their phenotypic role in mitosis. By rendering light-sheet microscopy operational for high-throughput screening applications, this workflow enables target gene characterization or drug candidate evaluation in tissue-like 3D cell culture models.

Aparna Sherlekar, Gayatri Mundhe, Prachi Richa, Bipasha Dey, Swati Sharma, and Richa Rikhy

Branched actin networks driven by Arp2/3 collaborate with actomyosin filaments in processes such as cell migration. The syncytial Drosophila blastoderm embryo also shows expansion of apical caps by Arp2/3 driven actin polymerization in interphase and buckling at contact edges by MyosinII to form furrows in metaphase. Here we study the role of Syndapin (Synd), an F-BAR domain containing protein in apical cap remodelling prior to furrow extension. synd depletion showed larger apical caps. STED super-resolution and TIRF microscopy showed long apical actin protrusions in caps in interphase and short protrusions in metaphase in control embryos. synd depletion led to sustained long protrusions even in metaphase. Loss of Arp2/3 function in synd mutants partly reverted defects in apical cap expansion and protrusion remodelling. MyosinII levels were decreased in synd mutants and MyosinII mutant embryos have been previously reported to have expanded caps. We propose that Syndapin function limits branching activity during cap expansion and affects MyosinII distribution in order to shift actin remodeling from apical cap expansion to favor lateral furrow extension.

Relativistic electron diffraction depends on linear and quadratic terms in the electric potential, the latter being neglected in the frequently used relativistically corrected Schrödinger equation. The quadratic electric potential term modifies atomic scattering amplitudes in particular for large-angle scattering and backscattering. The respective correction increases with increasing scattering angle, increasing atomic number and increasing kinetic energy. Conventional tabulations for electron scattering and its large-angle extrapolations can be amended in closed form by a universal correction based on the screened Coulomb potential squared.

A novel approach for finding and evaluating structural models of small metallic nanoparticles is presented. Rather than fitting a single model with many degrees of freedom, libraries of clusters from multiple structural motifs are built algorithmically and individually refined against experimental pair distribution functions. Each cluster fit is highly constrained. The approach, called cluster-mining, returns all candidate structure models that are consistent with the data as measured by a goodness of fit. It is highly automated, easy to use, and yields models that are more physically realistic and result in better agreement to the data than models based on cubic close-packed crystallographic cores, often reported in the literature for metallic nanoparticles.

In this study, the atomic structure of the ternary icosahedral ZnMgTm quasicrystal (QC) is investigated by means of single-crystal X-ray diffraction. The structure is found to be a member of the Bergman QC family, frequently found in Zn–Mg–rare-earth systems. The ab initio structure solution was obtained by the use of the Superflip software. The infinite structure model was founded on the atomic decoration of two golden rhombohedra, with an edge length of 21.7 Å, constituting the Ammann–Kramer–Neri tiling. The refined structure converged well with the experimental diffraction diagram, with the crystallographic R factor equal to 9.8%. The Bergman clusters were found to be bonded by four possible linkages. Only two linkages, b and c, are detected in approximant crystals and are employed to model the icosahedral QCs in the cluster approach known for the CdYb Tsai-type QC. Additional short b and a linkages are found in this study. Short interatomic distances are not generated by those linkages due to the systematic absence of atoms and the formation of split atomic positions. The presence of four linkages allows the structure to be pictured as a complete covering by rhombic triacontahedral clusters and consequently there is no need to define the interstitial part of the structure (i.e. that outside the cluster). The 6D embedding of the solved structure is discussed for the final verification of the model.

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.

Dr. Thomas R. Watters of the Center for Earth and Planetary Studies at the Smithsonian's National Air and Space Museum talks about his research in astronomy, particularly our moon. More about space science at http://www.nasm.si.edu

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Here come the stinkbugs...With the cooler temperatures of fall the brown marmorated stinkbug begins a determined quest to find a warm place to spend the winter. Crowding around window screens and searching for other ways to get inside, homeowners in the United States will share their indoor living space this winter with millions of brown marmorated stinkbugs. In this video Gary Hevel, an entomolgist at the Smithsonian's National Museum of Natural History, shares some information about these interesting creatures, as well as some advice about how to deal with those that inevitably gain entry to your home.

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"I'm getting paid to do what I like doing," says entomologist David Roubik. He loved nature and being outdoors when he was a kid, and now he does fieldwork in the tropical forests of Panama. He loves to travel, and his research takes him around the world. Can his work, then, be called a job?

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Tom Crouch, Senior curator in the National Air and Space Museum's Aeronautics Division, discusses Thaddeus Lowe and the birth of American aerial reconnaissance during the Civil War. This presentation was recorded on May 11, 2011 on the National Mall.

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