The product of microbial uranium reduction includes multiple species with U(IV)-phosphate coordination

Until recently, the reduction of U(VI) to U(IV) during bioremediation was assumed to produce solely the sparingly soluble mineral uraninite, UO2(s). However, results from several laboratories reveal other species of U(IV) characterized by the absence of an EXAFS U-U pair correlation (referred to here as noncrystalline U(IV)). Because it lacks the crystalline structure of uraninite, this species is likely to be more labile and susceptible to reoxidation. In the case of single species cultures, analyses of U extended X-ray fine structure (EXAFS) spectra have previously suggested U(IV) coordination to carboxyl, phosphoryl or carbonate groups. In spite of this evidence, little is understood about the species that make up noncrystalline U(IV), their structural chemistry and the nature of the U(IV)-ligand interactions. Here, we use infrared spectroscopy (IR), uranium L-III-edge X-ray absorption spectroscopy (XAS), and phosphorus K-edge XAS analyses to constrain the binding environments of phosphate and uranium associated with Shewanella oneidensis MR-1 bacterial cells. Systems tested as a function of pH included: cells under metal-reducing conditions without uranium, cells under reducing conditions that produced primarily uraninite, and cells under reducing conditions that produced primarily biomass-associated noncrystalline U(IV). P X-ray absorption near-edge structure (XANES) results provided clear and direct evidence of U(IV) coordination to phosphate. Infrared (IR) spectroscopy revealed a pronounced perturbation of phosphate functional groups in the presence of uranium. Analysis of these data provides evidence that U(IV) is coordinated to a range of phosphate species, including monomers and polymerized networks. U EXAFS analyses and a chemical extraction measurements support these conclusions. The results of this study provide new insights into the binding mechanisms of biomass-associated U(IV) species which in turn sheds light on the mechanisms of biological U(VI) reduction. (C) 2014 Elsevier Ltd. All rights reserved

Influence of crystallographic orientation of biogenic calcite on in situ Mg XANES analyses

Micro X-ray absorption near-edge spectroscopy at the Mg K-edge is a useful technique for acquiring information about the environment of Mg2+ in biogenic calcite. These analyses can be applied to shell powders or intact shell structures. The advantage of the latter is that the XANES analyses can be applied to specific areas, at high (e. g. micrometre) spatial resolution, to determine the environment of Mg2+ in a biomineral context. Such in situ synchrotron analysis has to take into account the potential effect of crystallographic orientation given the anisotropy of calcite crystals and the polarized nature of X-rays. Brachiopod shells of species with different crystallographic orientations are used to assess this crystallographic effect on in situ synchrotron measurements at the Mg Kedge. Results show that, owing to the anisotropy of calcite, in situ X-ray absorption spectra (XAS) are influenced by the crystallographic orientation of calcite crystals with a subsequent potentially erroneous interpretation of Mg2+ data. Thus, this study demonstrates the importance of crystallography for XAS analyses and, therefore, the necessity to obtain crystallographic information at high spatial resolution prior to spectroscopic analysis.</p

Magnesium in the lattice of calcite-shelled brachiopods

Palaeoclimate information is often extracted from Rhynchonelliform brachiopod shell calcite, in particular the inner secondary layer, via the delta O-18 composition, which is a proxy for seawater temperature. Compared to delta O-18, the potential for Mg/Ca ratio, as a brachiopod seawater temperature proxy, has been neglected. The use of Mg/Ca ratio as a temperature proxy assumes that, with increasing temperature, more Mg Substitutes for Ca in the calcite lattice. Brachiopod shells, like all biominerals, are composites of organic and inorganic components. This raises the possibility that magnesium is hosted by the organic components. Alternatively, magnesium may be present as a separate mineral phase, rather than a true component of the calcite lattice, or incorporated into calcite in non-ideal or variable coordination. Here we use synchrotron X-ray absorption Near Edge Spectroscopy (XANES) at the Mg K-edge to determine the local environment of magnesium in two species of brachiopod with low Mg-calcite shells, Terebratulina retusa and Notosaria nigricans and one species with a high Mg-calcite shell, Novocrania anomala. XANES at the Mg K-edge of a Suite of Mg-bearing standards fingerprints the local environment of magnesium in the brachiopod shell powders as well as in situ analyses. In all cases, it is evident that magnesium is not hosted by organic components but is within the inorganic component of the shell. These data support the possibility of using brachiopod Mg/Ca ratios as a temperature proxy. (C) 2008 Published by Elsevier B.V.</p

Irradiation effects in helium implanted silicon carbide measured by X-ray absorption spectrometry

Silicon carbide (SiC) is investigated as a possible structural material for future nuclear power plants. It is utilized as fibre and/or as matrix in ceramic composite materials. The fibre reinforcement is necessary to provide the required ductility. In this work, the behaviour of pure SiC under irradiation by He implantation is studied. Samples are investigated by means of the extended X-ray absorption fine structure (EXAFS) spectroscopy, performed at the Si K-edge. The Fourier transforms of the EXAFS data indicate a decrease of the Si–Si bond related shells around the absorbing Si. The possible damage features are discussed and the three most probable ones for the irradiation conditions are selected for future modelling work

Strontium hydroxyapatite and strontium carbonate as templates for the precipitation of calcium-phosphates in the absence and presence of fluoride

The heterogeneous precipitation of calcium phosphates on calcium hydroxyapariLe (Ca-10(PO4)(4)OH)(2) or HAP) in the presence arid absence of fluoride is important in the formation of bone and teeth, protection against tooth decay, dental and skeletal fluorosis and defluoridaLion of drinking wafer. Strontium hyclroxyapariLe (Sr-10(PO4)(6)(OH)(2) or SrHAP) and strontium carbonate (SrCO3) were used as calcium free seed templates in precipitation experiments conducted with varying initial calcium-Lophosphate (Ca/P) or calcium-Lo-phosphaLe-Lo-fluoride (Ca/P/F) ratios. Suspensions of SrHAP or SrCO3 seed templates (which were calcium limited for both templates and phosphate limited in the case of SECO3) were reacted at pH 7.3 (25 degrees C) over 3 days. The resulting solids were examined with Scanning Transmission Electron Microscopy (STEM), X-ray Diffraction (XRD), Fourier Transform Infrared (MR), and X-ray Photoelectron Spectroscopy (XPS), X-ray Absorption Near Edge Structure (XANES), and Extended X-ray Absorption Fine Structure spectroscopy (EXAFS). Calcium apatite was the predominant phase identified by all techniques independent of the added Ca/P ratios and of the presence of fluoride. It was not possible to make an unambiguous distinction between HAP and fluorapatite (Ca-10(PO4)(6)F-2, FAP). The apatite was calcium-deficient and probably contained some strontium. (C) 2014 Elsevier B.V. All rights reserved

Sulphur poisoning of Ni catalysts in the SNG production from biomass: A TPO/XPS/XAS study

Ni-based catalysts are prone to deactivation (poisoning) of their active surface sites by sulphur and carbon species contained in the gas fed to the reactor. This study focuses on Ni/Al2O3-based catalyst samples which had allegedly been deactivated by sulphur poisoning. The samples had been collected from a 10 kW methanation reactor fed with producer gas from the industrial biomass gasifier in Gussing (Austria). The samples allowed intensive investigation using several analytical tools to identify the chemical nature (inorganic, organic) of the S-poisoning species. Temperature-programmed oxidation (TPO) allowed quantification of the sulphur content, but not the identification of the S species responsible. S 2p X-ray photoelectron spectroscopy (XPS) pointed at the presence of sulphide and sulphate, but the data were too noisy to reach more specific conclusions. Ni K-edge X-ray absorption spectroscopy (XAS) in the fine structure (EXAFS) region suggested the presence of elemental or thiophenic sulphur, but the contribution was masked heavily by other backscattering paths. Only S Kedge analysis in the near edge (XANES) region showed unambiguously that the catalyst could not have been deactivated by inorganic H2S only. This conclusion is supported by S K-edge XANES results with model catalysts which had either been poisoned by H2S or thiophene (C4H4S), representing a cyclic, aromatic S compound. Short-term H2S poisoning in the absence of air led to a white-line position characteristic for sulphide (2470 eV), whereas with thiophene the white-line position started at 3 eV higher energy. The XANES signatures changed with the catalyst samples after contacting air, but remained unique for each of the two S-poison types studied here. (C) 2009 Elsevier B.V. All rights reserved

TORO Indexer: A PyTorch-Based Indexing Algorithm for kHz Serial Crystallography

Serial Crystallography (SX) involves the processing of thousands of diffraction patterns coming from crystals in random orientations. To compile a complete dataset, these patterns must be indexed (i.e., determine orientation), integrated, and merged. We introduce the TORO (TOrch-powered Robust Optimization) Indexer, a robust and adaptable indexing algorithm developed using the PyTorch framework. TORO Indexer is capable of operating on GPUs, CPUs, and other hardware accelerators supported by PyTorch, ensuring compatibility with a wide variety of computational setups. In our tests, TORO outpaces existing solutions indexing thousands of frames per second when running on GPUs, positioning it as an attractive candidate to produce real-time indexing and user feedback. Our algorithm streamlines some of the ideas introduced by previous indexers like DIALS real grid search and XGandalf, and refines them using faster and principled robust optimization techniques which result in a concise codebase consisting of less than 500 lines. Based on our evaluations across four proteins, TORO consistently matches and, in certain instances, outperforms established algorithms such as XGandalf and MOSFLM, occasionally amplifying the quality of the consolidated data while achieving indexing rates that are orders of magnitude higher. The inherent modularity of TORO, and the versatility of Pytorch code bases, facilitate its deployment into a wide array of architectures, software platforms and bespoke applications, highlighting its prospective significance in SX

Unique Dynamic Changes of Fe Cationic Species under NH₃-SCR Conditions

The type and location of Fe cations in zeolite BEA and their structural changes under NH₃-SCR conditions are reported, as they are important catalysts for the selective catalytic reduction of NO_<i>x</i> with NH₃. Adsorption of basic probe molecules such as NH₃ and pyridine shows that additional Brønsted acid sites are formed at the expense of Lewis acidic octahedrally coordinated Fe cations during the aging cycle. The formation of new tetrahedrally coordinated Fe suggests that Fe cations are incorporated into the zeolite framework at tetrahedral positions. UV/vis, XAFS, and IR spectra indicate that these species, however, exist only when the samples are cooled to room temperature under NH₃-SCR conditions. In situ EXAFS shows Fe cations forming bridging Fe–O–Fe species at cation exchange sites above 573 K under reaction conditions. This indicates that the Fe cations undergo a unique reversible transformation during temperature cycles under NH₃-SCR conditions