A software package for the analysis of X‐ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl ...programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high‐quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.
The development of useful structure-function relationships for materials that exhibit correlated nanoscale disorder requires adequately large atomistic models which today are obtained mainly via ...theoretical simulations. Here, we exploit our recent advances in structure-refinement methodology to demonstrate how such models can be derived directly from simultaneous fitting of 3D diffuse- and total-scattering data, and we use this approach to elucidate the complex nanoscale atomic correlations in the classical relaxor ferroelectric PbMg
Nb
O
(PMN). Our results uncover details of ordering of Mg and Nb and reveal a hierarchical structure of polar nanoregions associated with the Pb and Nb displacements. The magnitudes of these displacements and their alignment vary smoothly across the nanoregion boundaries. No spatial correlations were found between the chemical ordering and the polar nanoregions. This work highlights a broadly applicable nanoscale structure-refinement method and provides insights into the structure of PMN that require rethinking its existing contentious models.
Muffin‐tin potentials are the standard tool for calculating the potential surface of a cluster of atoms for use in the analysis of extended X‐ray absorption fine‐structure (EXAFS) data. The set of ...Cartesian coordinates used to define the positions of atoms in the cluster and to calculate the muffin‐tin potentials is commonly also used to enumerate the scattering paths used in the EXAFS data analysis. In this paper, it is shown that these muffin‐tin potentials are sufficiently robust to be used to examine quantitatively contributions to the EXAFS data from scattering geometries not represented in the original cluster.
In recent years, the ability to interpret and analyze X-ray absorption spectroscopy data has progressed dramatically due, in large part, to the rapid development of ab initio theories of the ...absorption spectrum. One such theory, the
feff program, has proven especially successful and is in wide use throughout the world. This paper presents an outline of the real-space, multiple-scattering theory used by
feff and explains how
feff is applied to both the near-edge and extended portions of the absorption spectrum. This paper is intended to be both practical and accessible. It is by a synchrotron experimentalist and intended for synchrotron experimentalists.
Membrane proteins, particularly G-protein coupled receptors (GPCRs), are notoriously difficult to express. Using commercial E. coli cell-free systems with the detergent Brij-35, we could rapidly ...produce milligram quantities of 13 unique GPCRs. Immunoaffinity purification yielded receptors at >90% purity. Secondary structure analysis using circular dichroism indicated that the purified receptors were properly folded. Microscale thermophoresis, a novel label-free and surface-free detection technique that uses thermal gradients, showed that these receptors bound their ligands. The secondary structure and ligand-binding results from cell-free produced proteins were comparable to those expressed and purified from HEK293 cells. Our study demonstrates that cell-free protein production using commercially available kits and optimal detergents is a robust technology that can be used to produce sufficient GPCRs for biochemical, structural, and functional analyses. This robust and simple method may further stimulate others to study the structure and function of membrane proteins.
A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their ...stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.
We propose a standard data format for the interchange of XAFS data. The XAFS Data Interchange (XDI) standard is meant to encapsulate a single spectrum of XAFS along with relevant metadata. XDI is a ...text-based format with a simple syntax which clearly delineates metadata from the data table in a way that is easily interpreted both by a computer and by a human. The metadata header is inspired by the format of an electronic mail header, representing metadata names and values as an associative array. The data table is represented as columns of numbers. This format can be imported as is into most existing XAFS data analysis, spreadsheet, or data visualization programs. Along with a specification and a dictionary of metadata types, we provide an application-programming interface written in C and bindings for programming dynamic languages.
A theory program intended for use with extended X‐ray‐absorption fine structure (EXAFS) spectroscopy and based on the popular FEFF8 is presented. It provides an application programming interface ...designed to make it easy to integrate high‐quality theory into EXAFS analysis software. This new code is then used to examine the impact of self‐consistent scattering potentials on EXAFS data analysis by methodical testing of theoretical fitting standards against a curated suite of measured EXAFS data. For each data set, the results of a fit are compared using a well characterized structural model and theoretical fitting standards computed both with and without self‐consistent potentials. It is demonstrated that the use of self‐consistent potentials has scant impact on the results of the EXAFS analysis.
The use of self‐consistency in the computation of scattering potentials has scant impact on EXAFS analysis.
A suite of uranium brannerites for the disposal of MOX residues, formulated (U
0.9
Ce
0.1
)
1−
x
M
x
Ti
2
O
6
(M = Ca
2+
and/or Gd
3+
), were prepared using a mixed oxide route under oxidising, inert ...and reducing atmospheres (air, argon and H
2
/N
2
). Gd
3+
was added to act as a neutron absorber in the final Pu bearing wasteform and Ce added to function as a structural analogue for Pu. X-ray powder diffraction of the synthesised specimens found that phase distribution was strongly affected by the processing atmosphere and Gd content. In all cases prototypical brannerite was formed, accompanied by different secondary phases dependent on processing atmosphere. Microstructural analysis (SEM) of the sintered samples confirmed the results of the X-ray powder diffraction. Bulk XANES found that Ti remained in the Ti
4+
oxidation state whereas Ce was uniformly reduced to the Ce
3+
oxidation state regardless of processing conditions or stoichiometry. Micro-focus XANES was used to determine U oxidation in the brannerite phase and showed that U oxidised to higher U oxidation states to charge compensate. It was concluded that the charge balance mechanism was a combination of U oxidation and A-site vacancies.
This work presents the synthesis and characterisation of novel brannerite ceramics designed for the disposal of mixed oxide fuel residues.
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