June 2013 issue
An efficient and robust algorithm for the comparison of clusters is presented. Several illustrative example applications are given, including the screening of sets of clusters generated during global optimizations and Monte Carlo/molecular dymanics simulations, the identification of specific structure fragments inside large clusters, and the study of structure–substructure relations of periodic crystals.
Fast Fourier transformation calculations, used in direct space refinement, are presented using graphical processing units (GPUs) and compared with the speed achieved using normal central processing unit calculations.
High-quality single crystals of Zr–Fe co-doped lithium niobate have been grown by the Czochralski method using an automatic diameter-controlled crystal puller. The grown crystals have been assessed by various X-ray techniques to determine the lattice parameter, strain, crystalline perfection and composition variation. The optical properties were investigated and a thermal analysis was conducted to identify the potential for device fabrication.
A theoretical concept for the sin2ψ-based analysis of residual stress depth gradients providing high lateral resolution is presented. Simulations for very small gauge volumes are presented for the energy-dispersive case of diffraction.
The experimental implementation of the concept introduced in part I of this series is demonstrated. The range of applications and the relevance of considering the gauge volume geometry are discussed.
A new analytical model for the surface effect in strain analysis by neutron diffraction has been developed. Spurious strains are calculated from primary parameters of the instrument to a precision allowing for reliable data corrections.
An alternative configuration for a ψ-circle diffractometer is discussed, such that the sample normal is along the χ-circle axis. Reciprocal space calculations for specular and nonspecular surface diffraction are described in detail.
Crystallographic changes in polycrystalline samples of Yb1−xTbxMnO3 were analyzed using the Rietveld method. Site occupancy models were tested in the double-phase cases.
An algorithm for determining the element-selective charge density is developed using multi-wavelength anomalous synchrotron X-ray powder diffraction data. The method is employed in order to resolve the disordered structure of yttrium in (Y@C82)(C6H5CH3).
The potential for first-princples molecular dynamics simulations to predict thermal-motion parameters has been illustrated by good agreement between theoretical and neutron-diffraction-determined anisotropic displacement parameters of benzophenone.
A method is described for the estimation of background level and separation of background pixels from signal pixels in a Poisson-distributed data set by statistical analysis.
The performance of a novel synchrotron-class X-ray tabletop microsource has been tested for the collection of small-angle X-ray scattering (SAXS) data, by inspecting the nanoscale structural order of air-dried rat-tail tendon. Reciprocal space information up to the 22nd diffraction order (q = 0.21 Å−1, d = 29 Å) was retrieved for SAXS data collected over 8–10 h integration times, with a significant gain in the diffraction peak visibility found for patterns collected for only 0.5 h.
The Monte Carlo X-ray simulation package McXtrace is described, and examples of its use for generic virtual X-ray experiments are given. These include tomography using a laboratory source, synchrotron beam evolution through compound refractive lenses, Laue protein crystallography, powder diffraction, an EXAFS and surface diffraction beamline optics study, and time-resolved disordered diffraction.
A new reactor-based neutron single-crystal diffractometer was developed based on a large-area curved position-sensitive detector with a delay-line readout method. The instrumentation details are presented, including diffractometer construction, measurement method, raw data treatment and calibration, and various applications for structural studies are given to exploit the strengths of the diffractometer.
A self-assembly process is demonstrated that results in the formation of an anisotropic lattice of regularly ordered Ge quantum dots in an amorphous alumina matrix. The prepared material shows a strong anisotropy of the electrical transport properties.
Variant selection in friction-stir-welded high-strength low-alloy steels has been studied using electron backscatter diffraction and prior austenite reconstruction techniques. A hypothesis for variant selection has been proposed on the basis of grain-boundary interfacial energy and misorientation.
A denoising method is reported for the treatment of neutron scattering data obtained with position-sensitive detectors, which enhances the information obtained from weak and very weak Bragg peaks.
Alloys made from equimolar mixtures of more than five elements exhibit an improved thermal diffusivity at elevated temperatures, and the improvement reaches 20% at 423 K and 50% at 573 K. This phenomenon is identified from the lengthened mean free path upon thermal expansion, and lengthening scales with lattice dilation over a wide range of temperatures.
Visual analysis with a motorized microscope coupled to image processing software is used to measure the positions of crystals in their crystallization plates. Crystals, still in their crystallization drop, can then be rapidly centered in the beam for in situ X-ray analysis.
A system for growing Ga-doped yttrium iron garnet (YIG) single crystals by the edge-defined film-fed growth method was designed and constructed, and the mechanism of crystal growth was also preliminarily studied. The Ga3+ dopant concentration, the Curie temperature and the transmission spectra of as-grown crystals were investigated to evaluate their potential application in magneto-optical devices.
Ru particle sizes in supported ruthenium catalysts have been studied by small-angle X-ray scattering (SAXS). Using new masking liquids with a relatively low X-ray radiation absorption, it was possible to achieve practically quantitative agreement between SAXS and transmission electron microscopy data.
The pressure-induced phase transformations up to 40 GPa of a well characterized form of amorphous silicon were examined using in situ synchrotron X-ray radiation. The phase-transformation pathway was found to be critically dependent on the impurity content, which explains the diversity in phase-transformation pathways reported in previous high-pressure studies on amorphous silicon.
General guidelines are given for the application of resonant X-ray diffraction in order to determine the element distribution in compounds lacking X-ray scattering contrast, including cases where more than two `similar' elements are involved.
The big bang–big crunch optimization method has been revised, combined with the simulated annealing technique and implemented in the latest version of the EXPO program for solving crystal structure from powder diffraction data.
Real-space magnetic small-angle neutron scattering data from nanocrystalline cobalt and nickel have been analysed in terms of a recently developed micromagnetic theory for the autocorrelation function of the spin misalignment.
The proof of concept for using a 4% broad-bandpass beam, which is planned for the new SwissFEL facility, for the structural characterization of nonbiological materials is shown.
Forty-seven main reagents included in a large set of macromolecular crystallization conditions are shown to have a similar impact overall on the yield of crystal structures. It is also shown that the conditions formulated with such reagents are under-sampled.
The electron diffraction technique was employed to unambiguously clarify the crystal symmetries of ferroelectric Bi4Ti3O12 and Bi3.15Nd0.85Ti3O12 single crystals at room temperature. On the basis of the monoclinic space group B1a1, the lattice parameters of both the ferroelectrics were calculated by the Rietveld refinement of powder X-ray diffraction data.
Software to compute the angle between corresponding directions in a twinned crystal from a known twin element or vice versa is presented.
A system for the automatic reduction of single- and multi-position macromolecular crystallography data is presented.
An open-source Fortran90 program is presented for creating the Wulff construction (resulting from a user-defined list of facets) in a general and efficient way using a simple algorithm, which is explained. The output files contain all the detailed structural information required to define the solid completely. The code is made freely available to the crystallographic community for immediate use.
The preparation of a desiccant array by dispensing and then drying droplets of aqueous salt solutions on a tape is presented as a means of enhancing the efficiency and the applicability of the gradual desiccation method in protein crystallization screening.
An unexpected phase transition observed during low-temperature X-ray diffraction measurements of the negative thermal expansion material ScF3 is a result of stresses arising from the large thermal expansion mismatch with the GE-7031 varnish used as a thermally conducting sample matrix.
A bespoke capillary sample holder is described that attaches to the cold head of a commercially manufactured (PheniX) closed-cycle helium cryostat originally intended for flat-plate geometry. The new holder allows high-resolution synchrotron powder diffraction data to be collected from samples in Debye–Scherrer geometry over the temperature range 11–295 K.
A straightforward low-cost device with a specially engineered multi-channel tip allows the dispensing of very small volumes of viscous lipidic cubic phases (LCPs) more efficiently. The device lowers the threshold for LCP crystallization of membrane proteins/peptides
This article describes protein crystallization under the influence of an electric field using a sitting-drop and vapor-diffusion experimental setup.