2016-08-10This paper reports on the fabrication and characterization of X-ray waveguide beamsplitters. The waveguide channels were manufactured by electron-beam lithography, reactive ion etching and wafer bonding techniques, with an empty (air) channel forming the guiding layer and silicon the cladding material. A focused synchrotron beam is efficiently coupled into the input channel. The beam is guided and split into two channels with a controlled (and tunable) distance at the exit of the waveguide chip. After free-space propagation and diffraction broadening, the two beams interfere and form a double-slit interference pattern in the far-field. From the recorded far-field, the near-field was reconstructed by a phase retrieval algorithm (error reduction), which was found to be extremely reliable for the two-channel setting. By numerical propagation methods, the reconstructed field was then propagated along the optical axis, to investigate the formation of the interference pattern from the two overlapping beams. Interestingly, phase vortices were observed and analysed.
2016-07-15Volume A of International Tables for Crystallography is the reference for space-group information. However, the content is not exhaustive because for many space groups a variety of settings may be chosen but not all of them are described in detail or even fully listed. The use of alternative settings may seem an unnecessary complication when the purpose is just to describe a crystal structure; however, these are of the utmost importance for a number of tasks, such as the investigation of structure relations between polymorphs or derivative structures, the study of pseudo-symmetry and its potential consequences, and the analysis of the common substructure of twins. The aim of the article is twofold: (i) to present a guide to expressing the symmetry operations, the Hermann–Mauguin symbols and the Wyckoff positions of a space group in an alternative setting, and (ii) to point to alternative settings of space groups of possible practical applications and not listed in Volume A of International Tables for Crystallography.
2016-07-15An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.
2016-07-28A Rodrigues vector is a triplet of real numbers used for parameterizing rotations or orientations in three-dimensional space. Because of its properties (e.g. simplicity of fundamental regions for misorientations) this parameterization is frequently applied in analysis of orientation maps of polycrystalline materials. By conventional definition, the Rodrigues parameters are specified in orthonormal coordinate systems, whereas the bases of crystal lattices are generally non-orthogonal. Therefore, the definition of Rodrigues parameters is extended so they can be directly linked to non-Cartesian bases of a crystal. The new parameters are co- or contravariant components of vectors specified with respect to the same basis as atomic positions in a unit cell. The generalized formalism allows for redundant crystallographic axes. The formulas for rotation composition and the relationship to the rotation matrix are similar to those used in the Cartesian case, but they have a wider range of applicability: calculations can be performed with an arbitrary metric tensor of the crystal lattice. The parameterization in oblique coordinate frames of lattices is convenient for crystallographic applications because the generalized parameters are directly related to indices of rotation-invariant lattice directions and rotation-invariant lattice planes.
2016-07-28Inferring structural information from the intensity of a small-angle scattering (SAS) experiment is an ill-posed inverse problem. Thus, the determination of a solution is in general non-trivial. In this work, the indirect Fourier transform (IFT), which determines the pair distance distribution function from the intensity and hence yields structural information, is discussed within two different statistical inference approaches, namely a frequentist one and a Bayesian one, in order to determine a solution objectively From the frequentist approach the cross-validation method is obtained as a good practical objective function for selecting an IFT solution. Moreover, modern machine learning methods are employed to suppress oscillatory behaviour of the solution, hence extracting only meaningful features of the solution. By comparing the results yielded by the different methods presented here, the reliability of the outcome can be improved and thus the approach should enable more reliable information to be deduced from SAS experiments.
2016-08-31Topological coordinate systems are used to address all cells of abstract cell complexes. In this paper, a topological coordinate system for cells in the diamond cubic grid is presented and some of its properties are detailed. Four dependent coordinates are used to address the voxels (triakis truncated tetrahedra), their faces (hexagons and triangles), their edges and the points at their corners. Boundary and co-boundary relations, as well as adjacency relations between the cells, can easily be captured by the coordinate values. Thus, this coordinate system is apt for implementation in various applications, such as visualizations, morphological and topological operations and shape analysis.
2016-08-10In this paper a method is suggested for naming any convex polyhedron by a numerical code arising from the adjacency matrix of its edge graph. A polyhedron is uniquely fixed by its name and can be built using it. Classes of convex n-acra (i.e. n-vertex polyhedra) are strictly ordered by their names.