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July 2006 issue
Cover illustration: Determination of a one-dimensional structure by the charge flipping algorithm. Bottom curves: grey is the initial electron density obtained with a random choice of structure-factor phases; white is the result of charge flipping, i.e. the sign of the density below a threshold is reversed. Top curves: electron density after convergence (blue) and its flipped counterpart (red). Only the three atomic regions correspond to the true structure, small oscillations do not. See Oszlányi & Süto [Acta Cryst. (2004), A60, 134-141; (2005), A61, 147-152].
research papers
An approach for obtaining precise simulations of HAADF STEM images for elements with large atomic numbers and thick specimens is proposed. The method utilizes two types of optical potential to describe the thermal diffuse scattering from a crystal that is represented by multiple layers. The validity of the method is demonstrated for elements with the diamond structure (Si, Ge and α-Sn) and for the perovskite BaTiO3.
Six-beam pinhole topographs of a floating-zone silicon crystal were experimentally obtained with the incidence of synchrotron X-rays whose polarization state was controlled using an X-ray phase-retarder system which can generate an arbitrary state of polarization. The topographs agreed quantitatively with computer-simulated images based on an n-beam Takagi–Taupin equation for which the derivation procedure is described in detail.
Details of the algorithm used in the reconstruction of a yeast cell image are given.
Extension of FFT methods to all angular variables in AMoRe permits accurate and faster calculations of the rotation function at high angular resolution.
The capsid of the icosahedral virion is encapsulated between two polyhedra scaled according to the golden mean, each being composed of an icosahedron and a dodecahedron. Structural units of the coat proteins are enclosed into forms whose projections along the icosahedral symmetry axes obey the crystallographic law of rational indices.
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An MX3 stoichiometry salt, LaCl3, is shown to fill carbon nanotubes, of varying diameter, via molecular dynamics computer simulations to produce low-dimension crystals. The filled crystal structures allow a full atomistic comparison to be made with experimental high-resolution transmission electron micrographs, and the emergence of new, non-bulk, crystal structures is predicted.
Combined analyser-based/propagation-based X-ray phase-contrast image formation and phase/amplitude reconstruction are re-examined and extended using rigorous wave-optical formalism. The derived algorithms are applied for quantitative analysis of simulated and experimental phase-contrast images.
A method is reported for the parameterization of bulk charge density exploiting density functional calculations which can be used to generate an improvement over a neutral atom model.
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