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Biomedical subjects

John C H Spence

Publications and source records attributed to John C H Spence.

12 recordsLinked to original sources
PubMed2006

Ab initio phasing of X-ray powder diffraction patterns by charge flipping.

Determining crystal structures from powder X-ray diffraction data remains a challenging problem in materials science. By embedding a Le-Bail-like procedure within the recently discovered charge-flipping phasing algorithm, an extremely simple, fast and effective ab initio method has been developed to determine phases directly from indexed powder diffraction patterns. The algorithm solves the degeneracy problem by applying spherical averaging for overlapping Bragg reflections, while solving the phase problem by using the Oszlányi-Süto charge-flipping algorithm. The processes of peak decomposition and phasing are integrated within the same iteration, and a dynamic support is used. The Fienup hybrid input-output algorithm is also incorporated to minimize stagnation. The ability of the algorithm to find structure-factor phases rapidly is found to assist with the fundamental problem of degeneracy (overlapping reflections) which is intrinsic to powder diffraction data. Space-group and chemical-composition information are not needed as inputs, and can be determined from the result. The method is illustrated using several experimental powder patterns of indifferent quality.

Journal Article↗
PubMed2006

High-resolution ab initio three-dimensional x-ray diffraction microscopy.

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

Algorithms↗
PubMed2005

Diffractive electron imaging of nanoparticles on a substrate.

The observation of the detailed atomic arrangement within nanostructures has previously required the use of an electron microscope for imaging. The development of diffractive (lensless) imaging in X-ray science and electron microscopy using ab initio phase retrieval provides a promising tool for nanostructural characterization. We show that it is possible experimentally to reconstruct the atomic-resolution complex image (exit-face wavefunction) of a small particle lying on a thin carbon substrate from its electron microdiffraction pattern alone. We use a modified iterative charge-flipping algorithm and an estimate of the complex substrate image is subtracted at each iteration. The diffraction pattern is recorded using a parallel beam with a diameter of approximately 50 nm, illuminating a gold nanoparticle of approximately 13.6 nm diameter. Prior knowledge of the boundary of the object is not required. The method has the advantage that the reconstructed exit-face wavefunction is free of the aberrations of the objective lens normally used in the microscope, whereas resolution is limited only by thermal vibration and noise.

Algorithms↗
PubMed2005

Interpretation of Oxygen K pre-edge peak in complex oxides.

A controversial pre-edge peak has often been observed at the O K-edge in absorption spectra from complex oxides. We study this feature in both K(2)O-SiO(2) glass and MgAl(2)O(4) spinel crystals. Our time-resolved energy-loss spectroscopy (EELS) results indicate that the pre-edge peak is due to radiation damage, rather than from any intrinsic feature of the material. It is assigned to the pi* peak due to the O-O interaction.

Journal Article↗
PubMed2005

Experimental and theoretical improvements on understanding of the O K-edge of TeO2.

Using an electron monochromator attached to an electron microscope, high energy-resolution electron energy-loss spectra collected from TeO2 have revealed new features in the Oxygen K-edge. Using density-functional theory in the local density and the generalized gradient approximation, we find that core-hole strength of 1.3 gives an excellent fit to our high-resolution experimental data. This indicates that screening is not weak in this oxide, as normally assumed, and that neither the ground state nor a full core-hole model is adequate in quantitative reproduction of the O K-edge in the TeO2 system.

Journal Article↗
PubMed2005

Electron diffraction from laser-aligned beams of large hydrated molecules.

We consider X-ray or electron diffraction from a molecular beam of hydrated proteins. These are aligned by the polarized field of a powerful continuous infrared laser. The laser power, temperature and molecular size needed to obtain sufficient alignment accuracy for sharp diffraction patterns is estimated using a thermal average, and the resulting Dawson integral compared with the estimate based on equipartition used in our previous work. The conditions determined allow sub-nanometer resolution charge-density maps to be reconstructed from phased diffraction patterns, so that the secondary structure of the proteins can be observed.

Journal Article↗
PubMed2005

Phasing diffraction data from a stream of hydrated proteins.

We consider the problem of phase determination for continuous diffraction patterns obtained from a beam of identical, aligned large molecules (such as proteins), each coated with a layer of water or vitreous ice. Many laser-aligned molecules are assumed to lie within a wide continuous x-ray beam at any instant. An iterative phasing method is developed to extract the common target structure in three dimensions from diffraction patterns of these doped ice balls. Several measurements of the diffraction intensity in reciprocal space are needed. We found iteratively two boundaries (supports) (between protein and ice and the outer iceball support) by using the charge-flipping and multiple hybrid input-output algorithms, working with multiple sets of measured data. The approach is applied to simulated data from hydrated lysozyme proteins generated by the serial crystallography method of laser-aligned protein-beam diffraction proposed by Spence and Doak [Phys. Rev. Lett. 92, 198102 (2004)]. We consider also the effect of empty ice balls on the patterns. The algorithm can also be used to align images with different randomly chosen origins, so that the same embedded subunits overlap.

Algorithms↗
PubMed2004

SPEDEN: reconstructing single particles from their diffraction patterns.

SPEDEN is a computer program that reconstructs the electron density of single particles from their X-ray diffraction patterns, using a single-particle adaptation of the holographic method in crystallography [Szöke, Szöke & Somoza (1997). Acta Cryst. A53, 291-313]. The method, like its parent, is unique because it does not rely on 'back' transformation from the diffraction pattern into real space and on interpolation within measured data. It is designed to deal successfully with sparse, irregular, incomplete and noisy data. It is also designed to use prior information for ensuring sensible results and for reliable convergence. This article describes the theoretical basis for the reconstruction algorithm, its implementation, and quantitative results of tests on synthetic and experimentally obtained data. The program could be used for determining the structures of radiation-tolerant samples and, eventually, of large biological molecular structures without the need for crystallization.

Algorithms↗
PubMed2002

One-step synthesis and structure of an oligo(spiro-orthocarbonate).

The reaction of pentaerythritol and tetraethylorthocarbonate at 260 degrees C for 12 h yields a white crystalline material that was characterized by 13C CPMAS NMR, CHN analysis, FT-IR, electron and X-ray powder diffraction, and Rietveld analysis. The white crystalline material was found to have the formula C6H8O4 and a crystal structure with a monoclinic cell [a = 9.167 A, b = 5.681 A, c = 5.880 A, beta = 90.0 degrees , space group I2] of hexagonally arranged spiro-oligomeric chains.

Journal Article↗
PubMed2002

Resonance effect in ELNES from perovskite-type manganites BiMnO3 and LaMnO3.

Fine structures in electron energy-loss spectra, observed 30-40 eV beyond the threshold of oxygen K-edges in perovskite-type manganites BiMnO3 and LaMnO3, are discussed. LaMnO3 with orthorhombic symmetry (space group Pbnm) shows a clear peak in this region. However, BiMnO3 with a heavily distorted perovskite-type structure (monoclinic, space group C2) does not show an appreciable peak. It is demonstrated that peaks in this energy region arise from the resonance effect of ejected core electrons and that the shape is sensitive to the environment of neighbouring oxygen atoms in the perovskite-type structures.

Journal Article↗