Anomalous diffraction at ultra-high energy for protein crystallography

2006 ◽  
Vol 39 (6) ◽  
pp. 831-841 ◽  
Author(s):  
Jean Jakoncic ◽  
Marco Di Michiel ◽  
Zhong Zhong ◽  
Veijo Honkimaki ◽  
Yves Jouanneau ◽  
...  
Keyword(s):  
Electron Density ◽  
Three Dimensional ◽  
High Energy ◽  
Anomalous Scattering ◽  
X Rays ◽  
Ultra High Energy ◽  
High Quality ◽  
Electronic Density ◽  
Standard Equipment ◽  
Anomalous Diffraction

Single-wavelength anomalous diffraction (SAD), multiwavelength anomalous diffraction (MAD) and single isomorphous replacement with anomalous scattering (SIRAS) phasing at ultra-high X-ray energy, 55 keV, are used successfully to determine a high-quality and high-resolution experimental electronic density map of hen egg-white lysozyme, a model protein. Several combinations, between single- and three-wavelength, with native data were exploited to demonstrate that standard phasing procedures with standard equipment and software can successfully be applied to three-dimensional crystal structure determination of a macromolecule, even at these very short wavelengths. For the first time, a high-quality three-dimensional molecular structure is reported from SAD phasing with ultra-high-energy X-rays. The quality of the crystallographic data and the experimental electron density maps meet current standards. The 2.7% anomalous signal from three Ho atoms, at the HoKedge, was sufficient to obtain a remarkable electron density and build the first lanthanide structure for HEWL in its entirety.

Multi-wavelength anomalous diffraction method for I and Xe atoms using ultra-high-energy X-rays from SPring-8

2004 ◽  
Vol 37 (6) ◽  
pp. 925-933 ◽  
Author(s):  
Kazuki Takeda ◽  
Hideyuki Miyatake ◽  
Sam-Yong Park ◽  
Masahide Kawamoto ◽  
Nobuo Kamiya ◽  
...  
Keyword(s):  
Diffraction Method ◽  
High Energy ◽  
X Rays ◽  
Ultra High Energy ◽  
Anomalous Diffraction ◽  
Egg White Lysozyme ◽  
Density Maps ◽  
Mad Phasing ◽  
Multi Wavelength ◽  
Lysozyme Crystals

The first successful multi-wavelength anomalous diffraction (MAD) experiments using ultra-high-energy X-rays (∼35 keV) were performed for iodine and xenon derivatives of hen egg-white lysozyme crystals. The beamline BL41XU of SPring-8 enabled the collection of high-quality MAD data, which led to the calculation of anomalous or dispersive difference Patterson maps that determined the positions of iodine and xenon atoms. The electron density maps obtained by the density modification method for both cases proved to be of sufficient quality for building molecular models. I-MAD and Xe-MAD phasing are now available at SPring-8, and the utilization of ultra-high-energy X-rays will make a significant contribution to the solution of the phase problem in protein crystallography.

Monte Carlo studies on electromagnetic cascades in extensive air showers

1968 ◽  
Vol 46 (10) ◽  
pp. S189-S196 ◽  
Author(s):  
K. O. Thielheim ◽  
E. K. Schlegel ◽  
R. Beiersdorf
Keyword(s):  
Monte Carlo ◽  
Electron Density ◽  
Three Dimensional ◽  
High Energy ◽  
Extensive Air Showers ◽  
Air Showers ◽  
Energy Distributions ◽  
The Core ◽  
Fragmentation Mechanisms ◽  
Monte Carlo Studies

Three-dimensional Monte Carlo calculations have been performed on the trajectories of high-energy hadrons in extensive air showers. The central electron density and gradient of distribution are obtained for individual electromagnetic cascades together with coordinates at the level of observation. Various assumptions concerning primary mass number and energy, distributions of strong interaction parameters, and fragmentation mechanisms are discussed with respect to the production of steep maxima of electron density by single electromagnetic cascades in the core region of extensive air showers.

scholarly journals Counter-based pseudorandom number generators for CORSIKA 8

2021 ◽  
Vol 251 ◽  
pp. 03039
Author(s):  
A. Augusto Alves ◽  
Anton Poctarev ◽  
Ralf Ulrich
Keyword(s):  
Secondary Particle ◽  
High Energy ◽  
Massively Parallel ◽  
Random Numbers ◽  
Ultra High Energy ◽  
Simulation Framework ◽  
Performance Measurements ◽  
Astroparticle Physics ◽  
Lazy Evaluation ◽  
High Quality

This document is devoted to the description of advances in the generation of high-quality random numbers for CORSIKA 8, which is being developed in modern C++17 and is designed to run on modern multi-thread processors and accelerators. CORSIKA 8 is a Monte Carlo simulation framework to model ultra-high energy secondary particle cascades in astroparticle physics. The aspects associated with the generation of high-quality random numbers on massively parallel platforms, like multi-core CPUs and GPUs, are reviewed and the deployment of counter-based engines using an innovative and multi-thread friendly API are described. The API is based on iterators providing a very well known access mechanism in C++, and also supports lazy evaluation. Moreover, an upgraded version of the Squares algorithm with highly efficient internal 128 as well as 256 bit counters is presented in this context. Performance measurements are provided, as well as comparisons with conventional designs are given. Finally, the integration into CORSIKA 8 is commented.

Hybrid Measurement of CT and Strain Distribution of Internal Crack Using Synchrotron High-Energy Monochromatic X-Rays

2010 ◽  
Vol 652 ◽  
pp. 202-209
Author(s):  
Keisuke Tanaka ◽  
Takahisa Shobu ◽  
Hiroshi Kimachi
Keyword(s):  
Strain Distribution ◽  
Crack Opening ◽  
Three Dimensional ◽  
Crack Tip ◽  
High Energy ◽  
Internal Crack ◽  
X Rays ◽  
Crack Face ◽  
Dimensional Shape ◽  
Three Dimensional Shape

Using high-energy monochromatic X-rays of energy 66.4keV from the synchrotron radiation source, SPring-8, we have developed a system to perform a hybrid measurement of imaging of cracks and strain distribution around cracks. This system was applied to a fatigue crack made in a round bar made of carbon steel with a diameter of 4 mm. Computed tomography of the specimen gave the three-dimensional shape of a thumb-nail crack. High tensile strain ahead of the crack was measured at the applied maximum stress, while the strain on the crack face was low because of stress relief due to crack opening. The full width at half maximum (FWHM) increased near the crack tip under loading, and then decreased after unloading. The recoverable part of FWHM by unloading was caused by the steep distribution of the applied stress in the vicinity of the crack tip. The FWHM increased by plastic deformation does not change when unloaded. The measured distributions of the lattice strain and FWHM agreed well with those of the elastic and plastic strains calculated by the finite element method, respectively.

Accurate charge densities from powder X-ray diffraction – a new version of the Aarhus vacuum imaging-plate diffractometer

2017 ◽  
Vol 73 (4) ◽  
pp. 521-530 ◽  
Author(s):  
Kasper Tolborg ◽  
Mads R. V. Jørgensen ◽  
Sebastian Christensen ◽  
Hidetaka Kasai ◽  
Jacob Becker ◽  
...  
Keyword(s):  
Electron Density ◽  
High Energy ◽  
Imaging Plate ◽  
High Symmetry ◽  
X Rays ◽  
X Ray Diffraction ◽  
Core Electron ◽  
X Ray ◽  
Peak Broadening ◽  
Structure Factors

In recent years powder X-ray diffraction has proven to be a valuable alternative to single-crystal X-ray diffraction for determining electron-density distributions in high-symmetry inorganic materials, including subtle deformation in the core electron density. This was made possible by performing diffraction measurements in vacuum using high-energy X-rays at a synchrotron-radiation facility. Here we present a new version of our custom-built in-vacuum powder diffractometer with the sample-to-detector distance increased by a factor of four. In practice this is found to give a reduction in instrumental peak broadening by approximately a factor of three and a large improvement in signal-to-background ratio compared to the previous instrument. Structure factors of silicon at room temperature are extracted using a combined multipole–Rietveld procedure and compared withab initiocalculations and the results from the previous diffractometer. Despite some remaining issues regarding peak asymmetry, the new diffractometer yields structure factors of comparable accuracy to the previous diffractometer at low angles and improved accuracy at high angles. The high quality of the structure factors is further assessed by modelling of core electron deformation with results in good agreement with previous investigations.

scholarly journals The Pierre Auger Observatory: Studying the Highest Energy Frontier

2019 ◽  
Vol 64 (7) ◽  
pp. 646
Author(s):  
I. Valiño
Keyword(s):  
Cosmic Rays ◽  
High Energy ◽  
Pierre Auger Observatory ◽  
Quality Data ◽  
Ultra High Energy ◽  
High Quality ◽  
High Quality Data ◽  
High Energy Cosmic Rays ◽  
Energy Frontier ◽  
The Universe

We highlight the main results obtained by the Pierre Auger Collaboration in its quest to unveil the mysteries associated with the nature and origin of the ultra-high energy cosmic rays, the highest-energy particles in the Universe. The observatory has steadily produced high-quality data for more than 15 years, which have already led to a number of major breakthroughs in the field contributing to the advance of our understanding of these extremely energetic particles. The interpretation of our measurements so far opens new questions which will be addressed by the on-going upgrade of the Pierre Auger Observatory.

POVScript+: a program for model and data visualization using persistence of vision ray-tracing

2003 ◽  
Vol 36 (3) ◽  
pp. 944-947 ◽  
Author(s):  
T. D. Fenn ◽  
D. Ringe ◽  
G. A. Petsko
Keyword(s):  
Structural Analysis ◽  
Ray Tracing ◽  
Electron Density ◽  
Data Visualization ◽  
Visual Information ◽  
Three Dimensional ◽  
Input Output ◽  
High Quality ◽  
Rank Tensor ◽  
Volumetric Rendering

Macromolecular visualization is hampered by the fragmented set of available programs and the lack of cooperativity among them. The amount of visual information required for robust structural analysis is relatively difficult to generate and rarely allows further high-quality three-dimensional graphic rendering. Here, a modification ofMolScript[Kraulis (1991).J. Appl. Cryst.24, 946–950] is presented which contains the capability of the originalMolScript, the ability to carry out a majority of the options available in most other crystallographic visualization packages, as well as several new features of its own.POVScript+(currently version 1.62) allows anisotropic displacement ellipsoid rendering (read in as a second-rank tensor from a PDB file), electron-density polygonization (in several formats derived from a `marching tetrahedra' approach), volumetric rendering of electron density and GRASP/MSMS surface-map input/output. Finally,POVRayoutput is supported (viaa modified version ofPovScript) to generate high-quality renderings that are easily modified for any of a number of purposes (e.g.animations or altered textures).POVScript+provides a marked increase in the amount of structural and atomic detail possible, while still allowing a straightforward means of generating this information.

scholarly journals Anomalous diffraction in crystallographic phase evaluation

2014 ◽  
Vol 47 (1) ◽  
pp. 49-93 ◽  
Author(s):  
Wayne A. Hendrickson
Keyword(s):  
Electron Density ◽  
De Novo ◽  
Resonance Phenomenon ◽  
Sufficient Information ◽  
Anomalous Scattering ◽  
Biological Macromolecules ◽  
Anomalous Diffraction ◽  
Atomic Structures ◽  
Diffracted Waves ◽  
Diffraction Patterns

AbstractX-ray diffraction patterns from crystals of biological macromolecules contain sufficient information to define atomic structures, but atomic positions are inextricable without having electron-density images. Diffraction measurements provide amplitudes, but the computation of electron density also requires phases for the diffracted waves. The resonance phenomenon known as anomalous scattering offers a powerful solution to this phase problem. Exploiting scattering resonances from diverse elements, the methods of MAD (multiwavelength anomalous diffraction) and SAD (single-wavelength anomalous diffraction) now predominate for de novo determinations of atomic-level biological structures. This review describes the physical underpinnings of anomalous diffraction methods, the evolution of these methods to their current maturity, the elements, procedures and instrumentation used for effective implementation, and the realm of applications.

Three-Dimensional X-Ray Diffraction Microscopy Using High-Energy X-Rays

MRS Bulletin ◽  
2004 ◽  
Vol 29 (3) ◽  
pp. 166-169 ◽  
Author(s):  
Henning F. Poulsen ◽  
Dorte Juul Jensen ◽  
Gavin B.M. Vaughan
Keyword(s):  
Materials Science ◽  
Three Dimensional ◽  
High Energy ◽  
Polycrystalline Materials ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Reconstruction Methods ◽  
The Individual ◽  
Individual Grains

AbstractThree-dimensional x-ray diffraction (3DXRD) microscopy is a tool for fast and nondestructive characterization of the individual grains, subgrains, and domains inside bulk materials. The method is based on diffraction with very penetrating hard x-rays (E ≥ 50 keV), enabling 3D studies of millimeter-to-centimeter-thick specimens.The position, volume, orientation, and elastic and plastic strain can be derived for hundreds of grains simultaneously. Furthermore, by applying novel reconstruction methods, 3D maps of the grain boundaries can be generated. The 3DXRD microscope in use at the European Synchrotron Radiation Facility in Grenoble, France, has a spatial resolution of ∼5 μm and can detect grains as small as 150 nm. The technique enables, for the first time, dynamic studies of the individual grains within polycrystalline materials. In this article, some fundamental materials science applications of 3DXRD are reviewed: studies of nucleation and growth kinetics during recrystallization, recovery, and phase transformations, as well as studies of polycrystal deformation.

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