scholarly journals X-ray diffraction evidence for the existence of 102.0- and 230.0-nm transverse periodicities in striated muscle.

1987 ◽  
Vol 105 (3) ◽  
pp. 1311-1318 ◽  
Author(s):  
J Bordas ◽  
G R Mant ◽  
G P Diakun ◽  
C Nave
Keyword(s):  
Electron Density ◽  
Striated Muscle ◽  
Diffraction Theory ◽  
Optical Microscope ◽  
Sartorius Muscle ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Diffraction Patterns ◽  
Integrated Intensities

Synchrotron radiation techniques have enabled us to record meridional x-ray diffraction patterns from frog sartorius muscle at resolutions ranging from approximately 2,800 to 38 nm (i.e., overlapping with the optical microscope and the region normally accessible with low angle diffraction cameras). These diffraction patterns represent the transform of the low resolution structure of muscle projected on the sarcomere axis and sampled by its repeat. Altering the sarcomere length results in the sampling of different parts of this transform, which induces changes in the positions and the integrated intensities of the diffraction maxima. This effect has been used to determine the transform of the mass projection on the muscle axis in a quasicontinuous fashion. The results reveal the existence of maxima arising from long-range periodicities in the structure. Determination of the zeroes in the transforms has been used to obtain phase information from which electron density maps have been calculated. The x-ray diffraction diagrams and the resulting electron density maps show the existence of a series of mass bands, disposed transversely to the sarcomere axis and distributed at regular intervals. A set of these transverse structures is associated with thin filaments, and their 102.0-nm repeat suggests a close structural relationship with their known molecular components. A second set, spaced by approximately 230.0 nm, is also present; from diffraction theory one has to conclude that this repeat simultaneously exists in thick and thin filament regions.

A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation

2017 ◽  
Vol 24 (5) ◽  
pp. 1024-1038 ◽  
Author(s):  
Yuki Sekiguchi ◽  
Saki Hashimoto ◽  
Amane Kobayashi ◽  
Tomotaka Oroguchi ◽  
Masayoshi Nakasako
Keyword(s):  
Diffraction Pattern ◽  
Electron Density ◽  
Figure Of Merit ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Diffraction Imaging ◽  
Density Map ◽  
Diffraction Patterns ◽  
Electron Density Map

Coherent X-ray diffraction imaging (CXDI) is a technique for visualizing the structures of non-crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X-rays can be reconstructed only from the diffraction pattern by using phase-retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small-angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X-ray detection. To date, X-ray free-electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non-crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.

scholarly journals Thermal History of Matrix Forsterite Grains from Murchison Based on High-resolution Tomography

2021 ◽  
Vol 922 (2) ◽  
pp. 256
Author(s):  
Giulia Perotti ◽  
Henning O. Sørensen ◽  
Henning Haack ◽  
Anja C. Andersen ◽  
Dario Ferreira Sanchez ◽  
...  
Keyword(s):  
High Resolution ◽  
Electron Density ◽  
Chemical Compositions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Maps ◽  
Thermally Processed ◽  
The Matrix ◽  
History Of ◽  
Chondrule Formation

Abstract Protoplanetary disks are dust- and gas-rich structures surrounding protostars. Depending on the distance from the protostar, this dust is thermally processed to different degrees and accreted to form bodies of varying chemical compositions. The primordial accretion processes occurring in the early protoplanetary disk such as chondrule formation and metal segregation are not well understood. One way to constrain them is to study the morphology and composition of forsteritic grains from the matrix of carbonaceous chondrites. Here, we present high-resolution ptychographic X-ray nanotomography and multimodal chemical microtomography (X-ray diffraction and X-ray fluorescence) to reveal the early history of forsteritic grains extracted from the matrix of the Murchison CM2.5 chondrite. The 3D electron density maps revealed, at unprecedented resolution (64 nm), spherical inclusions containing Fe–Ni, very little silica-rich glass and void caps (i.e., volumes where the electron density is consistent with conditions close to vacuum) trapped in forsterite. The presence of the voids along with the overall composition, petrological textures, and shrinkage calculations is consistent with the grains experiencing one or more heating events with peak temperatures close to the melting point of forsterite (∼2100 K), and subsequently cooled and contracted, in agreement with chondrule-forming conditions.

Electron Density Distribution in LiB3O5 at 293 K

1997 ◽  
Vol 53 (6) ◽  
pp. 870-879 ◽  
Author(s):  
C. Le Hénaff ◽  
N. K. Hansen ◽  
J. Protas ◽  
G. Marnier
Keyword(s):  
Density Distribution ◽  
Electron Density ◽  
Electron Density Distribution ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hartree Fock ◽  
Density Maps ◽  
Symmetry Constraints ◽  
Net Charges ◽  
Good Agreement

The electron density distribution in lithium triborate LiB3O5 has been studied at room temperature by X-ray diffraction using Ag K \alpha radiation up to 1.02 Å−1 [1439 unique reflections with I > 3\sigma(I)]. Conventional refinements with a free-atom model yield R(F) = 0.0223, wR(F) = 0.0299, S = 1.632. Atom charge refinements show that the lithium should be considered a monovalent ion. Multipolar refinements were undertaken up to fourth order, imposing local non-crystallographic symmetry constraints in order to avoid phase problems leading to meaningless multipole populations due to the non-centrosymmetry of the structure (space group: Pn a21). The residual indices decreased to: R(F) = 0.0147, wR(F) = 0.0193, S = 1.106. The net charges are in good agreement with what can be expected in borate chemistry. Deformation density maps are analysed in terms of \sigma and \pi bonding. The experimental electron distribution in the p z orbitals of triangular B atoms and surrounding O atoms has been analysed by introducing idealized hybridized states. In parallel, the electron density has been determined from ab initio Hartree–Fock calculations on fragments of the structure. Agreement with the X-ray determination is very good and confirms the nature of bonding in the crystal. The amount of transfer of \pi electrons from the oxygen to the triangular B atoms is estimated to be 0.22 electrons by theory.

Comments on determining X-ray diffraction-based volume fractions of retained austenite in steels

2001 ◽  
Vol 16 (4) ◽  
pp. 198-204 ◽  
Author(s):  
C. K. Lowe-Ma ◽  
W. T. Donlon ◽  
W. E. Dowling
Keyword(s):  
Retained Austenite ◽  
Volume Fraction ◽  
X Ray Diffraction ◽  
Experimental Conditions ◽  
X Ray ◽  
Profile Fitting ◽  
Diffraction Peaks ◽  
Diffraction Patterns ◽  
Heat Treatment Regimes ◽  
Integrated Intensities

Retained austenite is an important characteristic of properly heat-treated steel components, particularly gears and shafts, that will be subjected to long-term use and wear. Normally, either X-ray diffraction or optical microscopy techniques are used to determine the volume percent of retained austenite present in steel components subjected to specific heat-treatment regimes. As described in the literature, a number of phenomenological, experimental, and calculation factors can influence the volume fraction of retained austenite determined from X-ray diffraction measurements. However, recent disagreement between metallurgical properties, microscopy, and service laboratory values for retained austenite led to a re-evaluation of possible reasons for the apparent discrepancies. Broad, distorted X-ray peaks from un-tempered martensite were found to yield unreliable integrated intensities whereas diffraction peaks from tempered samples were more amenable to profile fitting with standard shape functions, yielding reliable integrated intensities. Retained austenite values calculated from reliable integrated intensities were found to be consistent with values obtained by Rietveld refinement of the diffraction patterns. The experimental conditions used by service laboratories combined with a poor choice of diffraction peaks were found to be sources of retained austenite values containing significant bias.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography

2010 ◽  
Vol 66 (5) ◽  
pp. 558-567 ◽  
Author(s):  
Anna S. Gardberg ◽  
Alexis Rae Del Castillo ◽  
Kevin L. Weiss ◽  
Flora Meilleur ◽  
Matthew P. Blakeley ◽  
...  
Keyword(s):  
Neutron Diffraction ◽  
Electron Density ◽  
Pyrococcus Furiosus ◽  
X Ray Diffraction ◽  
Neutron Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Improved Model

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3-protonated perdeuterated crystals ofPyrococcus furiosusrubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high-confidence positions for D atoms than 1.1 Å resolution X-ray data at 100 K or RT. At or above the 1.0σ level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0σ level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

Photoinduced structural dynamics of polar solids studied by femtosecond X-ray diffraction

2010 ◽  
Vol 66 (2) ◽  
pp. 168-178 ◽  
Author(s):  
Thomas Elsaesser ◽  
Michael Woerner
Keyword(s):  
Real Time ◽  
Structural Changes ◽  
Bragg Diffraction ◽  
X Ray Diffraction ◽  
Crystalline Materials ◽  
X Ray ◽  
Density Maps ◽  
Diffraction Patterns ◽  
Superlattice Structures ◽  
Work Done

Femtosecond X-ray diffraction allows for real-time mapping of structural changes in condensed matter on atomic length and timescales. Sequences of diffraction patterns provide both transient geometries and charge-density maps of crystalline materials. This article reviews recent progress in this field, the main emphasis being on experimental work done with laser-driven hard X-ray sources. Both Bragg diffraction techniques for bulk and nanostructured single crystals as well as the recently implemented powder diffraction from polycrystalline samples are discussed. In ferroelectric superlattice structures, coherent phonon motions and the driving stress mechanisms are observed in real time. In molecular crystals charge-transfer processes and the concomitant changes of the lattice geometry are analyzed.

Cross-sectional texture of carbon fibres analysed by scanning microbeam X-ray diffraction

2001 ◽  
Vol 34 (4) ◽  
pp. 473-479 ◽  
Author(s):  
Oskar Paris ◽  
Dieter Loidl ◽  
Martin Müller ◽  
Helga Lichtenegger ◽  
Herwig Peterlik
Keyword(s):  
Quantitative Description ◽  
Fibre Diameter ◽  
Orientation Distribution ◽  
Carbon Fibres ◽  
X Ray Diffraction ◽  
Cross Sectional ◽  
X Ray ◽  
The Cross ◽  
Diffraction Patterns ◽  
Integrated Intensities

Scanning microbeam X-ray diffraction analysis of single carbon fibres allows the cross-sectional orientation distribution (texture) of the carbon layers to be determined, even when the fibre axis is oriented perpendicular to the X-ray beam (fibre geometry). The fibre is scanned across a microbeam with a diameter significantly smaller than the fibre diameter, and fibre diffraction patterns are recorded for every scanning step. The cross-sectional texture information is obtained from the integrated intensities of two different equatorial reflections as a function of the position on the fibre. As an example, results from two different types of carbon fibres are presented: a polyacrylonitrile-based fibre, with random cross-sectional texture, and a fibre based on mesophase pitch, which exhibits a radially folded cross-sectional texture. Detailed modelling of the diffraction data allows a quantitative description of the radial folded texture.

Fourier Electron Density Maps for Nanostructured TiO2 and TiO2-CeO2 Sol-Gel Solid

2009 ◽  
Vol 5 ◽  
pp. 87-94 ◽  
Author(s):  
Félix Galindo-Hernández ◽  
Ricardo Gómez
Keyword(s):  
Crystallite Size ◽  
Electron Density ◽  
Annealing Temperature ◽  
Anatase Phase ◽  
Sol Gel ◽  
X Ray Diffraction ◽  
Electronic Density ◽  
X Ray ◽  
Density Maps ◽  
Gel Preparation

Sol-gel TiO2 and TiO2–CeO2 materials were synthesized at pH3 using HNO3 as hydrolysis catalysts. Gels were annealed at 473, 673 and 873 K for 4h. X-ray diffraction Rietveld refinement was used to determine the mean crystallite size, TiO2 stoichiometry (titanium deficiency) and Fourier electronic density maps. It has been found that the fractal surface dimension diminishes on TiO2 a nd TiO2–CeO2 surfaces as the annealing temperature increases. The X-ray diffraction patterns showed nanocrystalline anatase phase in the range of 8.9 to 43.6 nm in depending of the annealing temperature. A dependency between the crystallite size and the titanium deficiency [V+Ti4+] per unit cell was found, as lowest is the crystallite highest is the titanium deficiency. Strong differences on the Fourier electron density map were found on TiO2 and TiO2–CeO2 materials. It was concluded that the sol-gel preparation method favors the formation of nanosized TiO2 with high Ti4+ stoichiometry deficiency.

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