Absorption correction based on a three-dimensional model reconstruction from visual images

2008 ◽  
Vol 41 (4) ◽  
pp. 729-737 ◽  
Author(s):  
Ricardo M. F. Leal ◽  
Susana C. M. Teixeira ◽  
Vicente Rey ◽  
V. Trevor Forsyth ◽  
Edward P. Mitchell
Keyword(s):  
Three Dimensional ◽  
Incident Beam ◽  
Empirical Method ◽  
General Interest ◽  
Three Dimensional Model ◽  
X Ray ◽  
Camera Systems ◽  
Crystal Model ◽  
Path Lengths ◽  
Incident Beam Energy

The results are presented of a feasibility study for the application of absorption corrections to macromolecular crystallographic X-ray diffraction data using a three-dimensional crystal model generated photographically. The model allows path lengths through the crystal, the solvent and the crystal mount system to be determined. The approach has been tested on the macromolecular crystallography beamline ID23-1 at the ESRF in Grenoble using a model insulin system with the standard mini diffractometer facilities, which incorporate high-quality camera systems for sample alignment. Data from the insulin crystal at low incident beam energy (6.0 keV or 2.1 Å) were recorded and processed using this approach. The resulting data are compared against those treated using an empirical method and show significant improvement. The methods described here are of general interest, particularly for long-wavelength X-ray work, and may also be applied to account for absorption effects in neutron crystallography.

Optimizing conditions for x-ray microchemical analysis in analytical electron microscopy

1978 ◽  
Vol 36 (1) ◽  
pp. 548-549 ◽  
Author(s):  
N. J. Zaluzec
Keyword(s):  
Solid Angle ◽  
Analytical Electron Microscopy ◽  
Incident Beam ◽  
Thin Foil ◽  
Experimental Conditions ◽  
X Ray ◽  
Microchemical Analysis ◽  
Analytical Electron ◽  
Image Position ◽  
Incident Beam Energy

The ultimate sensitivity of microchemical analysis using x-ray emission rests in selecting those experimental conditions which will maximize the measured peak-to-background (P/B) ratio. This paper presents the results of calculations aimed at determining the influence of incident beam energy, detector/specimen geometry and specimen composition on the P/B ratio for ideally thin samples (i.e., the effects of scattering and absorption are considered negligible). As such it is assumed that the complications resulting from system peaks, bremsstrahlung fluorescence, electron tails and specimen contamination have been eliminated and that one needs only to consider the physics of the generation/emission process.The number of characteristic x-ray photons (Ip) emitted from a thin foil of thickness dt into the solid angle dΩ is given by the well-known equation

A new model for packing of type-I collagen molecules in the native fibril

1981 ◽  
Vol 1 (10) ◽  
pp. 801-810 ◽  
Author(s):  
Karl A. Piez ◽  
Benes L. Trus
Keyword(s):  
Type I Collagen ◽  
Hexagonal Lattice ◽  
Three Dimensional ◽  
Equatorial Region ◽  
Type I ◽  
X Ray Diffraction ◽  
X Ray ◽  
Left Handed ◽  
Crystal Model ◽  
Collagen Molecules

A specific fibril model is presented consisting of bundles of five-stranded microfibrils, which are usually disordered (except axially) but under lateral compression become ordered. The features are as follows (where D = 234 residues or 67 nm): (1) D-staggered collagen molecules 4.5 D long in the helical microfibril have a left-handed supercoil with a pitch of 400–700 residues, but microfibrils need not have helical symmetry. (2) Straight-tilted 0.5-D overlap regions on a near-hexagonal lattice contribute the discrete x-ray diffraction reflections arising from lateral order, while the gap regions remain disordered. (3) The overlap regions are equivalent, but are crystallographically distinguished by systematic displacements from the near-hexagonal lattice. (4) The unit cell is the same as in a recently proposed three-dimensional crystal model, and calculated intensities in the equatorial region of the x-ray diffraction pattern agree with observed values.

Diffraction by crystals

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Three Dimensional ◽  
Incident Beam ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Angle Of Incidence ◽  
X Ray ◽  
Max Von Laue ◽  
The Fourier Transform

In Chapter 4 many two-dimensional examples were shown, in which a diffraction pattern represents the Fourier transform of the scattering object. When a diffracting object is three-dimensional, a new effect arises. In diffraction by a repetitive object, rays are scattered in many directions. Each unit of the lattice scatters, but a diffracted beam arises only if the scattered rays from each unit are all in phase. Otherwise the scattering from one unit is cancelled out by another. In two dimensions, there is always a direction where the scattered rays are in phase for any order of diffraction (just as shown for a one-dimensional scatterer in Fig. 4.1). In three dimensions, it is only possible for all the points of a lattice to scatter in phase if the crystal is correctly oriented in the incident beam. The amplitudes and phases of all the scattered beams from a three-dimensional crystal still provide the Fourier transform of the three-dimensional structure. But when a crystal is at a particular angular orientation to the X-ray beam, the scattering of a monochromatic beam provides only a tiny sample of the total Fourier transform of its structure. In the next section, we are going to find what is needed to allow a diffracted beam to be generated. We shall follow a treatment invented by Lawrence Bragg in 1913. Max von Laue, who discovered X-ray diffraction in 1912, used a different scheme of analysis; and Paul Ewald introduced a new way of looking at it in 1921. These three methods are referred to as the Laue equations, Bragg’s law and the Ewald construction, and they give identical results. All three are described in many crystallographic text books. Bragg’s method is straightforward, understandable, and suffices for present needs. I had heard J.J. Thomson lecture about…X-rays as very short pulses of radiation. I worked out that such pulses…should be reflected at any angle of incidence by the sheets of atoms in the crystal as if these sheets were mirrors.…It remained to explain why certain of the atomic mirrors in the zinc blende [ZnS] crystal reflected more powerfully than others.

scholarly journals Preliminary crystallographic studies of aSchistosoma mansoniantigen (Sm21.7) dynein light-chain (DLC) domain

2014 ◽  
Vol 70 (6) ◽  
pp. 803-807 ◽  
Author(s):  
M. A. F. Costa ◽  
F. T. G. Rodrigues ◽  
B. C. A. Chagas ◽  
C. M. F. Rezende ◽  
A. M. Goes ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Monomethyl Ether ◽  
Dynein Light Chain ◽  
X Ray Diffraction ◽  
Three Dimensional Model ◽  
Major Health Problem ◽  
X Ray ◽  
Cell Parameters ◽  
Terminal Domain ◽  
Drug Of Choice

Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) fromSchistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed inEscherichia coliand the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space groupP6122, with similar unit-cell parametersa=b= 108.5,c= 55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS–PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine.

Low Beam Energy X-Ray Micro Analysis: How Useful Is It?

1997 ◽  
Vol 3 (S2) ◽  
pp. 881-882 ◽  
Author(s):  
Dale E. Newbury
Keyword(s):  
Electron Beam ◽  
Beam Energy ◽  
Strong Dependence ◽  
Incident Beam ◽  
X Ray ◽  
Upper Limit ◽  
History Of ◽  
Incident Beam Energy ◽  
Micro Analysis ◽  
Electron Range

Throughout the history of electron-beam X-ray microanalysis, analysts have made good use of the strong dependence of electron range on incident energy (R ≈ E1,7) to optimize the analytical volume when attacking certain types of problems, such as inclusions in a matrix or layered specimens. The “conventional” energy range for quantitative electron beam X-ray microanalysis can be thought of as beginning at 10 keV and extending to the upper limit of the accelerating potential, typically 30 - 50 keV depending on the instrument. The lower limit of 10 keV is selected because this is the lowest incident beam energy for which there is a satisfactory analytical X-ray peak excited from the K-, L-, or M- shells (in a few cases, two shells are simultaneously excited, e.g., Fe-K and Fe-L) for every element in the Periodic Table that is accessible to X-ray spectrometry, beginning with Be (Ek =116 eV) and extending to the transuranic elements. This criterion is based upon establishing a minimum overvoltage U = E0/Ec > 1.25, which is the practical minimum for useful excitation.

Simulation of small-angle X-ray scattering from thylakoid membranes

2009 ◽  
Vol 42 (4) ◽  
pp. 649-659 ◽  
Author(s):  
J. J. K. Kirkensgaard ◽  
J. K. Holm ◽  
J. K. Larsen ◽  
D. Posselt
Keyword(s):  
Experimental Data ◽  
Small Angle ◽  
Virtual Instrument ◽  
Three Dimensional ◽  
Thylakoid Membranes ◽  
Three Dimensional Model ◽  
General Applicability ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) patterns are calculated from a three-dimensional model of photosynthetic thylakoid membranes. The intricate structure of the thylakoids is represented by sampling random `electron density points' on geometric surfaces. The simulation setup works as a virtual instrument, allowing direct comparison with experimental data. The simulations qualitatively reproduce experimental data and thus clarify the structural origin of the scattering features. This is used to explain recent SAXS measurements and as a guideline for new experiments and future quantitative modeling. The setup has general applicability for model testing purposes when modeling scattering from membrane systems of complex geometries.

X-ray characterization of contact holes for block copolymer lithography

2019 ◽  
Vol 52 (1) ◽  
pp. 106-114
Author(s):  
Daniel F. Sunday ◽  
Florian Delachat ◽  
Ahmed Gharbi ◽  
Guillaume Freychet ◽  
Christopher D. Liman ◽  
...  
Keyword(s):  
Self Assembly ◽  
Low Cost ◽  
Ion Beam ◽  
Three Dimensional ◽  
Incident Beam ◽  
Residual Layer ◽  
Processing Conditions ◽  
Dimensional Metrology ◽  
Grid Pattern ◽  
X Ray

The directed self-assembly (DSA) of block copolymers (BCPs) is a promising low-cost approach to patterning structures with critical dimensions (CDs) which are smaller than can be achieved by traditional photolithography. The CD of contact holes can be reduced by assembling a cylindrical BCP inside a patterned template and utilizing the native size of the cylinder to dictate the reduced dimensions of the hole. This is a particularly promising application of the DSA technique, but in order for this technology to be realized there is a need for three-dimensional metrology of the internal structure of the patterned BCP in order to understand how template properties and processing conditions impact BCP assembly. This is a particularly challenging problem for traditional metrologies owing to the three-dimensional nature of the structure and the buried features. By utilizing small-angle X-ray scattering and changing the angle between the incident beam and sample we can reconstruct the three-dimensional shape profile of the empty template and the residual polymer after self-assembly and removal of one of the phases. A two-dimensional square grid pattern of the holes results in scattering in both in-plane directions, which is simplified by converting to a radial geometry. The shape is then determined by simulating the scattering from a model and iterating that model until the simulated and experimental scattering profiles show a satisfactory match. Samples with two different processing conditions are characterized in order to demonstrate the ability of the technique to evaluate critical features such as residual layer thickness and sidewall height. It was found that the samples had residual layer thicknesses of 15.9 ± 3.2 nm and 4.5 ± 2.2 nm, which were clearly distinguished between the two different DSA processes and in good agreement with focused ion beam scanning transmission electron microscopy (FIBSTEM) observations. The advantage of the X-ray measurements is that FIBSTEM characterizes around ten holes, while there are of the order of 800 000 holes illuminated by the X-ray beam.

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