Theoretical Fraunhofer light diffraction patterns calculated from three-dimensional sarcomere arrays imaged from isolated cardiac cells at rest

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

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Electrophysiology of the Sodium-Potassium-ATPase in Cardiac Cells

Physiological Reviews ◽

10.1152/physrev.2001.81.4.1791 ◽

2001 ◽

Vol 81 (4) ◽

pp. 1791-1826 ◽

Cited By ~ 141

Author(s):

Helfried Günther Glitsch

Keyword(s):

Cell Membrane ◽

Potential Gradient ◽

Outward Current ◽

Pump Current ◽

Cardiac Cells ◽

Animal Cells ◽

Excitable Cells ◽

Extracellular Medium ◽

Enzymatic Isolation ◽

Isolated Cardiac Cells

Like several other ion transporters, the Na+-K+ pump of animal cells is electrogenic. The pump generates the pump current I p. Under physiological conditions, I p is an outward current. It can be measured by electrophysiological methods. These methods permit the study of characteristics of the Na+-K+ pump in its physiological environment, i.e., in the cell membrane. The cell membrane, across which a potential gradient exists, separates the cytosol and extracellular medium, which have distinctly different ionic compositions. The introduction of the patch-clamp techniques and the enzymatic isolation of cells have facilitated the investigation of I p in single cardiac myocytes. This review summarizes and discusses the results obtained from I p measurements in isolated cardiac cells. These results offer new exciting insights into the voltage and ionic dependence of the Na+-K+ pump activity, its effect on membrane potential, and its modulation by hormones, transmitters, and drugs. They are fundamental for our current understanding of Na+-K+ pumping in electrically excitable cells.

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2D X-ray diffraction and molecular modelling of the crystalline structure of polyesters under uniaxial stress

Polymers and Polymer Composites ◽

10.1177/0967391121998225 ◽

2021 ◽

pp. 096739112199822

Author(s):

Ahmed I Abou-Kandil ◽

Gerhard Goldbeck

Keyword(s):

Crystalline Structure ◽

Molecular Modelling ◽

Three Dimensional ◽

Uniaxial Stress ◽

X Ray Diffraction ◽

X Ray ◽

Wide Range ◽

Modelling Techniques ◽

Diffraction Patterns

Studying the crystalline structure of uniaxially and biaxially drawn polyesters is of great importance due to their wide range of applications. In this study, we shed some light on the behaviour of PET and PEN under uniaxial stress using experimental and molecular modelling techniques. Comparing experiment with modelling provides insights into polymer crystallisation with extended chains. Experimental x-ray diffraction patterns are reproduced by means of models of chains sliding along the c-axis leading to some loss of three-dimensional order, i.e. moving away from the condition of perfect register of the fully extended chains in triclinic crystals of both PET and PEN. This will help us understand the mechanism of polymer crystallisation under uniaxial stress and the appearance of mesophases in some cases as discussed herein.

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Heteroepitaxial Nucleation and Growth of Ge ON Si(100) Surfaces Using Remote Plasma Enhanced Chemical Vapor Deposition

MRS Proceedings ◽

10.1557/proc-116-519 ◽

1988 ◽

Vol 116 ◽

Cited By ~ 2

Author(s):

R.A. Rudder ◽

S.V. Hattangady ◽

D.J. Vitkavage ◽

R.J. Markunas

Keyword(s):

Chemical Vapor Deposition ◽

Vapor Deposition ◽

Photoelectron Spectroscopy ◽

Three Dimensional ◽

Chemical Vapor ◽

Layer By Layer ◽

Heteroepitaxial Growth ◽

Remote Plasma ◽

Dimensional Growth ◽

Diffraction Patterns

Heteroepitaxial growth of Ge on Si(100) has been accomplished using remote plasma enhanced chemical vapor deposition at 300*#x00B0;C. Reconstructed surfaces with diffraction patterns showing non-uniform intensity variations along the lengths of the integral order streaks are observed during the first 100 Å of deposit. This observation of an atomically rough surface during the initial stages of growth is an indication of three-dimensional growth. As the epitaxial growth proceeds, the diffraction patterns become uniform with extensive streaking on both the integral and fractional order streaks. Subsequent growth, therefore, takes place in a layer-by-layer, two-dimensional mode. X-ray photoelectron spectroscopy of the early nucleation stages, less than 80 Å, show that there is uniform coverage with no evidence of island formation.

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Hard X-ray polarizer to enable simultaneous three-dimensional nanoscale imaging of magnetic structure and lattice strain

Journal of Synchrotron Radiation ◽

10.1107/s1600577516009632 ◽

2016 ◽

Vol 23 (5) ◽

pp. 1210-1215 ◽

Cited By ~ 3

Author(s):

Jonathan Logan ◽

Ross Harder ◽

Luxi Li ◽

Daniel Haskel ◽

Pice Chen ◽

...

Keyword(s):

Magnetic Circular Dichroism ◽

Three Dimensional ◽

Control Sample ◽

Magnetic Ordering ◽

X Rays ◽

Diffractive Imaging ◽

X Ray ◽

Coherent Diffractive Imaging ◽

Diffraction Patterns ◽

A New Technique

Recent progress in the development of dichroic Bragg coherent diffractive imaging, a new technique for simultaneous three-dimensional imaging of strain and magnetization at the nanoscale, is reported. This progress includes the installation of a diamond X-ray phase retarder at beamline 34-ID-C of the Advanced Photon Source. The performance of the phase retarder for tuning X-ray polarization is demonstrated with temperature-dependent X-ray magnetic circular dichroism measurements on a gadolinium foil in transmission and on a Gd5Si2Ge2crystal in diffraction geometry with a partially coherent, focused X-ray beam. Feasibility tests for dichroic Bragg coherent diffractive imaging are presented. These tests include (1) using conventional Bragg coherent diffractive imaging to determine whether the phase retarder introduces aberrations using a nonmagnetic gold nanocrystal as a control sample, and (2) collecting coherent diffraction patterns of a magnetic Gd5Si2Ge2nanocrystal with left- and right-circularly polarized X-rays. Future applications of dichroic Bragg coherent diffractive imaging for the correlation of strain and lattice defects with magnetic ordering and inhomogeneities are considered.

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Light Induced Ferroelectric Domain Nucleation in LiNbO3 Crystal

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.79-82.1383 ◽

2009 ◽

Vol 79-82 ◽

pp. 1383-1386

Author(s):

Yun Lin Chen ◽

Hai Wei Li ◽

Yuan An Li

Keyword(s):

Light Intensity ◽

Lithium Niobate ◽

Visible Light ◽

Lithium Niobate Crystal ◽

Ferroelectric Domain ◽

Light Diffraction ◽

Far Field ◽

Light Wavelength ◽

Irradiation Intensity ◽

Diffraction Patterns

Using the tightly focused visible light (wavelength λ=488nm) illuminating, the ferroelectric domain patterns of the undoped lithium niobate crystal have been demonstrated. The influence of the visible light intensity on the domain nucleation field was investigated. The reduction of nucleation field decreases exponentially with increasing incident irradiation intensity. Once a domain is nucleated it can be dictated by the far-field light diffraction patterns. An assumption is proposed that the reduction of nucleation field is directly related to the defects mobility and structure of the crystals.

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Nearly uniform sampling of crystal orientations

Journal of Applied Crystallography ◽

10.1107/s1600576718009019 ◽

2018 ◽

Vol 51 (4) ◽

pp. 1162-1173 ◽

Cited By ~ 10

Author(s):

Romain Quey ◽

Aurélien Villani ◽

Claire Maurice

Keyword(s):

Dimensional Space ◽

Three Dimensional ◽

Uniform Distributions ◽

Orientation Space ◽

Unit Quaternions ◽

Spatial Uniformity ◽

Unit Hypersphere ◽

Open Source Software Package ◽

Diffraction Patterns ◽

Thomson Problem

A method is presented for generating nearly uniform distributions of three-dimensional orientations in the presence of symmetry. The method is based on the Thomson problem, which consists in finding the configuration of minimal energy of N electrons located on a unit sphere – a configuration of high spatial uniformity. Orientations are represented as unit quaternions, which lie on a unit hypersphere in four-dimensional space. Expressions of the electrostatic potential energy and Coulomb's forces are derived by working in the tangent space of orientation space. Using the forces, orientations are evolved in a conventional gradient-descent optimization until equilibrium. The method is highly versatile as it can generate uniform distributions for any number of orientations and any symmetry, and even allows one to prescribe some orientations. For large numbers of orientations, the forces can be computed using only the close neighbourhoods of orientations. Even uniform distributions of as many as 106 orientations, such as those required for dictionary-based indexing of diffraction patterns, can be generated in reasonable computation times. The presented algorithms are implemented and distributed in the free (open-source) software package Neper.

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Determination of Tilt Parameters in Electron Diffraction Patterns of 3D-Microcrystals

Microscopy and Microanalysis ◽

10.1017/s1431927600012137 ◽

1997 ◽

Vol 3 (S2) ◽

pp. 1049-1050

Author(s):

E. Dimmeler ◽

K.C. Holmes ◽

R.R. Schröder

Keyword(s):

Reciprocal Lattice ◽

Three Dimensional ◽

Diffraction Spot ◽

Spot Intensity ◽

Crystal Face ◽

Ewald Sphere ◽

Exact Determination ◽

Current Experimental Data ◽

Diffraction Patterns

Electron crystallography of thin three-dimensional (3D) protein crystals requires very exact determination of tilt angles and spot profiles to obtain correct merging of diffraction spot amplitudes. The reciprocal lattice of 3D microcrystals consists of ellipsoidal spot profiles which are very extended in the direction normal to the crystal face (z*). To extrapolate from the intensity measured in a section to the total spot intensity, two features need to be known very exactly: 1. the orientation of reciprocal lattice relative to the Ewald sphere, 2. the 3D-shape of the spot cloud.Fig. 1 shows a tilt series of one frozen hydrated catalase crystal, in the order of recording. The third diffraction pattern gives the highest resolution because it is untilted and therefore the electrons have the shortest path length. In the current experimental data taken at 120 keV electron energy inelastic scattering within the crystal leads to a dramatic loss of elastic information in highly tilted patterns.

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VESTA: a three-dimensional visualization system for electronic and structural analysis

Journal of Applied Crystallography ◽

10.1107/s0021889808012016 ◽

2008 ◽

Vol 41 (3) ◽

pp. 653-658 ◽

Cited By ~ 2780

Author(s):

Koichi Momma ◽

Fujio Izumi

Keyword(s):

Structural Model ◽

Three Dimensional ◽

Electronic Energy ◽

Oxidation States ◽

Chemical Information ◽

Volumetric Data ◽

Visualization System ◽

Cross Platform ◽

Diffraction Patterns ◽

Physical Quantities

A cross-platform program,VESTA, has been developed to visualize both structural and volumetric data in multiple windows with tabs.VESTArepresents crystal structures by ball-and-stick, space-filling, polyhedral, wireframe, stick, dot-surface and thermal-ellipsoid models. A variety of crystal-chemical information is extractable from fractional coordinates, occupancies and oxidation states of sites. Volumetric data such as electron and nuclear densities, Patterson functions, and wavefunctions are displayed as isosurfaces, bird's-eye views and two-dimensional maps. Isosurfaces can be colored according to other physical quantities. Translucent isosurfaces and/or slices can be overlapped with a structural model. Collaboration with external programs enables the user to locate bonds and bond angles in the `graphics area', simulate powder diffraction patterns, and calculate site potentials and Madelung energies. Electron densities determined experimentally are convertible into their Laplacians and electronic energy densities.

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The CCP13FibreFixprogram suite: semi-automated analysis of diffraction patterns from non-crystalline materials

Journal of Applied Crystallography ◽

10.1107/s0021889806048643 ◽

2007 ◽

Vol 40 (1) ◽

pp. 178-184 ◽

Cited By ~ 21

Author(s):

Ganeshalingam Rajkumar ◽

Hind A. AL-Khayat ◽

Felicity Eakins ◽

Carlo Knupp ◽

John M. Squire

Keyword(s):

Structural Information ◽

Protein Crystallography ◽

Three Dimensional ◽

Automated Analysis ◽

Crystalline Materials ◽

Space Groups ◽

Naturally Occurring ◽

Single User ◽

Diffraction Patterns ◽

User Friendly

The extraction of useful information from recorded diffraction patterns from non-crystalline materials is non-trivial and is not a well defined operation. Unlike protein crystallography where one expects to see well behaved diffraction spots in predictable positions defined by standard space groups, the diffraction patterns from non-crystalline materials are very diverse. They can range from uniaxially oriented fibre patterns which are completely sampled as Bragg peaks, but rotationally averaged around the fibre axis, to fibre patterns that are completely unsampled, to either kind of pattern with considerable axial misalignment (disorientation), to liquid-like order and even to mixtures of these various structure types. In the case of protein crystallography, the specimen is generated artificially and only used if the degree of order is sufficient to yield a three-dimensional density map of high enough resolution to be interpreted sensibly. However, with non-crystalline diffraction, many of the specimens of interest are naturally occurring (e.g.cellulose, rubber, collagen, muscle, hair, silk) and to elucidate their structure it is necessary to extract structural information from the materials as they actually are and to whatever resolution is available. Even when synthetic fibres are generated from purified components (e.g.nylon, polyethylene, DNA, polysaccharides, amyloidsetc.) and diffraction occurs to high resolution, it is rarely possible to obtain perfect uniaxial alignment. The CCP13 project was established in the 1990s to generate software which will be generally useful for analysis of non-crystalline diffraction patterns. Various individual programs were written which allowed separate steps in the analysis procedure to be carried out. Many of these programs have now been integrated into a single user-friendly package known asFibreFix, which is freely downloadable from http://www.ccp13.ac.uk. Here the main features ofFibreFixare outlined and some of its applications are illustrated.

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