scholarly journals Inelastic scattering and solvent scattering reduce dynamical diffraction in biological crystals

2019 ◽  
Vol 75 (4) ◽  
pp. 523-531 ◽  
Author(s):  
Tatiana Latychevskaia ◽  
Jan Pieter Abrahams
Keyword(s):  
Inelastic Scattering ◽  
Three Dimensional ◽  
Theory And Practice ◽  
Apparent Discrepancy ◽  
Electron Crystallography ◽  
Dynamical Diffraction ◽  
Structure Solution ◽  
Unit Cells ◽  
Phase Differences ◽  
Exit Beam

Multi-slice simulations of electron diffraction by three-dimensional protein crystals have indicated that structure solution would be severely impeded by dynamical diffraction, especially when crystals are more than a few unit cells thick. In practice, however, dynamical diffraction turned out to be less of a problem than anticipated on the basis of these simulations. Here it is shown that two scattering phenomena, which are usually omitted from multi-slice simulations, reduce the dynamical effect: solvent scattering reduces the phase differences within the exit beam and inelastic scattering followed by elastic scattering results in diffusion of dynamical scattering out of Bragg peaks. Thus, these independent phenomena provide potential reasons for the apparent discrepancy between theory and practice in protein electron crystallography.

Crystal Structure Analysis of Cu-Zr Alloys by Convergent Beam Diffraction

1981 ◽  
Vol 39 ◽  
pp. 354-355
Author(s):  
A. F. Marshall ◽  
J. W. Steeds ◽  
D. Bouchet ◽  
S. L. Shinde ◽  
R. G. Walmsley
Keyword(s):  
Crystal Structure ◽  
Point Group ◽  
Intermetallic Phase ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Ion Milling ◽  
Composition And Structure ◽  
Unit Cells ◽  
Sputter Deposited ◽  
Convergent Beam

Convergent beam electron diffraction is a powerful technique for determining the crystal structure of a material in TEM. In this paper we have applied it to the study of the intermetallic phases in the Cu-rich end of the Cu-Zr system. These phases are highly ordered. Their composition and structure has been previously studied by microprobe and x-ray diffraction with sometimes conflicting results.The crystalline phases were obtained by annealing amorphous sputter-deposited Cu-Zr. Specimens were thinned for TEM by ion milling and observed in a Philips EM 400. Due to the large unit cells involved, a small convergence angle of diffraction was used; however, the three-dimensional lattice and symmetry information of convergent beam microdiffraction patterns is still present. The results are as follows:1) 21 at% Zr in Cu: annealed at 500°C for 5 hours. An intermetallic phase, Cu3.6Zr (21.7% Zr), space group P6/m has been proposed near this composition (2). The major phase of our annealed material was hexagonal with a point group determined as 6/m.

Defocus ramp correction in spot-scan imaging

1992 ◽  
Vol 50 (1) ◽  
pp. 130-131
Author(s):  
Kenneth H. Downing
Keyword(s):  
Computer Control ◽  
Three Dimensional ◽  
Sufficient Accuracy ◽  
Objective Lens ◽  
Electron Crystallography ◽  
Contrast Transfer Function ◽  
Tilt Axis ◽  
Specimen Height ◽  
The Difference ◽  
Envelope Functions

Three-dimensional structures of a number of samples have been determined by electron crystallography. The procedures used in this work include recording images of fairly large areas of a specimen at high tilt angles. There is then a large defocus ramp across the image, and parts of the image are far out of focus. In the regions where the defocus is large, the contrast transfer function (CTF) varies rapidly across the image, especially at high resolution. Not only is the CTF then difficult to determine with sufficient accuracy to correct properly, but the image contrast is reduced by envelope functions which tend toward a low value at high defocus.We have combined computer control of the electron microscope with spot-scan imaging in order to eliminate most of the defocus ramp and its effects in the images of tilted specimens. In recording the spot-scan image, the beam is scanned along rows that are parallel to the tilt axis, so that along each row of spots the focus is constant. Between scan rows, the objective lens current is changed to correct for the difference in specimen height from one scan to the next.

Image formation analysis of thick biological specimens using three-dimensional power-spectra of through focus series

1994 ◽  
Vol 52 ◽  
pp. 124-125
Author(s):  
Karen F. Han
Keyword(s):  
Inelastic Scattering ◽  
Imaging Techniques ◽  
Mass Density ◽  
Relative Proportion ◽  
Three Dimensional ◽  
Power Spectra ◽  
Image Formation ◽  
Energy Filtering ◽  
Ewald Sphere ◽  
Nonlinear Imaging

The primary focus in our laboratory is the study of higher order chromatin structure using three dimensional electron microscope tomography. Three dimensional tomography involves the deconstruction of an object by combining multiple projection views of the object at different tilt angles, image intensities are not always accurate representations of the projected object mass density, due to the effects of electron-specimen interactions and microscope lens aberrations. Therefore, an understanding of the mechanism of image formation is important for interpreting the images. The image formation for thick biological specimens has been analyzed by using both energy filtering and Ewald sphere constructions. Surprisingly, there is a significant amount of coherent transfer for our thick specimens. The relative amount of coherent transfer is correlated with the relative proportion of elastically scattered electrons using electron energy loss spectoscopy and imaging techniques.Electron-specimen interactions include single and multiple, elastic and inelastic scattering. Multiple and inelastic scattering events give rise to nonlinear imaging effects which complicates the interpretation of collected images.

scholarly journals Structure Solution of Nano-Crystalline Small Molecules Using MicroED and Solid-State NMR Dipolar-Based Experiments

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4652
Author(s):  
Nghia Tuan Duong ◽  
Yoshitaka Aoyama ◽  
Katsumi Kawamoto ◽  
Toshio Yamazaki ◽  
Yusuke Nishiyama
Keyword(s):  
Spin Dynamics ◽  
Double Resonance ◽  
Three Dimensional ◽  
Saturation Pulse ◽  
X Ray Crystallography ◽  
Nano Crystalline ◽  
Structure Solution ◽  
Validation Procedure ◽  
R Factors ◽  
Shift Calculation

Three-dimensional electron diffraction crystallography (microED) can solve structures of sub-micrometer crystals, which are too small for single crystal X-ray crystallography. However, R factors for the microED-based structures are generally high because of dynamic scattering. That means R factor may not be reliable provided that kinetic analysis is used. Consequently, there remains ambiguity to locate hydrogens and to assign nuclei with close atomic numbers, like carbon, nitrogen, and oxygen. Herein, we employed microED and ssNMR dipolar-based experiments together with spin dynamics numerical simulations. The NMR dipolar-based experiments were 1H-14N phase-modulated rotational-echo saturation-pulse double-resonance (PM-S-RESPDOR) and 1H-1H selective recoupling of proton (SERP) experiments. The former examined the dephasing effect of a specific 1H resonance under multiple 1H-14N dipolar couplings. The latter examined the selective polarization transfer between a 1H-1H pair. The structure was solved by microED and then validated by evaluating the agreement between experimental and calculated dipolar-based NMR results. As the measurements were performed on 1H and 14N, the method can be employed for natural abundance samples. Furthermore, the whole validation procedure was conducted at 293 K unlike widely used chemical shift calculation at 0 K using the GIPAW method. This combined method was demonstrated on monoclinic l-histidine.

Prediction of internal geometry and tensile behavior of 3D woven solid structures by mathematical coding

2021 ◽  
pp. 152808372110013
Author(s):  
Vivek R Jayan ◽  
Lekhani Tripathi ◽  
Promoda Kumar Behera ◽  
Michal Petru ◽  
BK Behera
Keyword(s):  
Volume Fraction ◽  
Three Dimensional ◽  
Areal Density ◽  
Woven Fabrics ◽  
Tensile Behavior ◽  
Geometrical Parameters ◽  
Fiber Volume ◽  
Acceptable Error ◽  
Internal Geometry ◽  
Unit Cells

The internal geometry of composite material is one of the most important factors that influence its performance and service life. A new approach is proposed for the prediction of internal geometry and tensile behavior of the 3 D (three dimensional) woven fabrics by creating the unit cell using mathematical coding. In many technical applications, textile materials are subjected to rates of loading or straining that may be much greater in magnitude than the regular household applications of these materials. The main aim of this study is to provide a generalized method for all the structures. By mathematical coding, unit cells of 3 D woven orthogonal, warp interlock and angle interlock structures have been created. The study then focuses on developing code to analyze the geometrical parameters of the fabric like fabric thickness, areal density, and fiber volume fraction. Then, the tensile behavior of the coded 3 D structures is studied in Ansys platform and the results are compared with experimental values for authentication of geometrical parameters as well as for tensile behavior. The results show that the mathematical coding approach is a more efficient modeling technique with an acceptable error percentage.

The crystal structure of myoglobin. VI. Seal myoglobin

1960 ◽  
Vol 258 (1293) ◽  
pp. 181-201 ◽  
Keyword(s):  
Tertiary Structure ◽  
Heavy Atom ◽  
Three Dimensional ◽  
Sperm Whale ◽  
Fourier Synthesis ◽  
Heavy Atoms ◽  
Isomorphous Replacement ◽  
Unit Cells ◽  
The Common ◽  
Sperm Whale Myoglobin

Myoglobin from the common seal ( Phoca vitulina ) when crystallized from ammonium sulphate forms monoclinic crystals with space group the unit cell, a = 57·9Å, b = 29·6Å, c = 106·4Å, β = 102°15', contains four molecules. The method of isomorphous replacement has been used in an investigation of the centrosymmetric b -axis projection in which it has been possible to determine signs for nearly all the h0l reflexions having spacings greater than 4Å. Three independent heavy-atom derivatives were employed and the signs so determined have been used to compute a map of the electron density projected on the (010) plane. This projection has been interpreted in terms of the molecule of sperm-whale myoglobin, as deduced by Bodo, Dintzis, Kendrew & Wyckoff (1959) from a three-dimensional Fourier synthesis to 6Å resolution. The results of the interpretation show that the two myoglobin molecules are very similar in form (tertiary structure) in spite of the differences in their amino-acid composition. The relative orientation of the two unit cells with respect to the myoglobin molecule is given and a comparison is made of the positions of the heavy atoms in each molecule.

Measurement of Angular Acceleration of a Rigid Body Using Linear Accelerometers

1975 ◽  
Vol 42 (3) ◽  
pp. 552-556 ◽  
Author(s):  
A. J. Padgaonkar ◽  
K. W. Krieger ◽  
A. I. King
Keyword(s):  
Experimental Data ◽  
Rigid Body ◽  
Simple Procedure ◽  
Three Dimensional ◽  
Angular Acceleration ◽  
Theory And Practice ◽  
Body Segments ◽  
Impact Biomechanics ◽  
The Stability ◽  
Definition Of

The computation of angular acceleration of a rigid body from measured linear accelerations is a simple procedure, based on well-known kinematic principles. It can be shown that, in theory, a minimum of six linear accelerometers are required for a complete definition of the kinematics of a rigid body. However, recent attempts in impact biomechanics to determine general three-dimensional motion of body segments were unsuccessful when only six accelerometers were used. This paper demonstrates the cause for this inconsistency between theory and practice and specifies the conditions under which the method fails. In addition, an alternate method based on a special nine-accelerometer configuration is proposed. The stability and superiority of this approach are shown by the use of hypothetical as well as experimental data.

Inelastic scattering of interstellar silyl cyanide (SiH3CN) by helium atoms : cross-sections and rate coefficients for A- and E-SiH3CN

2021 ◽  
Vol 507 (4) ◽  
pp. 5264-5271
Author(s):  
Manel Naouai ◽  
Abdelhak Jrad ◽  
Ayda Badri ◽  
Faouzi Najar
Keyword(s):  
Inelastic Scattering ◽  
Total Energy ◽  
Cross Sections ◽  
Three Dimensional ◽  
Basis Set ◽  
Rate Coefficients ◽  
Close Coupling ◽  
Explicitly Correlated ◽  
Correlation Consistent ◽  
Triple Excitation

ABSTRACT Rotational inelastic scattering of silyl cyanide (SiH3CN) molecule with helium (He) atoms is investigated. Three-dimensional potential energy surface (3D-PES) for the SiH3CN–He interacting system is carried out. The ab initio 3D-PES is computed using explicitly correlated coupled cluster approach with single, double, and perturbative triple excitation CCSD(T)-F12a connected to augmented-correlation consistent-polarized valence triple zeta Gaussian basis set. A global minimum at (R = 6.35 bohr; θ = 90○; ϕ = 60○) with a well depth of 52.99 cm−1 is pointed out. Inelastic rotational cross-sections are emphasized for the 22 first rotational levels for total energy up to 500 cm−1 via close coupling (CC) approach in the case of A-SiH3CN and for the 24 first rotational levels for total energy up to 100 cm−1 via CC and from 100 to 500 cm−1 via coupled states (CS) in the case of E-SiH3CN. Rate coefficients are derived for temperature until 80 K for both A- and E-SiH3CN–He systems. Propensity rules are obtained for |ΔJ| = 2 processes with broken parity for A-SiH3CN and for |ΔJ| = 2 processes with |ΔK| = 0 and unbroken parity for E-SiH3CN.

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