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Title: Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots

Abstract

Two independent approaches to calculate the angular distribution of X-ray diffusion scattering from a crystalline medium with spheroidal quantum dots (QDs) have been proposed. The first method is based on the analytical solution involving the multipole expansion of elastic strain fields beyond QDs. The second approach is based on calculations of atomic displacements near QDs by the Green’s function method. An analysis of the diffuse scattering intensity distribution in the reciprocal space within these two approaches shows that both methods yield similar results for the chosen models of QD spatial distribution.

Authors:
;  [1]
  1. Russian Academy of Sciences, Komi Science Center, Ural Branch (Russian Federation)
Publication Date:
OSTI Identifier:
22472330
Resource Type:
Journal Article
Resource Relation:
Journal Name: Crystallography Reports; Journal Volume: 60; Journal Issue: 2; Other Information: Copyright (c) 2015 Pleiades Publishing, Inc.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
United States
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 77 NANOSCIENCE AND NANOTECHNOLOGY; ANALYTICAL SOLUTION; ANGULAR DISTRIBUTION; ATOMIC DISPLACEMENTS; DIFFUSE SCATTERING; DIFFUSION; GREEN FUNCTION; QUANTUM DOTS; SPATIAL DISTRIBUTION; STRAINS; X-RAY DIFFRACTION

Citation Formats

Punegov, V. I., E-mail: vpunegov@dm.komisc.ru, and Sivkov, D. V. Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots. United States: N. p., 2015. Web. doi:10.1134/S1063774515010198.
Punegov, V. I., E-mail: vpunegov@dm.komisc.ru, & Sivkov, D. V. Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots. United States. doi:10.1134/S1063774515010198.
Punegov, V. I., E-mail: vpunegov@dm.komisc.ru, and Sivkov, D. V. Sun . "Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots". United States. doi:10.1134/S1063774515010198.
@article{osti_22472330,
title = {Methods for calculating X-ray diffuse scattering from a crystalline medium with spheroidal quantum dots},
author = {Punegov, V. I., E-mail: vpunegov@dm.komisc.ru and Sivkov, D. V.},
abstractNote = {Two independent approaches to calculate the angular distribution of X-ray diffusion scattering from a crystalline medium with spheroidal quantum dots (QDs) have been proposed. The first method is based on the analytical solution involving the multipole expansion of elastic strain fields beyond QDs. The second approach is based on calculations of atomic displacements near QDs by the Green’s function method. An analysis of the diffuse scattering intensity distribution in the reciprocal space within these two approaches shows that both methods yield similar results for the chosen models of QD spatial distribution.},
doi = {10.1134/S1063774515010198},
journal = {Crystallography Reports},
number = 2,
volume = 60,
place = {United States},
year = {Sun Mar 15 00:00:00 EDT 2015},
month = {Sun Mar 15 00:00:00 EDT 2015}
}
  • No abstract prepared.
  • The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at q=0.28 A ring {sup -1} originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of {alpha}-helix pitch and inter-{beta}-strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involvemore » potentially functional active-site deformations.« less
  • X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less
  • X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. The decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. In conclusion, diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less
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  • X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculationsmore » of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein–solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.« less