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Related Concept Videos

Atomic Absorption Spectroscopy: Instrumentation01:22

Atomic Absorption Spectroscopy: Instrumentation

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An atomic absorption spectrophotometer (AAS) comprises several components: a radiation source, an atomizer, a monochromator, and a detector. The radiation source can be a hollow-cathode lamp (HCL) or an electrodeless-discharge lamp (EDL), both of which provide a narrow emission line of the required wavelength. However, some instruments use continuum sources and high-resolution monochromators to achieve a narrow range of radiation.
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X-ray Crystallography02:18

X-ray Crystallography

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The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...
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Atomic Absorption Spectroscopy: Overview01:27

Atomic Absorption Spectroscopy: Overview

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Atomic absorption spectroscopy (AAS) is a technique used to analyze elements by measuring electromagnetic radiation (EMR) absorbed by atoms, which causes them to transition to a higher-energy orbit. The most crucial step in AAS is atomization, where the analyte is converted into gas-phase atoms, typically through a flame or furnace. Some of these atoms become thermally excited in the flame, while most remain in the ground state.
When irradiated by EMR of a particular wavelength, these...
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Atomic Absorption Spectroscopy: Atomization Methods01:25

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Atomic Absorption Spectroscopy (AAS) atomizes samples through flame atomization or electrothermal atomization. Flame atomization typically involves a nebulizer and spray chamber assembly to combine the sample with a fuel–oxidant mixture, creating a fine aerosol mist that enters a burner. Typically, the fuel and oxidant are combined in an approximately stoichiometric ratio. However, for atoms that are easily oxidized, a fuel-rich mixture may be more advantageous. Only about 5% of the...
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X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal...
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Atomic Absorption Spectroscopy: Interference01:25

Atomic Absorption Spectroscopy: Interference

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Interference leads to systematic error in atomic absorption (AA) measurements by enhancing or diminishing the analytical signal or the background. These interferences can be grouped into three main categories: spectral interference, chemical interference, and physical interference.
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AnACor2.0: a GPU-accelerated open-source software package for analytical absorption corrections in X-ray

Yishun Lu1, Karel Adámek1, Tihana Stefanic2

  • 1Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, OxfordOX1 3QG, United Kingdom.

Journal of Applied Crystallography
|December 4, 2024
PubMed
Summary
This summary is machine-generated.

Analytical absorption corrections are crucial for crystallography. The AnACor2.0 software package significantly accelerates these calculations using novel ray-tracing and sampling methods, reducing computation time by up to 175x.

Keywords:
CUDA accelerationabsorption correctionlong-wavelength crystallographyray-tracingsoftware

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Area of Science:

  • Crystallography and Materials Science
  • Computational Science and Engineering

Background:

  • Analytical absorption corrections are essential for processing diffraction data from highly absorbing crystalline samples, particularly in long-wavelength crystallography.
  • Traditional empirical corrections are often inadequate, and existing analytical methods can be computationally intensive due to ray-tracing complexities.

Purpose of the Study:

  • To develop and evaluate AnACor2.0, an accelerated software package for calculating analytical absorption corrections.
  • To significantly reduce the computational time required for absorption correction calculations without compromising accuracy.

Main Methods:

  • AnACor2.0 employs ray-tracing of X-ray paths through a voxelized 3D sample model.
  • Acceleration is achieved through systematic sampling of crystal voxels and modifications to standard ray-tracing algorithms.
  • The bisection method (reducing complexity to O(log2 n)) and gridding with interpolation are utilized, alongside optimized CUDA implementations for NVIDIA GPUs.

Main Results:

  • Execution time for analytical absorption corrections was reduced by up to 175x compared to previous methods.
  • Absorption factor calculations for datasets like insulin were completed in under 10 seconds.
  • Systematic sampling yielded accurate results with minimal variance (mean difference ≤ 2% for absorption factors, ≤ 1% for anomalous peak heights).

Conclusions:

  • AnACor2.0 effectively refines and accelerates the analytical absorption correction process.
  • Innovative sampling and computational techniques ensure high efficiency and accuracy for crystallographic data analysis.
  • The software provides a significant advancement for handling highly absorbing samples in X-ray diffraction studies.