New analytical scattering-factor functions for free atoms and ions

Metallic glasses with conventional glass-forming ability (Al-Fe-Nd, Fe-Zr-B, Fe-B-Nb compositions) and bulk metallic glasses (Ca-Mg-Cu compositions) were studied by synchrotron X-ray diffraction during annealing throughout glass transition and crystallization temperatures.The analysis of the first diffraction peak position during the annealing process allowed us to follow the free volume change during relaxation and glass transition. The structure factor and the radial distribution function of the glasses were obtained from the X-ray measurements. The structural changes occurred during annealing are analyzed and discussed.

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“…[8,9] compiled in the DABAX data base [10]. The reduced radial distribution function was then obtained by Fourier transformation…”

Section: Methodsmentioning

confidence: 99%

Structural study of conventional and bulk metallic glasses during annealing

Pineda

Hidalgo

Bruna

et al. 2009

Journal of Alloys and Compounds

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“…The sample was sealed in a silica glass tube ͑2 Ϯ 0.05 mm inner diameter and 0.21Ϯ 0.05 mm wall thickness͒, and diffraction patterns of samples in this tube and an empty tube were measured in vacuum in a transmission geometry. The collected data were corrected using a standard program, 21 and the absorption coefficients, 22 incoherent-scattering functions, 23 and atomic scattering factors 24 were used for correction and normalization, leading to the Faber-Ziman total structure factor S͑Q͒. 25 The radial distribution function ͑RDF͒ or pair-correlation function g͑r͒ is the spherically averaged distribution of interatomic vectors,…”

Section: High-energy X-ray Diffractionmentioning

confidence: 99%

Density variations in liquid tellurium: Roles of rings, chains, and cavities

et al. 2010

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Liquid tellurium has been studied by density-functional/molecular-dynamics simulations at 560, 625, 722, and 970 K and by high-energy x-ray diffraction ͑HEXRD͒ at 763 K and 973 K. The HEXRD measurements agree very well with earlier neutron-scattering data of Menelle et al. The density maximum near the melting point ͑722 K͒ reflects the competition between twofold and threefold local coordination, which results in chain formation and changed ring statistics at lower T, and the variation with T of the volume of cavities ͑26-35 % of the total͒. A higher-order gradient expansion of the exchange-correlation functional is needed to describe structural details. Changes in the electronic properties ͑band gap and dc conductivity͒ upon cooling are consistent with a transition from a high-temperature metal to a semiconductor.

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“…First, the model density distribution is calculated using one of the available approximations (Neutron News, 1992;Maslen et al, 1992;Waasmaier & Kirfel, 1995;Grosse--Kunstleve, Sauter et al, 2004;Peng et al, 1996;Peng, 1998). Then a set of Fourier coefficients is calculated from the distribution up to the resolution limit specified by the target map 2 .…”

Section: Model--to--map Target ( !"#" )mentioning

confidence: 99%

Real-space refinement in Phenix for cryo-EM and crystallography

Afonine

Poon

Read

et al. 2018

Preprint

532

640

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SynopsisA description of the implementation of real--space refinement in the phenix.real_space_refine program from the Phenix suite and its application to re--refinement of cryo--EM derived models.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/249607 doi: bioRxiv preprint first posted online Jan. 17, 2018; peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/249607 doi: bioRxiv preprint first posted online Jan. 17, 2018; AbstractThis article describes the implementation of real--space refinement in the phenix.real_space_refine program from the Phenix suite. Use of a simplified refinement target function enables fast calculation, which in turn makes it possible to identify optimal data--restraints weight as part of routine refinements with little runtime cost. Refinement of atomic models against low--resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary--structure and rotamer--specific restraints, as well as restraints or constraints on internal molecular symmetry. Re--refinement of 385 cryo--EM derived models available in the PDB at resolutions of 6 Å or better shows significant improvement of models and the fit of these models to the target maps.

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New analytical scattering-factor functions for free atoms and ions

Cited by 591 publications

References 3 publications

Structural study of conventional and bulk metallic glasses during annealing

Structural study of conventional and bulk metallic glasses during annealing

Density variations in liquid tellurium: Roles of rings, chains, and cavities

Real-space refinement in Phenix for cryo-EM and crystallography

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