• Issue

    Journal of Applied Crystallography: Volume 56, Issue 4

    910-1312
    August 2023

research papers

Open Access

AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank

  • Pages: 910-926
  • First Published: 20 July 2023
AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank

A rapid ensemble modelling method that optimizes the fit to the small-angle X-ray scattering (SAXS)-derived pair-wise distance distribution function [P(r) versus r] and the measured intensity profile [I(q) versus q] has been used to account for differences between AlphaFold-predicted and experimental SAXS profiles. By considering the confidence levels that come with the predicted structures, a conformational ensemble with potentially flexible linkers between stable folded domains can be optimized to provide representative structures.

Novel methodology to determine thermal properties of nanoparticles exclusively based on SAXS measurements applied to Bi nanocrystals and nanodroplets in a glass matrix

  • Pages: 927-938
  • First Published: 16 June 2023
Novel methodology to determine thermal properties of nanoparticles exclusively based on SAXS measurements applied to Bi nanocrystals and nanodroplets in a glass matrix

A novel methodology using solely small-angle X-ray scattering (SAXS) measurements at multiple temperatures is proposed to determine the coefficients of thermal expansion of confined spherical nanocrystals and/or nanodroplets and the radius dependence of the melting temperature of spherical nanocrystals.

Open Access

Small-angle X-ray scattering in the era of fourth-generation light sources

  • Pages: 939-946
  • First Published: 23 June 2023
Small-angle X-ray scattering in the era of fourth-generation light sources

This article presents some representative examples illustrating the performance of small-angle X-ray scattering and X-ray photon correlation spectroscopy methods with the Extremely Brilliant Source at the European Synchrotron Radiation Facility.

Open Access

Extended Q-range small-angle neutron scattering to understand the morphology of proton-exchange membranes: the case of the functionalized syndiotactic-polystyrene model system

  • Pages: 947-960
  • First Published: 25 July 2023
Extended Q-range small-angle neutron scattering to understand the morphology of proton-exchange membranes: the case of the functionalized syndiotactic-polystyrene model system

Semi-crystalline polymers present a hierarchical organization of structural levels from ångströms to hundreds of nanometres. By combining small- and wide-angle neutron scattering at the same instrument, such complex morphologies can be resolved under application of relevant humidity and temperature conditions.

Open Access

Implication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures

  • Pages: 961-966
  • First Published: 16 June 2023
Implication of the double-gating mode in a hybrid photon counting detector for measurements of transient heat conduction in GaAs/AlAs superlattice structures

Use of the double-gating mode implemented on the modern hybrid photon counting system EIGER2 helps to suppress the influence of beam fluctuations in pump–probe experiments at synchrotron radiation facilities and provides better data quality.

Open Access

In situ biaxial loading and multi-scale deformation measurements of nanostructured materials at the CoSAXS beamline at MAX IV Laboratory

  • Pages: 967-975
  • First Published: 30 June 2023
In situ biaxial loading and multi-scale deformation measurements of nanostructured materials at the CoSAXS beamline at MAX IV Laboratory

A novel biaxial tensile tester designed to work in combination with 2D synchrotron-based scanning small- and wide-angle X-ray scattering and digital image correlation is described. The available biaxial modes and a proposed sample geometry are discussed.

Microstructural changes in building materials after various consolidation treatments studied by small-angle neutron scattering, mercury intrusion porosimetry and scanning electron microscopy

  • Pages: 976-987
  • First Published: 14 July 2023
Microstructural changes in building materials after various consolidation treatments studied by small-angle neutron scattering, mercury intrusion porosimetry and scanning electron microscopy

Small-angle neutron scattering is used to characterize the microstructural changes in building materials treated by various specialist consolidating agents.

Open Access

Revealing cholesterol effects on PEGylated HSPC liposomes using AF4–MALS and simultaneous small- and wide-angle X-ray scattering

  • Pages: 988-993
  • First Published: 25 July 2023
Revealing cholesterol effects on PEGylated HSPC liposomes using AF4–MALS and simultaneous small- and wide-angle X-ray scattering

Small- and wide-angle X-ray scattering and asymmetric flow field-flow fractionation integrated with multi-angle light scattering (AF4–MALS) are used to characterize PEGylated liposomes of hydrogenated soy phosphatidylcholine (HSPC) that have potential for drug delivery. Observed local and global structural changes of the phospholipid bilayers reveal the effects of cholesterol on PEGylated HSPC liposomes.

Open Access

Upgraded D22 SEC–SANS setup dedicated to the biology community

  • Pages: 994-1001
  • First Published: 12 June 2023
Upgraded D22 SEC–SANS setup dedicated to the biology community

This publication describes the stable version of a liquid chromatography system combined with the small-angle neutron scattering (SANS) instrument D22 at Institut Laue–Langevin to run size-exclusion chromatography (SEC) immediately before SANS measurement.

Open Access

Alterations promoted by acid straightening and/or bleaching in hair microstructures

  • Pages: 1002-1014
  • First Published: 01 August 2023
Alterations promoted by acid straightening and/or bleaching in hair microstructures

A systematic investigation on alterations promoted by acid straightening and/or bleaching in hair microstructures is presented. By combining X-ray scattering methods and microcomputed tomography, among several other methods, innovative results were obtained on the structure and thermodynamics of human hair subjected to cosmetic procedures.

Water distribution in human hair microstructure elucidated by spin contrast variation small-angle neutron scattering

  • Pages: 1015-1031
  • First Published: 30 June 2023
Water distribution in human hair microstructure elucidated by spin contrast variation small-angle neutron scattering

Contrast variation small-angle neutron scattering by dynamic nuclear polarization is applied to the study of human hair microstructure.

Open Access

Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography

  • Pages: 1038-1045
  • First Published: 12 June 2023
Mix-and-extrude: high-viscosity sample injection towards time-resolved protein crystallography

3D-printed mixing high-viscosity extruder devices address time-resolved membrane protein crystallography challenges via compact dual-flow lipidic cubic phase injection.

Open Access

Robust phase determination in complex solid solutions using diffuse multiple scattering

  • Pages: 1046-1050
  • First Published: 12 June 2023
Robust phase determination in complex solid solutions using diffuse multiple scattering

A new fingerprinting methodology is presented for phase discrimination in complex solid solutions near the morphotropic phase boundary.

Exploring the impact of incoherent Compton scattering on X-ray pair distribution function analysis of disordered materials

  • Pages: 1051-1056
  • First Published: 16 June 2023
Exploring the impact of incoherent Compton scattering on X-ray pair distribution function analysis of disordered materials

This paper discusses the effects of incoherent Compton scattering and fluorescence on X-ray pair distribution function analysis and shows that a noise-to-signal ratio of approximately 1% is the minimum threshold for satisfactory results when analyzing disordered structures with a high Qmax.

Open Access

Equilibration of precipitants in a counter-diffusion apparatus for protein crystallization

  • Pages: 1057-1065
  • First Published: 23 June 2023
Equilibration of precipitants in a counter-diffusion apparatus for protein crystallization

A cost-effective capillary dialysis apparatus (Toledo Capillary Box) was developed for biomacromolecule crystal growth in microgravity and unit gravity environments to provide slow equilibration between the precipitant reservoir and capillary solutions. Analytical and semi-analytical models allow the prediction of precipitant equilibration of capillary and reservoir solutions under diffusion-controlled transport and show good agreement with experimental results.

Open Access

In situ neutron diffraction to investigate the solid-state synthesis of Ni-rich cathode materials

  • Pages: 1066-1075
  • First Published: 23 June 2023
In situ neutron diffraction to investigate the solid-state synthesis of Ni-rich cathode materials

In situ neutron diffraction is demonstrated as a suitable technique to track phase evolution during synthesis of layered oxide compounds. The synthesis of a series of cathode materials for Li-ion batteries with different Ni/Mn ratio is investigated, in batches comparable to standard laboratory conditions, demonstrating the delayed onset of lithiation with increasing Mn content.

Open Access

Texture-based residual stress analysis of laser powder bed fused Inconel 718 parts

  • Pages: 1076-1090
  • First Published: 30 June 2023
Texture-based residual stress analysis of laser powder bed fused Inconel 718 parts

In this article, a texture-based characterization of surface, sub-surface and bulk residual stress in laser powder bed fused Inconel 718 alloy is carried out. It is shown that, in the case of this nickel-based superalloy, the texture affects the residual stress determination only when it has sufficient strength.

First-principles study on the electronic structure of siligraphene on a ZnO monolayer

  • Pages: 1091-1098
  • First Published: 30 June 2023
First-principles study on the electronic structure of siligraphene on a ZnO monolayer

New heterostructures of ZnO monolayers and siligraphene with tunable band gaps for various applications are reported.

Particle-size polydispersity analysis based on the unified exponential/power-law approach to small-angle scattering

  • Pages: 1099-1107
  • First Published: 30 June 2023
Particle-size polydispersity analysis based on the unified exponential/power-law approach to small-angle scattering

This article introduces a generalized approach to determine polydispersity characteristics from small-angle scattering analysis based on the Beaucage model without numerical integration of experimental data.

Orientation mapping of YbSn3 single crystals based on Bragg-dip analysis using a delay-line superconducting sensor

  • Pages: 1108-1113
  • First Published: 14 July 2023
Orientation mapping of YbSn3 single crystals based on Bragg-dip analysis using a delay-line superconducting sensor

It is demonstrated that a newly developed superconducting neutron detector, called a current-biased kinetic inductance detector, can be used for crystal orientation mapping based on the Bragg dips observed in a neutron transmission spectrum. The neutron transmission spectra of YbSn3 single crystals were observed up to 100 eV, and crystal orientations were determined.

Open Access

Insights into the precipitation kinetics of CaCO3 particles in the presence of polystyrene sulfonate using in situ small-angle X-ray scattering

  • Pages: 1114-1124
  • First Published: 14 July 2023
Insights into the precipitation kinetics of CaCO3 particles in the presence of polystyrene sulfonate using in situ small-angle X-ray scattering

The kinetics of precipitation of CaCO3 particles in the presence of polystyrene sulfonate was studied by small- and wide-angle X-ray scattering. Employment of the Porod invariant and the Hurd–Flower model provides essential information on the kinetics.

Structure evolution of Bi4O7 under high pressure

  • Pages: 1125-1130
  • First Published: 20 July 2023
Structure evolution of Bi4O7 under high pressure

Two isostructural phase transitions were observed for Bi4O7 during compression under high pressure. The pressure–volume curve was found to be discontinuous at the two pressure transition boundaries. Fitting the curves of the three different stages revealed large differences in the bulk moduli, confirming the two isostructural phase changes.

Open Access

Combining synchrotron X-ray diffraction, mechanistic modeling and machine learning for in situ subsurface temperature quantification during laser melting

  • Pages: 1131-1143
  • First Published: 20 July 2023
Combining synchrotron X-ray diffraction, mechanistic modeling and machine learning for in situ subsurface temperature quantification during laser melting

A new methodology is demonstrated for analyzing spatial temperature distributions using modeling and machine learning. The method is applied to X-ray data gathered during in situ laser melting.

Open Access

Representative volume elements of strain/stress fields measured by diffraction techniques

  • Pages: 1144-1167
  • First Published: 20 July 2023
Representative volume elements of strain/stress fields measured by diffraction techniques

Representative volume elements for diffraction-based stress/strain distributions in polycrystalline materials are compared with direct-space values of these quantities using numerical modelling. The results indicate that these volumes and their stress states are equivalent under very specific conditions.

Quantifying molecular deformation in polymer melts by a generalized Zimm plot approach

  • Pages: 1168-1179
  • First Published: 25 July 2023
Quantifying molecular deformation in polymer melts by a generalized Zimm plot approach

A generalized Zimm plot approach is outlined for quantifying molecular deformation of polymer melts. Combined with the spherical harmonic expansion technique, the proposed method provides several benefits for understanding the small-angle neutron scattering spectra of deformed polymers, including a tensorial extension of the Guinier law and direct visualization of spatially dependent deformation.

Design of multi-shell nested fully annular quasi-ellipsoidal focusing mirrors for small-angle neutron scattering

  • Pages: 1180-1191
  • First Published: 25 July 2023
Design of multi-shell nested fully annular quasi-ellipsoidal focusing mirrors for small-angle neutron scattering

This study describes ten-shell nested fully annular quasi-ellipsoidal focusing mirrors with an m = 3 Ni/Ti supermirror coating for small-angle neutron scattering. The proposed mirrors have been developed to gain enough neutrons on a sample for the specified minimum wavevector transfer Q and the results demonstrate adaptability for instruments with changeable sources.

Symmetry-mode analysis for local structure investigations using pair distribution function data

  • Pages: 1192-1199
  • First Published: 25 July 2023
Symmetry-mode analysis for local structure investigations using pair distribution function data

Symmetry-mode analysis is used to detect and characterize structural distortions from pair distribution function data by refining mode amplitudes directly. This approach is successfully applied to a subtle but long-range distortion in TiSe2 and also to a large but highly localized distortion in MnTe. Two new open-source Python packages, isopydistort and isopytools, were used to carry out this analysis within the open-source DiffPy framework.

Open Access

Progress in detection of and correction for low-energy contamination

  • Pages: 1200-1220
  • First Published: 25 July 2023
Progress in detection of and correction for low-energy contamination

A new robust indicator for low-energy contamination is presented and applied to experimental data. The standard correction procedure for low-energy contamination is improved.

Open Access

Towards scanning nanostructure X-ray microscopy

  • Pages: 1221-1228
  • First Published: 28 July 2023
Towards scanning nanostructure X-ray microscopy

A semi-automated workflow is described for rapid-scanning powder X-ray diffraction and pair distribution function experiments. The software infrastructure saves metadata and raw and analyzed files into a collection stored on the local hard drive for easier reuse.

CrysFieldExplorer: rapid optimization of the crystal field Hamiltonian

  • Pages: 1229-1241
  • First Published: 28 July 2023
CrysFieldExplorer: rapid optimization of the crystal field Hamiltonian

An approach to fast fitting of crystal electric field parameters to any experimental data is presented. This approach is implemented in a lightweight Python-based program, CrysFieldExplorer.

Open Access

In situ neutron diffraction for analysing complex coarse-grained functional materials

  • Pages: 1242-1251
  • First Published: 01 August 2023
In situ neutron diffraction for analysing complex coarse-grained functional materials

This work reports in situ neutron diffraction experiments on a broad range of grain sizes of barium titanate. The study reveals the grain-size-dependent strain mechanisms and shows the competitiveness of neutron diffraction with high-resolution synchrotron diffraction.

Design of a three-detector system on LUOSHU: a small-angle neutron scattering instrument at China Mianyang Research Reactor

  • Pages: 1252-1260
  • First Published: 01 August 2023
Design of a three-detector system on LUOSHU: a small-angle neutron scattering instrument at China Mianyang Research Reactor

The LUOSHU small-angle neutron scattering instrument is designed to provide a wide scattering vector magnitude (Q) range of four orders of magnitude by 46 m total length, for studies of nano-particles ranging from the sub-nanometre to the sub-micrometre scale in numerous fields. A high dynamic Q range (Qmax/Qmin) is realized by a unique three-detector system, for better efficiency in experiments. High-flux and high-resolution modes are ensured by two switchable velocity selectors, for more flexibility in different situations.

short communications

Open Access

Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10

  • Pages: 1261-1266
  • First Published: 16 June 2023
Diffraction anisotropy and paired refinement: crystal structure of H33, a protein binder to interleukin 10

The paired refinement procedure was applied on diffraction data from binder H33 corrected for strong diffraction anisotropy.

computer programs

Open Access

TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation

  • Pages: 1267-1276
  • First Published: 14 July 2023
TEMGYM Basic: transmission electron microscopy simulation software for teaching and training of microscope operation

TEMGYM Basic is a Python-based ray-tracing tool for novel experiment visualization and an interactive learning environment for using transmission electron microscopes.

Open Access

MILK: a Python scripting interface to MAUD for automation of Rietveld analysis

  • Pages: 1277-1286
  • First Published: 20 July 2023
MILK: a Python scripting interface to MAUD for automation of Rietveld analysis

The MAUD Interface Language Kit (MILK) provides a Python interface to the Rietveld software MAUD, enabling scriptable refinements. The MILK framework includes parallel computing and folder management which enable high-throughput Rietveld analysis, visualization and validation.

Open Access

Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes

  • Pages: 1287-1294
  • First Published: 28 July 2023
Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes

Shape2SAS allows the user to simulate solution small-angle scattering data and pair distance distributions from user-defined shapes. The program is available as a web application, and is useful for teaching and tutorials, as well as for checking the validity of analytical form factors.

Open Access

Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations

  • Pages: 1295-1303
  • First Published: 28 July 2023
Upgrade of D+ software for hierarchical modeling of X-ray scattering data from complex structures in solution, fibers and single orientations

An upgrade to the D+ software is presented, simulating the 2D scattering pattern from structures with a single orientation or fibers. An upgraded independent D+ Python API is described, including structure factor, polydispersity and several other features.

crystallographers

Jimpei Harada (1931–2023)

  • Pages: 1306-1307
  • First Published: 23 June 2023
Jimpei Harada (1931–2023)

Obituary for Jimpei Harada.