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Wide-range X-ray scattering datasets and analyses for all samples described in the 2020 publication "Gold and silver dichroic nanocomposite in the quest for 3D printing the Lycurgus cup". These datasets are composed by combining multiple small-angle x-ray scattering and wide-angle x-ray scattering curves into a single dataset. They have been analyzed using McSAS to extract polydispersities and volume fractions. They have been collected using the MOUSE project (instrument and methodology).
he main objective of the nPSize project is to improve the measurement capabilities for nanoparticle size based on both measurement methods traceable to SI units and new reference materials. Two basic approaches have been used in order to develop measurement procedures resulting in traceable results of the nanoparticle size distribution: physical modelling for the methods used in the project (TSEM, SEM, AFM and SAXS) and machine learning.
Physical modelling: In this part, the physical models associated with different shape measurements for the techniques TSEM, SEM, AFM and SAXS have been collected and further developed with the aim to simulate the resulting signal as measured by the individual methods. Uncertainties and traceability associated with each model were investigated and evaluated. In the following, the progress on these physical models is reported for each individual method.
Machine Learning modelling: The aim of this part is to use machine learning to enable automatic measurement of nanoparticle shape from expert a-priori information only. No physical model will be used as a-priori information in this task.
The accuracy and traceability of the size results obtained by each technique will be analyzed and compared with the physical modelling. A machine learning database will then be used to create automatic detection algorithms.
In recent years, we have come to appreciate the astounding intricacy of the formation process of minerals from ions in aqueous solutions. In this context, a number of studies have revealed that nucleation in the calcium sulfate system is non-classical, involving the aggregation and reorganization of nanosized prenucleation particles. In a recent work we have shown that this particle-mediated nucleation pathway is actually imprinted in the resultant single micron-sized CaSO4 crystals. This property of CaSO4 minerals provides us with an unique opportunity to search for evidence of non-classical nucleation pathways in geological environments. In particular, we focused on the quintessential single crystals of anhydrite extracted from the Naica mine in Mexico. We elucidated the growth history from this mineral sample by mapping growth defects at different length scales. Based on these data we argue that the nano-scale misalignment of the structural sub-units observed in the initial calcium sulfate crystal seed propagate through different length-scales both in morphological, as well as strictly crystallographic aspects, eventually causing the formation of large mesostructured single crystals of anhydrite. Hence, the nanoparticle mediated nucleation mechanism introduces a 'seed of imperfection', which leads to a macroscopic single crystal, in which its fragments do not fit together at different length-scales in a self-similar manner. Consequently, anisotropic voids of various sizes are formed with very well-defined walls/edges. But, at the same time the material retains its essential single crystal nature. These findings shed new light on the longstanding concept of crystal structure.
OpenSCAD, STL and technical drawings for the capillary flow-through cell designed primarily for use with The MOUSE instruments.
This flow-through cell can be used in conjunction with:
- Modular sample holder (10.5281/zenodo.7499416)
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Laser-cut sample holder (10.5281/zenodo.7499437)
Technical drawings and documents for building a compact, heated, vacuum compatible flow-through sample holder. This holder is in use at the BAM MOUSE instrument as well as at the I22 beamline at the Diamond Light Source (see references for instrument details).
This holder has several features:
- The holder can be used in vacuum environments as well as in atmosphere
- It has two G 1/4" UNF fittings to attach HPLC tubing for (optionally) flowing a medium through the sample cell
- There are two additional (unflowed) sample positions for backgrounds and calibrants, held at the same temperature
- The low-mass design coupled with a 250W heating element can achieve heating rates of 1 degree C per second, when coupled (for example) with an Omron E5CC PID controller.
- The sample holder insert can be made from various materials depending on the application. Sealing the sample from the vacuum can be achieved using kapton, teflon or Magic tape, depending on the temperature requirements. The inlet and outlet holes will need to be punctured with a needle to enable flow.
- Large exit cones ensure a clear exit angle of at least 45 degrees two theta.
- It has been tested with temperatures up to 400 degrees C.
- Compression area has been raised and polished to ensure a good vacuum seal.
OpenSCAD, STL and technical drawings for the solid sample rack designed primarily for use with The MOUSE instruments.
This solid sample rack can be used in conjunction with:
- Laser-cut sample holder (10.5281/zenodo.7499437)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
PDF file for the laser-cut sample holder designed primarily for use with The MOUSE instruments.
This sample holder can be used in conjunction with:
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
The SPONGE
(2020)
This dataset is a complete set of raw, processed and analyzed data, complete with Jupiter notebooks, associated with the manuscript mentioned in the title.
In the manuscript, we provide a "systems architecture"-like overview and detailed discussions of the methodological and instrumental components that, together, comprise the "MOUSE" project (Methodology Optimization for Ultrafine Structure Exploration). Through this project, we aim to provide a comprehensive methodology for obtaining the highest quality X-ray scattering information (at small and wide angles) from measurements on materials science samples.
This paper reports a systematic study into the effect of different biomass-derived precursors on the structure and porosity of carbons prepared via catalytic graphitization. Glucose, starch and cellulose are combined with iron nitrate and heated under a nitrogen atmosphere to produce Fe3C nanoparticles, which catalyze the conversion of amorphous carbon to graphitic nanostructures. The choice of organic precursor provides a means of controlling the catalyst particle size, which has a direct effect on the porosity of the material. Cellulose and glucose produce mesoporous carbons, while starch produces a mixture of micro- and mesopores under the same conditions and proceeds via a much slower graphitization step, generating a mixture of graphitic nanostructures and turbostratic carbon. Porous carbons are critical to energy applications such as batteries and electrocatalytic processes. For These applications, a simple and sustainable route to those carbons is essential. Therefore, the ability to control the precise structure of a biomass-derived carbon simply through the choice of precursor will enable the production of a new generation of energy materials.
This dataset is a complete set of raw, processed and analyzed data, associated with the manuscript mentioned in the title.
All associated metadata and processing history has been added. Particle size distribution analyses using McSAS are included as well.
The samples consisted of a 4.2 mass% dispersion of yttria-stabilized zirconia nanoparticles in a cross-linked matrix. The measurements show a good dispersion with minimal agglomeration. The wide-angle region shows diffraction information consistent with zirconia.
OpenSCAD, STL and technical drawings for the Modular sample holder designed primarily for use with The MOUSE instruments.
This modular sample holder can be used in conjunction with the following:
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Laser-cut sample holder (10.5281/zenodo.7499437)
X-ray scattering datasets for samples described in the 2020 publication "Molecular Dynamics of Janus Polynorbornenes: Glass Transitions and Nanophase Separation". This dataset includes both raw and processed X-ray scattering data for samples PTCHSiO-Pr, Bu, Hx, Oc and De, alongside background measurements files (BKG). This data was collected using the MOUSE project (instrument and methodology).
X-ray scattering datasets for samples described in the 2022 publication "Molecular Mobility of Polynorbornenes with Trimethylsiloxysilyl side groups: Influence of the Polymerization Mechanism". This dataset includes both raw and processed X-ray scattering data for samples APTCN and MPTCN, alongside background measurements files (BKG).
X-ray scattering datasets for samples described in the 2022 publication "Side chain length dependent dynamics and conductivity in self assembled ion channels". This dataset includes both raw and processed X-ray scattering data for samples ILC8, ILC10, ILC12, ILC14 and ILC16 alongside background measurement files (BKG).
These are four datasets that were made available to the participants of the Small-angle Scattering data analysis round robin. The intent was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset.
In this repository, there are:
1) a PDF document with more details for the study,
2) the datasets for people to try and fit
3) an Excel spreadsheet to document the results.
Datasets 1 and 2 were modified from: Deumer, Jerome, & Gollwitzer, Christian. (2022). npSize_SAXS_data_PTB (Version 5) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5886834
Datasets 3 and 4 were collected in-house on the MOUSE instrument.
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is on the same scale as the scattering intensity, may offer a novel pathway for determining the degree of crystallinity.
The "Ultima Ratio" strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from Q < 0.01 1/nm up to Q < 150 1/nm, with a resolution of 0.16 Angstrom. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to 8000^3 voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-Q behaviour. The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder. While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts.
## Summary:
This notebook and associated datasets (including VASP details) accompany a manuscript available on the ArXiv (https://doi.org/10.48550/arXiv.2303.13435) and hopefully soon in a journal as short communication as well. Most of the details needed to understand this notebook are explained in that paper with the same title as above. For convenience, the abstract is repeated here:
## Paper abstract:
We demonstrate a strategy for simulating wide-range X-ray scattering patterns, which spans the small- and wide scattering angles as well as the scattering angles typically used for Pair Distribution Function (PDF) analysis. Such simulated patterns can be used to test holistic analysis models, and, since the diffraction intensity is presented coupled to the scattering intensity, may offer a novel pathway for determining the degree of crystallinity.
The ``Ultima Ratio'' strategy is demonstrated on a 64-nm Metal Organic Framework (MOF) particle, calculated from $Q<0.01$\,$\mathrm{nm}^{-1}$ up to $Q\approx150$\,$\mathrm{nm}^{-1}$, with a resolution of 0.16\,\AA. The computations exploit a modified 3D Fast Fourier Transform (3D-FFT), whose modifications enable the transformations of matrices at least up to $8000^3$ voxels in size. Multiple of these modified 3D-FFTs are combined to improve the low-$Q$ behaviour.
The resulting curve is compared to a wide-range scattering pattern measured on a polydisperse MOF powder.
While computationally intensive, the approach is expected to be useful for simulating scattering from a wide range of realistic, complex structures, from (poly-)crystalline particles to hierarchical, multicomponent structures such as viruses and catalysts.
Electric Safety Interlock
(2023)
This interlock is designed to prevent electrical shock from high voltage (>60V) equipment.
While the general safety interlock can be generically applied, this particular example employs an external vacuum-activated switch. It is for safeguarding human operations inside a vacuum sample chamber while the chamber doors are open. The circuit is closed (output is active) when a sufficient level of vacuum is reached, i.e. when all accessible openings are necessarily closed.
The initial application is to interrupt power to a 220V, 250W heating cartridge (itself mounted inside a small sample holder with potentially exposed contacts) when the sample chamber is open.
The external circuit can be modified to use different interlock mechanisms as needed. Note that the external interlock circuit is only a single circuit (with two signal lines) and thus is not protected against external shorts.
To accomodate a range of safety interlocks, the 4-pin M12 connector is wired as follows: Pin 1 (Brown): +24V for power supply, max current 0.6A Pin 2 (White): Safety interlock system signal 1 (0 or 24V) Pin 3 (Blue) : Safety interlock system signal 2 (0 or 24V) Pin 4 (Black): 0V for power supply
The safety is interlocked (output active) when both signal pins are set high (24V), with sufficient current to activate the two relays. Pin 1 and 4 can be used to power safety hardware (such as light curtains or proximity detectors) with 24VDC up to a current of 0.6A. A larger power supply can be installed when higher currents are needed, while staying within the current limits imposed by the wiring cross-section.
This is a set of use examples for the HDF5Translator framework. This framework lets you translate measurement files into a different (e.g. NeXus-compatible) structure, with some optional checks and conversions on the way. For an in-depth look at what it does, there is a blog post here.
The use examples provided herein are each accompanied by the measurement data necessary to test and replicate the conversion. The README.md files in each example show the steps necessary to do the conversion for each.
We encourage those who have used or adapted one or more of these exampes to create their own conversion, to get in touch with us so we may add your example to the set.
Small-angle Scattering Data Analysis Round Robin: anonymized results, figures and Jupyter notebook
(2023)
The intent of this round robin was to find out how comparable results from different researchers are, who analyse exactly the same processed, corrected dataset.
This zip file contains the anonymized results and the jupyter notebook used to do the data processing, analysis and visualisation. Additionally, TEM images of the samples are included
A Round Robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions, and two from powders.
Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population mean entries within 1.5 % and half of the population width entries within 40 %, respectively. Due to the added complexity of the structure factor, much fewer people submitted answers on the powder datasets.
For those that did, half of the entries for the means and widths were within 44 % and 86 % respectively. This Round Robin experiment highlights several causes for the discrepancies, for which solutions are proposed.
Ultra-SAXS can enhance the capabilities of existing SAXS/WAXS beamlines and laboratory instruments. A compact Ultra-SAXS module has been developed, which extends the measurable q-range with 0:0015 < q 1/nm) < 0:2, allowing structural dimensions between 30 < D(nm) < 4000 to be probed in addition to the range covered by a high-end SAXS/WAXS instrument. By shifting the module components in and out on their respective motor stages, SAXS/WAXS measurements can be easily and rapidly interleaved with USAXS measurements.