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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.
By automatically recording as much information as possible in automated laboratory setups, reproducibility and traceability of experiments are vastly improved. This presentation shows what such an approach means for the quality of experiments in an X-ray scattering laboratory and an automated synthesis set-up.
Impact of organic phosphates on the structure and composition of short-range ordered iron nanophases
(2024)
Organic phosphates (OP) are important nutrient components for living cells in natural environments, where they readily interact with ubiquitous iron phases such as hydrous ferric oxide, ferrihydrite (FHY). FHY partakes in many key bio(geo)chemical reactions including iron-mediated carbon storage in soils, or iron-storage in living organisms. However, it is still unknown how OP affects the formation, structure and properties of FHY. Here, we document how β-glycerophosphate (GP), a model OP ligand, affects the structure and properties of GP–FHY nanoparticles synthesized by coprecipitation at variable nominal molar P/Fe ratios (0.01 to 0.5). All GP–FHY precipitates were characterized by a maximum solid P/Fe ratio of 0.22, irrespective of the nominal P/Fe ratio. With increasing nominal P/Fe ratio, the specific surface area of the GP–FHY precipitates decreased sharply from 290 to 3 m2 g−1, accompanied by the collapse of their pore structure. The Fe–P local bonding environment gradually transitioned from a bidentate binuclear geometry at low P/Fe ratios to monodentate mononuclear geometry at high P/Fe ratios. This transition was accompanied by a decrease in coordination number of edge-sharing Fe polyhedra, and the loss of the corner-sharing Fe polyhedra. We show that Fe(III) polymerization is impeded by GP, and that the GP–FHY structure is highly dependent on the P/Fe ratio. We discuss the role that natural OP-bearing Fe(III) nanophases have in biogeochemical reactions between Fe–P and C species in aquatic systems.
This presentation highlights ongoing scientific misconduct as found in academic literature. This includes data- and image manipulation, and paper mills. Starting with an expose of examples, it delves deeper into the causes and metrics driving this phenomenon. Finally a range of possible tools is presented, that the young researcher can use to prevent themselves from sliding into the dark scientific methods.
Trinamic TMCL IOC is a Python package designed for controlling stepper motors connected to a Trinamic board using the TMCL language (all boards supported by PyTrinamic should now work, has been tested on the TMCM 6110 and the TMCM 6214). Since it is implementing the TMCL protocol, it should be easy to adapt to other Trinamic motor controller boards. This package assumes the motor controller is connected over a machine network via a network-to-serial converter, but the underlying PyTrinamic package allows for other connections too.
This allows the control of attached motors via the EPICS Channel-Access virtual communications bus. If EPICS is not desired, plain Pythonic control via motion_control should also be possible. An example for this will be provided in the example.ipynb Jupyter notebook.
This package leverages Caproto for EPICS IOCs and a modified PyTrinamic library for the motor board control, and interfaces between the two via an internal set of dataclasses. Configuration for the motors and boards are loaded from YAML files (see tests/testdata/example_config.yaml).
The modifications to PyTrinamic involved extending their library with a socket interface. This was a minor modification that should eventually find its way into the official package (a pull request has been submitted).