17 materials found
Resource type:
slides
Collection of photon science slides
No short description available.
Resource type: Moodle course, e-learning, slides
Collection of photon science slides
https://pan-learning.org/moodle/course/view.php?id=82
https://pan-training.eu/materials/collection-of-photon-science-slides
No short description available.
Neutrons for Magnetic Nanostructures on Surfaces: Beyond the Specular Intensity Wars
Polarized Neutron Reflectometry (PNR) is a great method to study magnetism of surface near structures on the nm scale. It is especially useful for functional materials and fundamentals of nano magnetism. The applications of the technique and the related grazing incidence scattering include...
Scientific topics: polarized neutron reflectometry, grazing incidence small angle neutron scattering
Keywords: polarized neutron reflectometry, grazing incidence scattering, magnetic nanoparticles, GISANS
Resource type: video, slides
Neutrons for Magnetic Nanostructures on Surfaces: Beyond the Specular Intensity Wars
https://www.youtube.com/watch?v=7qTk8FjmQmo
https://pan-training.eu/materials/neutrons-for-magnetic-nanostructures-on-surfaces-beyond-the-specular-intensity-wars
Polarized Neutron Reflectometry (PNR) is a great method to study magnetism of surface near structures on the nm scale. It is especially useful for functional materials and fundamentals of nano magnetism. The applications of the technique and the related grazing incidence scattering include multiferroic heterostructures, correlated electron systems, exchange bias, superconductors, magnetic nanoparticles and spin textures like skyrmions. Many of these systems have in common that the sample sizes are small, leading to intensity limited experiments. [...]
polarized neutron reflectometry
grazing incidence small angle neutron scattering
polarized neutron reflectometry, grazing incidence scattering, magnetic nanoparticles, GISANS
Seeing the chemistry in biology using neutron crystallography
New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while...
Keywords: macromolecular neutron crystallography, biological macromolecules, neutron
Resource type: video, slides, scientific article
Seeing the chemistry in biology using neutron crystallography
https://www.youtube.com/watch?v=eL63fo5O-vk
https://pan-training.eu/materials/seeing-the-chemistry-in-biology-using-neutron-crystallography
New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged from recent neutron structures; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.
macromolecular neutron crystallography, biological macromolecules, neutron
Neutron crystallography to inform drug design targeting SARS-CoV-2 main protease
Talk from one of the ILL colloqia. See colloquia list at the bottom for other talks.
COVID-19, caused by SARS-CoV-2, remains a global health threat after two years of the pandemic even with available vaccines and therapeutic options. The viral main protease (Mpro) is indispensable for the...
Keywords: COVID research, neutron, drug development, neutron crystallography
Resource type: video, slides
Neutron crystallography to inform drug design targeting SARS-CoV-2 main protease
https://www.youtube.com/watch?v=G-vPWwh5NKs
https://pan-training.eu/materials/neutron-crystallography-to-inform-drug-design-targeting-sars-cov-2-main-protease
Talk from one of the ILL colloqia. See colloquia list at the bottom for other talks.
COVID-19, caused by SARS-CoV-2, remains a global health threat after two years of the pandemic even with available vaccines and therapeutic options. The viral main protease (Mpro) is indispensable for the virus replication and thus is an important target for small-molecule antivirals. Computer-assisted and structure-based drug design strategies rely on atomic scale understanding of the target biomacromolecule traditionally derived from X-ray crystallographic data collected at cryogenic temperatures. Conventional protein X-ray crystallography is limited by possible cryo-artifacts and its inability to locate the functional hydrogen atoms crucial for understanding chemistry occurring in enzyme active sites. Neutrons are ideal probes to observe the protonation states of ionizable amino acids at near-physiological temperature, directly determining their electric charges – crucial information for drug design. Our room-temperature X-ray crystal structures of Mpro brought rapid insights into the reactivity of the catalytic cysteine, malleability of the active site, and binding modes with clinical protease inhibitors. The neutron crystal structures of ligand-free and inhibitor-bound Mpro were determined allowing the direct observation of protonation states of all residues in a coronavirus protein for the first time [1,2]. At rest, the catalytic Cys-His dyad exists in the reactive zwitterionic state (Fig. 1), with both Cys145 and His41 charged, instead of the anticipated neutral state. Covalent inhibitor binding results in modulation of the protonation states. This information was used to design nanomolar hybrid reversible covalent inhibitors with robust antiviral properties. High-throughput virtual screening, utilizing ORNL’s supercomputing capabilities, in conjunction with in vitro assays identified a lead noncovalent compound with sub-micromolar affinity. The neutron structure of Mpro in complex with the noncovalent inhibitor was used in a structure-activity relationship (SAR) study guided by virtual reality structure analysis to novel Mpro inhibitors with imporved affinity to the enzyme [3]. Our research is providing real-time data for atomistic design and discovery of Mpro inhibitors to combat the COVID-19 pandemic and prepare for future threats from pathogenic coronaviruses.
[1] D.W. Kneller et al. Unusual zwitterionic catalytic site of SARS-CoV-2 main protease revealed by neutron crystallography. J. Biol. Chem.295, 17365-17373 (2020).
[2] D.W. Kneller et al. Direct observation of protonation state modulation in SARS-CoV-2 main protease upon inhibitor binding with neutron crystallography. J. Med. Chem.64, 4991-5000 (2021).
[3] D.W. Kneller et al. Structural, electronic and electrostatic determinants for inhibitor binding to subsites S1 and S2 in SARS-CoV-2 main protease. J. Med. Chem.64, 17366-17383 (2021).
The authors acknowledge support by the National Virtual Biotechnology Laboratory, US Department of Energy.
COVID research, neutron, drug development, neutron crystallography
Workshop on Metadata Catalogues
Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022.
Keywords: data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing
Resource type: slides, video
Workshop on Metadata Catalogues
https://zenodo.org/record/6414117
https://pan-training.eu/materials/workshop-on-metadata-catalogues
Presentations from the Workshop on Metadata Catalogues, which took place virtually via Zoom on the 4th April 2022.
data catalogue, SciCat, ICAT, expands, panet, PaNOSC, metadata, data management, data processing
data curator
data managers
research data engineer
ExPaNDS and PaNOSC project members
PaN users
PaN Community
ExPaNDS mid-term review
Slides of the presentations done during the ExPaNDS midterm review.
Keywords: expands
Resource type: slides
ExPaNDS mid-term review
https://indico.desy.de/event/30039/
https://pan-training.eu/materials/expands-mid-term-review
Slides of the presentations done during the ExPaNDS midterm review.
expands
ExPaNDS and PaNOSC project members
DAPHNE4NFDI: Science driven data management solutions for the user community
Slides (and other resources) of the presentations done at this workshop, including a presentation of ICAT and SciCat.
Keywords: ICAT, SciCat, PaNOSC, expands
Resource type: slides
DAPHNE4NFDI: Science driven data management solutions for the user community
https://github.com/ExPaNDS-eu/ExPaNDS/tree/master/WP3/DAPHNE4NFDI_20220124
https://pan-training.eu/materials/daphne4nfdi-science-driven-data-management-solutions-for-the-user-community
Slides (and other resources) of the presentations done at this workshop, including a presentation of ICAT and SciCat.
ICAT, SciCat, PaNOSC, expands
PaN Community
ExPaNDS and PaNOSC project members
PaN users
data curator
data managers
research data engineer
engineers
Persistent Identifiers for Facilities Research Workshop
Our workshop on Persistent Identifiers (PIDs) reflected on practices of PIDs used in facilities research, an update on state-of-the art and recent developments about PIDs elsewhere and discussions around the actual and desired levels of PIDs adoption across facilities research lifecycle.
You...
Keywords: pid, persistent identifiers, expands
Resource type: video, slides
Persistent Identifiers for Facilities Research Workshop
https://vimeo.com/676015892
https://pan-training.eu/materials/persistent-identifiers-for-facilities-research-workshop
Our workshop on Persistent Identifiers (PIDs) reflected on practices of PIDs used in facilities research, an update on state-of-the art and recent developments about PIDs elsewhere and discussions around the actual and desired levels of PIDs adoption across facilities research lifecycle.
You can read our report and view the presentations in the links below.
pid, persistent identifiers, expands
facility staff
Librarian Symposium
Our Librarian Symposium was aimed at librarians and data managers who work with and support PaN science facilities. In particular, the symposium focused on the interface between publications and data. How can we bring these together better for the benefit of all? Where are the gaps? What do we...
Keywords: expands, open data, persistent identifiers, pid, PUMA project, publishing experiments, F-UJI tool, FAIR, FAIR metrics
Resource type: video, slides
Librarian Symposium
https://vimeo.com/675857001
https://pan-training.eu/materials/librarian-symposium-am-session
Our Librarian Symposium was aimed at librarians and data managers who work with and support PaN science facilities. In particular, the symposium focused on the interface between publications and data. How can we bring these together better for the benefit of all? Where are the gaps? What do we need to bridge them?
Watch our video recordings for the AM and PM sessions, you can also find our report and presentations below.
expands, open data, persistent identifiers, pid, PUMA project, publishing experiments, F-UJI tool, FAIR, FAIR metrics
librarians
data managers
data curator
Beamline FAIRness Assessment Presentation
The presentation which took place on the 15th November 2021, organised by the ExPaNDS project where Markus Kubin and Gerrit Guenther gave an overview of "Assessing the FAIRness of a prototypical PaN instrument at BESSY II".
Keywords: BESSY II, FAIR, expands, open data
Resource type: video, slides
Beamline FAIRness Assessment Presentation
https://vimeo.com/647450948
https://pan-training.eu/materials/beamline-fairness-assessment-presentation
The presentation which took place on the 15th November 2021, organised by the ExPaNDS project where Markus Kubin and Gerrit Guenther gave an overview of "Assessing the FAIRness of a prototypical PaN instrument at BESSY II".
BESSY II, FAIR, expands, open data
McStas and McXtrace schools
This repository contains teaching material related to McStas and McXtrace schools 2019-
Keywords: McStas, McXtrace, simulation, neutron simulation, x-ray simulation
Resource type: git, tutorial, slides, e-learning
McStas and McXtrace schools
https://github.com/McStasMcXtrace/Schools
https://pan-training.eu/materials/mcstas-and-mcxtrace-schools
This repository contains teaching material related to McStas and McXtrace schools 2019-
McStas, McXtrace, simulation, neutron simulation, x-ray simulation
PaN Community
beamline users
DOI, FAIR and MX COVID-19 use case
Frank von Delft presents: DOI, FAIR and MX COVID-19 use case at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Keywords: COVID research, FAIR, fragalysis, drug development, XChem, PDB, zenodo
Resource type: video, slides
DOI, FAIR and MX COVID-19 use case
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-Frank-vonDelft-DiamondMX-UseCase.pdf?download=1
https://pan-training.eu/materials/doi-fair-and-mx-covid-19-use-case
Frank von Delft presents: DOI, FAIR and MX COVID-19 use case at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
COVID research, FAIR, fragalysis, drug development, XChem, PDB, zenodo
Machine Learning-based Spectra Classification
Yue Sun presents: Machine Learning-based Spectra Classification at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Scientific topics: spectroscopy
Keywords: machine learning, XFEL, FAIR, large dataset, NeXus, spectroscopy
Resource type: video, slides
Machine Learning-based Spectra Classification
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-YueSun-UseCase.pdf?download=1
https://pan-training.eu/materials/machine-learning-based-spectra-classification
Yue Sun presents: Machine Learning-based Spectra Classification at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
spectroscopy
machine learning, XFEL, FAIR, large dataset, NeXus, spectroscopy
PaN Community
scientists
TELBE data analysis workflow and the PaN training platform UX
Jan-Christoph Deinert presents: TELBE data analysis workflow and the PaN training platform UX at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Keywords: training platform, workflow, TELBE, FAIR, data correction
Resource type: video, slides
TELBE data analysis workflow and the PaN training platform UX
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-JanChristophDeiner-TELBE-UseCase.pdf?download=1
https://pan-training.eu/materials/telbe-data-analysis-workflow-and-the-pan-training-platform-ux
Jan-Christoph Deinert presents: TELBE data analysis workflow and the PaN training platform UX at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
training platform, workflow, TELBE, FAIR, data correction
Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection
Mousumi Upadhyay Kahaly presents: Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Scientific topics: neutron diffraction, inelastic scattering
Keywords: McStas, simulation, inelastic neutron scattering, ab-initio, neutron scattering, neutron, neutron diffraction, defect detection, structural analysis
Resource type: video, slides
Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-MousumiUpadhyayKahaly-UseCase.pdf?download=1
https://pan-training.eu/materials/neutron-diffraction-from-boro-carbon-for-efficient-structural-analysis-and-defect-detection
Mousumi Upadhyay Kahaly presents: Neutron diffraction from Boro-carbon for efficient structural analysis and defect detection at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
neutron diffraction
inelastic scattering
McStas, simulation, inelastic neutron scattering, ab-initio, neutron scattering, neutron, neutron diffraction, defect detection, structural analysis
PaN Community
scientists
Tomography Case Study
Kamel Madi presents: Tomography Case Study at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Keywords: tomography, pid, doi, FAIR, large dataset, 3Dmagination
Resource type: video, slides
Tomography Case Study
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-KamelMadi-3DmaginationAthena.pdf?download=1
https://pan-training.eu/materials/tomography-case-study
Kamel Madi presents: Tomography Case Study at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
tomography, pid, doi, FAIR, large dataset, 3Dmagination
Describe data by scripts for future reuse
Petr Čermák presents: Describe data by scripts for future reuse at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
Keywords: metadata, open data, FAIR, figshare, binder, data processing
Resource type: video, slides
Describe data by scripts for future reuse
https://zenodo.org/record/5636331/files/20211026-PaN-EOSC-Symposium2021-PetrCermak-UseCase.pdf?download=1
https://pan-training.eu/materials/describe-data-by-scripts-for-future-reuse
Petr Čermák presents: Describe data by scripts for future reuse at the 2nd PaNOSC and ExPaNDS PaN EOSC Symposium (October 2021).
metadata, open data, FAIR, figshare, binder, data processing