ILL's PhD talks
This YouTube playlist displays the ILL PhD seminars, recorded in winter and spring 2021.
We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Valerie Duchasténier and Steph Monfront.
Scientific topics: neutron scattering, small angle neutron scattering, time-of-flight spectrometry, magnetism technique, neutron time of flight technique
Keywords: neutron scattering theorie, neutron transport , monochromization, polarized neutrons, multi grid detectors, guide fields and solenoids, quasi-elastic neutron scattering, Small Angle Neutron Scattering, time-of-flight, magnetism and neutrons, ultra cold neutrons, Nuclear Physics
Resource type: video
ILL's PhD talks
https://www.youtube.com/playlist?list=PLA2s_idZ6bwFdB-HUrmKllBq7Uhsl3gpX
https://pan-training.eu/materials/ill-s-phd-talks
This YouTube playlist displays the ILL PhD seminars, recorded in winter and spring 2021.
We thank all the speakers who have agreed to have their presentation shared in this collection, curated by Valerie Duchasténier and Steph Monfront.
neutron scattering
small angle neutron scattering
time-of-flight spectrometry
magnetism technique
neutron time of flight technique
neutron scattering theorie, neutron transport , monochromization, polarized neutrons, multi grid detectors, guide fields and solenoids, quasi-elastic neutron scattering, Small Angle Neutron Scattering, time-of-flight, magnetism and neutrons, ultra cold neutrons, Nuclear Physics
PhD students
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
Neutrons4Science: Enter the world of neutrons! Just be curious!
Enter the world of neutrons! They are a powerful and highly acclaimed tool not only for the study of condensed matter (the world we live in) but also for confirming our current understanding of physics. What's more, you don't even need to be a scientist to use Neutrons4Science. Just be...
Keywords: neutron, ILL ThALES, neutron spectrometer, Magnons, gravitational spectrometer, GRANIT
Resource type: tool
Neutrons4Science: Enter the world of neutrons! Just be curious!
https://www.ill.eu/fr/users/support-labs-infrastructure/software-scientific-tools/neutrons4science
https://pan-training.eu/materials/neutrons4science-enter-the-world-of-neutrons-just-be-curious
Enter the world of neutrons! They are a powerful and highly acclaimed tool not only for the study of condensed matter (the world we live in) but also for confirming our current understanding of physics. What's more, you don't even need to be a scientist to use Neutrons4Science. Just be curious!
Neutrons and protons are elementary particles constituting the nucleus of atoms. The neutron has no electric charge but has a spin and a magnetic moment. Neutron beams - like beams of X-rays, electrons or muons - are valuable tools for studying the multitude of materials that surround us in our daily lives (alloys, magnets, superconductors, polymers, colloids, proteins, biological systems, …). However, the way neutrons interact with matter is quite unique and, as a result, it can often reveal to us what is normally hidden. With Neutrons4Science you can discover one of the many types of neutron spectroscopy.
The neutron also answers questions on the very foundations of physics, helping us to solve some of the great mysteries of the universe (Is the Grand Unified Theory valid? Is there a fifth fundamental force? ...) As an example, Neutrons4Science gives you insights to a brand new method of neutron spectroscopy that takes advantage of the quantum states of this light neutral particle.
Neutrons4Science lets you experience neutron science through three interactive 3D animations:
• ThALES: Use a neutron spectrometer (ILL ThALES) as if you were performing a real experiment.
• Magnons: Discover the spin waves that exist inside magnetic materials and understand how ThALES can observe them.
• GRANIT: Discover an innovative gravitational spectrometer (ILL GRANIT) based on neutron quantum states in a gravitational field.
These three educational animations were developed with the help of scientists at the "Institut Laue-Langevin", one of the world's flagship facilities for neutron science.
This project was funded by the ILL and the LPSC and developed by Ipter (out of business since 2015).
neutron, ILL ThALES, neutron spectrometer, Magnons, gravitational spectrometer, GRANIT
general public
vDiffraction: A serious game about diffraction and crystals
#### This game is a fun way to discover the world of crystals and their symmetries through diffraction.
Crystals are all around us: in our environment (rocks and minerals, etc), in our bodies (sugar, bones, gallstones, etc.) and in technology (metals and alloys, silicon and quartz used for...
Scientific topics: crystallography
Keywords: game, diffraction, crystal diffraction, software
Resource type: game
vDiffraction: A serious game about diffraction and crystals
https://www.ill.eu/users/support-labs-infrastructure/software-scientific-tools/vdiffraction
https://pan-training.eu/materials/vdiffraction-a-serious-game-about-diffraction-and-crystals
#### This game is a fun way to discover the world of crystals and their symmetries through diffraction.
Crystals are all around us: in our environment (rocks and minerals, etc), in our bodies (sugar, bones, gallstones, etc.) and in technology (metals and alloys, silicon and quartz used for microelectronics, etc.). By successively discovering the diffraction of X-rays, neutrons and electrons, scientists in the twentieth century threw the door to the microscopic world wide open by demonstrating that crystals are made up of atoms and molecules and explaining their structure.
Crystals are characterised by the fact that their constituents are arranged in a highly ordered structure. This internal order and its symmetry is clearly visible in the diffraction patterns produced by any crystal. It is this symmetry which is also gives crystals their often amazing shapes, making them highly prized by rockhounds.
Whether you are a senior scientist, a student, or just curious about science, vDiffraction is a serious game that will let you try your hand at crystal diffraction so that you can begin to understand how scientists identify the symmetry characteristics of a crystal. This is the first, crucial step towards understanding the atomic and molecular structure of a crystalline material, in other words what type of atoms and molecules make up the crystal and how they are organised.
crystallography
game, diffraction, crystal diffraction, software
Machine learning in electronic-structure theory
Machine Learning approaches are increasingly being used across many fields of science, with electronic structure theory being no exception. They offer novel approaches to age-old problems. In recent years they have been used in construction of trial wavefunctions, in computing Hamiltonians, and...
Keywords: machine learning, electronic-structure theory
Resource type: video
Machine learning in electronic-structure theory
https://www.youtube.com/watch?v=Sgp0w74k9kQ
https://pan-training.eu/materials/machine-learning-in-electronic-structure-theory
Machine Learning approaches are increasingly being used across many fields of science, with electronic structure theory being no exception. They offer novel approaches to age-old problems. In recent years they have been used in construction of trial wavefunctions, in computing Hamiltonians, and in direct calculation of properties and forces.
These methods are highly versatile and computationally efficient, yet many questions regarding their interpretability and ability to extrapolate information remains unanswered.
How are they being used in electronic structure theory today, and how do they fit into the bigger picture? Would electronic structure theory have looked anything different if it was conceived in the age of machine learning? This seminar seeks to answer these kinds of questions, and was originally given as a trial lecture at the Hylleraas Centre of Quantum Molecular Sciences at the University of Oslo.
machine learning, electronic-structure theory
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
PaNdata software catalogue
PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments.
Scientific topics: photon and neutron technique, crystallography, imaging, macromolecular crystallography, nuclear resonant scattering, powder diffraction, ptychography, radiotherapy, small angle x-ray scattering, small angle inelastic scattering, single crystal diffraction, surface crystallography, tomography
Keywords: software, FAIR, catalogue
Resource type: tool
PaNdata software catalogue
https://software.pan-data.eu/
https://pan-training.eu/materials/pandata-software-catalogue
PaNdata software catalogue is a database of software used mainly for data analysis of neutron and photon experiments.
photon and neutron technique
crystallography
imaging
macromolecular crystallography
nuclear resonant scattering
powder diffraction
ptychography
radiotherapy
small angle x-ray scattering
small angle inelastic scattering
single crystal diffraction
surface crystallography
tomography
software, FAIR, catalogue
scientists
neutron community
Photon Community
research data scientist