en: Myelin insulates neuronal axons and enables fast signal transmission, constituting a key component of brain development, aging and disease. Yet, myelin-specific imaging of macroscopic samples remains a challenge. Here, we exploit myelin’s nanostructural periodicity, and use small-angle X-ray scattering tensor tomography (SAXS-TT) to simultaneously quantify myelin levels, nanostructural integrity and axon orientations in nervous tissue. Proof-of-principle is demonstrated in whole mouse brain, mouse spinal cord and human white and gray matter samples. Outcomes are validated by 2D/3D histology and compared to MRI measurements sensitive to myelin and axon orientations. Specificity to nanostructure is exemplified by concomitantly imaging different myelin types with distinct periodicities. Finally, we illustrate the method’s sensitivity towards myelin-related diseases by quantifying myelin alterations in dysmyelinated mouse brain. This non-destructive, stain-free molecular imaging approach enables quantitative studies of myelination within and across samples during development, aging, disease and treatment, and is applicable to other ordered biomolecules or nanostructures.

en: Nanostructure-specific X-ray tomography reveals myelin levels, integrity and axon orientations in mouse and human nervous tissue


$oid: OBSOLETE

en: The aim of this proposal is to image the complex vascular lesions seen in human pulmonary hypertension (PH). High resolution 3D image data can by itself, or when combined with subsequent sectioning and immunohistochemical analyses of the same specimen, create a detailed map of the distribution of pathology in 3D space. This project has the potential to advance our understanding of PH pathophysiology and increase our chances of finding relevant targets for drug development.

en:
Synchrotron Imaging of Complex Vascular Lesions in Human Pulmonary Hypertension:
Pathology Distribution in 3D Space

approval_status: approved

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.

en: PSI Data Catalog

de: PSI Data Catalog

fr: PSI Data Catalog

it: PSI Data Catalog

political_level: other

state: active

type: organization

psi

capacity: public

de: PSI Open Data Provider

type: dataset

key: guid

key: uri

value: DCAT Harvester SciCat

envi

de: Umwelt

en: Environment

fr: Environnement

it: Ambiente


en:
Particle accelerators are enabling tools for scientific exploration and discovery in various disciplines.  Finding optimized operation points for these complex machines is a challenging task, however, due to the large number of parameters involved and the underlying non-linear dynamics. Here, we introduce two families of data-driven surrogate models, based on deep and invertible neural networks, that can replace the expensive physics computer models.
These models are employed in multi-objective optimisations to find Pareto optimal operation points for two fundamentally different types of particle accelerators. Our approach reduces the time-to-solution for a multi-objective accelerator optimisation up to a factor of 640 and the computational cost up to 98%. The framework established here should pave the way for future on-line and real-time multi-objective optimisation of particle accelerators.

en: Data for the paper: "Fast,  efficient  and  flexible  particle  accelerator  optimisation using densely connected and invertible neural networks"


en: Pump-probe experiment on antiferromagnetic Bragg peak

en: NaOsO3 magnetism SACLA XFEL experiment 2017/04


en:
We present a detailed low-energy muon spin rotation and x-ray magnetic circular dichroism (XMCD) investigation of the magnetic structure in ultrathin tetragonal (T)-CuO films. The measured muon-spin polarization decay indicates an antiferromagnetic (AFM) order with a transition temperature higher than 200 K. The XMCD signal obtained around the Cu L2,3 edges indicates the presence of pinned Cu
2+ moments that are parallel to the sample surface, and additionally, isotropic paramagnetic moments. The pinning of some of the Cu moments is caused by an AFM ordering consisting of moments that lie most likely in plane of the film. Moreover, pinned moments show a larger orbital magnetic moment contribution with an approximate ratio of m_orb/m_spin=1.5, indicating that these spins are located at sites with reduced symmetry. Some fractions of the pinned moments remain pinned from an AFM background even at 360 K, indicating that TN>360K. We propose a simple model that explains these experimental findings, showing that the magnetic order of the T-CuO ultrathin films differs from the theoretical predictions.

en: Magnetic order of tetragonal CuO ultrathin films


en: The associated article to these datasets describes a new genus and species, Skyttegaardia galtieri E.M.Friis, P.R.Crane & E.M.Friis. The fossils were isolated from dark clay of the early-mid Berriasian Skyttegård Member of the Rabekke Formation, collected at the Skyttegård and Arnager Bay localities, Bornholm, Denmark. The fossils were studied using SEM. Internal structures of the fossils were also investigated using synchrotron radiation X-ray tomographic microscopy at the TOMCAT Beamline, Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland. The new taxon is based on small microsporangiophores consisting of a proximal fertile portion and a distal sterile extension. The fertile portion is stalk-like with two sporangia deeply sunken into two cavities in the presumed abaxial surface. The sterile distal tip is long, horn-shaped and tapers to a slender point. Pollen grains in situ are of the Monosulcites/Cycadopites type, monocolpate, tectate-psilate. General organisation and details of epidermal features, as well as pollen morphology, are consistent with a possible relationship of Skyttegaardia galtieri to extant Cycadales. However, in the low number of partially embedded sporangia Skyttegaardia is distinct from the microsporophores of extant cycads, in which the sporangia are usually crowded on the surface of the microsporangiophores, typically in groups of two to five.

en: Synchrotron radiation X-ray tomographic microscopy datasets for a putative cycad from the earliest Cretaceous (Berriasian) of the isle of Bornholm, Denmark


en: THz FTIR spectroscopy on LiYF4:Tm


en: We present a theoretical framework to model the generation and shaping of carrier-envelope phase stable narrowband pulses by means of difference frequency generation from independently tunable optical parametric amplifiers. The simulations apply group delay dispersion (GDD) to infrared (IR) pulses to generate second-order phase-modulated mid-IR pulses. The modulation of the second-order phase of the mid-IR is dependent on the relative second-order phase of the mixed IR pulses. Changing the relative second-order phase can produce linearly chirped or Fourier-limited narrowband mid-IR pulses. The bandwidth of the mid-IR is dependent on the pulse-shaped IR pulses and the central frequency of the mid-IR pulses are unaffected by the chirp. The delay between the optical parametric amplifiers offers another degree of tunability. The introduction of a delay changes the central frequency of the generated mid-IR pulse. It also has limited impact on the bandwidth of the mid-IR and does not change the dependence of the second-order phase of the mid-IR on the relative second-order phase of the IR pulses.

en: Simulated Generation of Tunable and Shaped Narrowband THz Pulses using Difference Frequency Generation


en: Understanding ultrafast magnetization dynamics on the microscopic level is of strong current interest due to the potential for applications in information storage. In recent years, the spin-lattice coupling has been recognized to be essential for ultrafast magnetization dynamics. Magnetoelectric multiferroics of type II possess intrinsic correlations among magnetic sublattices and electric polarization (P) through spin-lattice coupling, enabling fundamentally coupled dynamics between spins and lattice. Here we report on ultrafast magnetization dynamics in a room-temperature multiferroic hexaferrite possessing ferrimagnetic and antiferromagnetic sublattices, revealed by time-resolved resonant x-ray diffraction. A femtosecond above-bandgap excitation triggers a coherent magnon in which the two magnetic sublattices entangle and give rise to a transient modulation of P. A novel microscopic mechanism for triggering the coherent magnon in this ferrimagnetic insulator based on the spin-lattice coupling is proposed. Our finding opens up a novel but general pathway for ultrafast control of magnetism.

en: Optical excitation of electromagnons in hexaferrite


en: Chloride transport by microbial rhodopsins is an essential process of which the molecular details have remained elusive, such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light powered chloride ion pump.

en: Dynamics and mechanism of a light-driven chloride pump - SSX datasets


en: Dynamics and mechanism of a light-driven chloride pump - datasets collected with 13.7 keV X-ray energy

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.

en: PSI Data Catalog


en:
A Muon Induced Xray Measurement (MIXE) of a hetero-structured sample of known elements and thicknesses.
The target consisted of a three-layered sandwich sample of iron (Fe), titanium (Ti), and copper (Cu) plates and was placed in vacuum.
Each layer was 500 μm thick with a diameter of 26.5 mm.
The sample was used to characterize the capabilities of MIXE at PSI. This sample emphasizes the quality of a continuous beam, and the exceptional SNR at high rates.

en: MIXE 2018 Fe/Ti/Cu sandwich sample raw data

en: Environment


en:
We report on element-resolved ultrafast magnetization dynamics in multiferroic CoCr2O4 and
Co0.975Ge0.025Cr2O4 after optical excitation above the electronic band gap. We observe demagnetization dynamics
in the range of several picoseconds, up to two orders of magnitude faster than previously reported
demagnetization in other ferrimagnetic insulators. Moreover, we find that the dynamics of the two magnetic
ions differ significantly just below the Curie point. The dynamics of the low-temperature multiferroic phase
are almost two times slower than those in the ferrimagnetic phase. This suggests that the additional magnetic
cycloidal component, which is coupled to electric polarization at low temperatures, might influence the ultrafast
magnetization dynamics.

en: Ultrafast probe of magnetization dynamics in multiferroic CoCr2O4 and Co0.975Ge0.025Cr2O4


en:
Here we report a resonant x-ray diffraction (RXD) study at the Cu L3 edge on the multichiral system CsCuCl3, exhibiting helical magnetic order in a chiral crystal structure. RXD is a powerful technique to disentangle electronic degrees of freedom due to its sensitivity to electric monopoles (charge), magnetic dipoles (spin),
and electric quadrupoles (orbital). We characterize electric quadrupole moments around Cu ascribed to the unoccupied Cu 3d orbital, whose quantization axis is off the basal plane. Detailed investigation of magnetic reflections reveals additional sinusoidal modulations along the principal axis superimposed on the reported
helical structure, i.e., a longitudinal conical (helical-butterfly) structure. The out-of-plane modulations imply significant spin-orbit interaction despite S = 1/2 of Cu2+.

en: Conical spin order with chiral quadrupole helix in CsCuCl3


en: The recently discovered superconducting nickelates are already looking quite different to their cousins, the cuprates. One big reason is the magnetic order. First, the undoped parent compound NdNiO2 appears to be non-magnetic, unlike the undoped cuprates, which are antiferromagnetic. Secondly, the hole-doped Nd1-xSrxNiO2 seems to host antiferromagnetic order as well as superconductivity and these coexisting phenomena are rare in hole-doped cuprates. Low energy muon spin relaxation provides the ideal tool to probe the magnetism in this new family of superconductors.

en: Determining the nature of the magnetism in infinite layer nickelate superconductors


en: Incomplete cancellation of collinear antiparallel spins gives rise to ferrimagnetism. Even if the oppositely polarized spins are owing to the equal number of a single magnetic element having the same valence state, in principle, a ferrimagnetic state can still arise from the crystallographic inequivalence of the host ions. However, experimental identification of such a state as “ferrimagnetic” is not straightforward because of the tiny magnitude expected for M and the requirement for a sophisticated technique to differentiate similar magnetic sites. We report a synchrotron-based x-ray investigation on an epitaxial film of CaFe2O4, which exhibits two magnetic phases with similar energies, performed at the Fe L2,3 edges. We find that while one phase of CaFe2O4 is antiferromagnetic, the other one is “ferrimagnetic” with an antiparallel arrangement of an equal number of spins between two distinct crystallographic sites with very similar local coordination environments. Our results further indicate two distinct origins of an overall minute M; one is intrinsic, from distinct Fe3+ sites, and the other one is extrinsic, arising from defective Fe2+ likely forming weakly-coupled ferrimagnetic clusters. These two origins are uncorrelated and have very different coercive fields. Hence, this work provides a direct experimental demonstration of “ferrimagnetism” solely due to crystallographic inequivalence of the Fe3+ as the origin of the weak M of CaFe2O4.

en: Ferrimagnetism in CaFe2O4


en: In the corresponding article to these data sets, we explore the flow dynamics for two-phase flow in a porous medium (a bioclastic carbonate rock). We use state-of-the-art synchrotron X-ray tomography to capture the fluid dynamics within the pore space, with a temporal resolution of 1 s. The rock sample was initially saturated with brine (DI water doped with 15%wt. KI) before brine and nitrogen gas were injected simultaneously. As the gas establishes a path through the pore space, the flow dynamics are transient. Eventually, an equilibrium is established, where the gas saturation oscillates about a constant mean value; this is referred to as steady state. There are 9 data sets, with all the dynamics captured during steady state. We explore 3 total flow rates (brine flow rate + nitrogen flow rate): 0.1ml/min, 0.4ml/min, 0.7ml/min. With 3 fractional flows (brine flow rate / total flow rate) explored for each total flow rate: 0.85, 0.7 and 0.5. The images were captured with a voxel size of 2.75 µm3. In these data sets we observe the development of intermittent flow pathways, and the stability of these pathways when perturbed by a change in the flow rate .

en: The development and stability of intermittent fluid flow pathways during multiphase flow in porous media - initial state data


en: Understanding the ultrashort time scale structural dynamics of the FeRh metamagnetic phase transition is a key element in developing a complete explanation of the mechanism driving the evolution from an antiferromagnetic to ferromagnetic state. Using an X‐ray free electron laser we determine, with sub‐ps time resolution, the time evolution of the (–101) lattice diffraction peak following excitation using a 35 fs laser pulse. The dynamics at higher laser fluence indicates the existence of a transient lattice state distinct from the high temperature ferromagnetic phase. By extracting the lattice temperature and comparing it with values obtained in a quasi‐static diffraction measurement, we estimate the electron–phonon coupling in FeRh thin films as a function of laser excitation fluence. A model is presented which demonstrates that the transient state is paramagnetic and can be reached by a subset of the phonon bands. A complete description of the FeRh structural dynamics requires consideration of coupling strength variation across the phonon frequencies.

en: Raw data of the SACLA XFEL experiment 2021/05, Proposal Number: 2021A8026 on FeRh (Determination of sub‐ps lattice dynamics in FeRh thin films)


en: We present a detailed atomistic picture of the oxidation mechanism of Co nanoparticles and its impact on magnetism by experimentally following the evolution of the structure, chemical composition, and magnetism of individual, gas-phase grown Co nanoparticles during controlled oxidation. The early stage oxidation occurs in a two-step process characterized by (i) the initial formation of small CoO crystallites randomly distributed across the nanoparticle surface, until their coalescence leads to structural completion of the oxide shell and passivation of the metallic core; (ii) progressive conversion of the CoO shell to Co3O4, accompanied by void formation due to the nanoscale Kirkendall effect. The Co nanoparticles remain highly reactive toward oxygen during phase (i), demonstrating the absence of a pressure gap whereby a low reactivity at low pressures is postulated. Our results provide an important benchmark for an improved understanding of the magnetism of oxidized cobalt nanoparticles, with potential implications on their performance in catalytic reactions.

en: Absence of a pressure gap and atomistic mechanism of the oxidation of pure Co nanoparticles

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


chiral-phonons-probed-by-x-rays

en: The concept of quasiparticles is a landmark of condensed matter physics. The symmetry of quasiparticles is of particular importance to attaining emergent phenomena in both equilibrium and nonequilibrium states. Whereas recent exploration has demonstrated chiral fermions and their relevance in emergent phenomena closely relating to topology, the experimental verification of chiral phonons (bosons) remains challenging despite their expected strong impact on fundamental physical properties. Here we show experimental proof of chiral phonons by means of resonant inelastic X-ray scattering with circularly polarized X rays. We show how intrinsically chiral circularly polarized X rays couple to circular phonons at different positions in reciprocal space, principally being able to determine the chiral dispersion of a lattice mode. Our experimental proof of chiral phonons demonstrates a new degree of freedom in condensed matter that is not only of fundamental importance but also of inspiring unconventional ideas to extract emergent phenomena.

en: Chiral phonons probed by X rays

en: PSI Data Catalog

title_for_slug: chiral-phonons-probed-by-x-rays


en: The data available here consists of XPEEM and HR-STEM raw data that was used for a publication entitled "Absence of a pressure gap and atomistic mechanism of the oxidation of pure Co nanoparticles" by Jaianth Vijayakumar, Tatiana M. Savchenko, David M. Bracher, Gunnar Lumbeeck, Armand Beche, Jo Verbeeck, Stefan Vajda, Frithjof Nolting, C.A.F. Vaz, and Armin Kleibert. A detailed list of contents is provided in the "Content of source files and raw data collection" document.

en: Raw data for publication: "Absence of a pressure gap and atomistic mechanism of the oxidation of pure Co nanoparticles"

envi

en: Environment


en: The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we have captured the release of azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of tubulin-binding drugs against gout, cancer, and COVID-19.

en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 10 nanoseconds after photoactivation.


en: Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs). A photon is absorbed by the 11-cis retinal chromophore of rhodopsin which isomerises within 200 femtoseconds to the all-trans conformation, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains elusive. In this work, we use ultrafast time-resolved crystallography at room temperature to determine how an isomerised twisted all-trans retinal stores the photon energy required to initiate protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at 1 ps time-delay of photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Strikingly, the very early structural motions in the protein side chains of rhodopsin appear in regions involved in later stages of the conserved Class A GPCR activation mechanism. Our work sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.

en: ULTRAFAST STRUCTURAL CHANGES DIRECT THE FIRST MOLECULAR EVENTS OF VISION. Gruhl et al. 2023, Nature.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 1 nanosecond after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 100 nanoseconds after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 1 microsecond after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 100 microseconds after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 1 millisecond after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 10 milliseconds after photoactivation.


en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: Apo state

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


en: Calibrated and reconstructed data for the SciFi sub-detector of the Mu3e experiment


en: The files contain the calibrated and reconstructed data collected during test beam campaigns at PSI in 2020 and 2021 intended to characterize the performance of the SciFi subdetector of the Mu3e experiment

en: Development of the Scintillating Fiber Timing Detector for the Mu3e Experiment

en: PSI Data Catalog


en: Electromagnons are emergent collective excitations that involve both vibrational and magnetic characters, arising from strong coupling between the lattice and spins. Although previous experimental studies have successfully observed the spin dynamics of a coherent electromagnon, the associated atomic motions have not been directly observed. Here we use time-resolved hard X-ray diffraction to directly measure the ultrafast structural motion following the excitation of a coherent electromagnon by an intense THz pulse in a multiferroic hexaferrite. Comparing the dynamics of two different components, one striking outcome is the different phase shifts relative to the driving field, gives deeper insights into the excitation process of the electromagnons. The observation of combined lattice and magnetization dynamics of the electromagnon resonance paves the way to access the magnetoelectric coupling strength in ultrafast timescales, which remains a missing fundamental parameter for ultrafast control of magnetism in multiferroics.

en: Non-equilibrium dynamics of spin-lattice coupling

en: Environment


en: Dark and light CrystFEL stream files for every timepoint collected during beamtime 19638

en: stream files produced from experiment p19638


en: NavCt crystal pictures taken by light microscope at the PSI crystallisation facility.

en: 3D Crystal pictures of NavCT voltage-gated sodium channel


en: Test of scicat

en: Test 2


en: In this dataset the catalytic fast pyrolysis of ortho-methoxyphenol isomers was investigated over different zeolites. The data is part of a manuscript submitted to the journal Nat. Commun., entitled " Tuning the Zeolite Acidity Enables Selectivity Control by Suppressing Ketene Formation in Lignin Catalytic Pyrolysis". This work is supported by the Swiss National Science Foundation (project number 200021_178952).

en: Data: Tuning the Zeolite Acidity Enables Selectivity Control by Suppressing Ketene Formation in Lignin Catalytic Pyrolysis


en: Data to reproduce the experiments described in the paper: "Image2Reg: Linking Chromatin Images to Gene Regulation using Genetic perturbations screens" by Daniel Paysan, Adityanarayanan Radhakrishnan, G.V. Shivashankar and Caroline Uhler. The raw imaging data from Rohban et al. (2017) and from the Joint Undertaking in Morphological Profiling Cell Painting Consortium (Chandrasekaran et al., 2023) used in the study was obtained from IDR0033 available at "http://idr-demo.openmicroscopy.org/webclient/?show=screen-1751" , respectively from the Cell Painting Gallery on the Registry of Open Data on AWS "https://registry.opendata.aws/cellpainting-gallery/". Please note that these data resources need to be appropriately referenced if this dataset is used. Please refer to the above mentioned paper for a complete list of the used data sets.

en: Data set for the manuscript: Image2Reg - Linking Chromatin Images to Gene Regulation using Genetic Perturbation Screens


en: We present a detailed study of the magnetic, spectroscopic and structural properties of ultrathin LaMnO3 films deposited on SrTiO3(001) substrates by oxide molecular beam epitaxy. We find that the as-grown LaMnO3 films are slightly reduced and present a significant magnetic moment, while annealing to 600 oC fully oxidises and enhances its magnetic properties. From synchrotron x-ray photoemission spectromicroscopy, we find the presence of Sr, Ca and Si in the LaMnO3 film that diffuse from the SrTiO3 substrate; these impurities act as hole dopants, and can explain the presence of ferromagnetism in LaMnO3. This work highlights the importance of cation mobility at the elevated growth temperature in modifying the magnetic properties of ultrathin LaMnO3 films.

en: Role of interdiffusion on the magnetism of ultrathin LaMnO3 films

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


en: Acoustic levitation has attracted attention in terms of chemical and biochemical analysis in combination with various analytical methods because of its unique container-less environment for samples that is not reliant on specific material characteristics. However, loading samples with very high viscosity is difficult. To expand the scope, we propose the use of polymer thin films as sample holders, whereby the sample is dispensed on a film that is subsequently loaded onto an acoustic levitator. When applied for protein crystallography experiments, rotation controllability and positional stability are important prerequisites. We therefore study the acoustic levitation and rotation of thin films with an aspect ratio (the diameter-to-thickness ratio) of 80–240, which is an order of magnitude larger than those reported previously. For films with empirically optimized shapes, we find that it is possible to control the rotation speed in the range of 1–4 rotations per second while maintaining a positional stability of 12 ± 5 µm. The acoustic radiation force acting on the films is found to be a factor of 26–30 higher than that for same-volume water droplets. We propose use cases of the developed films for protein crystallography experiments and demonstrate data collections for large single crystal samples at room temperature.

en: Data for Acoustic levitation and rotation of thin films and their application for room temperature protein crystallography

en: PSI Data Catalog


en:
Ductal carcinoma in situ (DCIS) is a pre-invasive tumor that can give rise to invasive breast cancer, a
leading cause of cancer death. We generated a large-scale tissue microarray imaging dataset, stained for
chromatin using DAPI, from 560 tissue samples from 122 patients at 3 disease stages and 11 phenotypic
categories of the tumor during DCIS progression. We investigated what cell or tissue features mark DCIS
progression and if such features could be obtained from chromatin images alone without the use of
highly multiplexed staining or high-throughput sequencing. Using unsupervised representation learning
methods, we identified eight distinct morphological cell states just based on the chromatin images and
showed that these distinct cell states were associated with interpretable nuclear and chromatin features.
All cell states were observed in all 3 disease stages and 11 phenotypic categories with different
proportions, indicating that cell states that are enriched in invasive cancer already exist in small fractions
in normal breast tissue. Tissue-level analysis revealed that the spatial organization of the cell states, in
terms of a cell state’s position relative to the ducts and relative to each other, were significantly altered
during DCIS progression. Importantly, we showed that disease stage and phenotypic category could be
accurately predicted just based on statistics of cell state neighborhoods. Collectively, our analysis
demonstrates that chromatin imaging represents a powerful measure of cell state and disease stage of
DCIS, thereby providing a simple and effective imaging-based biomarker for tumor progression.

en: Imaging data related to the paper "Unsupervised representation learning of chromatin images identifies changes in cell state and tissue organization during DCIS progression"

en: Environment


en: We report the observation of fully magnetically polarized ultrathin La0.8Sr0.2MnO3 films by using LaMnO3 and La0.45Sr0.55MnO3 buffer layers grown epitaxially on SrTiO3(001) substrates by molecular beam epitaxy. Specifically, we show that La0.8Sr0.2MnO3 films grown on 12-unit-cell LaMnO3 have bulk-like magnetic moments starting from a single unit cell thickness, while for the 15-unit-cell La0.45Sr0.55MnO3 buffer layer, the La0.8Sr0.2MnO3 transitions from an antiferromagnetic state to a fully spin-polarized ferromagnetic state at 4 unit cells. The magnetic results are confirmed by X-ray magnetic circular dichroism, while linear dichroic measurements carried out for the La0.8Sr0.2MnO3/La0.45Sr0.55MnO3 series show the presence of an orbital reorganization at the transition from the antiferromagnetic to ferromagnetic state corresponding to a change from a preferred in-plane orbital hole occupancy, characteristic of the A-type antiferromagnetic state of La0.45Sr0.55MnO3, to preferentially out of plane. We interpret our findings in terms of the different electronic charge transfers between the adjacent layers, confined to the unit cell in the case of insulating LaMnO3 and extended to a few unit cells in the case of conducting La0.45Sr0.55MnO3. Our work demonstrates an approach to growing ultrathin mixed-valence manganite films that are fully magnetically polarized from the single unit cell, paving the way to fully exploring the unique electronic properties of this class of strongly correlated oxide materials.

en: Fully Magnetically Polarized Ultrathin La0.8Sr0.2MnO3 Films


en: Reconstruction code for burst ptychography and tomography used at the at the cSAXS beamline, Swiss Light Source in Paul Scherrer Institute.

en: X-ray Tomography of a Data Processing Chip at 4 nm Resolution


en: Data of a computer chip obtained by using Ptychographic X-ray computed tomography (PXCT) with a 4.2 nm voxel size in 3D. The sample pillar diameter was 5 micrometers and the sample was acquired at the cSAXS beamline, Swiss Light Source in Paul Scherrer Institute.


en: The evolution of the magnetic ground state of ultrathin 0–10 unit cells (uc) thick La0.8Sr0.2MnO3 films interfaced to an antiferromagnetic La0.45Sr0.55MnO3/SrTiO3(001) buffer layer was investigated with x-ray photoemission electron microscopy. For 0–3 uc La0.8Sr0.2MnO3, we observe antiferromagnetic domains but no ferromagnetic contrast, showing that nominally ferromagnetic La0.8Sr0.2MnO3 adopts the antiferromagnetic ground state of the buffer layer. For larger thicknesses, ferromagnetic domains emerge, confirming that the additional layers revert to the ferromagnetic ground state. We also observe a drastic increase in the complexity of the domain configuration between 3 and 5 uc, which we attribute to competing magnetic and electronic ground states in the system. We attribute the interfacial modified magnetic ground state to charge sharing at the interface due to the chemical potential mismatch, which leads to hole doping at the La0.8Sr0.2MnO3 interface. The present work sheds light on the impact of charge sharing at the interface of complex oxide materials, in particular on the magnetic and electronic states, and presents a strategy for modulating the electronic ground state properties at metallic interfaces.

en: Charge-exchange-driven interfacial antiferromagnetic ground state in La0.8Sr0.2MnO3 ultrathin films


en: Morphology and defects in 3D self-assembled diamond networks


en: The resonant excitation of electronic transitions with coherent laser sources creates quantum coherent superpositions of the involved electronic states. Most time-resolved studies have focused on gases or isolated subsystems embedded in insulating solids, aiming for applications in quantum information1–6. Here, we focus on the coherent control of orbital wavefunctions in the correlated quantum material Tb2Ti2O7, which forms an interacting spin liquid ground state. We show that resonant excitation with a strong THz pulse creates a coherent superposition of the lowest energy Tb 4f states. The coherence manifests itself as a macroscopic oscillating magnetic dipole, which is detected by ultrafast resonant x-ray diffraction. We envision the coherent control of orbital wavefunctions demonstrated here to become a new tool for the ultrafast manipulation and investigation of quantum materials.

en: Coherent control of rare earth 4f shell wavefunctions in the quantum spin liquid Tb2Ti2O7 Source Data


en: The interaction of magnetic order and spontaneous polarization is a fundamental coupling with the prospect for the control of electronic properties and magnetism. The connection among magnetic order, charge localization and associated metal-insulator transition (MIT) are cornerstones for materials control. Materials that combine both effects are therefore of great interest for testing models that claim the occurrence of spontaneous polarization from and magnetic charge order. One class of materials proposed to combine these functionalities is the family of RNiO3 (R: lanthanide or Y), whose members show a clear MIT and an antiferromagnetic ground state and for which an electric polarization has been predicted. Using resonant magnetic x-ray scattering with circular polarization and an applied electric field we show that YNiO3 possess a magnetic structure containing domains of spin-rotations that are consistent with an electric polarization. We show a reversal of the magnetic structure with the applied electric field confirming that charge ordered RNiO3 are magnetoelectric type II multiferroics with a MIT.

en: Magnetoelectric effect in multiferroic nickelate perovskite YNiO3

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


en: In this paper we present a model system built out of artificially layered materials, allowing us to understand the interrelation of magnetic phases with the metallic-insulating phase at long length scales, and enabling new strategies for the design and control of materials in devices. The artificial model system consists of superlattices made of SmNiO3 and NdNiO3 layers, – two members of the fascinating rare earth nickelate family, having different metal-to-insulator and magnetic transition temperatures. By combining two complementary techniques—resonant elastic x-ray scattering and muon spin relaxation—we show how the magnetic order evolves, in this complex multicomponent system, as a function of temperature and superlattice periodicity. We demonstrate that the length scale of the coupling between the antiferromagnetic and paramagnetic phases is longer than that of the electronic metal-insulator phase transition—despite being subsidiary to it. This can be explained via a Landau theory—where the bulk magnetic energy plus a gradient cost between magnetic and nonmagnetic phases is considered. These results provide a clear understanding of the coupling of magnetic transitions in systems sharing identical order parameters.

en: Coupling of magnetic phases at nickelate interfaces (SNO-NNO)

en: PSI Data Catalog


en: In this study, we explore the intricate interplay between the electronic properties within the solid and field emission beams characteristics. By examining the fundamental principles governing field emission, we investigate how transverse momentum impact the propagation of the emitted electron beams. We demonstrate that transverse momentum and the spatial coherence of the emission source significantly affect beam properties, leading to notable changes in interference patterns.

en: Beam Divergence and Interference Characteristics of Field Emission Beam

en: Environment


en: Acoustic tweezers comprising a surface acoustic wave chip and a disposable silicon microfluidic chip are potentially advantageous to stable and cost-effective acoustofluidic experiments while avoiding the cross-contamination by reusing the surface acoustic wave chip and disposing of the microfluidic chip. For such a device, it is important to optimize the chip-to-chip bonding and the size and shape of the microfluidic chip to enhance the available acoustic pressure. In this work, aiming at studying samples with the size of a few tens of microns, we explore the device structure and assembly method of acoustic tweezers. By using a polymer bonding layer and shaping the silicon microfluidic chip via deep reactive ion etching, we were able to attain the acoustic pressure up to 2 MPa with a corresponding acoustic radiation pressure of 0.2 kPa for 50 MHz ultrasound, comparable to reported values at lower ultrasound frequencies. We utilized the fabricated acoustic tweezers for non-contact viscoelastic deformation experiments of soft matter and  trapping of highly motile cells. These results suggests that the feasibility of the hybrid chip approach to attaining the high acoustic force required to conduct acoustomechanical testing of small soft matters and cells.

en: Dataset for Surface-acoustic-wave driven silicon microfluidic chips for acoustic tweezing of motile cells and viscoelastic microbeads


en: Resonant X-ray diffraction (RXD) provides a unique capability to investigate electronic ordered states in matter. The circular dichroism in RXD can determine the absolute chirality formed by anisotropic multipole arrangement. Here, we demonstrate that the scattering interference between distinct atomic electric multipoles can create circular contrast in resonant RXD even in a non-chiral crystal. These general considerations are applied to 1T-TiSe2, where recently reported circular dichroism in RXD was used to claim chiral charge density wave order. We show that the experimental observations are well reproduced by our ab initio calculations on the basis of the centrosymmetric crystal structure. Our results not only illuminate a way for a better understanding of possible chiral electronic order but also propose a general approach to extract buried high-order atomic multipoles via circular contrast in RXD. Besides, we discuss the difference in the circular dichroism of RXD originated by crystal chirality in chiral crystals and the interference effect in non-chiral crystals.

en: Non-chiral 1T-TiSe2 creates circular dichroism in resonant X-ray diffraction via multipole scattering interference


en: This dataset contains tomographic data (grayscale and segmented) of the commercial Fumasep bipolar membrane assembled in a CO2-electrolyzer. One sample is a fully functional cell, while the other does not contain catalyst layers to avoid metal artifacts. The samples were imaged in dry and water saturated state.

en: Laboratory source X-ray tomographic microscopy of bipolar membrane swelling in an assembled CO2-electrolyzer


cd-rixs-data-on-cuo

en: Resonant inelastic x-ray scattering (RIXS) has become a prominent technique to study quasiparticle excitations. With advances in polarization analysis capabilities at different facilities, RIXS offers exceptional potential for investigating symmetry-broken quasiparticles like chiral phonons and magnons. At optical wavelengths birefringence can severely affect polarization states in low-symmetry systems. Here we show its importance for soft x-ray resonances. Given the growing interest in Circular Dichroism (CD) in RIXS, it is important to evaluate how birefringence may affect the RIXS spectra of anisotropic systems. We investigate CuO, a well-known anisotropic material, using Cu L3-edge RIXS and detect significant CD in both magnetic and orbital excitations in the collinear antiferromagnetic phase. We demonstrate that the CD can be modeled by a proper treatment of RIXS scattering amplitudes derived from single-ion calculations with birefringence. Recognizing these effects is crucial for unambiguous identification of subtle dichroic effects induced by symmetry-broken quasiparticles. Furthermore, the combined sensitivity of RIXS and birefringence to local symmetry presents an opportunity to study microscopic changes driven by external perturbations.

en: CD RIXS data on CuO

title_for_slug: cd-rixs-data-on-cuo


en: Chirality is a fundamental symmetry element existing at disparate scales and in many categories of scientific fields. Even though symmetry breaking is an indispensable concept for describing qualitatively distinct phenomena, symmetry cannot quantitatively predict measurable quantities. Since chirality is ternary, i.e., left-handed, right-handed, or achiral, the role of its “amplitude” in material properties is habitually not addressed. Considering the role of “amplitude” for time-reversal symmetry breaking, which can be described by magnetization, chirality amplitude is intuitively a key quantity for controlling emergent phenomena. Here, we propose two types of chiral order parameters and demonstrate the tunability of their amplitude at ultrafast timescales. Resonant X-ray diffraction with circular polarization is an established technique to measure crystal chirality directly. Extending this technique to the time domain, we quantify the ultrafast change in chirality amplitude in real time after an optical excitation. Besides, using a THz excitation, we observe oscillations in the resonant diffraction intensities with specific phonon frequencies. This indicates the creation of additional asymmetry, which could also be described as an enhancement in chirality amplitude. Our proposed concept of chirality amplitude and its ultrafast control may lead to a unique approach to control chirality-induced emergent phenomena at ultrafast timescales.

en: Tuning chirality amplitude at ultrafast timescales


en: The purpose of this experiment was to measure a brain specimen by nf-PXCT, with the aim to measure it afterwards at the ID16A beamline of the ESRF.

en: Raw datasets corresponding to the near-field ptychographic X-ray computed tomography acquisition of a resin-embedded, heavy-metal stained brain speciamen of about 100 micron diameter

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


en: Van der Waals (vdW) materials exhibit a variety of states that can be switched with low power at low temperatures, offering a viable cryogenic "flash memory" required for the classical control electronics for solid-state quantum information processing. In 1T-TaS2, a non-volatile metallic 'hidden' state can be induced from an insulating equilibrium charge-density wave ground state using either optical or electrical pulses. Given that conventional memristors form localized, filamentary channels which support the current, a key question for design concerns the geometry of the conduction region in highly energy-efficient 1T-TaS2 devices. Here, we report in operando micro-beam X-ray diffraction, fluorescence, and concurrent transport measurements, allowing us to spatially image the non-thermal hidden state induced by electrical switching of 1T-TaS2. Our results reveal a long-range ordered, non-filamentary switched state that extends well below the electrodes, implying that the self-organized, collective growth of the hidden phase is driven by a combination of charge flow and lattice strain. Our unique combination of techniques showcases the potential of non-destructive, three-dimensional X-ray imaging to study bulk switching properties in microscopic detail, namely electrical control of the vdW layer stacking.

en: Imaging of electrically controlled van der Waals layer stacking in 1T-TaS2

en: PSI Data Catalog


en: Raw data associated with the paper entitled 'Pinning of antiferromagnetic domain walls and domain structure in ultrathin La0.45Sr0.55MnO3 films'.

envi

en: Environment


en: Aligned complex-valued projections and tomographic datasets from 3 PXCT acquisitions on the same catalyst specimen primarily composed of zeolite, alumina, and nickel, acquired at 3 different photon energies close to the nickel absorption edge. The file information.txt contains a description of the data. We also include the software scripts used to process the data.

en: Aligned complex-valued projections and 3D tomographic datasets from a catalyst specimen


en: Ptychographic and tomographic reconstructions of a triblock copolymer soft matter crystal replicated into gold


en: The data available here consists of XPEEM, SQUID, transport, RHEED, and atomic force probe microscopy raw data that was used for a publication entitled "Direct Imaging of the Magnetoelectric Coupling in BaTiO3/La0.9Ba0.1MnO3 Multiferroic Heterostructures" by F. Stramaglia, G. Panchal, L. Tovaglieri, C. Lichtensteiger, F. Nolting, and C. A. F. Vaz.


en: The binding and release of ligands from their protein targets is central to fundamental biological processes as well as to drug discovery. Photopharmacology introduces chemical triggers that allow the changing of ligand affinities and thus biological activity by light. Insight into the molecular mechanisms of photopharmacology is largely missing because the relevant transitions during the light-triggered reaction cannot be resolved by conventional structural biology. Using time-resolved serial crystallography at a synchrotron and X-ray free-electron laser, we have captured the release of azo-combretastatin A4 and the resulting conformational changes in tubulin. Nine structural snapshots from 1 ns to 100 ms complemented by simulations show how cis-to-trans isomerization of the azobenzene bond leads to a switch in ligand affinity, opening of an exit channel, and collapse of the binding pocket upon ligand release. The resulting global backbone rearrangements are related to the action mechanism of tubulin-binding drugs against gout, cancer, and COVID-19.

en: Watching the release of a photopharmacological drug from tubulin using time-resolved serial crystallography: 10 microseconds after photoactivation.


en: Raw data from dataset C319_EPL1_cSAXS_273_S01394-S02309, obtained at the cSAXS beamline at the Swiss Light Source during beamtime 20190654 (e17964).

en: Non-destructive X-ray tomography of brain tissue ultrastructure. Supporting raw data. Dataset C319_EPL1_cSAXS_273_S01394-S02309.


en: The associated article to this dataset describes a new genus and species, Renbernia zhoui E.M.Friis, P.R.Crane & K.R.Pedersen from the Early Cretaceous (early-middle Albian) mesofossil flora collected in Potomac Group sediments at the Puddledock locality, Virginia, U.S.A. The new taxon is based on microsporangiate structures with Decussosporites-type pollen in situ in densely arranged microsporangiophores. The microsporangia are elongate with extrorse and valvate dehiscence. Synchrotron radiation X-ray tomographic microscopy shows that they are bisporangiate. The in situ Decussosporites-type pollen is elliptical with an unusual arrangement of apertures. On the presumed distal face there is a long median colpus flanked laterally by two equally long lateral colpi. On the presumed proximal side there is a short transverse colpus perpendicular to the longitudinal colpi. Renbernia zhoui is compared to Brenneria potomacensis, another microsporangiate structure from the Potomac Group sediments with Decussosporites-type pollen in situ. B. potomacensis is slightly older than Renbernia zhoui and is distinguished by the more rounded microsporangia and the pollen is more distinctly saccate. A comparison with the extinct pollen genus Eucommiidites and a possible link of Renbernia zhoui to the Bennettitales-Erdtmanithecales-Gnetales group, which is diverse and common in the Puddledock mesofossil flora, is discussed.

en: Extinct seed plant diversity in the Early Cretaceous: An enigmatic new microsporangiate fossil with Decussosporites pollen in situ


en:
Circular dichroism observed by resonant x-ray diffraction at the Cu L3 edge was investigated in a chiral antiferromagnet, Pb(TiO)Cu4(PO4)4, which shows magnetic quadrupole order (TN = 7K). At temperatures
above TN, space-group-forbidden reflection 100 is observed due to the anisotropic tensor of susceptibility (ATS) scattering. With decreasing temperature, the reflection intensity shows substantial circular dichroism below
TN. We found one-to-one correspondence between the sign of the circular dichroism and that of the sample’s crystallographic chirality. In addition, the reflection intensity depends on the product of poling magnetic and
electric fields. The circular dichroism observed in this study is interpreted as the interference between the ATS and the magnetic scatterings. This finding shows that the interference scattering probes both the chirality and the
order parameter of the magnetic quadrupole order in this chiral antiferromagnetic.

en: Chirality and magnetic quadrupole order in Pb(TiO)Cu4(PO4)4 probed by interference scattering in resonant x-ray diffraction


en: Data to reproduce the experiments described in the paper: "Image2Reg: Linking Chromatin Images to Gene Regulation using Genetic perturbations screens" by Daniel Paysan, Adityanarayanan Radhakrishnan, G.V. Shivashankar and Caroline Uhler. The raw imaging data from Rohban et al. (2017) and from the Joint Undertaking in Morphological Profiling Cell Painting Consortium (Chandrasekaran et al., 2023) used in the study was obtained from IDR0033 available at "http://idr-demo.openmicroscopy.org/webclient/?show=screen-1751" , respectively from the Cell Painting Gallery on the Registry of Open Data on AWS "https://registry.opendata.aws/cellpainting-gallery/". Please note that these data resources need to be appropriately referenced if this dataset is used. Please refer to the above mentioned paper for a complete list of the used data sets.

en: Data for Image2Reg

en: The PSI Data Catalog is the central repository directory for scientific metadata generated at the Paul Scherrer Institut (PSI). Powered by SciCat—a community-driven, open-source metadata management framework co-developed by PSI—the catalog provides discoverability and standardized access pathways to petabyte-scale datasets produced across PSI’s large-scale research facilities, including the Swiss Light Source (SLS), the Swiss Spallation Neutron Source (SINQ), and the SwissFEL X-ray free-electron laser.


en: Multiple genomic and proteomic studies have suggested that peripheral blood mononuclear cells (PBMCs) respond to tumor secretomes and thus could provide possible avenues for tumor prognosis and treatment evaluation. We hypothesized that the chromatin organization of PBMCs obtained from liquid biopsies, which integrates secretome signals with gene expression programs, provides efficient biomarkers to characterize tumor signals and the efficacy of proton therapy in tumor patients. In the paper associated to the enclosed data set, we show that chromatin imaging of PBMCs combined with machine learning methods provides such robust and predictive chromatin biomarkers. Our work shows that such chromatin biomarker enable the accurate diagnoses of different tumor types and monitoring of treatment effects of patients undergoing proton therapy and thus highlights their potential for accurate cancer diagnostics and therapy evaluation.

en: Imaging data related to the paper: "Imaging and AI based Chromatin Biomarkers for Diagnosis and Therapy Evaluation from Liquid Biopsies" by Kiran Challa* and Daniel Paysan*, Dominic Leiser, Nadia Sauder, Damien C. Weber and G.V. Shivashankar.

en: PSI Data Catalog


en: The controlled rotation of acoustically levitated samples is beneficial for analyzing sample properties, e.g., in a recently reported room temperature x-ray diffraction experiment, wherein thin film sample holders comprising thin film disks with short blades attached around their circumference were utilized. However, the mechanism of producing the torque and the determinant factor of the rotation direction for these planar ultrasonic rotors have been elusive. We, therefore, study the impact of the size and shape on the rotation characteristics of these ultrasonic rotors in air and further study the influence of the viscosity of fluid. Theory and experiment demonstrate the essential role of the short blades in producing the acoustic torque both in air and water. In the airborne case, the shape and arrangement of the blades are found to determine the rotation direction. In water, with a dynamic viscosity 55 times higher than that of air, we demonstrate that ultrasonic rotors down to 25-μm-disk-diameter function in an optimized experimental geometry with approximately the same actuation efficiency as in air. Our results will be beneficial to further improve the applicability of the ultrasonic rotors as sample holders for airborne experiments and to explore the micrometer-scale ultrasonic rotors in liquid.

en: Data for Size and shape dependent rotation characteristics of thin film ultrasonic rotors

en: Environment


en: In this work, we present a comprehensive dataset designed to facilitate the prediction of metal fatigue life using deep learning techniques. The dataset includes detailed experimental data from 40 different metallic materials, comprising a total of 1195 data points under 48 distinct loading paths. Each data point is stored in a CSV file, capturing the loading path as a time-series with axial and tangential stress or strain values.The primary purpose of this dataset is to support the development and validation of deep learning models aimed at accurately predicting the fatigue life of metals under various loading conditions. This dataset includes stress-controlled and strain-controlled data, ensuring a broad representation of experimental scenarios. Additionally, an Excel file accompanies the dataset, providing detailed mechanical properties of each material, such as elastic modulus, tensile strength, yield strength, and Poisson's ratio, along with references to the original experimental sources.This dataset is intended for researchers in materials science and mechanical engineering, offering a robust foundation for training and testing deep learning algorithms in fatigue analysis. By making this dataset publicly available, we aim to foster collaboration and further advancements in the field of metal fatigue prediction. Researchers are encouraged to utilize and contribute to the dataset, thereby enhancing its scope and applicability.

en: A deep learning dataset for metal multiaxial fatigue life prediction

materialscloud

en:
Materials Cloud is a platform built to enable the seamless sharing and dissemination of resources in computational materials science, offering educational, research, and archiving tools; simulation software and services; and curated and raw data. These underpin published results and empower data-based discovery, compliant with data management plans and the FAIR principles.

In the Materials Cloud you can browse, explore, download, or deposit raw and curated data (in the Discover, Explore, and Archive sections); you can access cloud or redeployable simulation services (from AiiDAlab turnkey simulations to the Quantum Mobile virtual machine, the AiiDA registry of plugins and workflows, and the OSSCAR notebooks, in the Work section), and you can use all our educational material, tutorials and lectures (in the Learn section).

en: Materials Cloud

de: Materials Cloud

fr: Materials Cloud

it: Materials Cloud

value: DCAT Harvester Materials Cloud

deep-learning

display_name: deep-learning

fatigue-life-prediction

display_name: fatigue-life-prediction

metal-fatigue

display_name: metal-fatigue

multiaxial-fatigue

display_name: multiaxial-fatigue


en: A transient state of the excess electron in liquid water preceding the development of the solvation shell, the so-called wet electron, has been invoked to explain spectroscopic observations, but its binding energy and atomic structure have remained highly elusive. Here, we carry out hybrid functional molecular dynamics to unveil the ultrafast solvation mechanism leading to the hydrated electron. In the pre-hydrated regime, the electron is found to repeatedly switch between a quasi-free electron state in the conduction band and a localized state with a binding energy of 0.26 eV, which we assign to the wet electron. This transient state self-traps in a region of the liquid which extends up to ∼4.5 Å and involves a severe disruption of the hydrogen-bond network. Our picture provides an unprecedented view on the nature of the wet electron, which is instrumental to understand the properties of this fundamental species in liquid water.

en: Picture of Wet Electron: A Localized Transient State in Liquid Water

first-principles

display_name: first-principles

hydrated-electron

display_name: hydrated-electron

liquid-water

display_name: liquid-water

molecular-dynamics

display_name: molecular-dynamics

wet-electron

display_name: wet-electron


en:
Project Abstract: For applications of metal-organic frameworks (MOFs) such as gas storage and separation, flexibility is often seen as a parameter that can tune material performance. In this work we aim to determine the optimal flexibility for the shape selective separation of similarly sized molecules (e.g., Xe/Kr mixtures). To obtain systematic insight into how the flexibility impacts this type of separation we develop a simple analytical model that predicts a material's Henry regime adsorption and selectivity as a function of flexibility. We elucidate the complex dependence of selectivity on a framework's intrinsic flexibility whereby performance is either improved or reduced with increasing flexibility, depending on the material's pore size characteristics. However, the selectivity of a material with the pore size and chemistry that already maximizes selectivity in the rigid approximation is continuously diminished with increasing flexibility, demonstrating that the globally optimal separation exists within an entirely rigid pore. Molecular simulations show that our simple model predicts performance trends that are observed when screening the adsorption behavior of flexible MOFs. These flexible simulations provide better agreement with experimental adsorption data in a high performance material that is not captured when modeling this framework as rigid, an approximation typically made in high-throughput screening studies. We conclude that, for shape selective adsorption applications, the globally optimal material will have the optimal pore size/chemistry and minimal intrinsic flexibility even though other non-optimal materials' selectivity can actually be improved by flexibility. Equally important, we find that flexible simulations can be critical for correctly modeling adsorption in these types of systems.

About this entry: You can find the Xe/Kr Henry coefficients and the infinite dilution selectivity of more than 2000 CoRE MOF structures obtained via computational screening when materials are simulated as both flexible and rigid.  For details about the methods used to obtain these results, please see the corresponding paper (DOI: 10.1021/jacs.7b01688).  The data provided here was used to create the scatter plots presented in the original paper and can be used to find the adsorption properties for any material in the CoRE MOF screening.

Version 2 includes a minor formatting correction to make the CIF files compliant with the CIF standard.

en: The Influence of Intrinsic Framework Flexibility on Adsorption in Nanoporous Materials (Data Download)

flexibility

display_name: flexibility

nanoporous-materials

display_name: nanoporous-materials

xekr-separations

display_name: xekr-separations


en:
Project abstract: In this work, a theoretical framework is developed to explain and predict changes in the product distribution of the propene dimerization reaction, which yields a mixture of C6 olefin isomers, resulting from the use of different porous materials as catalysts. The MOF-74 class of materials has shown promise in catalyzing the dimerization of propene with high selectivity for valuable linear olefin products. We show that experimentally observed changes in the product distribution can be explained in terms of the contribution of the pores to the free energy of formation, which are directly computed using molecular simulation. Our model is used to screen a library of 118 existing and hypothetical MOF and zeolite structures to study how product distribution can be tuned by changing pore size, shape, and composition of porous materials. Using these molecular descriptors, catalyst properties are identified that increase the selective reaction of linear olefin isomers, which are valued as industrial feedstocks. A pore size commensurate with the size of the desired linear products enhances linear conversion by sterically hindering the branched isomers. Another promising feature is the presence of open metal sites, which interact with the olefin π-bond to provide favorable binding sites for the linear isomers.

About this entry: We provide the geometrical framework descriptors, linear conversions, and thermodynamic data for the 118 frameworks screened in this study, as well as thermodynamics of adsorption properties computed for 12 C6 olefin isomers in each framework. For details about the methods used to obtain these data, please see the corresponding paper (DOI: 10.1021/acscatal.7b00712). The data provided here was used to create the scatter plots in the original paper and can be used to find the product distribution and adsorption properties for all of the materials considered in the study.

en: Predicting Product Distribution of Propene Dimerization in Nanoporous Materials (Data Download)

metalorganic-frameworks

display_name: metalorganic-frameworks

molecular-simulation

display_name: molecular-simulation

monte-carlo

display_name: monte-carlo

product-distribution

display_name: product-distribution

propene-dimerization

display_name: propene-dimerization

zeolites

display_name: zeolites


en: The leucine-lysine amphiphilic peptide LKα14 has been used to study fundamental driving forces in processes such as peptide-surface binding and biomineralization. Here, we employ molecular dynamics (MD) simulations in tandem with replica exchange metadynamics to probe the binding mechanism and thermodynamics of LKα14 on silica. We also investigate the effect that the nature of the silica surface – crystalline vs. amorphous, has on the binding properties and peptide-surface conformations. We find that water adsorbs differently on both surfaces; it forms a denser interfacial layer on the crystalline surface, compared to the amorphous surface. This causes the peptide to bind more strongly on the amorphous surface than the crystalline surface. Cluster analysis shows that the peptide adopts a helical conformation at both surfaces, with a greater distribution of states on the crystalline surface. Peptide binding is primarily through lysine interactions, in line with prior experimental results.

en: Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations

enhanced-sampling

display_name: enhanced-sampling

molecular-dynamics-simulations

display_name: molecular-dynamics-simulations

peptide-surface-interactions

display_name: peptide-surface-interactions


en: Molecular self-assembly plays a very important role in various aspects of technology as well as in biological systems. Governed by covalent, hydrogen or van der Waals interactions - self-assembly of alike molecules results in a large variety of complex patterns even in two dimensions (2D). Prediction of pattern formation for 2D molecular networks is extremely important, though very challenging, and so far, relied on computationally involved approaches such as density functional theory, classical molecular dynamics, Monte Carlo, or machine learning. Such methods, however, do not guarantee that all possible patterns will be considered and often rely on intuition. Here we introduce a much simpler, though rigorous, hierarchical geometric model founded on the mean-field theory of 2D polygonal tessellations to predict extended network patterns based on molecular-level information. Based on graph theory, this approach yields pattern classification and pattern prediction within well-defined ranges. When applied to existing experimental data, our model provides an entirely new view of self-assembled molecular patterns, leading to interesting predictions on admissible patterns and potential additional phases. While developed for hydrogen-bonded systems, an extension to covalently bonded graphene-derived materials or 3D structures such as fullerenes is possible, significantly opening the range of potential future applications.

en: Polygonal tessellations as predictive models of molecular monolayers

molecular-self-assembly

display_name: molecular-self-assembly

tesselation

display_name: tesselation


en: Covalent organic frameworks (COFs) are a class of advanced nanoporous polymeric materials which combine the crystallinity of metal–organic frameworks (MOFs) with the stability and potentially low-cost organic chemistry of porous polymer networks (PPNs). Like other advanced porous materials, COFs can potentially be designed to meet the needs of a variety of applications, from energy, to security, to human health. In this work, we construct in silico a database of hypothetical three-dimensional, crystalline COFs. In constructing this library we generate novel COFs using only established synthetic routes, previously utilized tetrahedral building units, and commercially available bridging "linker" molecules. This ensures that there are no known chemical barriers to synthesizing all materials in our database. We relaxed all materials in our database through semiempirical electronic structure calculations. In addition, for those structures that allow interpenetration, we designed interpenetrated versions of the basic structure. Then, we characterized the porosity of each of these structures. The final set of 4147 structures (based on 620 unique noninterpenetrated structures) and their computed properties are publicly available and can be screened to identify promising materials for a wide variety of applications. Here, we assess the suitability of our COFs for vehicular methane storage by performing molecular simulations to predict the equilibrium methane uptake.

en: In silico design of three-dimensional porous covalent organic frameworks via known synthesis routes and commercially available species

cofs

display_name: cofs

covalent-organic-frameworks

display_name: covalent-organic-frameworks

database

display_name: database

dc

display_name: dc

deliverable-capacities

display_name: deliverable-capacities

gcmc

display_name: gcmc

grand-canonical-monte-carlo

display_name: grand-canonical-monte-carlo

high-throughput

display_name: high-throughput

methane-storage

display_name: methane-storage

nanoporous

display_name: nanoporous

three-dimensional

display_name: three-dimensional


en: Metal-organic frameworks (MOFs) have emerged as versatile materials for applications ranging from gas separation and storage, catalysis, and sensing. The attractive feature of MOFs is that by changing the ligand and/or metal, they can be chemically tuned to perform optimally for a given application. In most, if not all, of these applications one also needs a material that has a sufficient mechanical stability, but our understanding of how changes in the chemical structure influence mechanical stability is limited. In this work, we rationalize how the mechanical properties of MOFs are related to framework bonding topology and ligand structure. We illustrate that the functional groups on the organic ligands can either enhance the mechanical stability through formation of a secondary network of non-bonded interactions, or soften the material by destabilizing the bonded network of a MOF. In addition, we show that synergistic effect of the bonding network of the material and the secondary network is required to achieve optimal mechanical stability of a MOF. The developed molecular insights in this work can be used for systematic improvement of the mechanical stability of the materials by careful selection of the functional groups.

en: Improving the Mechanical Stability of Metal-Organic Frameworks Using Chemical Caryatids

envi

en: Environment

marvel

display_name: marvel

mechanical-properties

display_name: mechanical-properties

nanoporous-materials

display_name: nanoporous-materials

stability

display_name: stability


en:
This entry includes the surface structures of some prototypical semiconductors obtained via structural optimizations using the PBE density functional. The structures were initially used for benchmarking ionization potentials calculated with hybrid density functionals and GW approximation.

Seven semiconductor surfaces are provided in the form of Quantum ESPRESSO input: Si(111), C(111),  GaAs(110), GaP(110), ZnSe(110), ZnO(10-10), and TiO2(110).

en: Atomic structures of semiconductor surfaces

materialscloud

en:
Materials Cloud is a platform built to enable the seamless sharing and dissemination of resources in computational materials science, offering educational, research, and archiving tools; simulation software and services; and curated and raw data. These underpin published results and empower data-based discovery, compliant with data management plans and the FAIR principles.

In the Materials Cloud you can browse, explore, download, or deposit raw and curated data (in the Discover, Explore, and Archive sections); you can access cloud or redeployable simulation services (from AiiDAlab turnkey simulations to the Quantum Mobile virtual machine, the AiiDA registry of plugins and workflows, and the OSSCAR notebooks, in the Work section), and you can use all our educational material, tutorials and lectures (in the Learn section).

ionization-potential

display_name: ionization-potential

semiconductor

display_name: semiconductor

surface

display_name: surface


en: Weyl semimetals in three-dimensional crystals provide the paradigm example of topologically protected band nodes. It is usually taken for granted that a pair of colliding Weyl points annihilate whenever they carry opposite chiral charges. In stark contrast, here we report that Weyl points in systems symmetric under the composition of time-reversal with a π-rotation are characterized by a non-Abelian topological invariant. The topological charges of the Weyl points are transformed via braid phase factors which arise upon exchange inside symmetric planes of the reciprocal momentum space. We elucidate this process with an elementary two-dimensional tight-binding model implementable in cold-atoms setups and in photonic systems. In three dimensions, interplay of the non-Abelian topology with point-group symmetry is shown to enable topological phase transitions in which pairs of Weyl points may scatter or convert into nodal-line rings. By combining our theoretical arguments with first-principles calculations, we predict that Weyl points occurring near the Fermi level of zirconium telluride (ZrTe) carry non-trivial values of the non-Abelian charge, and that uniaxial compression strain drives a non-trivial conversion of the Weyl points into nodal lines.

en: Non-Abelian reciprocal braiding of Weyl points and its manifestation in ZrTe

materialscloud

en: Materials Cloud

epfl

display_name: epfl

non-abelian-braiding

display_name: non-abelian-braiding

snsf

display_name: snsf

taas

display_name: taas

weyl-semimetal

display_name: weyl-semimetal

zrte

display_name: zrte


en: Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these states by a large set of descriptors and employ neural networks to compress this information in a lower-dimensional space, using Fisher's linear discriminant as an objective function to maximize the discriminative power of the network. We test this method on alanine dipeptide, using the non-linearly separable dataset composed by atomic distances. We then study an intermolecular aldol reaction characterized by a concerted mechanism. The resulting variables are able to promote sampling by drawing non-linear paths in the physical space connecting the fluctuations between metastable basins. Lastly, we interpret the behavior of the neural network by studying its relation to the physical variables. Through the identification of its most relevant features, we are able to gain chemical insight into the process.

en: Data-Driven Collective Variables for Enhanced Sampling

collective-variables

display_name: collective-variables

enhanced-sampling

display_name: enhanced-sampling

erc

display_name: erc

metadynamics

display_name: metadynamics

neural-networks

display_name: neural-networks

opes

display_name: opes

plumed

display_name: plumed


en: This repository contains the PLUMED-2 input files required to generate the data used in the ITRE publications. ITRE is a method to reweight Molecular Dynamics trajectory biased with a history-dependent potential (such as Metadynamics), and calculate unbiased thermodynamic observables. Since it uses the trajectory itself as a proxy of a grid, its scaling does not depend on the dimensionality of the space explored. In addition, thanks to its formulation, it is less affected by out-of-equilibrium points that characterize the early stages of a biased calculation and are usually discarded. Thanks to this feature, it can be used to increase the statistics when evaluating a thermodynamic observable from biased calculation.

en: Iterative unbiasing of quasi-equilibrium sampling

molecular-dynamics

display_name: molecular-dynamics

statistical-mechanics

display_name: statistical-mechanics


en: Weyl semimetals are crystals in which electron bands cross at isolated points in momentum space. Associated with each crossing point (or Weyl node) is an integer topological invariant known as the Berry monopole charge. The discovery of new classes of Weyl materials is driving the search for novel properties that derive directly from the Berry charge. The circular photogalvanic effect (CPGE), whereby circular polarized light generates a current whose direction depends on the helicity of the absorbed photons, is a striking example of a macroscopic property that emerges from Weyl topology. Recently, it was predicted that the rate of current generation associated with optical transitions near a Weyl node is proportional to its monopole charge. In Weyl semimetals that retain mirror symmetry the current is strongly suppressed by contributions from energy equivalent nodes of opposite charge. However, when all mirror symmetries are broken, as in chiral Weyl systems, nodes with opposite topological charge are no longer degenerate, opening a window of photon energies where the CPGE derived from the topological band structure can emerge. In this work we report the photon-energy dependence of the CPGE in the chiral Weyl semimetal RhSi. The spectrum reveals a helicity-sensitive response in a low-energy window that closes at 0.65 eV, in quantitative agreement with the bandstucture recently predicted from DFT calculations.

en: Helicity-dependent photocurrents in the chiral Weyl semimetal RhSi

cpge

display_name: cpge

rhsi

display_name: rhsi

thz

display_name: thz

weyl

display_name: weyl


en: We present a scheme to extract the adsorption energy, adsorbate interaction parameter and the saturation coverage from temperature programmed desorption (TPD) experiments. We propose that the coverage dependent adsorption energy can be fit using a functional form including the configurational entropy and linear adsorbate-adsorbate interaction terms. As one example of this scheme, we analyze TPD of CO desorption on Au(211) and Au(310) surfaces. We determine that under atmospheric CO pressure, the steps of both facets adsorb between 0.4-0.9 ML coverage of CO*. We compare this result against energies obtained from five density functionals, RPBE, PBE, PBE-D3, RPBE-D3 and BEEF-vdW. We find that the energies and equilibrium coverages from RPBE-D3 and PBE are closest to the values determined from the TPD. This dataset contains all the DFT calculations run using AiiDA.

en: How to extract adsorption energies, adsorbate-adsorbate interaction parameters, and saturation coverages from temperature programmed desorption experiments

benchmark

display_name: benchmark

catalysis

display_name: catalysis


en: Blending organic molecules to tune their energy levels is currently investigated as an approach to engineer the bulk and interfacial optoelectronic properties of organic semiconductors. It has been proven that the ionization energy (IE) and electron affinity (EA) can be equally shifted in the same direction by electrostatic effects controlled by blending similar halogenated derivatives with different energetics. Here, we show that the energy gap of organic semiconductors can be tuned by blending as well. We use oligothiophenes with different numbers of thiophene rings as example and investigate their structure and electronic properties. Photoelectron spectroscopy and inverse photoelectron spectroscopy show tunability of the single-particle gap, with the optical gaps showing similar, but smaller effects. Theoretical analysis shows that this tuning is mainly caused by a change in the dielectric constant with blend ratio. Further studies will explore the practical impact of this energy-level engineering strategy in optoelectronic devices.

en: Band gap engineering in blended organic semiconductor films based on dielectric interactions

dielectric-interactions

display_name: dielectric-interactions

energy-level-tuning

display_name: energy-level-tuning

photoelectron-spectroscopy

display_name: photoelectron-spectroscopy

theoretical-simulations

display_name: theoretical-simulations


en: The solar water splitting process assisted by semiconductor photocatalysts attracts growing research interests worldwide for the production of hydrogen as a clean and sustainable energy carrier. Due to their optical and electrical properties several oxynitride materials show great promise for the fabrication of efficient photocatalysts for solar water splitting. This study reports a comparative investigation of particle- and thin films-based photocatalysts using three different oxynitride materials. The absolute comparison of the photoelectrochemical activities favors the particle-based electrodes due to the better absorption properties and larger electrochemical surface area. However, thin films surpass the particle-based photoelectrodes due to their more suitable morphological features that improve the separation and mobility of the photo-generated charge carriers. Our analysis identifies what specific insights into the properties of materials can be achieved with the two complementary approaches.

en: Oxynitride thin films versus particle-based photoanodes: a comparative study for photoelectrochemical solar water splitting

envi

en: Environment

marvel

display_name: marvel

oxynitride-photoanode

display_name: oxynitride-photoanode

pulsed-laser-deposition

display_name: pulsed-laser-deposition

solar-fuel

display_name: solar-fuel

solar-water-splitting

display_name: solar-water-splitting


en: The formation of large polarons has been proposed as reason for the high defect tolerance, low mobility, low charge carrier trapping and low nonradiative recombination rates of lead halide perovskites. Recently, direct evidence for large-polaron formation has been reported from a 50% effective mass enhancement in angle-resolved photoemission of CsPbBr₃ over theory for the orthorhombic structure. We present in-depth band dispersion measurements of CsPbBr₃ and GW calculations which lead to almost identical effective masses at the valence band maximum of 0.203+/-0.016 m₀ in experiment and 0.217 m₀ in orthorhombic theory. We argue that the effective mass can be explained solely on the basis of electron-electron correlation and large polaron formation cannot be concluded from photoemission data.

en: Is there a polaron signature in angle-resolved photoemission of CsPbBr₃?

materialscloud

en:
Materials Cloud is a platform built to enable the seamless sharing and dissemination of resources in computational materials science, offering educational, research, and archiving tools; simulation software and services; and curated and raw data. These underpin published results and empower data-based discovery, compliant with data management plans and the FAIR principles.

In the Materials Cloud you can browse, explore, download, or deposit raw and curated data (in the Discover, Explore, and Archive sections); you can access cloud or redeployable simulation services (from AiiDAlab turnkey simulations to the Quantum Mobile virtual machine, the AiiDA registry of plugins and workflows, and the OSSCAR notebooks, in the Work section), and you can use all our educational material, tutorials and lectures (in the Learn section).

large-polaron

display_name: large-polaron


en:
The resolving power of solid-state nuclear magnetic resonance (NMR) crystallography depends heavily on the accuracy of the computational prediction of NMR chemical shieldings of candidate structures, which are usually taken to be local minima in the potential energy surface.
To test the limits of this approximation, we perform a systematic study of the role of finite-temperature and quantum nuclear fluctuations on 1H, 13C, and 15N chemical shieldings in molecular crystals -- considering the paradigmatic examples of the different polymorphs of benzene, glycine, and succinic acid.
We find the effect of quantum fluctuations to be comparable in size to the typical errors of predictions of chemical shieldings for static nuclei with respect to experimental measurements, and to improve the match between experiments and theoretical predictions, translating to more reliable assignment of the NMR spectra to the correct candidate structure.
Thanks to the use of integrated machine-learning models trained on both first-principles configurational energies and chemical shieldings, the accurate sampling of thermal and quantum fluctuations of the structures can be achieved at an affordable cost, setting a new standard for the calculations that underlie solid-state structural determination by NMR.

This archive contains the machine-learning potentials and shielding models, sample inputs, and scripts to reproduce the results discussed in the manuscript. It further contains the reference data and scripts to reconstruct the shielding models.

en: The importance of nuclear quantum effects for NMR crystallography

materialscloud

en: Materials Cloud

first-principles-gipaw-dft

display_name: first-principles-gipaw-dft

machine-learning

display_name: machine-learning

molecular-crystals

display_name: molecular-crystals

nmr-chemical-shielding

display_name: nmr-chemical-shielding

nuclear-quantum-effects

display_name: nuclear-quantum-effects

snsf

display_name: snsf


en: Skutterudites are crystals with a cagelike structure that can be augmented with filler atoms ("rattlers"), usually leading to a reduction in thermal conductivity that can be exploited for thermoelectric applications. Here, we leverage the recently introduced Wigner formulation of thermal transport to elucidate the microscopic physics underlying heat conduction in skutterudites, showing that filler atoms can drive a crossover from the Boltzmann to the Wigner regimes of thermal transport, i.e., from particlelike conduction to wavelike tunneling. At temperatures where the thermoelectric efficiency of skutterudites is largest, wavelike tunneling can become comparable to particlelike propagation. We define a Boltzmann deviation descriptor able to differentiate the two regimes and relate the competition between the two mechanisms to the materials' chemistry, providing a design strategy to select rattlers and identify optimal compositions for thermoelectric applications.

en: Crossover from Boltzmann to Wigner thermal transport in thermoelectric skutterudites

phonons

display_name: phonons

thermal-conductivity

display_name: thermal-conductivity

thermoelectrics

display_name: thermoelectrics


en: The electronic density of states (DOS) provides information regarding the distribution of electronic energy levels in a material, and can be used to approximate its optical and electronic properties and therefore guide computational material design. Given its usefulness and relative simplicity, it has been one of the first electronic properties used as target for machine-learning approaches going beyond interatomic potentials. A subtle but important point, well-appreciated in the condensed matter community but usually overlooked in the construction of data-driven models, is that for bulk configurations the absolute energy reference of single-particle energy levels is ill-defined. Only energy differences matter, and quantities derived from the DOS are typically independent on the absolute alignment. We introduce an adaptive scheme that optimizes the energy reference of each structure as part of the training process, and show that it consistently improves the quality of ML models compared to traditional choices of energy reference, for different classes of materials and different model architectures. On a practical level, we trace the improved performance to the ability of this self-aligning scheme to match the most prominent features in the DOS. More broadly, we believe that this work highlights the importance of incorporating insights on the nature of the physical target into the definition of the architecture and of the appropriate figures of merit for machine-learning models, that translate in better transferability and overall performance.

en: Adaptive energy reference for machine-learning models of the electronic density of states

density-of-states

display_name: density-of-states

electronic-structure

display_name: electronic-structure

epfl

display_name: epfl

erc

display_name: erc


en: We present an ab initio modeling framework to simulate Majorana transport in 2D semiconducting materials, paving the way for topological qubits based on 2D nanoribbons. By combining density-functional-theory and quantum transport calculations, we show that the signature of Majorana bound states (MBSs) can be found in 2D material systems as zero-energy modes with peaks in the local density-of-states. The influence of spin-orbit coupling and external magnetic fields on Majorana transport is studied for two relevant 2D materials, WSe2 and PbI2. To illustrate the capabilities of the proposed ab initio platform, a device structure capable of hosting MBSs is created from a PbI2 nanoribbon and carefully investigated. These results are compared to InSb nanowires and used to provide design guidelines for 2D topological qubits.

en: Ab initio modeling framework for Majorana transport in 2D materials: towards topological quantum computing

ab-initio

display_name: ab-initio

majorana

display_name: majorana

quantum-transport

display_name: quantum-transport


en: We use a data-driven approach to study the magnetic and thermodynamic properties of van der Waals (vdW) layered materials. We investigate monolayers of the form A2B2X6, based on the known material Cr2Ge2Te6, using density functional theory (DFT) calculations and determine their magnetic properties, such as magnetic order and magnetic moment. We also examine formation energies and use them as a proxy for chemical stability.

en: Data-driven studies of magnetic two-dimensional materials

magnetic-materials

display_name: magnetic-materials

two-dimensional-materials

display_name: two-dimensional-materials


en: High Entropy Alloys (HEAs) are a new broad class of near-random solid solution alloys that can possess some impressive mechanical and physical properties including high stability against grain growth (i.e. low grain boundary (GB) mobility). Here, it is shown that an initially flat GB in an HEA can become spontaneously rough, driven by natural local compositional fluctuations. Roughening lowers the total GB energy and thus can inhibit migration. A parameter-free theoretical framework is developed to demonstrate the energetics and size scales of the roughening in terms of solute/GB interaction energies and GB disconnection energies. Above a critical level of solute/GB interactions, a planar GB is predicted to roughen down to the scale of the GB periodic unit. A similar theory for 1D GBs (minimum periodic length in one direction) is also developed since such geometries are common in atomistic simulations. Specific predictions are made for the symmetric tilt boundaries Σ17 [100] (530) and Σ5 [100] (310) in a model CoCuFeNi alloy and atomistic simulations demonstrate roughening consistent with the theory. Analysis of the stresses needed to drive migration shows how migration can be inhibited or enhanced, rationalizing variations in mobility of GBs in HEAs.

en: Theory of spontaneous grain boundary roughening in high entropy alloys

grain-boundaries

display_name: grain-boundaries

high-entropy-alloys

display_name: high-entropy-alloys

pinning

display_name: pinning

spontaneous-roughening

display_name: spontaneous-roughening


en:
The uploaded archive provides a ML-ready data set extracted from the juHemd database (see references) augmented with supplemental data for atomic descriptors. Descriptors provided in this data set include structural, magnetic, atomic quantities as well as derived (summed) quantities. In total, 118 possible descriptors are included of which 12 are DFT generated. For each simulation type (LDA/GGA) there is also a data set cleaned from DFT data available.

After data cleaning and preprocessing we extracted 387 LDA calculated magnetic Heusler structures as well as 408 GGA structures which have a full structural and magnetic data set. As we only aim at magnetic compounds, we chose to filter out compounds from the original JuHemd which have at least 0.1 Bohr magneton as total absolute magnetic moment. For each data file there is an existing descriptor file naming all the descriptors included in the data set.

en: ML-ready Curie temperatures and descriptors extracted from the JuHemd database

envi

en: Environment

critical-temperature

display_name: critical-temperature

curie-temperature

display_name: curie-temperature

density-functional-theory

display_name: density-functional-theory

heusler-alloy

display_name: heusler-alloy

judft

display_name: judft

kkr

display_name: kkr

machine-learning

display_name: machine-learning

magnetic

display_name: magnetic

magnetic-phase-transition

display_name: magnetic-phase-transition

magnetic-structure

display_name: magnetic-structure

max

display_name: max

monte-carlo

display_name: monte-carlo