en:
The extinct plant group Bennettitales (Cycadeoidales) was a prominent part of Mesozoic vegetation. The group has been studied extensively and for more than 100 years it has been central in discussions of the relationships among the major groups of seed plants in which extinct plants were also considered. Despite much effort the phylogenetic position of the Bennettitales is still unresolved with a major obstacle being uncertainty about how to interpret the organisation and structure of the seed. The most widely accepted interpretation has been that the seed, like the seeds of most conifers, has a single integument around the nucellus and lacks any additional coverings. An alternative interpretation is that the seed integument is surrounded by an envelope comparable to the situation in extant Gnetales and extinct Erdtmanithecales. The petrified seed cone of Cycadeoidea (Bennettites) morierei described in the late nineteenth century from the Early Cretaceous of Normandy is one of the most informative bennettitalean reproductive structures with its superb preservation offering great potential for resolving the unsettled discussion regarding seed structure in Bennettitales.
	C. morierei was carefully documented by Octave Lignier in his monumental study “Végétaux fossiles de Normandie. Structure et affinités du Bennettites morierei Sap. & Mar. (sp.)” from 1894, but despite his meticulous analysis of the fossil, Lignier left certain questions open in his interpretation and in his widely cited reconstruction of the structure of the seed. In the paper associated with the datasets provided here we have re-examined fragments of Cycadeoidea morierei using synchrotron X-ray tomographic microscopy (SRXTM) to attempt to answer some of these open questions.
	Cycadeoidea morierei is based on a single petrified seed cone. The specimen was fractured by Lignier, who prepared several thin sections, in longitudinal as well as transverse directions in preparing his account. The original material was stored at the University of Caen, France, but most was lost during the second World War. However, several larger and smaller fragments of the seed cone were later recovered at the university and made available for the present study. Among the fragments studied using SRXTM were small isolated, abraded seeds and interseminal scales (e.g., fragments 6 and 8) and a few small groups of fractured seeds and interseminal scales still tightly packed together (e.g., fragment 17). Typically, these small fragments are broken at the base and only rarely are remains of the seed stalk preserved. One larger fragment (fragment 24) consists of several seeds with seed stalks intact. For comparison with Cycadeoidea morierei we also examined a fragment of another classic petrified seed cone, Cycadeoidea gibsoniana from the Early Cretaceous of isle of Wight, Southern England, using SRXTM. The results, combined with a comparative survey of other fossil material, indicate that the seeds of Bennettitales had at least one, perhaps two, envelopes covering the integument, comparable to what is seen among extant Gnetales, extinct Erdtmanithecales, and diverse fossil seeds recovered from Early Cretaceous mesofossil assemblages. Most of the SRXTM analyses of the Cycadeoidea material were carried during 2009-2023 on the TOMCAT beamline, SLS, Paul Scherrer Institute, Villigen, Switzerland. Fragment 24 was analysed at the new I-TOMCAT beamline at SLS in November 2025.

en: Synchrotron radiation X-ray tomographic microscopy datasets for seed structure in Cycadeoidea morierei

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.


$oid: OBSOLETE

en: Plasticity in amorphous SiO2 at the micro-scale is an unsolved problem. We aim to study the responsible deformation mechanisms (densification, shear flow, and shear band formation) and propose a Ptychographic X-ray Computed Tomography (PXCT) experiment to image the three-dimensional density distribution in plastically deformed silica micro-pillars. Understanding the spatial extend and geometric aspects of these mechanisms will contribute to the technological exploitation of these phenomena.

en: Direct observation of micro-plasticity in fused silica glass

approval_status: approved

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: This dataset has been used in the work titled ‘Metamorphic fabrics can be formed by stress without significant strain’ by Gilgannon et al. (2023). It was acquired at the TOMCAT beamline as part of a long term science proposal called ‘Implementing novel X-ray transparent triaxial deformation rigs to study fluid-rock interaction at mid-crustal conditions’. This research was funded through NERC standard grant NE/T001615/1.

en: Metamorphic fabrics can be formed by stress without significant strain - sample VA17


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 - SFX datasets


en:
This repository contains the complete dataset and associated software supporting the publication:
“In-Situ Ptychographic Nanotomography Captures Activation, Mobility, and Deactivation of Supported Catalysts”

The data were acquired using in-situ ptychographic X-ray computed nanotomography (PXCT) and used to investigate structural evolution of Pd-on-silica catalysts under methane oxidation conditions.
Experiments were performed at the cSAXS beamline of the SLS.

The dataset includes raw diffraction data, reconstructed projections, 3D electron density tomograms, and analysis/reconstruction codes.

Codes:
cxs_software_ptychography/  Contains ptychographic reconstruction routines (phase retrieval, scan handling, preprocessing).
cxs_software_tomography/    Contains tomographic reconstruction and 3D volume processing tools.

Raw Data
S03000-03999_ID ...     Raw diffraction datasets acquired during in-situ scanning nanotomography experiments

Reconstructed Data
analysis_S03000-03999 ...    Includes phase and/or amplitude porjection reconstructions
reconstructed_tomograms    Volumetric datasets derived from ptychographic projections used for analysis

en: Data and Software Supporting: In-Situ Ptychographic Nanotomography Captures Activation, Mobility, and Deactivation of Supported Catalysts

heterogeneous-catalysis

display_name: heterogeneous-catalysis

x-ray-ptychography

display_name: x-ray-ptychography

x-ray-tomography

display_name: x-ray-tomography


en: Metamorphic fabrics can be formed by stress without significant strain - sample VA10


en: Metamorphic fabrics can be formed by stress without significant strain - sample VA_A


en:
The experimental realisation of unconventional superconductivity and charge order
in kagome systems AV3Sb5 is of critical importance. This work presents the most
systematic study to date, employing tuning parameters such as doping, hydrostatic
pressure, magnetic fields, and depth, using muon spin rotation, AC susceptibility, and
STM, to uncover tunable exotic magnetism in the normal state of Cs(V1−xNbx)3Sb5
with x=0.07 (Nb0.07-CVS), which transitions to a chiral superconducting state under
pressure. Our findings reveal that the bulk of Nb0.07-CVS (at depths >20 nm from the
surface) experiences time-reversal symmetry (TRS) breaking below T ∗ = 40 K, lower
than the charge order onset temperature, TCO = 58 K. However, near the surface (<20
nm), the TRS breaking signal doubles and onsets at TCO, indicating that Nb-doping
decouples TRS breaking from charge order in the bulk but synchronises them near
the surface. Additionally, Nb-doping raises the superconducting critical temperature
TC from 2.5 K to 4.4 K. Applying hydrostatic pressure enhances both TC and the
superfluid density by a factor of two, with a critical pressure pcr ≃ 0.85 GPa, suggesting
competition with charge order. Notably, above pcr, we observe nodeless electron pairing
and weak internal fields below TC, pointing to chiral superconducting pairing. Overall,
these results demonstrate a highly unconventional normal state with a tunable onset of
TRS breaking, and a transition to chiral superconductivity under low pressures, with
an unconventional correlation between TC and the superfluid density.

en: Pressure induced transition from chiral charge order to time-reversal symmetry-breaking superconducting state in Nb-doped CsV3Sb5 - LEM data


en: The small size, the location (embedded in the temporal bone), and the tiny movements of the three ossicles of the human middle ear make the study of sound transmission through the human auditory system extremely challenging. From the encouraging results of our previous investigations with dynamic synchrotron-based phase-contrast microtomography (proposal 20200954), we aim to further characterize the biomechanics of the human middle ear. The goal is to stimulate the middle ear with a broad range of sound frequencies, covering a wider spectrum of the human voice, together with a range of sound intensities meeting physiological criteria.

en: DYNAMITE: DYNamic phAse-contrast MIcro-Tomography of the human middle Ear


en:
In the original article associated with this dataset, we present synchrotron radiation-based X-ray phase-contrast imaging (X-PCI) as an efficient and non-destructive imaging technique to provide high resolution, three-dimensional (3D) information on myocardial microstructure in left ventricular hypertrophy. In the pilot study, the methodology was applied on tissue samples obtained from three patients that underwent septal myectomy. This technique allows for multi-scale investigation - to localize regions of interest, low resolution overlapping scans, at 5.8um effective pixel size, were achieved to cover the entire sample, whereas high resolution datasets, at 0.65 um pixel size, were collected locally allowing assessment of myocyte organization, 3D connective tissue distribution and vasculature.
X-PCI data was visualized and analyzed. 3D myocyte arrangement, interstitial fibrosis, collagen disarray, and vascular remodelling were identified and related to findings of non-invasive cardiac imaging. The integration of imaging data data illustrates the correspondence of macrostructural and functional non-invasive phenotypes with invasive microstructural phenotypes, suggesting the potential clinical utility of non-invasive myocardial deformation patterns in phenotyping left ventricular hypertrophy.

en: Etiology-Discriminative Multimodal Imaging of Left Ventricular Hypertrophy and Synchrotron-Based Assessment of Microstructural Tissue Remodeling

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: 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: Dark state

en: PSI Data Catalog


en: The associated article to these datasets describes a new genus and two new species from the Late Cretaceous (Campanian-Maastrichtian) Mira locality, District of Coimbra, Portugal. The new taxa are based on small lignitized and charcoalified flower buds, post-anthetic flowers and a fruit. Internal structures of the fossils were investigated using synchrotron radiation X-ray tomographic microscopy at the TOMCAT Beamline, Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland. Internal structures and other details provide clear evidence for a phylogenetic position of the fossils in the family Primulaceae of the order Ericales. A key distinctive feature that is critical for placing the fossils in the Primulaceae s. l., is the free, central dome-shaped placenta that bears numerous, densely spaced ovules. The fruit matured into a capsule containing many, minute, reticulate seeds. Phylogenetic analyses using external and internal features of the fossils confirm their relationship to Primulaceae s. l. and indicate a position as sister to the genus Samolus of the subfamily Theophrastoideae. The occurrence of these fossils in the Late Cretaceous calls into question a previous hypothesis that the Theophrastoideae originated in the Neotropics and dispersed relatively recently into other regions.

en: Synchrotron radiation X-ray tomographic microscopy datasets for primuloid flowers from the Late Cretaceous of Portugal

envi

en: Environment


en: Data of the paper "Global sensitivity analysis on numerical solver parameters of Particle-In-Cell models in particle accelerator systems" published in Computer Physics Communications. The data is generated as part of the PhD thesis funded by the Swiss National Science Foundation (SNSF) under contract number 200021_159936.

en: Data of of a global sensitivity study of the PSI Injector 2, PSI Ring Cyclotron, IsoDAR and AWA RF gun


en: This dataset has been used in the work titled ‘Metamorphic fabrics can be formed by stress without significant strain’ by Gilgannon et al. (2023). It was acquired at the TOMCAT beamline as part of a long term science proposal called ‘Implementing novel X-ray transparent triaxial deformation rigs to study fluid-rock interaction at mid-crustal conditions’. This research was funded through NERC standard grant NE/T001615/1.

en: Metamorphic fabrics can be formed by stress without significant strain - sample VA18


en: The ability of photofunctional organic molecules to perform chemical/mechanical work or convert photons into electrons results from a complex interplay between charge transfer and transient atomic rearrangements involving the local environment. These ultrafast structural dynamics have remained elusive experimentally, preventing a mechanistic understanding of the electronic-nuclear couplings. We will use the high X-ray photon flux and sub ps time resolution of the SwissFEL to realize the first X-ray scattering observation of solute-solvent dynamics following photoinduced charge transfer in an organic chromophore. The sensitivity of the scattering to changes in atomic distances will be exploited not only to track in real time the intra- and intermolecular structural dynamics but also to identify the electronic changes that trigger them. The results will pave the way for a better understanding of the factors governing the outcomes of photoreactions across chemistry and biology.

en: Photoinduced intramolecular and solvation dynamics of an organic chromophore in polar solvent


en:
Two-dimensional magnetic materials attract a lot of attention since
they potentially exhibit new magnetic properties due to, e.g., strongly
enhanced spin fluctuations. However, the suppression of the long-range
magnetic order in two dimensions due to long-wavelength spin fluctuations,
as suggested by the Mermin-Wagner theorem, has been questioned
for finite-size laboratory samples. Here we study the magnetic properties
of a dimensional crossover in superlattices composed of the antiferromagnetic
LaFeO3 and SrTiO3 that, thanks to their large lateral size, allowed
examination using a sensitive magnetic probe — muon spin rotation spectroscopy.
We show that the iron electronic moments in superlattices with
3 and 2 monolayers of LaFeO3 exhibit a static antiferromagnetic order. In
contrast, in the superlattices with single LaFeO3 monolayer, the moments
do not order and fluctuate to the lowest measured temperature as expected
from the Mermin-Wagner theorem. Our work shows how dimensionality
can be used to tune the magnetic properties of ultrathin films.

en: Magnetic properties of LaFeO3/SrTiO3 superlattices


en:
Tomography data published in A. Mularczyk et al. (2020). 'Droplet and Percolation Network Interactions in a Fuel Cell Gas Diffusion Layer', Journal of The Electrochemical Society 167(8): 084506. https://doi.org/10.1149/1945-7111/ab8c85
###### The tomographic data of liquid water observed in the flow field channel was used also in Andersson, M., et al. (2018). "Modeling and synchrotron imaging of droplet detachment in gas channels of polymer electrolyte fuel cells." Journal of Power Sources 404: 159-171. https://doi.org/10.1016/j.jpowsour.2018.10.021
###### The tomographic data of liquid water observed in the GDL and flow field channel was also used in Niblett, D., et al. (2020). "Two-phase flow dynamics in a gas diffusion layer - gas channel - microporous layer system." Journal of Power Sources 471: 228427.  https://doi.org/10.1016/j.jpowsour.2020.228427
###### A small ROI segmentation around the water cluster in GDL of this dataset can be accessed under https://doi.org/10.16907/13dc29a3-733b-419b-ad61-838d17ddfa47
###### The Raw CT data of this dataset can be accessed under https://doi.org/10.16907/63ac1a63-8ab6-4a92-be5a-db499c9e7e6a

en: Tomographic data set of dynamic liquid water injection into SGL 25 BA gas diffusion layer: Large ROI segmentation

lamibracmularczyk-paper

display_name: lamibracmularczyk-paper

liquid-injection

display_name: liquid-injection

sgl

display_name: sgl

tomcat

display_name: tomcat


en: The experimental realisation of unconventional superconductivity and charge order in kagome systems AV3Sb5 is of critical importance. This work presents the most systematic study to date, employing tuning parameters such as doping, hydrostatic pressure, magnetic fields, and depth, using muon spin rotation, AC susceptibility, and STM, to uncover tunable exotic magnetism in the normal state of Cs(V1−xNbx)3Sb5 with x=0.07 (Nb0.07-CVS), which transitions to a chiral superconducting state under pressure. Our findings reveal that the bulk of Nb0.07-CVS (at depths >20 nm from the surface) experiences time-reversal symmetry (TRS) breaking below T ∗ = 40 K, lower than the charge order onset temperature, TCO = 58 K. However, near the surface (<20 nm), the TRS breaking signal doubles and onsets at TCO, indicating that Nb-doping decouples TRS breaking from charge order in the bulk but synchronises them near the surface. Additionally, Nb-doping raises the superconducting critical temperature TC from 2.5 K to 4.4 K. Applying hydrostatic pressure enhances both TC and the superfluid density by a factor of two, with a critical pressure pcr ≃ 0.85 GPa, suggesting competition with charge order. Notably, above pcr, we observe nodeless electron pairing and weak internal fields below TC, pointing to chiral superconducting pairing. Overall, these results demonstrate a highly unconventional normal state with a tunable onset of TRS breaking, and a transition to chiral superconductivity under low pressures, with an unconventional correlation between TC and the superfluid density.

en: Pressure induced transition from chiral charge order to time-reversal symmetry-breaking superconducting state in Nb-doped CsV3Sb5 - GPS data

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.

gps

display_name: gps

smus

display_name: smus


en: In the associate article to these data sets, we present an X-ray tomographic imaging method that is well suited for pulmonary disease studies in animal models, to resolve the full pathway from gas intake to gas exchange. Current state-of-the-art synchrotron-based tomographic phase-contrast imaging methods allow for three-dimensional microscopic imaging data to be acquired non-destructively in scan times of the order of seconds with good soft tissue contrast. However, when studying multi-scale hierarchically structured objects, such as the mammalian lung, the overall sample size typically exceeds the field of view illuminated by the X-rays in a single scan, and the necessity for achieving a high spatial resolution conflicts with the need to image the whole sample. Several image-stitching and calibration techniques to achieve extended high-resolution fields of view have been reported, but those approaches tend to fail when imaging non-stable samples, thus precluding tomographic measurements of large biological samples, which are prone to degradation and motion during extended scan times. In this work, we demonstrate a full-volume three-dimensional reconstruction of an intact rat lung under immediate post mortem conditions and at an isotropic voxel size of (2.75 µm)^3. We present the methodology for collecting multiple local tomographies with 360 degree extended field of view scans followed by locally non-rigid volumetric stitching. Applied to the lung, it allows to resolve the entire pulmonary structure from the trachea down to the parenchyma in a single dataset.

en: Micrometer-resolution X-ray tomographic imaging of a complete intact post mortem juvenile rat lung

en: PSI Data Catalog


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

envi

en: Environment


en: Low-energy muSR (LE-muSR) enables depth-resolved studies of magnetic and electronic properties from the surface into the near-surface region, but the measured transverse-field asymmetry is not an intrinsic constant but depends on implantation energy and beamline conditions. Following an upgrade of the single-muon tagging system at the LEM beamline at PSI in 2023, updated asymmetry calibrations are required. Here, we present updated reference measurements that establish the energy-dependent maximum asymmetry using a silver reference and quantify spurious contributions from reflected muons using a nickel reference. In addition, we address systematic reductions of the measured asymmetry arising from incomplete beam--sample overlap by introducing a sample-size-dependent correction factor. This factor is obtained from musrSim/Geant4 simulations incorporating an updated electrostatic field map of the sample environment and is benchmarked using implantation-energy scans on SrTiO3 samples of different dimensions. Together, these updated calibrations and the simulation-based overlap correction provide a practical and up-to-date framework for LE-muSR data correction under current beam conditions and enable quantitative depth-resolved analysis of (dia)magnetic volume fractions.

en: Correcting the Depth-Dependent Asymmetry in Low-Energy muSR


en:
This time-resolved tomographic microscopy dataset captures disintegration dynamics of pharmaceutical tablets. A diverse set of mini-tablets of 2 mm diameter with compositions varied according to a full factorial design of experiments were individually imaged as they underwent disintegration in water. We established a predominantly GPU based software pipeline for raw data reconstruction, including phase contrast filtering, and reconstructed image segmentation to enable visualization and quantitative analysis. The experimental system was highly dynamic, such that the quality of reconstructed images is impeded by motion artefacts, especially at advanced stages of tablet disintegration. To meet the challenges of varying image quality, we devised and trained a convolutional neural network (CNN) based on the U-Net architecture to segment the reconstructed images. Only the segmented data enables visualization for qualitative analysis and allows for quantification of the captured disintegration process.

Detailed descriptions of data acquisition parameters, the custom software pipeline used for image reconstruction and image segmentation, as well as a sample analysis of the data are discussed in the associated publicaton : https://doi.org/10.1016/j.heliyon.2024.e26025
The source code of the software pipeline used to reconstruct and segment the data is available here: https://github.com/walsam00/4D_CT_code
Videos visualizing the entire dataset are available here: https://zenodo.org/doi/10.5281/zenodo.7180040 as well as here:
https://www.youtube.com/watch?v=yESTXXv6wbM&list=PLPnSoY_iHSc410wtWpewTeFN3koH3gkQw&index=1

en: Three - dimensional reconstruction of time-resolved disintegration process in pharmaceutical tablets


en: In this work, we map the charge carrier concentration as a function of depth and electric field across the SiO2/Si interface up to a depth of 100 nm in Si-based MOS capacitors using low-energy muons. The results show that the formation of the anisotropic bond-centered muonium MuBC state in Si serves as a direct measure of the local changes in electronic structures, which were detected and scanned for a range of depths. In general, any muonium state in a semiconductor can be used as a sensitive probe for the presence of free charge carriers. Therefore, our work represents a significant extension of the application of the muon spin rotation technique (μSR) and lays the foundation for further research on direct observation of charge carrier density manipulation at technologically important semiconductor device interfaces.

en: Charge carrier distribution observation and manipulation in Si-MOS


en: This dataset has been used in the work titled ‘Metamorphic fabrics can be formed by stress without significant strain’ by Gilgannon et al. (2023). It was acquired at the TOMCAT beamline as part of a long term science proposal called ‘Implementing novel X-ray transparent triaxial deformation rigs to study fluid-rock interaction at mid-crustal conditions’. This research was funded through NERC standard grant NE/T001615/1.

en: Metamorphic fabrics can be formed by stress without significant strain - sample VA_B


en: The data is part of a manuscript submitted to the journal Chem. Sci., entitled "Isomer-dependent catalytic pyrolysis mechanism of the lignin model compounds catechol, resorcinol and hydroquinone". [DOI	https://doi.org/10.1039/D1SC00654A, Chem. Sci., 2021,12, 3161-3169 ] This work is supported by the Swiss National Science Foundation (project number 200021_178952).

en: Dataset: Isomer-dependent catalytic pyrolysis mechanism of the lignin model compounds catechol, resorcinol and hydroquinone


en: Metamorphic fabrics can be formed by stress without significant strain - sample VA19

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: Analyzing the structure and dynamics of the human middle ear is crucial for understanding biomechanics and improving clinical practice; however, characterizing middle ear structures is challenging due to their small sizes, location inside the temporal bone, and minute displacements. Synchrotron radiation-based X-ray microtomography can visualize both the soft and hard tissues of the entire intact middle ear with micrometer resolution. Unfortunately, access to synchrotron radiation facilities is limited and handling the related TB-scale data volumes requires high performance computing infrastructure. Data sharing efforts can increase accessibility and encourage development of new research directions. Here, we share static microtomography datasets covering the entire middle ear and surroundings for 15 fresh-frozen human temporal bones with voxel sizes of 2.75 or 5.8 µm. These datasets allow for the analysis of rich anatomical information across a range of specimens.

en: Static synchrotron X-ray microtomography of 15 intact human middle ears

en: x-ray-microtomography hearing-research synchrotron-radiation middle-ear anatomy

anatomy

display_name: anatomy

hearing-research

display_name: hearing-research

middle-ear

display_name: middle-ear

synchrotron-radiation

display_name: synchrotron-radiation

x-ray-microtomography

display_name: x-ray-microtomography


en: Metamorphic fabrics can be formed by stress without significant strain - sample VA22

en: PSI Data Catalog


en:
The articles based on this dataset discuss wicking in polyethylene terephthalate (PET) yarns using time-resolved X-ray tomographic microscopy. Wicking is a two-phase flow phenomenon in porous media where a wetting fluid replaces spontaneously the non-wetting fluid, here water and air.
The employed setup provides high-quality four-dimensional imaging of water uptake in yarns in a FOV of 3.3 mm height at 2.75 um voxel size and up to one full scan per second. The segmented data gives the detailed inter-fiber pore structure and allows to track the evolution of the water configuration at pore level with its evolution of free (interfacial) energy. We find that water wicking in yarns happens as network propagation with two types of steps: rapid pore filling events and long delays between those events. The long delays are caused by an unfavorable free energy evolution at structure-induced quasi-equilibria. Due to the sparsity of the pore network and the lack of alternative propagation paths, macroscopic wicking in yarns shows irregular step-wise dynamics with high variability.

en: Wicking dynamics in complex yarn pore networks

envi

en: Environment


en: Recently, we have fabricated heterostructures formed by a ferromagnetic topological insulator Cr-doped (Bi,Sb)2Te3 (CBST) and a non-superconducting antiferromagnet FeTe. Combining electrical transport and ARPES measurements, we demonstrate the coexistence of emergent superconductivity, ferromagnetism, and topological order in these heterostructures; these three essential ingredients make this an ideal candidate to host chiral topological superconductivity. We propose performing low-energy muSR measurements to study the nature of this interface-induced superconducting state, and to determine whether the superconductivity and magnetic order coexist in the same region.

en: Coexistence of Superconductivity and Magnetic Order in Magnetic Topological Insulator Heterostructures


en: High-temperature and high-magnetic-field-induced re-entrant superconductivity has been discovered in the infinite-layer nickelate Sm1−x−yEuxCayNiO2 (SECNO). Infinite-layer nickelates are the closest known analogues of high-Tc cuprate superconductors, yet they host distinct magnetic ground states. Using low-energy muon spin relaxation and polarized neutron reflectometry, we reveal the magnetic order in SECNO. We find that magnetic freezing occurs at a higher-temperature than in other nickelate compounds, and that a substantial net magnetization of 55 kA m−1 ±10 kA m−1 emerges and remains largely unchanged across the superconducting transition. The magnetism in SECNO is disordered and nonuniform.

en: Net Magnetization and Inhomogeneous Magnetic Order in a High-Tc Nickelate Superconductor


en: This dataset contains time-resolved X-ray tomographic microscopy on wicking in interlacing polyethylene terephthalate (PET) yarns.  Wicking is a two-phase flow phenomenon in porous media where a wetting fluid replaces spontaneously the non-wetting fluid, here water and air. The employed setup provides high-quality four-dimensional imaging of water uptake in yarn interlaces in a FOV of 5.5 mm height at 2.75 um voxel size and up to 2.5 full scans per second. The segmented data gives the detailed inter-fiber pore structure and allows to track the evolution of the water configuration at pore level with its evolution of free (interfacial) energy.  Yarn-to-yarn transition is found to coincide with slow water advance in a thin interface zone at the yarn contact. The pore spaces of the two yarns merge within this interface zone and provide a transition path. A deep capillary pressure minimum occurs while water passes through the center of the interface zone, effectively delaying the wicking flow.

en: Wicking through complex interfaces at interlacing yarns


en: The article associated with the datasets provided here presents a summary of the diverse and abundant occurrence of chloranthoid fossils from Cretaceous strata, along with the description of three new genera from the Early Cretaceous of Portugal and North America; the pistillate floral structures of Swamyflora and Wasmyflora and the staminate floral structures of Asterostemon. All three genera are related to extant Hedyosmum and extinct Hedyflora. The diversity of extinct chloranthoids during the Cretaceous is considerable and has revealed a number of unexpected features that help clarify the evolution of several unusual floral features of extant Chloranthaceae. Swamyflora and Wasmyflora, together with the previously described fossils of Hedyflora, are of particular importance in understanding the divergent seed coat anatomy and unusual hypanthial outgrowths of extant Hedyosmum. The description of the new Hedyosmum-like fossils is based on synchrotron radiation X-ray tomographic microscopy (SRXTM) of seven specimens of Swamyflora (PP56596, PP57072, PP57073, PP57100, PP57101, PP57106, PP57747 from the Puddledock mesofossil flora) and one specimen of Wasmyflora (S266319 from the Vale de Água mesofossil flora). The datasets supporting the descriptions are provided here together with datasets for four specimens of Hedyflora also studied using SRXTM (Hedyflora crystallifera: S172328 from the Buarcos mesofossil flora and S174186 from the Vale de Água mesofossil flora; Hedyflora sp. A: PP44116 from the Puddledock mesofossil flora; Hedyflora sp. B: PP54022 from Kenilworth mesofossil flora).

en: Synchrotron radiation X-ray tomographic microscopy datasets for Early Cretaceous Hedyosmum-like fossils from Portugal and North America


en: Here we present 1,000 structures each of a water monomer, water dimer, Zundel cation and bulk water used to train tensorial machine-learning models in Phys. Rev. Lett. 120, 036002 (2018). The archive entry contains files in extended-XYZ format including the structures and several tensorial properties: for the monomer, dimer and Zundel cation, the dipole moment, polarizability and first hyperpolarizability are included, and for bulk water the dipole moment, polarizability and dielectric tensor are given.

en: Symmetry-Adapted Machine Learning for Tensorial Properties of Atomistic Systems

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

bulk

display_name: bulk

dielectric-tensor

display_name: dielectric-tensor

dipole-moment

display_name: dipole-moment

hyperpolarizability

display_name: hyperpolarizability

machine-learning

display_name: machine-learning

molecular

display_name: molecular

polarizability

display_name: polarizability

water

display_name: water


en: Biomolecular simulations have a great potential in protein engineering, drug discovery and many other fields. Unfortunately, this method is computationally expensive, so many interesting processes cannot be routinely studied. In order to address this problem we developed Flying Gaussian method [Journal of Chemical Theory and Computation 12, 4644-4650 (2016)]. This method simultaneously simulates multiple replicas of the studied system and disfavor replicas with similar structures by artificial bias potential. The question arises how to calculate an unbiased free energy surface from a biased simulation. This dataset demonstrates together with mathematical arguments supports application of Umbrella Sampling reweighing method, despite the fact that this method is designed for methods with a time-independent bias potential.

en: Free-Energy Surface Prediction by Flying Gaussian Method: Numerical Proof

flying-gaussian-method

display_name: flying-gaussian-method

metadynamics

display_name: metadynamics

molecular-dynamics-simulation

display_name: molecular-dynamics-simulation

sampling

display_name: sampling


en: We report a large-scale density-functional-theory study of the configuration space of water ice. We geometry optimise 74,963 ice structures, which are selected and constructed from over five million tetrahedral networks listed in the databases of Treacy and Deem, and the International Zeolite Association database. All prior knowledge of ice is set aside and we introduce generalised convex hulls to identify configurations stabilised by appropriate thermodynamic constraints. We thereby rediscover all known phases (I to XVII, i, 0 and the quartz phase) except the metastable ice IV. Crucially, we also find promising candidates for ices XVIII through LI. Using the sketch-map dimensionality-reduction algorithm we construct an a priori, navigable map of configuration space, which reproduces similarity relations between structures and highlights the novel candidates. By relating the known phases to the tractably small, yet structurally diverse set of synthesisable candidate structures, we provide an excellent starting point for identifying formation pathways.

en: Mapping uncharted territory in ice from zeolite networks to ice structures

database

display_name: database

dft

display_name: dft

first-principles

display_name: first-principles

high-throughput

display_name: high-throughput

ice

display_name: ice

three-dimensional

display_name: three-dimensional


en: The nature of the bulk hydrated electron has been a challenge for both experiment and theory due to its short lifetime and high reactivity, and the need for a high-level of electronic structure theory to achieve predictive accuracy. The lack of a classical atomistic structural formula makes it exceedingly difficult to model the solvated electron using conventional empirical force fields, which describe the system in terms of interactions between point particles associated with atomic nuclei. Here we overcome this problem using a machine-learning model, that is sufficiently flexible to describe the effect of the excess electron on the structure of the surrounding water, without including the electron in the model explicitly. The resulting potential is not only able to reproduce the stable cavity structure but also recovers the correct localization dynamics that follow the injection of an electron in neat water. The machine learning model achieves the accuracy of the state-of-the-art correlated wave function method it is trained on. It is sufficiently inexpensive to afford a full quantum statistical and dynamical description and allows us to achieve accurate determination of the structure, diffusion mechanisms, and vibrational spectroscopy of the solvated electron.

en: Simulating the ghost: quantum dynamics of the solvated electron

envi

en: Environment

cscs

display_name: cscs

marvel

display_name: marvel

moller-plesset-perturbation-theory

display_name: moller-plesset-perturbation-theory

quantum-dynamics

display_name: quantum-dynamics

snsf

display_name: snsf

solvated-electron

display_name: solvated-electron


en: We introduce and discuss the phenomenon of adatom-induced surface local melting, using extensive first-principles molecular dynamics simulations of Al(100) taken as a paradigmatic case of a non-premelting surface that nevertheless displays facile adatom diffusion with single and multiple exchange pathways. Here, a single adatom deposited on the surface is sufficient to nucleate a localized and diffusing liquid-like region that remains confined to the surface layer, but with an area that increases with temperature; in the absence of the adatom, the surface instead remains crystalline until reaching the bulk melting temperature.

en: Adatom-Induced Local Melting

aluminum

display_name: aluminum

defects

display_name: defects

first-principles-molecular-dynamics

display_name: first-principles-molecular-dynamics

surface-melting

display_name: surface-melting


en: Solid-state electrolytes for Li-ion batteries are attracting growing interest as they allow building safer batteries, also using lithium-metal anodes. Here, we studied a compound in the lithium superionic conductor (LISICON) family, i.e. Li₄₋ₓGe₁₋ₓPₓO₄ (LGPO). Thin films were deposited via pulsed laser deposition, and their electrical properties were compared to those of ceramic pellets. A detailed characterization of their microstructures shows that thin films can be deposited fully crystalline at higher temperatures but also partially amorphous at room temperature. The conductivity is not strongly influenced by the presence of grain boundaries, exposure to air, or lithium deficiencies. First-principles molecular dynamics simulations were employed to calculate the lithium-ion diffusion profile and the conductivity at various temperatures of the ideal LGPO crystal. Simulations give the upper limit of conductivity for a defect-free crystal, which is in the range of 10–2 S cm–1 at 300 °C. The ease of thin-film fabrication and room-temperature Li-ion conductivity in the range of a few μS cm–1 make LGPO a very appealing electrolyte material for thin-film all-solid-state all-oxide microbatteries.

en: Li₄₋ₓGe₁₋ₓPₓO₄, a potential solid-state electrolyte for all-oxide microbatteries

big-map

display_name: big-map

ionic-transport

display_name: ionic-transport

lgpo

display_name: lgpo

lisicon

display_name: lisicon

microbatteries

display_name: microbatteries

solid-state-electrolytes

display_name: solid-state-electrolytes

thin-films

display_name: thin-films


en:
Project abstract: Frustrated magnets are one class of fascinating materials that host many intriguing phases such as spin ice, spin liquid and complex long-range magnetic orderings at low temperatures. In this work we use first-principles calculations to find that in a wide range of magnetically frustrated oxides, at zero temperature a number of non-collinear magnetic orderings are more stable than the type-I collinear ordering that is observed at finite temperatures. The emergence of non-collinear orderings in those complex oxides is due to higher-order exchange interactions that originate from second-row and third-row transition metal elements. This implies a collinear-to-noncollinear spin transition at sufficiently low temperatures in those frustrated complex oxides. Furthermore, we find that in a particular oxide Ba2YOsO6, experimentally feasible uniaxial strain can tune the material between two different non-collinear magnetic orderings. Our work predicts new non- collinear magnetic orderings in frustrated complex oxides at very low temperatures and provides a mechanical route to tuning complex non-collinear magnetic orderings in those materials.

About this entry:  We provide the input files of our DFT calculations for the studied complex oxides.  The structures in POSCAR format and the INCAR files for all stabilized magnetic orderings in our study are all included. These files can be directly used into DFT calculations with VASP.

en: The complex non-collinear magnetic orderings in Ba2YOsO6: A new approach to tuning spin-lattice interactions and controlling magnetic orderings in frustrated complex oxides

double-perovskite

display_name: double-perovskite

first-principles-calculations

display_name: first-principles-calculations

frustrated-complex-oxides

display_name: frustrated-complex-oxides

non-collinear-magnetic-ordering

display_name: non-collinear-magnetic-ordering

spin-orbital-coupling

display_name: spin-orbital-coupling


en:
Here we present 69,840 covalent organic frameworks (COFs) assembled in silico from a set of 666 distinct organic linkers into 2D-layered and 3D configurations. We investigate the feasibility of using these frameworks for methane storage by using grand-canonical Monte Carlo (GCMC) simulations to calculate their deliverable capacities (DCs). From these calculations, we predict that the best structure in the database is linker91_C_linker91_C_tbd, a structure composed of carbon-carbon bonded triazine linkers in the tbd topology. This structure has a predicted 65-bar DC of 216 v STP/v, greater than that of the best current methane storage material. We also predict other top performing materials, with 305 structures having DCs of over 190 v STP/v, and 34 of these having DCs of over 200 v STP/v.
This archive entry contains the database of assembled COF structures (in CIF file format) together with all of their properties, which can be explored using interactive figures. Among the calculated properties for each structure are the framework density, the methane heats of desorption at the storage and depletion pressures, the methane uptakes at the storage and deplation pressures, the supercell volume, and the geometric surface area. Structures are also labeled according to their bond types (amide, amine, imine, carbon-carbon, or mixed) and their dimensionalities (2D or 3D).

en: In Silico Design of 2D and 3D Covalent Organic Frameworks for Methane Storage Applications

cof

display_name: cof

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

layered

display_name: layered

marvel

display_name: marvel

methane-storage

display_name: methane-storage

nanoporous

display_name: nanoporous

three-dimensional

display_name: three-dimensional

two-dimensional

display_name: two-dimensional


the-geometric-blueprint-of-perovskites

en: Perovskite minerals form an essential component of the Earth's mantle, and synthetic crystals are ubiquitous in electronics, photonics, and energy technology. The extraordinary chemical diversity of these crystals raises the question of how many and which perovskites are yet to be discovered. Here we show that the "no-rattling" principle postulated by Goldschmidt in 1926, describing the geometric conditions under which a perovskite can form, is much more effective than previously thought and allows us to predict perovskites with a fidelity of 80%. By supplementing this principle with inferential statistics and internet data mining we establish that currently known perovskites are only the tip of the iceberg, and we enumerate 90,000 hitherto-unknown compounds awaiting to be studied. Our results suggest that geometric blueprints may enable the systematic screening of millions of compounds and offer untapped opportunities in structure prediction and materials design.

en: The geometric blueprint of perovskites

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).

title_for_slug: the-geometric-blueprint-of-perovskites

data-mining

display_name: data-mining

goldschmidt

display_name: goldschmidt

perovskites

display_name: perovskites

structure-predictions

display_name: structure-predictions


en: We report a methodology using machine learning to capture chemical intuition from a set of (partially) failed attempts to synthesize a metal organic framework. We define chemical intuition as the collection of unwritten guidelines used by synthetic chemists to find the right synthesis conditions. As (partially) failed experiments usually remain unreported, we have reconstructed a typical track of failed experiments in a successful search for finding the optimal synthesis conditions that yields HKUST-1 with the highest surface area reported to date. We illustrate the importance of quantifying this chemical intuition for the synthesis of novel materials.

en: Capturing chemical intuition in synthesis of metal-organic frameworks

materialscloud

en: Materials Cloud

genetic-algorithms

display_name: genetic-algorithms

machine-learning

display_name: machine-learning

metal-organic-frameworks

display_name: metal-organic-frameworks

optimisation

display_name: optimisation

robotic-synthesi

display_name: robotic-synthesi

synthesis

display_name: synthesis


en: Biomolecular simulations are computationally expensive. This limits their application in drug or protein design and related fields. Several methods have been developed to address this problem. These methods often use an artificial force or potential acting on selected degrees of freedom known as collective variables. This requires explicit calculation of a collective variable (and its derivatives) from molecular structure. For collective variables that cannot be calculated explicitly or such calculations is slow we developed anncolvar package (https://github.com/spiwokv/anncolvar). This package approximates collective variables using artificial neural networks. It was tested on Isomap low dimensional representation of cyclooctane derivative or solvent-accessible surface area of Trp-cage miniprotein.

en: Approximation of Collective Variables by anncolvar

artificial-neural-networks

display_name: artificial-neural-networks

collective-variable

display_name: collective-variable

metadynamics

display_name: metadynamics


en: Biomolecular simulations are computationally expensive. This limits their application in protein folding simulations, protein engineering, drug design and related fields. Enhanced sampling techniques such as metadynamics accelerates slow events in molecular simulation. This and other method apply artificial forces in directions of collective degrees of freedom (aka collective variables). Path collective variables and Property Map collective variables are defined using a series of reference structures of the studied molecular system. They require a huge number of mean square deviation calculations along the simulation. Close Structure algorithm reduces the number of these operations.

en: Reducing the Number of Mean-Square Deviation Calculations with Floating Close Structure in Metadynamics

envi

en: Environment

mean-square-deviation

display_name: mean-square-deviation


en:
Charge equilibration (Qeq) methods can estimate the electrostatic potential of molecules and periodic frameworks by assigning point charges to each atom, using only a small fraction of the resources needed to compute density functional (DFT)-derived charges. This makes possible, for example, the computational screening of thousands of microporous structures to assess their performance for the adsorption of polar molecules. Recently, different variants of the original Qeq scheme were proposed to improve the quality of the computed point charges. One focus of this research was to improve the gas adsorption predictions in Metal Organic Frameworks (MOFs), for which many different structures are available. In this work, we review the evolution of the method from the original Qeq scheme, understanding the role of the different modifications on the final output. We evaluated the result of combining different protocols and set of parameters, by comparing the Qeq charges with high quality DFT-derived DDEC charges for 2338 MOF structures. We focused on the systematic errors that are attributable to specific atom types to quantify the final precision that one can expect from Qeq methods in the context of gas adsorption where the electrostatic potential plays a significant role, namely CO2 and H2S adsorption. In conclusion, both the type of algorithm and the input parameters have a large impact on the resulting charges and we draw some guidelines to help the user to choose the proper combination of the two for obtaining a meaningful set of charges. We show that, considering this set of MOFs, the accuracy of the original Qeq scheme is often still comparable with the most recent variants, even if it clearly fails in the presence of certain atom types, such as alkali metals.

Version 2 of the record adds the data underlying the figures in CSV format.

en: Evaluating charge equilibration methods to generate electrostatic fields in nanoporous materials

charge-equilibration-methods

display_name: charge-equilibration-methods

marvel

display_name: marvel

partial-charges

display_name: partial-charges

qeq

display_name: qeq


en: Project Abstract: Pore volume is one of the main properties for the characterization of microporous crystals. It is experimentally measurable and it can also be obtained from the refined unit cell by a number of computational techniques. In this work we assess the accuracy and the discrepancies between the different computational methods which are commonly used for this purpose, i.e, geometric, helium and probe center pore volume, by studying a database of more than 5000 frameworks. We developed a new technique to fully characterize the internal void of a microporous material and to compute the probe accessible and occupiable pore volume. We show that unlike the other definitions of pore volume, the occupiable pore volume can be directly related to the experimentally measured pore volumes from nitrogen isotherms.

en: Accurate Characterization of the Pore Volume in Microporous Crystalline Materials (Data Download)

nanoporous-materials

display_name: nanoporous-materials

pore-volume

display_name: pore-volume

void-fraction

display_name: void-fraction


en: Zeolite-templated carbons (ZTCs) comprise a relatively recent material class synthesized via the chemical vapor deposition of a carbon-containing precursor on a zeolite template, followed by the removal of the template. We have developed a theoretical framework to generate a ZTC model from any given zeolite structure, which we show can successfully predict the structure of known ZTCs. We use our method to generate a library of ZTCs from all known zeolites, to establish criteria for which zeolites can produce experimentally accessible ZTCs, and to identify over 10 ZTCs that have never before been synthesized. We show that ZTCs partition space into two disjoint labyrinths that can be described by a pair of interpenetrating nets. Since such a pair of nets also describes a triply periodic minimal surface (TPMS), our results establish the relationship between ZTCs and schwarzites—carbon materials with negative Gaussian curvature that resemble TPMSs—linking the research topics and demonstrating that schwarzites should no longer be thought of as purely hypothetical materials.

en: Generating carbon schwarzites via zeolite-templating

carbon-materials

display_name: carbon-materials

schwarzites

display_name: schwarzites

tpms

display_name: tpms

ztc

display_name: ztc


en: The application of modern machine learning to challenges in atomistic simulation is gaining attraction. We present new machine learning models that can predict the energy of the oxidative addition process between a transition metal complex and a substrate for C-C cross-coupling reaction. In turn, this quantity can be used as a descriptor to estimate the activity of homogeneous catalysts using molecular volcano plots. The versatility of this approach is illustrated for vast libraries of organometallic catalysts based on Pt, Pd, Ni, Cu, Ag, and Au combined with 91 ligands. Out-of-sample machine learning predictions were made on a total of 18,062 compounds leading to 557 catalyst candidates falling into the ideal thermodynamic window. This number was further refined by searching for candidates with an estimated price lower than 10 US$/mmol. The 37 catalyst finalists are dominated by palladium phosphine ligand combinations but also include earth abundant (Cu) transition metal with less common ligands. Our results indicate that modern statistical learning techniques can be applied to the computational discovery of readily available and promising catalyst candidates.

en: Machine learning meets volcano plots: Computational discovery of cross-coupling catalysts

homogeneous-catalysis

display_name: homogeneous-catalysis

machine-learning

display_name: machine-learning

transition-metal-complexes

display_name: transition-metal-complexes

volcano-plot

display_name: volcano-plot


en:
Classical turning surfaces of Kohn-Sham potentials separate classically-allowed regions (CARs) from classically-forbidden regions (CFRs). They are useful for understanding many chemical properties of molecules, but need not exist in solids, where the density never decays to zero. At equilibrium geometries, we find that CFRs are absent in perfect metals, rare in covalent semiconductors at equilibrium, but common in ionic and molecular crystals. In all materials, CFRs appear or grow as the internuclear distances are uniformly expanded. They can also appear at a monovacancy in a metal. Calculations with several approximate density functionals and codes confirm these behaviors. A classical picture of conduction suggests that CARs should be connected in metals, and disconnected in wide-gap insulators, and is confirmed in the limits of extreme compression and expansion. Surprisingly, many semiconductors have no CFR at equilibrium, a key finding for density functional construction. Nonetheless, a strong correlation with insulating behavior can still be inferred. Moreover, equilibrium bond lengths for all cases can be estimated from the bond type and the sum of the classical turning radii of the free atoms or ions.

This record contains machine readable data for this work

en: Calculation and interpretation of classical turning surfaces in solids

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).

density-functional-theory

display_name: density-functional-theory

dft

display_name: dft

kohn-sham-potential

display_name: kohn-sham-potential

turning-surface

display_name: turning-surface


en:
We provide the input files to reproduce the data presented in the work:
Hidden Beneath the Surface: Origin of the Observed Enantioselective Adsorption on PdGa(111)
The files are subdivided in directories named after the figures/table of the manuscript
A. V. Yakutovich, J. Hoja, D. Passerone, Alexandre Tkatchenko, C. A. Pignedoli
J. Am. Chem. Soc., 140, 1401-1408 (2018) DOI: 10.1021/jacs.7b10980
In the work, we unravel the origin of the recently observed striking enantioselectivity of the PdGa(111) surface with respect to the adsorption of a small organic molecule, 9-ethynylphenanthrene, using first-principles calculations. It turns out that the key ingredient to understand the experimental evidence is the appropriate description of van der Waals interactions beyond the widely employed atomic pairwise approximation. A recently developed van der Waals-inclusive density functional method, which encompasses dielectric screening effects, reveals the origin of the experimentally observed enantioselectivity and provides conclusive evidence of chiral recognition on a bimetallic surface driven by dispersion interactions.

materialscloud

en: Materials Cloud

chirality

display_name: chirality

many-body-dispersion

display_name: many-body-dispersion

marvel

display_name: marvel

pdga

display_name: pdga


en:
Fast-charging batteries typically employ electrodes capable of accommodating lithium continuously via solid-solution transformation because they have few kinetic barriers apart from Li+ diffusion. One exception is lithium titanate, an anode that exhibits extraordinary rate capability seemingly inconsistent with its two-phase reaction and slow diffusion within the two phases. Through real-time tracking of Li+ migration using operando electron energy-loss spectroscopy (EELS) along with simulation of the EELS spectra, we observe that the kinetic pathway that enables facile ionic transport in lithium titanate consists of distorted Li polyhedra in metastable intermediate states. Thus, fast-charging electrodes may not be controlled solely by the intrinsic ionic diffusivity of macroscopic phases, but also by the transport via kinetically accessible low-energy landscapes.

In order to understand the origin of various EELS spectra features, we simulate EELS spectra using the Vienna Ab initio Simulation (VASP) package. For a specific Li in a given configuration, this is done by calculating the DOS and integrated DOS considering a Li core-hole on the position of the specific Li and calculating the EELS based on the DOS. We also calculated the minimum energy paths (MEP) and migration energy of Li in various compositions, including Li4Ti5O12 with an additional Li carrier, Li5Ti5O12 with an additional Li carrier, and Li7Ti5O12 with a Li vacancy carrier. The calculation was performed using the nudged elastic band (NEB) method in VASP. Analysis of the VASP outputs was done using scripts from Transition State Tools for VASP (VTST, https://theory.cm.utexas.edu/vtsttools/index.html). We present here the relevant input and output files from the VASP calculations, the python code used to generate EELS spectra from VASP outputs, and the outputs of the VTST scripts that were used to generate MEP plots.

en: Kinetic Pathways of Ionic Transport in Fast Charging Lithium Titanate

ionic-transport

display_name: ionic-transport

nudged-elastic-band

display_name: nudged-elastic-band

vasp

display_name: vasp


en: The study of organic molecular crystals under high pressure provides fundamental insight into crystal packing distortions and reveals mechanisms of phase transitions and the crystallization of polymorphs. These solid state transformations can be monitored directly by analyzing electron charge densities that are experimentally obtained at high pressure. However, restricting the analysis to the featureless electron density does not reveal the chemical bonding nature and the existence of intermolecular interactions. This shortcoming can be resolved by the use of the DORI (Density Overlap Region Indicator) descriptor, which is capable of detecting simultaneously both covalent patterns and non-covalent interactions from electron density and its derivatives. Using the biscarbonyl[14]annulene crystal under pressure as an example, we demonstrate how DORI can be exploited on experimental electron densities to reveal and monitor changes in electronic structure patterns resulting from molecular compression. A novel approach based on a flood fill type algorithm is proposed for analyzing the topology of the DORI isosurface. This approach avoids the arbitrarily selection of DORI isovalues and provides an intuitive way to assess how compression packing affects covalent bonding in organic solids.

en: DORI reveals the influence of non-covalent interactions on covalent bonding patterns in molecular crystals under pressure

high-pressure

display_name: high-pressure

molecular-scalar-fields

display_name: molecular-scalar-fields

organic-crystals

display_name: organic-crystals

topology

display_name: topology


en: Ice nucleation is a process of great relevance in physics, chemistry, technology, and environmental sciences; much theoretical effort has been devoted to its understanding, but it still remains a topic of intense research. We shed light on this phenomenon by performing atomistic based simulations. Using metadynamics and a carefully designed set of collective variables, reversible transitions between water and ice are able to be simulated. We find that water freezes into a stacking disordered structure with the all-atom transferable intermolecular potential with 4 points/ice (TIP4P/ice) model, and the features of the critical nucleus of nucleation at the microscopic level are revealed. We have also estimated the ice nucleation rates along with other nucleation parameters at different undercoolings. Our results are in agreement with recent experimental and other theoretical works, and they confirm that nucleation is preceded by a large increase in tetrahedrally coordinated water molecules.

en: Temperature Dependence of Homogeneous Nucleation in Ice

envi

en: Environment

enhanced-sampling

display_name: enhanced-sampling

erc

display_name: erc

homegenous-nucleation

display_name: homegenous-nucleation

ice

display_name: ice

metadynamics

display_name: metadynamics

molecular-dynamics

display_name: molecular-dynamics

plumed

display_name: plumed


en: We describe a double helical conformation in the densely charged aromatic polyamide poly(2,2'- disulfonyl-4,4'-benzidine terephthalamide) or PBDT. This double helix macromolecule represents one of the most rigid simple molecular structures known, exhibiting an extremely high axial persistence length (~ 1 micrometer).

en: Double helix PBDT polymer - Submitted manuscript, simulations and other source data

ionic

display_name: ionic

nematic

display_name: nematic

nmr

display_name: nmr

polymer

display_name: polymer

simulations

display_name: simulations

x-ray

display_name: x-ray


en: We present a derivation of the exact expression for Pulay forces in density-functional theory calculations augmented with extended Hubbard functionals, and arising from the use of orthogonalized atomic orbitals as projectors for the Hubbard manifold. The derivative of the inverse square root of the orbital overlap matrix is obtained as a closed-form solution of the associated Lyapunov (Sylvester) equation. The expression for the resulting contribution to the forces is presented in the framework of ultrasoft pseudopotentials and the projector-augmented-wave method, and using a plane wave basis set. We have benchmarked the present implementation with respect to finite differences of total energies for the case of NiO, finding excellent agreement. Owing to the accuracy of Hubbard-corrected density-functional theory calculations - provided the Hubbard parameters are computed for the manifold under consideration - the present work paves the way for systematic studies of solid-state and molecular transition-metal and rare-earth compounds.

en: Pulay forces in density-functional theory with extended Hubbard functionals: from nonorthogonalized to orthogonalized manifolds

cscs

display_name: cscs

density-functional-theory

display_name: density-functional-theory

dftu

display_name: dftu

dftuv

display_name: dftuv

hubbard-corrections

display_name: hubbard-corrections

hubbard-forces

display_name: hubbard-forces

hubbard-manifold

display_name: hubbard-manifold

hubbard-parameters

display_name: hubbard-parameters

lowdin-orthogonalization-method

display_name: lowdin-orthogonalization-method

lyapunov-equation

display_name: lyapunov-equation

marvel

display_name: marvel

orbital-overlap-matrix

display_name: orbital-overlap-matrix

pulay-forces

display_name: pulay-forces

self-interaction-corrections

display_name: self-interaction-corrections

sylvester-equation

display_name: sylvester-equation


en:
Thermodynamic properties of liquid water as well as hexagonal (Ih) and cubic (Ic) ice are predicted based on density functional theory at the hybrid-functional level, rigorously taking into account quantum nuclear motion, anharmonic fluctuations and proton disorder. This is made possible by combining advanced free energy methods and state-of-the-art machine learning techniques. The ab initio description leads to structural properties in excellent agreement with experiments, and reliable estimates of the melting points of light and heavy water. We observe that nuclear quantum effects contribute a crucial 0.2 meV/H2O to the stability of ice Ih, making it more stable than ice Ic. Our computational approach is general and transferable, providing a comprehensive framework for quantitative predictions of ab initio thermodynamic properties using machine learning potentials as an intermediate step.

In this set of supplemental materials, we have included the neural network potential for bulk water, including its training set in two different formats. We have also included the input files for running free energy calculations.

en: Ab initio thermodynamics of liquid and solid water: supplemental materials

free-energy-calculation-input-files

display_name: free-energy-calculation-input-files

machine-learning-potential

display_name: machine-learning-potential

machine-learning-potential-training-set

display_name: machine-learning-potential-training-set


en: We present a large dataset of adsorption of H, C, N, O and S onto more than 2,000 metallic and bimetallic alloy surfaces, consisting of approximately 90,000 DFT calculations performed in Quantum Espresso. The alloys are constructed from all possible combinations of 37 metals into AB and A3B stoichiometries, in the L1_0 and L1_2 structures respectively, where the 37 metals in the A1 structure are included as well. Slabs are cleaved along the 111 facet for A1 and L1_2 and along the 101 facet for L1_0, and all possible adsorption sites are sampled. In addition to the monoatomic adsorbates, adsorption of CH, CH2, CH3, NH, NH2, OH, H2O and SH  is sampled for a smaller subset of alloys.

en: High-throughput calculations of catalytic properties of bimetallic alloy surfaces

chemisorption

display_name: chemisorption

dft

display_name: dft

heterogeneous-catalysis

display_name: heterogeneous-catalysis

surfaces

display_name: surfaces


dopant-discovery-in-cuprous-iodide

en: Computational data to support an extensive study of prospective dopants in the zinc blende (gamma) phase of cuprous iodide. This phase of CuI holds the current record hole conductivity for intrinsic transparent p-type semiconductors. In the corresponding scientific article, a high-throughput approach was employed to systematically explore strategies for enhancing CuI further by impurity incorporation. Our objectives were to identify a practical approach for increasing hole conductivity in CuI thin films and to explore the possibility for ambivalent doping. A total of 64 chemical elements was investigated. This materials cloud record contains all optimized defective structures for Cu and I substitutional sites, calculation settings and some of the output (LOCPOT files, required for electrostatic correction calculations are not included due to their large size).  Chalcogen elements were found to display acceptor character when substituting iodine. Further eight impurities suitable for n-type doping were also discovered. Unfortunately, our work further revealed that donor doping is hindered by compensating native defects.

en: Dopant discovery in cuprous iodide

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).

title_for_slug: dopant-discovery-in-cuprous-iodide

cui

display_name: cui

defects

display_name: defects

dopants

display_name: dopants

supercell

display_name: supercell

transparent-conductors

display_name: transparent-conductors


en: This is a LAMMPS readable EAM type potential file for Hf-Nb-Ta-Zr based high-entropy alloys (HEAs). In this potential file the elements are sequenced as Hf, Nb, Ta and Zr, respectively. This potential was previously used to model the HEA for the local lattice distortions due to short-range order clustering found in the alloy after long-term annealing at high-temperature. The input to build this potential is based on the physical properties of pure elements such as the lattice parameter, cohesive energy, elastic constants etc and the details are discussed in the associated reference. Units used are in eV/atom for energy and Angstrom for distance.

en: EAM potential for Hf-Nb-Ta-Zr high-entropy alloy

materialscloud

en: Materials Cloud

eam-potential

display_name: eam-potential

high-entropy-alloys

display_name: high-entropy-alloys

lammps

display_name: lammps

refractory-elements

display_name: refractory-elements


en: Zethrenes are model diradicaloids with potential applications in spintronics and optoelectronics. Despite a rich chemistry in solution, on-surface synthesis of zethrenes has never been demonstrated. This record contains data to support our recent publication where we report the on-surface synthesis of super-heptazethrene on Au(111). Scanning tunneling spectroscopy investigations reveal that super-heptazethrene exhibits an exceedingly low HOMO–LUMO gap of 230 meV and, in contrast to its open-shell singlet ground state in the solution phase and in the solid-state, likely adopts a closed-shell ground state on Au(111).

en: On-surface synthesis of super-heptazethrene

ab-initio

display_name: ab-initio

cscs

display_name: cscs

diradicaloid

display_name: diradicaloid

erc

display_name: erc

on-surface-synthesis

display_name: on-surface-synthesis

snsf

display_name: snsf


en: Two-dimensional transition metal dichalcogenides (TMDs) of Mo and W in their 1T′ crystalline phase host the quantum spin Hall (QSH) insulator phase. We address the electronic properties of the QSH edge states by means of first-principles calculations performed on realistic models of edge terminations of different stoichiometries. The QSH edge states show a tendency to have complex band dispersions and coexist with topologically trivial edge states. We nevertheless identify two stable edge terminations that allow isolation of a pair of helical edge states within the band gap of TMDs, with monolayer 1T′-WSe2 being the most promising material. We also characterize the finite-size effects in the electronic structure of 1T′-WSe2 nanoribbons. Our results provide guidance to the experimental studies and possible practical applications of QSH edge states in monolayer 1T′-TMDs.

en: Controlling the quantum spin Hall edge states in two-dimensional transition metal dichalcogenides

envi

en: Environment

edge-states

display_name: edge-states

epfl

display_name: epfl

marvel

display_name: marvel

quantum-spin-hall-effect

display_name: quantum-spin-hall-effect

topological-insulators

display_name: topological-insulators

transition-metal-dichalcogenides

display_name: transition-metal-dichalcogenides


en: We propose a general method to calculate the average misfit volumes of atoms in any random alloy via DFT calculations. The method is validated with an example of a 6-component equi-composition high entropy alloy. The special quasi-random structures (SQSs) used in our work are reported here.

en: Special quasi-random structures for the 6-component high entropy alloys

misfit-volumes

display_name: misfit-volumes

random-alloys

display_name: random-alloys

special-quasi-random-structures-sqss

display_name: special-quasi-random-structures-sqss


en: Metal-Organic Frameworks (MOFs) are highly versatile materials owing to their vast structural and chemical tunability. These hybrid inorganic-organic crystalline materials offer an ideal platform to incorporate light-harvesting and catalytic centers and thus, exhibit a great potential to be exploited in solar-driven photocatalytic processes such as H2 production and CO2 reduction. To be photocatalytically active, UV-visible optical absorption and appropriate band alignment with respect to the target redox potential is required. Despite fulfilling these criteria, the photocatalytic performance of MOFs is still limited by their ability to produce long-lived electron-hole pairs and long-range charge transport. In this work, we present a computational strategy to address these two descriptors in MOF structures and translate them into charge transfer numbers and effective mass values. We apply our approach to 15 MOF structures from the literature that encompass the main strategies used in the design of efficient photocatalysts including different metals, ligands, and topologies. Our results capture the main characteristics previously reported for these MOFs and enable us to identify promising candidates. In the quest of novel photocatalytic systems, high-throughput screening based on charge separation and charge mobility features is envisioned to be applied in large databases of both experimentally and in silico generated MOFs.

en: Charge separation and charge carrier mobility in photocatalytic metal-organic frameworks

charge-transfer

display_name: charge-transfer

mof

display_name: mof

photocatalysis

display_name: photocatalysis


en: The most successful and popular machine learning models of atomic-scale properties derive their transferability from a locality ansatz. The properties of a large molecule or a bulk material are written as a sum over contributions that depend on the configurations within finite atom-centered environments. The obvious downside of this approach is that it cannot capture nonlocal, nonadditive effects such as those arising due to long-range electrostatics or quantum interference. We propose a solution to this problem by introducing nonlocal representations of the system, which are remapped as feature vectors that are defined locally and are equivariant in O(3). We consider, in particular, one form that has the same asymptotic behavior as the electrostatic potential. We demonstrate that this framework can capture nonlocal, long-range physics by building a model for the electrostatic energy of randomly distributed point-charges, for the unrelaxed binding curves of charged organic molecular dimers, and for the electronic dielectric response of liquid water. By combining a representation of the system that is sensitive to long-range correlations with the transferability of an atom-centered additive model, this method outperforms current state-of-the-art machine-learning schemes and provides a conceptual framework to incorporate nonlocal physics into atomistic machine learning.

en: Incorporating long-range physics in atomic-scale machine learning

long-range-interactions

display_name: long-range-interactions

machine-learning

display_name: machine-learning


en: We investigate formation energies of C, Si, and Ge defects in β-Ga2O3 through hybrid functional calculations. We find that the interstitial defects of these elements generally occur at higher energies than their substitutional counterparts, while they are more stable at low Fermi energies in Ga-rich conditions. In n-type and Ga-rich conditions, interstitials of Si and Ge show significantly higher formation energies than their substitutional form, but this difference is less pronounced for C. Charge transition levels of interstitial defects lie in the upper part of the band-gap, and account for several measured levels in unintentionally doped and Ge-doped samples of β-Ga2O3.

en: Defect Formation Energies of Interstitial C, Si, and Ge Impurities in β-Ga2O3

defects

display_name: defects

hybrid-functional

display_name: hybrid-functional


en: In this work, we investigate the transverse magnetoresistance of materials by combining the Fermi surfaces calculated from first principles with the Boltzmann transport theory approach relying on the semiclassical model and the relaxation time approximation. We first consider a series of simple model Fermi surfaces to provide a didactic introduction into the charge-carrier compensation and open-orbit mechanisms leading to nonsaturating magnetoresistance. We then address in detail magnetotransport in three representative materials: (i) copper,  (ii) bismuth,  and (iii) tungsten diphosphide. Furthermore, the calculations allow for a full interpretation of the observed features in terms of the Fermi surface topology. Our study thus establishes guidelines to clarifying the physical mechanisms underlying the magnetotransport properties in a broad range of materials.

en: Magnetoresistance from Fermi surface topology

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).

boltzmann-transport-theory

display_name: boltzmann-transport-theory

fermi-surface

display_name: fermi-surface

first-principles

display_name: first-principles

magnetoresistance

display_name: magnetoresistance

wanniertools

display_name: wanniertools


en: Maximally-localised Wannier functions (MLWFs) are routinely used to compute from first-principles advanced materials properties that require very dense Brillouin zone integration and to build accurate tight-binding models for scale-bridging simulations. At the same time, high-throughput (HT) computational materials design is an emergent field that promises to accelerate the reliable and cost-effective design and optimisation of new materials with target properties. The use of MLWFs in HT workflows has been hampered by the fact that generating MLWFs automatically and robustly without any user intervention and for arbitrary materials is, in general, very challenging. We address this problem directly by proposing a procedure for automatically generating MLWFs for HT frameworks. Our approach is based on the selected columns of the density matrix method (SCDM) and we present the details of its implementation in an AiiDA workflow. We apply our approach to a dataset of 200 bulk crystalline materials that span a wide structural and chemical space. We assess the quality of our MLWFs in terms of the accuracy of the band-structure interpolation that they provide as compared to the band-structure obtained via full first-principles calculations. We provide here an AiiDA export file with the full provenance of all simulations run in the project. Moreover, we provide a downloadable virtual machine that allows to reproduce the results of this paper and also to run new calculations for different materials, including all first-principles and atomistic simulations and the computational workflows.

materialscloud

en: Materials Cloud

aiida-workflow

display_name: aiida-workflow

automated-wannierisation

display_name: automated-wannierisation

band-structure-interpolation

display_name: band-structure-interpolation

high-throughput-simulations

display_name: high-throughput-simulations

marvelosp

display_name: marvelosp

maximally-localised-wannier-functions

display_name: maximally-localised-wannier-functions

scdm

display_name: scdm


en: Nonbenzenoid carbocyclic rings are postulated to serve as important structural elements toward tuning the chemical and electronic properties of extended polycyclic aromatic hydrocarbons (PAHs, or namely nanographenes), necessitating a rational and atomically precise synthetic approach toward their fabrication. This record contains data supporting a recent work where, using a combined bottom-up in-solution and on-surface synthetic approach, we report the synthesis of nonbenzenoid open-shell nanographenes containing two pairs of embedded pentagonal and heptagonal rings.

en: Open-shell Non-benzenoid Nanographenes Containing Two Pairs of Pentagonal and Heptagonal Rings

ab-initio

display_name: ab-initio

nanographene

display_name: nanographene

on-surface-synthesis

display_name: on-surface-synthesis

polycyclic-aromatic-hydrocarbons

display_name: polycyclic-aromatic-hydrocarbons

scanning-tunneling-microscopy

display_name: scanning-tunneling-microscopy


en:
We present a workflow that traces the path from the bulk structure of a crystalline material to assessing its performance in carbon capture from coal's postcombustion flue gases. This workflow is applied to a database of 324 covalent−organic frameworks (COFs) reported in the literature, to characterize their CO2 adsorption properties using the following steps:
(1) optimization of the crystal structure (atomic positions and unit cell) using density functional theory,
(2) fitting atomic point charges based on the electron density,
(3) characterizing the pore geometry of the structures before and after optimization,
(4) computing carbon dioxide and nitrogen isotherms using grand canonical Monte Carlo simulations with an empirical interaction potential, and finally,
(5) assessing the CO2 parasitic energy via process modeling.

The full workflow has been encoded in the Automated Interactive Infrastructure and Database for Computational Science (AiiDA). Both the workflow and the automatically generated provenance graph of our calculations are made available on the Materials Cloud, allowing peers to inspect every input parameter and result along the workflow, download structures and files at intermediate stages, and start their research right from where this work has left off. In particular, our set of CURATED (Clean, Uniform, and Refined with Automatic Tracking from Experimental Database) COFs, having optimized geometry and high-quality DFT-derived point charges, are available for further investigations of gas adsorption properties. We plan to update the database as new COFs are being reported.

*** UPDATE December 2019 ***
 - Database extended to  include 417 COFs (from papers published until September 1st 2019)
- Migration to AiiDA-v1.0.0
- Using the publicly available plugin aiida-lsmo

*** UPDATE February 2020 ***
 - Database extended to  include 505 COFs (from papers published until February 1st 2020)
 - Including AiiDA Groups for quick interactive visualization

*** UPDATE June 2020 ***
 - Database extended to include 574 COFs (from papers published until June 1st 2020)

*** UPDATE September 2020 ***
 - Include other applications than CCS, considering the same set of 574 COFs

*** UPDATE October 2020 ***
 - Database extended to include 626 COFs (from papers published until October 1st 2020)

*** UPDATE February 2021 ***
 - Database extended to include 632 COFs (from papers published until February 1st 2021). We added a total of 61 new structures but we discarded 55: see CURATED-COFs GitHub for more details.

*** UPDATE June 2021 ***
 - Database extended to include 648 valid COFs (from papers published until June 1st 2021) plus 80 discarded: see CURATED-COFs GitHub for more details.

*** UPDATE July 2022 ***
 - Database extended to include 871 valid COFs (from papers published until July 1st 2022) plus 110 discarded: see CURATED-COFs GitHub for more details.

en: Building a consistent and reproducible database for adsorption evaluation in Covalent-Organic Frameworks

aiida

display_name: aiida

covalent-organic-framework

display_name: covalent-organic-framework

erc

display_name: erc

reproducibility

display_name: reproducibility

workflows

display_name: workflows


en: Oxygen vacancies are a common source of excess electrons in complex oxides. In Mott insulators, these additional electrons can induce a metal-insulator transition (MIT), fundamentally altering the electronic properties of the  system. Here we study the effect of oxygen vacancies in LaTiO3, a prototypical Mott insulator close to the MIT. We show that the introduction of oxygen vacancies creates a vacancy-related band immediately below the partially filled Ti-t 2g bands. We study the effect of this additional band on the Mott MIT  using a combination of density functional theory and dynamical mean-field theory (DFT+DMFT), employing a minimal correlated subspace consisting of effective Ti-t 2g orbitals plus an additional Wannier function centered on the vacancy site. We find that the Mott insulating state in LaTiO3 is robust to the presence of the vacancy band, which remains fully occupied even in the presence of a local Coulomb repulsion, and therefore does not cause a doping of the Mott insulator

en: DFT+DMFT study of oxygen vacancies in a Mott insulator

envi

en: Environment

defects

display_name: defects

dftdmft

display_name: dftdmft

electronic-structure

display_name: electronic-structure

mott-insulators

display_name: mott-insulators

oxygen-vacancies

display_name: oxygen-vacancies


en: We investigate the synergy occurring in photocatalytic water splitting between the metal-organic framework MIL-125-NH2 and two co-catalysts, namely NiO and Ni2P, by calculating their band edge alignment with respect to the redox levels of liquid water. For the NiO/H2O and Ni2P/H2O interfaces, we employ an explicit atomistic description of water and perform molecular dynamics simulations considering both molecular and dissociated water adsorbed at the co-catalyst surface. For the MIL-125-NH2/NiO and MIL-125-NH2/Ni2P interfaces, we rely on the concept of charge neutrality and use a scheme combining the electron affinities and the charge neutrality levels of the interface components. We provide a description of the underlying fundamental processes that is consistent with photoluminescence and intrinsic activity experiments and that supports NiO and Ni2P as suitable co-catalysts for MIL-125-NH2 as far as the hydrogen evolution reaction is concerned.

en: Unraveling the synergy between metal-organic frameworks and co-catalysts in photocatalytic water splitting

co-catalyst

display_name: co-catalyst

density-functional-calculations

display_name: density-functional-calculations

first-principles-calculations

display_name: first-principles-calculations

hydrogen-evolution

display_name: hydrogen-evolution

metal-organic-frameworks

display_name: metal-organic-frameworks

molecular-dynamics

display_name: molecular-dynamics

photocatalysis

display_name: photocatalysis

water-splitting

display_name: water-splitting


en: Singlet Fission (SF) has demonstrated significant promise for boosting the power conversion efficiency (PCE) of solar cells. Traditionally, SF is targeted as an intermolecular process, however its dependence on crystal packing makes molecular design difficult. In contrast, intramolecular SF (iSF) enables the exploration of tunable bi-chromophoric systems following well-defined structure-property relationships. In this work, we propose a set of parameters to screen conjugated donor-acceptor copolymer candidates with potential iSF behaviour. We focus our analysis on the E(S1)>2E(T1) thermodynamic condition and on the appropriate charge transfer (CT) character of S1. We map the CT character with respect to the frontier molecular orbital (FMO) energies of the constituent monomers, providing a cost-effective protocol for an accelerated screening of promising iSF donor-acceptor pairs, while minimizing the number of computations. These parameters are applied to a chemically diverse, curated library of 81 truncated dimers of synthetically feasible donor-acceptor copolymers. From our dataset, four candidates are flagged for iSF, two of which were previously experimentally reported. This protocol is envisioned to be scaled up for the high-throughput screening of large databases of donor-acceptor dimers for the design and identification of conjugated polymers capable of iSF.

en: Designing Singlet Fission Candidates from Donor-Acceptor Copolymers

da-copolymers

display_name: da-copolymers

dft-computations

display_name: dft-computations

epfl

display_name: epfl

screening-descriptors

display_name: screening-descriptors

singlet-fission

display_name: singlet-fission


en: We investigate the solvation effect of water on the overpotentials of the oxygen evolution reaction on rutile TiO2 by applying the thermodynamic integration method on atomistic model interfaces with and without the water molecules. We compare the results at the vacuum interface with the commonly used computational hydrogen electrode method, finding overall good agreement. The effect of the solvent is found to be twofold. First, the explicit treatment of the solvent can lead to equilibrium configurations differing from the relaxed structures without solvent. Second, the overpotentials can be affected by up to 0.5 eV. The energetics are subject to electrostatic effects at the interface rather than to modifications in the hydrogen bond network. These results provide a promising perspective for treating the solvent with implicit models.

en: Effect of the Solvent on the Oxygen Evolution Reaction at the TiO2-Water Interface

explicit-solvent

display_name: explicit-solvent

oxygen-evolution-reaction

display_name: oxygen-evolution-reaction

rutile

display_name: rutile

solvation-effect

display_name: solvation-effect

water

display_name: water