Using federated data sources and Varian Learning Portal framework to train a neural network model for automatic organ segmentation.

PURPOSE: In this study we trained a deep neural network model for female pelvis organ segmentation using data from several sites without any personal data sharing. The goal was to assess its prediction power compared with the model trained in a centralized manner. METHODS: Varian Learning Portal (VLP) is a distributed machine learning (ML) infrastructure enabling privacy-preserving research across hospitals from different regions or countries, within the framework of a trusted consortium. Such a framework is relevant in the case when there is a high level of trust among the participating sites, but there are legal restrictions which do not allow the actual data sharing between them. We trained an organ segmentation model for the female pelvic region using the synchronous data distributed framework provided by the VLP. RESULTS: The prediction performance of the model trained using the federated framework offered by VLP was on the same level as the performance of the model trained in a centralized manner where all training data was pulled together in one centre. CONCLUSIONS: VLP infrastructure can be used for GPU-based training of a deep neural network for organ segmentation for the female pelvic region. This organ segmentation instance is particularly difficult due to the high variation in the organs' shape and size. Being able to train the model using data from several clinics can help, for instance, by exposing the model to a larger range of data variations. VLP framework enables such a distributed training approach without sharing protected health information.

Hydrogen adsorption trends on various metal-doped Ni2P surfaces for optimal catalyst design.

In this study, we looked at the hydrogen evolution reaction on Mg-, Mo-, Fe-, Co-, V-, and Cu-doped Ni3P2 and Ni3P2 + P terminated Ni2P surfaces. The DFT calculated hydrogen adsorption free energy was employed as a predictor of the materials' catalytic HER activity. Our results indicate that doping can substantially improve the catalytic activity of the Ni3P2 terminated surface. In contrast, the Ni3P2 + P terminated one seems to be catalytically active irrespective of the type of doping, including in the absence of doping. Based on our doping energy and adsorption free energy calculations, the most promising dopants are iron and cobalt, whereas copper is less likely to function well as a doping element.

Hydrogen adsorption trends on Al-doped Ni2P surfaces for optimal catalyst design.

Nanoparticles of nickel phosphide are promising materials to replace the currently used rare Pt-group metals at cathode-side electrodes in devices for electrochemical hydrogen production. Chemical modification by doping can be used to fine-tune the electrocatalytic activity, but this path requires theoretical, atomic-level support which has not been widely available for Ni-P. We present a density functional theory analysis of Al-doped Ni2P surfaces to identify structural motifs that could contribute to the improved behavior of the catalyst. Based on the formation energies of substitutionally Al-doped Ni sublattices, we find doping to take place preferably at the topmost layers. The Ni-Ni bridge and the P-top sites are the optimal ones in terms of hydrogen bonding energies. The Ni-Ni bridge site is not present on pristine surfaces but is a consequence of Al doping and provides a candidate to explain the experimentally observed high activities in doped Ni-P nanoparticles. Similar structural motifs can be recommended to be engineered for other Ni-P structures for improved electrocatalytic activity.

Hydrogen adsorption on doped MoS2 nanostructures.

Electrochemical devices for efficient production of hydrogen as energy carrier rely still largely on rare platinum group metal catalysts. Chemically and structurally modified metal dichalcogenide MoS2 is a promising substitute for these critical raw materials at the cathode side where the hydrogen evolution reaction takes place. For precise understanding of structure and hydrogen adsorption characteristics in chemically modified MoS2 nanostructures, we perform comprehensive density functional theory calculations on transition metal (Fe, Co, Ni, Cu) doping at the experimentally relevant MoS2 surfaces at substitutional Mo-sites. Clear benefits of doping the basal plane are found, whereas at the Mo- and S-edges complex modifications at the whole edge are observed. New insight into doping-enhanced activity is obtained and guidance is given for further experiments. We study a machine learning model to facilitate the screening of suitable structures and find a promising level of prediction accuracy with minimal structural input.

Hydrogen adsorption on MoS2-surfaces: a DFT study on preferential sites and the effect of sulfur and hydrogen coverage.

We report a comprehensive computational study of the intricate structure-property relationships governing the hydrogen adsorption trends on MoS2 edges with varying S- and H-coverages, as well as provide insights into the role of individual adsorption sites. Additionally, the effect of single- and dual S-vacancies in the basal plane on the adsorption energetics is assessed, likewise with an emphasis on the H-coverage dependency. The employed edge/site-selective approach reveals significant variations in the adsorption free energies, ranging between ∼±1.0 eV for the different edges-types and S-saturations, including differences of even as much as ∼1.2 eV between sites on the same edge. The incrementally increasing hydrogen coverage is seen to mainly weaken the adsorption, but intriguingly for certain configurations a stabilizing effect is also observed. The strengthened binding is seen to be coupled with significant surface restructuring, most notably the splitting of terminal S2-dimers. Our work links the energetics of hydrogen adsorption on 2H-MoS2 to both static and dynamic geometrical features and quantifies the observed trends as a function of H-coverage, thus illustrating the complex structure/activity relationships of the MoS2 catalyst. The results of this systematical study aims to serve as guidance for experimentalists by suggesting feasible edge/S-coverage combinations, the synthesis of which would potentially yield the most optimally performing HER-catalysts.

Density functional simulation of resonant inelastic X-ray scattering experiments in liquids: acetonitrile.

In this paper we report an experimental and computational study of liquid acetonitrile (H3C-C[triple bond, length as m-dash]N) by resonant inelastic X-ray scattering (RIXS) at the N K-edge. The experimental spectra exhibit clear signatures of the electronic structure of the valence states at the N site and incident-beam-polarization dependence is observed as well. Moreover, we find fine structure in the quasielastic line that is assigned to finite scattering duration and nuclear relaxation. We present a simple and light-to-evaluate model for the RIXS maps and analyze the experimental data using this model combined with ab initio molecular dynamics simulations. In addition to polarization-dependence and scattering-duration effects, we pinpoint the effects of different types of chemical bonding to the RIXS spectrum and conclude that the H2C-C[double bond, length as m-dash]NH isomer, suggested in the literature, does not exist in detectable quantities. We study solution effects on the scattering spectra with simulations in liquid and in vacuum. The presented model for RIXS proved to be light enough to allow phase-space-sampling and still accurate enough for identification of transition lines in physical chemistry research by RIXS.

Resonant X-ray emission with a standing wave excitation.

The Borrmann effect is the anomalous transmission of x-rays in perfect crystals under diffraction conditions. It arises from the interference of the incident and diffracted waves, which creates a standing wave with nodes at strongly absorbing atoms. Dipolar absorption of x-rays is thus diminished, which makes the crystal nearly transparent for certain x-ray wave vectors. Indeed, a relative enhancement of electric quadrupole absorption via the Borrmann effect has been demonstrated recently. Here we show that the Borrmann effect has a significantly larger impact on resonant x-ray emission than is observable in x-ray absorption. Emission from a dipole forbidden intermediate state may even dominate the corresponding x-ray spectra. Our work extends the domain of x-ray standing wave methods to resonant x-ray emission spectroscopy and provides means for novel spectroscopic experiments in d- and f-electron systems.

Intramolecular structure and energetics in supercooled water down to 255 K.

We studied the structure and energetics of supercooled water by means of X-ray Raman and Compton scattering. Under supercooled conditions down to 255 K, the oxygen K-edge measured by X-ray Raman scattering suggests an increase of tetrahedral order similar to the conventional temperature effect observed in non-supercooled water. Compton profile differences indicate contributions beyond the theoretically predicted temperature effect and provide a deeper insight into local structural changes. These contributions suggest a decrease of the electron mean kinetic energy by 3.3 ± 0.7 kJ (mol K)(-1) that cannot be modeled within established water models. Our surprising results emphasize the need for water models that capture in detail the intramolecular structural changes and quantum effects to explain this complex liquid.

Sulphur Kß emission spectra reveal protonation states of aqueous sulfuric acid.

In this paper we report an X-ray emission study of bulk aqueous sulfuric acid. Throughout the range of molarities from 1 M to 18 M the sulfur Kß emission spectra from H2SO4 (aq) depend on the molar fractions and related deprotonation of H2SO4. We compare the experimental results with results from emission spectrum calculations based on atomic structures of single molecules and structures from ab initio molecular dynamics simulations. We show that the S Kß emission spectrum is a sensitive probe of the protonation state of the acid molecules. Using non-negative matrix factorization we are able to extract the fractions of different protonation states in the spectra, and the results are in good agreement with the simulation for the higher part of the concentration range.

Probing the thermal stability and the decomposition mechanism of a magnesium-fullerene polymer via X-ray Raman spectroscopy, X-ray diffraction and molecular dynamics simulations.

We report the microscopic view of the thermal structural stability of the magnesium intercalated fullerene polymer Mg2C60. With the application of X-ray Raman spectroscopy and X-ray diffraction, we study in detail the decomposition pathways of the polymer system upon annealing at temperatures between 300 and 700 °C. We show that there are at least two energy scales involved in the decomposition reaction. Intermolecular carbon bonds, which are responsible for the formation of a 2D fullerene polymer, are broken with a relatively modest thermal energy, while the long-range order of the original polymer remains intact. With an increased thermal energy, the crystal structure in turn is found to undergo a transition to a novel intercalated cubic phase that is stable up to the highest temperature studied here. The local structure surrounding magnesium ions gets severely modified close to, possibly at, the phase transition. We used density functional theory based calculations to study the thermodynamic and kinetic aspects of the collapse of the fullerene network, and to explain the intermediate steps as well as the reaction pathways in the break-up of this peculiar C60 intermolecular bonding architecture.

X-ray induced dimerization of cinnamic acid: Time-resolved inelastic X-ray scattering study.

A classic example of solid-state topochemical reactions is the ultraviolet-light induced photodimerization of α-trans-cinnamic acid (CA). Here, we report the first observation of an X-ray-induced dimerization of CA and monitor it in situ using nonresonant inelastic X-ray scattering spectroscopy (NRIXS). The time-evolution of the carbon core-electron excitation spectra shows the effects of two X-ray induced reactions: dimerization on a short time-scale and disintegration on a long time-scale. We used spectrum simulations of CA and its dimerization product, α-truxillic acid (TA), to gain insight into the dimerization effects. From the time-resolved spectra, we extracted component spectra and time-dependent weights corresponding to CA and TA. The results suggest that the X-ray induced dimerization proceeds homogeneously in contrast to the dimerization induced by ultraviolet light. We also utilized the ability of NRIXS for direct tomography with chemical-bond contrast to image the spatial progress of the reactions in the sample crystal. Our work paves the way for other time-resolved studies on chemical reactions using inelastic X-ray scattering.

Protonation Dynamics and Hydrogen Bonding in Aqueous Sulfuric Acid.

Hydration of sulfuric acid plays a key role in new-particle formation in the atmosphere. It has been recently proposed that proton dynamics is crucial in the stabilization of these clusters. One key question is how water molecules mediate proton transfer from sulfuric acid, and hence how the deprotonation state of the acid molecule behaves as a function concentration. We address the proton transfer in aqueous sulfuric acid with O K edge and S L edge core-excitation spectra recorded using inelastic X-ray scattering and with ab initio molecular dynamics simulations in the concentration range of 0-18.0 M. Throughout this range, we quantify the acid-water interaction with atomic resolution. Our simulations show that the number of donated hydrogen bonds per Owater increases from 1.9 to 2.5 when concentration increases from 0 to 18.0 M, in agreement with a rapid disappearance of the pre-edge feature in the O K edge spectrum. The simulations also suggest that for 1.5 M sulfuric acid SO4(2-) is most abundant and that its concentration falls monotonously with increasing concentration. Moreover, the fraction of HSO4(-) peaks at ∼12 M.

Inelastic x-ray scattering in heterostructures: electronic excitations in LaAlO3/SrTiO3.

We present an investigation of the valence-electron excitation spectra including the collective plasmon modes of SrTiO3, LaAlO3 and their heterostructures with non-resonant inelastic x-ray scattering. We analyse the spectra using calculations based on first principles and atomic multiplet models. We demonstrate the feasibility of performing valence IXS experiments in a total reflection geometry. Surprisingly, we find that the plasmon, interband and semicore excitations in multilayers are well described as a superposition of bulk-compound spectra even in a superstructure composing of layers of only one atomic layer thickness.

Identification of the dye adsorption modes in dye-sensitised solar cells with X-ray spectroscopy techniques: a computational study.

Adsorption geometry of dye molecules can have a substantial impact on the efficiency and functional lifespan of a dye-sensitised solar cell (DSSC) and therefore, its reliable assessment is an important step in engineering more efficient DSSCs. X-ray photoelectron spectroscopy (XPS) of oxygen is empirically proved to be the most efficient technique in distinguishing between the two most occurring adsorption geometries, i.e. monodentate and bidentate. In this computational study, we provide a comprehensive analysis of XPS and X-ray absorption spectroscopy (XAS) of carbon and oxygen for these binding modes in a perylene-sensitised TiO2. We confirm that O 1s XPS has an excellent sensitivity in mode identification. Moreover, we show that adsorption has a great impact on the XPS binding energies and reduces them by ∼4 eV, and using this effect, we extend the XPS usage to study dye desorption in the cell. Finally, our results for XAS indicate that although less sensitive, the spectra from carbon can be used in mode detection.

Effect of the hydrophobic alcohol chain length on the hydrogen-bond network of water.

The microscopic structure of the hydrogen-bond network of water-alcohol mixtures was studied using X-ray Raman scattering (XRS). To systematically examine how the hydrogen-bond network of water is affected by an increasing size of the hydrophobic group, small linear alcohols (methanol, ethanol, and propanol) in constant mole fractions were studied. The oxygen K-edge spectra were not altered upon hydration of the alcohols beyond a simple superposition of signals from alcohol and water. The experiment thus indicates that alcohols do not have a substantial effect on the structure of the hydrogen-bond network of water. In particular, no apparent breaking or forming of the hydrogen bonds is observed to take place in the overall structure. In addition, there is no indication of changes in the tetrahedrality of the hydrogen-bond network of water in the vicinity of alcohol molecules.

Molecular-level changes of aqueous poly(N-isopropylacrylamide) in phase transition.

We report a Compton scattering study on the molecular-level structural changes of aqueous poly(N-isopropylacrylamide) (PNIPAM) across the conformational phase transition. PNIPAM is a thermoresponsive polymer that changes its conformation in water from the hydrophilic coil state to the collapsed hydrophobic globule state at 32 °C. Combined with density functional theory calculations, the Compton scattering experiments detect two type of changes in the phase transition. The amount of hydrogen bonds is found to reduce, and an elongation of the internal covalent bond lengths is observed. The elongation of the bonds indicates that not only the hydrogen bonding changes but there are other processes, most likely related to hydrophobic interaction, that should be taken into account in the phase transition.

Interplay between temperature-activated vibrations and nondipolar effects in the valence excitations of the CO2 molecule.

We report a study on the temperature dependence of the valence electron excitation spectrum of CO2 performed using nonresonant inelastic X-ray scattering spectroscopy. The excitation spectra were measured at the temperatures of 300 and 850 K with momentum-transfer values of 0.4-4.8 Å(-1), i.e., from the dipole limit to the higher-multipole regime, and were simulated using high-level coupled cluster calculations on the dipole and quadrupole level. The results demonstrate the emergence of dipole-forbidden excitations owing to temperature-induced bending mode activation and finite momentum transfer.

Crystal-field excitations in NiO under high pressure studied by resonant inelastic x-ray scattering.

We report a study on charge-neutral crystal-field (dd) excitations in NiO as a function of applied pressure up to 55 GPa, using resonant inelastic x-ray scattering spectroscopy at the Ni K edge. We find distinct signatures of the pressure-induced modifications to the 3d orbital energies as a function of pressure. These modifications are experimentally evidenced by a subtle splitting of the dd-excitation resonance energies. We compare the experimental results to a charge-transfer cluster-model calculation, and a LSDA + U calculation of the ground state as a function of lattice constant. We thus show how resonant inelastic x-ray scattering spectroscopy is able to give insights into the manifold of excited states even in conditions that are difficult to access with many traditional experimental techniques.

Saturation behavior in X-ray Raman scattering spectra of aqueous LiCl.

We report a study on the hydrogen-bond network of water in aqueous LiCl solutions using X-ray Raman scattering (XRS) spectroscopy. A wide concentration range of 0-17 mol/kg was covered. We find that the XRS spectral features change systematically at low concentrations and saturate at 11 mol/kg. This behavior suggests a gradual destruction in the hydrogen-bond network until the saturation concentration. The surprisingly large concentration required for the saturation supports an interpretation in which the ions affect the structure of water only within their first hydration shell. The study is complemented by density-functional-theory calculations and molecular dynamics simulations.

Microscopic structure of water at elevated pressures and temperatures.

We report on the microscopic structure of water at sub- and supercritical conditions studied using X-ray Raman spectroscopy, ab initio molecular dynamics simulations, and density functional theory. Systematic changes in the X-ray Raman spectra with increasing pressure and temperature are observed. Throughout the studied thermodynamic range, the experimental spectra can be interpreted with a structural model obtained from the molecular dynamics simulations. A spatial statistical analysis using Ripley's K-function shows that this model is homogeneous on the nanometer length scale. According to the simulations, distortions of the hydrogen-bond network increase dramatically when temperature and pressure increase to the supercritical regime. In particular, the average number of hydrogen bonds per molecule decreases to ≈ 0.6 at 600 °C and p = 134 MPa.