Monte Carlo model for ion mobility and diffusion for characteristic electric fields in nanodosimetry

The quantification of the effects of space radiation for manned spaceflight can be approximated by nanodosimetric measurements. For the development of nanodosimetric detectors, a Monte Carlo model for ion mobility and diffusion for characteristic electric fields is presented. This model can be used to describe the interactions of ions in their parent gas based solely on commonly known input parameters, such as the ionization potential, kinetic diameter, molar mass, and polarizability of the gas. A model for approximating the resonant charge exchange cross section has been proposed, requiring only the ionization energy and mass of the parent gas as input parameters. The method proposed in this work was tested against experimental drift velocity data for a wide range of gases (helium, neon, nitrogen, argon, krypton, carbon monoxide, carbon dioxide, oxygen, propane). The transverse diffusion coefficients were compared to experimental values for helium, nitrogen, neon, argon, and propane gas. With the Monte Carlo code and resonant charge exchange cross section approximation model presented in this work, it is now possible to calculate an estimate of the drift velocities, transverse diffusion, and thus the ion mobility of ions in their parent gas. This is essential for further nanodosimetric detector development, as those parameters are often not well known for the gas mixtures used in nanodosimetry.

Benchmark of the PenRed Monte Carlo framework for HDR brachytherapy

PURPOSE

The purpose of this study is to validate the PenRed Monte Carlo framework for clinical applications in brachytherapy. PenRed is a C++ version of Penelope Monte Carlo code with additional tallies and utilities.

METHODS AND MATERIALS

Six benchmarking scenarios are explored to validate the use of PenRed and its improved bachytherapy-oriented capabilities for HDR brachytherapy. A new tally allowing the evaluation of collisional kerma for any material using the track length kerma estimator and the possibility to obtain the seed positions, weights and directions processing directly the DICOM file are now implemented in the PenRed distribution. The four non-clinical test cases developed by the Joint AAPM-ESTRO-ABG-ABS WG-DCAB were evaluated by comparing local and global absorbed dose differences with respect to established reference datasets. A prostate and a palliative lung cases, were also studied. For them, absorbed dose ratios, global absorbed dose differences, and cumulative dose-volume histograms were obtained and discussed.

RESULTS

The air-kerma strength and the dose rate constant corresponding to the two sources agree with the reference datatests within 0.3% (Sk) and 0.1% (Λ). With respect to the first three WG-DCAB test cases, more than 99.8% of the voxels present local (global) differences within ±1%(±0.1%) of the reference datasets. For test Case 4 reference dataset, more than 94.9%(97.5%) of voxels show an agreement within ±1%(±0.1%), better than similar benchmarking calculations in the literature. The track length kerma estimator scorer implemented increases the numerical efficiency of brachytherapy calculations two orders of magnitude, while the specific brachytherapy source allows the user to avoid the use of error-prone intermediate steps to translate the DICOM information into the simulation. In both clinical cases, only minor absorbed dose differences arise in the low-dose isodoses. 99.8% and 100% of the voxels have a global absorbed dose difference ratio within ±0.2% for the prostate and lung cases, respectively. The role played by the different segmentation and composition material in the bone structures was discussed, obtaining negligible absorbed dose differences. Dose-volume histograms were in agreement with the reference data.

CONCLUSIONS

PenRed incorporates new tallies and utilities and has been validated for its use for detailed and precise high-dose-rate brachytherapy simulations.

espm: A Python library for the simulation of STEM-EDXS datasets

We present two open-source Python packages: "electron spectro-microscopy" (espm) and "electron microscopy tables" (emtables). The espm software enables the simulation of scanning transmission electron microscopy energy-dispersive X-ray spectroscopy datacubes, based on user-defined chemical compositions and spatial abundance maps of constituent phases. The simulation process uses X-ray emission cross-sections generated via state-of-the-art calculations made with emtables. These tables are designed to be easily modifiable, either manually or using espm. The simulation framework is designed to test the application of decomposition algorithms for the analysis of STEM-EDX spectrum images with access to a known ground truth. We validate our approach using the case of a complex geology-related sample, comparing raw simulated and experimental datasets and the outputs of their non-negative matrix factorization. In addition to testing machine learning algorithms, our packages will also help experimental design, for instance, predicting dataset characteristics or establishing minimum counts needed to measure nanoscale features.

Application of nano-radiosensitizers in combination cancer therapy

Radiosensitizers are compounds or nanostructures, which can improve the efficiency of ionizing radiation to kill cells. Radiosensitization increases the susceptibility of cancer cells to radiation-induced killing, while simultaneously reducing the potentially damaging effect on the cellular structure and function of the surrounding healthy tissues. Therefore, radiosensitizers are therapeutic agents used to boost the effectiveness of radiation treatment. The complexity and heterogeneity of cancer, and the multifactorial nature of its pathophysiology has led to many approaches to treatment. The effectiveness of each approach has been proven to some extent, but no definitive treatment to eradicate cancer has been discovered. The current review discusses a broad range of nano-radiosensitizers, summarizing possible combinations of radiosensitizing NPs with several other types of cancer therapy options, focusing on the benefits and drawbacks, challenges, and future prospects.

Realistic nuclear charge distribution model function for analytic nuclear attraction integrals in Gaussian basis functions

In electronic structure theory, the charge distribution of a nucleus is usually approximated by point charge, Gaussian function, or homogeneously charged sphere, because they have an analytical nuclear attraction integral (NAI) formula. However, these functions do not always provide good approximations for nuclei with large mass number. The two-parameter Fermi (2pF) distribution and more realistic distributions describe well even nuclei with large mass number but do not have analytical NAI formulas. We propose a new function model called augmented Gaussian 12 (AG12), which has sufficient number of parameters and analytical NAI formulas. With the proposed fitting scheme, the AG12 charge distribution model optimally reproduces 2pF and the more realistic charge distributions. Moreover, AG12 fitted to 2pF model reproduces the energy difference of hydrogen-like ions well between the Gaussian distribution and 2pF models. Calculations using AG12 also suggested necessity to use more realistic nuclear charge distributions than 2pF.

Properties of Naked Silver Clusters with Up to 100 Atoms as Found with Embedded-Atom and Density-Functional Calculations

The structural and energetic properties of small silver clusters Agn with n = 2-100 atoms are reported. For n = 2-100 the embedded atom model for the calculation of the total energy of a given structure in combination with the basin-hopping search strategy for an unbiased structure optimization has been used to identify the energies and structures of the three energetically lowest-lying isomers. These optimized structures for n = 2-11 were subsequently studied further through density-functional-theory calculations. These calculations provide additional information on the electronic properties of the clusters that is lacking in the embedded-atom calculations. Thereby, also quantities related to the catalytic performance of the clusters are studied. The calculated properties in comparison to other available theoretical and experimental data show a good agreement. Previously unidentified magic (i.e., particularly stable) clusters have been found for n>80. In order to obtain a more detailed understanding of the structural properties of the clusters, various descriptors are used. Thereby, the silver clusters are compared to other noble metals and show some similarities to both copper and nickel systems, and also growth patterns have been identified. All vibrational frequencies of all the clusters have been calculated for the first time, and here we focus on the highest and lowest frequencies. Structural effects on the calculated frequencies were considered.

Isotropic and Anisotropic Monolayer Structures in RF Discharge Plasma

We present the results of an experimental and analytical study of the structural and dynamic properties of a monolayer consisting of dust grains in an electrostatic trap in an RF discharge plasma. The possibility of forming a monolayer with an isotropic distribution for interparticle distance and kinetic energy of particles in the structure has been experimentally shown. Isotropy has crucial importance for the study of various processes in such systems, including the kinetics of phase transitions, the formation of directed flows, wave propagation, and others.

GRASP Manual for Users

grasp is a software package in Fortran 95, adapted to run in parallel under MPI, for research in atomic physics. The basic premise is that, given a wave function, any observed atomic property can be computed. Thus, the first step is always to determine a wave function. Different properties challenge the accuracy of the wave function in different ways. This software is distributed under the MIT Licence.

Attosecond Monitoring of Nonadiabatic Molecular Dynamics by Transient X-ray Transmission Spectroscopy

Tracing the evolution of molecular coherences can provide a direct, unambiguous probe of nonadiabatic molecular processes, such as the passage through conical intersections of electronic states. Two techniques, attosecond transient absorption spectroscopy (ATAS) and Transient Redistribution of Ultrafast Electronic Coherences in Attosecond Raman Signals (TRUECARS), have been used or proposed for monitoring nonadiabatic molecular dynamics. Both techniques employ the transmission of a weak attosecond extreme-ultraviolet or X-ray probe to interrogate the molecule at controllable time delays with respect to an optical pump, thereby extracting dynamical information from transient spectral features. The connection between these techniques has not been firmly established yet. In this theoretical study, we provide a unified description of both transient transmission techniques, establishing their relationship as limits of the same pump-probe spectroscopy technique for different pulse parameter regimes. We demonstrate this by quantum dynamical simulations of thiophenol photodissociation and show how complementary coherence information can be revealed by the two techniques.

Combinatorial Synthesis of AlTiN Thin Films

Nitrides of aluminum (Al) and titanium (Ti) mixtures have long been studied and used as commercial coatings because of their high hardness and high oxidation resistance due to the formation of an alumina layer on the coating surface. To fully understand the contribution of Al and Ti to the properties of the film, a combinatorial deposition approach was employed using half-disk targets. Film growth was carried out using a magnetron sputtering system powered by a 13.56 MHz radio frequency power supply with varying argon (Ar) and nitrogen (N2) gas ratios. Depending on the location of the substrate relative to the target, atomic percent gradients of 0.60–0.70 Al and 0.30–0.40 Ti across the substrate surface were obtained from energy dispersive X-ray spectral analysis. X-ray diffraction peaks at 43.59°, 74.71° (face-centered cubic), and 50.60° (wurtzite) confirmed the presence of aluminum titanium nitride (AlTiN) mixtures, with an increasing amount of wurtzite phase at higher Al concentrations. For all samples, cauliflower-like nanograins were obtained and samples of the 80:20 Ar:N2 gas pressure ratio showed the smallest grain size among the three gas ratio combinations. The 80:20 Ar:N2 films revealed a relatively high hardness compared to the other gas ratios. All thin films exhibited good adhesion to 304 stainless steel substrates.

Atomic Data Assessment with PyNeb: Radiative and Electron Impact Excitation Rates for [Fe ii] and [Fe iii]

We use the PyNeb 1.1.16 Python package to evaluate the atomic datasets available for the spectral modeling of [Fe ii] and [Fe iii], which list level energies, A-values, and effective collision strengths. Most datasets are reconstructed from the sources, and new ones are incorporated to be compared with observed and measured benchmarks. For [Fe iii], we arrive at conclusive results that allow us to select the default datasets, while for [Fe ii], the conspicuous temperature dependency on the collisional data becomes a deterrent. This dependency is mainly due to the singularly low critical density of the 3d7a4F9/2 metastable level that strongly depends on both the radiative and collisional data, although the level populating by fluorescence pumping from the stellar continuum cannot be ruled out. A new version of PyNeb (1.1.17) is released containing the evaluated datasets.

Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions

Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core-shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements.

On the Utmost Importance of the Basis Set Choice for the Calculations of the Relativistic Corrections to NMR Shielding Constants

The investigation of the sensitivity of the relativistic corrections to the NMR shielding constants (σ) to the configuration of angular spaces of the basis sets used on the atoms of interest was carried out within the four-component density functional theory (DFT). Both types of relativistic effects were considered, namely the so-called heavy atom on light atom and heavy atom on heavy atom effects, though the main attention was paid to the former. As a main result, it was found that the dependence of the relativistic corrections to σ of light nuclei (exemplified here by 1H and 13C) located in close vicinity to a heavy atom (exemplified here by In, Sn, Sb, Te, and I) on the basis set used on the light spectator atom was very much in common with that of the Fermi-contact contribution to the corresponding nonrelativistic spin-spin coupling constant (J). In general, it has been shown that the nonrelativistic J-oriented and σ-oriented basis sets, artificially saturated in the tight s-region, provided much better accuracy than the standard nonrelativistic σ-oriented basis sets when calculating the relativistic corrections to the NMR shielding constants of light nuclei at the relativistic four-component level of the DFT theory.

Time-Dependent Density-Functional Theory for Determining the Electron-Capture Cross Section for Protons Impacting on Atoms and Molecules

The use of the Time-Dependent Density-Functional Theory (TDDFT) has increased in the atomic collision field. Calculating the electron-capture cross section (ECCS) for protons is an important question in hadrontherapy and plasma physics, among other areas. In previous studies, it was shown that the approach based on the Local Density Approximation (LDA) fails in the 1-50 keV region, requiring the use of the Optimized Effective Potential (OEP) method. In this work, the ECCS values for 1-50 keV protons impacting on isolated hydrogen, carbon, nitrogen, oxygen, and nitrogenous atoms were determined using the TDDFT. It is shown that adding the Self Interaction Correction to the LDA (LDA-Sic) allows obtaining results close to those provided by the OEP and experiments, with the advantage that the LDA-Sic consumes less computational time. In addition, it was demonstrated that it is imperative to include the spin correction for the specific helium and oxygen cases, in order to get good results for the ECCS using the TDDFT. Theoretical results obtained in this work show excellent agreement with experimental values.

Refined theoretical values of field and mass isotope shifts in thallium to extract charge radii of Tl isotopes

Electronic factors for the field and mass isotope shifts in the 6p ²P_3/2 → 7s ²S_1/2 (535 nm), 6p ²P_1/2 → 6d ²D_3/2 (277 nm), and 6p ²P_1/2 → 7s ²S_1/2 (378 nm) transitions in neutral thallium were calculated within the high-order relativistic coupled cluster approach. These factors were used to reinterpret previous experimental isotope shift measurements in terms of charge radii of a wide range of Tl isotopes. Good agreement between theoretical and experimental King-plot parameters was found for the 6p ²P_3/2 → 7s ²S_1/2 and 6p ²P_1/2 → 6d ²D_3/2 transitions. It was shown that the value of the specific mass shift factor for the 6p ²P_3/2 → 7s ²S_1/2 transition is not negligible compared with the value of normal mass shift in contrast to what had been suggested previously. Theoretical uncertainties in the mean square charge radii were estimated. They were substantially reduced compared with the previously ascribed ones and amounted to less than 2.6%. The achieved accuracy paves the way for a more reliable comparison of the charge radii trends in the lead region.

Role of the Cohen-Fano interference in recoil-induced rotation

We study the rotational dynamics induced by the recoil effect in diatomic molecules using time-resolved two-color x-ray pump-probe spectroscopy. A short pump x-ray pulse ionizes a valence electron inducing the molecular rotational wave packet, whereas the second time-delayed x-ray pulse probes the dynamics. An accurate theoretical description is used for analytical discussions and numerical simulations. Our main attention is paid to the following two interference effects that influence the recoil-induced dynamics: (i) Cohen-Fano (CF) two-center interference between partial ionization channels in diatomics and (ii) interference between the recoil-excited rotational levels manifesting as the rotational revival structures in the time-dependent absorption of the probe pulse. The time-dependent x-ray absorption is computed for the heteronuclear CO and homonuclear N₂ molecules as showcases. It is found that the effect of CF interference is comparable with the contribution from independent partial ionization channels, especially for the low photoelectron kinetic energy case. The amplitude of the recoil-induced revival structures for the individual ionization decreases monotonously with a decrease in the photoelectron energy, whereas the amplitude of the CF contribution remains sufficient even at the photoelectron kinetic energy below 1 eV. The profile and intensity of the CF interference depend on the phase difference between the individual ionization channels related to the parity of the molecular orbital emitting the photoelectron. This phenomenon provides a sensitive tool for the symmetry analysis of molecular orbitals.

Reducing Exact Two-Component Theory for NMR Couplings to a One-Component Approach: Efficiency and Accuracy

The self-consistent and complex spin-orbit exact two-component (X2C) formalism for NMR spin-spin coupling constants [ J. Chem. Theory Comput. 17, 2021, 3874-3994] is reduced to a scalar one-component ansatz. This way, the first-order response term can be partitioned into the Fermi-contact (FC) and spin-dipole (SD) interactions as well as the paramagnetic spin-orbit (PSO) contribution. The FC+SD terms are real and symmetric, while the PSO term is purely imaginary and antisymmetric. The relativistic one-component approach is combined with a modern density functional treatment up to local hybrid functionals including the response of the current density. Computational demands are reduced by factors of 8-24 as shown for a large tin compound consisting of 137 atoms. Limitations of the current ansatz are critically assessed for Sn, Pb, Pd, and Pt compounds, i.e. the one-component treatment is not sufficient for tin compounds featuring a few heavy halogen atoms.

The Electronic Nature of Cationic Group 10 Ylidyne Complexes

We report a broad theoretical study on [(PMe3)3MER]+ complexes, with M = Ni, Pd, Pt, E = C, Si, Ge, Sn, Pb, and R = ArMes, Tbb, (ArMes = 2,6-dimesitylphenyl; Tbb = C6H2-2,6-[CH(SiMe3)2]2-4-tBu). A few years ago, our group succeeded in obtaining heavier homologues of cationic group 10 carbyne complexes via halide abstraction of the tetrylidene complexes [(PMe3)3M=E(X)R] (X = Cl, Br) using a halide scavenger. The electronic structure and the M-E bonds of the [(PMe3)3MER]+ complexes were analyzed utilizing quantum-chemical tools, such as the Pipek–Mezey orbital localization method, the energy decomposition analysis (EDA), and the extended-transition state method with natural orbitals of chemical valence (ETS-NOCV). The carbyne, silylidyne complexes, and the germylidyne complex [(PMe3)3NiGeArMes]+ are suggested to be tetrylidyne complexes featuring donor–acceptor metal tetrel triple bonds, which are composed of two strong π(M→E) and one weaker σ(E→M) interaction. In comparison, the complexes with M = Pd, Pt; E = Sn, Pb; and R = ArMes are best described as metallotetrylenes and exhibit considerable M−E−C bending, a strong σ(M→E) bond, weakened M−E π-components, and lone pair density at the tetrel atoms. Furthermore, bond cleavage energy (BCE) and bond dissociation energy (BDE) reveal preferred splitting into [M(PMe3)3]+ and [ER] fragments for most complex cations in the range of 293.3–618.3 kJ·mol−1 and 230.4–461.6 kJ·mol−1, respectively. Finally, an extensive study of the potential energy hypersurface varying the M−E−C angle indicates the presence of isomers with M−E−C bond angles of around 95°. Interestingly, these isomers are energetically favored for M = Pd, Pt; E = Sn, Pb; and R = ArMes over the less-bent structures by 13–29 kJ·mol−1.

Renal enhanced CT images reveal the tandem mechanism between tumor cells and immunocytes based on bulk/single-cell RNA sequencing

Metabolic reprogramming is essential for establishing the tumor microenvironment (TME). Glutamine has been implicated in cancer metabolism, but its role in clear cell renal carcinoma (ccRCC) remains unknown. Transcriptome data of patients with ccRCC and single-cell RNA sequencing (scRNA-seq) data were obtained from The Cancer Genome Atlas (TCGA, 539 ccRCC samples and 59 normal samples) database and GSE152938 (5 ccRCC samples). Differentially expressed genes related to glutamine metabolism (GRGs) were obtained from the MSigDB database. Consensus cluster analysis distinguished metabolism-related ccRCC subtypes. LASSO-Cox regression analysis was used to construct a metabolism-related prognostic model. The ssGSEA and ESTIMATE algorithms evaluated the level of immune cell infiltration in the TME, and the immunotherapy sensitivity score was obtained from TIDE. Cell-cell communication analysis was used to observe the distribution and effects of the target genes in the cell subsets. An image genomics model was constructed using imaging feature extraction and a machine learning algorithm. Results: Fourteen GRGs were identified. Overall survival and progression-free survival rates were lower in metabolic cluster 2, compared with those in cluster 1. The matrix/ESTIMATE/immune score in C1 decreased, but tumor purity in C2 increased. Immune cells were more active in the high-risk group, in which CD8 + T cells, follicular helper T cells, Th1 cells, and Th2 cells were significantly higher than those in the low-risk group. The expression levels of immune checkpoints were also significantly different between the two groups. RIMKL mainly appeared in epithelial cells in the single-cell analysis. ARHGAP11B was sparsely distributed. The imaging genomics model proved effective in aiding with clinical decisions. Glutamine metabolism plays a crucial role in the formation of immune TMEs in ccRCC. It is effective in differentiating the risk and predicting survival in patients with ccRCC. Imaging features can be used as new biomarkers for predicting ccRCC immunotherapy.

Werner Eissner (1930–2022): A Pioneer in Computational Atomic Physics

Werner Eissner (Figure 1), a pioneer in computational atomic physics, was born on 16 October 1930 in the city of Görlitz, Germany, to Bernhard and Frieda (née Eckert) Eissner [...]

Mass absorption coefficient in the 200-800 eV region of sp(3) carbon atoms measured using self-standing polyethylene thin films

To experimentally determine the mass absorption coefficient (μ) of a sp³-carbon (C) atom in the soft X-ray region, soft X-ray absorption spectra (XAS) in the 200-800 eV and C K regions of 200-nm-thick self-standing polyethylene (PE) films were measured in the transmission and total electron yield (TEY) modes. PE films were prepared by a spin-coating method. Their experimentally measured thickness and density are 200 nm and 0.920 g/cm³, respectively. Soft X-ray absorption measurements were performed in beamline BL-6.3.2 at the Advanced Light Source. Although surface oxygen can be slightly observed in the O K and C K regions in TEY-XAS, it cannot be observed in absorbance-XAS. The absorbance-XAS profiles agree well with the calculated profiles, except in the C K threshold. Hence, it can be confirmed that the absorption-XAS measurements are achieved. From the absorbance, μ of sp³-C in PE is 7 × 10⁴ cm²/g near 288 eV and 294 eV.

Wet to Dry Controls Lanthanide Scandate Synthesis

The choice of temperature and gas conditions used in a water pressure-controlled reactor is guided by density functional theory (DFT) to synthesize nearly phase-pure lanthanide scandate nanoparticles (LnScO₃, Ln = La, Nd, Sm, Gd). In this synthetic method, low water-vapor partial pressures, well below water's gas liquidus, inhibit particle growth, while an excess of water vapor results in undesired rare-earth hydroxide and oxyhydroxide secondary phases. The optimal humidity for high-purity LnScO₃ particle synthesis is shown to vary with the lanthanide; DFT is used to calculate the thermodynamics of secondary phase formation for each lanthanide tested such that the role of water vapor may be quantified and used to maintain phase purity (greater than 96 mol %) across the series. The combination of thermodynamic calculation and experimental confirmation with this pressure-controlled reactor provides an opportunity to explore analogous syntheses of other inorganic perovskite nanoparticles.

Intensity Ratio of Kβ/Kα in Selected Elements from Mg to Cu, and the Chemical Effects of Cr Kα1,2 Diagram Lines and Cr Kβ/Kα Intensity Ratio in Cr Compounds

Kα,β X-ray lines from photon excitation were measured in selected elements from Mg to Cu using a high-resolution double-crystal X-ray spectrometer with a proportional counter, and the Kβ/Kα intensity ratio for each element was obtained, after correcting for self-absorption, detection efficiency, and crystal reflectance. This intensity ratio increases rapidly from Mg to Ca but, in the 3d elements region, the increase becomes slower. This is related to the intensity of the Kβ line involving valence electrons. The slow increase of this ratio in the 3d elements region is thought to be due to the correlation between 3d and 4s electrons. Moreover, the chemical shifts, FWHM, asymmetry indices, and Kβ/Kα intensity ratios of the Cr compounds, due to different valences, were also investigated using the same double-crystal X-ray spectrometer. The chemical effects were clearly observed, and the Kβ/Kα intensity ratio was found to be compound-dependent for Cr.

Raman and NMR spectroscopic and theoretical investigations of the cubic laves-phases REAl2 (RE = Sc, Y, La, Yb, Lu)

The cubic Laves-phase aluminides REAl₂ with RE = Sc, Y, La, Yb and Lu were prepared from the elements by arc-melting or using refractory metal ampoules and induction heating. They all crystallize in the cubic crystal system with space group Fd3̄m and adopt the MgCu₂ type structure. The title compounds were characterized by powder X-ray diffraction and spectroscopically investigated using Raman and ²⁷Al and in the case of ScAl₂ by ⁴⁵Sc solid-state MAS NMR. In both, the Raman and NMR spectra, the aluminides exhibit only one signal due to the crystal structure. DFT calculations were used to calculate Bader charges illustrating the charge transfer in these compounds along with NMR parameters and densities of states. Finally, the bonding situation was assessed by means of ELF calculations rendering these compounds aluminides with positively charged RE^δ+ cations embedded in an [Al₂]^δ- polyanion.

Identification of Visible Lines in Pm-like W13+

To provide spectroscopic data for W13+, the present work is focused on the analysis of spectra observed in the visible range, using a compact electron beam ion trap (CoBIT). Line identification is done by using a collisional radiative model, along with sophisticated structure calculations from FAC and GRASP2018. Most of the identified lines belong to magnetic dipole (M1) transitions between the levels of the 4f125p1 and 4f13 configurations.

Photoionization and Electron–Ion Recombination in Astrophysical Plasmas

Photoionization and its inverse, electron–ion recombination, are key processes that influence many astrophysical plasmas (and gasses), and the diagnostics that we use to analyze the plasmas. In this review we provide a brief overview of the importance of photoionization and recombination in astrophysics. We highlight how the data needed for spectral analyses, and the required accuracy, varies considerably in different astrophysical environments. We then discuss photoionization processes, highlighting resonances in their cross-sections. Next we discuss radiative recombination, and low and high temperature dielectronic recombination. The possible suppression of low temperature dielectronic recombination (LTDR) and high temperature dielectronic recombination (HTDR) due to the radiation field and high densities is discussed. Finally we discuss a few astrophysical examples to highlight photoionization and recombination processes.

Energy loss function of samarium

We present a combined experimental and theoretical work to obtain the energy loss function (ELF) or the excitation spectrum of samarium in the energy loss range between 3 and 200 eV. At low loss energies, the plasmon excitation is clearly identified and the surface and bulk contributions are distinguished. For the precise analysis the frequency-dependent energy loss function and the related optical constants (n and k) of samarium were extracted from the measured reflection electron energy loss spectroscopy (REELS) spectra by the reverse Monte Carlo method. The ps- and f-sum rules with final ELF fulfils the nominal values with 0.2% and 2.5% accuracy, respectively. It was found that a bulk mode locates at 14.2 eV with the peak width ~6 eV and the corresponding broaden surface plasmon mode locates at energies of 5-11 eV.

Using Collocation to Solve the Schrödinger Equation

We review the collocation approach to the solution of the Schrödinger equation and its uses in applications. Interrelations between collocation and other methods are highlighted. We also stress advantages and disadvantages of the rectangular collocation formulation. Using collocation makes it possible to use any, e.g. optimized, coordinates and basis functions, including nonintegrable basis functions, and provides a straightforward way of dealing with singularities in the potential. In addition, we stress that using collocation facilitates tuning the shape of basis functions and the placement of points, both of which can be done with machine-learning methods. Applications to electronic and vibrational problems are reviewed focusing on calculations for molecules on surfaces for which there are few variational calculations. Collocation has advantages when potential energy surfaces are unavailable, in particular, for molecule-surface systems, and for systems for which standard direct product quadrature grids, often used with variational methods, are costly.

Long-range interactions of aromatic molecules with alkali-metal and alkaline-earth-metal atoms

The isotropic and anisotropic coefficients C_n ^l,m of the long-range spherical expansion ∼1/Rⁿ (R-the intermolecular distance) of the dispersion and induction intermolecular energies are calculated using the first principles for the complexes containing an aromatic molecule (benzene, pyridine, furan, and pyrrole) and alkali-metal (Li, Na, K, Rb, and Cs) or alkaline-earth-metal (Be, Mg, Ca, Sr, and Ba) atoms in their electronic ground states. The values of the first- and second-order properties of the aromatic molecules are calculated using the response theory with the asymptotically corrected LPBE0 functional. The second-order properties of the closed-shell alkaline-earth-metal atoms are obtained using the expectation-value coupled cluster theory and of the open-shell alkali-metal atoms using analytical wavefunctions. These properties are used for the calculation of the dispersion C_n,disp ^l,m and induction C_n,ind ^l,m coefficients (C_n ^l,m=C_n,disp ^l,m+C_n,ind ^l,m) with n up to 12 using the available implemented analytical formulas. It is shown that the inclusion of the coefficients with n > 6 is important for reproducing the interaction energy in the van der Waals region at R ≈ 6 Å. The reported long-range potentials should be useful for constructing the analytical potentials valid for the whole intermolecular interaction range, which are needed for spectroscopic and scattering studies.

A relativistic relationship between parity-violating nuclear spin-rotation tensors and parity-violating NMR shielding tensors

The nuclear-spin-dependent parity-violation contributions to the nuclear magnetic resonance shielding and nuclear spin-rotation tensors (σ^PV and M^PV, respectively) are known to be formally related to one another in the non-relativistic regime. In this work, the polarization propagator formalism and the linear response within the elimination of small components model are used to show a new and more general relationship between them, which is valid within the relativistic framework. The full set of the zeroth- and first-order relativistic contributions to σ^PV and M^PV are also given here for the first time, and these results are compared with previous findings. According to four-component relativistic calculations, the electronic spin-orbit effects are the most significant ones for the isotropic values of σ^PV and M^PV in the H₂X₂ series of molecules (with X = O, S, Se, Te, and Po). When only scalar relativistic effects are taken into account, the non-relativistic relationship between σ^PV and M^PV does hold. However, when the spin-orbit effects are taken into consideration, this old non-relativistic relationship breaks down, and therefore, the new one must be considered.

Dual Role of Glutathione as a Reducing Agent and Cu-Ligand Governs the ROS Production by Anticancer Cu-Thiosemicarbazone Complexes

α-Pyridyl thiosemicarbazones (TSC) such as Triapine (3AP) and Dp44mT are a promising class of anticancer agents. Contrary to Triapine, Dp44mT showed a pronounced synergism with Cu^II, which may be due to the generation of reactive oxygen species (ROS) by Dp44mT-bound Cu^II ions. However, in the intracellular environment, Cu^II complexes have to cope with glutathione (GSH), a relevant Cu^II reductant and Cu^I-chelator. Here, aiming at rationalizing the different biological activity of Triapine and Dp44mT, we first evaluated the ROS production by their Cu^II-complexes in the presence of GSH, showing that Cu^II-Dp44mT is a better catalyst than Cu^II-3AP. Furthermore, we performed density functional theory (DFT) calculations, which suggest that a different hard/soft character of the complexes could account for their different reactivity with GSH.

Insights into the Effect of Metal Ratio on Cooperative Redox Enhancement Effects over Au- and Pd-Mediated Alcohol Oxidation

The aerobic oxidation of alcohols and aldehydes over supported heterogeneous catalysts can be considered as comprising two complementary and linked processes: dehydrogenation and oxygen reduction. Significant rate enhancements can be observed when these processes are catalyzed by independent active sites, coupled by electron transport between the two catalysts. This effect, termed cooperative redox enhancement (CORE), could significantly influence how researchers approach catalyst design, but a greater understanding of the factors which influence it is required. Herein, we demonstrate that the Au/Pd ratio used in physical mixtures of monometallic catalysts and phase-separated Au and Pd bimetallic catalysts dramatically influences the degree to which CORE effects can promote alcohol oxidation. Perhaps more interestingly, the roles of Au and Pd in this coupled system are determined to be interchangeable. Preliminarily, we hypothesize that this is attributed to the relative rates of the coupled reactions and demonstrate how physical properties can influence this. This deeper understanding of the factors which influence CORE is an important development in bimetallic catalysis.

EUV Beam–Foil Spectra of Germanium and a Blind-Spot Problem in Spectroscopy

Beam–foil extreme-ultraviolet survey spectra of Ge (Z=32) are presented. The data have been garnered at the performance limit of the heavy-ion accelerator available, with a correspondingly limited statistical and calibrational reliability. However, the Ge spectra have been recorded at various delays after excitation, and this technique points to a possible blind spot in some other spectroscopic techniques, and thus in the literature coverage. A similarly patchy coverage can be noted in various atomic structure computations. The experimental and theoretical gaps seem to be correlated.

Precise characterization of a corridor-shaped structure in Khufu's Pyramid by observation of cosmic-ray muons

Khufu's Pyramid is one of the largest archaeological monument all over the world, which still holds many mysteries. In 2016 and 2017, the ScanPyramids team reported on several discoveries of previously unknown voids by cosmic-ray muon radiography that is a non-destructive technique ideal for the investigation of large-scale structures. Among these discoveries, a corridor-shaped structure has been observed behind the so-called Chevron zone on the North face, with a length of at least 5 meters. A dedicated study of this structure was thus necessary to better understand its function in relation with the enigmatic architectural role of this Chevron. Here we report on new measurements of excellent sensitivity obtained with nuclear emulsion films from Nagoya University and gaseous detectors from CEA, revealing a structure of about 9 m length with a transverse section of about 2.0 m by 2.0 m.

Low-energy Ar+ ion-beam-induced chemical vapor deposition of silicon dioxide films using tetraethyl orthosilicate

This study was conducted to determine whether the simultaneous injections of Ar⁺ ions and tetraethyl orthosilicate (TEOS) to a substrate are able to fabricate a film on the substrate. The Ar⁺ ion energy was 100 eV. After the injections, we found a film deposited on the substrate. Following the analyses of the film with X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy, it was found that the deposited film was silicon dioxide (SiO₂). We conclude that the low-energy Ar⁺ ion-beam-induced deposition method using TEOS is useful for the growth of SiO₂ films.

Determination of Electron Beam Energy in Measuring the Electron-Impact Ionization Cross Section of He-like Fe24+

In an effort to measure electron-impact ionization (EII) cross-sections of He-like Fe24+ at the electron beam ion trap (EBIT) facility of the National Institute of Standards and Technology (NIST), we have experimentally determined the corrections to the nominal beam energy determined by the voltages applied to the EBIT. High-resolution X-ray spectra were recorded at nominal electron beam energies between 6660 eV and 6750 eV using X-ray microcalorimetry based upon an array of 192 transition-edge sensors (TES). A large-scale collisional-radiative simulation of the non-Maxwellian EBIT plasma using relevant atomic data calculated with Flexible Atomic Code allowed us to determine the space-charge correction due to the electron beam including the neutralization factor by the ion cloud of the EBIT.

Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures

X-ray crystallography has been invaluable in delivering structural information about proteins. Previously, an approach has been developed that allows high-quality X-ray diffraction data to be obtained from protein crystals at and above room temperature. Here, this previous work is built on and extended by showing that high-quality anomalous signal can be obtained from single protein crystals using diffraction data collected at 220 K up to physiological temperatures. The anomalous signal can be used to directly determine the structure of a protein, i.e. to phase the data, as is routinely performed under cryoconditions. This ability is demonstrated by obtaining diffraction data from model lysozyme, thaumatin and proteinase K crystals, the anomalous signal from which allowed their structures to be solved experimentally at 7.1 keV X-ray energy and at room temperature with relatively low data redundancy. It is also demonstrated that the anomalous signal from diffraction data obtained at 310 K (37°C) can be used to solve the structure of proteinase K and to identify ordered ions. The method provides useful anomalous signal at temperatures down to 220 K, resulting in an extended crystal lifetime and increased data redundancy. Finally, we show that useful anomalous signal can be obtained at room temperature using X-rays of 12 keV energy as typically used for routine data collection, allowing this type of experiment to be carried out at widely accessible synchrotron beamline energies and enabling the simultaneous extraction of high-resolution data and anomalous signal. With the recent emphasis on obtaining conformational ensemble information for proteins, the high resolution of the data allows such ensembles to be built, while the anomalous signal allows the structure to be experimentally solved, ions to be identified, and water molecules and ions to be differentiated. Because bound metal-, phosphorus- and sulfur-containing ions all have anomalous signal, obtaining anomalous signal across temperatures and up to physiological temperatures will provide a more complete description of protein conformational ensembles, function and energetics.

Direct Observation of Charge, Energy, and Hydrogen Transfer between the Backbone and Nucleobases in Isolated DNA Oligonucleotides

Understanding how charge and energy, as well as protons and hydrogen atoms, are transferred in molecular systems as a result of an electronic excitation is fundamental for understanding the interaction between ionizing radiation and biological matter on the molecular level. To localize the excitation at the atomic scale, it was chosen to target phosphorus atoms in the backbone of gas-phase oligonucleotide anions and cations, by means of resonant photoabsorption at the L- and K-edges. The ionic photoproducts of the excitation process were studied by a combination of mass spectrometry and X-ray spectroscopy. The combination of absorption site selectivity and photoproduct sensitivity allowed the identification of X-ray spectral signatures of specific processes. Moreover, charge and/or energy as well as H transfer from the backbone to nucleobases has been directly observed. Although the probability of one versus two H transfer following valence ionization depends on the nucleobase, ionization of sugar or phosphate groups at the carbon K-edge or the phosphorus L-edge mainly leads to single H transfer to protonated adenine. Moreover, our results indicate a surprising proton-transfer process to specifically form protonated guanine after excitation or ionization of P 2p electrons.

Pseudopotential analysis on hyperfine splitting frequency shift of alkali-metal atoms in noble gases, revisited

Theoretical pseudopotentials and dispersion potentials are used to study ground-state hyperfine splitting frequencies of alkali-metal atoms (Li, Na, K, Rb, and Cs) in noble gases (He, Ne, Ar, Kr, and Xe) in all combinations. With a single fitting parameter, calculations based on first-order perturbation theory qualitatively present each temperature dependence of the measured frequency shift. With this parameter and excitation energies of alkali-metal and noble-gas atoms, the hyperfine splitting frequency of alkali-metal atoms is suitable for investigating the properties of noble-gas atoms, such as the s-wave scattering length of electrons, the electric-dipole polarizability, and the van der Waals radius. This study suggests the possibility of improving excitation energies and van der Waals potentials of colliding pairs.