Atomic Calculations Research Articles

4f photoabsorption in Pt+ to Pt4+

Detailed knowledge of the inner-shell atomic structure of lowly-ionised species is lacking for most elements along the sixth row of the periodic table, from hafnium to bismuth. This paper presents 4f-photoabsorption spectra of Pt+ to Pt4+ ions, recorded between 69 and 127 eV (9.8 nm and 18 nm) using the dual laser plasma method. Analysis of the spectra was supported by atomic structure calculations using the Cowan suite of codes, by relativistic time-dependent local-density approximation (RTDLDA) calculations, and by comparison along isoelectronic series, particularly with spectra of lowly-ionised gold plasmas. The RTDLDA calculations account for the influence of photoionisation and photoexcitation on the recorded spectra. The spectra show 4f 5d, 6d, and 7d transitions, broadened by autoionisation.

Serially improved GTOs for molecular applications (SIGMA): Basis sets from H to Ne.

A new approach for generating Gaussian basis sets is reported and tested for atoms from H to Ne. The basis sets thus calculated, named SIGMA basis sets, range from DZ to QZ sizes and have the same composition per shell as Dunning basis sets but with different treatment of the contractions. The standard SIGMA basis sets and their augmented versions have proven to be very suitable for providing good results in atomic and molecular calculations. The performance of the new basis sets is analyzed in terms of total, correlation, and atomization energies, equilibrium distances, and vibrational frequencies in several molecules, and the results are compared at several computational levels with those obtained with the corresponding Dunning and other basis sets.

Thermal contribution to measured g-factors in alkali atoms

In this paper, we consider a one-loop thermal correction to the g-factors of the ground and low-lying excited states in atomic systems with one valence s electron. As an example, we carried out calculations for Rb and Cs atoms, where optical measurements of transition frequencies set the metrological level of accuracy. With the development of atomic systems as the most accurate tool for spectroscopic experiments, it has become increasingly important to improve the accuracy of measuring the electron g-factor, which is currently at10−12. The rapid progress in this field in recent years requires analysis not only of various relativistic, quantum electrodynamics, and other effects, but also theoretical studies of phenomena stimulated by the external thermal environment. We can expect that the thermal contribution to the g-factor calculated in our work may be of interest in the near future.

Anisotropic excitonic photocurrent in β−Ga2O3

Polarization-dependent photocurrent spectra are measured on a (001) $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$ Schottky photodetector, where the linear polarization of light is rotated within the ab plane. Three spectral peaks at 4.92, 5.15, and 5.44 eV are observed that vary in intensity with the optical polarization direction. The peak transition energies are consistent with excitons previously reported in $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$ due to interband transitions modified by the valence-band $p$-orbital anisotropy and the electron-hole Coulombic attraction. The measured polarization dependence of the photocurrent matches our predictions based on electromagnetic simulations of anisotropic absorption using the complex dielectric function tensor extracted from previous ellipsometry studies. These results illustrate the dominance of excitonic absorption and photocurrent in $\ensuremath{\beta}\text{\ensuremath{-}}{\mathrm{Ga}}_{2}{\mathrm{O}}_{3}$ both below and above the band gap, demonstrate a combined theoretical/experimental understanding of anisotropic photocarrier generation, and validate previous atomistic band-structure calculations in this low-symmetry ultrawide-band-gap semiconductor.

MolTwister – a molecular systems construction, manipulation and statistical mechanical calculation tool

To perform molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, quantum mechanical (QM) electronic structure calculations, or similar atomistic calculations, it is necessary to first construct and define the molecular system of interest. This involves creating an initial configuration of atoms, where MD and MC simulations require forcefield assignments, for example in the form of non-bonded, bonded, angular and dihedral potentials. Once simulations or calculations have been performed, large sets of data are available (often several gigabytes). These contain atomic trajectories and other relevant static or dynamic information, from which static and dynamic properties (such as density profiles, vibrational density of states and velocity autocorrelation functions) can be obtained through statistical mechanical calculations. MolTwister is an open source software platform that addresses the construction of molecular systems, basic 3D visualization of these, the generation of input files for selected MD packages, as well as calculation of properties from atomistic simulation data. It also contains a GPU accelerated MD simulator suited for smaller tasks such as molecular thermalization. The software package is written in C++14 and can be used as a basis for further development, where efforts have been made to make access to underlying functionality easy. Moreover, it supports Python, where scripts have access to the majority of program functionality. Program summaryProgram Title: MolTwisterCPC Library link to program files:https://doi.org/10.17632/ph6pwst9mn.1Developer's repository link:http://moltwister.comLicensing provisions: GPLv3 or laterProgramming language: C++14Nature of problem: Lack of SW tools for easy construction of complex molecular systems, as well as tools enabling analysis of long molecular trajectories.Solution method: Developed command line tool with associated 3D view, where molecular construction commands can be executed in complex manners through a Python interface. The program also has commands for analysis of molecular data that process one molecular time-frame at a time, thus enabling analysis of long molecular trajectories. Moreover, the program structure is designed for easy implementation of new commands by other researchers.Additional comments including restrictions and unusual features: Supported file formats: xyz, pdb, mtt (MolTwister trajectory), dcd, xtc, qepos, python, script (MolTwister scripts)Supported MD engines: HOOMD-blue, LAMMPS, MolTwister internal (moldyn)

Atomistic study of the properties and behavior under uniaxial tensile stress of some representative UO[formula omitted] grain boundaries

In irradiated polycrystalline uranium dioxide (UO2), the pressure generated at high temperature by the noble gases in the intergranular bubbles as well as the thermomechanical stresses due to temperature gradients cause the fracture of the grain boundaries. In this study, one analyzes through atomistic calculations of static and molecular dynamics type the properties of three UO2 grain boundaries and their behavior under uniaxial tensile loading up to fracture. In these atomistic simulations, the interactions between atoms are described using a many-body variable charge potential. Structural analysis, performed on the three grain boundary structures under uniaxial tensile stresses and over a wide temperature range, reveals no source of plasticity. This suggests a brittle behavior at fracture, in agreement with recent experimental studies carried out on micrometer size specimens containing grain boundaries. A method based on thermodynamic considerations is used to build normal cohesive zone laws for the UO2 grain boundaries using molecular dynamics simulation data. The cohesive zone laws will be employed in a future study in failure simulations at higher scales.

Cocrystallization of Dasatinib with different acids improves the solubility and physicochemical properties: A combined experimental and theoretical studies

Dasatinib (DAS) is a tyrosine kinase inhibitor that is categorized as a class-II drug by Biopharmaceutical Classification System (BCS). It is used to treat Chronic Myeloid Leukemia (CML). The present work aimed to use the cocrystallization technique to enhance DAS's physicochemical characteristics. By applying the slow evaporation approach, we reported three DAS cocrystals with different structures of co-formers such as 4 hydroxybenzoic acid, 4-chlorobenzene acid, and Sorbic acid. Single Crystal X-ray Diffraction (SCXRD), Powder X-ray Diffraction (PXRD), Differential Scanning Calorimetry (DSC), Thermo Gravimetric Analysis (TGA), and Fourier Transform Infrared Spectroscopy (FT-IR) were used to analyze the three obtained cocrystals. The solubility of DAS cocrystals was investigated and found to be ideally enhanced up to 6-fold, 4.5-fold, and 3.5-fold higher than DAS. According to the findings, the DAS cocrystal system has strong hydrogen bonding and stacking interactions. We also performed quantum chemical calculation and quantum theory of atoms in molecules (QTAIM) analysis to understand the strength of intermolecular interactions. From this study, we observed that cocrystallization was a promising technique for changing the physicochemical properties of DAS.

Spatial-Temporal Self-Attention Transformer Networks for Battery State of Charge Estimation

Over the past ten years, breakthroughs in battery technology have dramatically propelled the evolution of electric vehicle (EV) technologies. For EV applications, accurately estimating the state-of-charge (SOC) is critical for ensuring safe operation and prolonging the lifespan of batteries, particularly under complex loading scenarios. Despite progress in this area, modeling and forecasting the evaluation of multiphysics and multiscale electrochemical systems under realistic conditions using first-principles and atomistic calculations remains challenging. This study proposes a solution by designing a specialized Transformer-based network architecture, called Bidirectional Encoder Representations from Transformers for Batteries (BERTtery), which only uses time-resolved battery data (i.e., current, voltage, and temperature) as an input to estimate SOC. To enhance the Transformer model’s generalization, it was trained and tested under a wide range of working conditions, including diverse aging conditions (ranging from 100% to 80% of the nominal capacity) and varying temperature windows (from 35 °C to −5 °C). To ensure the model’s effectiveness, a rigorous test of its performance was conducted at the pack level, which allows for the translation of cell-level predictions into real-life problems with hundreds of cells in-series conditions possible. The best models achieve a root mean square error (RMSE) of less than 0.5 test error and approximately 0.1% average percentage error (APE), with maximum absolute errors (MAE) of 2% on the test dataset, accurately estimating SOC under dynamic operating and aging conditions with widely varying operational profiles. These results demonstrate the power of the self-attention Transformer-based model to predict the behavior of complex multiphysics and multiscale battery systems.

Liver-cell protective pyridones from the fungi Tolypocladium album dws120

Five previously undescribed pyridone derivatives, tolypyridones I–M, were identified from the solid rice medium fermented by Tolypocladium album dws120, along with two known compounds tolypyridone A (or trichodin A) and pyridoxatin. Their planar structures and partial relative configurations have been determined by careful interpretation of their spectroscopic data. The full assignment of the relative and absolute configurations of tolypyridones I–M was achieved by gauge-independent atomic orbital 13C NMR calculation, quantitative nuclear Overhauser effects based interatomic distance calculation, and electronic circular dichroism calculation. In addition, we have fully determined the configuration of tolypyridone A by X-ray diffraction analysis. In bioassay, tolypyridones I was able to restore cell viability and inhibit the release of alanine aminotransferase and aspartate aminotransferase for ethanol-induced LO2 cells, suggesting its potential as a liver protective agent.

Wedge disclination description of emergent core-shifted grain boundaries at free surfaces

Emergent grain boundaries at free surface control material properties such as nanomaterial strength, catalysis, and corrosion. Recently the restructuring of emergent boundaries on copper (111) surfaces was discovered experimentally and atomic calculations point to its universality in fcc metal systems. Restructuring is due to a preference for boundaries to shift their tilt axis across the (11¯0) plane towards [112] and ultimately to form low energy [112] core shifted boundaries (CSBs). However, the observed geometry of these emergent boundaries is not reproduced by atomic calculations and the driving force is still controversial due to inconsistencies between the computational continuum analysis and atomic calculations. Here, using atomic calculations that involve a methodical shift of the dislocation core, we confirmed the geometry of emergent boundaries observed in experiment and reconciled the atomic calculations with the elastic analysis through the inclusion of a straight wedge disclination at the free surface.

Néel vector switching and terahertz spin-wave excitation in Mn2Au due to femtosecond spin-transfer torques

Efficient and fast manipulation of antiferromagnets has to date remained a challenging task, hindering their application in spintronic devices. For ultrafast operation of such devices, it is highly desirable to be able to control the antiferromagnetic order within picoseconds - a timescale that is difficult to achieve with electrical circuits. Here, we demonstrate that bursts of spin-polarized hot-electron currents emerging due to laser-induced ultrafast demagnetization are able to efficiently excite spin dynamics in antiferromagnetic Mn$_2$Au by exerting a spin-transfer torque on femtosecond timescales. We combine quantitative superdiffusive transport and atomistic spin-model calculations to describe a spin-valve-type trilayer consisting of Fe$|$Cu$|$Mn$_2$Au. Our results demonstrate that femtosecond spin-transfer torques can switch the Mn$_2$Au layer within a few picoseconds. In addition, we find that spin waves with high frequencies up to several THz can be excited in Mn$_2$Au.

Exploring the experimental study and density functional theory calculations of symmetric and asymmetric chalcogen atoms interacted molybdenum dichalcogenides for lithium-ion batteries

Two-dimensional asymmetric chalcogen atoms attached to Janus nanoparticles have fascinated research attention owing to their distinctive properties and characteristics for various applications. This paper proposed a facile synthesis to produce efficient molybdenum-based symmetric and asymmetric chalcogens bounded by XMoX and TeMoX nanostructures. Subsequently, the fabricated XMoX and TeMoX nanostructures were employed as anodes for lithium-ion batteries (LIBs). Assembled LIBs using TeMoS and TeMoSe Janus anodes achieved 2610 and 2073 mAh g–1 reversible capacity at 0.1 A g–1, respectively for the half-cell configuration, which is outstanding performance compared with previous reports. Superior rate capability performances at 0.1–20 A g–1 and exceptional cycling solidity confirmed high charge and discharge capacities for TeMoX Janus lithium-ion battery anodes. In addition, the full cell device with TeMoS//LiCoO2 configuration explored the discharge capacity of 1605 mAh g−1 at 0.1 A g–1 which suggests their excellent electrochemical characteristics. The density functional theory approximations established the significance of assembled symmetric and asymmetric chalcogen atoms interacted with XMoX and TeMoX anode materials for LIBs. Thus, the present investigation supports a new approach to creating two-dimensional materials based on asymmetric chalcogen atoms with core metal to effectively increase desirable energy storage characteristics.

The Interaction of Factor Xa and IXa with Non-Activated Antithrombin in Michaelis Complex: Insights from Enhanced-Sampling Molecular Dynamics Simulations.

The interaction between coagulation factors Xa and IXa and the activated state of their inhibitor, antithrombin (AT),have been investigated using X-ray diffraction studies. However, only mutagenesis data are available for non-activated AT. Our aim was to propose a model based on docking and advanced-sampling molecular dynamics simulations that can reveal the conformational behavior of the systems when AT is not binding a pentasaccharide. We built the initial structure for non-activated AT-FXa and AT-FIXa complexes using HADDOCK 2.4. The conformational behavior was studied using Gaussian accelerated molecular dynamics simulations. In addition to the docked complexes, two systems based on the X-ray structures were also simulated, with and without the ligand. The simulations revealed large variability in conformation for both factors. In the docking-based complex of AT-FIXa, conformations with stable Arg150-AT interactions can exist for longer time periods but the system also has a higher tendency for reaching states with very limited interaction with the "exosite" of AT. By comparing simulations with or without the pentasaccharide, we were able to gain insights into the effects of conformational activation on the Michaelis complexes. RMSF analysis and correlation calculations for the alpha-carbon atoms revealed important details of the allosteric mechanisms. Our simulations provide atomistic models for better understanding the conformational activation mechanism of AT against its target factors.

Spin-phonon interactions induced anomalous thermal conductivity in nickel (II) oxide

Nickel (II) oxide is a prominent candidate for spintronic and spin-caloritronic applications operating at room temperature. Although there are extensive studies on nickel oxide, the roles of magnon- and spin-phonon interactions on thermal transport are not well understood. In the present work, the relationship between spin-phonon interactions and thermal transport is investigated by performing inelastic neutron scattering, time-domain thermoreflectance thermal conductivity measurements, and atomistic thermal transport calculations. Inelastic neutron scattering measurements of the magnon lifetime imply that magnon thermal conductivity is trivial, and so heat is conducted only by phonons. Time-domain thermoreflectance measurements of the thermal conductivity vs. temperature follow T−1.5 in the antiferromagnetic phase. This temperature dependence cannot be explained by phonon-isotope and phonon-defect scattering or phonon softening. Instead, we attribute this to magnon-phonon scattering and spin-induced dynamic symmetry breaking. The spin-phonon interactions are saturated in the paramagnetic phase and lead to a weaker temperature dependence of T−1.0 at 550–700 K. These results reveal the importance of spin-phonon interactions on lattice thermal transport, shedding light on the engineering of functional antiferromagnetic spintronic and spin-caloritronic materials through these interactions.

Atomic Electronic Structure Calculations with Hermite Interpolating Polynomials.

We have recently described the implementation of atomic electronic structure calculations within the finite element method with numerical radial basis functions of the form χμ(r) = r-1Bμ(r), where high-order Lagrange interpolating polynomials (LIPs) were used as the shape functions Bμ(r). In this work, we discuss how χμ(r) can be evaluated in a stable manner at small r and also revisit the choice of the shape functions Bμ(r). Three kinds of shape functions are considered: in addition to the continuous LIPs, we consider the analytical implementation of first-order Hermite interpolating polynomials (HIPs) that are continuous, as well as numerical implementations of n-th order ( continuous) HIPs that are expressed in terms of an underlying high-order LIP basis. Furnished with the new implementation, we demonstrate that the first-order HIPs are reliable even with large numbers of nodes and that they also work with nonuniform element grids, affording even better results in atomic electronic structure calculations than LIPs with the same total number of basis functions. We demonstrate that discontinuities can be observed in the spin-σ local kinetic energy τσ in small LIP basis sets, while HIP basis sets do not suffer from such issues; however, either set can be used to reach the complete basis set limit with smooth τσ. Moreover, we discuss the implications of HIPs on calculations with meta-GGA functionals with a number of recent meta-GGA functionals, and we find most Minnesota functionals to be ill-behaved. We also examine the potential usefulness of the explicit control over the derivative in HIPs for forming numerical atomic orbital basis sets, but we find that confining potentials are still likely a better option.

Single-size and cluster dynamics modeling of intra-granular fission gas bubbles in UO[formula omitted

We perform simulations of intra-granular fission gas bubble evolution in UO2 using both a relatively simple, computationally inexpensive single-size model and a detailed cluster dynamics model. Simulations encompass 36 experimental cases from 4 different databases, covering various temperature and burnup levels. We systematically compare results from the two models to each other and to post-irradiation experimental data of bubble average size and number density. Overall, the model-to-model comparisons reveal an excellent agreement across the set of simulations. This outcome indicates that, in spite of the underlying assumptions, the single-size model provides a good approximation of the complex physical behavior that is more rigorously described by the cluster dynamics model. Qualitatively, both models reproduce the trends of the experimental data with temperature and burnup correctly. Quantitatively, calculated results are either in good agreement with the data or within errors that appear consistent with the inherent uncertainties. Moreover, for the single-size model, we demonstrate and assess a multiscale approach whereby values for the fission gas atom diffusion coefficient from separate atomistic calculations are used. Systematic comparisons to experimental data point out a credible accuracy of the multiscale model.

Meta-GGA Density Functional Calculations on Atoms with Spherically Symmetric Densities in the Finite Element Formalism.

Density functional calculations on atoms are often used for determining accurate initial guesses as well as generating various types of pseudopotential approximations and efficient atomic-orbital basis sets for polyatomic calculations. To reach the best accuracy for these purposes, the atomic calculations should employ the same density functional as the polyatomic calculation. Atomic density functional calculations are typically carried out employing spherically symmetric densities, corresponding to the use of fractional orbital occupations. We have described their implementation for density functional approximations (DFAs) belonging to the local density approximation (LDA) and generalized gradient approximation (GGA) levels of theory as well as Hartree-Fock (HF) and range-separated exact exchange [Lehtola, S. Phys. Rev. A 2020, 101, 012516]. In this work, we describe the extension to meta-GGA functionals using the generalized Kohn-Sham scheme, in which the energy is minimized with respect to the orbitals, which in turn are expanded in the finite element formalism with high-order numerical basis functions. Furnished with the new implementation, we continue our recent work on the numerical well-behavedness of recent meta-GGA functionals [Lehtola, S.; Marques, M. A. L. J. Chem. Phys. 2022, 157, 174114]. We pursue complete basis set (CBS) limit energies for recent density functionals and find many to be ill-behaved for the Li and Na atoms. We report basis set truncation errors (BSTEs) of some commonly used Gaussian basis sets for these density functionals and find the BSTEs to be strongly functional dependent. We also discuss the importance of density thresholding in DFAs and find that all of the functionals studied in this work yield total energies converged to 0.1 μEh when densities smaller than 10-11a0-3 are screened out.

Screening Topological Quantum Cathode Materials for K-Ion Batteries by Graph Neural Network and First-Principles Calculations

Among the key parts of metal-ion batteries, cathode materials significantly affect the energy density and cycling stability. However, due to the large size of K+, not much progress has been made on cathode materials for K-ion batteries (KIBs). In this study, using the Atomistic Line Graph Neural Network and first-principles calculations, for the first time we screen cathode materials for KIBs from 7385 topological quantum materials with high electronic conductivity and reversible capacity. The experimentally synthesized K2MnS2 is discovered to have a reversible capacity of 203.8 mAh/g, an energy density of 564.5 Wh/kg, a small volume change of 6.4%, and multiple channels for K+ transport with fast dynamics. Furthermore, K2MnS2 shows high electrochemical interface stability with the reported solid electrolytes of K4V2O7, and K3NbP2O9. These findings suggest that topological quantum materials expand the design space of battery cathodes.

Observation of an Inner-Shell Orbital Clock Transition in Neutral Ytterbium Atoms.

We observe a weakly allowed optical transition of atomic ytterbium from the ground state to the metastable state 4f^{13}5d6s^{2} (J=2) for all five bosonic and two fermionic isotopes with resolved Zeeman and hyperfine structures. This inner-shell orbital transition has been proposed as a new frequency standard as well as a quantum sensor for new physics. We find magic wavelengths through the measurement of the scalar and tensor polarizabilities and reveal that the measured trap lifetime in a three-dimensional optical lattice is 1.9(1)s, which is crucial for precision measurements. We also determine the g factor by an interleaved measurement, consistent with our relativistic atomic calculation. This work opens the possibility of an optical lattice clock with improved stability and accuracy as well as novel approaches for physics beyond the standard model.

Precise dd excitations and commensurate intersite Coulomb interactions in the dissimilar cuprates YBa2Cu3O7–y and La2–xSrxCuO4

Using high-resolution extreme ultraviolet resonant inelastic X-ray scattering (EUVRIXS) spectroscopy at Cu M-edge, we observed the doping dependent spectral shifts of inter-orbital (dd) excitations of YBa_2Cu_3O_(7-x) and La_(2-x)Sr_xCuO_4. With increasing hole doping level from undoped to optimally doped superconducting compositions, the leading edge of dd excitations is found to shift towards lower energy loss in a roughly linear trend that is irrespective to the cuprate species. The magnitude of energy shift can be explained by including a 0.15 eV Coulomb attraction between Cu 3d_(x^2-y^2) electrons and the doped holes on the surrounding oxygens in the atomic multiplet calculations. The consistent energy shift between distinct cuprate families suggests that this inter-site Coulomb interaction energy scale is relatively material-independent, and provides an important reference point for understanding charge density wave phenomena in the cuprate phase diagram.