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Atomic structures and adatom geometries of surfaces encode information about the thermodynamics and kinetics of the processes that lead to their formation, and which can be captured by a generative physical model. In this work, we develop a workflow based on a machine-learning-based analysis of scanning tunneling microscopy images to reconstruct the atomic and adatom positions, and a Bayesian optimization procedure to minimize statistical distance between the chosen physical models and experimental observations. We optimize the parameters of a 2- and 3-parameter Ising model describing surface ordering and use the derived generative model to make predictions across the parameter space. For concentration dependence, we compare the predicted morphologies at different adatom concentrations with the dissimilar regions on the sample surfaces that serendipitously had different adatom concentrations. The proposed workflow can be used to reconstruct the thermodynamic models and associated uncertainties from the experimental observations of materials microstructures. The code used in the manuscript is available at https://github.com/saimani5/Adatom_interactions.
We have calculated electron collisional excitation strengths for all electric dipole forbidden, semi-forbidden, and allowed transitions among the lowest 17 LS states 3s(exp 2)3p(exp 2) P-3, D-1, S-1, 3s3p(exp 3)S-5(exp 0), D-3(exp 0), P-3(exp 0), P-1(exp 0), S-3(exp 0), D-1(exp 0), 3S(exp 2)3p3d D-1(exp 0), F-3(exp 0), P-3(exp 0), D-3(exp 0), F-3(exp 0), P-1(exp 0), and 3S(exp 2)3p4S P-3(exp 0), P-l(exp 0) of S III using the R-matrix method. These S m states are represented by fairly extensive configuration-interaction wave functions that yield excited state energies in close agreement with recent laboratory measurements. Rydberg series of resonances converging to the excited state thresholds are explicitly included in the scattering calculation. The effective collision strengths are determined assuming Maxwellian distribution of electron energies. These are listed over a wide temperature range ([0.5-10] x 10(exp 4) K) and compared, where possible, with other available calculations. Subject headings: atomic data - atomic processes
UV emission from B-like N and O ions a rather rare opportunity for recording spectral lines in a narrow wavelength range that can potentially be used to derive temperatures relevant to the solar transition region. In these ions, the line intensity ratios of the type (2s2p(sup 2) - 2p(sup 3)) / (2s(sup 2)2p - 2s2p(sup 2)) are very sensitive to the electron temperature. Additionally, the lines involving the ratios fall within a range of only - 12 A; in N III the lines fall in the 980 - 992 A range and in O IV in the 780 - 791 A range. In this work, we explore the use of these atomic systems, primarily in N III, for temperature diagnostics of the transition region by analyzing UV spectra obtained by the Solar Ultraviolet Measurements of Emitted Radiation (SUMER) spectrometer flown on the Solar and Heliospheric Observatory (SOHO). The N III temperature-sensitive line ratios are measured in more than 60 observations. Most of the measured ratios correspond to temperatures in the range 5.7x10(exp 4) - 6.7x10(exp 4) K. This range is considerably lower than the calculated temperature of maximum abundance of N III, which is approx. 7.6x10(exp 4) K. Detailed analysis of the spectra further indicates that the measured ratios are probably somewhat overestimated due to resonant scattering effects in the 2s(sup 2)2p - 2s2p(sup 2) lines and small blends in the 2s2p(sup 2) - 2p3 lines. Actual lower ratios would only increase the disagreement between the ionization balance calculations and present temperature measurements based on a collisional excitation model. In the case of the O IV spectra, we determined that due to the close proximity in wavelength of the weak line (2s2p(sup 2)-2p3 transitions) to a strong Ne VIII line, sufficiently accurate ratio measurements cannot be obtained. Subject headings: atomic data --- atomic processes --- Sun: transition region --- Sun: U V radiation --- techniques: spectroscopic
Data on neutral atomic species are analyzed for the purpose of inferring relative elemental abundances and depletions in diffuse cloud cores, where it is assumed that densities are enhanced in comparison with mean densities over integrated lines of sight. Column densities of neutral atoms are compared to yield relative column densities of singly ionized species, which are assumed dominant in cloud cores. This paper incorporates a survey of literature data on neutral atomic abundances with the result that no systematic enhancement in the depletions of calcium or iron in cloud cores is found, except for zeta Ophiuchi. This may imply that depletions are not influenced by density, but other data argue against this interpretation. It is concluded either that in general all elements are depleted together in dense regions so that their relative abundances remain constant, or that typical diffuse clouds do not have significant cores, but instead are reasonably homogeneous. The data show a probable correlation between cloud-core depletion and hydrogen-molecular fraction, supporting the assumption that overall depletions are a function of density.
Advanced theoretical methods can accurately calculate various atomic observables and predict electronic structure. Still, systematic computations of the radiative and non-radiative transition probabilities and energies are missing for the actinides and all the transfermium elements. However, these compilations are needed for comprehensive Monte-Carlo simulations (such as GEANT4) of the radioactive decay of transfermium nuclei. These simulations can forma basis for data analysis of experiments, especially with complex detection setups. Investigation of the transfermium nuclei is crucial for understanding the nature of the nuclear force. In this study, simulations based on data from the Jena Atomic Calculator (JAC) and the data from the Evaluated Atomic Data Library (EADL) present in GEANT4 were found compatible for the three elements Ba(Z = 56), U(Z = 92), and Fm(Z = 100), thus, validating the JAC calculations. For Z> 100, we also found sound agreement between simulations that used data generated with JAC and experimental results involving No(Z = 102) and Rf(Z = 104) isotopes. In conclusion, these results demonstrate that JAC can produce reliable atomic data sets for transfermium elements, which will assist in analyzing nuclear-decay-spectroscopy experiments.
ABSTRACT Even though the electromagnetic counterpart AT2017gfo to the binary neutron star merger GW170817 is powered by the radioactive decay of r-process nuclei, only few tentative identifications of light r-process elements have been made so far. One of the major limitations for the identification of heavy nuclei is incomplete or missing atomic data. While substantial progress has been made on lanthanide atomic data over the last few years, for actinides there has been less emphasis, with the first complete set of opacity data only recently published. We perform atomic structure calculations of neodymium (Z = 60) as well as the corresponding actinide uranium (Z = 92). Using two different codes [flexible atomic code (fac) and hartree–fock-relativistic (hfr)] for the calculation of the atomic data, we investigate the accuracy of the calculated data (energy levels and electric dipole transitions) and their effect on kilonova opacities. For the fac calculations, we optimize the local central potential and the number of included configurations and use a dedicated calibration technique to improve the agreement between theoretical and available experimental atomic energy levels (AELs). For ions with vast amounts of experimental data available, the presented opacities agree quite well with previous estimations. On the other hand, the optimization and calibration method cannot be used for ions with only few available AELs. For these cases, where no experimental nor benchmarked calculations are available, a large spread in the opacities estimated from the atomic data obtained with the various atomic structure codes is observed. We find that the opacity of uranium is almost double the neodymium opacity.
Producing enantioenriched molecules from racemic mixtures is essential for manufacturing. Traditional methods such as resolution, deracemization and enantioconvergent catalysis primarily involve separating or converting enantiomers without altering their structures, or functionalization of stereocentres at or proximal to functional groups. However, there are challenges in enantioselectively forging C–H bonds that are remote from functional groups via hydrogen atom transfer (HAT) with these methods. Here we introduce a strategy for the photoenzymatic stereoablative enantioconvergence of γ-chiral oximes using repurposed flavin-dependent ene-reductases. A photoinduced single-electron reduction of the γ-chiral oxime by an ene-reductase generates an iminyl radical, which then undergoes stereoablative 1,5-HAT at the γ-stereocentre. Subsequent chiral reconstruction through enzymatic HAT and spontaneous imine hydrolysis yields the γ-chiral ketone with high enantioselectivity. This work provides a robust method for remote stereoablative enantioconvergent HAT and broadens the synthetic utility of photobiocatalysis.
In this work, we present Aurora, an open-source package for particle transport, neutrals and radiation modeling in magnetic confinement fusion plasmas. Aurora's modern multi-language interface enables simulations of 1.5D impurity transport within high-performance computing frameworks, particularly for the inference of particle transport coefficients. A user-friendly Python library allows simple interaction with atomic rates from the Atomic Data and Atomic Structure database as well as other sources. This enables a range of radiation predictions, both for power balance and spectroscopic analysis. We discuss here the superstaging approximation for complex ions, as a way to group charge states and reduce computational cost, demonstrating its wide applicability within the Aurora forward model and beyond. Aurora also facilitates neutral particle analysis, both from experimental spectroscopic data and other simulation codes. Leveraging Aurora's capabilities to interface SOLPS-ITER results, we demonstrate that charge exchange is unlikely to affect the total radiated power from the ITER core during high performance operation. Finally, we describe the ImpRad module in the one modeling framework for integrated task framework, developed to enable experimental analysis and transport inferences on multiple devices using Aurora.
The precise atomic structure and therefore the wavelength-dependent opacities of lanthanides are highly uncertain. This uncertainty introduces systematic errors in modeling transients like kilonovae and estimating key properties such as mass, characteristic velocity, and heavy metal content. Here, we quantify how atomic data from across the literature as well as choices of thermalization efficiency of r-process radioactive decay heating impact the light curve and spectra of kilonovae. Specifically, we analyze the spectra of a grid of models produced by the radiative transfer code Sedona that span the expected range of kilonova properties to identify regions with the highest systematic uncertainty. Our findings indicate that differences in atomic data have a substantial impact on estimates of lanthanide mass fraction, spanning approximately 1 order of magnitude for lanthanide-rich ejecta, and demonstrate the difficulty in precisely measuring the lanthanide fraction in lanthanide-poor ejecta. Mass estimates vary typically by 25%–40% for differing atomic data. Similarly, the choice of thermalization efficiency can affect mass estimates by 20%–50%. Observational properties such as color and decay rate are highly model dependent. Velocity estimation, when fitting solely based on the light curve, can have a typical error of ∼100%. Atomic data of light r-process elements can strongly affect blue emission. Even for well-observed events like GW170817, the total lanthanide production estimated using different atomic data sets can vary by a factor of ∼6.
Atomic hydrogen dayglow Lyman alpha structure of Mars exosphere from Mariner 6 and 7 UV spectrometric observations
Unstructured volumetric meshes serve as fundamental data representations in various scientific simulations and analyses. They play a crucial role in representing complex computational domains and are essential for important numerical techniques, such as finite element analysis. Whenever such a mesh is read from a file, streamed in-situ, or generated by algorithms, scientific visualization libraries rely on calculating the external surface of a geometry, named “external facelist”, to produce a polygonal mesh for rendering. Consequently, external facelist calculation has become one of the most widely used algorithms in the scientific visualization domain, necessitating optimal performance. In this paper, we explore relevant work on external facelist calculation algorithms in two common visualization libraries, VTK and Viskores, assess their performance and memory constraints, and introduce a novel memory-aware external facelist calculation algorithm employing an atomic hash counting approach. This algorithm fully leverages Viskores' data-parallel primitive operations, facilitating its execution across diverse many-core architectures. Our algorithm features the lowest memory footprint on the GPU and the second-lowest on the CPU among all evaluated methods, and it also delivers the fastest performance on both CPU and GPU. It has been made available under an open-source license in the VTK and Viskores visualization systems.
Lyman continuum absorption shortward of 912 A in the quiet sun solar transition region is investigated by combining spectra obtained from the Apollo Telescope Mount experiments on Skylab. The most recent atomic data are used to compute line intensities for lines that fall on both sides of the Lyman limit. Lines of O III, O IV, O V, and S IV are considered. The computed intensity ratios of most lines from O IV, O V, and S IV agree with the experimental ratios to within a factor of 2. However, the discrepancies show no apparent wavelength dependence. From this fact, it is concluded that at least part of the discrepancy between theory and observation for lines of these ions can be accounted for by uncertainties in instrumental calibration and atomic data. However, difficulties remain in reconciling observation and theory, particularly for lines of O III, and one line of S IV. The other recent results of Schmahl and Orrall (1979) are also discussed in terms of newer atomic data.
Cosmic EUV/x-ray spectroscopists, including both solar and astrophysical analysts, have a wide range of high-resolution and high-sensitivity tools in use and a number of new facilities in development for launch. As this bandpass requires placing the spectrometer beyond the Earth’s atmosphere, each mission represents a major investment by a national space agency such as NASA, ESA, or JAXA, and more typically a collaboration between two or three. In general justifying new mission requires an improvement in capabilities of at least an order of magnitude, but the sensitivity of these existing missions are already taxing existing atomic data quantity and accuracy. This roadmap reviews the existing missions, showing how in a number of areas atomic data limits the science that can be performed. The missions that will be launched in the coming Decade will without doubt require both more and improved measurements of wavelengths and rates, along with theoretical calculations of collisional and radiative cross sections for a wide range of processes.
In this paper we reanalayze the full-disk quiet-sun spectrum of Mallinovsky & Heroux (1973) with modern atomic data. The purposes of this are to check our atomic data and methods in other investigations using data from nearby stars obtained with the NASA Extreme Ultraviolet Explorer (EUVE) satellite, and to confirm that the solar first ionization potential (FIP) effect investigated by previous authors studying discrete solar regions is the same as that found in full-disk spectra. We recover the usual solar FIP effect of a coronal abundance enhancement of elements with a low FIP of a factor approximately 3-4 for lines formed at temperatures greater than approximately 10(exp 6) K. For lower temperatures, the FIP effect seems to be substantially smaller, in qualitative agreement with other data. Comparing our full-disk result with those from discrete solar structures suggest that the FIP effect is a function of altitude, with the lower temperature full-disk emission being dominated by the super-granulation network. We also compare the recent ionization balance of Arnaud & Raymond (1992) with that of Arnaud & Rothenflug (1985).
Astrophysical Plasma Emission Database - APED consists of atomic data, primarily theoretical, needed to calculate X-ray through optical emission spectra of hot thermal plasmas. These data are supplemented by experimental values, such as laboratory plasma wave- lengths, and are validated by experiment only rarely. Thus the comparison of predicted spectra to astrophysical spectra serves as invaluable feedback on the quality of the models. Following up on unfavorable comparisons, we have communicated atomic data needs to atomic theorists and experimental plasma physicists so that improvements can be made to the database. The database is now reasonably complete from approx. 1 to 30 A, and from - 90 to 180 A, with significant gaps remaining in the range 30 to 90 A. Astrophysical Plasma Emission Code - APEC uses the APED data as inputs and computes level populations and line emissivities using a rate matrix solver. Tabulated models for a fine grid of temperatures and densities can be applied to observational data. The current public version of APEC output uses an input ionization balance model, assuming CIE; however, we have a working version to calculate the ionization state of the gas. We will begin testing non-equilibrium ionization (NEI) models over the next year - we are now finalizing the atomic database needed to perform the ionization state calculations. At that time, the code will be made public. We have developed optimized error codes, additional testing protocols and substantial documentation, in preparation for this public release. Secondarily, we have begun to investigate the use of APED and APEC for X-ray photoionized plasma, beginning with opacity modeling (e.g. warm absorbers). Application to bright AGN Chandra grating spectra suggests that the accurate wavelengths in APED are of great importance to fitting the data. We are exploring additional subroutines to APEC to extend its usefulness for X-ray photoionized plasma, e.g. to include collisional or photo-excitation of metastable levels for absorption.
Accurate particle and power deposition profiles of neutral beam injection (NBI) are essential to transport studies, and that information is usually acquired through Monte Carlo simulations with a given collisional model. The deposition process of the energetic beam particles leads to the informative electron temperature (T e ) evolution trajectory, which can be captured by electron cyclotron emission (ECE) system due to its good spatial and temporal resolution. Previously, some work has been done to interpret the T e responses to the pulsed NBI as a linear heating source with Fourier-based techniques, although that approach fell short when the fast ion slowing-down time becomes significant (~100 ms). It has been observed in DIII-D that the modulated NBI pulses (10–50 Hz) reduce local core T e values ~0.1 keV through cold electron dilution in high-T e (>2 keV) plasmas alongside accumulative heating. Here, a novel approach to interpret the T e response to NBI was developed by linearizing and modeling the detailed T e evolution trajectory using coherently averaged ECE data based on the different time scales of the terms in the local power and particle balance equations. The technique does not require absolute calibrations of ECE and is independent of collisional models. The resulting beam deposition profiles show good consistency and reasonable agreement with Monte Carlo calculations based on the atomic data from the Atomic Data and Analysis Structure (ADAS). Local electron density response measured by Thomson scattering (TS) also suggests the same features when the beam pulse is large enough for that diagnostic to resolve. The remaining discrepancies are also discussed.
The University of Alabama in Huntsville (UAH) experiment which flew on the STS-8 mission had several objectives which were mostly of a speculative nature since so little was known of the processes of interest. The experiment provided original, if limited, data on: (1) oxidation of metal surfaces, (2) reaction rates of atomic oxygen with carbon and other surfaces and the dependence of these rates on temperature, and (3) the angular distribution of 5eV atoms scattered off a solid surface. Provided is a review of the results, with reference given to fuller published accounts where these are available.