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At least 145 records · Page 8

Magnetic property of transition metal-Si atomic line on silicon Σ3 grain boundary: A theoretical study

Using first-principles calculations within density functional theory, we investigate the electronic and magnetic properties of different 3d transition metal-Si atomic lines on silicon Σ3 (112) grain boundary, which can be formed through grain boundary segregation. We find that (i) Fe atoms occupy the substitutional sites at the grain boundary and form an Fe-Si atomic line, but the interaction between the Fe atoms is antiferromagnetic. (ii) The ferromagnetic stability increases with the atomic number of the transition metals and Co-Si atomic line is more stable in the ferromagnetic phase and shows a semimetallic behavior. We suggest that this special TM-Si atomic line formed by thermodynamically favorable transition metal segregation on Si grain boundary could be used in design of spin-dependent quantum devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A diagnostic to measure time-resolved atom column density and Doppler temperature in atomic vapors produced by laser ablation

We report on the development of a diagnostic to measure the time-resolved column density and Doppler temperature of atomic vapors produced by laser ablation. The diagnostic is based on the strong frequency dependence of the atomic susceptibility near an electronic transition in the interrogated atomic species. Interference on the face of a fast photodetector between the several frequency components present in a sinusoidally phase-modulated probe beam will produce a time signature uniquely determined by the column density of atoms in the probed atomic state and the Doppler temperature of the atomic vapor. With the extensive, high precision atomic spectroscopy data available in the literature, it is possible to model the vapor and extract the desired parameters through comparison of the model result with the experimental data.

47 OTHER INSTRUMENTATION↗

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Abstract Motivation The state-of-art protein structure prediction methods such as AlphaFold are being widely used to predict structures of uncharacterized proteins in biomedical research. There is a significant need to further improve the quality and nativeness of the predicted structures to enhance their usability. In this work, we develop ATOMRefine, a deep learning-based, end-to-end, all-atom protein structural model refinement method. It uses a SE(3)-equivariant graph transformer network to directly refine protein atomic coordinates in a predicted tertiary structure represented as a molecular graph. Results The method is first trained and tested on the structural models in AlphaFoldDB whose experimental structures are known, and then blindly tested on 69 CASP14 regular targets and 7 CASP14 refinement targets. ATOMRefine improves the quality of both backbone atoms and all-atom conformation of the initial structural models generated by AlphaFold. It also performs better than two state-of-the-art refinement methods in multiple evaluation metrics including an all-atom model quality score—the MolProbity score based on the analysis of all-atom contacts, bond length, atom clashes, torsion angles, and side-chain rotamers. As ATOMRefine can refine a protein structure quickly, it provides a viable, fast solution for improving protein geometry and fixing structural errors of predicted structures through direct coordinate refinement. Availability and implementation The source code of ATOMRefine is available in the GitHub repository (https://github.com/BioinfoMachineLearning/ATOMRefine). All the required data for training and testing are available at https://doi.org/10.5281/zenodo.6944368.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray atomic mapping of quantum dots

We report a model-independent atomic-mapping technique for quantum dots (QDs) by combining Bragg reflection x-ray standing wave (XSW) and grazing incidence diffraction (GID) measurements. In this study, we choose GaAs capped InGaAs QDs/GaAs(001) as a model system to show the locations and arrangements of indium atoms within the QDs along various [hkl] directions. This technique directly reveals the actual amount of positional anisotropy and ordering fraction of indium atoms within the QDs by probing the (1¯11), (111), (311), (1¯31), (113), and (1¯13) crystallographic planes. We find that indium atoms are outwardly shifted along the [001] direction by small fractions of the lattice constant, 0.04a GaAs and 0.06a GaAs from Ga sites for 50- and 150-Å GaAs capped InGaAs QDs, respectively. We observe that an improved coherency factor of the indium atoms within the QDs by 45–60% along the [001] and [011] directions reduces the photoluminescence linewidth by 22%, thus making the QDs efficient for QD-laser and optoelectronic device applications. Here, we also find that the position and ordering of In atoms along the (113) and (1¯13) planes are most sensitive to the thickness of the GaAs cap layer. Our XSW-based results are supported by numerical calculations using a QD-macroscopic structural model based on our GID study. We thus show that this atomic-mapping technique will be useful for studying various quantum structures and tuning their properties.

36 MATERIALS SCIENCE↗

Plasma enhanced atomic layer deposition and atomic layer etching of gallium oxide using trimethylgallium

Atomic layer etching driven by self-limiting thermal reactions has recently been developed as a highly conformal and isotropic technique for low damage atomic scale material removal by sequential exposures of vapor phase reactants. Gallium oxide (Ga2O3) is currently among the materials of interest due to a large variety of applications including power electronics, solar cells, gas sensors, and photon detectors. In this study, Ga2O3 was deposited by plasma enhanced atomic layer deposition using trimethylgallium [TMG, Ga(CH3)3] and O2 plasma at a substrate temperature of 200 °C. We report a newly developed method for Ga2O3 thermal atomic layer etching, in which surface modification is achieved through HF exposure resulting in a gallium fluoride surface layer, and then removed through volatile product formation via ligand exchange with TMG. Saturation of the precursor exposure at a substrate temperature of 300 °C resulted in an etch rate of 1.0 ± 0.1 Å/cycle for amorphous Ga2O3. Uniformity and conformality of the atomic layer etching process were confirmed via atomic force microscopy with a measured surface roughness of 0.55 ± 0.05 nm that remains unchanged after etching. The use of TMG for etching may expand available precursors for atomic layer etching processes, while allowing for both etching and deposition of Ga2O3 using the same metalorganic precursor.

Hatch, Kevin A. (ORCID:0000000283118623)↗

Materials selection for long life in LEO: A critical evaluation of atomic oxygen testing with thermal atom systems

The use of thermal atom test methods as a materials selection and screening technique for low-Earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined to be in thermal atom environments are compared to those observed in LEO and in high quality LEO simulations. Reaction efficiencies measured in a new type of thermal atom apparatus are one-hundredth to one-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of 8 in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain specific thermal test environments can be used as reliable materials screening tools. Using thermal atom methods to predict material lifetime in LEO requires direct calibration of the method against LEO data or high quality simulation data for each material.

Koontz, S. L.↗

Materials selection for long life in low earth orbit - A critical evaluation of atomic oxygen testing with thermal atom systems

The use of thermal atom test methods as a materials selection and screening technique for low-earth orbit (LEO) spacecraft is critically evaluated. The chemistry and physics of thermal atom environments are compared with the LEO environment. The relative reactivities of a number of materials determined in thermal atom environments are compared with those observed in LEO and in high-quality LEO simulations. Reaction efficiencies (cu cm/atom) measured in a new type of thermal atom apparatus are one-thousandth to one ten-thousandth those observed in LEO, and many materials showing nearly identical reactivities in LEO show relative reactivities differing by as much as a factor of eight in thermal atom systems. A simple phenomenological kinetic model for the reaction of oxygen atoms with organic materials can be used to explain the differences in reactivity in different environments. Certain speciic thermal atom test environments can be used as reliable materials screening tools.

Koontz, S. L.↗

Atomic oxygen testing with thermal atom systems - A critical evaluation

The use of thermal atom (kinetic energy near 0.04 eV) test methods as a materials selection and screening technique for LEO spacecraft is critically evaluated in this paper. The physics and chemistry of the thermal atom environments are shown to produce specific mass loss rates (mg/sq cm per min) and reaction efficiencies (Re) radically different from those produced in the LEO environment. A response surface study shows that specific mass loss rates change rapidly with plasma-asher parameters and seldom agree with flight data. FEP Teflon is shown to react by a different mechanism than Kapton, polyethylene, or graphite. The Re (Re = volume of material removed/oxygen atom) of Kapton, polyethylene, Mylar, Tedlar, FEP Teflon, and graphite measured in a flowing afterglow apparatus are 0.001 to 0.0001 those measured with high-energy atoms (kinetic energy 1.5 eV or greater) in beam systems or in LEO. The effect of sample temperature and atom impact energy on Re is discussed. A simple kinetic model describing the reaction of atomic oxygen with polymer surfaces is developed. Guidelines and recommendations for thermal atom testing and interpretation of test results are presented.

Koontz, Steven L.↗

Sensitive Technique Developed Using Atomic Force Microscopy to Measure the Low-Earth-Orbit Atomic Oxygen Erosion of Polymers

A recession measurement technique has been developed at the NASA Glenn Research Center to determine the atomic oxygen durability of polymers exposed to the space environment for short durations. Polymers such as polyimide Kapton and Teflon FEP (fluorinated ethylene propylene, DuPont) are commonly used in spacecraft because of their desirable properties, such as flexibility, low density, and in the case of FEP, low solar absorptance and high thermal emittance. Polymers on the exterior of spacecraft in the low- Earth-orbit environment are exposed to energetic atomic oxygen, resulting in erosion and potential structural loss. It is, therefore, important to understand the atomic oxygen erosion yield (E, the volume loss per incident oxygen atom) of polymers being considered in spacecraft design. Because long-term space exposure data are rare and very costly, short-term exposures, such as on the space shuttles, are often relied on for atomic oxygen erosion determination. The most common technique for determining E is through mass-loss measurements. For limited-duration exposure experiments, such as shuttle flight experiments, the atomic oxygen fluence is often so small that mass-loss measurements are not sensitive enough. Therefore, a recession measurement technique has been developed at Glenn to obtain accurate erosion yields of polymers exposed to low atomic oxygen fluences.

deGroh, Kim D.↗

Mass production of high-performance single atomic FeNC electrocatalysts via sequenced ultrasonic atomization and pyrolysis process

Mass production of highly efficient, durable, and inexpensive single atomic catalysts is currently the major challenge associated with the oxygen reduction reaction (ORR) for fuel cells. In this study, we develop a general strategy that uses a simple ultrasonic atomization coupling with pyrolysis and calcination process to synthesize single atomic FeNC catalysts (FeNC SACs) at large scale. The microstructure characterizations confirm that the active centers root in the single atomic Fe sites chelating to the four-fold pyridinic N atoms. The identified specific Fe active sites with the variable valence states facilitate the transfer of electrons, endowing the FeNC SACs with excellent electrochemical ORR activity. The FeNC SACs were used as cathode catalysts in a homemade Zn-air battery, giving an open-circuit voltage (OCV) of 1.43 V, which is substantially higher than that of commercial Pt/C catalysts. This study provides a simple approach to the synthesis of single atomic catalysts at large scale.

36 MATERIALS SCIENCE↗

The interaction of 193-nm excimer laser radiation with single-crystal zinc oxide: The generation of atomic Zn line emission at laser fluences below breakdown

The production of gas phase atomic and ionic line spectra accompanying the high laser fluence irradiation of solid surfaces is well known and is most often due to the production and interaction of high densities of atoms, ions, and electrons generated from laser-induced breakdown. The resulting plasma expands and moves rapidly away from the irradiated spot and is accompanied by intense emission of light. This type of “plume” is well studied and is frequently exploited in the technique of chemical analysis known as laser induced breakdown spectroscopy. Here, we describe a similar but weaker emission of light generated in vacuum by the laser irradiation of single crystal ZnO at fluences well below breakdown; this emission consists entirely of optical line emission from excited atomic Zn. We compare the properties of the resulting laser-generated gas-phase light emission (above and below breakdown) and describe a mechanism for the production of the low-fluence optical emission resulting from a fortuitous choice of material and laser wavelength.

36 MATERIALS SCIENCE↗

Correlation consistent basis sets for actinides. I. The Th and U atoms

New correlation consistent basis sets based on both pseudopotential (PP) and all-electron Douglas-Kroll-Hess (DKH) Hamiltonians have been developed from double- to quadruple-zeta quality for the actinide atoms thorium and uranium. Sets for valence electron correlation (5f6s6p6d), cc − pV nZ − PP and cc − pV nZ − DK3, as well as outer-core correlation (valence + 5s5p5d), cc − pwCV nZ − PP and cc − pwCV nZ − DK3, are reported (n = D, T, Q). The -PP sets are constructed in conjunction with small-core, 60-electron PPs, while the -DK3 sets utilized the 3rd-order Douglas-Kroll-Hess scalar relativistic Hamiltonian. Both series of basis sets show systematic convergence towards the complete basis set limit, both at the Hartree-Fock and correlated levels of theory, making them amenable to standard basis set extrapolation techniques. To assess the utility of the new basis sets, extensive coupled cluster composite thermochemistry calculations of ThF{sub n} (n = 2 − 4), ThO{sub 2}, and UF{sub n} (n = 4 − 6) have been carried out. After accurately accounting for valence and outer-core correlation, spin-orbit coupling, and even Lamb shift effects, the final 298 K atomization enthalpies of ThF{sub 4}, ThF{sub 3}, ThF{sub 2}, and ThO{sub 2} are all within their experimental uncertainties. Bond dissociation energies of ThF{sub 4} and ThF{sub 3}, as well as UF{sub 6} and UF{sub 5}, were similarly accurate. The derived enthalpies of formation for these species also showed a very satisfactory agreement with experiment, demonstrating that the new basis sets allow for the use of accurate composite schemes just as in molecular systems composed only of lighter atoms. The differences between the PP and DK3 approaches were found to increase with the change in formal oxidation state on the actinide atom, approaching 5-6 kcal/mol for the atomization enthalpies of ThF{sub 4} and ThO{sub 2}. The DKH3 atomization energy of ThO{sub 2} was calculated to be smaller than the DKH2 value by ∼1 kcal/mol.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effects of relativity for atomization and isomerization energies of seaborgium carbonyl SgCO and seaborgium isocarbonyl SgOC: Relativity predicts SgOC to be more stable than SgCO

Our ab initio all-electron fully relativistic Dirac-Fock (DF) and nonrelativistic Hartree-Fock (NR) calculations for seaborgium isocarbonyl SgOC predict atomization energy (AE) of 13.04 and 11.05 eV, respectively. However, the corresponding DF and NR atomization energies for the seaborgium carbonyl SgCO are predicted as 12.75 and 12.45 eV, respectively. This is the first such result in Chemistry where an isocarbonyl (and especially for a system of superheavy element Sg) is predicted to be more stable at the DF level of theory than the corresponding carbonyl. The predicted energy for the formation of the carbonyl SgCO at the relativistic DF and NR levels of theory is -54.90 and -50.95 kJ /mol, whereas the corresponding energy of formation of the isocarbonyl SgOC is -64.44 and -18.64 kJ/mol, respectively. Ours are the first results of relativistic effects for isomerization and atomization energies of the superheavy seaborgium isocarbonyl SgOC and its isomer SgCO. Lastly, the formation of isocarbonyl SgOC, should be favored over the carbonyl isomer SgCO in the first step of the reaction Sg+CO →SgOC.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atoms in Flight: The Remarkable Connections between Atomic and Hadronic Physics

Atomic physics and hadron physics are both based on Yang Mills gauge theory; in fact, quantum electrodynamics can be regarded as the zero-color limit of quantum chromodynamics. I review a number of areas where the techniques of atomic physics provide important insight into the theory of hadrons in QCD. For example, the Dirac-Coulomb equation, which predicts the spectroscopy and structure of hydrogenic atoms, has an analog in hadron physics in the form of light-front relativistic equations of motion which give a remarkable first approximation to the spectroscopy, dynamics, and structure of light hadrons. The renormalization scale for the running coupling, which is unambiguously set in QED, leads to a method for setting the renormalization scale in QCD. The production of atoms in flight provides a method for computing the formation of hadrons at the amplitude level. Conversely, many techniques which have been developed for hadron physics, such as scaling laws, evolution equations, and light-front quantization have equal utility for atomic physics, especially in the relativistic domain. I also present a new perspective for understanding the contributions to the cosmological constant from QED and QCD.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Targeted Single-Site MOF Node Modification: Trivalent Metal Loading via Atomic Layer Deposition

Postsynthetic functionalization of metal organic frameworks (MOFs) enables the controlled, high-density incorporation of new atoms on a crystallographically precise framework. Leveraging the broad palette of known atomic layer deposition (ALD) chemistries, ALD in MOFs (AIM) is one such targeted approach to construct diverse, highly functional, few-atom clusters. We here demonstrate the saturating reaction of trimethylindium (InMe3) with the node hydroxyls and ligated water of NU-1000, which takes place without significant loss of MOF crystallinity or internal surface area. We computationally identify the elementary steps by which trimethylated trivalent metal compounds (ALD precursors) react with this Zr-based MOF node to generate a uniform and well characterized new surface layer on the node itself, and we predict a final structure that is fully consistent with experimental X-ray pair distribution function (PDF) analysis. We further demonstrate tunable metal loading through controlled number density of the reactive handles (-OH and -OH2) achieved through node dehydration at elevated temperatures.

atomic layer deposition in MOF↗

Atomic and electronic structures of lattice mismatched Cu 2 O/TiO 2 interfaces

Heterojunction interfaces between metal oxides are often highly lattice mismatched. The atomic and electronic structures of such interfaces, however, are not well understood. Here, we have synthesized Cu 2 O/TiO 2 heterojunction thin films with 13% lattice mismatch and studied the interface via experimental methods and large-scale density function theory calculations of supercells containing 1300 atoms. We find that an interface of epitaxial quality is formed via a coincidence site lattice of 8 Cu 2 O unit cells matching 9 TiO 2 unit cells. Calculations reveal the existence of a dislocation core of the O sublattices at the interface and a random arrangement of one layer of interfacial Cu atoms. The interfacial electronic structure is found to be mostly determined by the interfacial Cu distribution, rather than by the O dislocation core. The conduction band minimum and valence band maximum states are spatially separated, and there is no strongly localized state near the core.

74 ATOMIC AND MOLECULAR PHYSICS↗

Characterization of an atomic hydrogen source for charge exchange experiments

We characterized the dissociation fraction of a thermal dissociation atomic hydrogen source by injecting the mixed atomic and molecular output of the source into an electron beam ion trap containing highly charged ions and recording the x-ray spectrum generated by charge exchange using a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchange state-selective capture cross sections are very different for atomic and molecular hydrogen incident on the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Spin-squeezing-enhanced dual-species atom interferometric accelerometer employing large momentum transfer for precision test of the equivalence principle

Here, we theoretically investigate the feasibility of applying spin squeezing to a light pulse atom interferometer in the presence of large momentum transfer using off resonant Raman transitions, in order to enhance the sensitivity of accelerometry close to the Heisenberg limit. We also show how to implement this scheme in a dual-species atom interferometer for a precision test of the equivalence principle by measuring the Eötvös parameter, and to identify the spin squeezing protocol that is best suited for such an experiment. For a space borne platform in low Earth orbit, such a scheme may eventually enable the measurement of the Eötvös parameter with a sensitivity of the order of 10 -20 within 150 days when 10 5 atoms are employed in each cycle of the experiment.

79 ASTRONOMY AND ASTROPHYSICS↗