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NASA NTRS1994

NLTE model stellar atmospheres with line blanketing near the series limits

In this paper we study the influence of line-merging regions at the intermediate long-wavelength side of a continuum threshold on the computed model atmosphere structure and predicted spectrum. In order to model these regions sufficiently accurately, we have developed two concepts. First, we have extended the occupation probability formalism of Hummer and Mihalas to non-local thermodynamic equilibrium (non-LTE) plasmas. Second, in order to treat the very complicated opacity in the line merging region, we have generalized the concept of opacity distribution functions to treat non-LTE situations. All Rydberg states are consistently included within this framework, so that no arbitrary cutoff of high (LTE) levels is made. We have calculated several pure hydrogen models atmospheres for two effective temperatures, T(sub eff) = 20000 and 35000 K, and discussed the differences between models calculated with various treatments of the line merging. In particular, we have shown that the error in the predicted profiles of Balmer lines resulting from the neglect of line merging is typically of the order of 3-4%, while the errors in the far-UV portion of the Balmer continuum reaches 15-35%. The errors generally decrease with increasing effective temperature. At the same time, the internal accuracy of the models is shown to be about or below 0.5% for all predicted spectral features. We conclude that for interpreting current high-accuracy spectrophotometric observations models including the line merging are necessary, and that the formalism developed in this paper is capable of providing a sufficiently accurate and robust modeling technique.

Hubeny, I.↗
DOE OSTI2024

Generalized Bayesian MARS: Tools for Stochastic Computer Model Emulation

The multivariate adaptive regression spline (MARS) approach of Friedman and its Bayesian counterpart are effective approaches for the emulation of computer models. The traditional assumption of Gaussian errors limits the usefulness of MARS, and many popular alternatives, when dealing with stochastic computer models. Here, we propose a generalized Bayesian MARS (GBMARS) framework which admits the broad class of generalized hyperbolic distributions as the induced likelihood function. This allows us to develop tools for the emulation of stochastic simulators which are parsimonious, scalable, and interpretable and require minimal tuning, while providing powerful predictive and uncertainty quantification capabilities. GBMARS is capable of robust regression with t distributions, quantile regression with asymmetric Laplace distributions, and a general form of “Normal-Wald” regression in which the shape of the error distribution and the structure of the mean function are learned simultaneously. We demonstrate the effectiveness of GBMARS on various stochastic computer models, and we show that it compares favorably to several popular alternatives.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2015

Energetics of intrinsic defects in NiO and the consequences for its resistive random access memory performance

Energetics for a variety of intrinsic defects in NiO are calculated using state-of-the-art ab initio hybrid density functional theory calculations. At the O-rich limit, Ni vacancies are the lowest cost defect for all Fermi energies within the gap, in agreement with the well-known p-type behaviour of NiO. However, the ability of the metal electrode in a resistive random access memory metal-oxide-metal setup to shift the oxygen chemical potential towards the O-poor limit results in unusual NiO behaviour and O vacancies dominating at lower Fermi energy levels. Calculated band diagrams show that O vacancies in NiO are positively charged at the operating Fermi energy giving it the advantage of not requiring a scavenger metal layer to maximise drift. Ni and O interstitials are generally found to be higher in energy than the respective vacancies suggesting that significant recombination of O vacancies and interstitials does not take place as proposed in some models of switching behaviour.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Solitons and protein folding: An In Silico experiment

Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

The complexity of { 11 2 ¯ 1 } twin interface structure and energetics in HCP materials

Here, the quest for a deeper understanding of the mechanical properties of HCP alloys has been an ongoing effort. Due to the lack of a sufficient number of slip systems, twin nucleation and migration originate as a substantial plastic deformation mechanism in HCP metals. The paper uncovers the energetics and atomistic mechanism of the {$11\overline{2}1$} < $11\overline{2}6$ > which is one of the most prominent twin modes in HCP materials that has not been fully understood. In view of corrugated {$11\overline{2}1$} interfaces, the positioning of lattice/motif atoms needs to be clarified. First, we establish the initial twin boundary (TB) structure unambiguously via the lattice offsets resulting in volume invariancy and correct relative positioning of the twin variants. Secondly, the TB migration mechanism is determined from a crystallographic (zero net shuffle, $Σ\vec{s}$ = 0) and energetic standpoints (minimum energy path). The Generalized Planar Fault Energy (GPFE) curves are calculated for Ti, Hf, Mg, and Zr. Such GPFE curves for this twin mode are calculated for the first time, and point to unusually high unstable energies (300-850 mJ/m 2 ), and low migration barriers (<60 mJ/m 2 ) for twinning accompanied with large shuffle magnitudes, |$\vec{s}$|, comparable to the Burger’s vector (|$\vec{s}$| ≅ $b_e$ > 0.44Å)

36 MATERIALS SCIENCE↗
DOE OSTI2019

Collective charge and spin dynamics in low-dimensional itinerant electron systems with spin-orbit coupling

This research project in theoretical condensed-matter physics aims to study the collective charge and spin excitations of itinerant quasi-two-dimensional electronic systems such as doped semiconductor nanostructures and carbon-based materials, in the presence of impurities and spin-orbit coupling. In previous work under DOE support, we had discovered an interesting interplay between many-body effects and Rashba and Dresselhaus spin-orbit interactions: contrary to many situation in spintronics where spin-orbit interactions lead to loss of spin coherence, collective spin modes are robust against such coherence losses, and behave as macroscopic quantum objects with a collective magnetic moment precessing about an effective spin-orbit magnetic field. Experimental data for GaAs and CdMnTe quantum wells, obtained by our collaborators at the University Pierre et Marie Curie in Paris, confirmed our predictions and suggested that the observed effect is universal. However, a full theoretical explanation of the effect is still missing, and a wealth of new experimental data remains to be analyzed. We therefore plan to address the following three interrelated objectives: 1. Theory of collective modes in chiral systems. We will explore the various ways in which spin-orbit interactions affect collective spin-density and spin-flip excitations in semiconductor quantum wells. The goal will be to develop a universal formalism for chiral collective modes, with a particular emphasis on analytic results for dispersion relations, which will be compared with experimental results from inelastic light scattering. We will calculate the linewidths of spin plasmons and spin-flip waves due to impurity scattering and spin Coulomb drag from first principles. 2.Many-body effects in noncollinear magnetism. We will describe electronic many-body effects using time-dependent density-functional theory (TDDFT) in the linear-response regime. Quantum wells with spin-orbit coupling are noncollinear itinerant magnetic systems at the crossover between two and three dimensions, which poses subtle challenges for standard exchange-correlation (xc) functionals such as the local-density approximation (LDA). We will develop new orbital-dependent xc functionals for noncollinear magnetic systems by generalizing the so-called STLS approach. 3. Beyond single semiconductor quantum wells. We will consider quantum well bilayer or multilayer systems with spin-orbit coupling, where the coupling between the quasi-2D electron systems leads to acoustic and optical modes (in phase and out of phase). How are these modes affected if the two layers have the same or different chirality? Plasmon modes have been widely studied in graphene and other topological materials, and we will study collective spin excitations in graphene and other carbon-based materials in the presence of spin-orbit coupling and magnetic fields. The potential impact of the proposed research will be both on a fundamental and a practical level. A universal theory of chiral collective modes will advance our understanding of the interplay between many-body effects and spin-orbit interactions in a wide variety of materials and systems. A generalized STLS approach for noncollinear magnetism will be of wide interest beyond the systems studied here. This work may also point towards new ways of manipulating and controlling spin waves in low-dimensional itinerant electron systems: this could be used to encode, transport and process information, which would be of interest to the field of magnon spintronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Analysis of the multipactor effect in circular waveguides excited by two orthogonal polarization waves

Circular waveguides, either employed as resonant cavities or as irises connecting adjacent guides, are widely present in many passive components used in different applications (i.e., particle accelerators and satellite subsystems). In this paper, we present the study of the multipactor effect in circular waveguides considering the coexistence of the two polarizations of the fundamental TE{sub 11} circular waveguide mode. For a better understanding of the problem, only low multipactor orders have been explored as a function of the polarization ellipse eccentricity. Special attention has been paid to the linear and circular polarizations, but other more general configurations have also been explored.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Exchange-correlation functional challenges in modeling quaternary chalcogenides

The development of next-generation quaternary chalcogenides, such as Cu2ZnSnS4 (CZTS) and Cu2ZnGeS4 (CZGS), for solar energy and thermoelectric applications hinges upon both careful experimentation and accurate quantum mechanical modeling. To address the latter, many have turned to density functional theory (DFT), which offers several choices for the approximate treatment of electron exchange and correlation (XC). Popular XC functionals include the Perdew-Burke-Ernzerhof (PBE) generalized gradient approximation (GGA) and the recently developed strongly constrained and appropriately normed (SCAN) meta-GGA. Extensions of DFT functionals, such as adding a Hubbard U correction and introducing a fraction of the Fock exchange (hybrid functionals), have been used widely to model systems containing 3d metal ions. However, no studies yet have compared comprehensively PBE(+U) and SCAN(+U) in the quality of their predictions of the bulk and defect thermodynamics of quaternary chalcogenides, which play a critical role in device fabrication and performance. Hence, here we calculate the (i) 0 K formation energies of bulk Ge compounds and (ii) neutral defect formation energies including charge-balanced (e.g., CuZn + ZnCu) and charge-imbalanced (e.g., CuSn) combinations of antisites and vacancies in CZTS and CZGS using the PBE, PBE +U, SCAN, SCAN +U, and the hybrid Heyd-Scuseria-Ernzerhof XC frameworks. We find that the formation energies of charge-imbalanced defects are more sensitive to the choice of the XC functional than those of charge-balanced defects, which can be explained by the differences in the extent of penalization of defect-generated delocalized electrons/holes by PBE, PBE +U, SCAN, and SCAN +U. Additionally, our results show that SCAN systematically underbinds Ge-containing compounds, thus highlighting the need for even further improvement of XC functionals. Based on our findings, we recommend the use of SCAN for modeling quaternary chalcogenides because its errors are systematic, and it has the firmest theoretical underpinning. Our work provides guidance for future modeling of quaternary chalcogenides.

14 SOLAR ENERGY↗
DOE OSTI2019

Pseudo-differential representation of the metaplectic transform and its application to fast algorithms

The metaplectic transform (MT), also known as the linear canonical transform, is a unitary integral mapping that is widely used in signal processing and can be viewed as a generalization of the Fourier transform. For a given function $ψ$ on an $N$-dimensional continuous space q , the MT of $ψ$ is parameterized by a rotation (or more generally, a linear symplectic transformation) of the 2$N$-dimensional phase space ( q,p ), where p is the wavevector space dual to q . In this study, we derive a pseudo-differential form of the MT. For small-angle rotations, or near-identity transformations of the phase space, it readily yields asymptotic differential representations of the MT, which are easy to compute numerically. Rotations by larger angles are implemented as successive applications of $K \gg 1$ small-angle MTs. The algorithm complexity scales as $O(KN^3N_p)$ where $N_p$ is the number of grid points. Here, we present a numerical implementation of this algorithm and discuss how to mitigate the associated numerical instabilities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression

Cropping soils vary in extent of natural suppression of soil-borne plant diseases. However, it is unknown whether similar variation occurs across pastoral agricultural systems. We examined soil microbial community properties known to be associated with disease suppression across 50 pastoral fields varying in management intensity. The composition and abundance of the disease-suppressive community were assessed from both taxonomic and functional perspectives. Pseudomonas bacteria were selected as a general taxonomic indicator of disease suppressive potential, while genes associated with the biosynthesis of a suite of secondary metabolites provided functional markers (GeoChip 5.0 microarray analysis). The composition of both the Pseudomonas communities and disease suppressive functional genes were responsive to land use. Underlying soil properties explained 37% of the variation in Pseudomonas community structure and up to 61% of the variation in the abundance of disease suppressive functional genes. Notably, measures of soil organic matter quality, C:P ratio, and aromaticity of the dissolved organic matter content (carbon recalcitrance), influenced both the taxonomic and functional disease suppressive potential of the pasture soils. Our results suggest that key components of the soil microbial community may be managed on-farm to enhance disease suppression and plant productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Photoacoustic tomography based on the Green's function retrieval with ultrasound interferometry for sample partially behind an acoustically scattering layer

Acoustically inhomogeneous mediums with multiple scattering are often the nightmare of photoacoustic tomography. In order to break this limitation, a photoacoustic tomography scheme combining ultrasound interferometry and time reversal is proposed to achieve images in acoustically scattering medium. An ultrasound interferometry is developed to determine the unknown Green's function of strong scattering tissue. Using the determined Greens' function, a time-reversal process is carried out to restore images behind an acoustically inhomogeneous layer from the scattering photoacoustic signals. This method effectively decreases the false contrast, noise, and position deviation of images induced by the multiple scattering. Phantom experiment is carried out to validate the method. Therefore, the proposed method could have potential value in extending the biomedical applications of photoacoustic tomography in acoustically inhomogeneous tissue.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Structural stability and defect energetics of ZnO from diffusion quantum Monte Carlo

We have applied the many-body ab initio diffusion quantum Monte Carlo (DMC) method to study Zn and ZnO crystals under pressure and the energetics of the oxygen vacancy, zinc interstitial, and hydrogen impurities in ZnO. We show that DMC is an accurate and practical method that can be used to characterize multiple properties of materials that are challenging for density functional theory (DFT) approximations. DMC agrees with experimental measurements to within 0.3 eV, including the band-gap of ZnO, the ionization potential of O and Zn, and the atomization energy of O{sub 2}, ZnO dimer, and wurtzite ZnO. DMC predicts the oxygen vacancy as a deep donor with a formation energy of 5.0(2) eV under O-rich conditions and thermodynamic transition levels located between 1.8 and 2.5 eV from the valence band maximum. Our DMC results indicate that the concentration of zinc interstitial and hydrogen impurities in ZnO should be low under n-type and Zn- and H-rich conditions because these defects have formation energies above 1.4 eV under these conditions. Comparison of DMC and hybrid functionals shows that these DFT approximations can be parameterized to yield a general correct qualitative description of ZnO. However, the formation energy of defects in ZnO evaluated with DMC and hybrid functionals can differ by more than 0.5 eV.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structure prediction of epitaxial inorganic interfaces by lattice and surface matching with Ogre

We present a new version of the Ogre open source Python package with the capability to perform structure prediction of epitaxial inorganic interfaces by lattice and surface matching. In the lattice matching step, a scan over combinations of substrate and film Miller indices is performed to identify the domain-matched interfaces with the lowest mismatch. Subsequently, surface matching is conducted by Bayesian optimization to find the optimal interfacial distance and in-plane registry between the substrate and the film. For the objective function, a geometric score function is proposed based on the overlap and empty space between atomic spheres at the interface. The score function reproduces the results of density functional theory (DFT) at a fraction of the computational cost. The optimized interfaces are pre-ranked using a score function based on the similarity of the atomic environment at the interface to the bulk environment. Final ranking of the top candidate structures is performed with DFT. Ogre streamlines DFT calculations of interface energies and electronic properties by automating the construction of interface models. The application of Ogre is demonstrated for two interfaces of interest for quantum computing and spintronics, Al/InAs and Fe/InSb.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Non-free gas of dipoles of non-singular screw dislocations and the shear modulus near the melting

The behavior of the shear modulus caused by proliferation of dipoles of non-singular screw dislocations with finite-sized core is considered. The representation of two-dimensional Coulomb gas with smoothed-out coupling is used, and the stress–stress correlation function is calculated. A convolution integral expressed in terms of the modified Bessel function K{sub 0} is derived in order to obtain the shear modulus in approximation of interacting dipoles. Implications are demonstrated for the shear modulus near the melting transition which are due to the singularityless character of the dislocations. - Highlights: • Thermodynamics of dipoles of non-singular screw dislocations is studied below the melting. • The renormalization of the shear modulus is obtained for interacting dipoles. • Dependence of the shear modulus on the system scales is presented near the melting.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Study on transport properties of silicene monolayer under external field using NEGF method

We investigate the current-voltage (I-V) characteristics of a pristine monolayer silicene using non-equilibrium Green function (NEGF) method combining with density functional theory (DFT). This method succeeded in showing the relationship of I and V on silicene corresponding to the electronic characteristics such as density of states. The external field perpendicular to the silicene monolayer affects in increasing of the current. Under 0.2 eV external field, the current reaches the maximum peak at Vb = 0.3 eV with the increase is about 60% from what it is in zero external field.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

On the avalanche generation of runaway electrons during tokamak disruptions

A simple zero dimensional model for a tokamak disruption is developed to evaluate the avalanche multiplication of a runaway primary seed during the current quench phase of a fast disruptive event. Analytical expressions for the plateau runaway current, the energy of the runaway beam, and the runaway energy distribution function are obtained allowing the identification of the parameters dominating the formation of the runaway current during disruptions. The effect of the electromagnetic coupling to the vessel and the penetration of the external magnetic energy during the disruption current quench as well as of the collisional dissipation of the runaway current at high densities are investigated. Current profile shape effects during the formation of the runaway beam are also addressed by means of an upgraded one-dimensional model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Scale-invariant curvature fluctuations from an extended semiclassical gravity

We present an extension of the semiclassical Einstein equations which couple n-point correlation functions of a stochastic Einstein tensor to the n-point functions of the quantum stress-energy tensor. We apply this extension to calculate the quantum fluctuations during an inflationary period, where we take as a model a massive conformally coupled scalar field on a perturbed de Sitter space and describe how a renormalization independent, almost-scale-invariant power spectrum of the scalar metric perturbation is produced. Furthermore, we discuss how this model yields a natural basis for the calculation of non-Gaussianities of the considered metric fluctuations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

{sup 90}Y -PET imaging: Exploring limitations and accuracy under conditions of low counts and high random fraction

Purpose: {sup 90}Y -positron emission tomography (PET) imaging is becoming a recognized modality for postinfusion quantitative assessment following radioembolization therapy. However, the extremely low counts and high random fraction associated with {sup 90}Y -PET may significantly impair both qualitative and quantitative results. The aim of this work was to study image quality and noise level in relation to the quantification and bias performance of two types of Siemens PET scanners when imaging {sup 90}Y and to compare experimental results with clinical data from two types of commercially available {sup 90}Y microspheres. Methods: Data were acquired on both Siemens Biograph TruePoint [non-time-of-flight (TOF)] and Biograph microcomputed tomography (mCT) (TOF) PET/CT scanners. The study was conducted in three phases. The first aimed to assess quantification and bias for different reconstruction methods according to random fraction and number of true counts in the scan. The NEMA 1994 PET phantom was filled with water with one cylindrical insert left empty (air) and the other filled with a solution of {sup 90}Y . The phantom was scanned for 60 min in the PET/CT scanner every one or two days. The second phase used the NEMA 2001 PET phantom to derive noise and image quality metrics. The spheres and the background were filled with a {sup 90}Y solution in an 8:1 contrast ratio and four 30 min acquisitions were performed over a one week period. Finally, 32 patient data (8 treated with Therasphere{sup ®} and 24 with SIR-Spheres{sup ®}) were retrospectively reconstructed and activity in the whole field of view and the liver was compared to theoretical injected activity. Results: The contribution of both bremsstrahlung and LSO trues was found to be negligible, allowing data to be decay corrected to obtain correct quantification. In general, the recovered activity for all reconstruction methods was stable over the range studied, with a small bias appearing at extremely high random fraction and low counts for iterative algorithms. Point spread function (PSF) correction and TOF reconstruction in general reduce background variability and noise and increase recovered concentration. Results for patient data indicated a good correlation between the expected and PET reconstructed activities. A linear relationship between the expected and the measured activities in the organ of interest was observed for all reconstruction method used: a linearity coefficient of 0.89 ± 0.05 for the Biograph mCT and 0.81 ± 0.05 for the Biograph TruePoint. Conclusions: Due to the low counts and high random fraction, accurate image quantification of {sup 90}Y during selective internal radionuclide therapy is affected by random coincidence estimation, scatter correction, and any positivity constraint of the algorithm. Nevertheless, phantom and patient studies showed that the impact of number of true and random coincidences on quantitative results was found to be limited as long as ordinary Poisson ordered subsets expectation maximization reconstruction algorithms with random smoothing are used. Adding PSF correction and TOF information to the reconstruction greatly improves the image quality in terms of bias, variability, noise reduction, and detectability. On the patient studies, the total activity in the field of view is in general accurately measured by Biograph mCT and slightly overestimated by the Biograph TruePoint.

60 APPLIED LIFE SCIENCES↗