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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Automation of Active Space Selection for Multireference Methods via Machine Learning on Chemical Bond Dissociation

Predicting and understanding the chemical bond is one of the major challenges of computational quantum chemistry. Kohn–Sham density functional theory (KS-DFT) is the most common method, but approximate density functionals may not be able to describe systems where multiple electronic configurations are equally important. Multiconfigurational wave functions, on the other hand, can provide a detailed understanding of the electronic structures and chemical bonds of such systems. In the complete active space self-consistent field (CASSCF) method, one performs a full configuration interaction calculation in an active space consisting of active electrons and active orbitals. However, CASSCF and its variants require the selection of these active spaces. This choice is not black box; it requires significant experience and testing by the user, and thus active space methods are not considered particularly user-friendly and are employed only by a minority of quantum chemists. Our goal is to popularize these methods by making it easier to make good active space choices. Here, we present a machine learning protocol that performs an automated selection of active spaces for chemical bond dissociation calculations of main group diatomic molecules. The protocol shows high prediction performance for a given target system as long as a properly correlated system is chosen for training. Good active spaces are correctly predicted with a considerably better success rate than random guess (larger than 80% precision for most systems studied). Our automated machine learning protocol shows that a “black-box” mode is possible for facilitating and accelerating the large-scale calculations on multireference systems where single-reference methods such as KS-DFT cannot be applied.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Kohn–Sham Density in a Slater Orbital Basis Set

Finite, atom-centered Slater basis sets are used to determine approximate Kohn–Sham molecular orbitals. This is achieved by minimizing the kinetic energy plus the sum-squared difference between the Kohn–Sham density and the full configuration interaction density. As a result of the finite basis, a weight factor is introduced to balance the two minimization components. Results herein show that this can be done systematically, without sensitive dependence on the choice of scaling factor. In addition, the algorithm is applied to the LiH diatomic for fractional electron counts, where stretching the bond introduces significant reorganization of the electron density. As a result, the analysis will show the correct KS orbital structure and reveal the effects of correlation and electron locality on the KS solutions.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Exact and Model Exchange-Correlation Potentials for Open-Shell Systems

The conventional approaches to the inverse density functional theory problem typically assume nondegeneracy of the Kohn–Sham (KS) eigenvalues, greatly hindering their use in open-shell systems. Here, we present a generalization of the inverse density functional theory problem that can seamlessly admit degenerate KS eigenvalues. Additionally, we allow for fractional occupancy of the Kohn–Sham orbitals to also handle noninteracting ensemble-v-representable densities, as opposed to just noninteracting pure-v-representable densities. We present the exact exchange-correlation (XC) potentials for six open-shell systems–four atoms (Li, C, N, and O) and two molecules (CN and CH 2 )–using accurate ground-state densities from configuration interaction calculations. We compare these exact XC potentials with model XC potentials obtained using nonlocal (B3LYP, SCAN0) and local/semilocal (SCAN, PBE, PW92) XC functionals. Although the relative errors in the densities obtained from these DFT functionals are of $O$(10 –3 to 10 –2 ), the relative errors in the model XC potentials remain substantially large–$O$(10 –1 to 10 0 ).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Electronic structure prediction of multi-million atom systems through uncertainty quantification enabled transfer learning

The ground state electron density — obtainable using Kohn-Sham Density Functional Theory (KS-DFT) simulations — contains a wealth of material information, making its prediction via machine learning (ML) models attractive. However, the computational expense of KS-DFT scales cubically with system size which tends to stymie training data generation, making it difficult to develop quantifiably accurate ML models that are applicable across many scales and system configurations. Here, we address this fundamental challenge by employing transfer learning to leverage the multi-scale nature of the training data, while comprehensively sampling system configurations using thermalization. Our ML models are less reliant on heuristics, and being based on Bayesian neural networks, enable uncertainty quantification. We show that our models incur significantly lower data generation costs while allowing confident — and when verifiable, accurate — predictions for a wide variety of bulk systems well beyond training, including systems with defects, different alloy compositions, and at multi-million-atom scales. Moreover, such predictions can be carried out using only modest computational resources.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Real-space Kohn–Sham density functional theory for complex energy applications

Real-space Kohn-Sham density functional theory (real-space KS-DFT) enables large-scale electronic structure simulations that is particularly well-suited for the modern high-performance computing (HPC) architectures. This feature article reviews its theoretical foundations, highlights the algorithmic advances and recent developments, and showcases applications in complex nano systems. We aim to provide a perspective on the trajectory of real-space KS-DFT as an emerging tool for computational chemistry and materials science in the exascale era.

Zhang, Zeyi↗
DOE OSTI2021

Probing Systematic Bias in Low-redshift Type Ia Supernova Measurements by Cross Analyzing Surface Brightness and Hubble Residuals

For low-redshift (z < 0.1) SN Ia samples used in several cosmological analyses over the past decade, we probe for systematic bias by looking for correlations between surface brightness (SB) measurements and Hubble residuals (HR). For 292 SNe Ia, we measure SB at the location of the SN Ia from publicly available Pan-STARRS (PS1) images. The Hubble residuals are from two recent measurements with low-z SNe Ia that overlap the PS1 footprint: (1) the DES 3 yr cosmology analysis, with 120 overlapping low-z SNe Ia from the Harvard-Smithsonian Center for Astrophysics surveys and Carnegie Supernova Project, and (2) the PS1 single-telescope analysis, with 172 overlapping low-z SNe Ia from the Foundation Supernova Survey. This study is motivated by previous reports of anomalous inefficiencies and flux scatter for transients on bright galaxies. Here, we compare HR distributions of the bright and faint halves of the SB distribution: the mean HR values differ by ${\rm{\Delta }}\overline{\mathrm{HR}}$ = 0.031 ± 0.018, consistent with no difference at the 2σ level. We also perform a Kolmogorov–Smirnov (KS) test for the bright and faint half HR distributions, and conclude that the two distributions are statistically consistent with a KS p-value of 0.07. However, if future studies with larger data sets find ${\rm{\Delta }}\overline{\mathrm{HR}}\sim 0.03$ with high significance, this difference would be a leading systematic uncertainty in measurements of the dark energy equation of state, w.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

The Gaia DR2 parallax zero-point: hierarchical modelling of red clump stars

ABSTRACT The systematic offset of Gaia parallaxes has been widely reported with Gaia’s second data release, and it is expected to persist in future Gaia data. In order to use Gaia parallaxes to infer distances to high precision, we develop a hierarchical probabilistic model to determine the Gaia parallax zero-point offset along with the calibration of an empirical model for luminosity of red clump stars by combining astrometric and photometric measurements. Using a cross-matched sample of red clump stars from the Apache Point Observatory Galactic Evolution Experiment and Gaia Data Release 2 (DR2), we report the parallax zero-point offset in DR2 to be $\varpi _0 = -48 \pm 1\,\mu \text{as}$. We infer the red clump absolute magnitude to be −1.622 ± 0.004 in Ks, 0.435 ± 0.004 in G, −1.019 ± 0.004 in J, and −1.516 ± 0.004 in H. The intrinsic scatter of the red clump is ∼0.09 mag in J, H, and Ks, or ∼ 0.12 mag in G. We tailor our models to accommodate more complex analyses such as investigating the variations of the parallax zero-point with each source’s observed magnitude, observed colour, and sky position. In particular, we find fluctuations of the zero-point across the sky to be of order or less than a few 10s of $\mu \text{as}$.

Chan, Victor C.↗
DOE OSTI2022

A deep, multi-epoch Chandra HETG study of the ionized outflow from NGC 4051

Actively accreting supermassive black holes significantly impact the evolution of their host galaxies, truncating further star formation by expelling large fractions of gas with wide-angle outflows. The X-ray band is key to understanding how these black hole winds affect their environment, as the outflows have high temperatures ~10 5–8 K). We have developed a Bayesian framework for characterizing active galactic nucleus outflows with an improved ability to explore parameter space and perform robust model selection. We applied this framework to a new 700 ks and an archival 315 ks Chandra High Energy Transmission Gratings observation of the Seyfert galaxy NGC 4051. We have detected six absorbers intrinsic to NGC 4051. These wind components span velocities from 400 to 30000 km s -1 . We have determined that the most statistically significant wind component is purely collisionally ionized, which is the first detection of such an absorber. This wind has T ≈ 10 7 K and v ≈ 880 km s -1 and remains remarkably stable between the two epochs. Other slow components also remain stable across time. Fast outflow components change their properties between 2008 and 2016, suggesting either physical changes or clouds moving in and out of the line of sight. For one of the fast components, we obtain one of the tightest wind density measurements to date, log n/(cm -3 ) = 13.0$^{+0.01}_{-0.02}$, and determine that it is located at ~240 gravitational radii. The estimated total outflow power surpasses 5 percent of the bolometric luminosity (albeit with large uncertainties) making it important in the context of galaxy–black hole interactions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Kaposi's sarcoma herpesvirus exploits the DNA damage response to circularize its genome

Abstract To establish lifelong, latent infection, herpesviruses circularize their linear, double-stranded, DNA genomes through an unknown mechanism. Kaposi's sarcoma (KS) herpesvirus (KSHV), a gamma herpesvirus, is tightly linked with KS, primary effusion lymphoma, and multicentric Castleman's disease. KSHV persists in latently infected cells as a multi-copy, extrachromosomal episome. Here, we show the KSHV genome rapidly circularizes following infection, and viral protein expression is unnecessary for this process. The DNA damage response (DDR) kinases, ATM and DNA-PKcs, each exert roles, and absence of both severely compromises circularization and latency. These deficiencies were rescued by expression of ATM and DNA-PKcs, but not catalytically inactive mutants. In contrast, γH2AX did not function in KSHV circularization. The linear viral genomic ends resemble a DNA double strand break, and non-homologous DNA end joining (NHEJ) and homologous recombination (HR) reporters indicate both NHEJ and HR contribute to KSHV circularization. Last, we show, similar to KSHV, ATM and DNA-PKcs have roles in circularization of the alpha herpesvirus, herpes simplex virus-1 (HSV-1), while γH2AX does not. Therefore, the DDR mediates KSHV and HSV-1 circularization. This strategy may serve as a general herpesvirus mechanism to initiate latency, and its disruption may provide new opportunities for prevention of herpesvirus disease.

Li, Shijun↗
DOE OSTI2021

Density-functional theory of material design: fundamentals and applications-I

This article is part-I of a review of density-functional theory (DFT) that is the most widely used method for calculating electronic structure of materials. The accuracy and ease of numerical implementation of DFT methods has resulted in its extensive use for materials design and discovery and has thus ushered in the new field of computational material science. In this article, we start with an introduction to Schrödinger equation and methods of its solutions. After presenting exact results for some well-known systems, difficulties encountered in solving the equation for interacting electrons are described. How these difficulties are handled using the variational principle for the energy to obtain approximate solutions of the Schrödinger equation is discussed. The resulting Hartree and Hartree–Fock theories are presented along with results they give for atomic and solid-state systems. We then describe Thomas–Fermi theory and its extensions which were the initial attempts to formulate many-electron problem in terms of electronic density of a system. Having described these theories, we introduce modern DFT by discussing Hohenberg–Kohn theorems that form its foundations. We then go on to discuss Kohn–Sham (KS) formulation of DFT in its exact form. Next, local density approximation (LDA) is introduced and solutions of KS equation for some representative systems, obtained using the LDA, are presented. We end part-I of the review describing the contents of part-II.

36 MATERIALS SCIENCE↗
DOE OSTI2025

XRISM view of a stellar flare: High-resolution Fe K spectra of HR 1099, an RS CVn-type star

A high-resolution X-ray spectroscopic observation was made of the RS CVn-type binary star HR 1099 using the Resolve instrument onboard XRISM for its calibration purposes. During the $\sim$400 ks telescope time covering 1.5 binary orbit, a flare lasting for $\sim$100 ks was observed with a released X-ray radiation energy of ${\sim }10^{34}$ erg, making it the first stellar flare ever observed with an X-ray microcalorimeter spectrometer. The flare peak count rate is 6.4 times higher than that in quiescence and is distinguished clearly in time thanks to the long telescope time. Many emission lines were detected in the 1.7–10 keV range both in the flare and quiescent phases. Using the high spectral resolution of Resolve in the Fe K band (6.5–7.0 keV), we resolved the inner-shell lines of Fe XIX-XXVI as well as the outer-shell lines of Fe XXV-XXVI . These lines have peaks in the contribution functions at different temperatures over a wide range, allowing us to construct the differential emission measure (DEM) distribution over the electron temperature of 1–10 keV (roughly 10–100 MK) based only on Fe lines, thus without an assumption of the elemental abundance. The reconstructed DEM has a bimodal distribution, and only the hotter component increased during the flare. The elemental abundance was derived based on the DEM distribution thus constructed. A significant abundance increase was observed during the flare for Ca and Fe, which are some of the elements with the lowest first ionization potential among those analyzed, but not for Si, S, and Ar. This behavior is seen in some giant solar flares and the present result is a clear example in stellar flares.

Astronomy and AstroPhysics↗
DOE OSTI2021

Seawater exposure causes hydraulic damage in dying Sitka-spruce trees

Sea-level rise is one of the most critical challenges facing coastal ecosystems under climate change. Observations of elevated tree mortality in global coastal forests are increasing, but the mechanism of salinity-stress induced tree mortality is currently unknown. We monitored progressive mortality and associated gas exchange and hydraulic shifts in Sitka-spruce (Picea sitchensis) trees located within a salinity gradient under an ecosystem-scale change of seawater exposure in Washington State, USA. Percentage of live foliated crown (PLFC) decreased and tree mortality increased with increasing soil salinity during the study period. A strong reduction in gas exchange and xylem hydraulic conductivity (Ks) occurred during tree death, with an increase of the percentage loss of xylem conductivity (PLC) and turgor loss point (ptlp). Hydraulic and osmotic shifts reflected that hydraulic function declined from seawater exposure and dying trees were unable to support osmotic adjustment. Constrained gas exchange was strongly related to hydraulic damage at both stem and leaf levels. Significant correlations between foliar sodium (Na+) concentration and gas exchange and key hydraulic parameters (Ks, PLC and ptlp ) suggest that cellular injury related to the toxic effects of ion accumulation impacted the physiology of these dying trees. This study provides evidence of toxic effects on cellular function that become manifest in all aspects of plant functioning, leading to unfavourable osmotic and hydraulic conditions.

Zhang, Hongxia↗
DOE OSTI2022

Conditional probability density functional theory

Here we present conditional probability (CP) density functional theory (DFT) as a formally exact theory. In essence, CP-DFT determines the ground-state energy of a system by finding the CP density from a series of independent Kohn-Sham (KS) DFT calculations. By directly calculating CP densities, we bypass the need for an approximate XC energy functional. In this paper we discuss and derive several key properties of the CP density and corresponding CP-KS potential. Illustrative examples are used throughout to help guide the reader through the various concepts and theory presented. We explore a suitable CP-DFT approximation and discuss exact conditions, limitations, and results for selected examples.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Efficient core-excited state orbital perspective on calculating x-ray absorption transitions in determinant framework

X-ray absorption spectroscopy (XAS) is an explicit probe of the unoccupied electronic structure of materials and an invaluable tool for fingerprinting various electronic properties and phenomena. Computational methods capable of simulating and analyzing such spectra are therefore in high demand for complementing experimental results and for extracting valuable insights therefrom. In particular, a recently proposed first-principles approach titled many-body XAS (MBXAS), which approximates the final (initial) state as a Slater determinant constructed from Kohn-Sham (KS) orbitals optimized in the absence (presence) of the relevant core electron has shown promising prospects in evaluating the transition amplitudes. In this article, we show that the MBXAS approach can be rederived using a transition operator expressed entirely in the basis of core-excited state KS orbitals and that this reformulation offers substantial practical and conceptual advantages. In addition to circumventing previous issues of convergence with respect to the number of unoccupied ground-state orbitals, the aforementioned representation reduces the computational expense by rendering the calculation of such orbitals unnecessary altogether. Furthermore, the reformulated approach also provides a direct pathway for comparing the many-body approximation with the so-called single-particle treatment and indicates the relative importance in observed XAS intensity of the relaxation of the valence occupied subspace induced by the core excitation. Finally, using the core-excited state basis, we define auxiliary orbitals for x-ray absorption and demonstrate their utility in explaining the spectral intensity by contrasting them with single-particle approximations to the excited state.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2023

Development of a machine-learning-based ionic-force correction model for quantum molecular dynamic simulations of warm dense matter

In this work Δ learning is used to map orbital-free density functional theory (OF-DFT) ionic forces to the corresponding Kohn-Sham (KS) DFT ionic forces. The development of the approximate force difference in terms of the ion positions is constructed and serves as a stand in for the ground truth force difference. Descriptor vectors for ion configurations are constructed using all distance between ions in conjunction with an indexing based on a nearest neighbor ranking. It is demonstrated that such a scheme of descriptors can uniquely describe an ionic configuration up to a rotation and reflection when no ambiguity in the nearest neighbor ranking exists. How to handle the case when an ambiguity exists in the nearest neighbor ranking is discussed. As a proof of principle, the model is trained and tested on warm dense hydrogen at temperatures between 1 and 15 eV. Once tested, the model was used to perform molecular dynamic simulations of warm dense hydrogen. Furthermore, the resulting energies and pressures are within 1% and 2% of their respective target KS values.

36 MATERIALS SCIENCE↗
DOE OSTI2021

DNA Viral Diversity, Abundance, and Functional Potential Vary across Grassland Soils with a Range of Historical Moisture Regimes

Soil viruses are abundant, but the influence of the environment and climate on soil viruses remains poorly understood. Here, we addressed this gap by comparing the diversity, abundance, lifestyle, and metabolic potential of DNA viruses in three grassland soils with historical differences in average annual precipitation, low in eastern Washington (WA), high in Iowa (IA), and intermediate in Kansas (KS). Bioinformatics analyses were applied to identify a total of 2,631 viral contigs, including 14 complete viral genomes from three deep metagenomes (1 terabase [Tb] each) that were sequenced from bulk soil DNA. An additional three replicate metagenomes (~0.5 Tb each) were obtained from each location for statistical comparisons. Identified viruses were primarily bacteriophages targeting dominant bacterial taxa. Both viral and host diversity were higher in soil with lower precipitation. Viral abundance was also significantly higher in the arid WA location than in IA and KS. More lysogenic markers and fewer clustered regularly interspaced short palindromic repeats (CRISPR) spacer hits were found in WA, reflecting more lysogeny in historically drier soil. More putative auxiliary metabolic genes (AMGs) were also detected in WA than in the historically wetter locations. The AMGs occurring in 18 pathways could potentially contribute to carbon metabolism and energy acquisition in their hosts. Structural equation modeling (SEM) suggested that historical precipitation influenced viral life cycle and selection of AMGs. The observed and predicted relationships between soil viruses and various biotic and abiotic variables have value for predicting viral responses to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

HfZr_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys hafnium-zirconium (Hf-Zr). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP). Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Hf and Zr. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions.

36 MATERIALS SCIENCE↗
DOE OSTI2026

NbTi_BCC_SolidSolution_128atoms_VASP6

We performed density functional theory (DFT) calculations for body-centered-cubic (BCC) structures with 128 lattices sites of solid solution binary alloys niobium-titanium (Nb-Ti). The electronic structures of alloys have been calculated using Vienna Ab initio Simulation Package (VASP), https://github.com/ORNL/ScalableWorkflow_VASP_Calculations. Within this package the DFT approach is used to reduce many-body Schrodinger equation to set of single particle Kohn-Sham (KS) equations. The generalized electronic exchange-correlation functional is described by generalized gradient approximation with the Perdew-Burke-Ernzerhof parametrization. The electron-ion interactions is described by pseudopotentials developed within the plane-wave basis projector augmented-wave (PAW) approach. These pseudopotentials are available at the VASP portal (http://cms.mpi.univie.ac.at/vasp/). Our calculations have been run with the pseudopotentials treating s and p semi-core states as valence in case for the elements Nb and Ti. The electronic densities and potentials are expanded over plane-waves with energy cutoff of 350 eV. 2x2x2 k-mesh and normal precision were used. The alloys were modeled by supercell containing 128 randomly distributed atoms. At initial step the atoms occupy perfect bcc lattice cites. This initial structure was optimized until energy changes less than 1e-6 eV, while forces acting on atoms don't exceed 1e-2 eV/angstrom. The electron-ion interaction is described by PAW pseudopotentials. The calculations have been collected by sampling chemical compositions across the entire compositional range. The chemical compositions have been sampled by progressively changing the number of atoms per constituent by 4. For each chemical composition of binaries and ternaries, the first-principle calculations have been run for 100 randomized arrangements of the constituents on the BCC lattice sites. We collected data for a total of 3,100 randomized atomic structures over 31 chemical compositions. The calculations have been collected on Air Force HPC11 cluster using the VASP 6.5.1. Additional methodology and file structure information is available in the dataset README.txt file.

36 MATERIALS SCIENCE↗