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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to each patient's biomolecular characteristics. Although scientific data about coding and non-coding RNA molecules are constantly produced and available from public repositories, they are scattered across different databases and a centralized, uniform, and semantically consistent representation of the "RNA world" is still lacking. We propose RNA-KG, a knowledge graph (KG) encompassing biological knowledge about RNAs gathered from more than 60 public databases, integrating functional relationships with genes, proteins, and chemicals and ontologically grounded biomedical concepts. To develop RNA-KG, we first identified, pre-processed, and characterized each data source; next, we built a meta-graph that provides an ontological description of the KG by representing all the bio-molecular entities and medical concepts of interest in this domain, as well as the types of interactions connecting them. Finally, we leveraged an instance-based semantically abstracted knowledge model to specify the ontological alignment according to which RNA-KG was generated. RNA-KG can be downloaded in different formats and also queried by a SPARQL endpoint. A thorough topological analysis of the resulting heterogeneous graph provides further insights into the characteristics of the "RNA world". RNA-KG can be both directly explored and visualized, and/or analyzed by applying computational methods to infer bio-medical knowledge from its heterogeneous nodes and edges. The resource can be easily updated with new experimental data, and specific views of the overall KG can be extracted according to the bio-medical problem to be studied.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Prediction of Quantum Anomalous Hall Insulator in half-fluorinated GaBi Honeycomb

Using first-principles electronic structure calculations, we predict half-fluorinated GaBi honeycomb under tensile strain to harbor a quantum anomalous Hall (QAH) insulator phase. We show that this QAH phase is driven by a single inversion in the band structure at the Γ point. Moreover, we have computed the electronic spectrum of a half-fluorinated GaBi nanoribbon with zigzag edges, which shows that only one edge band crosses the Fermi level within the band gap. In conclusion, our results suggest that half-fluorination of the GaBi honeycomb under tensile strain could provide a new platform for developing novel spintronics devices based on the QAH effect.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Attainment of a stable, fully detached plasma state in innovative divertor configurations

A computational study of long-legged tokamak divertor configurations is performed with the edge transport code UEDGE. Several divertor configurations are considered, with radially or vertically extended, tightly baffled, outer divertor legs and with or without a secondary X-point in the divertor leg volume. For otherwise identical conditions, a scan of the input power from the core plasma is performed. As the power is reduced to a threshold value, the plasma in the outer leg transitions to a fully detached state, which defines the upper limit on the power for detached divertor operation. Reducing the power further results in the detachment front shifting upstream but remains stable. At low power, the detachment front eventually moves all the way to the primary X-point, which is usually associated with degradation of the core plasma, and this defines the lower limit on the power for the detached divertor operation. For the studied parameters, for long-legged divertors, the detached operation window is quite large, in particular, for the X-point target configuration using a secondary X-point in the divertor leg volume, allowing a factor of 5–10 variations in the input power. For the same parameters, for the standard divertor configuration, the detached operation window is very small or even non-existent. In conclusion, the present modeling results suggest the possibility of stable fully detached divertor operation for a tokamak with tightly baffled extended divertor legs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Spatially separating redox centers on 2D carbon nitride with cobalt single atom for photocatalytic H 2 O 2 production

Redox cocatalysts play crucial roles in photosynthetic reactions, yet simultaneous loading of oxidative and reductive cocatalysts often leads to enhanced charge recombination that is detrimental to photosynthesis. This study introduces an approach to simultaneously load two redox cocatalysts, atomically dispersed cobalt for improving oxidation activity and anthraquinone for improving reduction selectivity, onto graphitic carbon nitride (C 3 N 4 ) nanosheets for photocatalytic H 2 O 2 production. Spatial separation of oxidative and reductive cocatalysts was achieved on a two-dimensional (2D) photocatalyst, by coordinating cobalt single atom above the void center of C 3 N 4 and anchoring anthraquinone at the edges of C 3 N 4 nanosheets. Such spatial separation, experimentally confirmed and computationally simulated, was found to be critical for enhancing surface charge separation and achieving efficient H 2 O 2 production. This center/edge strategy for spatial separation of cocatalysts may be applied on other 2D photocatalysts that are increasingly studied in photosynthetic reactions.

2D photocatalyst↗
DOE OSTI2019

Divertor currents during type-I edge-localized modes on the DIII-D tokamak

Measurements of divertor currents on DIII-D lead to new insights in nonlinear edge-localized mode (ELM) dynamics and a possible mechanism to explain their explosive growth. Rapidly oscillating currents flowing into the divertor before a significant increase in divertor heat flux occurs are measured with an array of shunted tiles and characterized. Extrapolation results in total n = 0 currents of 5–10 kA flowing into a concentric circle near the strike point. The detected Fourier harmonics appear consistent with a mix of low- n modes ( n < 4) with currents up to 4 kA. A heuristic framework for ELM currents is developed based on thermoelectric origin of the tile currents with flow through regions inside of the nominal separatrix and found consistent with the current measurements. A current flow through the confined plasma leading to increased stochasticity and transport at the plasma edge could provide a mechanism for additional nonlinear growth as sought for in computational ELM simulations. Results also imply that ELM currents may open the possibility to manipulate the ELM character by perturbations through non-axisymmetric divertor bias or tile insulation.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Sphynx

Sphynx is a software library for parallel graph partitioning and load balancing. It partitions a set of vertices in a graph such that the vertex parts are balanced, and the edge cut is approximately minimized. The primary use case is to partition a computational graph into smaller tasks that can be assigned to processors (cores) for efficient parallel computing. Sphynx is based on the Trilinos scientific computing toolkit so can run on both multi-CPU and multi-GPU systems. SAND2020-12183 M Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Boman, Erik↗
DOE OSTI2018

Edge Simulation Laboratory

The goal of the Edge Simulation Laboratory (ESL) multi-institutional project is to advance scientific understanding of the edge plasma region of magnetic fusion devices via a coordinated effort utilizing modern computing resources, advanced algorithms, and ongoing theoretical development. The UCSD team was involved in the development of the COGENT code for kinetic studies across a magnetic separatrix. This work included a kinetic treatment of electrons and multiple ion species (impurities) and accurate collision operators.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

DUNE Software and Computing Research and Development

The international collaboration designing and constructing the Deep Underground Neutrino Experiment (DUNE) at the Long-Baseline Neutrino Facility (LBNF) has developed a two-phase strategy toward the implementation of this leading-edge, large-scale science project. The ambitious physics program of Phase I and Phase II of DUNE is dependent upon deployment and utilization of significant computing resources, and successful research and development of software (both infrastructure and algorithmic) in order to achieve these scientific goals. This submission discusses the computing resources projections, infrastructure support, and software development needed for DUNE during the coming decades as an input to the European Strategy for Particle Physics Update for 2026. The DUNE collaboration is submitting four main contributions to the 2026 Update of the European Strategy for Particle Physics process. This submission to the 'Computing' stream focuses on DUNE software and computing. Additional inputs related to the DUNE science program, DUNE detector technologies and R&D, and European contributions to Fermilab accelerator upgrades and facilities for the DUNE experiment, are also being submitted to other streams.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2019

Parafermions, induced edge states, and domain walls in fractional quantum Hall effect spin transitions

Search for parafermions and Fibonacci anyons, which are excitations obeying non-Abelian statistics, is driven both by the quest for deeper understanding of nature and prospects for universal topological quantum computation. However, physical systems that can host these exotic excitations are rare and hard to realize in experiments. Here we study the domain walls and the edge states formed in spin transitions in the fractional quantum Hall effect. Effective theory approach and exact diagonalization in a disk and torus geometries proves the existence of the counterpropagating edge modes with opposite spin polarizations at the boundary between the two neighboring regions of the two-dimensional electron liquid in spin-polarized and spin-unpolarized phases. By analytical and numerical analysis, we argue that these systems can host parafermions when coupled to an 𝑠-wave superconductor and are experimentally feasible. We investigate settings based on 𝜈 = 2/3, 4/3, and 5/3 spin transitions and analyze spin-flipping interactions that hybridize counterpropagating modes. Lastly, we discuss spin-orbit interactions of composite fermions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Differentially Private Synthesis and Sharing of Network Data Via Bayesian Exponential Random Graph Models

Abstract Network data often contain sensitive relational information. One approach to protecting sensitive information while offering flexibility for network analysis is to share synthesized networks based on the information in originally observed networks. We employ differential privacy (DP) and exponential random graph models (ERGMs) and propose the DP-ERGM method to synthesize network data. We apply DP-ERGM to two real-world networks. We then compare the utility of synthesized networks generated by DP-ERGM, the DyadWise Randomized Response (DWRR) approach, and the Synthesis through Conditional distribution of Edge given nodal Attribute (SCEA) approach. In general, the results suggest that DP-ERGM preserves the original information significantly better than two other approaches in network structural statistics and inference for ERGMs and latent space models. Furthermore, DP-ERGM satisfies node DP through modeling the global network structure with ERGM, a stronger notion of privacy than the edge DP under which DWRR and SCEA operate.

graph synthesis↗
DOE OSTI2023

Detailed studies of the processes in low energy H irradiation of Li and Li-compound surfaces

We have used a combination of pico-to-nano temporal/spatial scale computational physics and chemistry modeling of plasma–material interfaces in the tokamak fusion plasma edges to unravel the evolving characteristics, not readily accessible by empirical means, of lithium-, oxygen-, and hydrogen-containing materials of plasma-facing components under irradiation by hydrogen and its isotopes. In the present calculation, amorphous lithium compound surfaces containing oxygen, Li 2 O, and LiOH were irradiated by 1-100 eV particles at incident angles on the surface ranging from perpendicular to almost grazing angles. Consequential surface processes, reflection, retention, and sputtering were studied at “the same footing” and compared to earlier results from amorphous Li and LiH surfaces. In conclusion, the critical role of charging dynamics of lithium, oxygen, and hydrogen atoms in the surface chemistry during hydrogen-fuel irradiation was found to drive the kinetics and dynamics of these surfaces in unexpected ways that ultimately could have profound effects on fusion plasma confinement behavior and surface erosion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Navigating Large Chemical Spaces Using Graph Theory and Integer Programming

Navigating and analyzing large chemical spaces are necessary to accelerate the design and discovery of new molecules and chemical processes. In this work, we introduce a computational framework that integrates graph theory and integer programming to enable the efficient navigation of large chemical spaces. Our framework represents the chemical space as a graph, wherein nodes represent molecules and edges represent the degree of similarity or connectivity based on domain-specific information. Using the graph representation, we identify representative molecules by computing the so-called minimum dominating set (MDS), which in our context is the minimum set of molecules that is connected to all other molecules. We present a suite of solution strategies for the MDS problem including heuristic and rigorous integer programming (IP) approaches. We show that these approaches allow us to capture physicochemical properties and domain-specific logic and constraints, facilitating the identification of molecules with the target properties. We demonstrate the effectiveness of the proposed approach by navigating the chemical space of per- and polyfluoroalkyl substances (PFAS); this comprises approximately 15,000 molecular structures. We compare our framework against traditional dimensionality reduction and clustering methods such as t-SNE and K-means clustering.

Chemical structure↗
DOE OSTI2019

Using first principles calculations to interpret XANES experiments: extracting the size-dependence of the ( p , T ) phase diagram of sub-nanometer Cu clusters in an O 2 environment

Here, we have used ab initio density functional theory together with ab initio atomistic thermodynamics, and in situ X-ray absorption near edge spectroscopy (XANES) experiments, to study the oxidation of sub-nanometer clusters of Cu n O x supported on a hydroxylated amorphous alumina substrate in an O 2 -rich environment. We obtain ( p , T ) phase diagrams; these differ notably for the nanoclusters compared to the bulk. Both theory and experiment suggest that in the presence of oxygen, the cluster will oxidize from its elemental state to the oxidized state as temperature decreases. We obtain a clear trend for the transition Cu n → Cu n O n/2 : we see that smaller the cluster, greater is the tendency toward oxidation. However, we do not see a monotonic size-dependent trend for the transition Cu n O n/2 → Cu n O n . We suggest that theoretically computed Bader charges constitute a simple yet quantitative way to align experimental measures of XANES edges with theoretical calculations, so as to yield oxidation states for nanoclusters. Our results have important implications for the use of small clusters in fields such as nanocatalysis and nanomedicine.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Computationally Guided Discovery of Axis-Dependent Conduction Polarity in NaSnAs Crystals

Most electronic materials exhibit a single dominant charge carrier type, either holes or electrons, along all crystallographic directions. However, there are a small number of compounds, mostly metals, that exhibit simultaneous p-type and n-type conduction behavior along different crystallographic directions. We demonstrate that the experimental discovery of semiconductors with this axis-dependent conduction polarity can be facilitated by identifying a large anisotropy of either the electron or hole effective masses (m*) or both, providing the electron and hole masses dominate along different crystallographic directions. We calculated the layered semiconductor NaSnAs to have a lower electron m* in-plane than the cross-plane and a very large hole m* in-plane and small hole m* cross-plane. We established the growth of >3 mm-sized NaSnAs crystals via Sn flux and confirmed the band gap to be 0.65 eV, in agreement with theory. NaSnAs exhibits p-type thermopowers cross-plane and n-type thermopowers in-plane, confirming that the large anisotropy in the effective mass at the band edges is an excellent indicator for axis-dependent conduction polarity. Altogether, this work shows that the discovery of semiconductors with such a phenomenon can be accelerated by computationally evaluating the anisotropic curvatures of the band edges, paving the way for their future discovery and application.

30 DIRECT ENERGY CONVERSION↗
DOE OSTI2022

Time-Resolved Optical Pump-Resonant X-ray Probe Spectroscopy of 4-Thiouracil: A Simulation Study

We theoretically monitor the photoinduced ππ* → nπ* internal conversion process in 4-thiouracil (4TU), triggered by an optical pump. The element-sensitive spectroscopic signatures are recorded by a resonant X-ray probe tuned to the sulfur, oxygen, or nitrogen K-edge. We employ high-level electronic structure methods optimized for core-excited electronic structure calculation combined with quantum nuclear wavepacket dynamics computed on two relevant nuclear modes, fully accounting for their quantum nature of nuclear motions. We critically discuss the capabilities and limitations of the resonant technique. For sulfur and nitrogen, we document a pre-edge spectral window free from ground-state background and rich with ππ* and nπ* absorption features. The lowest sulfur K-edge shows strong absorption for both ππ* and nπ*. In the lowest nitrogen K-edge window, we resolve a state-specific fingerprint of the ππ* and an approximate timing of the conical intersection via its depletion. A spectral signature of the nπ* transition, not accessible by UV–vis spectroscopy, is identified. The oxygen K-edge is not sensitive to molecular deformations and gives steady transient absorption features without spectral dynamics. Here, the ππ*/nπ* coherence information is masked by more intense contributions from populations. Altogether, element-specific time-resolved resonant X-ray spectroscopy provides a detailed picture of the electronic excited-state dynamics and therefore a sensitive window into the photophysics of thiobases.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Toward a Machine Learning Approach to Interpreting X-ray Spectra of Trace Impurities by Converting XANES to EXAFS

The fact that the photoabsorption spectrum of a material contains information about the atomic structure, commonly understood in terms of multiple scattering theory, is the basis of the popular extended X-ray absorption spectroscopy (EXAFS) technique. How much of the same structural information is present in other complementary spectroscopic signals is not obvious. Here we use a machine learning approach to demonstrate that within theoretical models that accurately predict the EXAFS signal, the extended near-edge region does indeed contain the EXAFS-accessible structural information. We do this by exhibiting deep operator neural networks (DeepONets) that have learned the relationship between the extended and near edge portions of the X-ray absorption spectrum to predict the former from the latter. We find that we can accurately predict the EXAFS spectrum between 6 and 14 Å –1 from the first 6 Å –1 (≈100 eV) of the absorption spectrum of Cu 2 + substitutional defects in the Fe 3+ mineral hematite (α-Fe 2 O 3 ). This surprising finding implies that theoretical analyses of X-ray absorption spectra could be implemented that extract the same conclusions as high-quality EXAFS studies from spectra collected over a much smaller range of photon energies. This relaxes a host of experimental limitations related to the X-ray source and measurement sample, including collection time, minimum dopant concentration, source brilliance, and energy range. We describe the theoretical data sets and DeepONet construction and show that the resulting DeepONets produce EXAFS that recovers linear combination fits to experimental data with accuracy approaching the original ab initio calculations. We discuss the implications of our findings for minor constituent characterization and for understanding the information content of spectroscopic data more broadly, including how this approach might be applied to measured experimental spectra. In conclusion, to encourage similar efforts, the simulated X-ray spectra, machine learning, and fitting code are publicly available.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

The PAC-MAN model: Benchmark case for linear acoustics in computational physics

Benchmark cases in the field of computational physics, on the one hand, have to contain a certain complexity to test numerical edge cases and, on the other hand, require the existence of an analytical solution, because an analytical solution allows the exact quantification of the accuracy of a numerical simulation method. This dilemma causes a need for analytical sound field formulations of complex acoustic problems. A well known example for such a benchmark case for harmonic linear acoustics is the “Cat's Eye model”, which describes the three-dimensional sound field radiated from a sphere with a missing octant analytically. In this paper, a benchmark case for two-dimensional (2D) harmonic linear acoustic problems, viz., the “PAC-MAN model”, is proposed. The PAC-MAN model describes the radiated and scattered sound field around an infinitely long cylinder with a cut out sector of variable angular width. While the analytical calculation of the 2D sound field allows different angular cut-out widths and arbitrarily positioned line sources, the computational cost associated with the solution of this problem is similar to a 1D problem because of a modal formulation of the sound field in the PAC-MAN model. - Highlights: • A benchmark case for 2D harmonic linear acoustic problems is proposed. • The PAC-MAN geometry is used as emitter/scatterer in this benchmark. • An analytic formulation of radiated and scattered sound is derived. • Line and disk sources, plane waves, and surface vibrations are considered.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗