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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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At least 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs

We report that community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

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

Production of warm ions in electron beam generated E × B plasma

Several recent experiments have demonstrated low-damage processing of 2D materials, such as graphene and single crystal diamond, using electron beam (e-beam) generated plasmas with applied crossed electric and magnetic (E × B) fields. Here, the low damage of these sensitive materials is commonly attributed to the low energy of ions incident to the substrate surface and the ion confinement in E x B fields. In this work, measurements of atom and ion velocity distribution functions in an e-beam E × B plasma at sub-mTorr argon pressures using a laser-induced fluorescence diagnostic revealed the presence of a warm population of ions with temperatures of ~ 1 eV that are sufficient to destroy the ion confinement in E × B fields and drive the ion flux by cross field diffusion in the direction opposite to the applied electric field, toward the plasma-bounded walls or substrate. Thus, it is this nearly ambipolar diffusion process that is responsible for the flux of charged particles impinging on the wall/substrate surface.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2026

Analog-to-digital converter based on voltage-controlled superconducting devices

The increasing demand for cryogenic electronics in superconducting and quantum computing systems calls for ultra-energy-efficient data conversion architectures that remain functional at deep cryogenic temperatures. Here, in this work, we present the first design of a voltage-controlled superconducting flash analog-to-digital converter (ADC) based on a voltage-controlled quantum-enhanced Josephson junction field-effect transistor (JJFET). Exploiting its strong gate tunability and transistor-like behavior, the JJFET offers a scalable alternative to conventional current-controlled superconducting devices while aligning naturally with CMOS-style design methodologies. Building on our previously developed Verilog-A compact model calibrated to experimental data, we design and simulate a three-bit JJFET-based flash ADC targeted for integration within cryogenic control and readout circuitry in quantum computing. The core comparator block is realized through careful bias current selection and augmented with a three-terminal nanocryotron to precisely define reference voltages. Cascaded JJFET comparators ensure robust voltage gain, cascadability, and logic-level restoration across stages. Simulation results demonstrate accurate quantization behavior with ultra-low power dissipation, underscoring the feasibility of voltage-driven superconducting mixed-signal circuits. This work establishes a critical step toward unifying superconducting logic and data conversion, paving the way for scalable cryogenic architectures in quantum–classical co-processors, low-power artificial intelligence accelerators, and next-generation energy-constrained computing platforms.

Analog-to-digital converter↗
DOE OSTI2023

Dominant heterocyclic composition of dissolved organic nitrogen in the ocean: A new paradigm for cycling and persistence

Marine dissolved organic nitrogen (DON) is one of the planet’s largest reservoirs of fixed N, which persists even in the N-limited oligotrophic surface ocean. The vast majority of the ocean’s total DON reservoir is refractory (RDON), primarily composed of low molecular weight (LMW) compounds in the subsurface and deep sea. However, the composition of this major N pool, as well as the reasons for its accumulation and persistence, are not understood. Past characterization of the analytically more tractable, but quantitatively minor, high molecular weight (HMW) DON fraction revealed a functionally simple amide-dominated composition. While extensive work in the past two decades has revealed enormous complexity and structural diversity in LMW dissolved organic carbon, no efforts have specifically targeted LMW nitrogenous molecules. Here, we report the first coupled isotopic and solid-state NMR structural analysis of LMW DON isolated throughout the water column in two ocean basins. Together these results provide a first view into the composition, potential sources, and cycling of this dominant portion of marine DON. Our data indicate that RDON is dominated by 15N-depleted heterocyclic-N structures, entirely distinct from previously characterized HMW material. This fundamentally new view of marine DON composition suggests an important structural control for RDON accumulation and persistence in the ocean. The mechanisms of production, cycling, and removal of these heterocyclic-N-containing compounds now represents a central challenge in our understanding of the ocean’s DON reservoir.

58 GEOSCIENCES↗
DOE OSTI2023

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Abstract Motivation Proteins interact to form complexes to carry out essential biological functions. Computational methods such as AlphaFold-multimer have been developed to predict the quaternary structures of protein complexes. An important yet largely unsolved challenge in protein complex structure prediction is to accurately estimate the quality of predicted protein complex structures without any knowledge of the corresponding native structures. Such estimations can then be used to select high-quality predicted complex structures to facilitate biomedical research such as protein function analysis and drug discovery. Results In this work, we introduce a new gated neighborhood-modulating graph transformer to predict the quality of 3D protein complex structures. It incorporates node and edge gates within a graph transformer framework to control information flow during graph message passing. We trained, evaluated and tested the method (called DProQA) on newly-curated protein complex datasets before the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) and then blindly tested it in the 2022 CASP15 experiment. The method was ranked 3rd among the single-model quality assessment methods in CASP15 in terms of the ranking loss of TM-score on 36 complex targets. The rigorous internal and external experiments demonstrate that DProQA is effective in ranking protein complex structures. Availability and implementation The source code, data, and pre-trained models are available at https://github.com/jianlin-cheng/DProQA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Including massive neutrinos in thermal Sunyaev Zeldovich power spectrum and cluster counts analyses

We consistently include the effect of massive neutrinos in the thermal Sunyaev Zeldovich (SZ) power spectrum and cluster counts analyses, highlighting subtle dependencies on the total neutrino mass and data combination. In particular, we find that using the transfer functions for cold dark matter (CDM) + baryons in the computation of the halo mass function, instead of the transfer functions including neutrino perturbations, as prescribed in recent work, yields an ≈0.25 percent downward shift of the σ 8 constraint from tSZ power spectrum data, with a fiducial neutrino mass Σm ν = 0.06 eV. In ΛCDM, with an X-ray mass bias corresponding to the expected hydrostatic mass bias, i.e. (1 - b) ≃ 0.8, our constraints from Planck SZ data are consistent with the latest results from SPT, DES-Y1, and KiDS+VIKING-450. In νΛCDM, our joint analyses of Planck SZ with Planck 2015 primary CMB yield a small improvement on the total neutrino mass bound compared to the Planck 2015 primary CMB constraint, as well as (1 - b) = 0.64 ± 0.04 (68 percent CL). For forecasts, we find that competitive neutrino mass measurements using cosmic variance limited SZ power spectrum require masking the heaviest clusters and probing the small-scale SZ power spectrum up to ℓ max ≈ 10 4 . Although this is challenging, we find that SZ power spectrum can realistically be used to tightly constrain intracluster medium properties: we forecast a 2 percent determination of the X-ray mass bias by combining CMB-S4 and our mock SZ power spectrum with ℓ max = 10 3 .

Astronomy & Astrophysics↗
DOE OSTI2020

Crystal structure of an atypical cobalamin riboswitch reveals RNA structural adaptability as basis for promiscuous ligand binding

Cobalamin riboswitches encompass a structurally diverse group of cis-acting, gene regulatory elements found mostly in bacterial messenger RNA and are classified into subtypes based on secondary and tertiary characteristics. An unusual variant of the cobalamin riboswitch with predicted structural features was identified in Bacillus subtilis over a decade ago, but its structure and mechanisms of cobalamin selectivity and translational control have remained unsolved. We present the crystal structure of the aptamer domain of this atypical cobalamin riboswitch and a model for the complete riboswitch, including its expression platform domain. We demonstrate that this riboswitch binds to multiple cobalamin derivatives and correlate its promiscuous behavior to its structure and unique arrangement of peripheral elements. Comparative structural analyses between conventional cobalamin riboswitches and the B. subtilis cobalamin riboswitch reveal that the likely basis for this promiscuous ligand binding is intrinsic structural adaptability encoded in the RNA structure. It suggests that cobalamin selectivity might ultimately be viewed as existing on a spectrum of affinity for each derivative rather than as belonging to distinct types based on ligand specificities. Our work provides an interesting and notable example of functional coupling of ligand-sensing and adaptive folding by a structured RNA molecule.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Streamlined spatial and environmental expression signatures characterize the minimalist duckweed Wolffia australiana

Single-cell genomics permits a new resolution in the examination of molecular and cellular dynamics, allowing global, parallel assessments of cell types and cellular behaviors through development and in response to environmental circumstances, such as interaction with water and the light–dark cycle of the Earth. Here, we leverage the smallest, and possibly most structurally reduced, plant, the semiaquaticWolffia australiana, to understand dynamics of cell expression in these contexts at the whole-plant level. We examined single-cell-resolution RNA-sequencing data and foundWolffiacells divide into four principal clusters representing the above- and below-water-situated parenchyma and epidermis. Although these tissues share transcriptomic similarity with model plants, they display distinct adaptations thatWolffiahas made for the aquatic environment. Within this broad classification, discrete subspecializations are evident, with select cells showing unique transcriptomic signatures associated with developmental maturation and specialized physiologies. Assessing this simplified biological system temporally at two key time-of-day (TOD) transitions, we identify additional TOD-responsive genes previously overlooked in whole-plant transcriptomic approaches and demonstrate that the core circadian clock machinery and its downstream responses can vary in cell-specific manners, even in this simplified system. Distinctions between cell types and their responses to submergence and/or TOD are driven by expression changes of unexpectedly few genes, characterizingWolffiaas a highly streamlined organism with the majority of genes dedicated to fundamental cellular processes.Wolffiaprovides a unique opportunity to apply reductionist biology to elucidate signaling functions at the organismal level, for which this work provides a powerful resource.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Block Lanczos algorithm for lattice QCD spectroscopy and matrix elements

Recent work introduced a new framework for analyzing correlation functions with improved convergence and signal-to-noise properties, as well as rigorous quantification of excited-state effects, based on the Lanczos algorithm and spurious eigenvalue filtering with the Cullum-Willoughby test. Here, we extend this framework to the analysis of correlation-function matrices built from multiple interpolating operators in lattice quantum chromodynamics (QCD) by constructing an oblique generalization of the block Lanczos algorithm, as well as a new physically motivated reformulation of the Cullum-Willoughby test that generalizes to block Lanczos straightforwardly. The resulting block Lanczos method directly extends generalized eigenvalue problem (GEVP) methods, which can be viewed as applying a single iteration of block Lanczos. Block Lanczos provides qualitative and quantitative advantages over GEVP methods analogous to the benefits of Lanczos over the standard effective mass, including faster convergence to ground- and excited-state energies, explicitly computable two-sided error bounds, straightforward extraction of matrix elements of external currents, and asymptotically constant signal-to-noise. No fits or statistical inference are required. Proof-of-principle calculations are performed for noiseless mock-data examples as well as two-by-two proton correlation-function matrices in lattice QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2022

Electronic structure of Humble defects in Ge and Ge 0.8⁢ Si 0.2

The group-IV diamond-structure elements are known to host a variety of planar defects, including {001} planar defects in C and {001}, {111}, and {113} planar defects in Si and Ge. Among the {001} planar defects, the Humble defect, known for some time to occur in Ge, has recently also been observed in Si-Ge alloys, but the details of its electronic structure remain poorly understood. Here, in this work, we perform first-principles density-functional calculations to study Humble defects in both Ge and Ge 0.8⁢ Si 0.2 . We also measure the Si L 2,3 -edge electron energy-loss spectra both at the defect and in a bulk-like region far from the defect and compare with theoretical calculations on corresponding Si sites in our first-principles calculations. We find that inclusion of core-hole effects in the theory is essential for reproducing the observed L 2,3 edge spectra, and that once they are included, the results provide a set of fingerprints for different types of local atomic bonding environments in Ge 0.8⁢ Si 0.2 . Our first-principles calculations reveal that the Humble defects have a tendency to enlarge the electronic band gap, which may have potential uses in band engineering. The use of hybrid functionals for an improved description of the band gap in these systems is also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Crystallizing Kagome Artificial Spin Ice

Artificial spin ices are engineered arrays of dipolarly coupled nanobar magnets. They enable direct investigations of fascinating collective phenomena from their diverse microstates. However, experimental access to ground states in the geometrically frustrated systems has proven difficult, limiting studies and applications of novel properties and functionalities from the low energy states. In this work, we introduce a convenient approach to control the competing diploar interactions between the neighboring nanomagnets, allowing us to tailor the vertex degeneracy of the ground states. We achieve this by tuning the length of selected nanobar magnets in the spin ice lattice. We demonstrate the effectiveness of our method by realizing multiple low energy microstates in a kagome artificial spin ice, particularly the hardly accessible long range ordered ground state—the spin crystal state. Our strategy can be directly applied to other artificial spin systems to achieve exotic phases and explore new emergent collective behaviors.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Monolayer 2D semiconducting tellurides for high-mobility electronics

Discovery and design of two-dimensional (2D) materials with suitable band gaps and high carrier mobility are of vital importance for the photonics, optoelectronics, and high-speed electronics. In this work, based on first principles calculations using density functional theory with Perdew-Burke-Ernzerhof and Heyd-Scuseria-Ernzerhoffunctionals, we introduce a family of monolayer isostructural semiconducting tellurides MNTe 4 , with M={Ti,Zr,Hf} and N={Si,Ge}. We find that these compounds have been identified to possess direct band gaps from 1.0 to 1.31 eV, which are well suited for photonics and optoelectronics applications. Additionally, anisotropic in-plane transport behavior is observed, and small electron and hole (0.11–0.15m e ) effective masses are identified along the dominant transport direction. Ultrahigh carrier mobility is predicted for this family of 2D compounds, which host great promise for potential applications in high-speed electronic devices. Furthermore, detailed analysis of electronic structures reveals the origins of the promising properties of this unique class of 2D telluride materials.

2-dimensional systems↗
DOE OSTI2021

Point Adversarial Self-Mining: A Simple Method for Facial Expression Recognition

In this article, we propose a simple yet effective approach, called point adversarial self mining (PASM), to improve the recognition accuracy in facial expression recognition (FER). Unlike previous works focusing on designing specific architectures or loss functions to solve this problem, PASM boosts the network capability by simulating human learning processes: providing updated learning materials and guidance from more capable teachers. Specifically, to generate new learning materials, PASM leverages a point adversarial attack method and a trained teacher network to locate the most informative position related to the target task, generating harder learning samples to refine the network. The searched position is highly adaptive since it considers both the statistical information of each sample and the teacher network capability. Other than being provided new learning materials, the student network also receives guidance from the teacher network. After the student network finishes training, the student network changes its role and acts as a teacher, generating new learning materials and providing stronger guidance to train a better student network. Here, the adaptive learning materials generation and teacher/student update can be conducted more than one time, improving the network capability iteratively. Extensive experimental results validate the efficacy of our method over the existing state of the arts for FER.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Unveiling the Mechanism of Photodamage to Sphingolipid Molecules via Laser Flash Photolysis and EPR

Abstract Sphingolipids are involved in the maintenance of the skin barrier function and regulate cellular processes of keratinocytes. The work reported here is designed to uncover details of the mechanism of damage to such lipids by UV radiation. Our approach employs laser flash photolysis and electron paramagnetic resonance (EPR) spectrometry to explore the mechanism of the decay reactions, and to determine the associated kinetic parameters. To interpret our experiments, we computed both excitation energies and EPR parameters of radicals formed during photolysis. Employing the spin‐trap EPR method confirmed the formation of both carbon‐ and nitrogen‐centered radicals. Thus, we can conclude that the photodecomposition of sphingolipids and their analogues proceeds by Norrish type I reactions with the formation of both nitrogen‐centered and alkyl radicals.

Biochemistry & Molecular Biology↗
DOE OSTI2024

Quantum control of exciton wave functions in 2D semiconductors

Excitons—bound electron-hole pairs—play a central role in light-matter interaction phenomena and are crucial for wide-ranging applications from light harvesting and generation to quantum information processing. A long-standing challenge in solid-state optics has been to achieve precise and scalable control over excitonic motion. We present a technique using nanostructured gate electrodes to create tailored potential landscapes for excitons in 2D semiconductors, enabling in situ wave function shaping at the nanoscale. Our approach forms electrostatic traps for excitons in various geometries, such as quantum dots, rings, and arrays thereof. We show independent spectral tuning of spatially separated quantum dots, achieving degeneracy despite material disorder. Owing to the strong light-matter coupling of excitons in 2D semiconductors, we observe unambiguous signatures of confined exciton wave functions in optical reflection and photoluminescence measurements. This work unlocks possibilities for engineering exciton dynamics and interactions at the nanometer scale, with implications for optoelectronic devices, topological photonics, and quantum nonlinear optics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Defining the Expression, Production, and Signaling Roles of Specialized Metabolites during Bacillus subtilis Differentiation

Bacterial specialized (or secondary) metabolites are structurally diverse molecules that mediate intra- and interspecies interactions by altering growth and cellular physiology and differentiation. Bacillus subtilis, a Gram-positive model bacterium commonly used to study biofilm formation and sporulation, has the capacity to produce more than 10 specialized metabolites. Some of these B. subtilis specialized metabolites have been investigated for their role in facilitating cellular differentiation, but only rarely has the behavior of multiple metabolites been simultaneously investigated. In this study, we explored the interconnectivity of differentiation (biofilm and sporulation) and specialized metabolites in B. subtilis. Specifically, we interrogated how development influences specialized metabolites and vice versa. Using the sporulation-inducing medium DSM, we found that the majority of the specialized metabolites examined are expressed and produced during biofilm formation and sporulation. Additionally, we found that six of these metabolites (surfactin, ComX, bacillibactin, bacilysin, subtilosin A, and plipastatin) are necessary signaling molecules for proper progression of B. subtilis differentiation. This study further supports the growing body of work demonstrating that specialized metabolites have essential physiological functions as cell-cell communication signals in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold

Exoribonuclease-resistant RNAs (xrRNAs) are discrete elements that block the progression of 5' to 3' exoribonucleases using specifically folded RNA structures. A recently discovered class of xrRNA is widespread in several genera of plant-infecting viruses, within both noncoding and protein-coding subgenomic RNAs. The structure of one such xrRNA from a dianthovirus revealed three-dimensional details of the resistant fold but did not answer all questions regarding the conservation and diversity of this xrRNA class. Here, we present the crystal structure of a representative polerovirus xrRNA that contains sequence elements that diverge from the previously solved structure. This new structure rationalizes previously unexplained sequence conservation patterns and shows interactions not present in the first structure. Together, the structures of these xrRNAs from dianthovirus and polerovirus genera support the idea that these plant virus xrRNAs fold through a defined pathway that includes a programmed intermediate conformation. This work deepens our knowledge of the structure-function relationship of xrRNAs and shows how evolution can craft similar RNA folds from divergent sequences.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Bayesian Monte Carlo Evaluation Framework for Imperfect Nuclear Data

Bayesian evaluation of resolved resonance region (RRR) nuclear data has historically been carried out using the generalized least squares (GLS) formalism, as implemented in, e.g., SAMMY. We have recently developed a prototype of Bayesian Monte Carlo (BMC) evaluation framework, implemented using a Markov Chain Monte Carlo (MCMC) method with a Metropolis-Hastings (MH) acceptance criterion. This was done in order to remove the approximations underlying the conventional GLS evaluations, namely, the linear approximation, and the approximation that all probability density functions (PDFs) are of the normal kind. Recent works by others have used similar stochastic approaches to quantify cross section uncertainties from ENDF evaluated co-variances, and/or, from integral benchmark data, but those have not been conceived as an evaluation framework like the one presented here.

97 MATHEMATICS AND COMPUTING↗