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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 955 records · Page 53
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The physical origin of dark energy constraints from rubin observatory and CMB-S4 lensing tomography

ABSTRACT We seek to clarify the origin of constraints on the dark energy equation of state parameter from CMB lensing tomography, that is the combination of galaxy clustering and the cross-correlation of galaxies with CMB lensing in a number of redshift bins. We focus on the analytic understanding of the origin of the constraints. Dark energy information in these data arises from the influence of three primary relationships: distance as a function of redshift (geometry), the amplitude of the power spectrum as a function of redshift (growth), and the power spectrum as a function of wavenumber (shape). We find that the effects from geometry and growth play a significant role and partially cancel each other out, while the shape effect is unimportant. We also show that Dark Energy Task Force figure of merit forecasts from the combination of LSST galaxies and CMB-S4 lensing are comparable to the forecasts from cosmic shear in the absence of the CMB lensing map, thus providing an important independent check. Compared to the forecasts with the LSST galaxies alone, combining CMB lensing and LSST clustering information increases the FoM by roughly a factor of 3–4 in the optimistic scenario where systematics are fully under control. We caution that achieving these forecasts will likely require a full analysis of higher-order biasing, photometric redshift uncertainties, and stringent control of other systematic limitations, which are outside the scope of this work, whose primary purpose is to elucidate the physical origin of the constraints.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

An intergalactic medium temperature from a giant radio galaxy

ABSTRACT The warm–hot intergalactic medium (warm–hot IGM, or WHIM) pervades the filaments of the Cosmic Web and harbours half of the Universe’s baryons. The WHIM’s thermodynamic properties are notoriously hard to measure. Here we estimate a galaxy group–WHIM boundary temperature using a new method. In particular, we use a radio image of the giant radio galaxy (giant RG, or GRG) created by NGC 6185, a massive nearby spiral. We analyse this extraordinary object with a Bayesian 3D lobe model and deduce an equipartition pressure Peq = 6 × 10−16 Pa – among the lowest found in RGs yet. Using an X-ray-based statistical conversion for Fanaroff–Riley II RGs, we find a true lobe pressure $P = 1.5\substack{+1.7\\ -0.4}\times 10^{-15}\ \mathrm{Pa}$. Cosmic Web reconstructions, group catalogues, and MHD simulations furthermore imply an Mpc–scale IGM density $1 + \delta _\mathrm{IGM} = 40\substack{+30\\ -10}$. The buoyantly rising lobes are crushed by the IGM at their inner side, where an approximate balance between IGM and lobe pressure occurs: PIGM ≈ P. The ideal gas law then suggests an IGM temperature $T_\mathrm{IGM} = 11\substack{+12\\-5} \times 10^6\ \mathrm{K}$, or $k_\mathrm{B}T_\mathrm{IGM} = 0.9\substack{+1.0\\-0.4}\ \mathrm{keV}$, at the virial radius – consistent with X-ray-derived temperatures of similarly massive groups. Interestingly, the method is not performing at its limit: in principle, estimates TIGM ∼ 4 × 106 K are already possible – rivalling the lowest X-ray measurements available. The technique’s future scope extends from galaxy group outskirts to the WHIM. In conclusion, we demonstrate that observations of GRGs in Cosmic Web filaments are finally sensitive enough to probe the thermodynamics of galaxy groups and beyond.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

The Human Phenotype Ontology in 2021

The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange. The HPO has grown steadily since its inception due to considerable contributions from clinical experts and researchers from a diverse range of disciplines. Here, we present recent major extensions of the HPO for neurology, nephrology, immunology, pulmonology, newborn screening, and other areas. For example, the seizure subontology now reflects the International League Against Epilepsy (ILAE) guidelines and these enhancements have already shown clinical validity. We present new efforts to harmonize computational definitions of phenotypic abnormalities across the HPO and multiple phenotype ontologies used for animal models of disease. These efforts will benefit software such as Exomiser by improving the accuracy and scope of cross-species phenotype matching. The computational modeling strategy used by the HPO to define disease entities and phenotypic features and distinguish between them is explained in detail. We also report on recent efforts to translate the HPO into indigenous languages. Finally, we summarize recent advances in the use of HPO in electronic health record systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami

Wireframe DNA origami assemblies can now be programmed automatically from the top-down using simple wireframe target geometries, or meshes, in 2D and 3D, using either rigid, six-helix bundle (6HB) or more compliant, two-helix bundle (DX) edges. While these assemblies have numerous applications in nanoscale materials fabrication due to their nanoscale spatial addressability and high degree of customization, no easy-to-use graphical user interface software yet exists to deploy these algorithmic approaches within a single, standalone interface. Further, top-down sequence design of 3D DX-based objects previously enabled by DAEDALUS was limited to discrete edge lengths and uniform vertex angles, limiting the scope of objects that can be designed. Here, we introduce the open-source software package ATHENA with a graphical user interface that automatically renders single-stranded DNA scaffold routing and staple strand sequences for any target wireframe DNA origami using DX or 6HB edges, including irregular, asymmetric DX-based polyhedra with variable edge lengths and vertices demonstrated experimentally, which significantly expands the set of possible 3D DNA-based assemblies that can be designed. ATHENA also enables external editing of sequences using caDNAno, demonstrated using asymmetric nanoscale positioning of gold nanoparticles, as well as providing atomic-level models for molecular dynamics, coarse-grained dynamics with oxDNA, and other computational chemistry simulation approaches.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ADAR activation by inducing a syn conformation at guanosine adjacent to an editing site

Abstract ADARs (adenosine deaminases acting on RNA) can be directed to sites in the transcriptome by complementary guide strands allowing for the correction of disease-causing mutations at the RNA level. However, ADARs show bias against editing adenosines with a guanosine 5′ nearest neighbor (5′-GA sites), limiting the scope of this approach. Earlier studies suggested this effect arises from a clash in the RNA minor groove involving the 2-amino group of the guanosine adjacent to an editing site. Here we show that nucleosides capable of pairing with guanosine in a syn conformation enhance editing for 5′-GA sites. We describe the crystal structure of a fragment of human ADAR2 bound to RNA bearing a G:G pair adjacent to an editing site. The two guanosines form a Gsyn:Ganti pair solving the steric problem by flipping the 2-amino group of the guanosine adjacent to the editing site into the major groove. Also, duplexes with 2′-deoxyadenosine and 3-deaza-2′-deoxyadenosine displayed increased editing efficiency, suggesting the formation of a Gsyn:AH+anti pair. This was supported by X-ray crystallography of an ADAR complex with RNA bearing a G:3-deaza dA pair. This study shows how non-Watson–Crick pairing in duplex RNA can facilitate ADAR editing enabling the design of next generation guide strands for therapeutic RNA editing.

Doherty, Erin E.↗
DOE OSTI2025

The Natural Products Magnetic Resonance Database (NP-MRD) for 2025

The Natural Products Magnetic Resonance Database or NP-MRD (https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction and retrieval of nuclear magnetic resonance (NMR) data on natural products. The NP-MRD was initially established to support compound de-replication and data dissemination for the natural products community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics and nutrition science fields. Indeed, since its launch in 2021, the NP-MRD has expanded enormously in size, scope and popularity. The current version of NP-MRD now contains nearly 7X more compounds (281,859 vs. 40,908) and 7X more NMR spectra (5.1 million vs. 817,000) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11,000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from a 165 spectra per year to more than 10,000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20,000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, important improvements to the visualization and display of NMR spectra, notable updates to the database’s spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD’s database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned.

Artifical Intelligence↗
DOE OSTI2024

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code development continues in line with the Galaxy Project roadmap, with improvements to job scheduling and the user interface. Environmental impact assessment is also helping engage users and developers, reminding them of their role in sustainability, by displaying estimated CO 2 emissions generated by each Galaxy job.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Metal-organic frameworks as effective sensors and scavengers for toxic environmental pollutants

Abstract Metal-organic frameworks (MOFs) constructed from a rich library of organic struts and metal ions/clusters represent promising candidates for a wide range of applications. The unique structure, porous nature, easy tunability and processability of these materials make them an outstanding class of materials for tackling serious global problems relating to energy and environment. Among them, environmental pollution is one aspect that has increased at an alarming rate in the past decade or so. With rapid urbanization and industrialization, toxic environmental pollutants are constantly released and accumulated leading to serious contamination in water bodies and thereby having adverse effects on human health. Recent studies have shown that many toxic pollutants, as listed by the World Health Organization and the US Environmental Protection Agency, can be selectively detected, captured, sequestered and removed by MOFs from air and aquatic systems. Most of these sensing/capture processes in MOFs are quantifiable and effective for even a trace amount of the targeted chemical species. The functional sites (ligands and metals) play a critical role in such recognition processes and offer an extensive scope of structural tunability for guest (pollutants, toxic entities) recognition. Whereas on the one hand, the underlying mechanisms governing such sensing and capture are important, it is also crucial to identify MOFs that are best suited for commercial applications for the future. In this review article, we provide an overview of the most recent progress in the sensing, capture and removal of various common toxic pollutants, including neutral and ionic, inorganic and organic species, with brief discussions on the mechanism and efficacy of selected MOFs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Complementing model species with model clades

Abstract Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a “model clade.” These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a “model clade” and make suggestions for building global networks to support future studies in the model order Brassicales.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Viral delivery of recombinases activates heritable genetic switches in plants

Viral vectors provide an increasingly versatile platform for transformation-free reagent delivery to plants. RNA viral vectors can be used to induce gene silencing, overexpress proteins, or introduce gene editing reagents; however, they are often constrained by carrying capacity or restricted tropism in germline cells. Site-specific recombinases that catalyze precise genetic rearrangements are powerful tools for genome engineering that vary in size and, potentially, efficacy in plants. In this work, we show that viral vectors based on tobacco rattle virus (TRV) deliver and stably express four recombinases ranging in size from ~0.6kb to ~1.5kb and achieve simultaneous marker removal and reporter activation through targeted excision in transgenic Nicotiana benthamiana lines. TRV vectors with Cre, FLP, CinH, and Integrase13 efficiently mediated recombination in infected somatic tissue and led to heritable modifications at high frequency. Here, an excision-activated Ruby reporter enabled simple and high-resolution tracing of infected cell lineages without the need for molecular genotyping. Together, our experiments broaden the scope of viral recombinase delivery and offer insights into infection dynamics that may be useful in developing future viral vectors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The Belle II Physics Book

The Belle II Theory Interface Platform (B2TiP) was created as a physics prospects working group of the Belle II collaboration in June 2014. It offered a platform where theorists and experimentalists could work together to elucidate the potential impacts of the Belle II program, which includes a wide scope of physics topics: B physics, charm, τ, quarkonium physics, electroweak precision measurements, and dark sector searches.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Cooperative effects in thin dielectric layers: Long-range Dicke superradiance

The realization and control of collective quantum effects so far have predominantly focused on cold atomic ensembles. Quantum photonic platforms, with their engineered Green's functions and integration capability of advanced solid-state quantum emitters, provide opportunities to explore regimes of light-matter interaction beyond the scope of atomic systems. In this work, we demonstrate that embedding quantum emitters within a thin dielectric layer fundamentally alters their collective radiative behavior. The optical modes in the dielectric layer mediate long-range dipole-dipole interactions between emitters, enabling both total and directional superradiance between emitters separated by several wavelengths. Crucially, this mechanism supports Dicke superradiance even in parameter regimes where standard settings fail to support an interaction, unveiling a dimensionality-driven enhancement of cooperative effects. By bridging many-body quantum optics and photonic engineering, our work reveals a distinct interplay between surrounding dimensionality and collective quantum dynamics. Experimental realization of these predictions, readily achievable in solid-state quantum optics platforms, paves the way for scalable, directional quantum light sources and frontiers in many-body quantum optics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Baryon-baryon, meson-meson, and meson-baryon interactions in nonrelativistic QCD

Van der Waals potentials describing interactions between color-singlet mesons and/or baryons vanish at leading order in potential nonrelativistic quantum chromodynamics (pNRQCD). This result and constraints from Gauss’s law are used to prove that weakly coupled pNRQCD van der Waals potentials in generic non-Abelian gauge theories with only heavy quarks are too weak to form bound states whose color state is a product of color singlets. Quantum Monte Carlo calculations of four, five, and six quarks with equal masses provide numerical evidence that exotic color configurations are higher energy than products of color-singlet hadrons, suggesting that equal-mass fully heavy tetraquark, pentaquark, and hexaquark bound states do not exist at next-to-leading order in pNRQCD and at all orders in QCD-like theories in which all quark masses are asymptotically large. Mechanisms for generating hadron-hadron bound states are identified, which necessarily involve large quark-mass hierarchies, relativistic effects arising from the presence of sufficiently light quarks, or nonperturbative effects outside the scope of weakly coupled pNRQCD.

Effective field theory↗
DOE OSTI2025

New Constraints on Cosmic Ray-Boosted Dark Matter from the LUX-ZEPLIN Experiment

While dual-phase xenon time projection chambers have driven the sensitivity toward weakly interacting massive particles at the GeV/c 2 to TeV/c 2 mass scale, the scope for sub-GeV/c 2 dark matter particles is hindered by a limited nuclear recoil energy detection threshold. One approach to probe for lighter candidates is to consider cases where they have been boosted by collisions with cosmic rays in the Milky Way, such that the additional kinetic energy lifts their induced signatures above the nominal threshold. In this Letter, we report first results of a search for cosmic ray-boosted dark matter (CRDM) with a combined 4.2 metric ton/yr exposure from the LUX-ZEPLIN experiment. We observe no excess above the expected backgrounds and establish world-leading constraints on the spin-independent CRDM-nucleon cross section as small as 3.9×10 −33 cm 2 at 90% confidence level for sub-GeV/c 2 masses.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Performance analysis of superconductor-constriction-superconductor transmon qubits

Here, this work presents a computational analysis of a superconducting transmon qubit design, in which the superconductor-insulator-superconductor (SIS) Josephson junction is replaced by a coplanar, superconductor-constriction-superconductor (ScS) nanobridge junction. Within the scope of Ginzburg-Landau theory, we find that the nanobridge ScS transmon has an improved charge dispersion compared to the SIS transmon, with a tradeoff of smaller anharmonicity. These calculations provide a framework for estimating the superconductor material properties and junction dimensions compatible with gigahertz frequency ScS transmon operation.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Orbital design of flat bands in non-line-graph lattices via line-graph wave functions

Line-graph (LG) lattices are known for having flat bands (FBs) from the destructive interference of Bloch wave functions encoded in only lattice symmetry. In this work, we develop a generic atomic/molecular orbital design principle for FBs in non-LG lattices. Based on linear combination of atomic orbital theory, we demonstrate that the underlying wave-function symmetry of FBs in a LG lattice can be transformed into the atomic/molecular orbital symmetry in a non-LG lattice. We illustrate such orbital-designed topological FBs in three 2D non-LG, square, trigonal, and hexagonal lattices, where the designed orbitals faithfully reproduce the corresponding lattice symmetries of checkerboard, kagome, and diatomic-kagome lattices, respectively. Interestingly, systematic design of FBs with a high Chern number is also achieved based on the same principle. Fundamentally our theory enriches the FB physics; practically, it significantly expands the scope of FB materials, since most materials have multiple atomic/molecular orbitals at each lattice site, rather than a single s orbital mandated in graph theory and generic lattice models.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Stability of fractional Chern insulators with a non-Landau level continuum limit

The stability of fractional Chern insulators is widely believed to be predicted by the resemblance of their single-particle spectra to Landau levels. Here we investigate the scope of this geometric stability hypothesis by analyzing the stability of a set of fractional Chern insulators that explicitly do not have a Landau level continuum limit. By computing the many-body spectra of Laughlin states in a generalized Hofstadter model, we analyze the relationship between single-particle metrics, such as trace inequality saturation, and many-body metrics, such as the magnitude of the many-body and entanglement gaps. We show numerically that the geometric stability hypothesis holds for Chern bands that are not continuously connected to Landau levels, as well as conventional Chern bands, albeit often requiring larger system sizes to converge for these configurations.

2-dimensional systems↗
DOE OSTI2022

Entanglement and seniority

In quantum mechanics entanglement is the most striking phenomenon which has no counterpart in classical systems. Although, different approaches have already been developed to study correlations in the case of indistinguishable particles, the exploration of the so-called mode entanglement is still in its initial stage in nuclear physics. Study of mode-entanglement in the seniority model, derivation of analytic formulas for the one-body reduced density matrix of states with seniority $ν$ = 0, 1, 2, and $ν$ = 3, and also determination of the particle number dependence of the one-body reduced density matrix for arbitrary seniority. In addition, comparison of the predictions of the seniority model with the results of the shell model to gain insight into the structure and correlations of the ground and lowest yrast states. In the seniority model the analytic results are calculated using the quasi-spin formalism. The numerical shell model calculations are carried out in the standard shell model framework using an inert core. The applied realistic effective interactions are derived earlier using the $G$-matrix formalism. The density matrix renormalization group method is also applied in order to directly calculate the mode entropies. In the seniority model simple analytical expressions are given for the mode entropies. The peculiar behavior of the half-filled shells and the seniority-zero states are revealed. Numerical results are presented for the lightest stable calcium isotopes and for 94 Ru nucleus. For 94 Ru, the seniority model accounts for the 0$g$ 9/2 mode entropies, but seniority mixing is important for certain yrast states. Furthermore, interaction induced quantum fluctuations decrease the occupation of the 0$f$ 5/2 , 1$p$ 3/2 and 1$p$ 1/2 shells, and amount in non-negligible mode entropies on these shells, too, clearly outside the scope of the simple (0$g$ 9/2 ) 4 seniority model. The 0$f$ 7/2 shell-based seniority model is more accurate for the Ca isotopes, but seniority mixing is substantial for some 44 Ca yrast states, too. Mode and one-body entanglement entropies are useful tools to investigate the structure of quantum correlations in nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗