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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 1,045 records · Page 58
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗
DOE OSTI2022

RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Burley, Stephen K.↗
DOE OSTI2020

Herbaspirillum rubrisubalbicans as a Phytopathogenic Model to Study the Immune System of Sorghum bicolor

Herbaspirillum rubrisubalbicans is the causal agent of red stripe disease (RSD) and mottle stripe disease of sorghum and sugarcane, respectively. In all, 63 genotypes of Sorghum bicolor were inoculated with H. rubrisubalbicans, with 59 showing RSD symptoms. Quantitative trait loci (QTL) analysis in a recombinant inbred line (RIL) population identified several QTL associated with variation in resistance to RSD. RNA sequencing analysis identified a number of genes whose transcript levels were differentially regulated during H. rubrisubalbicans infection. Among those genes that responded to H. rubrisubalbicans inoculation were many involved in plant–pathogen interactions such as leucine-rich repeat receptors, mitogen-activated protein kinase 1, calcium-binding proteins, transcriptional factors (ethylene-responsive element binding factor), and callose synthase. Pretreatment of sorghum leaves with the pathogen-associated molecular pattern (PAMP) molecules flg22 and chitooctaose provided protection against subsequent challenge with the pathogen, suggesting that PAMP-triggered immunity plays an important role in the sorghum immunity response. These data present baseline information for the use of the genetically tractable H. rubrisubalbicans–sorghum pathosystem for the study of innate immunity and disease resistance in this important grain and bioenergy crop. Information gained from the use of this system is likely to be informative for other monocots, including those more intractable for experimental study (e.g., sugarcane).

Biochemistry & Molecular Biology↗
DOE OSTI2019

In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria

Over the past decades, crop yields have risen in parallel with increasing use of fossil-fuel derived nitrogen (N) fertilizers, but with concomitant negative impacts on climate and water resources. There is a need for more sustainable agricultural practices, and biological nitrogen fixation (BNF) could be part of the solution. A variety of nitrogen-fixing, epiphytic and endophytic plant growth promoting bacteria (PGPB) are known to stimulate plant growth. However, compared to the rhizobium-legume symbiosis, little mechanistic information is available as to how PGPB affect plant metabolism. Therefore, we investigated the metabolic changes in roots of the model grass species Setaria viridis upon endophytic colonization by Herbaspirillum seropedicae SmR1 (fix + ) or a fix - mutant strain (SmR54), compared to uninoculated roots. Endophytic colonization of the root is highly localized and, hence, analysis of whole root segments dilutes the metabolic signature of those few cells impacted by the bacteria. Therefore, we utilized in situ laser ablation electrospray ionization mass spectrometry (LAESI-MS) to sample only those root segments at or adjacent to the sites of bacterial colonization. We report netabolites involved in purine, zeatin, and riboflavin pathways were significantly more abundant in inoculated plants while metabolites indicative of nitrogen, starch, and sucrose metabolism were reduced in roots inoculated with the fix - strain or uninoculated, presumably due to N limitation. Interestingly, compounds, involved in indole-alkaloid biosynthesis were more abundant in the roots colonized by the fix - strain, perhaps reflecting a plant defense response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

On the Necessity of Adopting Irradiation Protocols Recommended by the Compatibility in Irradiation Research Protocols Expert Roundtable (CIRPER) in Published Research and Why It Matters to Health Physicists

The National Nuclear Security Administration (NNSA) seeks to assist and support all partners in the fields of radiobiology, health physics, radiation physics, and related areas to transition from cesium-137 chloride-based technologies that can potentially be used in an act of terrorism to X-ray technologies. The absence of information on experimental procedures, equipment, and irradiation parameters directly and negatively impacts the reproducibility and translatability of a sizable portion of radiation biology studies. It also discourages researchers from adopting new tools that eliminate the risks of a radiological dispersal device.

Stern, Warren [Brookhaven National Laboratory (BNL↗
DOE OSTI2025

First Evidence of Solar Neutrino Interactions on 13 C

The SNO+ Collaboration reports the first evidence of 8 B solar neutrinos interacting on 13 C nuclei. The charged current interaction proceeds through 13 C +𝜈 𝑒 → 13 N+𝑒 − which is followed, with a 10 minute half life, by 13 N → 13 C +𝑒 + +𝜈 𝑒 . The detection strategy is based on the delayed coincidence between the electron and the positron. Evidence for the charged current signal is presented with a significance of 4.2⁢𝜎. Using the natural abundance of 13 C present in the scintillator, 5.7 metric tons of 13 C over 231 days of data were used in this analysis. The 5.6$^{+3.0}_{−2.3}$ observed events in the data set are consistent with the expectation of 4.7$^{+0.6}_{−1.3}$ events. This result is the second real-time measurement of CC interactions of 8 B neutrinos with nuclei and constitutes the lowest energy observation of neutrino interactions on 13 C generally. This enables the first direct measurement of the CC 𝜈 𝑒 reaction to the ground state of 13 N , yielding an average cross section of (16.1$^{+8.5}_{−6.7}$⁢(stat.)$^{+1.6}_{−2.7}$⁢(syst.))×10 −43 cm 2 over the relevant 8 B solar neutrino energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Effects of chemical disorder and spin-orbit coupling on the electronic-structure and Fermi-surface topology of YbSb-based monopnictides

Here, in this work, we study the influence of disorder on the electronic structure of YbSb—a rare-earth monopnictide featuring a simple rocksalt (B1) crystal structure and a well-defined Fermi-surface topology—by employing first-principles density-functional theory. We focus on chemical disorder introduced through Te and Al doping, selected based on their thermodynamic stability in alloyed configurations, to understand how such perturbations modify the electronic states of YbSb. Our results indicate that Te doping predominantly introduces electronlike states at the 𝑋 and 𝐿 points, while Al doping leads to a suppression of holelike states at Γ, effectively driving the system from a semimetallic state to one characterized by very narrow-gap behavior at Γ. This modulation of the Fermi surface, particularly the reduction of central hole pockets at Γ, plays a central role in altering interpocket scattering—a mechanism critical for tuning quantum transport properties, including superconductivity. This disorder-driven modulation of the Fermi surface, particularly the suppression of central hole pockets at Γ, controls interpocket scattering, which is essential for optimizing quantum transport properties, including superconductivity. Our results show that disorder can be effectively used for engineering band topology, thereby tuning quantum related response through a tailored electronic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Beta-Decay Half-Lives beyond 54 Ca: A Systematic Survey of Decay Properties Approaching the Neutron Dripline

In an experiment performed at the Facility for Rare Isotope Beams (FRIB) using the FRIB Decay Station initiator, 15 new half-lives of isotopes near 54 Ca were measured. A new method of extracting lifetimes from experimental data, taking into account the unknown 𝛽-delayed neutron emission branches of very neutron-rich nuclei, was developed to enable systematic uncertainty analysis. The experiment observed a dramatic change in the half-life systematics for the isotopes with neutron number 𝑁 = 34. Beyond 𝑁 = 34, the decline of nuclear lifetime is much slower, leading to longer than anticipated lifetimes for near-dripline nuclei. State-of-the-art shell-model calculations can explain the experimental results, revealing the imprint of shell effects and the need for modification of single-particle neutron states. In conclusion, the results from a newly developed quasiparticle random phase approximation model with potential for making global predictions were also tested against the experimental results and good agreement was found.

Physics - Nuclear physics and radiation physics↗
DOE OSTI2025

Universal Effective Charges in the 𝑠⁢𝑑 and 𝑓⁡𝑝 Shells

The 247-keV state in 54 Sc, populated in the 𝛽 decay of 54 Ca, is reported here as a nanosecond isomer with a half-life of 26.0(22) ns. The state is interpreted as the 1 + member of the 𝜋⁢𝑓 7/2 ⊗ 𝜈⁢𝑓 5/2 spin-coupled multiplet, which decays to the 3 + ,𝜋⁢𝑓 7/2 ⊗ 𝜈⁢𝑝 1/2 ground state. The new half-life corresponds to a pure 𝐸⁢2 transition with a strength of 1.93(16) W.u., providing the most precise, unambiguous 𝐵⁡(𝐸⁢2) value in the neutron-rich 𝑓⁡𝑝 region to date for a nucleus with valence protons above 𝑍 = 20. Notably, it is roughly 4 times larger than the 𝐵⁡(𝐸⁢2;1/2 − → 5/2 − ) value in 55 Ca. The results, as compared to semiempirical and ab initio shell-model calculations, indicate (1) a weak 𝑁 = 34 subshell gap relative to 𝑁 = 32, (2) a large 𝐸⁢2 enhancement in Sc as compared to Ca due to 1⁢𝑝 − 1⁢ℎ proton excitations across 𝑍 = 28, and (3) empirical effective proton and neutron charges 𝑒 𝜋 = 1.30⁢(8)⁢𝑒 and 𝑒 𝜈 = 0.452⁢(7)⁢𝑒, respectively, that are in contrast to reports of 𝑒 𝜋 ≈1.1–1.15⁢𝑒 and 𝑒 𝜈 ≈ 0.6–0.8⁢𝑒 for 𝑓⁡𝑝-shell nuclei near 𝑁 = 𝑍. Here, we demonstrate that these reports are erroneous and that, in fact, a universal set of effective charges can be used across the 𝑠⁢𝑑 and 𝑓⁡𝑝 shells.

Beta decay↗
DOE OSTI2026

Strain-Driven Evolution of Structural and Carrier Recombination Dynamics in Germanium

Strain engineering in group-IV semiconductors, in particular germanium (Ge), offers a promising route for advancing next-generation optoelectronic device performance. High minority carrier lifetime serves as a direct indicator of superior material quality and device efficiency. Several factors govern the minority carrier lifetime in both strained Ge and strained GeSn, such as strain level, epilayer thickness, defects, surface roughness, and Sn alloying. In this study, the impact of biaxial strain on effective minority carrier lifetimes of tensile-strained Ge (0% ..epsilon..-Ge/Al?As, 0.78% ..epsilon..-Ge/In0.115?Ga0.885?As, and 0.93% ..epsilon..-Ge/In0.16?Ga0.84?As) and compressively strained GeSn (-0.53% c-Ge0.97?Sn0.03/Al?As) epilayers, grown by molecular beam epitaxy, was experimentally investigated via the microwave-reflection photoconductive decay (..mu..-PCD) technique as a simultaneous function of thickness and strain. The structural and strain-relaxation properties were analyzed by high-resolution x-ray diffraction and Raman spectroscopy, while surface morphology analysis using atomic force microscopy provided insights into the surface roughness of strained Ge-based epilayers. Defect characterization by cross-section transmission electron microscopy revealed superior crystalline quality of ..epsilon..-Ge in one epilayer, while twin boundary formation was observed in the other. We investigated the carrier recombination dynamics in epitaxially strained Ge by extracting the bulk recombination lifetime and surface recombination velocity using the thickness-dependent minority carrier lifetime. High effective minority carrier lifetimes of approximately 60-340 ns were achieved at high strain levels with minimal dependence on the thickness of the strained Ge-based epilayers by means of the ..mu..-PCD technique. Minority carrier lifetimes in Ge-based epilayers exhibit a quadratic dependence on the biaxial strain, ranging from -0.88% (compressive) to +1.6% (tensile). The analysis of the carrier recombination dynamics in strained Ge-based heterostructures offers a pathway to designing group-IV based optoelectronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Correlated purification for restoring 𝑁-representability in quantum simulation

Experimentally measured reduced density matrices (RDMs) often violate constraints that ensure they represent N-electron states—known as N-representability conditions—because of statistical and hardware noise. In this work, we present a correlated purification framework based on semidefinite programming to restore the accuracy of a noisy, unphysical two-electron RDM (2-RDM). The method performs a bi-objective optimization that minimizes both the many-electron energy and the nuclear norm of the correction to the measured 2-RDM. The nuclear norm, often employed in matrix completion, promotes low-rank corrections, while the energy term acts as a regularization term that can improve the purity of the ground state. While the method is particularly effective for ground states, it can also be applied to excited and nonstationary states by decreasing the weight of the energy relative to the error norm. In an application to fermionic shadow tomography of large hydrogen chains, correlated purification yields substantial reductions in both energy and 2-RDM error, achieving chemical accuracy across dissociation curves. This framework provides a robust strategy for tomography in many-body quantum simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

X-ray-line coincidence photopumping in a potassium-chlorine mixed plasma

Exploiting the multiple long pulse capability and suite of x-ray diagnostics of the Orion laser, we have set out to explore line coincidence photopuming—the enhancement in population of an atomic level brought on by resonant absorption of x rays from a different emitting ion. Unlike previous work, the two ions are in the same plasma and so the experiment is an x-ray analog of the well-known Bowen resonance fluorescence mechanism that operates in astrophysical situations in the optical region. Herein, our measurements have shown enhanced fluorescence in a chlorine plasma, attributable to line coincident photopumping from co-mixed potassium ions. To detect this relatively low signal-to-noise phenomenon, the data from multiple shots are combined, and the statistical method of bootstrapping is used to assign a confidence value to the measured enhancement, resulting in an estimate of the enhancement of 39 ± 18 16 % compared to the null case, where no pumping occurs. The experimental results have been compared to coupled radiation-transport and radiation hydrodynamics simulations using the CRETIN code together with the NYM radiation hydrodynamics model and agreement has been found, with the simulations also predicting modest enhancement.

74 ATOMIC AND MOLECULAR PHYSICS↗