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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 1,351 records · Page 75
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Tertiary folds of the SL5 RNA from the 5 ' proximal region of SARS-CoV-2 and related coronaviruses

Coronavirus genomes sequester their start codons within stem-loop 5 (SL5), a structured, 5' genomic RNA element. In most alpha- and betacoronaviruses, the secondary structure of SL5 is predicted to contain a four-way junction of helical stems, some of which are capped with UUYYGU hexaloops. Here, using cryogenic electron microscopy (cryo-EM) and computational modeling with biochemically determined secondary structures, we present three-dimensional structures of SL5 from six coronaviruses. The SL5 domain of betacoronavirus severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2), resolved at 4.7 Å resolution, exhibits a T-shaped structure, with its UUYYGU hexaloops at opposing ends of a coaxial stack, the T’s “arms.” Further analysis of SL5 domains from SARS-CoV-1 and MERS (7.1 and 6.4 to 6.9 Å resolution, respectively) indicate that the junction geometry and inter-hexaloop distances are conserved features across these human-infecting betacoronaviruses. The MERS SL5 domain displays an additional tertiary interaction, which is also observed in the non-human-infecting betacoronavirus BtCoV-HKU5 (5.9 to 8.0 Å resolution). SL5s from human-infecting alphacoronaviruses, HCoV-229E and HCoV-NL63 (6.5 and 8.4 to 9.0 Å resolution, respectively), exhibit the same coaxial stacks, including the UUYYGU-capped arms, but with a phylogenetically distinct crossing angle, an X-shape. As such, all SL5 domains studied herein fold into stable tertiary structures with cross-genus similarities and notable differences, with implications for potential protein-binding modes and therapeutic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

High power density soft x-ray GaAs photodiodes with tailored spectral response

GaAs photodiode arrays have been designed for non-destructive monitoring of x-ray beam position in soft coherent beamline front ends in synchrotron light sources. A shallow p-on-n junction was employed to reduce the device photocurrent density to optimize the operation with beam power densities up to 20 W mm -2 , mainly coming from hard x-rays. With this approach, the photocurrent is primarily defined by the excess carriers generated by low-energy x-ray photons absorbed near the detector surface. The p–n junction structures were grown by molecular beam epitaxy and processed into 64-element linear photodiode arrays. The devices were characterized first in the visible range with a high-power Ar-ion laser and then tested in the soft and hard x-ray regions up to 10 keV at two beamlines of the National Synchrotron Light Source II. The responsivity was measured to be 0.16 A W -1 at 0.7 keV and 0.05 A W -1 at 6 keV in agreement with modeling. At higher x-ray energies the measured responsivity was lower than predicted in the framework of the carrier diffusion model; a possible explanation is discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Beyond the Anderson rule: importance of interfacial dipole and hybridization in van der Waals heterostructures

Vertical stacking of two-dimensional materials with weak van der Waals (vdW) interactions has laid the ground for breakthroughs in physics as well as in technological applications. Although vdW interactions dominate interlayer binding, interlayer electronic coupling may not be negligible and can lead to properties beyond the superposition of constituent monolayers. Here, studying heterobilayers of transition-metal dichalcogenides (MQ 2 ; M = Mo, Ni, Pt; Q = S, Se) by means of density functional theory calculations, we show two mechanisms that influence the band gaps of vdW heterostructures beyond the Anderson rule: (1) interfacial hybridization (mainly involving out-of-plane states, such as chalcogen p z -states), which leads to an upshift in the valence band maxima and accordingly a decrease in the band gap. (2) Formation of an interfacial electric dipole, resulting in an effective gap increase in type-II junctions. While the former is material specific, depending on the proximity of p z -states to each other and the valence band maxima, the latter can be generally described using a model based on the charge density decay outside the monolayers and the pristine band edge positions with respect to the vacuum level, irrespective of junction type.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Enhanced superconducting qubit performance through ammonium fluoride etch

The performance of superconducting qubits is often limited by dissipation and two-level systems (TLS) losses. The dominant sources of these losses are believed to originate from amorphous materials and defects at interfaces and surfaces, likely as a result of fabrication processes or ambient exposure. Here, we explore a novel wet chemical surface treatment at the Josephson junction-substrate and the substrate-air interfaces by replacing a buffered oxide etch (BOE) cleaning process with one that uses hydrofluoric acid followed by aqueous ammonium fluoride. We show that the ammonium fluoride etch process results in a statistically significant improvement in median $\text{T}_1$ by $\sim22\%$ (p = 0.002), and a reduction in the number of strongly-coupled TLS in the tunable frequency range. Microwave resonator measurements on samples treated with the ammonium fluoride etch after niobium deposition and etching also show $\sim33\%$ lower TLS-induced loss tangent compared to the BOE treated samples. As the chemical treatment primarily modifies the Josephson junction-substrate interface and substrate-air interface, we perform targeted chemical and structural characterizations to examine materials differences at these interfaces and identify multiple microscopic changes that could contribute to decreased TLS losses.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Chromoanagenesis in the asy1 meiotic mutant of Arabidopsis

Chromoanagenesis is a catastrophic event that involves localized chromosomal shattering and reorganization. In this study, we report a case of chromoanagenesis resulting from defective meiosis in the MEIOTIC ASYNAPTIC MUTANT 1 (asy1) background in Arabidopsis thaliana. We provide a detailed characterization of the genomic structure of this individual with a severely shattered segment of chromosome 1. We identified 260 novel DNA junctions in the affected region, most of which affect gene sequence on 1 or both sides of the junction. Our results confirm that asy1-related defective meiosis is a potential trigger for chromoanagenesis. This is the first example of chromoanagenesis associated with female meiosis and indicates the potential for genome evolution during oogenesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Crystal structure of a cap-independent translation enhancer RNA

In eukaryotic messenger RNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV 2 ) RNA in complex with our structural chaperone, Fab BL3–6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV 2 tertiary architecture is conserved among these homologs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biomechanical Analysis of Multilevel Posterior Cervical Spinal Fusion Constructs

Study Design: Controlled Laboratory Study Objective: To compare multilevel posterior cervical fusion (PCF) constructs stopping at C7, T1, and T2 under cyclic load to determine the range of motion (ROM) between the lowest instrumented level and lowest instrumented-adjacent level (LIV-1). Summary of Background Data: PCF is a mainstay of treatment for various cervical spine conditions. The transition between the flexible cervical spine and rigid thoracic spine can lead to construct failure at the cervicothoracic junction. There is little evidence to determine the most appropriate level at which to stop a multilevel PCF. Methods: Fifteen human cadaveric cervicothoracic spines were randomly assigned to 1 of 3 treatment groups: PCF stopping at C7, T1, or T2. Specimens were tested in their native state, following a simulated PCF, and after cyclic loading. Specimens were loaded in flexion-extension), lateral bending, and axial rotation. Three-dimensional kinematics were recorded to evaluate ROM. Results: The C7 group had greater flexion-extension motion than the T1 and T2 groups following instrumentation (10.17±0.83 degree vs. 2.77±1.66 degree and 1.06±0.55 degree, P <0.001), and after cyclic loading (10.42±2.30 degree vs. 2.47±0.64 degree and 1.99±1.23 degree, P <0.001). There was no significant difference between the T1 and T2 groups. The C7 group had greater lateral bending ROM than both thoracic groups after instrumentation (8.81±3.44 degree vs. 3.51±2.52 degree, P =0.013 and 1.99±1.99 degree, P =0.003) and after cyclic loading. The C7 group had greater axial rotation motion than the thoracic groups (4.46±2.27 degree vs. 1.26±0.69 degree, P =0.010; and 0.73±0.74 degree, P =0.003) following cyclic loading. Conclusion: Motion at the cervicothoracic junction is significantly greater when a multilevel PCF stops at C7 rather than T1 or T2. This is likely attributable to the transition from a flexible cervical spine to a rigid thoracic spine. Although this does not account for in vivo fusion, surgeons should consider extending multilevel PCF constructs to T1 when feasible. Level of Evidence: Not applicable.

Neurosciences & Neurology↗
DOE OSTI2026

Josephson dynamics in two-dimensional ring-shaped condensates

We investigate Josephson transport in a fully closed, two-dimensional superfluid circuit formed by a ring-shaped 87 Rb Bose-Einstein condensate that contains two optical barriers acting as movable weak links. Translating these barriers at controlled speeds imposes a steady bias current, enabling direct mapping of the current-chemical-potential (𝐼−Δ⁢𝜇) characteristics. For narrow junctions (𝑤 ≈ 1µ⁢m), the circuit exhibits a pronounced dc branch that terminates at a critical current 𝐼 𝑐 = 9⁢(1) × 10 3 s −1 ; above this threshold, the system switches to an ac, resistive regime. Classical-field simulations that include the moving barriers quantitatively reproduce both the nonlinear 𝐼−Δ⁢𝜇 curve and the measured 𝐼 𝑐 , validating the underlying microscopic picture. Analysis of the ensuing phase dynamics shows that dissipation is mediated by the nucleation and traversal of vortex-antivortex pairs through the junctions, while the bulk condensate remains globally phase locked—direct evidence of the ring's topological constraint enforcing quantized circulation. These results establish a cold-atom analog of a superconducting quantum interference device in which Josephson dynamics can be resolved at the single-vortex level, providing a versatile platform for atomtronic circuit elements, nonreciprocal Josephson devices, and on-chip Sagnac interferometers for multiaxis rotation sensing.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Understanding baryon stopping at the BNL Relativistic Heavy Ion Collider top energies

The nucleon exhibits a rich internal structure governed by quantum chromodynamics (QCD), where its electric charge arises from valence quarks, while its spin and mass emerge from complex interactions among valence quarks, sea (anti)quarks, and gluons. At the advent of QCD, an alternative hypothesis emerged suggesting, at high energies, the transport of a nucleon's baryon number could be traced by a nonperturbative configuration of gluon fields connecting its three valence quarks, forming a 𝑌-shaped topology known as the gluon junction. Recent measurements by the STAR experiment are compatible with this scenario. In light of these measurements, this study aims to explore the mechanisms of baryon transport in high-energy nuclear collisions using the pythia-8 framework, which incorporates a state-of-the-art hadronization model with advanced color flow (CF) and color reconnection (CR) mechanisms that mimic signatures of a baryon junction. Within this model setup, we investigate (i) the rapidity slope of the net-baryon distributions in photon-included processes (𝛾 + 𝑝) and (ii) baryon over charge transport in the isobaric (Ru + Ru and Zr + Zr) collisions. Our study highlights the importance of the CF and CR mechanisms in pythia-8, which play a crucial role in baryon transport. The results show that the CF and CR schemes significantly affect the isobaric baryon-to-charge ratio, leading to different predictions for baryon stopping and underscoring the need to account for CF and CR effects in comparisons with experimental measurements.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Flux-based three-dimensional electrodynamic modeling approach to superconducting circuits and materials

Modeling the behavior of superconducting electronic circuits containing Josephson junctions is crucial for the design of superconducting information processors and devices. In this paper, we introduce DEC-QED, a computational approach for modeling the electrodynamics of superconducting electronic circuits containing Josephson junctions in arbitrary three-dimensional electromagnetic environments. DEC-QED captures the nonlinear response and induced currents in BCS superconductors and accurately captures phenomena such as the Meissner effect, flux quantization, and Josephson effects. Using a spatial coarse-graining formulation based on discrete exterior calculus (DEC), DEC-QED can accurately simulate transient and long-time dynamics in superconductors. Finally, the expression of the entire electrodynamic problem in terms of the gauge-invariant flux field and charges makes the resulting classical field theory suitable for second quantization.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Powerful Terahertz Emission from a Bi 2 Sr 2 Ca Cu 2 O 8+ δ Mesa Operating Above 77 K

Mesa-shaped structures of the high critical temperature (high-T c ) superconductor Bi 2 Sr 2 CaCu 2 O 8+δ ; contain stacked intrinsic Josephson junctions. As such, they are a promising source of coherent radiation in the "terahertz gap" range, spanning from approximately 0.3 to 2.0 THz. Technological applications of these devices become far more practical if they can be operated at a cryogenic bath temperature of 77 K or higher. Previous works have reported emission from this type of device at high terahertz power levels at lower operating temperatures, 40-60 K, while at T bath >= 77 K observed power levels have generally been low. Here we report generation of 130 mu W of coherent power at 0.456 THz from a mesa of Bi 2 Sr 2 CaCu 2 O 8+δ ; doped with 0.16 holes per Cu atom, at a bath temperature of 77.4 K. Here, we find that the device radiates terahertz power when clearly identifiable cavity modes are excited, and that the frequency and bias voltage corresponding to each of these modes is almost independent of temperature. This is consistent with these modes having terahertz-frequency electric fields with very little dependence on vertical position within the mesa. We also find that the terahertz power radiated from any given mode decreases monotonically as the mesa temperature is increased. On the other hand, the low-frequency modes become inaccessible at low temperatures due to retrapping of the intrinsic Josephson junctions, and the maximum radiation power for the emitting mode is typically achieved at the temperature at which the retrapping voltage reaches the resonance voltage for this mode.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Majorana-based quantum computing in nanowire devices

The boundary of one-dimensional topological superconductors might lead to the appearance of Majorana zero modes, whose nontrivial exchange statistics can be used for quantum computing. In branched nanowire networks, one can exchange Majorana modes by time dependently tuning topologically nontrivial parameter regions. In this paper, we simulate the exchange of four Majorana modes in T-shaped junctions made out of $\textit{p}$-wave superconducting Rashba wires. Specifically, we derive concrete experimental predictions for (quasi-)adiabatic braiding times and determine geometric conditions for successful Majorana exchange processes. Moreover, we prove that, in the adiabatic limit, the gating time needs to be smaller than the inverse of the squared superconducting order parameter and scales linearly with the gating potential. Furthermore, we show how to circumvent the formation of additional Majorana modes in branched nanowire systems, arising at wire intersection points of narrow junctions. Finally, we propose a multiqubit setup, allowing for universal quantum computing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Easy-plane spin Hall nano-oscillators as spiking neurons for neuromorphic computing

Here we show analytically using a macrospin approximation that easy-plane spin Hall nano-oscillators excited by a spin current polarized perpendicularly to the easy plane have phase dynamics analogous to that of Josephson junctions. Similarly to Josephson junctions, they can reproduce the spiking behavior of biological neurons that is appropriate for neuromorphic computing. To take advantage of typical spin-orbit torques, we use a nanoconstriction geometry, in which the magnetostatic interaction and magnetocrystalline anisotropy are tuned to create an easy plane that includes the interface normal direction. We perform micromagnetic simulations of such oscillators realized in this geometry and show that the easy-plane spiking dynamics is preserved in this experimentally feasible architecture. Finally we simulate two elementary neural network blocks that implement operations essential for neuromorphic computing. First, we show that output spikes energies from two neurons can be summed and injected into a following layer neuron and second, we demonstrate that outputs can be multiplied by synaptic weights implemented by locally modifying the anisotropy.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Observation of Coulomb blockade and Coulomb staircases in superconducting Pr 0.8 Sr 0.2 NiO 2 films

Motivated by the discovery of superconductivity in the infinite-layer nickelate family, we report an experimental endeavor to clean the surface of nickelate superconductor Pr 0.8 Sr 0.2 NiO 2 films by Ar + ion sputtering and subsequent annealing, and we study their electronic structures by cryogenic scanning tunneling microscopy and spectroscopy. The annealed surfaces are characterized by nano-sized clusters and Coulomb staircases with periodicity inversely proportional to the projected area of the nanoclusters, consistent with a double-barrier tunneling junction model. Moreover, the dynamical Coulomb blockade effects are observed and result in well-defined energy gaps around the Fermi level, which correlate closely with the specific configuration of the junctions. These Coulomb blockade-related phenomena provide an alternative plausible cause of the observed gap structure that should be considered in the spectroscopic understanding of nickelate superconductors with the nano-clustered surface.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Longitudinal dynamics and particle production in relativistic nuclear collisions

This work presents a three-dimensional dynamical initialization model for relativistic heavy-ion collisions, implementing local energy-momentum conservation and baryon charge fluctuations at string junctions. Constraining parameters using experimental data from p + p collisions at various collision energies, the model provides a very good description of the charged hadron and net proton rapidity distributions in Au +Au collisions from 7.7 to 200 GeV and Pb + Pb collisions at 8.77 and 17.3 GeV. Here we demonstrate the importance of fluctuations of baryon densities to string junctions for describing net-proton distributions at collision energies of 62.4 and 200 GeV. Including this improved baryon stopping description along with the requirement of strangeness neutrality also yields a good description of identified particle yields as functions of the collision energy above 7.7 GeV. We further study asymmetric p + Al and (p,d, 3 He) + Au collisions at the top RHIC energy and p + Pb, Xe + Xe, and Pb + Pb collisions at LHC energies. We identify the produced particle rapidity distributions in asymmetric collision systems as particularly useful for constraining models of the early-time longitudinal dynamics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Treelike structure of symmetry topological field theories and multisector QFTs

The global symmetries of a D -dimensional quantum field theory (QFT) can, in many cases, be captured in terms of a ( D + 1 )-dimensional symmetry topological field theory (SymTFT). In this work we construct a ( D + 1 )-dimensional theory which governs the symmetries of QFTs with multiple sectors which have connected correlators that admit a decoupling limit. The associated symmetry field theory decomposes into a SymTree, namely a treelike structure of SymTFTs fused along possibly nontopological junctions. In string-realized multisector QFTs, these junctions are smoothed out in the extradimensional geometry, as we demonstrate in examples. We further use this perspective to study the fate of higher-form symmetries in the context of holographic large M averaging where the topological sectors of different large M replicas become dressed by additional extended operators associated with the SymTree. Published by the American Physical Society 2024

Astronomy & Astrophysics↗
DOE OSTI2025

Signal processing and spectral modeling for the BeEST experiment

The Beryllium Electron capture in Superconducting Tunnel junctions (BeEST) experiment searches for evidence of heavy neutrino mass eigenstates in the nuclear electron capture decay of 7 Be by precisely measuring the recoil energy of the 7 Li daughter. In Phase III, the BeEST experiment has been scaled from a singl superconducting tunnel junction (STJ) sensor to a 36-pixel array to increase sensitivity and mitigate gamma-induced backgrounds. Phase III also uses a new continuous data acquisition system that greatly increases the flexibility for signal processing and data cleaning. Here, we have developed procedures for signal processing and spectral fitting that are sufficiently robust to be automated for large datasets. Furthermore, this article presents the optimized procedures before unblinding the majority of the Phase III dataset to search for physics beyond the standard model.

6 ≤ A ≤ 19↗