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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 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2014

DISCOVERY OF A STRONG LENSING GALAXY EMBEDDED IN A CLUSTER AT z = 1.62

We identify a strong lensing galaxy in the cluster IRC 0218 (also known as XMM-LSS J02182–05102) that is spectroscopically confirmed to be at z = 1.62, making it the highest-redshift strong lens galaxy known. The lens is one of the two brightest cluster galaxies and lenses a background source galaxy into an arc and a counterimage. With Hubble Space Telescope (HST) grism and Keck/LRIS spectroscopy, we measure the source redshift to be z {sub S} = 2.26. Using HST imaging in ACS/F475W, ACS/F814W, WFC3/F125W, and WFC3/F160W, we model the lens mass distribution with an elliptical power-law profile and account for the effects of the cluster halo and nearby galaxies. The Einstein radius is θ{sub E}=0.38{sub −0.01}{sup +0.02} arcsec (3.2{sub −0.1}{sup +0.2} kpc) and the total enclosed mass is M {sub tot}(<θ{sub E})=1.8{sub −0.1}{sup +0.2}×10{sup 11} M{sub ⊙}. We estimate that the cluster environment contributes ∼10% of this total mass. Assuming a Chabrier initial mass function (IMF), the dark matter fraction within θ{sub E} is f{sub DM}{sup Chab}=0.3{sub −0.3}{sup +0.1}, while a Salpeter IMF is marginally inconsistent with the enclosed mass (f{sub DM}{sup Salp}=−0.3{sub −0.5}{sup +0.2}). The total magnification of the source is μ{sub tot}=2.1{sub −0.3}{sup +0.4}. The source has at least one bright compact region offset from the source center. Emission from Lyα and [O III] are likely to probe different regions in the source.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

ON THE RELATIONSHIP BETWEEN A HOT-CHANNEL-LIKE SOLAR MAGNETIC FLUX ROPE AND ITS EMBEDDED PROMINENCE

A magnetic flux rope (MFR) is a coherent and helical magnetic field structure that has recently been found likely to appear as an elongated hot channel prior to a solar eruption. In this Letter, we investigate the relationship between the hot channel and the associated prominence through analysis of a limb event on 2011 September 12. In the early rise phase, the hot channel was initially cospatial with the prominence. It then quickly expanded, resulting in a separation of the top of the hot channel from that of the prominence. Meanwhile, they both experienced an instantaneous morphology transformation from a Λ shape to a reversed-Y shape and the top of these two structures showed an exponential increase in height. These features are a good indication of the occurrence of kink instability. Moreover, the onset of kink instability is found to coincide in time with the impulsive enhancement of flare emission underneath the hot channel, suggesting that ideal kink instability likely also plays an important role in triggering fast flare reconnection besides initiating the impulsive acceleration of the hot channel and distorting its morphology. We conclude that the hot channel is most likely the MFR system and the prominence only corresponds to the cool materials that are collected in the bottom of the helical field lines of the MFR against gravity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

EpitopeVec: linear epitope prediction using deep protein sequence embeddings

Motivation: B-cell epitopes (BCEs) play a pivotal role in the development of peptide vaccines, immuno-diagnostic reagents and antibody production, and thus in infectious disease prevention and diagnostics in general. Experimental methods used to determine BCEs are costly and time-consuming. Therefore, it is essential to develop computational methods for the rapid identification of BCEs. Although several computational methods have been developed for this task, generalizability is still a major concern, where cross-testing of the classifiers trained and tested on different datasets has revealed accuracies of 51–53%. Results: We describe a new method called EpitopeVec, which uses a combination of residue properties, modified antigenicity scales, and protein language model-based representations (protein vectors) as features of peptides for linear BCE predictions. Extensive benchmarking of EpitopeVec and other state-of-the-art methods for linear BCE prediction on several large and small datasets, as well as cross-testing, demonstrated an improvement in the performance of EpitopeVec over other methods in terms of accuracy and area under the curve. As the predictive performance depended on the species origin of the respective antigens (viral, bacterial and eukaryotic), we also trained our method on a large viral dataset to create a dedicated linear viral BCE predictor with improved cross-testing performance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Efficient discontinuous finite difference meshes for 3-D Laplace–Fourier domain seismic wavefield modelling in acoustic media with embedded boundaries

Simulation of acoustic wave propagation in the Laplace–Fourier (LF) domain, with a spatially uniform mesh, can be computationally demanding especially in areas with large velocity contrasts. To improve efficiency and convergence, we use 3-D second- and fourth-order velocity-pressure finite difference (FD) discontinuous meshes (DM). Our DM algorithm can use any spatial discretization ratio between meshes. We evaluate direct and iterative parallel solvers for computational speed, memory requirements and convergence. Finally, benchmarks in realistic 3-D models and topographies show more efficient and stable results for DM with direct solvers than uniform mesh results with iterative solvers.

58 GEOSCIENCES↗
DOE OSTI2021

Supervised learning with word embeddings derived from PubMed captures latent knowledge about protein kinases and cancer

Abstract Inhibiting protein kinases (PKs) that cause cancers has been an important topic in cancer therapy for years. So far, almost 8% of >530 PKs have been targeted by FDA-approved medications, and around 150 protein kinase inhibitors (PKIs) have been tested in clinical trials. We present an approach based on natural language processing and machine learning to investigate the relations between PKs and cancers, predicting PKs whose inhibition would be efficacious to treat a certain cancer. Our approach represents PKs and cancers as semantically meaningful 100-dimensional vectors based on word and concept neighborhoods in PubMed abstracts. We use information about phase I-IV trials in ClinicalTrials.gov to construct a training set for random forest classification. Our results with historical data show that associations between PKs and specific cancers can be predicted years in advance with good accuracy. Our tool can be used to predict the relevance of inhibiting PKs for specific cancers and to support the design of well-focused clinical trials to discover novel PKIs for cancer therapy.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase

Bacillus subtilis forms organized multicellular communities known as biofilms wherein the individual cells are held together by a self-produced extracellular matrix. The environmental signals that promote matrix synthesis remain largely unknown. We discovered that one such signal is impaired respiration. Specifically, high oxygen levels suppressed synthesis of the extracellular matrix. In contrast, low oxygen levels, in the absence of an alternative electron acceptor, led to increased matrix production. The response to impaired respiration was blocked in a mutant lacking cytochromes caa(3) and bc and markedly reduced in a mutant lacking kinase KinB. Mass spectrometry of proteins associated with KinB showed that the kinase was in a complex with multiple components of the aerobic respiratory chain. We propose that KinB is activated via a redox switch involving interaction of its second transmembrane segment with one or more cytochromes under conditions of reduced electron transport. In addition, a second kinase (KinA) contributes to the response to impaired respiration. Evidence suggests that KinA is activated by a decrease in the nicotinamide adenine dinucleotide (NAD(+))/NADH ratio via binding of NAD(+) to the kinase in a PAS domain A-dependent manner. Thus, B. subtilis switches from a unicellular to a multicellular state by two pathways that independently respond to conditions of impaired respiration.

Kolodkin-Gal, I↗
DOE OSTI2011

Orthogonality catastrophe as a consequence of qubit embedding in an ultracold Fermi gas

We investigate the behavior of a two-level atom coupled to a one-dimensional, ultracold Fermi gas. The sudden switching on of the scattering between the two entities leads to the loss of any coherence in the initial state of the impurity and we show that the exact dynamics of this process is strongly influenced by the effect of the orthogonality catastrophe within the gas. We highlight the relationship between the Loschmidt echo and the retarded Green's function - typically used to formulate the dynamical theory of the catastrophe - and demonstrate that the effect is reflected in the impurity dynamics. We show that the expected nonexponential decay of the spectral function can be observed using Ramsey interferometry on the two-level atom and comment on finite temperature effects.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Quantum geometry embedded in unitarity of evolution: Revealing its impacts as geometric oscillation and dephasing in spin resonance and crystal bands

Quantum Hall effects provide intuitive ways of revealing the topology in crystals, i.e., each quantized “step” represents a distinct topological state. Here, we seek a counterpart for “visualizing” quantum geometry, which is a broader concept. Here we show how geometry emerges in quantum as an intrinsic consequence of unitary evolution, composing a framework compatible with quantum metric and independent of specific details or approximations, suggesting quantum geometry may have widespread applicability. Indeed, we exemplify geometric observables, such as oscillation, dephasing, in magnetic resonance or band driving scenarios. Anomalies, supported by both analytic and numerical solutions, underscore the advantages of adopting a geometric perspective, potentially yielding distinguishable experimental signatures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗