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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 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Adjusting the Energy Profile for CH–O Interactions Leads to Improved Stability of RNA Stem-Loop Structures in MD Simulations

The role of ribonucleic acid (RNA) in biology continues to grow, but insight into important aspects of RNA behavior is lacking, such as dynamic structural ensembles in different environments, how flexibility is coupled to function, and how function might be modulated by small molecule binding. In the case of proteins, much progress in these areas has been made by complementing experiments with atomistic simulations, but RNA simulation methods and force fields are less mature. It remains challenging to generate stable RNA simulations, even for small systems where well-defined, thermostable structures have been established by experiments. Further many different aspects of RNA energetics have been adjusted in force fields, seeking improvements that are transferable across a variety of RNA structural motifs. In this work, the role of weak CH···O interactions is explored, which are ubiquitous in RNA structure but have received less attention in RNA force field development. By comparing data extracted from high-resolution RNA crystal structures to energy profiles from quantum mechanics and force field calculations, it is shown that CH···O interactions are overly repulsive in the widely used Amber RNA force fields. A simple, targeted adjustment of CH···O repulsion that leaves the remainder of the force field unchanged was developed. Then, the standard and modified force fields were tested using molecular dynamics (MD) simulations with explicit water and salt, amassing over 300 μs of data for multiple RNA systems containing important features such as the presence of loops, base stacking interactions as well as canonical and noncanonical base pairing. In this work and others, standard force fields lead to reproducible unfolding of the NMR-based structures. Including a targeted CH···O adjustment in an otherwise identical protocol dramatically improves the outcome, leading to stable simulations for all RNA systems tested.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Ray-tracing image simulations of transparent objects with complex shape and inhomogeneous refractive index

Optical images of transparent three-dimensional objects can be different from a replica of the object’s cross section in the image plane, due to refraction at the surface or in the body of the object. Simulations of the object’s image are thus needed for the visualization and validation of physical models. We report ray tracing image simulations that achieved high physical fidelity, reproducing optical behaviors and image features not rendered in previous studies. We replicated brightfield microscopy images of drops with complex shapes, and images of pressure and shock waves traveling inside them. For high physical fidelity, the simulations must replicate the spatial and angular distribution of illumination rays, and both the experiment and the simulation must be designed for accurate optical modeling. The simulations are highly sensitive to the properties of the drops and can be used to diagnose and refine fluid dynamics models. The simulated images can also be optimized to extract multiple 3D properties from experimental images. Compared to specialized single-shot 3D imaging methods, this approach has the advantage that it preserves the experimental simplicity, the high resolution, and the visual interpretability characteristic to basic optical imaging. The techniques introduced here are directly applicable to optical microscopy, so they can be used in other fields, such as microfluidics and biology, to expand the type and the accuracy of three-dimensional information that can be extracted from basic optical images.

Cavitation↗
DOE OSTI2021

Coupled valence carrier and core-exciton dynamics in WS 2 probed by few-femtosecond extreme ultraviolet transient absorption spectroscopy

Few-femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy, performed with optical 500-1000 nm supercontinuum and broadband XUV pulses (30-50 eV), simultaneously probes dynamics of photoexcited carriers in WS$_{2}$ at the W O$_3$ edge (37-45 eV) and carrier-induced modifications of core-exciton absorption at the W N$_{6,7}$ edge (32-37 eV). Access to continuous core-to-conduction band absorption features and discrete core-exciton transitions in the same XUV spectral region in a semiconductor provides a novel means to investigate the effect of carrier excitation on core-exciton dynamics. The core-level transient absorption spectra, measured with either pulse arriving first to explore both core-level and valence carrier dynamics, reveal that core-exciton transitions are strongly influenced by the photoexcited carriers. A $1.2\pm0.3$ ps hole-phonon relaxation time and a $3.1\pm0.4$ ps carrier recombination time are extracted from the XUV transient absorption spectra from the core-to-conduction band transitions at the W O$_{3}$ edge. Global fitting of the transient absorption signal at the W N$_{6,7}$ edge yields $\sim 10$ fs coherence lifetimes of core-exciton states and reveals that the photoexcited carriers, which alter the electronic screening and band filling, are the dominant contributor to the spectral modifications of core-excitons and direct field-induced changes play a minor role. This work provides a first look at the modulations of core-exciton states by photoexcited carriers and advances our understanding of carrier dynamics in metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

MOSCATO Development and Integration in Fiscal Year 2022

During FY21, we conducted ongoing development work for the MOSCATO (Molten Salt Chemistry and Transport) solver. The code development work primarily consisted of transitioning capabilities from the original version of the solver, which was written in OpenFOAM, into Nek5000. In doing so, a fast, highly parallelizable solver was created that is capable of complex chemistry and corrosion simulations for engineering-scale molten salt systems. The Nek5000 version of MOSCATO is now fully featured and capable of higher-fidelity simulations than were previously possible. Demonstration cases including a thermal convection loop have been simulated to test these new capabilities. We built upon the work for FY22 and improved the code from several different perspectives. First, we improved the user interface by adding a new component to the official Nek5000 input file (.par). This new part contains documents parameters like, salt properties (density, viscosity, Cp, thermal conductivity), diffusion coefficients, standard potential, etc. Second, we built a conversion script to extract salt properties from the MSTDB-TP salt database and write to MOSCATO input file. Third, we migrated the code to NekRS, which is the GPU branch of Nek5000 and suitable for next generation supercomputers. Verification and Validation (V&V) work was also continued in FY22. Two tasks were performed. The first V&V task involved the validation of the Poisson-Nernst-Planck equation solver and Butler-Volmer electrode kinetics, by comparing with numerical and experimental data about thermoelectric cells. The second task involved the comparisons to corrosion results from a thermal convection loop run during the MSRE era. Satisfactory agreement was obtained from both tasks.

Yuan, Haomin↗
DOE OSTI2020

ContourNet: Salient Local Contour Identification for Blob Detection in Fusion Plasma Simulation Data

We present ContourNet, a deep learning approach to identify salient local isocontours as blobs in large-scale 5D gyrokinetic tokamak simulation data. Blobs-regions of high turbulence that run along the edge wall down toward the diverter and can damage the tokamak-are non-well-defined features but have been empirically localized by isocontours in 2D normalized fluctuating density fields. The key of our study is to train ContourNet to follow the empirical rules to detect blobs over the time-varying simulation data. The architecture of ContourNet is a convolutional neural segmentation network: the inputs are the density field and a rasterized isocontour; the output is a set of isocontour encircling blobs. At the training stage, we feed the network with manually identified isocontours and propagated labels. At the inference stage, we extract isocontours from the segmented blob regions. Results show that our approach can achieve both high accuracy and performance, which enables scientists to understand the blob dynamics influencing the confinement of the plasma.

Blob detection↗
DOE OSTI2025

Femtoscopic study of the proton-proton and proton-deuteron systems in heavy-ion collisions at the LHC

This work reports femtoscopic correlations of p – – p ($\overline{p}$ – – $\overline{p}$) and p – – d ($\overline{p}$ – – $\overline{d}$) pairs measured in Pb–Pb collisions at center-of-mass energy per nucleon $\sqrt{s_{NN}}$ = 5.02 TeV in the ALICE Collaboration. A fit to the measured proton-proton correlation functions allows one to extract the dependence of the nucleon femtoscopic radius of the particle-emitting source on the pair transverse mass (m T ) and on the average charge particle multiplicity $\langle$dN ch /dη$\rangle$ 1/3 for three centrality intervals (0–10%, 10 – – 30 %, 30 – – 50 %). In both cases, the expected power-law and linear scalings are observed, respectively. The measured p–d correlations can be described by both two- and three-body calculations, indicating that the femtoscopy observable is not sensitive to the short-distance features of the dynamics of the p-(p-n) system, due to the large inter-particle distances in Pb–Pb collisions at the LHC. Indeed, in this study, the minimum measured femtoscopic source sizes for protons and deuterons have a minimum value at 2.73$^{+0.05}_{–0.05}$ and 3.10$^{+1.04}_{–0.86}$ fm, respectively, for the 30–50% centrality collisions. Moreover, the m T -scaling obtained for the p–p and p–d systems is compatible within 1σ of the uncertainties. These findings provide new input for fundamental studies on the production of light (anti)nuclei under extreme conditions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2016

Effects of oxygen partial pressure, deposition temperature, and annealing on the optical response of CdS:O thin films as studied by spectroscopic ellipsometry

Ex-situ spectroscopic ellipsometry measurements are made on radio frequency magnetron sputtered oxygenated cadmium sulfide (CdS:O) thin films. Films are deposited onto glass substrates at room temperature and at 270 °C with varying oxygen to total gas flow ratios in the sputtering ambient. Ellipsometric spectra from 0.74 to 5.89 eV are collected before and after annealing at 607 °C to simulate the thermal processes during close-space sublimation of overlying cadmium telluride in that solar cell configuration. Complex dielectric function (ε = ε{sub 1} + iε{sub 2}) spectra are extracted for films as a function of oxygen gas flow ratio, deposition temperature, and post-deposition annealing using a parametric model accounting for critical point transitions and an Urbach tail for sub-band gap absorption. The results suggest an inverse relationship between degree of crystallinity and oxygen gas flow ratio, whereas annealing is shown to increase crystallinity in all samples. Direct band gap energies are determined from the parametric modeling of ε and linear extrapolations of the square of the absorption coefficient. As-deposited samples feature a range of band gap energies whereas annealing is shown to result in gap energies ranging only from 2.40 to 2.45 eV, which is close to typical band gaps for pure cadmium sulfide.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Characterizing Sub-Cohorts via Data Normalization and Representation Learning

The process of identifying a cohort of interest is a very challenging task. It requires manually inspecting many patient records of complex structure that might include medical coding errors and missing data. This paper presents a computational pipeline for refining the process of cohort selection based on medical concepts recorded in the electronic health records (EHRs). The pipeline extracts EHR data for a given cohort and normalizes this data using standard vocabularies. Then a stacked denoising autoencoder is used to embed the normalized patient vectors in a low dimensional space, where the patients are subsequently clustered into sub-cohorts. The goal is to represent the cohort in a standard format and abstract variants of sub-populations. As a use-case, we applied the pipeline to 1.8 million Veterans diagnosed with major depressive disorder (MDD), and identified four meaningful sub-cohorts using the features learned by the autoencoder. Then, each sub-cohort was explored using a set of keywords for interpretation.

Rush III, Everett↗
DOE OSTI2024

Development of message passing-based graph convolutional networks for classifying cancer pathology reports

Abstract Background Applying graph convolutional networks (GCN) to the classification of free-form natural language texts leveraged by graph-of-words features (TextGCN) was studied and confirmed to be an effective means of describing complex natural language texts. However, the text classification models based on the TextGCN possess weaknesses in terms of memory consumption and model dissemination and distribution. In this paper, we present a fast message passing network (FastMPN), implementing a GCN with message passing architecture that provides versatility and flexibility by allowing trainable node embedding and edge weights, helping the GCN model find the better solution. We applied the FastMPN model to the task of clinical information extraction from cancer pathology reports, extracting the following six properties: main site, subsite, laterality, histology, behavior, and grade. Results We evaluated the clinical task performance of the FastMPN models in terms of micro- and macro-averaged F1 scores. A comparison was performed with the multi-task convolutional neural network (MT-CNN) model. Results show that the FastMPN model is equivalent to or better than the MT-CNN. Conclusions Our implementation revealed that our FastMPN model, which is based on the PyTorch platform, can train a large corpus (667,290 training samples) with 202,373 unique words in less than 3 minutes per epoch using one NVIDIA V100 hardware accelerator. Our experiments demonstrated that using this implementation, the clinical task performance scores of information extraction related to tumors from cancer pathology reports were highly competitive.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

ATR-SEIRAS Reveals Potential Inversion and Associated Electron Transfer Kinetics in the Reduction of Surface-Confined Anthraquinone

The detection of stable semiquinone radicals on an anthraquinone (AQ) layer chemically grafted to an electrode surface in aqueous electrolytes has been elucidated by using attenuated total reflection surface enhanced infrared absorption spectroscopy (ATR-SEIRAS). In very alkaline conditions (pH 13), the reduction of the AQ involves no proton transfer, but surface sensitive infrared spectroscopy reveals that the anthraquinone dianion forms a strong hydrogen bonding network with coadsorbed water, leading to irreversible features in the voltammetry. The potential dependence of the IR band assigned to the AQ radical is consistent with the enhanced hydrogen bonding network causing increased stabilization of the quinone radical and supports the predicted response of a system under mild potential inversion, whereby the formal potential for the reduction of the anthraquinone radical is positive of the reduction potential of the neutral AQ molecule. Time-resolved ATR-SEIRAS is used to measure the transient formation of the AQ •– radical, from which rate constant information can be extracted using the Butler–Volmer model involving two one-electron transfers without a direct disproportionation reaction. The potential dependence of the rate constants is consistent with the potential inversion and can be used to qualitatively simulate the measured cyclic voltammograms. In conclusion, the thermodynamic and kinetic analyses re-emphasize long established deficiencies associated with using one-electron reaction formalisms to characterize multi-electron systems.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
DOE OSTI2016

On the structural origin of the single-ion magnetic anisotropy in LuFeO 3

The electronic structure for the conduction bands of both hexagonal and orthorhombic LuFeO 3 thin films have been measured using x-ray absorption spectroscopy at oxygen K (O K) edge. Dramatic differences in both the spectral features and the linear dichroism are observed. These differences in the spectra can be explained using the differences in crystal field splitting of the metal (Fe and Lu) electronic states and the differences in O 2p-Fe 3d and O 2p-Lu 5d hybridizations. While the oxidation states have not changed, the spectra are sensitive to the changes in the local environments of the Fe 3+ and Lu 3+ sites in the hexagonal and orthorhombic structures. Using the crystal-field splitting and the hybridizations that are extracted from the measured electronic structures and the structural distortion information, we derived the occupancies of the spin minority states in Fe 3+ , which are non-zero and uneven. The single ion anisotropy on Fe 3+ sites is found to originate from these uneven occupancies of the spin minority states via spin–orbit coupling in LuFeO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2019

Spectral function of the Holstein polaron at finite temperature

Here we compute the Holstein polaron spectral function on a one-dimensional ring using the finite-temperature T Lanczos method. With increasing T additional features in the spectral function emerge even at temperatures below the phonon frequency. We observe a substantial spread of the spectral weight towards lower frequencies and the broadening of the quasiparticle (QP) peak. In the weak-coupling regime the QP peak merges with the continuum in the high-T limit. In the strong-coupling regime the main features of the low-T spectral function remain detectable up to the highest T used in our calculations. The effective polaron mass shows a nonmonotonic behavior as a function of T at small phonon frequency but increases with T at larger frequencies. The self-energy remains k independent even at elevated T in the frequency range corresponding to the polaron band, while at higher frequencies it develops a distinguishable k dependence. Analytical expressions for the first few frequency moments are derived, and they agree well with those extracted from numerical calculations in a wide-T regime.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Sampling Microbial Dynamics in the Salish Sea Estuary: Evaluating Methods to Capture Cyanobacteria and Cyanophage

Introduction: Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aquatic environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogencoevolution. Methods: We developed and refined methods to sample and sequence cyanobacteria, cyanophages, and measured features of their abiotic environment. Results: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol from this exploratory effort included a combination of in-line and single vacuum flask filtrations, which reduced filtration processing time by over threefold in some cases compared to other tested methods, such as a fully in-line sequence or in-site filtrations. We successfully extracted an average of approximately 400–1200 ng for all filter fractions, with some variations between kits. Discussion: The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons.

Salish Sea↗
DOE OSTI2017

Electrochemical Window of the Li-Ion Solid Electrolyte Li 7 La 3 Zr 2 O 12

The recent discovery of fast ion-conducting solid electrolytes could enable solid-state and other advanced battery chemistries with higher energy densities and enhanced safety. In addition to high ionic conductivity, a viable electrolyte should also exhibit an electrochemical window that is wide enough to suppress undesirable electronic transport (i.e., self-discharge and/or short circuiting) arising from charge injection or extraction from the electrodes. Here, direct current chronoamperometry, alternating current electrochemical impedance spectroscopy, and optical absorption band gap measurements are combined with first-principles calculations to systematically characterize the electrochemical window of the promising superionic conductor Li 7 La 3 Zr 2 O 12 (LLZO). Negligible electronic current was measured within LLZO for a wide range of voltages relevant for high-voltage cathodes. This auspicious behavior is consistent with both the large band gap (~6 eV) predicted for LLZO and the absolute positions of its band edges. These features imply that a wide electrochemical window is an intrinsic property of LLZO, facilitating its use in next-generation batteries.

Thompson, Travis↗
DOE OSTI2022

c -axis transport in UTe 2 : Evidence of three-dimensional conductivity component

Here we study the temperature dependence of electrical resistivity for currents directed along all crystallographic axes of the spin-triplet superconductor UTe 2 . We focus particularly on an accurate determination of the resistivity along the c axis (ρ c ) by using a generalized Montgomery technique that allows extraction of crystallographic resistivity components from a single sample. In contrast to expectations from the observed highly anisotropic band structure, our measurement of the absolute values of resistivities in all current directions reveals a surprisingly nearly isotropic transport behavior at temperatures above Kondo coherence, with ρ c ~ ρ b ~ 2 ρ a , that evolves to reveal qualitatively distinct behaviors on cooling. The temperature dependence of ρ c exhibits a peak at a temperature much lower than the onset of Kondo coherence observed in ρ a and ρ b , consistent with features in magnetotransport and magnetization that point to a magnetic origin. A comparison to the temperature-dependent evolution of the scattering rate observed in angle-resolved photoemission spectroscopy experiments provides important insights into the underlying electronic structure necessary for building a microscopic model of superconductivity in UTe 2 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Chameleon: An Adaptive Wear Balancer for Flash Clusters

NAND flash-based Solid State Devices (SSDs) offer the desirable features of high performance, energy efficiency, and fast growing capacity. Thus, the use of SSDs is increasing in distributed storage systems. A key obstacle in this context is that the natural unbalance in distributed I/O workloads can result in wear imbalance across the SSDs in a distributed setting. This, in turn can have significant impact on the reliability, performance, and lifetime of the storage deployment. Extant load balancers for storage systems do not consider SSD wear imbalance when placing data, as the main design goal of such balancers is to extract higher performance. Consequently, data migration is the only common technique for tackling wear imbalance, where existing data is moved from highly loaded servers to the least loaded ones. In this paper, we explore an innovative holistic approach, Chameleon, that employs data redundancy techniques such as replication and erasure-coding, coupled with endurance-aware write offloading, to mitigate wear level imbalance in distributed SSD-based storage. Chameleon aims to balance the wear among different flash servers while meeting desirable objectives of: extending life of flash servers; improving I/O performance; and avoiding bottlenecks. Evaluation with a 50 node SSD cluster shows that Chameleon reduces the wear distribution deviation by 81% while improving the write performance by up to 33%.

Zhao, Nannan↗
DOE OSTI2024

Role of slip in hydrogen-assisted crack initiation in Ni-based alloy 725

We conduct in situ tensile straining experiments to investigate the role of hydrogen and slip in crack initiation in nickel-based alloy 725. Our experiments reveal no tendency for hydrogen to enhance localized slip and no necessity of slip for crack initiation. We use electrochemical charging to introduce hydrogen into samples, melt extraction to measure hydrogen content, and digital image correlation to analyze localized plastic strains during in situ tensile tests in a scanning electron microscope. Cracks initiate both in regions with and without nearby localized slip. Moreover, the fraction of cracks initiating with no nearby slip is greater at higher hydrogen content. Slip-assisted crack initiation generally occurs at locations where intergranular slip is arrested, especially at intersections of slipping coherent twin boundaries with thin twin lamellae. Cracks that initiate without nearby slip occur at a wider variety of microstructural features, including inclusions, triple junctions, and surface flaws.

36 MATERIALS SCIENCE↗
DOE OSTI2016

On the solid phase crystallization of In{sub 2}O{sub 3}:H transparent conductive oxide films prepared by atomic layer deposition

Hydrogen-doped indium oxide (In{sub 2}O{sub 3}:H) has emerged as a highly transparent and conductive oxide, finding its application in a multitude of optoelectronic devices. Recently, we have reported on an atomic layer deposition (ALD) process to prepare high quality In{sub 2}O{sub 3}:H. This process consists of ALD of In{sub 2}O{sub 3}:H films at 100 °C, followed by a solid phase crystallization step at 150–200 °C. In this work, we report on a detailed electron microscopy study of this crystallization process which reveals new insights into the crucial aspects for achieving the large grain size and associated excellent properties of the material. The key finding is that the best optoelectronic properties are obtained by preparing the films at the lowest possible temperature prior to post-deposition annealing. Electron microscopy imaging shows that such films are mostly amorphous, but feature a very low density of embedded crystallites. Upon post-deposition annealing, crystallization proceeds merely from isotropic crystal grain growth of these embedded crystallites rather than by the formation of additional crystallites. The relatively high hydrogen content of 4.2 at. % in these films is thought to cause the absence of additional nucleation, thereby rendering the final grain size and optoelectronic properties solely dependent on the density of embedded crystallites. The temperature-dependent grain growth rate has been determined, from which an activation energy of (1.39 ± 0.04) eV has been extracted. Finally, on the basis of the observed crystallization mechanism, a simple model to fully describe the crystallization process has been developed. This model has been validated with a numerical implementation thereof, which accurately predicts the observed temperature-dependent crystallization behaviour.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗