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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Transposition of HOPPLA in siRNA-deficient plants suggests a limited effect of the environment on retrotransposon mobility in Brachypodium distachyon

Long terminal repeat retrotransposons (LTR-RTs) are powerful mutagens regarded as a major source of genetic novelty and important drivers of evolution. Yet, the uncontrolled and potentially selfish proliferation of LTR-RTs can lead to deleterious mutations and genome instability, with large fitness costs for their host. While population genomics data suggest that an ongoing LTR-RT mobility is common in many species, the understanding of their dual role in evolution is limited. Here, we harness the genetic diversity of 320 sequenced natural accessions of the Mediterranean grass Brachypodium distachyon to characterize how genetic and environmental factors influence plant LTR-RT dynamics in the wild. When combining a coverage-based approach to estimate global LTR-RT copy number variations with mobilome-sequencing of nine accessions exposed to eight different stresses, we find little evidence for a major role of environmental factors in LTR-RT accumulations in B. distachyon natural accessions. Instead, we show that loss of RNA polymerase IV (Pol IV), which mediates RNA-directed DNA methylation in plants, results in high transcriptional and transpositional activities of RLC_BdisC024 (HOPPLA) LTR-RT family elements, and that these effects are not stress-specific. This work supports findings indicating an ongoing mobility in B. distachyon and reveals that host RNA-directed DNA methylation rather than environmental factors controls their mobility in this wild grass model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Determining Exact RANS Operators with the Macroscopic Forcing Method (Final Report)

This report contains a compilation of key results and findings from the ACT project “Determining Exact RANS Operators with the Macroscopic Forcing Method.” The Macroscopic Forcing Method (MFM), a numerical tool for determining closure operators, is used to measure eddy diffusivity moments in Rayleigh-Taylor (RT) instability. It is first applied to low-Atwood 2D RT instability; that work is then extended to 3D RT at different finite Atwood numbers. It is found that nonlocality is important for modeling the mean scalar transport closure operator in RT mixing. Additionally, work is done to improve the statistical convergence of MFM for chaotic problems like RT mixing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Establishment of a reverse transcription real-time quantitative PCR method for Getah virus detection and its application for epidemiological investigation in Shandong, China

Getah virus (GETV) is a mosquito-borne, single-stranded, positive-sense RNA virus belonging to the genus Alphavirus of the family Togaviridae . Natural infections of GETV have been identified in a variety of vertebrate species, with pathogenicity mainly in swine, horses, bovines, and foxes. The increasing spectrum of infection and the characteristic causing abortions in pregnant animals pose a serious threat to public health and the livestock economy. Therefore, there is an urgent need to establish a method that can be used for epidemiological investigation in multiple animals. In this study, a real-time reverse transcription fluorescent quantitative PCR (RT-qPCR) method combined with plaque assay was established for GETV with specific primers designed for the highly conserved region of GETV Nsp1 gene. The results showed that after optimizing the condition of RT-qPCR reaction, the minimum detection limit of the assay established in this study was 7.73 PFU/mL, and there was a good linear relationship between viral load and Cq value with a correlation coefficient ( R 2 ) of 0.998. Moreover, the method has good specificity, sensitivity, and repeatability. The established RT-qPCR is 100-fold more sensitive than the conventional RT-PCR. The best cutoff value for the method was determined to be 37.59 by receiver operating characteristic (ROC) curve analysis. The area under the curve (AUC) was 0.956. Meanwhile, we collected 2,847 serum specimens from swine, horses, bovines, sheep, and 17,080 mosquito specimens in Shandong Province in 2022. The positive detection rates by RT-qPCR were 1%, 1%, 0.2%, 0%, and 3%, respectively. In conclusion, the method was used for epidemiological investigation, which has extensive application prospects.

Cao, Xinyu↗
DOE OSTI2022

A Machine Learning Framework to Predict Images of Edge-on Protoplanetary Disks

The physical structure and properties of protoplanetary disks are typically derived from spatially resolved disk images. Edge-on disks in particular provide an important view point on the vertical structure and degree of settling of disks. Such analyses rely on radiative transfer (RT) calculations that are generally computationally intensive due to the high optical depth of disks. Here we present a machine learning framework that has the potential to dramatically speed up the forward modeling process by approximating the results of RT calculations. This framework, trained on an initial set of RT calculations, utilizes an autoencoder neural network to enable the generation of synthetic scattered light images of edge-on disks directly from a set of physical parameters. We demonstrate that this framework generates synthetic images 2–3 orders of magnitude faster than using RT calculations. These machine learning-generated images appear to approximate the RT images well, in particular preserving their size and shape. We also find a strong correlation between the latent space representations of the generated disk images and several of their associated physical parameters. Finally, we discuss potential changes to the framework, such as methods to further improve the image quality, extending the framework to multiple wavelengths, and inverting the process to infer physical parameters from observed images. Overall, these new tools have the potential to enable a more efficient and uniform analysis of edge-on disk properties and the initial conditions of planet formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

The Effect of Spatially Varying Collision Frequency on the Development of the Rayleigh–Taylor Instability

Abstract The Rayleigh–Taylor (RT) instability is ubiquitously observed, yet has traditionally been studied using ideal fluid models. Collisionality can vary strongly across the fluid interface, and previous work demonstrates the necessity of kinetic models to completely capture dynamics in certain collisional regimes. Where previous kinetic simulations used spatially and temporally constant collision frequency, this work presents five-dimensional (two spatial, three velocity dimensions) continuum-kinetic simulations of the RT instability using a more realistic spatially varying collision frequency. Three cases of collisional variation are explored for two Atwood numbers: low to intermediate, intermediate to high, and low to high. The low-to-intermediate case exhibits no RT instability growth, while the intermediate-to-high case is similar to a fluid-limit kinetic case with interface widening biased toward the lower-collisionality region. A novel contribution of this work is the low-to-high collisionality case that shows significantly altered instability growth through an upward movement of the interface and damped spike growth due to increased free-streaming particle diffusion in the lower region. Contributions to the energy flux from the non-Maxwellian portions of the distribution function are not accessible to fluid models and are greatest in magnitude in the spike and regions of low collisionality. Increasing the Atwood number results in greater RT instability growth and reduced upward interface movement. Deviation of the distribution function from Maxwellian is inversely proportional to collision frequency and concentrated around the fluid interface. The linear phase of RT instability growth is well described by theoretical linear growth rates accounting for viscosity and diffusion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Near‐Unity Superradiant Emission from Delocalized Frenkel Excitons in a Two‐Dimensional Supramolecular Assembly

Abstract Three general effective strategies are shown to mitigate nonradiative losses in the superradiant emission from supramolecular assemblies. J‐aggregates of 5,5′,6,6′‐tetrachloro‐1,1′‐diethyl‐3,3′‐di(4–sulfobutyl)‐benzimidazolocarbocyanine (TDBC) are used to elucidate the nature of nonradiative processes. Self‐annealing at room temperature (RT), photo‐brightening, and purification of the dye monomers are shown to all lead to substantial increases in emission quantum yields (QYs) and a concomitant lengthening of the emission lifetime, with purification having the largest effect. Structural and optical measurements are used to support a microscopic model that emphasizes the deleterious effects of a small number of impurity and defect sites that serve as nonradiative recombination centers. This understanding has yielded a molecular fluorophore in solution at RT with an unprecedented combination of fast emissive lifetime and high QY. Superradiant emission with a QY of 82% and a lifetime of 174 ps is obtained from J‐aggregates of TDBC in solution at RT. This combination of high QY and fast lifetime at RT makes supramolecular assemblies of purified TDBC a model system for the study of fundamental superradiance phenomena. High QY J‐aggregates are uniquely suited for the development of applications that require high speed and high brightness fluorophores such as devices for high‐speed optical communication.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Incorporate day-ahead robustness and real-time incentives for electricity market design

In this paper, we propose a two-stage electricity market framework to explore the participation of distributed energy resources (DERs) in a day-ahead (DA) market and a real-time (RT) market. The objective is to determine the optimal bidding strategies of the aggregated DERs in the DA market and generate online incentive signals for DER-owners to optimize the social-welfare taking into account network operational constraints. Distributionally robust optimization is used to explicitly incorporate data-based statistical information of renewable forecasts into the supply/demand decisions in the DA market. We evaluate the conservativeness of bidding strategies distinguished by different risk aversion settings. In the RT market, a bi-level time-varying optimization problem is proposed to design the online incentive signals to tradeoff the RT imbalance penalty for distribution system operators (DSOs) and the costs of individual DER-owners. This enables tracking their optimal dispatch to provide fast balancing services, in the presence of time-varying network states while satisfying the voltage regulation requirement. Simulation results on both DA wholesale market and RT balancing market demonstrate the necessity of this two-stage design, and its robustness to uncertainties, the performance of convergence, the tracking ability and the feasibility of the resulting network operations.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Modeling framework for evaluating the impacts of hydrodynamic pressure on hydrologic exchange fluxes and residence time for a large-scale river section over a long-term period

Quantifying hydrologic exchange fluxes (HEF) at the river and subsurface interface and their residence times (RT) in subsurface are important for managing the water quality and ecosystem health in dynamic river corridor systems. In this study, a modeling framework is developed for coupling the three-dimensional (3D) multi-phase surface, subsurface flow transport, and numerical tracer model for RT in a large-scale river section over a long period. The framework is utilized to evaluate the impacts of hydrodynamic pressure on HEFs and RT for a 30 km section of the Columbia River in Washington State over a three-year period. Based on comparisons between model simulations with and without considering hydrodynamic pressure, we found that hydrodynamic pressure increases the net HEFs by 7% with river gaining water from the subsurface domain, and leads to slight reduction of RT.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Quality of Life: A Prospective Randomized Trial of Palliative Volumetric Arc Therapy Versus 3-Dimensional Conventional Radiation Therapy

Volumetric arc therapy (VMAT) is a radiation therapy (RT) technique that spares normal tissues from high and intermediate RT doses but increases the volume of tissues receiving low doses of RT compared with 3-dimensional conformal RT (3DCRT). We hypothesized that palliative VMAT would reduce the detriment to patient quality of life (QOL) compared with palliative 3DCRT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

COVID-19 Vaccine-Induced Radiation Recall Phenomenon

Radiation recall phenomenon (RRP) is an uncommon, late occurring, acute inflammatory skin reaction that emerges in localized areas coincident with previously irradiated radiation therapy (RT) treatment fields. RRP has been known to be triggered by a number of chemotherapy agents. To the best of our knowledge, this report is the first description of RRP after administration of the Pfizer-BioNTech vaccine for COVID-19, or any other currently available vaccine against COVID-19. Acute skin reactions were observed in 2 RT patients with differing timelines of RT and vaccinations. In both cases however, the RRP presented within days of the patient receiving the second dose of vaccine. For each RT course, the treatment planning dosimetry of the radiation fields was compared with the area of the observable RRP. RRP developed within the borders of treatment fields where prescription dose constraints were prioritized over skin sparing. Our observation is currently limited to 2 patients. The actual incidence of RRP in conjunction with Pfizer-BioNTech vaccine or any other vaccine against COVID-19 is unknown. For patients with cancer being treated with radiation with significant dose to skin, consideration should be given to the probability of RRP side effects from vaccinations against COVID-19.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Dose Escalated Radiation Therapy for Glioblastoma Multiforme: An International Systematic Review and Meta-Analysis of 22 Prospective Trials

Limited evidence is available on the utility of dose-escalated radiation therapy (DE-RT) with or without temozolomide (TMZ) versus standard-of-care radiation therapy (SoC-RT) for patients with newly diagnosed glioblastoma multiforme. We performed a systematic review/meta-analysis to compare overall survival (OS) and progression-free survival (PFS) between DE-RT and SoC-RT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Human DNA polymerase η promotes RNA-templated error-free repair of DNA double-strand breaks

A growing body of evidence indicates that RNA plays a critical role in orchestrating DNA double-strand break repair (DSBR). Recently, we showed that homologous nascent RNA can be used as a template for error-free repair of double-strand breaks (DSBs) in the transcribed genome and to restore the missing sequence at the break site via the transcription-coupled classical nonhomologous end-joining (TC-NHEJ) pathway. TC-NHEJ is a complex multistep process in which a reverse transcriptase (RT) is essential for synthesizing the DNA strand from template RNA. However, the identity of the RT involved in the TC-NHEJ pathway remained unknown. Here, we report that DNA polymerase eta (Pol η), known to possess RT activity, plays a critical role in TC-NHEJ. We found that Pol η forms a multiprotein complex with RNAP II and other TC-NHEJ factors, while also associating with nascent RNA. Moreover, purified Pol η, along with DSBR proteins PNKP, XRCC4, and Ligase IV can fully repair RNA templated 3'-phosphate-containing gapped DNA substrate. In addition, we demonstrate here that Pol η deficiency leads to accumulation of R-loops and persistent strand breaks in the transcribed genes. Finally, we determined that, in Pol η depleted but not in control cells, TC-NHEJ-mediated repair was severely abrogated when a reporter plasmid containing a DSB with several nucleotide deletion within the E. coli lacZ gene was introduced for repair in lacZ-expressing mammalian cells. Thus, our data strongly suggest that RT activity of Pol η is required in error-free DSBR.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson’s correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Long-term thermal stability and calibration of Type-II fiber Bragg grating array inscribed in radiation-hardened fibers

This paper investigates the long-term thermal stability of Type-II fiber Bragg grating (FBG) arrays, inscribed by femtosecond laser in radiation-hardened fiber, for potential applications as multiplexed sensors in high-temperature energy systems. The thermal stability of FBG sensors was assessed through 16 thermal cycles from room temperature (RT) to 750 ℃ about two months, involving 100 FBG sensors. The results show that the absolute temperature drift of FBG sensors can be reduced to less than 0.4 pm/day after 54 h thermal annealing process at a constant temperature of 800 ℃. As temperature sensors, the FBGs demonstrated stable performance, achieving a standard deviation (STD) of 1.8 pm (corresponding to a temperature resolution of 0.118 ℃) post-annealing. Repeated thermal cycles revealed a random drift of 2.3 pm in the FBG wavelength at RT. Polynomial fitting was explored as a calibration method to convert FBG wavelength shifts into absolute temperature measurements. By optimizing calibration temperature points (RT, 200 ℃, 400 ℃, and 750 ℃), the study shows that cubic polynomial calibration using four points yields an average R2 of 0.9997 and an RMSE of 3.58 ℃ across the entire temperature range (RT to 750 ℃). This approach represents an 11.53-fold improvement over empirical slope calibration and a 1.34-fold improvement over four-point piecewise fitting. The findings indicate that Type-II FBGs inscribed in radiation-hardened fibers can function as accurate temperature sensors, with performance on par with or exceeding that of thermocouples. With their multiplexing capability, robust signal transmission over long lead cables, and immunity to electromagnetic interference, FBG sensors offer a promising alternative to traditional electronic sensors for energy system monitoring.

Dominguez-Ontiveros, Elvis [ORNL] (ORCID:000000018↗
DOE OSTI2021

Rayleigh–Taylor and Richtmyer–Meshkov instabilities: A journey through scales

Hydrodynamic instabilities such as Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) instabilities usually appear in conjunction with the Kelvin–Helmholtz (KH) instability and are found in many natural phenomena and engineering applications. They frequently result in turbulent mixing, which has a major impact on the overall flow development and other effective material properties. This can either be a desired outcome, an unwelcome side effect, or just an unavoidable consequence, but must in all cases be characterized in any model. The RT instability occurs at an interface between different fluids, when the light fluid is accelerated into the heavy. The RM instability may be considered a special case of the RT instability, when the acceleration provided is impulsive in nature such as that resulting from a shock wave. Here in this pedagogical review, we provide an extensive survey of the applications and examples where such instabilities play a central role. First, fundamental aspects of the instabilities are reviewed including the underlying flow physics at different stages of development, followed by an overview of analytical models describing the linear, nonlinear and fully turbulent stages. RT and RM instabilities pose special challenges to numerical modeling, due to the requirement that the sharp interface separating the fluids be captured with fidelity. These challenges are discussed at length here, followed by a summary of the significant progress in recent years in addressing them. Examples of the pivotal roles played by the instabilities in applications are given in the context of solar prominences, ionospheric flows in space, supernovae, inertial fusion and pulsed-power experiments, pulsed detonation engines and Scramjets. Progress in our understanding of special cases of RT/RM instabilities is reviewed, including the effects of material strength, chemical reactions, magnetic fields, as well as the roles the instabilities play in ejecta formation and transport, and explosively expanding flows. The article is addressed to a broad audience, but with particular attention to graduate students and researchers who are interested in the state-of-the-art in our understanding of the instabilities and the unique issues they present in the applications in which they are prominent.

42 ENGINEERING↗
DOE OSTI2020

Real-Time Time-Dependent Nuclear–Electronic Orbital Approach: Dynamics beyond the Born–Oppenheimer Approximation

The quantum mechanical treatment of both electrons and nuclei is crucial in nona- diabatic dynamical processes such as proton-coupled electron transfer. The nuclear electronic orbital (NEO) method provides an elegant framework for including nuclear quantum effects beyond the Born-Oppenheimer approximation. To enable the study of nonequilibrium properties, we derive and implement a real-time NEO (RT-NEO) approach based on time-dependent Hatree-Fock or density functional theory, in which both the electronic and nuclear degrees of freedom are propagated in a time-dependent variational framework. Nuclear and electronic spectral features can be resolved from the time-dependent dipole moment computed using the RT-NEO method. The test cases demonstrate the dynamical interplay between the quantum nuclei and the electrons through vibronic coupling. Moreover, vibrational excitation in the RT-NEO approach is demonstrated by applying a resonant driving eld, and electronic excitation is demonstrated by simulating excited state intramolecular proton transfer. This work shows that the RT-NEO approach is a promising tool to study nonadiabatic quantum dynamical processes within a time-dependent variational description for the coupled electronic and nuclear degrees of freedom.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Investigating the Role π -Rich Solvents Play in the Growth of Cesium Lead Bromide Nanocrystals

In this report, the role that a high-boiling-point solvent type plays on the nucleation and growth, morphology, and crystal-phase transformation of cesium lead bromide nanocrystals (CsPbBr 3 ) is studied. The CsPbBr 3 products were compared between a one-pot growth mechanism at room temperature (RT) versus a hot-injection mechanism (HI) control using dibenzyl ether (DBE), diphenyl ether (DPE), dioctyl ether (DOE), or 1- octadecene (ODE). The coordination between these solvents and the PbBr 2 salt precursors resulted in different plumbate [PbSBr n ] 2−n precursors being formed. The S-to-Pb 2+ coordination within [PbSBr n ] 2−n was probed by UV−vis and solvent-phase 207 Pb NMR, both of which showed considerable coordination between [PbSBr n ] 2−n and the π-rich DBE and DPE, whose reactivity affected CsPbBr 3 growth. The effect was more pronounced for CsPbBr 3 prepared via RT, where the morphology was tunable, with π-rich solvents producing thin rod-like CsPbB r3 with a blue emission, compared to the green-emitting thicker platelets formed via HI. While XRD showed crystalline products for both RT and HI, with orthorhombic and cubic forms, respectively, the RT products had considerable surface defects, as was indicated by lower quantum yields, and to understand this the photoluminescent lifetimes were measured by time-correlated single photon counting.

207Pb NMR↗
DOE OSTI2024

Real-Time Time-Dependent Density Functional Theory for Simulating Nonequilibrium Electron Dynamics

The explicit real-time propagation approach for time-dependent density functional theory (RT-TDDFT) has increasingly become a popular first-principles computational method for modeling various time-dependent electronic properties of complex chemical systems. Here, in this Perspective, we provide a nontechnical discussion of how this first-principles simulation approach has been used to gain novel physical insights into nonequilibrium electron dynamics phenomena in recent years. Following a concise overview of the RT-TDDFT methodology from a practical standpoint, we discuss our recent studies on the electronic stopping of DNA in water and the Floquet topological phase as examples. Our discussion focuses on how RT-TDDFT simulations played a unique role in deriving new scientific understandings. We then discuss existing challenges and some new advances at the frontier of RT-TDDFT method development for studying increasingly complex dynamic phenomena and systems.

Hamiltonians↗