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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 721 records · Page 40
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Underwater Fish Detection using Deep Learning for Water Power Applications

Clean energy from oceans and rivers is becoming a reality with the development of new technologies like tidal and instream turbines that generate electricity from naturally flowing water. These new technologies are being monitored for effects on fish and other wildlife using underwater video. Methods for automated analysis of underwater video are needed to lower the costs of analysis and improve accuracy. We have trained a deep learning model, YOLO, to recognize fish in underwater video using three very different datasets recorded at real-world water power sites. Training and testing with examples from all three datasets resulted in a mean average precision (MAP) score of 0.5392. To test how well a model could generalize to new datasets, the model was trained using examples from only two of the datasets and then tested on examples from all three datasets. The resulting model could not recognize fish in the dataset that was not part of the training set. The MAP scores on the other two datasets that were included in the training set were higher than the scores achieved by the model trained on all three datasets. These results indicate that different methods are needed in order to produce a trained model that can generalize to new data sets such as those encountered in real world applications.

fish detection, underwater video, marine and hydro↗
DOE OSTI2021

Oregon Rivers Characterization Tool

DHS’s Regional Resiliency Assessment Program (RRAP) undertook the Oregon State Transportation Systems RRAP project between 2018-2021 to assess the seismic vulnerabilities of the state’s transportation system to a Cascadia Subduction Zone (CSZ) earthquake (CISA 2021). The project primarily focused on the effects of a CSZ earthquake on the mobility of emergency response efforts into the region. In the event that bridges located at crucial river crossings fail during a CSZ earthquake, rivers will become natural barriers affecting the ability to support response and recovery efforts. The characteristics of rivers (e.g., width, depth, and flow) are critical data to inform planning for the recovery of transportation systems across river barriers and determine reopening times following a CSZ earthquake. As part of the transportation system assessment, an Argonne National Laboratory (Argonne) project team developed a River Characterization Tool (RCT) to quantify the physical characteristics of the river system in Oregon, which can be used to inform a system-level analysis of transportation recovery and reopening times. This report mainly discusses approaches, methods, development, and applications of the RCT. The use of the river data generated from this tool for a system-level analysis of transportation recovery is discussed in the Oregon Transportation Systems RRAP Resiliency Assessment report (CISA 2021). The primary goal of the RCT is to generate statewide dataset of widths, depths, and flows for all rivers across Oregon to assess the effects of river barriers on emergency response and recovery efforts following a CSZ earthquake. The RCT leverages remote sensing data that multispectral sensors collect from satellites, employs a deep learning model to characterize river predictions, and computes river channel geometric dimensions with hydraulic relationships and river predictions. The entire process of river characterization is automated and implemented through the RCT.

58 GEOSCIENCES↗
DOE OSTI2024

Measurement of Nuclear Dependence in Inclusive Antineutrino Scattering

One of the fundamental questions in physics is the matter-antimatter asymmetry of the Universe, explored through charge-parity violation searches in neutrino oscillation experiments. Next-generation oscillation experiments like DUNE need to constrain the systematic uncertainties arising from our understanding of (anti)neutrino-nucleus scattering to within a few percent to achieve their physics goals. MINERvA, a dedicated (anti)neutrino-nucleus scattering experiment, plays a crucial role in constraining these uncertainties. This thesis presents MINERvA's first high-statistics direct measurement of nuclear dependence in charged-current inclusive antineutrino scattering on carbon, hydrocarbon, iron, and lead as a function of antimuon transverse momentum, $p_{\text{T}}$, and Bjorken~$x$. The analysis utilises interactions with a mean antineutrino energy of approximately~6~GeV, with reconstructed antimuons having a scattering angle of less than 17$^\circ$ relative to the antin eutrino beam and an antimuon energy of 2--20 GeV. The measured per-nucleon differential cross-sections are reported with a precision of 7--9\%, while the cross-section ratios of carbon, iron, and lead to hydrocarbon have uncertainties of 5\% or less. The cross-sections for iron and lead indicate strong suppression at low $p_{\text{T}}$ and Bjorken~$x$, and an enhancement at high $p_{\text{T}}$. These effects are observed to be more pronounced with the increasing size of the target nucleus and are not reproduced by the underlying simulation prediction. Comparisons to alternative models used in current (anti)neutrino interaction generators show some improvements in modelling over the base prediction model, yet they are still unable to fully reproduce the observed nuclear dependence in this analysis. Importantly, the analysis provides a direct test of nuclear effects in inclusive antineutrino scattering, with major contributions from resonant pion production, deep inelastic scattering, and the transition region between these channels, which will be significant in DUNE. This measurement also represents one of the largest antineutrino datasets in this energy regime analysed to date.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

A deep learning enabler for nonintrusive reduced order modeling of fluid flows

Here in this paper, we introduce a modular deep neural network (DNN) framework for data-driven reduced order modeling of dynamical systems relevant to fluid flows. We propose various DNN architectures which numerically predict evolution of dynamical systems by learning from either using discrete state or slope information of the system. Our approach has been demonstrated using both residual formula and backward difference scheme formulas. However, it can be easily generalized into many different numerical schemes as well. We give a demonstration of our framework for three examples: (i) Kraichnan-Orszag system, an illustrative coupled nonlinear ordinary differential equation, (ii) Lorenz system exhibiting chaotic behavior, and (iii) a nonintrusive model order reduction framework for the two-dimensional Boussinesq equations with a differentially heated cavity flow setup at various Rayleigh numbers. Using only snapshots of state variables at discrete time instances, our data-driven approach can be considered truly nonintrusive since any prior information about the underlying governing equations is not required for generating the reduced order model. Our a posteriori analysis shows that the proposed data-driven approach is remarkably accurate and can be used as a robust predictive tool for nonintrusive model order reduction of complex fluid flows.

42 ENGINEERING↗
DOE OSTI2017

Simultaneous Evolution of Gyre and Atlantic Meridional Overturning Circulation Anomalies as an Eigenmode of the North Atlantic System

Here, the authors observe an interdecadal oscillatory mode of the North Atlantic atmosphere–ocean system in a general circulation model (GFDL CM2.1) via a linear inverse model (LIM). The oscillation mechanism is mostly embedded in the subpolar gyre: anomalous advection generates density anomalies in the eastern subpolar gyre, which propagate along the mean gyre circulation and reach the subpolar gyre center around 10 years later, when associated anomalous advection of the opposite sign starts the other half cycle. While density anomalies reach the Labrador Sea deep convection region, Atlantic meridional overturning circulation (AMOC) anomalies are also induced. Both the gyre and AMOC anomalies then propagate equatorward slowly, following the advection of density anomalies. The oscillation is further demonstrated to be more likely an ocean-only mode while excited by the atmospheric forcing; in particular, it can be approximated as a linearly driven damped oscillator that is partly excited by the North Atlantic Oscillation (NAO). The slowly evolving interdecadal oscillation significantly improves and prolongs the LIM’s prediction skill of sea surface temperature (SST) evolution.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Deep learning models for interpretation of point of care ultrasound in military working dogs

Introduction: Military working dogs (MWDs) are essential for military operations in a wide range of missions. With this pivotal role, MWDs can become casualties requiring specialized veterinary care that may not always be available far forward on the battlefield. Some injuries such as pneumothorax, hemothorax, or abdominal hemorrhage can be diagnosed using point of care ultrasound (POCUS) such as the Global FAST® exam. This presents a unique opportunity for artificial intelligence (AI) to aid in the interpretation of ultrasound images. In this article, deep learning classification neural networks were developed for POCUS assessment in MWDs. Methods: Images were collected in five MWDs under general anesthesia or deep sedation for all scan points in the Global FAST® exam. For representative injuries, a cadaver model was used from which positive and negative injury images were captured. A total of 327 ultrasound clips were captured and split across scan points for training three different AI network architectures: MobileNetV2, DarkNet-19, and ShrapML. Gradient class activation mapping (GradCAM) overlays were generated for representative images to better explain AI predictions. Results: Performance of AI models reached over 82% accuracy for all scan points. The model with the highest performance was trained with the MobileNetV2 network for the cystocolic scan point achieving 99.8% accuracy. Across all trained networks the diaphragmatic hepatorenal scan point had the best overall performance. However, GradCAM overlays showed that the models with highest accuracy, like MobileNetV2, were not always identifying relevant features. Conversely, the GradCAM heatmaps for ShrapML show general agreement with regions most indicative of fluid accumulation. Discussion: Overall, the AI models developed can automate POCUS predictions in MWDs. Preliminarily, ShrapML had the strongest performance and prediction rate paired with accurately tracking fluid accumulation sites, making it the most suitable option for eventual real-time deployment with ultrasound systems. Further integration of this technology with imaging technologies will expand use of POCUS-based triage of MWDs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Regional-scale flows in mountainous terrain. Part 1: A numerical and observational comparison

This study uses observed data and a numerical simulation to examine the generation of thermally driven flows across the Colorado mountain barrier on meso-beta to meso-alpha scales. The observations were collected from remote surface observing systems at exposed mountaintop locations throughout the state of Colorado, over the summers of 1984-88, as part of the Rocky Mountain Peaks Experiment (ROMPEX). The data show the development of a recurrent circulation system across the Colorado mountain barrier, operating on a diurnal timescale. From the observations, the basic structure of the flow system appears as a daytime inflow toward the highest terrain, and a nocturnal outflow away from it. However, when examined in detail, the flow system exhibits more unusual behavior, especially west of the barrier crest. Here, winds in the early evening are occasionally observed to onset abruptly from an easterly direction, generally counter to the upper-level winds. Observations from ROMPEX for 26 August 1985 are used to provide comparison data for a numerical simulation with the Regional Atmospheric Modeling System (RAMS). This three-dimensional case study experiment is initialized with data from the National Meteorological Center and incorporates two-way interactive grid nesting. From the observed data and case study simulation, four distinct phases of the regional-scale circulation system have been identified. In the development phase, a deep mountain-plains solenoid is generated through terrain heating along the Front Range. This circulation system transforms in the late afternoon transition phase into a westward-propagating density current (WPDC). The third phase, called the 'density-current propagation phase,' occurs as the WPDC moves westward across the mountains, leaving in its wake strong southeasterly flow at the mountaintop level. This current appears to be the cause of the peculiar easterly component winds found in the ROMPEX mountaintop observations along the western slope. In the final late-night adjustment phase, the WPDC dissipates near the western edge of the Colorado mountains and steady southerly flow evolves over the high mountain terrain. This southerly flow is the steady response to the differential heating that develops between the low-lying plains and the intermountain region.

Bossert, James E.↗
DOE OSTI2024

Causes of Reduced Climate Sensitivity in E3SM From Version 1 to Version 2

The effective climate sensitivity in the Department of Energy's Energy Exascale Earth System Model (E3SM) has decreased from 5.3 K in version 1 to 4.0 K in version 2. This reduction is mainly due to a weaker positive cloud feedback that leads to a stronger negative radiative feedback. Present-day atmosphere-only experiments with uniform 4 K sea surface temperature warming are used to separate the contributions of individual model modifications to the reduced cloud feedback. We find that the reduced cloud feedback is mostly driven by changes over the tropical marine low cloud regime, mainly related to a new trigger function for the deep convection scheme and modifications in the cloud microphysics scheme. The new trigger function helps weaken the low cloud reduction by increasing the cloud water detrainment at low levels from deep convection under warming. Changes to the formula of autoconversion rate from liquid to rain and an introduced minimum cloud droplet number concentration threshold in cloud microphysical calculations help sustain clouds against dissipation by suppressing precipitation generation with warming. In the midlatitudes, the increased Wegener-Bergeron-Findeisen (WBF) efficiency strongly reduces present-day liquid water and leads to a stronger negative cloud optical depth feedback. The reduced trade cumulus cloud feedback in v2 is closer to estimates from recent observational and large-eddy modeling studies but might not be due to the right physical reasons. The reduced mid-latitude cloud feedback may be more plausible because more realistic present-day mixed-phase clouds are produced through the change in the WBF efficiency.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Enhanced Oblique Decision Tree Enabled Policy Extraction for Deep Reinforcement Learning in Power System Emergency Control

Deep reinforcement learning (DRL) algorithms have successfully solved many challenging problems in various power system control scenarios. However, their decision-making process is usually regarded as black-boxes. Furthermore, how DRL models interact with human intelligence remains an open problem. Thus, this paper proposes a policy extraction framework to extract a complex DRL model into an explainable policy. This framework includes three parts: 1) DRL training and data generation. We train an agent for a specific control task and generate data, which contains the control policy of the agent. 2) Policy extraction. We propose an information gain rate based weighted oblique decision tree (IGR-WODT) for DRL policy extraction. 3) Policy evaluation. We define three metrics to evaluate the performance of the proposed approach. A case study for the under-voltage load shedding problem shows that the IGR-WODT presents a performance enhancement compared with DRL, weighted oblique decision tree, and univariate decision tree. The proposed policy extraction method could provide an intuitive explanation of the neural network decision-making process to the dispatchers when making final decisions on power grid operation. Also, the resulted rule-based controller could replace the deep neural network-based controller in many field edge devices with limited computing resources, providing comparable performance.

deep reinforcement learning↗
DOE OSTI2021

Light, long-lived B - L gauge and Higgs bosons at the DUNE near detector

The low-energy U(1)B-L gauge symmetry is well-motivated as part of beyond Standard Model physics related to neutrino mass generation. We show that a light B - L gauge boson Z' and the associated U(1) B-L -breaking scalar φ can both be effectively searched for at high-intensity facilities such as the near detector complex of the Deep Underground Neutrino Experiment (DUNE). Without the scalar φ, the Z' can be probed at DUNE up to mass of 1 GeV, with the corresponding gauge coupling g BL as low as 10 -9 . In the presence of the scalar φ with gauge coupling to Z', the DUNE capability of discovering the gauge boson Z' can be significantly improved, even by one order of magnitude in g BL , due to additional production from the decay φ → Z'Z'. The DUNE sensitivity is largely complementary to other long-lived Z' searches at beam-dump facilities such as FASER and SHiP, as well as astrophysical and cosmological probes. On the other hand, the prospects of detecting φ itself at DUNE are to some extent weakened in presence of Z', compared to the case without the gauge interaction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2019

Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning

The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing Gaucher disease, an autosomal recessive disorder that displays profound genotype–phenotype nonconcordance. More than 250 disease-causing mutations in GBA1 , the gene encoding GCase, have been discovered, although only one of these, N370S, causes 70% of disease. In this work, we have used a knowledge-based docking protocol that considers experimental data of protein–protein binding to generate a complex between GCase and its known facilitator protein saposin C (SAPC). Multiscale molecular-dynamics simulations were used to study lipid self-assembly, membrane insertion, and the dynamics of the interactions between different components of the complex. Deep learning was applied to propose a model that explains the mechanism of GCase activation, which requires SAPC. Notably, we find that conformational changes in the loops at the entrance of the substrate-binding site are stabilized by direct interactions with SAPC and that the loss of such interactions induced by N370S and another common mutation, L444P, result in destabilization of the complex and reduced GCase activation. Our results provide an atomistic-level explanation for GCase activation and the precise mechanism through which N370S and L444P cause Gaucher disease.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Tree water uptake patterns across the globe

Plant water uptake from the soil is a crucial element of the global hydrological cycle and essential for vegetation drought resilience. Yet, knowledge of how the distribution of water uptake depth (WUD) varies across species, climates, and seasons is scarce relative to our knowledge of aboveground plant functions. With a global literature review, we found that average WUD varied more among biomes than plant functional types (i.e. deciduous/evergreen broadleaves and conifers), illustrating the importance of the hydroclimate, especially precipitation seasonality, on WUD. By combining records of rooting depth with WUD, we observed a consistently deeper maximum rooting depth than WUD with the largest differences in arid regions – indicating that deep taproots act as lifelines while not contributing to the majority of water uptake. The most ubiquitous observation across the literature was that woody plants switch water sources to soil layers with the highest water availability within short timescales. Hence, seasonal shifts to deep soil layers occur across the globe when shallow soils are drying out, allowing continued transpiration and hydraulic safety. While there are still significant gaps in our understanding of WUD, the consistency across global ecosystems allows integration of existing knowledge into the next generation of vegetation process models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Towards On-Chip Learning for Low Latency Reasoning with End-to-End Synthesis

The Software Defined Architectures (SODA) Synthesizer is an open-source compiler-based tool able to automatically generate domain-specialized systems targeting Application-Specific Integrated Circuits (ASICs) or Field Programmable Gate Arrays (FPGAs) starting from high-level programming. SODA is composed of a frontend, SODA-OPT, which leverages the multilevel intermediate representation (MLIR) framework to interface with productive programming tools (e.g., machine learning frame-works), identify kernels suitable for acceleration, and perform high-level optimizations, and of a state-of-the-art high-level synthesis backend, Bambu from the PandA framework, to generate custom accelerators. One specific application of the SODA Synthesizer is the generation of accelerators to enable ultra-low latency inference and control on autonomous systems for scientific discovery (e.g., electron microscopes, sensors in particle accelerators, etc.). This paper provides an overview of the flow in the context of the generation of accelerators for edge processing to be integrated in transmission electron microscopy (TEM) devices, focusing on use cases from precision material synthesis. We show the tool in action with an example of design space exploration for inference on reconfigurable devices with a conventional deep neural network model (LeNet). Finally, we discuss the research directions and opportunities enabled by SODA in the area of autonomous control for scientific experimental workflows.

Castellana, Vito G.↗
DOE OSTI2011

Using next generation transcriptome sequencing to predict an ectomycorrhizal metablome.

Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Evolution in Cloud Population Statistics of the MJO: From AMIE Field Observations to Global-Cloud Permitting Models Final Report

This is a multi-institutional, collaborative project using a three-tier modeling approach to bridge field observations and global cloud-permitting models, with emphases on cloud population structural evolution through various large-scale environments. Our contribution was in data analysis for the generation of high value cloud and precipitation products and derive cloud statistics for model validation. There are two areas in data analysis that we contributed: the development of a synergistic cloud and precipitation cloud classification that identify different cloud (e.g. shallow cumulus, cirrus) and precipitation types (shallow, deep, convective, stratiform) using profiling ARM observations and the development of a quantitative precipitation rate retrieval algorithm using profiling ARM observations. Similar efforts have been developed in the past for precipitation (weather radars), but not for the millimeter-wavelength (cloud) radar deployed at the ARM sites.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1991

Navier-Stokes calculations of transonic flows past cavities

Presented in this paper is a computational investigation of subsonic and transonic flows past three-dimensional deep and transitional cavities. Simulations of these self-induced oscillatory flows have been generated through time-accurate solutions of the Reynolds averaged, full Navier-Stokes equations, using the explicit MacCormack scheme. The Reynolds stresses have been included through the Baldwin-Lomax algebraic turbulence model with certain modifications. The computational results include instantaneous and time averaged flow properties. The results of an experimental investigation have been used not only to validate the time-averaged results, but also to investigate the effects of varying the Mach number and the incoming boundary-layer thickness. Time series analyses have been performed for the instantaneous pressure values on the cavity floor and compared with the results obtained by a predictive formula. While most of the comparisons have been favorable, some discrepancies have been observed, particularly on the rear face. The present results help understanding the three-dimensional and unsteady features of the separations, vortices, the shear layer, as well as some of the aeroacoustic phenomena of compressible cavity flows.

Baysal, O.↗