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NASA NTRS1999

Analysis of Unsteady Flow Phenomena: Shock - Vortex and Shock - Boundary Layer Interactions

The interaction of shock waves with vortices has received much attention in the past, mainly because shock-vortex interaction closely models the interaction of a shock wave with the coherent structures of a turbulent flow-field, and is a key feature in the broad-band shock noise for supersonic jets in off-project conditions. Chu and Kovasznay have shown that a weak disturbance in a viscous heat conducting fluid can be decomposed as the sum of three basic modes, namely acoustic, vortical and entropy mode; the interaction of any of these modes with a shock wave gives rise to all three disturbance modes downstream of the shock. The vortical mode is important since it constitutes the basis of the coherent structures that have been observed to dominate turbulence for low- to moderate-flow speed. Hollingsworth et al. have experimentally investigated the interaction of a cylindrical shock-induced starting vortex with a plane normal shock, and have shown that the interaction generates a cylindrical acoustic pulse that exhibits a quadrupolar structure consisting of four alternate compression and expansion regions centered around the transmitted vortex. The investigations of Hollingsworth and Richards have been extended by Dosanjh and Weeks that have analyzed the interaction of a columnar spiral vortex with a normal shock wave, thus obtaining quantitative measurements and confirming the generation of a progressive cylindrical wavefront of alternate compression-expansion nature. Naumann and Hermanns' have experimentally addressed the non-linear aspects of shock-vortex interaction, and have shown that the interaction causes both a diffraction and a reflection of the shock with a pattern consisting of either a regular-or a Mach-reflection depending on the shock and the vortex strengths. An attempt to theoretically explain the production of sound from the shock-vortex interaction was carried out by Ribner. Pao and Salas have numerically studied two-dimensional shock-vortex interactions.

Grasso, Francesco↗

DOE OSTI2020

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Triton: Igiugig Fish Video Analysis (Project Report)

This document summarizes the analysis of video data collected around the Ocean Renewable Power Company’s RivGen® device in the Kvichak River during July and August 2015. Human (manual) analysis of the data was undertaken and used to develop automated algorithms to detect fish in the frames and describe interaction behavior. In addition, a web application, EyeSea, was developed to combine manual and automated processing, so that ultimately the automated algorithms could be used to identify where human analysis was needed (i.e., when fish are present in video frames). The aim of the project was to develop algorithms that could identify video frames with fish present that could then be used to enable faster manual analysis. However, the project has also identified recommendations for future data collection, and research that could help analysis and interpretation. The manual analysis started to look at all data from the start of the deployment; this was to ensure rare events were seen, and initially focused on night-time data when more fish were present. This process highlighted the amount of time taken to identify fish, and ultimately only 42.33 hours of video were reviewed due to the time-consuming analysis. The data were classified as ‘Fish’, when the reviewer was confident it was a fish, and ‘Maybe’ fish, when it was difficult to distinguish. This was based on the movement, shape and color characteristics. ‘Fish’ were further classified as ‘adult’, ‘juvenile’, or ‘unidentifiable’. Behavioral attributes were noted, which were broadly divided into passive and avoidance activities. In over 42 hours data, there were only 20 potential contact interactions, of which 3 were ‘Maybe’ classifications, 12 were juveniles and 5 were adults; on only one occasion was an actual contact confirmed, and this was an adult fish with the camera, not the turbine itself. This also highlights the difficulties associated with confirming a strike or collision event as occurring or being a near-miss. More interactions were detected at night; this was probably biased by nighttime artificial light use, which may have attracted fish, but also could have increased detection probability as the light is reflected from the fish itself. For the algorithm development, background subtraction, optical flow, and deep learning techniques were considered. The deep learning approach was determined as needing too much training data for this application, and therefore was not continued. The optical flow analysis was considered promising, but did not give immediate results, so would need further investigation. Therefore, background subtraction was the main focus. Three methods of background subtraction were tried: Robust Principal Components Analysis (RPCA), Gaussian Mixture Model (GMM) and Video Background Extraction(ViBE). A classification technique was then applied to the foreground images to determine fish presence. Using this combination, it was found that fish could be accurately detected when occupying more pixels (>200 pixels, 98.2% correct; 100-200 pixels, 99.6% correct; 5-100 pixels, 85.4% correct; 2-5 pixels, 66.3% correct). In parallel, EyeSea was developed to convert the video data to a usable form and to enable manual and automated analysis of the data that would have a standardized output. Recommendations for further research, and standardized methods for data collection are given.

13 HYDRO ENERGY↗

DOE OSTI2016

A SYSTEMATIC SURVEY FOR BROADENED CO EMISSION TOWARD GALACTIC SUPERNOVA REMNANTS

We present molecular spectroscopy toward 50 Galactic supernova remnants (SNRs) taken at millimeter wavelengths in {sup 12}CO J = 2 − 1. These observations are part of a systematic survey for broad molecular line (BML) regions indicative of interactions with molecular clouds (MCs). We detected BML regions toward 19 SNRs, including 9 newly identified BML regions associated with SNRs (G08.3–0.0, G09.9–0.8, G11.2–0.3, G12.2+0.3, G18.6–0.2, G23.6+0.3, 4C–04.71, G29.6+0.1, and G32.4+0.1). The remaining 10 SNRs with BML regions confirm previous evidence for MC interaction in most cases (G16.7+0.1, Kes 75, 3C 391, Kes 79, 3C 396, 3C 397, W49B, Cas A, and IC 443), although we confirm that the BML region toward HB 3 is associated with the W3(OH) H ii region, not the SNR. Based on the systemic velocity of each MC, molecular line diagnostics, and cloud morphology, we test whether these detections represent SNR–MC interactions. One of the targets (G54.1+0.3) had previous indications of a BML region, but we did not detect broadened emission toward it. Although broadened {sup 12}CO J = 2 − 1 line emission should be detectable toward virtually all SNR–MC interactions, we find relatively few examples; therefore, the number of interactions is low. This result favors mechanisms other than supernova feedback as the basic trigger for star formation. In addition, we find no significant association between TeV gamma-ray sources and MC interactions, contrary to predictions that SNR–MC interfaces are the primary venues for cosmic ray acceleration.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2019

Programming Metabolite Exchange to Understand and Control Plant-Microbe Interactions

Many aspects of plant growth and survival are dependent upon beneficial interactions between plant tissues and bacterial species of the endophyte and rhizosphere. These associated microorganisms can contribute positively to plant growth, stress tolerance, metabolism and protection against plant pathogens. For example, an endosymbiotic bacterium Burkholderia phytofirmans PsJN was shown to colonize and promote growth of switchgrass under controlled conditions, suggesting it may be a promising candidate for improving bioenergy crop production (Kim et al., 2012). Despite the documented benefits of endophytic and rhizosphere microbes on plant fitness and photosynthetic productivity, there is still a gap in our understanding of specific molecular -and cellular-level processes that guide the development of beneficial plant-microbe interactions. As these interactions involve physical contact/metabolite exchange we also posit that directed co-localization of beneficial bacteria and plant cells will enhance these benefits. We propose to engineer bacterial species that co-localize with the plant tissue and then to measure cell growth as well as carry out –omics analysis to obtain information regarding the specifics of these beneficial interactions as well as their extent. This report describes our progress with these goals and the results.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1997

Full-Potential Modeling of Blade-Vortex Interactions

A study of the full-potential modeling of a blade-vortex interaction was made. A primary goal of this study was to investigate the effectiveness of the various methods of modeling the vortex. The model problem restricts the interaction to that of an infinite wing with an infinite line vortex moving parallel to its leading edge. This problem provides a convenient testing ground for the various methods of modeling the vortex while retaining the essential physics of the full three-dimensional interaction. A full-potential algorithm specifically tailored to solve the blade-vortex interaction (BVI) was developed to solve this problem. The basic algorithm was modified to include the effect of a vortex passing near the airfoil. Four different methods of modeling the vortex were used: (1) the angle-of-attack method, (2) the lifting-surface method, (3) the branch-cut method, and (4) the split-potential method. A side-by-side comparison of the four models was conducted. These comparisons included comparing generated velocity fields, a subcritical interaction, and a critical interaction. The subcritical and critical interactions are compared with experimentally generated results. The split-potential model was used to make a survey of some of the more critical parameters which affect the BVI.

Jones, Henry E.↗

DOE OSTI2024

Structural basis of tRNA recognition by the widespread OB fold

The widespread oligonucleotide/oligosaccharide-binding (OB)-fold recognizes diverse substrates from sugars to nucleic acids and proteins, and plays key roles in genome maintenance, transcription, translation, and tRNA metabolism. OB-containing bacterial Trbp and yeast Arc1p proteins are thought to recognize the tRNA elbow or anticodon regions. Here we report a 2.6 Å co-crystal structure of Aquifex aeolicus Trbp111 bound to tRNA Ile , which reveals that Trbp recognizes tRNAs solely by capturing their 3' ends. Structural, mutational, and biophysical analyses show that the Trbp/EMAPII-like OB fold precisely recognizes the single-stranded structure, 3' terminal location, and specific sequence of the 3' CA dinucleotide — a universal feature of mature tRNAs. Arc1p supplements its OB – tRNA 3' end interaction with additional contacts that involve an adjacent basic region and the tRNA body. This study uncovers a previously unrecognized mode of tRNA recognition by an ancient protein fold, and provides insights into protein-mediated tRNA aminoacylation, folding, localization, trafficking, and piracy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

A divergent Pumilio repeat protein family for pre-rRNA processing and mRNA localization

Pumilio/feminization of XX and XO animals (fem)-3 mRNA-binding factor (PUF) proteins bind sequence specifically to mRNA targets using a single-stranded RNA-binding domain comprising eight Pumilio (PUM) repeats. PUM repeats have now been identified in proteins that function in pre-rRNA processing, including human Puf-A and yeast Puf6. This is a role not previously ascribed to PUF proteins. In this paper we present crystal structures of human Puf-A that reveal a class of nucleic acid-binding proteins with 11 PUM repeats arranged in an “L”-like shape. In contrast to classical PUF proteins, Puf-A forms sequence-independent interactions with DNA or RNA, mediated by conserved basic residues. We demonstrate that equivalent basic residues in yeast Puf6 are important for RNA binding, pre-rRNA processing, and mRNA localization. Finally, PUM repeats can be assembled into alternative folds that bind to structured nucleic acids in addition to forming canonical eight-repeat crescent-shaped RNA-binding domains found in classical PUF proteins.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Photoluminescence and Confinement of Excitons in Disordered Porous Films

The exciton confinement effect in quantum dots at the surface of SiO{sub 2} spheres and the percolation phase transition in films based on a mixture of pure SiO{sub 2} spheres and spheres covered by CdS quantum dots (SiO{sub 2}/CdS nanoparticles) are studied. It is found that, due to the high surface energy of spheres, the quantum dots deposited onto their surface are distorted, which modifies the exciton confinement effect: the effect is retained only in one direction, the direction normal to the surface of the spheres. As a result, the energy of the exciton ground state exhibits a complex dependence on both the quantum-dot radius and sphere size. In the optical spectra of films based on this mixture, the clustering of small-sized nanoparticles and then, at a critical concentration of nanoparticles of ~60%, the formation of a percolation cluster are detected for the first time. The critical concentration is twice higher than the corresponding quantity given by the model of geometrical “colored percolation”, which is a consequence of interaction between submicrometer nanoparticles. The relation between the basic parameters of the percolation transition, such as the film porosity, coordination number, and the quantity defining the number of particles in the percolation cluster, is obtained and analyzed.

36 MATERIALS SCIENCE↗

DOE OSTI2022

A Theory for the Response of Tropical Moist Convection to Mechanical Orographic Forcing

Abstract Spatial patterns of tropical rainfall are strongly influenced by mountains. Although theories for precipitation induced by convectively stable upslope ascent exist for the midlatitudes, these do not represent the interaction of moist convection with orographic forcing. Here, we present a theory for convective precipitation produced by the mechanical interaction of a tropical ridge with a basic-state horizontal wind. Deviations from this basic state are represented as the sum of a “dry” perturbation, due to the stationary orographic gravity wave, and a “moist” perturbation that carries the convective response. The moist component dynamics are subject to the weak temperature gradient approximation; they are forced by the dry mode’s influence on lower-tropospheric moisture and temperature. Analytical solutions provide estimates of the precipitation distribution, including peak precipitation, upstream extent, and rain shadow extent. The theory can be used with several degrees of complexity depending on the technique used to compute the dry mode, which can be drawn from linear mountain wave theory or full numerical simulations. To evaluate the theory, we use a set of convection-permitting simulations with a flow-perpendicular ridge in a long channel. The theory makes a good prediction for the cross-slope precipitation profile, indicating that the organization of convective rain by orography can be quantitatively understood by considering the effect of stationary orographic gravity waves on a lower-tropospheric convective quasi-equilibrium state.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Human-System Interface Design Review Guidelines

The U.S. Nuclear Regulatory Commission (NRC) staff reviews the human factors engineering (HFE) aspects of nuclear power plants in accordance with the Standard Review Plan (NUREG-0800, Standard Review Plan for the Review of Safety Analysis Reports for Nuclear Power Plants: LWR Edition). The Human Factors Engineering Program Review Model (NUREG-0711, Revision 3, issued November 2012) contains detailed design review procedures. As part of the review process, the interfaces between plant personnel and the plant's systems and components are evaluated for conformance with HFE guidelines. This document, Human-System Interface Design Review Guidelines (NUREG-0700, Revision 3), provides the guidelines necessary to perform this evaluation. The review guidelines address the physical and functional characteristics of human-system interfaces (HSIs). Because these guidelines only address the HFE aspects of design and not other related considerations, such as instrumentation and control and structural design, they are referred to as HFE guidelines. In addition to the review of actual HSIs, the NRC staff can use the NUREG-0700 guidelines to evaluate a design-specific HFE guidelines document or style guide. The HFE guidelines are organized into four basic parts, which are divided into sections. Part I contains guidelines for the basic HSI elements: information displays, user-interface interaction and management, and analog displays and controls. These elements are used as building blocks to develop HSI systems to serve specific functions. Part II contains the guidelines for reviewing the following HSI systems: alarm system, safety parameter display system, group-view display system, soft control system, computer-based procedure system, automation system, and communication system. Part III provides guidelines for the review of workstations and workplaces. Part IV provides guidelines for the review of HSI support (i.e., maintainability of digital systems and degraded HSI and instrumentation and control conditions).

42 ENGINEERING↗

DOE OSTI2025

Optimal Uses of Magnetic Fields for Indirect-Drive Inertial Fusion

This project explored how applied magnetic fields can improve inertial confinement fusion (ICF), specifically the indirect-drive approach that uses a hohlraum. This has been proposed for several decades as potentially beneficial, due to thermal insulation (reduced losses) from the imploded hotspot. We performed the most advanced radiation-magneto-hydrodynamic modeling to date of magnetized ICF designs in the ignition regime. We found that adding technologically feasible fields up to 60 – 70 Tesla could increase the fusion yield of current igniting designs for the National Ignition Facility (NIF) by up to 8x. Also, simulations show that in certain cases relatively small fields of 3 – 5 Tesla could double the yield, and be implemented at much lower cost. Early work on re-optimizing NIF designs with magnetic fields, namely by using a thicker ablator with more mass remaining, could increase the yield of a sub-ignition target by 18x and bring it into the ignition regime. A separate benefit of magnetization besides reduced thermal loss is reduced hydrodynamic instability. Modeling work under this project shows this could be significant, though early experiments at NIF and the Omega Laser proved inconclusive. We designed and proposed an improved NIF experiment on magnetized mix, based on a large-amplitude imposed perturbation. The project also supported basic physics research into magnetized laser-plasma interactions, namely cross-beam energy transfer, both with experiments at Omega and theory / modeling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2019

In Situ Loading and Delivery of Short Single- and Double-Stranded DNA by Supramolecular Organic Frameworks

Short DNA represents an important class of biomacromolecules that are widely applied in gene therapy, editing, and modulation. However, the development of simple and reliable methods for their intracellular delivery remains a challenge. Herein, we describe that seven water-soluble, homogeneous supramolecular organic frameworks (SOFs) with a well-defined pore size and high stability in water that can accomplish in situ inclusion of single-stranded (ss) and double-stranded (ds) DNA (21, 23, and 58 nt) and effective intracellular delivery (including two noncancerous and six cancerous cell lines). Fluorescence quenching experiments for single and double end-labeled ss- and ds-DNA support that the DNA sequences can be completely enveloped by the SOFs. Confocal laser scanning microscopy and flow cytometry reveal that five of the SOFs exhibit excellent delivery efficiencies that, in most of the studied cases, outperform the commercial standard Lipo2000, even at low SOF–nucleic acid ratios. In addition to high delivery efficiencies, the water-soluble, self-assembled SOF carriers have a variety of advantages, including convenient preparation, high stability, and in situ DNA inclusion, which are all critical for practical applications in nucleic acid delivery.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1975

Sketch of a unifying auroral theory

On the basis of field and particle observations, it is suggested that a bright auroral display is a part of a magnetosphere-ionosphere current system which is fed by a charge-separation process in the outer magnetosphere (or the solar wind). The upward magnetic-field-aligned current is flowing out of the display, carried mainly by down-flowing electrons from the hot-particle populations in the outer magnetosphere (the ambient cold electrons being depleted at high altitudes). As a result of the magnetic mirroring of these downflowing current carriers, a large potential drop is set up along the magnetic field, increasing both the number flux and the kinetic energy of the precipitating electrons. It is found that this simple basic model, when combined with wave-particle interactions, may be able to explain a highly diversified selection of auroral particle observations. It may thus be possible to explain both inverted-V events and auroral rays in terms of a static parallel electric field, and the electric field may be compatible with a strongly variable pitch-angle distribution of the precipitating electrons, including distributions peaked at 90 deg as well as 0 deg. This model may also provide a simple explanation of the simultaneous precipitation of electrons and collimated positive ions.

Lennartsson, W.↗

NASA NTRS1977

Space processing on Skylab and ASTP

The Skylab and Apollo Soyuz Test Project (ASTP) missions provided the opportunity the influence of micro-gravity on the processing of various materials. The results of physical and engineering experiments in metallurgy, fluids handling and crystal growth on two space missions are discussed. The majority of the experiments concern the solidification of alloys, semiconductors, and composite materials or basic liquid-liquid and solid-liquid interactions necessary to understand complex processing. Potential advantages of space processing to several materials disciplines are identified.

Snyder, R. S.↗

NASA NTRS1976

On the role of magnetic mirroring in the auroral phenomena

Lennartsson, W.↗

NASA NTRS1981

ICAP - An Interactive Cluster Analysis Procedure for analyzing remotely sensed data

An Interactive Cluster Analysis Procedure (ICAP) was developed to derive classifier training statistics from remotely sensed data. ICAP differs from conventional clustering algorithms by allowing the analyst to optimize the cluster configuration by inspection, rather than by manipulating process parameters. Control of the clustering process alternates between the algorithm, which creates new centroids and forms clusters, and the analyst, who can evaluate and elect to modify the cluster structure. Clusters can be deleted, or lumped together pairwise, or new centroids can be added. A summary of the cluster statistics can be requested to facilitate cluster manipulation. The principal advantage of this approach is that it allows prior information (when available) to be used directly in the analysis, since the analyst interacts with ICAP in a straightforward manner, using basic terms with which he is more likely to be familiar. Results from testing ICAP showed that an informed use of ICAP can improve classification, as compared to an existing cluster analysis procedure.

Wharton, S. W.↗