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At least 415 records · Page 23

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DOE OSTI2021

A theoretical approach for transient shock strengthening in high-energy-density laser compression experiments

In high-energy-density shock compression experiments, the desired state of compression is typically achieved by passing shock waves through a sequence of different materials. Here, a theoretical approach for transiently strengthening such shocks passing through interfaces of experimentally relevant impedance ratios is examined. A semi-analytical method based on characteristics analysis is used to solve the problem of a shock passing from one material to another through an intermediate region of non-uniform impedance; by appropriately designing this region, a greater shock strength can be achieved in the second material for a finite duration than in the absence of this region. When a shock passes into a material of higher impedance, the shock strengthening increases to a maximum before decreasing to an asymptotic value as the strength of the incident shock is increased. For shocks passing into materials of decreasing impedance, the shock strengthening increases monotonically as the strength of the incident shock is increased when the impedance ratio is above a critical threshold. Incorporating multiple intermediate materials can further increase the strength of the transmitted shock, with an exponential discretization of intermediate material impedances being the most effective distribution for strengthening strong shocks. The results suggest that up to 25% and 9% increases in pressure behind the leading shock can be achieved for materials of increasing and decreasing impedance, respectively. The technique is applied to the design of laser-driven dynamic compression experiments, and the results of the analysis are verified via comparison to simulations performed with the HYADES hydrodynamics code.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2021

Elucidating Electron Storage and Distribution within the Pentaheme Scaffold of Cytochrome c Nitrite Reductase (NrfA)

Cytochrome c nitrite reductases (CcNIR or NrfA) play important roles in the global nitrogen cycle by conserving the usable nitrogen in the soil. Here, the electron storage and distribution properties within the pentaheme scaffold of Geobacter lovleyi NrfA were investigated via EPR spectroscopy coupled with chemical titration experiments. Initially, a chemical reduction method was established to sequentially add electrons to the fully oxidized protein, one equivalent at a time. The step–by–step reduction of the hemes was then followed using UV–Vis and EPR spectroscopy. EPR–spectral simulations elucidate the sequence of heme reduction within the pentaheme scaffold, and identify the signals of all five hemes in the EPR spectra. Electrochemical experiments ascertain the reduction potentials for each heme, observed in a narrow +11 (Heme 5) to –212 mV (Heme 3) range (vs SHE). Based on quantitative analysis/simulation of the EPR data, we demonstrate that Hemes 4 and 5 are reduced first (before the active site Heme 1) and serve the purpose of an electron storage unit within the protein. To probe the role of the central Heme 3, a H108M NrfA variant was generated where the reduction potential of Heme 3 is shifted positively (from –212 mV to +29 mV). Here, the H108M mutation significantly impacts the distribution of electrons within the pentaheme scaffold and the reduction potentials of the hemes, reducing the catalytic activity of the enzyme to 3% compared to wild–type. We propose that this is due to Heme 3’s important role as an electron gateway in the wild–type enzyme.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Natural Horizontal Gene Transfer of Antimicrobial Resistance Genes in Campylobacter spp. From Turkeys and Swine

Antibiotic-resistant Campylobacter constitutes a serious threat to public health. The clonal expansion of resistant strains and/or the horizontal spread of resistance genes to other strains and species can hinder the clinical effectiveness of antibiotics to treat severe campylobacteriosis. Still, gaps exist in our understanding of the risks of acquisition and spread of antibiotic resistance in Campylobacter. While the in vitro transfer of antimicrobial resistance genes between Campylobacter species via natural transformation has been extensively demonstrated, experimental studies have favored the use of naked DNA to obtain transformants. In this study, we used experimental designs closer to real-world conditions to evaluate the possible transfer of antimicrobial resistance genes between Campylobacter strains of the same or different species (Campylobacter coli or Campylobacter jejuni) and originating from different animal hosts (swine or turkeys). This was evaluated in vitro through co-culture experiments and in vivo with dual-strain inoculation of turkeys, followed by whole genome sequencing of parental and newly emerged strains. In vitro, we observed four independent horizontal gene transfer events leading to the acquisition of resistance to beta-lactams (blaOXA), aminoglycosides [aph(2")-If and rpsL] and tetracycline [tet(O)]. Observed events involved the displacement of resistance-associated genes by a mutated version, or the acquisition of genomic islands harboring a resistance determinant by homologous recombination; we did not detect the transfer of resistance-carrying plasmids even though they were present in some strains. In vivo, we recovered a newly emerged strain with dual-resistance pattern and identified the replacement of an existing non-functional tet(O) by a functional tet(O) in the recipient strain. Whole genome comparisons allowed characterization of the events involved in the horizontal spread of resistance genes between Campylobacter following in vitro co-culture and in vivo dual inoculation. Our study also highlights the potential for antimicrobial resistance transfer across Campylobacter species originating from turkeys and swine, which may have implications for farms hosting both species in close proximity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Modeling SARS-CoV-2 proteins in the CASP-commons experiment

Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on 10 proteins. The resulting models were released to the public. CASP community members also worked together to provide estimates of local and global accuracy and identify structure-based domain boundaries for some proteins. Subsequently, two of these structures (ORF3a and ORF8) have been solved experimentally, allowing assessment of both model quality and the accuracy estimates. Models from the AlphaFold2 group were found to have good agreement with the experimental structures, with main chain GDT_TS accuracy scores ranging from 63 (a correct topology) to 87 (competitive with experiment).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2013

Structural Dynamics Testing of Advanced Stirling Convertor Components

NASA Glenn Research Center has been supporting the development of Stirling energy conversion for use in space. Lockheed Martin has been contracted by the Department of Energy to design and fabricate flight-unit Advanced Stirling Radioisotope Generators, which utilize Sunpower, Inc., free-piston Advanced Stirling Convertors. The engineering unit generator has demonstrated conversion efficiency in excess of 20 percent, offering a significant improvement over existing radioisotope-fueled power systems. NASA Glenn has been supporting the development of this generator by developing the convertors through a technology development contract with Sunpower, and conducting research and experiments in a multitude of areas, such as high-temperature material properties, organics testing, and convertor-level extended operation. Since the generator must undergo launch, several launch simulation tests have also been performed at the convertor level. The standard test sequence for launch vibration exposure has consisted of workmanship and flight acceptance levels. Together, these exposures simulate what a flight convertor will experience. Recently, two supplementary tests were added to the launch vibration simulation activity. First was a vibration durability test of the convertor, intended to quantify the effect of vibration levels up to qualification level in both the lateral and axial directions. Second was qualification-level vibration of several heater heads with small oxide inclusions in the material. The goal of this test was to ascertain the effect of the inclusions on launch survivability to determine if the heater heads were suitable for flight.

Heaters↗

NASA NTRS2013

Structural Dynamics Testing of Advanced Stirling Convertor Components

Oriti, Sal↗

DOE OSTI2024

Collective modes of excitation in 64 Cu

Medium and high-spin level sequences in 64 Cu were investigated using the complex 26 Mg( 48 Ca, αp5nγ ) multinucleon transfer reaction. The experiment was performed at the ATLAS accelerator facility at the Argonne National Laboratory using the Gammasphere array and the fragment mass analyzer (FMA). Two high-spin, quasirotational bands consisting of stretched-E2 transitions were observed in coincidence with the known low-spin structure for the first time. These bands share remarkable similarities with highly deformed and/or superdeformed bands observed in the A ≈ 60–70 mass region. In addition, a regular dipole sequence with weak E2 crossover transitions was observed. A general discussion of the observed structures, complemented by theoretical calculations carried out within the framework of the adiabatic and configuration-fixed constrained covariant density functional theory and the quantum particle-rotor model, are presented. Furthermore, the results are interpreted in the context of shell-structure evolution and the collectivity in the mass region.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1984

Flat-plate solar array project process development area, process research of non-CZ silicon material

The program is designed to investigate the fabrication of solar cells on N-type base material by a simultaneous diffusion of N-type and P-type dopants to form an P(+)NN(+) structure. The results of simultaneous diffusion experiments are being compared to cells fabricated using sequential diffusion of dopants into N-base material in the same resistivity range. The process used for the fabrication of the simultaneously diffused P(+)NN(+) cells follows the standard Westinghouse baseline sequence for P-base material except that the two diffusion processes (boron and phosphorus) are replaced by a single diffusion step. All experiments are carried out on N-type dendritic web grown in the Westinghouse pre-pilot facility. The resistivities vary from 0.5 (UC OMEGA)cm to 5 (UC OMEGA)cm. The dopant sources used for both the simultaneous and sequential diffusion experiments are commercial metallorganic solutions with phosphorus or boron components. After these liquids are applied to the web surface, they are baked to form a hard glass which acts as a diffusion source at elevated temperatures. In experiments performed thus far, cells produced in sequential diffusion tests have properties essentially equal to the baseline N(+)PP(+) cells. However, the simultaneous diffusions have produced cells with much lower IV characteristics mainly due to cross-doping of the sources at the diffusion temperature. This cross-doping is due to the high vapor pressure phosphorus (applied as a metallorganic to the back surface) diffusion through the SiO2 mask and then acting as a diffusant source for the front surface.

Campbell, R. B.↗

NASA NTRS1991

Magellan mission planning and orbital operations

The goal of NASA's Magellan mission is to understand the geological and geophysical processes that have shaped the planet Venus. Through synthetic aperture radar, radiometric, altimetric, and gravity measurements, the scientific community hopes to improve its knowledge of the planet's topography and internal mass distribution. This paper provides an overview of the Magellan mission; describes the spacecraft sequence software design, development, and test; addresses the nominal operational flow of stored sequence design and generation; briefly describes the ground processing of engineering telemetry and imaging data; and then summarizes the Magellan operational experience with non-routine behavior of the spacecraft during the cruise and mapping portions of the prime mission.

Venus↗

DOE OSTI2018

Factors governing extracellular DNA degradation dynamics in soil

We examined the impacts of soil moisture, temperature, agricultural management and habitat type on the degradation dynamics of eDNA in soils. Synthetic eDNA was added to soil microcosms, and its disappearance over time was measured using both high-throughput sequencing and qPCR. The synthetic eDNA was degraded rapidly, but a small fraction remained detectable throughout the experiments (39–80 days). The eDNA degradation rate was positively correlated with moisture and temperature, but negatively correlated with soil organic carbon content. End-point stabilization of eDNA was highest at low moisture and temperature, but exhibited no relationship with soil organic carbon. Tilled soils had higher rates of degradation and less stabilization than no-till soils. Among different habitats we observed that forest soils had the slowest degradation rate, and meadow soils had the greatest stabilization of eDNA. While eDNA was detectable by qPCR in all treatments across all time-points, it became inconsistently detectable with high-throughput gene sequencing in less than 1 week. We conclude that eDNA degradation and stabilization dynamics vary with moisture, temperature and habitat characteristics, that small amounts of eDNA may persist in soils indefinitely, and that the ability of persistent eDNA to impact microbial community estimates depends on method sensitivity and experimental objectives.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP

DNA stable isotope probing (DNA-SIP) allows for the identification of microbes that assimilate isotopically labeled substrates into DNA. Here we describe the analysis of sequencing data using the multiple window high-resolution DNA-SIP method (MW-HR-SIP). MW-HR-SIP has improved accuracy over other methods and is easily implemented on the statistical platform R. Here, we also discuss key experimental parameters to consider when designing DNA-SIP experiments and how these parameters affect accuracy of analysis.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding

Microbial split-pool ligation transcriptomics (microSPLiT) is a high-throughput single-cell RNA sequencing method for bacteria. With four combinatorial barcoding rounds, microSPLiT can profile transcriptional states in hundreds of thousands of Gram-negative and Gram-positive bacteria in a single experiment without specialized equipment. As bacterial samples are fixed and permeabilized before barcoding, they can be collected and stored ahead of time. During the first barcoding round, the fixed and permeabilized bacteria are distributed into a 96-well plate, where their transcripts are reverse transcribed into cDNA and labeled with the first well-specific barcode inside the cells. The cells are mixed and redistributed two more times into new 96-well plates, where the second and third barcodes are appended to the cDNA via in-cell ligation reactions. Finally, the cells are mixed and divided into aliquot sub-libraries, which can be stored until future use or prepared for sequencing with the addition of a fourth barcode. It takes 4 days to generate sequencing-ready libraries, including 1 day for collection and overnight fixation of samples. Here, the standard plate setup enables single-cell transcriptional profiling of up to 1 million bacterial cells and up to 96 samples in a single barcoding experiment, with the possibility of expansion by adding barcoding rounds. The protocol requires experience in basic molecular biology techniques, handling of bacterial samples and preparation of DNA libraries for next-generation sequencing. It can be performed by experienced undergraduate or graduate students. Data analysis requires access to computing resources, familiarity with Unix command line and basic experience with Python or R.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Suppressing 1 H Spin Diffusion in Fast MAS Proton Detected Heteronuclear Correlation Solid-State NMR Experiments

Fast magic angle spinning (MAS) and indirect detection by high gyromagnetic ratio (γ) nuclei such as proton or fluorine are increasingly utilized to obtain 2D heteronuclear correlation (HETCOR) solid-state NMR spectra of spin-1/2 nuclei by using cross polarization (CP) for coherence transfer. However, one major drawback of CP HETCOR pulse sequences is that 1 H spin diffusion during the back X→ 1 H CP transfer step results in relayed correlations. This problem is particularly pronounced for the indirect detection of very low-γ nuclei such as 89 Y, 103 Rh, 109 Ag and 183 W where long contact times on the order of 10 to 30 ms are necessary for optimal CP transfer. In this work, we propose two methods that eliminate relayed correlations and allow more reliable distance information to be obtained from 2D HETCOR NMR spectra. The first method uses Lee-Goldburg (LG) CP during the X→ 1 H back-transfer step to suppress 1 H spin diffusion. We determine LG conditions compatible with fast MAS frequencies (ν rot ) of 40- 95 kHz and show that 1 H spin diffusion can be efficiently suppressed at low effective radiofrequency (RF) fields (ν 1,eff << 0.5ν rot ) and also at high effective RF fields (ν 1,eff >> 2ν rot ). We describe modified Hartmann-Hahn LG-CP match conditions compatible with fast MAS and suitable for indirect detection of moderate-γ nuclei such as 13 C, and low-γ nuclei such as 89 Y. The second method uses D-RINEPT (dipolar refocused insensitive nuclei enhanced by polarization transfer) during the X→ 1 H back-transfer step of the HETCOR pulse sequence. The effectiveness of these methods for acquiring HETCOR spectra with reduced relayed signal intensities is demonstrated with 1 H{ 13 C} HETCOR NMR experiments on L-histidine•HCl•H 2 O and 1 H{ 89 Y} HETCOR NMR experiments on an organometallic yttrium complex.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

NASA NTRS1990

Space Station Freedom: Dynamic instrumentation for a large space structure

A proposed approach called Modal Identification Experiment (MIE) for obtaining on-orbit dynamic response measurements on Space Station Freedom, the first of a family of large, flexible space structures is discussed. The Phase 2 conceptual design study which provides a conceptual design of a proposed measurement system and an experimental protocol for inobstrusively collecting dynamic response data critical to characterizing important vibration modes of Space Station Freedom were recently concluded. The case for conducting such a measurement program is presented and the specific MIE objectives that were identified, are listed. The sequence of discrete Space Station Freedom assembly configurations is described, and the Phase 2 conceptual design of the experiment and instrumentation system are defined. In addition, a plan to utilize a space station hydrid scale model in laboratory simulations as part of the design process are discussed.

Raney, John P.↗

NASA NTRS1988

Net current measurements and secondary electron emission characteristics of the Voyager plasma science experiment and their impact on data interpretation

The Voyager Plasma Science (PLS) instrument is capable of returning integral (DC) current measurements, similar in some respects to measurements made with a Langmuir probe or a retarding potential analyzer, although there are significant differences. The integral measurements were made during a calibration sequence in the solar wind, during Cruise Science Maneuvers, and within the magnetospheres of Jupiter and Saturn by Voyager 1. After the failure of the PLS experiment following the Saturn encounter, that instrument was placed in the DC return mode returning possibly usable data from early 1981 through early 1985. The DC return measurements are difficult to interpret and are above threshold values only for relatively large fluxes; the determination of the measured current level is dependent on the operating temperature of the preamplifiers which further complicates the interpretation. Nevertheless, these measurements can be used to determine the efficiency of the suppressor grid at preventing the loss of secondary electrons off the collector plate. Some DC return measurements have been invaluable in aiding in the interpretation of some electron plasma measurements not previously understood. It is found that electron spectra can be significantly modified by the presence of second generation secondary electrons produced by either first generation secondaries or photoelectrons on the support ring of the negative high voltage modulator grid within the instrument housing.

Mcnutt, Ralph L., Jr.↗

DOE OSTI2021

Glacier ice archives nearly 15,000-year-old microbes and phages

Background Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. Results We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants. Conclusions Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1974

Vectorcardiographic results from Skylab medical experiment M092: Lower body negative pressure

Vectorcardiograms were recorded via a modified Frank lead system from all crewmen of the three Skylab missions in conjuction with the Lower Body Negative Pressure - M092 Experiment. Data were analyzed by a specially developed computer program (VECTAN). Design of the test sequences allowed direct comparisons of supine resting, Earth based (reference) vectorcardiograms with those taken during lower body negative pressure stress and those obtained at rest in orbit, as well as combinations of these conditions. Results revealed several statistically significant space flight related changes; namely, increased testing and lower body negative pressure stressed heart rates, modestly increased PR interval and corrected QTC interval, and greatly increased P and QPS loop maximal amplitudes. In addition, orientation changes in the QRS maximum vector and the J-vector at rest in space seem quite consistent among crewmen and different from those caused by the application of lower body negative pressure. No clinical abnormalities were observed. Etiology of these findings is conjectured to be, at least in part, related to fluid mass shifts occurring in weightlessness and attendant alterations in cardiovascular dynamics and myocardial autonomic control mechanisms.

Hoffler, G. W.↗

NASA NTRS1976

Computer measurement and representation of the heart in two and three dimensions

Methods for the measurement and display by minicomputer of cardiac images obtained from fluoroscopy to permit an accurate assessment of functional changes are discussed. Heart contours and discrete points can be digitized automatically or manually, with the recorded image in a video, cine, or print format. As each frame is digitized it is assigned a code name identifying the data source, experiment, run, view, and frame, and the images are filed for future reference in any sequence. Two views taken at the same point in the heart cycle are used to compute the spatial position of the ventricle apex and the midpoint of the aortic valve. The remainder of the points on the chamber border are corrected for the linear distortion of the X-rays by projection to a plane containing the chord between the apex and the aortic valve center and oriented so that lines perpendicular to the chord are parallel to the image intensifier face. The image of the chamber surface is obtained by generating circular cross sections with diameters perpendicular to the major chord. The transformed two- and three-dimensional imagery can be displayed in either static or animated form using a graphics terminal.

Rasmussen, D.↗