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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 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Understanding the transient large amplitude oscillatory shear behavior of yield stress fluids

A full understanding of the sequence of processes exhibited by yield stress fluids under large amplitude oscillatory shearing is developed using multiple experimental and analytical approaches. A novel component rate Lissajous curve, where the rates at which strain is acquired unrecoverably and recoverably are plotted against each other, is introduced and its utility is demonstrated by application to the analytical responses of four simple viscoelastic models. Using the component rate space, yielding and unyielding are identified by changes in the way strain is acquired, from recoverably to unrecoverably and back again. The behaviors are investigated by comparing the experimental results with predictions from the elastic Bingham model that is constructed using the Oldroyd–Prager formalism and the recently proposed continuous model by Kamani, Donley, and Rogers in which yielding is enhanced by rapid acquisition of elastic strain. The physical interpretation gained from the transient large amplitude oscillatory shear (LAOS) data is compared to the results from the analytical sequence of physical processes framework and a novel time-resolved Pipkin space. The component rate figures, therefore, provide an independent test of the interpretations of the sequence of physical processes analysis that can also be applied to other LAOS analysis frameworks. Each of these methods, the component rates, the sequence of physical processes analysis, and the time-resolved Pipkin diagrams, unambigiously identifies the same material physics, showing that yield stress fluids go through a sequence of physical processes that includes elastic deformation, gradual yielding, plastic flow, and gradual unyielding.

Kamani, Krutarth M. (ORCID:0000000338975420)↗
DOE OSTI2017

Kinetic characterization of Vibrio cholerae ApbE: Substrate specificity and regulatory mechanisms

ApbE is a member of a novel family of flavin transferases that incorporates flavin mononucleotide (FMN) to subunits of diverse respiratory complexes, which fulfill important homeostatic functions. In this work a detailed characterization of Vibrio cholerae ApbE physiologic activity, substrate specificity and pH dependency was carried out. The data obtained show novel characteristics of the regulation and function of this family. For instance, our experiments indicate that divalent cations are essential for ApbE function, and that the selectivity depends largely on size and the coordination sphere of the cation. Our data also show that ApbE regulation by pH, ADP and potassium is an important mechanism that enhances the adaptation, survival and colonization of V. cholerae in the small intestine. Moreover, studies of the pH-dependency of the activity show that the reaction is favored under alkaline conditions, with a pKa of 8.4. These studies, together with sequence and structure analysis allowed us to identify His257, which is absolutely conserved in the family, as a candidate for the residue whose deprotonation controls the activity. Remarkably, the mutant H257G abolished the flavin transfer activity, strongly indicating that this residue plays an important role in the catalytic mechanism of ApbE.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Data Analysis of the 2020 Central Idaho Mainshock-Aftershock Sequence

In an effort to inform the Senior Seismic Hazard Analysis Committee for the Idaho National Laboratory, we provide an improved aftershock catalog related to the March 31, 2020, Mw6.5 Stanley, Idaho earthquake from picks related to a temporary network of two real-time and 15 non-telemetered seismometers within the epicentral area. From the permanent and temporary (XP) real-time network, the USGS cataloged 1,946 aftershocks between April 1, 2020 and October 31, 2020. To improve aftershock location and magnitudes, we manually picked arrival times of P and S waves from off-line stations in the XP temporary network, generated a new crustal velocity model, and independently relocated each event using the HypoDD double-difference earthquake algorithm. We created our new velocity model from existing broadband and active source seismic campaign data that were acquired near the epicentral region prior to the 2020 earthquake. We compare arrival time differences, epicentral locations and depths between aftershocks recorded with the two catalogs. We find the addition of local stations provides tighter aftershock clustering that suggests an improved aftershock locations. To detect lower magnitude events, we employed deep learning. Our method solves common problems associated with detecting many events that have a low signal-to-noise ratio. From the machine learning database, we detected more than 74,000 aftershocks. Based on the number of identified earthquakes and Gutenberg-Richter relationships derived from the USGS catalog, we estimate that we have reduced the completion magnitude for the Stanley earthquake sequence to below M1 using this machine learning approach. We located each aftershock with our new velocity model. Our new velocity model and picks suggests aftershocks occurred mostly at shallower depths than assessed in the USGS catalog. These aftershocks align along two linear trends that suggest the activation of two unnamed primary faults.

58 GEOSCIENCES↗
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Small-Magnitude Seismic Swarms in Central Utah (US): Interactions of Regional Tectonics, Local Structures and Hydrothermal Systems

Swarms in Central Utah are situated in the complex transition between the Basin and Range (BR) province and the Colorado Plateau. Transecting transverse structures, volcanic deposits, and hydrothermal systems complicate the extensional BR horst and graben structures and provide a multitude of plausible triggering mechanisms. Revisiting the catalog of the University of Utah Seismograph Stations (1981–2022), we analyze spatio-temporal patterns and characteristic features of seismic sequences. Swarms with alternating seismicity rates, bursts, and longer swarms with persistent moment release exhibit a remarkable diversity in temporal evolution. Swarm durations do not scale with cumulative seismic moment: swarms lasting less than 1 day can have similar cumulative seismic moments as month-long swarms. Here, we observe stationary swarms re-occurring for years (e.g., Mineral Mountains), as well as singular swarms in low-seismicity areas (e.g., activating a local structure). The swarms show a pronounced heterogeneity in triggering and driving mechanisms, observed in the detailed analysis of exemplary sequences (detections, relocations, moment tensors, waveform-based clustering, and repeater analysis). The 2022 Sevier Valley sequence activated a BR-related normal fault, the first resolved fault plane in the valley since 1983. The 2011 Circleville sequence is interpreted as a swarm triggered by mainshock-aftershock activity characterized by increasing magnitudes, changing rupture mechanisms, and a concentration of highly similar events in the second part of the sequence. By jointly discussing exemplary sequences and catalog statistics, we draw a comprehensive picture of swarm activity and its relation to geothermal and tectonic activity.

58 GEOSCIENCES↗
DOE OSTI2020

Diverse Thaumarchaeota Dominate Subsurface Ammonia-oxidizing Communities in Semi-arid Floodplains in the Western United States

Subsurface microbial communities mediate biogeochemical transformations that drive both local and ecosystem-level cycling of essential elements, including nitrogen. However, their study has been largely limited to the deep ocean, terrestrial mines, caves, and topsoils (< 30 cm). Here, we present regional insights into the microbial ecology of aerobic ammonia oxidation within the terrestrial subsurface of five semi-arid riparian sites spanning a 900-km N-S transect. We sampled sediments, profiled communities to depths of ≤10 m, and compared them to reveal trends regionally within and surrounding the Upper Colorado River Basin (CRB). The diversity and abundance of ammonia-oxidizing microbial communities were evaluated in the context of subsurface geochemistry by applying a combination of amoA (encoding ammonia monooxygenase subunit A) gene sequencing, quantitative PCR, and geochemical techniques. Analysis of 898 amoA sequences from ammonia-oxidizing archaea (AOA) and bacteria (AOB) revealed extensive ecosystem-scale diversity, including archaeal amoA sequences from four of the five major AOA lineages currently found worldwide as well as distinct AOA ecotypes associated with naturally reduced zones (NRZs) and hydrogeochemical zones (unsaturated, capillary fringe, and saturated). Overall, AOA outnumber AOB by 2- to 5000-fold over this regional scale, suggesting that AOA may play a prominent biogeochemical role in nitrification within terrestrial subsurface sediments.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Data for Intra- and inter-annual variability of nitrification in the rhizosphere of field-grown bioenergy sorghum

These data were collected in 2018 and 2019 at the University of Illinois Energy Farm (N 40.063607, W 88.206926). During each growing season, bulk and rhizosphere soil were collected from replicate Sorghum bicolor nitrogen use efficiency trial plots at three separate time points (approximately July 1, August 1, and September 1). We measured soil moisture, pH, soil nitrate and ammonium, potential nitrification, potential denitrification, and extracted and sequenced the V4 region of the 16S rRNA gene for microbial community analysis. All microbial sequence data is archived in the National Center for Biotechnology Information’s (NCBI) Sequence Read Archive (accession number SRP326979, project number PRJNA741261).

bioenergy↗
DOE OSTI2015

A systematic approach to the analysis of double faults within design basic accident methodology - 14501

Within the UK there is a general trend towards adopting Design Basis Accident (DBA) methodology for the assessment of radiological hazards, including criticality. DBA is a single fault methodology and comprises identifying the initiating event, its frequency and consequence. A fault with a very low initiating event frequency will not require further analysis. A fault sequence that terminates in a sub-critical configuration would also not require further analysis; although the identified passive features ensuring sub-criticality are subjected to engineering substantiation. Where faults do not pass this initial screening, two safety measures are generally required to ensure the fault does not progress to a criticality incident. This methodology provides a robust approach to single faults ensuring that an appropriate level and range of plant measures are identified and subjected to appropriate substantiation. However, a criticality is a cliff-edge effect and is dependent on multiple parameters. It is entirely possible under DBA to evaluate several single fault sequences and conclude that no measures are required because the single faults terminate in a sub-critical configuration. Importantly, for criticality safety, under DBA, there is no requirement to prevent important parameters from deviating from normal or upper bound 'safe' levels leaving the plant at greater risk in the event that further faults initiate. The combination of two faults could lead to a criticality incident but there is no current driver within DBA methodology to analyze these coincident or double faults. There is, therefore, potential to significantly under estimate the risk of criticality. This understanding is embodied within other methodologies such as the Double Contingency Principle. However, within the UK the DBA methodology has so significantly improved the analysis of single faults that, in some instances, consideration of double faults has taken a back seat. This is despite the UK regulator stating that 'criticality safety cases should employ the double contingency approach'. This paper presents a systematic approach to ensure that the potential for double faults or multiple parameter deviations to result in a criticality is effectively evaluated within the wider DBA methodology. The methodology determines which faults may be screened out from double fault analysis on the grounds of being 'unlikely' to initiate and being present for a 'short' duration. For those faults screened into double fault analysis, this guidance sets out the potential means of determining acceptable risk. These means include the specific evaluation of the risk of two criticality control parameters deviating simultaneously, the definition of additional safety measures and the definition of the boundary of safety for multiple parameters and the risk of exceeding this boundary. (authors)

42 ENGINEERING↗
DOE OSTI2016

A HIGH-RESOLUTION MULTIBAND SURVEY OF WESTERLUND 2 WITH THE HUBBLE SPACE TELESCOPE. II. MASS ACCRETION IN THE PRE-MAIN-SEQUENCE POPULATION

We present a detailed analysis of the pre-main-sequence (PMS) population of the young star cluster Westerlund 2 (Wd2), the central ionizing cluster of the H ii region RCW 49, using data from a high-resolution multiband survey with the Hubble Space Telescope. The data were acquired with the Advanced Camera for Surveys in the F555W, F814W, and F658N filters and with the Wide Field Camera 3 in the F125W, F160W, and F128N filters. We find a mean age of the region of 1.04 ± 0.72 Myr. The combination of dereddened F555W and F814W photometry in combination with F658N photometry allows us to study and identify stars with Hα excess emission. With a careful selection of 240 bona-fide PMS Hα excess emitters we were able to determine their Hα luminosity, which has a mean value L(Hα)=1.67×10{sup −31} erg s{sup −1}. Using the PARSEC 1.2S isochrones to obtain the stellar parameters of the PMS stars, we determined a mean mass accretion rate M-dot {sub acc}=4.43×10{sup −8} M{sub ⊙} yr{sup −1} per star. A careful analysis of the spatial dependence of the mass accretion rate suggests that this rate is ∼25% lower in the center of the two density peaks of Wd2 in close proximity to the luminous OB stars, compared to the Wd2 average. This rate is higher with increasing distance from the OB stars, indicating that the PMS accretion disks are being rapidly destroyed by the far-ultraviolet radiation emitted by the OB population.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Top-down analysis of protein samples by de novo sequencing techniques

MOTIVATION: Recent technological advances have made high-resolution mass spectrometers affordable to many laboratories, thus boosting rapid development of top-down mass spectrometry, and implying a need in efficient methods for analyzing this kind of data. RESULTS: We describe a method for analysis of protein samples from top-down tandem mass spectrometry data, which capitalizes on de novo sequencing of fragments of the proteins present in the sample. Our algorithm takes as input a set of de novo amino acid strings derived from the given mass spectra using the recently proposed Twister approach, and combines them into aggregated strings endowed with offsets. The former typically constitute accurate sequence fragments of sufficiently well-represented proteins from the sample being analyzed, while the latter indicate their location in the protein sequence, and also bear information on post-translational modifications and fragmentation patterns.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Sequence Length of HIV-1 Subtype B Increases over Time: Analysis of a Cohort of Patients with Hemophilia over 30 Years

We aimed to investigate whether the sequence length of HIV-1 increases over time. We performed a longitudinal analysis of full-length coding region sequences (FLs) during an HIV-1 outbreak among patients with hemophilia and local controls infected with the Korean subclade B of HIV-1 (KSB). Genes were amplified by overlapping RT-PCR or nested PCR and subjected to direct sequencing. Overall, 141 FLs were sequentially determined over 30 years in 62 KSB-infected patients. Phylogenetic analysis indicated that within KSB, two FLs from plasma donors O and P comprised two clusters, together with 8 and 12 patients with hemophilia, respectively. Signature pattern analysis of the KSB of HIV-1 revealed 91 signature nucleotide residues (1.1%). In total, 48 and 43 signature nucleotides originated from clusters O and P, respectively. Six positions contained 100% specific nucleotide(s) in clusters O and P. In-depth FL analysis for over 30 years indicated that the KSB FL significantly increased over time before combination antiretroviral therapy (cART) and decreased with cART. This increase occurred due to the significant increase in env and nef genes, originating in the variable regions of both genes. The increase in sequence length of HIV-1 over time suggests an evolutionary direction.

59 BASIC BIOLOGICAL SCIENCES↗