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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 1,063 records · Page 59

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DOE OSTI2016

A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp

Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data for An Orphan Gene BOOSTER Enhances Photosynthetic Efficiency and Plant Productivity

Seeds of Col-0 wild type, sig6 T-DNA mutants (CS877785, ABRC), PRL-1-OE, and sig6 T-DNA mutants transfected with PRL-1 (sig6::PRL-1) were planted in 1/2 MS media. Seedlings growth including chlorophyll development defects were investigated across the genotypes. Four-days-old-post-light exposure seedlings were harvested and performed RNAseq analysis with four biological replicates.

Biomass Analytics↗

DOE OSTI2019

Data from: Reduced snow cover increases wintertime nitrous oxide (N2O) emissions from an agricultural soil in the upper U.S. Midwest

Throughout most of the northern hemisphere, snow cover decreased in almost every winter month from 1967 to 2012. Because snow is an effective insulator, snow cover loss has likely enhanced soil freezing and the frequency of soil freeze–thaw cycles, which can disrupt soil nitrogen dynamics including the production of nitrous oxide (N2O). We used replicated automated gas flux chambers deployed in an annual cropping system in the upper Midwest US for three winters (December–March, 2011–2013) to examine the effects of snow removal and additions on N2O fluxes. Diminished snow cover resulted in increased N2O emissions each year; over the entire experiment, cumulative emissions in plots with snow removed were 69% higher than in ambient snow control plots and 95% higher than in plots that received additional snow (P < 0.001). Higher emissions coincided with a greater number of freeze–thaw cycles that broke up soil macroaggregates (250–8000 µm) and significantly increased soil inorganic nitrogen pools. We conclude that winters with less snow cover can be expected to accelerate N2O fluxes from agricultural soils subject to wintertime freezing.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Onset dynamics of air-water menisci on rock fracture surfaces

Information on menisci dynamics and equilibrium contact angles, θ e , is needed for modeling multiphase flow of fluids in geologic formations. The wettability of fracture faces is relevant to applications such as waterflooding in enhanced oil recovery and evaluation of caprock integrity for geologic carbon sequestration. We investigated the vertical capillary rise of air-water menisci on exposed fracture faces for a sandstone, a shale, and three granites. The experimental design approximated that employed in the Wilhelmy plate method. Replicate fracture faces were prepared by fracturing cylindrical rock cores using the Brazilian method and splitting the fractured cores apart along their fracture planes. Meniscus onset was imaged from a cross-sectional perspective using dynamic neutron radiography, and quantified with change point analysis. An existing model for meniscus onset fitted the experimental data very well (median R 2 = 0.96). Capillary rise was typified by t 2/3 scaling (where t is time), followed by a constant equilibrium height, z e . The average time taken for the menisci to reach z e was 0.39 s, with no differences between rock types. The menisci achieved a greater vertical extent on the fracture faces of the sedimentary rocks as compared to those of the granites. Apparent θ e values were calculated from the best fit estimates of z e using the Wilhelmy plate equation for a smooth and planar vertical surface. Despite the fractal roughness of some of the fracture faces, there was a significant linear relationship (R 2 = 0.80) between the apparent θ e values and intrinsic θ e values measured on polished surfaces of the same rocks using the sessile drop method. The regression equation indicated the apparent θ e values were consistently greater than the intrinsic values. This overestimation may be due to averaging of pixels at the air-water-solid interface, a required step in the image analysis. Further exploration of the range of applicability and measurement accuracy of this proposed new technique would be valuable.

58 GEOSCIENCES↗

DOE OSTI2019

Superluminous supernovae from the Dark Energy Survey

We present a sample of 21 hydrogen-free superluminous supernovae (SLSNe-I) and one hydrogen-rich SLSN (SLSN-II) detected during the five-year Dark Energy Survey (DES). These SNe, located in the redshift range 0.220 < z < 1.998, represent the largest homogeneously selected sample of SLSN events at high redshift. We present the observed g, r, i, z light curves for these SNe, which we interpolate using Gaussian processes. The resulting light curves are analyzed to determine the luminosity function of SLSNe-I, and their evolutionary time-scales. The DES SLSN-I sample significantly broadens the distribution of SLSN-I light-curve properties when combined with existing samples from the literature. We fit a magnetar model to our SLSNe, and find that this model alone is unable to replicate the behavior of many of the bolometric light curves. We search the DES SLSN-I light curves for the presence of initial peaks prior to the main light-curve peak. Using a shock breakout model, our Monte Carlo search finds that 3 of our 14 events with pre-max data display such initial peaks. However, 10 events show no evidence for such peaks, in some cases down to an absolute magnitude of <–16, suggesting that such features are not ubiquitous to all SLSN-I events. In conclusion, we also identify a red pre-peak feature within the light curve of one SLSN, which is comparable to that observed within SN2018bsz.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2014

Inferring Viral Dynamics in Chronically HCV Infected Patients from the Spatial Distribution of Infected Hepatocytes

Chronic liver infection by hepatitis C virus (HCV) is a major public health concern. Despite partly successful treatment options, several aspects of intrahepatic HCV infection dynamics are still poorly understood, including the preferred mode of viral propagation, as well as the proportion of infected hepatocytes. Answers to these questions have important implications for the development of therapeutic interventions. In this study, we present methods to analyze the spatial distribution of infected hepatocytes obtained by single cell laser capture microdissection from liver biopsy samples of patients chronically infected with HCV. By characterizing the internal structure of clusters of infected cells, we are able to evaluate hypotheses about intrahepatic infection dynamics. We found that individual clusters on biopsy samples range in size from 4-50 infected cells. In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension. These observations support the idea that HCV infection in the liver is seeded randomly (e.g. from the blood) and then spreads locally. Assuming that the amount of intracellular HCV RNA is a proxy for how long a cell has been infected, we estimate based on models of intracellular HCV RNA replication and accumulation that cells in clusters have been infected on average for less than a week. Further, we do not find a relationship between the cluster size and the estimated cluster expansion time. Lastly, our method represents a novel approach to make inferences about infection dynamics in solid tissues from static spatial data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

A Pervasive Parallel Processing Framework for Data Visualization and Analysis at Extreme Scale

The evolution of the computing world from teraflop to petaflop has been relatively effortless, with several of the existing programming models scaling effectively to the petascale. The migration to exascale, however, poses considerable challenges. All industry trends infer that the exascale machine will be built using processors containing hundreds to thousands of cores per chip. It can be inferred that efficient concurrency on exascale machines requires a massive amount of concurrent threads, each performing many operations on a localized piece of data. Currently, visualization libraries and applications are based off what is known as the visualization pipeline. In the pipeline model, algorithms are encapsulated as filters with inputs and outputs. These filters are connected by setting the output of one component to the input of another. Parallelism in the visualization pipeline is achieved by replicating the pipeline for each processing thread. This works well for today’s distributed memory parallel computers but cannot be sustained when operating on processors with thousands of cores. Our project investigates a new visualization framework designed to exhibit the pervasive parallelism necessary for extreme scale machines. Our framework achieves this by defining algorithms in terms of worklets, which are localized stateless operations. Worklets are atomic operations that execute when invoked unlike filters, which execute when a pipeline request occurs. The worklet design allows execution on a massive amount of lightweight threads with minimal overhead. Only with such fine-grained parallelism can we hope to fill the billions of threads we expect will be necessary for efficient computation on an exascale machine.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2016

Transient dynamics of terrestrial carbon storage: Mathematical foundation and numeric examples

Terrestrial ecosystems absorb roughly 30% of anthropogenic CO 2 emissions since preindustrial era, but it is unclear whether this carbon (C) sink will endure into the future. Despite extensive modeling, experimental, and observational studies, what fundamentally determines transient dynamics of terrestrial C storage under climate change is still not very clear. Here we develop a new framework for understanding transient dynamics of terrestrial C storage through mathematical analysis and numerical experiments. Our analysis indicates that the ultimate force driving ecosystem C storage change is the C storage capacity, which is jointly determined by ecosystem C input (e.g., net primary production, NPP) and residence time. Since both C input and residence time vary with time, the C storage capacity is time-dependent and acts as a moving attractor that actual C storage chases. The rate of change in C storage is proportional to the C storage potential, the difference between the current storage and the storage capacity. The C storage capacity represents instantaneous responses of the land C cycle to external forcing, whereas the C storage potential represents the internal capability of the land C cycle to influence the C change trajectory in the next time step. The influence happens through redistribution of net C pool changes in a network of pools with different residence times. Furthermore, this and our other studies have demonstrated that one matrix equation can exactly replicate simulations of most land C cycle models (i.e., physical emulators). As a result, simulation outputs of those models can be placed into a three-dimensional (3D) parameter space to measure their differences. The latter can be decomposed into traceable components to track the origins of model uncertainty. Moreover, the emulators make data assimilation computationally feasible so that both C flux- and pool-related datasets can be used to better constrain model predictions of land C sequestration. We also propose that the C storage potential be the targeted variable for research, market trading, and government negotiation for C credits.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1991

Pilot personality and crew coordination - Implications for training and selection

It is contended that past failures to find linkages between performance and personality were due to a combination of premature performance evaluation, inadequate statistical modeling, and/or the reliance on data gathered in contrived as opposed to realistic situations. The goal of the research presented is to isolate subgroups of pilots along performance-related personality dimensions and to document limits on the impact of crew coordination training between the groups. Three different profiles were identified through cluster analysis of personality scales that replicated across samples and predicted attitude change following training in crew coordination.

Chidester, Thomas R.↗

NASA NTRSDate not supplied

Validating Drag and Heating Coefficients for Hollow Reentry Objects in Continuum Flow Using a Mach 7 Ludwieg Tube

Drag and heating coefficient databases and models are crucial to destructive reentry simulation. The NASA Orbital Debris Program Office (ODPO) develops, maintains, and performs analysis with the Object Reentry Survival Analysis Tool (ORSAT), which comprises drag and heating models for free molecular, transitional, and continuum flow regimes. These models have, in the past, only included solid, convex, blunt shapes (such as boxes, spheres, and cylinders). Previous work led by ODPO includes the extension of these models to hollow cylinders and square boxes in free molecular and transitional flow using the Direct Simulation Monte Carlo (DSMC) method. Since 2019, the ODPO has continued its program of DSMC simulations and extended the project to include analyses with the NASA Data Parallel Line Relaxation (DPLR) program on hollow cylinders and boxes (with varying wall thickness-diameter ratio). In fall 2022, the ODPO began a collaboration with the University of Texas San Antonio (UTSA) to use the Mach 7 Ludwieg Tube facility to validate the model built using numerical simulations. This facility can replicate (at a scale of approximately 100:1) the conditions seen by reentering objects near typical demise altitudes. We present here the drag and heating coefficients derived from the continued DSMC simulations, the new DPLR simulations, and the 26-test series at UTSA.

Chris Ostrom↗

NASA NTRS2023

Validating Drag and Heating Coefficients for Hollow Reentry Objects in Continuum Flow Using a Mach 7 Ludwieg Tube

Chris Ostrom↗

DOE OSTI2022

Value Proposition of UV-Absorbers in PV Module Encapsulation

Various common crystalline silicon cell technologies were exposed to UVA radiation (1.24 Wm-2 nm-1 at 340 nm peak) on the front and back faces at 45 degrees Celsius for periods up to 3000 h, representing about 3 y of solar exposure in Phoenix, Arizona, USA. The resulting degradation of the open-circuit voltage and short-circuit current is presented. Of the various cell types examined, significant levels of degradation were seen in all cases. Less degradation was generally found after UV irradiation of cell fronts and older cell types, whereas a bifacial PERC type exposed on the rear showed about 25% degradation in short circuit current, attributable to lack of a diffused surface field. Selected cells were exposed to UV irradiation with the addition of long pass UV filters to replicate UV-absorbers in encapsulants. Modern cell designs are sensitive to UV-ID because of reduced or eliminated front and back surface field and increased dependence on high quality surface passivation. Single transformation of the independent variable (t, kW h/m^2) could be used to achieve a linear model of the data to extrapolate to 50 y. Solar Advisor Model (SAM) shows appropriate filtering of UV-irradiation can improve LCOE and net present value of plant. Some advanced cell types are seen to be UV-resistant (cell level solutions also exist). Solutions therefore exist on the cell, glass, and encapsulant level. Changes over time in each of these would also need to be considered (solarization, encapsulant browning...).

ENGINEERING,SOLAR ENERGY↗

DOE OSTI2022

Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

The xeroderma pigmentosum protein A (XPA) and replication protein A (RPA) proteins fulfill essential roles in the assembly of the preincision complex in the nucleotide excision repair (NER) pathway. We have previously characterized the two interaction sites, one between the XPA N-terminal (XPA-N) disordered domain and the RPA32 C-terminal domain (RPA32C), and the other with the XPA DNA binding domain (DBD) and the RPA70AB DBDs. Here, we show that XPA mutations that inhibit the physical interaction in either site reduce NER activity in biochemical and cellular systems. Combining mutations in the two sites leads to an additive inhibition of NER, implying that they fulfill distinct roles. Our data suggest a model in which the interaction between XPA-N and RPA32C is important for the initial association of XPA with NER complexes, while the interaction between XPA DBD and RPA70AB is needed for structural organization of the complex to license the dual incision reaction. Integrative structural models of complexes of XPA and RPA bound to single-stranded/double-stranded DNA (ss/dsDNA) junction substrates that mimic the NER bubble reveal key features of the architecture of XPA and RPA in the preincision complex. Most critical among these is that the shape of the NER bubble is far from colinear as depicted in current models, but rather the two strands of unwound DNA must assume a U-shape with the two ss/dsDNA junctions localized in close proximity. Our data suggest that the interaction between XPA and RPA70 is key for the organization of the NER preincision complex.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Soil viral production count, respiration, and amplicon data

This study aimed to quantify rates of viral production in aridisol soil under conditions as close to natural field soil as possible given the perturbations necessary to manipulate viral abundances. Viruses were removed from soil, then added back to virus-depleted soil to control the initial viral abundances at either 100% (field_abund) or 10% (reduced_abund) of measured field viral abundance to generate treatments with field-relevant and reduced viral infection pressure, respectively. Replicates of batch incubation jars were harvested every 8 hours for 48 hours to enumerate bacteria and viruses by microscopy (n=5) and profile bacterial community composition by 16S rRNA amplicon sequencing (n=3).

Zimmerman, Amy [Pacific Northwest National Laborat↗

DOE OSTI2024

Structure analysis of the telomere resolvase from the Lyme disease spirochete Borrelia garinii reveals functional divergence of its C-terminal domain

Borrelia spirochetes are the causative agents of Lyme disease and relapsing fever, two of the most common tick-borne illnesses. A characteristic feature of these spirochetes is their highly segmented genomes which consists of a linear chromosome and a mixture of up to approximately 24 linear and circular extrachromosomal plasmids. The complexity of this genomic arrangement requires multiple strategies for efficient replication and partitioning during cell division, including the generation of hairpin ends found on linear replicons mediated by the essential enzyme ResT, a telomere resolvase. Using an integrative structural biology approach employing advanced modelling, circular dichroism, X-ray crystallography and small-angle X-ray scattering, we have generated high resolution structural data on ResT from B. garinii. Our data provides the first high-resolution structures of ResT from Borrelia spirochetes and revealed active site positioning in the catalytic domain. We also demonstrate that the C-terminal domain of ResT is required for both transesterification steps of telomere resolution, and is a requirement for DNA binding, distinguishing ResT from other telomere resolvases from phage and bacteria. These results advance our understanding of the molecular function of this essential enzyme involved in genome maintenance in Borrelia pathogens.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

A Multidimensional Holistic Framework for the Security of Distributed Energy and Control Systems

The digitization of smart grid distributed generation and industrial control systems has prompted utilities to deploy tools with ubiquitous communications that potentially widen the attack surface. The utilities still continue to rely on the traditional cybersecurity technologies, such as firewalls, anti-malware tools, and passwords that do not ensure security across all dimensions of the information assurance model required for a strong cybersecurity business process. This paper proposes a multidimensional holistic framework that addresses this gap through advanced technologies, intelligent algorithms, and continued assessments. To show proof, the layered defense model, a solution dimension of the framework, is integrated into the National Renewable Energy Laboratory's Security and Resilience Testbed to replicate a utility's enterprise and substation networks. The model is used to evaluate the security and resilience of microgrid control systems, and, based on the insights gathered, recommend best practices for utility cybersecurity analysts for a strong business process. Here, with this baseline, the paper conceptually introduces intelligence-driven solutions comprising contextual data analysis and machine learning to respond to advanced persistent threats sponsored by campaign efforts.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2013

Short-Read Assembly of Full-Length 16S Amplicons Reveals Bacterial Diversity in Subsurface Sediments

In microbial ecology, a fundamental question relates to how community diversity and composition change in response to perturbation. Most studies have had limited ability to deeply sample community structure (e.g. Sanger-sequenced 16S rRNA libraries), or have had limited taxonomic resolution (e.g. studies based on 16S rRNA hypervariable region sequencing). Here, we combine the higher taxonomic resolution of near-full-length 16S rRNA gene amplicons with the economics and sensitivity of short-read sequencing to assay the abundance and identity of organisms that represent as little as 0.01% of sediment bacterial communities. We used a new version of EMIRGE optimized for large data size to reconstruct near-full-length 16S rRNA genes from amplicons sheared and sequenced with Illumina technology. The approach allowed us to differentiate the community composition among samples acquired before perturbation, after acetate amendment shifted the predominant metabolism to iron reduction, and once sulfate reduction began. Results were highly reproducible across technical replicates, and identified specific taxa that responded to the perturbation. All samples contain very high alpha diversity and abundant organisms from phyla without cultivated representatives. Surprisingly, at the time points measured, there was no strong loss of evenness, despite the selective pressure of acetate amendment and change in the terminal electron accepting process. However, community membership was altered significantly. The method allows for sensitive, accurate profiling of the "long tail" of low abundance organisms that exist in many microbial communities, and can resolve population dynamics in response to environmental change.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2017

The Integrated Impact of Diet On Human Immune Response, the Gut Microbiota, and Nutritional Status During Adaptation to a Spaceflight Analog

Spaceflight impacts human physiology, including well documented immune system dysregulation. Diet, immune function, and the microbiome are interlinked, but diet is the only one of these factors that we have the ability to easily, and significantly, alter on Earth or during flight. As we understand dietary impacts on physiology more thoroughly, we may then improve the spaceflight diet to improve crew health and potentially reduce flight-associated physiological alterations. It is expected that increasing the consumption of fruits and vegetables and bioactive compounds (e.g.,omega-3 fatty acids, lycopene, flavonoids) and therefore enhancing overall nutritional intake from the nominal shelf-stable, fully-processed space food system could serve as a countermeasure to improve human immunological profiles, the taxonomic profile of the gut microbiota, and nutritional status, especially where currently dysregulated during spaceflight. This interdisciplinary study will determine the effect of the current shelf-stable spaceflight diet compared to an "enhanced" shelf-stable spaceflight diet (25% more foods rich in omega-3 fatty acids, lycopene, flavonoids, fruits, and vegetables). The NASA Human Exploration Research Analog (HERA) 2017 missions, consisting of closed chamber confinement, realistic mission simulation, in a high-fidelity mock space vehicle, will serve as a platform to replicate mission stressors and the dysregulated physiology observed in astronauts. Biosampling of crew members will occur at selected intervals, with complete dietary tracking. Outcome measures will include immune markers (e.g., peripheral leukocyte distribution, inflammatory cytokine profiles, T cell function), the taxonomic and metatranscriptomic profile of the gut microbiome, and nutritional status biomarkers and metabolites. Data collection will also include complete dietary tracking. Statistical evaluations will determine physiological and biochemical shifts in relation to nutrient in take and study phase. Beneficial improvements will provide evidence of the impact of diet on crew health and adaptation to this spaceflight analog, and will aid in the design and development of more-efficient targeted dietary interventions.

Douglas, G. L.↗