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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 1,279 records · Page 71
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition: N-Terminal Region of M-MuLV Integrase

The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain, and the C-terminal domain. The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1–44) and an HHCC zinc-finger NTD (residues 45–105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1–105 (NTR1–105) and 8–105 (NTR8–105) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR1–105 packs as a dimer and NTR8–105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn2+ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn2+ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV. Proteins 2017; 85:647–656.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Norovirus RNA‐dependent RNA polymerase: A computational study of metal‐binding preferences

ABSTRACT Norovirus (NV) RNA‐dependent RNA polymerase (RdRP) is essential for replicating the genome of the virus, which makes this enzyme a key target for the development of antiviral agents against NV gastroenteritis. In this work, a complex of NV RdRP bound to manganese ions and an RNA primer‐template duplex was investigated using X‐ray crystallography and hybrid quantum chemical/molecular mechanical simulations. Experimentally, the complex crystallized in a tetragonal crystal form. The nature of the primer/template duplex binding in the resulting structure indicates that the complex is a closed back‐tracked state of the enzyme, in which the ‐end of the primer occupies the position expected for the post‐incorporated nucleotide before translocation. Computationally, it is found that the complex can accept a range of divalent metal cations without marked distortions in the active site structure. The highest binding energy is for copper, followed closely by manganese and iron, and then by zinc, nickel, and cobalt. Proteins 2017; 85:1435–1445. © 2017 Wiley Periodicals, Inc.

Shaik, Md Munan↗
DOE OSTI2019

Putative structural rearrangements associated with the interaction of macrocyclic inhibitors with norovirus 3CL protease

Human noroviruses are the primary cause of outbreaks of acute gastroenteritis worldwide. The problem is further compounded by the current lack of norovirus-specific antivirals or vaccines. Noroviruses have a single-stranded, positive sense 7 to 8 kb RNA genome which encodes a polyprotein precursor that is processed by a virus-encoded 3C-like cysteine protease (NV 3CLpro) to generate at least six mature nonstructural proteins. Processing of the polyprotein is essential for virus replication, consequently, NV 3CLpro has emerged as an attractive target for the discovery of norovirus therapeutics and prophylactics. We have recently described the structure-based design of macrocyclic transition state inhibitors of NV 3CLpro. In order to gain insight and understanding into the interaction of macrocyclic inhibitors with the enzyme, as well as probe the effect of ring size on pharmacological activity and cellular permeability, additional macrocyclic inhibitors were synthesized and high resolution cocrystal structures determined. The results of our studies tentatively suggest that the macrocyclic scaffold may hamper optimal binding to the active site by impeding concerted cross-talk between the S2 and S4 subsites.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

HSV ‐1 ICP0 dimer domain adopts a novel β‐barrel fold

Abstract Infected cell protein 0 (ICP0) is an immediate‐early regulatory protein of herpes simplex virus 1 (HSV‐1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C‐terminal dimer domain (residues 555–767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0's dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C‐terminus of ICP0 was purified from bacteria and analyzed by X‐ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β‐strands and two α‐helices. Interestingly, two adjacent β‐strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β‐barrel‐like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β‐strands of each dimer, creating a “stacking” of the β‐barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C‐terminal SUMO‐interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV‐1 life cycle.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Evaluation of the Quasi‐Biennial Oscillation in global climate models for the SPARC QBO‐initiative

Abstract Quasi‐biennial oscillations (QBOs) in thirteen atmospheric general circulation models forced with both observed and annually repeating sea surface temperatures (SSTs) are evaluated. In most models the QBO period is close to, but shorter than, the observed period of 28 months. Amplitudes are within ±20 % of the observed QBO amplitude at 10 hPa, but typically about half of that observed at lower altitudes (50 and 70 hPa). For almost all models, the oscillation's amplitude profile shows an overall upward shift compared to reanalysis and its meridional extent is too narrow. Asymmetry in the duration of eastward and westward phases is reasonably well captured, though not all models replicate the observed slowing of the descending westward shear. Westward phases are generally too weak, and most models have an eastward time mean wind bias throughout the depth of the QBO. The intercycle period variability is realistic and in some models is enhanced in the experiment with observed SSTs compared to the experiment with repeated annual cycle SSTs. Mean periods are also sensitive to this difference between SSTs, but only when parametrized non‐orographic gravity wave (NOGW) sources are coupled to tropospheric parameters and not prescribed with a fixed value. Overall, however, modelled QBOs are very similar whether or not the prescribed SSTs vary interannually. A portrait of the overall ensemble performance is provided by a normalized grading of QBO metrics. To simulate a QBO, all but one model used parametrized NOGWs, which provided the majority of the total wave forcing at altitudes above 70 hPa in most models. Hence the representation of NOGWs either explicitly or through parametrization is still a major uncertainty underlying QBO simulation in these present‐day experiments.

Bushell, A. C.↗
DOE OSTI2019

A note on the Bayesian analysis of experiments with correlated multiple responses using a matrix-logarithmic covariance model

In the literature, analysis of multiple responses from experiments with replicates has modeled the covariance matrix directly as linear models of the transformed variances and correlations, i.e., covariance modeling. This article considers models based on the matrix- logarithm of the covariance matrix. This so-called log-covariance modeling is illustrated with data from actual experiments and compared with the traditional covariance modeling.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

High-throughput mass spectrometry analysis using immediate drop-on-demand technology coupled with an open port sampling interface

Rationale: The sampling throughput of immediate drop-on-demand technology (I.DOT) coupled with an open port sampling interface (OPSI) is limited by software communication. To enable much-needed high-throughput mass spectrometry (MS) analysis capabilities, a novel software was developed that allows for flexible sample selection from a 96-well plate and for maximized analysis throughput using I.DOT/OPSI-MS coupling. Methods: Wells of a 96-well I.DOT plate were filled with propranolol solution and were used to test maximum sampling throughput strategies to minimize analysis time. Demonstration of chemical reaction monitoring was done using acid-catalyzed ring closure of 2,3-diaminonaphthalene (DAN) with nitrite to form 2,3-naphthotriazole (NAT). Analytes were detected in positive electrospray ionization mode using selected reaction monitoring. Results: A maximum throughput of 1.54 s/sample (7.41 min/96-well plate with three technical replicates) was achieved, and it was limited by the peak width of the MS signal resulting in an occasional slight overlap between the peaks. Further, relative standard deviation was 10 ± 1% with all tested sampling strategies. Chemical reaction monitoring of DAN to NAT using nitrite was successfully accomplished with 2 s/sample throughout showing almost complete transformation in 10 min with no signal overlap. Conclusions: This work illustrates the development of a noncontact, automated I.DOT/OPSI-MS system with improved throughput achieved through an optimized software interface. Its achievable analysis time and precision make it a viable approach for drug discovery and in situ reaction monitoring studies.

47 OTHER INSTRUMENTATION↗
DOE OSTI2020

No–till establishment improves the climate benefit of bioenergy crops on marginal grasslands

Expanding biofuel production is expected to accelerate the conversion of unmanaged marginal lands to meet biomass feedstock needs. Greenhouse gas production during conversion jeopardizes the ensuing climate benefits, but most research to date has focused only on conversion to annual crops and only following tillage. Here we report the global warming impact of converting USDA Conservation Reserve Program (CRP) grasslands to three types of bioenergy crops using no–till (NT) vs. conventional tillage (CT). We established replicated NT and CT plots in three CRP fields planted to continuous corn, switchgrass, or restored prairie. For the 2 yr following an initial soybean year in all fields, we found that, on average, NT conversion reduced nitrous oxide (N 2 O) emissions by 50% and CO 2 emissions by 20% compared with CT conversion. Differences were higher in Year 1 than in Year 2 in the continuous corn field, and in the two perennial systems the differences disappeared after Year 1. In all fields net CO 2 emissions (as measured by eddy covariance) were positive for the first 2 yr following CT establishment, but following NT establishment net CO 2 emissions were close to zero or negative, indicating net C sequestration. Overall, NT improved the global warming impact of biofuel crop establishment following CRP conversion by over 20–fold compared with CT (–6.01 Mg CO 2 e ha –1 yr –1 for NT vs. –0.25 Mg CO 2 e ha –1 yr –1 for CT, on average). We also found that Intergovernmental Panel on Climate Change estimates of N 2 O emissions (as measured by static chambers) greatly underestimated actual emissions for converted fields regardless of tillage. Policies should encourage adoption of NT for converting marginal grasslands to perennial bioenergy crops to reduce C debt and maximize climate benefits.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Importance of sample preparation on reliable surface characterisation of nano-objects: ISO Standard 20579-4

The international ISO Standard 20579-4, dealing with the history and preparation of nano-objects for surface analysis, has been developed to help address some of the replication and reproducibility issues caused by the fundamental nature of nano-objects. Although all types of samples requiring surface analysis need thoughtful preparation, nano-objects, for which many properties are controlled by their surfaces, present additional challenges in order to avoid variations and artefacts due to the handling and preparation of materials prior to analysis. This international standard is part of a series of standards related to preparation of samples for surface chemical analysis. Parts 1 and 2 of ISO Standard series 20579 address general issues that apply to many samples. Part 4 specifically considers issues that arise due to the inherent nature of nano-objects. Because of sensitivity to their environment, the standard indicates the minimum information that needs to be reported about the handling and preparation of nano-objects prior to surface analysis. This information should become part of sample provenance information that helps assure the reliability and usefulness of data obtained from surface-analysis in the context of the synthesis, processing and analysis history of a batch of material. Application of this standard can help address reproducibility and traceability issues associated with synthesis, processing, and characterization of nano-objects in research and commercial applications.

nano-object characterization, surface analysis, sa↗
DOE OSTI2022

Highly Symmetric, Self-Assembling 3D DNA Crystals with Cubic and Trigonal Lattices

The rational design of nanoscopic DNA tiles has yielded highly ordered crystalline matter in 2D and 3D. The most well-studied 3D tile is the DNA tensegrity triangle, which is known to self-assemble into macroscopic crystals. However, contemporary rational design parameters for 3D DNA crystals nearly universally invoke integer numbers of DNA helical turns and Watson–Crick (WC) base pairs. Here, in this study, 24-bp edges are substituted into a previously 21-bp (two helical turns of DNA) tensegrity triangle motif to explore whether such unconventional motif can self-assemble into 3D crystals. The use of noncanonical base pairs in the sticky ends results in a cubic arrangement of tensegrity triangles with exceedingly high symmetry, assembling a lattice from winding helical axes and diamond-like tessellation patterns. Reverting this motif to sticky ends with Watson–Crick pairs results in a trigonal hexagonal arrangement, replicating this diamond arrangement in a hexagonal context. These results showcase that the authors can generate unexpected, highly complex, pathways for materials design by testing modifications to 3D tiles without prior knowledge of the ensuing symmetry. This study expands the rational design toolbox for DNA nanotechnology; and it further illustrates the existence of yet-unexplored arrangements of crystalline soft matter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Accelerated Stress Testing of Perovskite Photovoltaic Modules: Differentiating Degradation Modes with Electroluminescence Imaging

Herein, electroluminescence (EL) and thermal imaging are used to examine p–i–n metal halide perovskite (MHP) photovoltaic (PV) mini-modules (MA0.6FA0.4PbI3, 20 cells, 78 cm2) before and after indoor-accelerated stress testing or outdoor deployment. Distinct spatial patterns in the EL images emerge, which depend on the external stress conditions experienced by the mini-module. Imaging results highlight a distribution of dark speckle features that dominate after UV stress, attributed to widespread interfacial contact degradation. Lateral intensity gradients across cells dominate after thermal cycling (TC) stress, attributed to current crowding near scribe defects. While current–voltage analysis alone does not give full insight on the degradation process, this study shows that distinct degradation modes can be further defined by multimodal electro-optical imaging (i.e., EL combined with photoluminescence and dark lock-in thermography). Neither UV exposure nor TC-accelerated stress testing alone replicates the same degradation signatures observed after outdoor deployment, suggesting that multiple degradation modes occur under concurrent stressors outdoors. Finally, spatial characterization of degradation modes in MHP PV mini-modules before and after accelerated stress testing lays the groundwork for developing targeted accelerated stress testing procedures through comparison with outdoor aging.

14 SOLAR ENERGY↗
DOE OSTI2023

The effect of reducing dietary lipid and food availability on precocious male maturation in Chinook Salmon: A production-scale hatchery experiment

Abstract Objective Age of maturation in Chinook Salmon Oncorhynchus tshawytscha is phenotypically plastic, influenced by both genotype and environmental factors, including the availability and composition of the diet. Salmon hatchery programs often rear fish under accelerated growth regimes using high-lipid diets that can result in earlier age at maturity, including increased prevalence of age-2 males (minijacks). The goal of this investigation was to compare alternative dietary regimes to mitigate for this shift in age at maturity in hatchery-reared Umatilla River fall Chinook Salmon. Methods Juvenile fish were reared at Bonneville Hatchery, Oregon, under four dietary treatments across four replicate brood years. Dietary treatments included two feeding frequencies (standard [fed 7 days/week] and reduced [fed 4 days/week]) and two dietary lipid levels (standard [18%] and reduced [12%]) in a 2 × 2 factorial design. Dietary treatments were applied for approximately 9 months, beginning in March (a month after fry emergence) and lasting until December of the first year, after which all fish were reared on the standard feeding regime (7 days–18%) until the time of release the following spring as yearlings. Result We observed significant interannual variation in the proportion of minijacks produced among dietary treatments. For all brood years, decreasing the feeding frequency from 7 to 4 days/week reduced the proportion minijacks by 35.9%, and lowering dietary lipid from 18% to 12% reduced the proportion minijacks by 30%. The combined effects of reducing the feeding frequency and lowering dietary lipid were additive, reducing the proportion minijacks by 65.5% compared to the standard rearing regime. Growth and energetic indices were monitored throughout and confirmed findings from previous laboratory-based studies indicating that physiological status 10–12 months prior to spawn timing is important for the “decision” to mature. Conclusion Results of this investigation provide useful insights for optimizing rearing regimes for the Umatilla River program and other Chinook Salmon hatchery programs.

Harstad, Deborah L. (ORCID:0000000202676085)↗
DOE OSTI2020

Algebraic expressions for estimating the impact depths of a surface barrier over a homogeneous soil

Engineered surface barriers are used to isolate subsurface contaminants for effective long-term containment of municipal solid waste, other nonhazardous solid and liquid waste, hazardous and toxic wastes, and radioactive waste. The impact depths of a surface barrier are affected by the pre-barrier recharge rate and the properties of the soil beneath the barrier. In this paper, the pore-size-specific (PSS) water velocity is defined and an algebraic expression of PSS velocity is derived based on the stream tube concept and the Brooks and Corey hydraulic retention model. Algebraic expressions are developed to estimate drainage velocities and barrier impact depths after the emplacement of a surface barrier. Four impact depth terms are used to convey the protective effect: drainage front, average drainage, the location with 50% impact, and drainage tail. The drainage front depth is the deepest point at which the barrier has a detectable impact at a specific time (also called the near zero-impact depth). The average-impact depth is the depth at which average drainage occurs. At the 50% impact depth, the water flux rate is reduced by half because of the surface barrier. Lastly, the drainage tail depth (also called the full-impact depth) is the deepest depth at which the water conditions above it are in equilibrium with the barrier. The algebraic expressions show that the average-impact depth is no more than 1/3 of near zero-impact depth, while the 50% impact depth is slightly larger than 1/2 of the near zero-impact depth. The full-impact depth, depending on the final recharge rate from the surface barrier, is usually much smaller than the other impact depths. These differences lead to a very large transition zone beneath a surface barrier. Numerical simulations were conducted to replicate the same conditions. The numerical results corroborated the analytical models by predicting very similar water content profiles and near zero-, average-, 50%, and full-impact depths. The algebraic expressions provided in this paper are useful for quickly identifying sites where the depth of the existing contaminants could be beyond the protection of a surface barrier.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Gravo-aeroelastic scaling of a 13-MW downwind rotor for 20% scale blades

A 105-m, 13-MW two-bladed downwind Segmented Ultralight Morphing Rotor (SUMR-13) blade was gravo-aeroelastically scaled by 20% to a 20.87-m-long demonstrator blade and confirmed through structural ground testing. The subscale model was achieved through geometric scaling and by aeroelastic scaling principles based on operational flapwise deflections combined with rotational and structural frequencies while retaining the turbine tip-speed ratio. In particular, the subscale demonstrator was designed to replicate, as closely as possible, the nondimensional geometry, the ratio of centrifugal to gravitational moments, the tip-speed ratio, and the nondimensional rotation rate. The intent for this demonstrator was to achieve the same nondimensional flapwise blade deflections and dynamics of the full-scale 13-MW rotor. The manufactured SUMR-D blade resulted in less than half of the mass of the conventional two-bladed Controls Advanced Research Turbine (CART2) rotor blade based on scaling and a lower power rating, though with some differences in mass and stiffness from the ideal scaled-down design to meet safety requirements at the test site. To achieve proper scaling, operational pitch control set points were altered to account for the differences by evaluating simulated operation of both the SUMR-13 and SUMR-D rotors. Structural testing of the SUMR-D blade investigated the response to well-defined flapwise loads and indicated that the subscale blade had the appropriate elastic properties needed for both scaling and for safe operational field testing.

17 WIND ENERGY↗
DOE OSTI2022

Parked aeroelastic field rotor response for a 20% scaled demonstrator of a 13‐MW downwind turbine

Abstract Aeroelastic parked testing of a unique downwind two‐bladed subscale rotor was completed to characterize the response of an extreme‐scale 13‐MW turbine in high‐wind parked conditions. A 20% geometric scaling was used resulting in scaled 20‐m‐long blades, whose structural and stiffness properties were designed using aeroelastic scaling to replicate the nondimensional structural aeroelastic deflections and dynamics that would occur for a lightweight, downwind 13‐MW rotor. The subscale rotor was mounted and field tested on the two‐bladed Controls Advanced Research Turbine (CART2) at the National Renewable Energy Laboratory's Flatiron Campus (NREL FC). The parked testing of these highly flexible blades included both pitch‐to‐run and pitch‐to‐feather configurations with the blades in the horizontal braked orientation. The collected experimental data includes the unsteady flapwise root bending moments and tip deflections as a function of inflow wind conditions. The bending moments are based on strain gauges located in the root section, whereas the tip deflections are captured by a video camera on the hub of the turbine pointed toward the tip of the blade. The experimental results are compared against computational predictions generated by FAST, a wind turbine simulation software, for the subscale and full‐scale models with consistent unsteady wind fields. FAST reasonably predicted the bending moments and deflections of the experimental data in terms of both the mean and standard deviations. These results demonstrate the efficacy of the first such aeroelastically scaled turbine test and demonstrate that a highly flexible lightweight downwind coned rotor can be designed to withstand extreme loads in parked conditions.

17 WIND ENERGY↗
DOE OSTI2023

Advanced wind turbine control development using field test analysis for generator overspeed mitigation

Abstract Turbulent and gusty wind conditions can cause generator overspeed peaks to exceed a threshold that then lead to wind turbine shutdowns, which then decrease the energy production of the wind turbines. We derive so‐called “gust measures” that predict when generator overspeed peaks may occur. These gust measures are then used to develop advanced controllers to mitigate generator overspeed peaks so that wind turbines can operate more robustly in difficult wind conditions without exceeding generator overspeed thresholds that would lead to turbine shutdown events. The advanced controllers are demonstrated in nonlinear aeroelastic simulations using the open‐source wind turbine simulation tool OpenFAST. To increase the realism of the simulations, they are run using field‐replicated wind conditions and a wind turbine model based on data from an experimental field campaign on a downscaled demonstrator of a novel extreme‐scale, two‐bladed, downwind rotor design.

17 WIND ENERGY↗
DOE OSTI2023

Breaking the Ice: A Review of Phages in Polar Ecosystems

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. In this study, understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage–host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

09 BIOMASS FUELS↗