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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Identification and preliminary characterization of conserved uncharacterized proteins from Chlamydomonas reinhardtii , Arabidopsis thaliana , and Setaria viridis

Abstract The rapid accumulation of sequenced plant genomes in the past decade has outpaced the still difficult problem of genome‐wide protein‐coding gene annotation. A substantial fraction of protein‐coding genes in all plant genomes are poorly annotated or unannotated and remain functionally uncharacterized. We identified unannotated proteins in three model organisms representing distinct branches of the green lineage (Viridiplantae): Arabidopsis thaliana (eudicot), Setaria viridis (monocot), and Chlamydomonas reinhardtii (Chlorophyte alga). Using similarity searching, we identified a subset of unannotated proteins that were conserved between these species and defined them as Deep Green proteins. Bioinformatic, genomic, and structural predictions were performed to begin classifying Deep Green genes and proteins. Compared to whole proteomes for each species, the Deep Green set was enriched for proteins with predicted chloroplast targeting signals predictive of photosynthetic or plastid functions, a result that was consistent with enrichment for daylight phase diurnal expression patterning. Structural predictions using AlphaFold and comparisons to known structures showed that a significant proportion of Deep Green proteins may possess novel folds. Though only available for three organisms, the Deep Green genes and proteins provide a starting resource of high‐value targets for further investigation of potentially new protein structures and functions conserved across the green lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Challenges and Opportunities in State‐of‐the‐Art Proteomics Analysis for Biomarker Development From Plasma Extracellular Vesicles

Extracellular vesicles (EVs) are membrane-bound particles secreted by cells, playing crucial roles in intercellular communication. The composition of EVs can undergo changes in response to stress and disease conditions, making them excellent biomarker candidates. However, extracting protein information from EVs can be challenging due to their low abundance in complex biofluids and copurification with contaminant proteins and particles. Techniques to enrich EVs have their strengths and limitations, without one being able to purify EVs to complete homogeneity. This can lead to compromised recovery rates and increased complexity, making data interpretation difficult. In this viewpoint article, we explore the concept that better characterization of EV composition, followed by quantification of EV proteins in complex samples, might be a more viable route for biomarker development. Mass spectrometers can provide reproducible deep coverage of the EV proteome, despite sample impurities. This paradigm shift presents opportunities to integrate advanced bioinformatics tools to refine the EV proteome landscape, identify novel biomarkers, and streamline validation processes in biomarker development. By focusing on leveraging technology rather than achieving absolute purity, this approach can transform current practices and open opportunities for robust biomarker discovery. Herein, we highlight not only such opportunities but also challenges to implement this concept.

Dakup, Panshak P. [Pacific Northwest National Labo↗
DOE OSTI2024

Chain extension epoxide polymerization to well‐defined block polymers using a N‐Al Lewis pair catalyst

Block polyethers comprised of poly(propylene oxide) (PPO) and poly(ethylene oxide) (PEG or PEO) segments form the basis of ABA-type PEO-b-PPO-b-PEO poloxamer materials. The inverse architecture with an internal hydrophilic PEO segment flanked by hydrophobic blocks can be difficult to prepare with control of architecture by use of traditional anionic polymerization. These oxyanionic polymerizations are plagued by chain-transfer-to-monomer side reactions that occur with substituted epoxides such as propylene oxide (PO). Herein, we report a new method for the preparation of block polymers through a controlled polymerization involving a N-Al Lewis adduct catalyst and an aluminum alkoxide macroinitiator. The Lewis pair catalyst was able to chain-extend commercial PEO macroinitiators to prepare di-, tri-, and pentablock polyethers with low dispersity and reasonable monomer tolerance. Chain extension was confirmed using size exclusion chromatography and diffusion ordered nuclear magnetic resonance spectroscopy. In conclusion, the resulting block polymers were additionally analyzed with small-angle X-ray scattering to correlate the morphology to molecular architecture.

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

Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning

Tree training systems for temperate fruit have been developed throughout history by pomologists to improve light interception, fruit yield, and fruit quality. These training systems direct crown and branch growth to specific configurations. Quantifying crown architecture could aid the selection of trees that require less pruning or that naturally excel in specific growing/training system conditions. Regarding peaches [Prunus persica (L.) Batsch], access tools such as branching indices have been developed to characterize tree-crown architecture. However, the required branching data (BD) to develop these indices are difficult to collect. Traditionally, BD have been collected manually, but this process is tedious, time-consuming, and prone to human error. These barriers can be circumnavigated by utilizing terrestrial laser scanning (TLS) to obtain a digital twin of the real tree. TLS generates three-dimensional (3D) point clouds of the tree crown, wherein every point contains 3D coordinates (x, y, z). To facilitate the use of these tools for peach, we selected 16 young peach trees scanned in 2021 and 2022. These 16 trees were then modeled and quantified using the open-source software TreeQSM. As a result, “in silico” branching and biometric data for the young peach trees were calculated to demonstrate the capabilities of TLS phenotyping of peach tree-crown architecture. The comparison and analysis of field measurements (in situ) and in silico BD, biometric data, and quantitative structural model branch uncertainty data were utilized to determine the reconstructive model’s reliability as a source substitute for field measurements. Mean average deviation when comparing young tree (YT) height was approx. 5.93%, with crown volume was approx. 13.26% across both 2021 and 2022. All point clouds of the YTs in 2022 showed residuals lower than 12 mm to cylinders fitted to all branches, and mean surface coverage greater than 40% for both the trunk and primary branching orders.

09 BIOMASS FUELS↗
DOE OSTI2025

Development of a Printable Prill Formulation Technique and Demonstration of Monomodal Prill Size on Compaction Density and Compressive Strength

Polymer-bonded explosive molding powder, or “prills,” are relied on for the fabrication of pressed high explosives since the 1950's. The wet granulation technique, also known as “slurry coating,” that is used to formulate prills, is a complex process that results in polydisperse and variable yields. This makes it difficult to study the mesoscale effect that prills have on the microstructure of a pressed article. The following study introduces a novel approach to energetic granulation that leverages techniques used in the additive manufacturing of paste-like energetic materials. This extrusion granulation, or prill printing technique, makes it possible to tailor the sizes and shapes of prills, allowing for their morphological influences to be studied in a controlled manner. The following work details the fabrication and characterization of four monomodal size lots of prills using an inert formulation (95 wt.% melamine, 5 wt.% polymer binder). Prills from each size lot were die-pressed using a fixed recipe to investigate how prill size impacts compaction density and therefore compressive strength. It was found that larger prills influence the pressing density by creating larger defects within the microstructure of a pressed article, resulting in a decrease in compressive strength.

direct ink write↗
DOE OSTI2022

Utilization of the Critic Subnetwork of a Generative Adversarial Network as Detector of Morphological Material Change in Image Data

The resolution of computed tomography (CT) has become high enough to monitor morphological changes due to aging in materials in long-term applications. For this work, we explored the utility of the critic of a generative adversarial network (GAN) to automatically detect such changes. The GAN was trained with images of pristine Pharmatose, which is used as a surrogate energetic material. It is important to note that images of the material with altered morphology were only used during the test phase. The GAN-generated images reproduced the microstructure of Pharmatose well, although some unrealistic particle fusion was seen. Calculated morphological metrics (volume fraction, interfacial line length, and local thickness) for the synthetic images also showed good agreement with the training data, albeit with signs of mode collapse in the interfacial line length. While the critic exposed changes in particle size, it showed limited ability to distinguish images by particle shape. The detection of shape differences was also a more challenging task for the selected morphological metrics that related to energetic material performance. We further tested the critic with images of aged Pharmatose. Subtle changes due to aging are difficult for the human analyst to detect; but both critic and morphological metrics analysis showed image differentiation.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Development of Parameters for the Particle Size Distribution of TATB

Laser light scattering (LLS), manual counting of scanning electron microscopy (SEM) images, and reduction of SEM images using ImageJ (open source program) to determine Feret (caliper) diameters were applied to determine particle size distribution (PSD) of four preparations of 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) and yttria‐stabilized zirconia (YSZ), an SEM certified standard. Mie theory was used to reduce the LLS data. The spherical nature of the YSZ made it a good candidate for LLS. Variations in n , the refractive index, and iκ, the imaginary component, produced very little change in the PSD. However, changing the carrier liquid from H 2 O to a 40% aqueous sucrose solution, thereby changing the carrier refractive index, n 0 , substantially affected the PSD. The Mie complex refractive indices for the YSZ were n = 2.200, iκ = 0.100, with a 40% aqueous sucrose solution, n 0 = 1.400. The triclinic crystal structure of TATB made refractive index determinations more difficult, so a study was conducted varying Mie parameters and comparing them to the same data reduced using the Fraunhofer theory. Changing the n and κ parameters produced PSD with a small concentration of particles less than 1 µm in size or none in this range. SEM images, Feret data, manual counting, and Fraunhofer data reduction indicate particles less than 1 µm are probably < 5% in concentration. The final selection of Mie parameters for TATB was n = 2.283, iκ = 0.1, and suspension medium, n 0 = 1.330. Finally, computations, using density functional theory produced similar parameters.

Feret diameter↗
DOE OSTI2021

Three-repeat and four-repeat tau isoforms form different oligomers

Different tauopathies are characterized by the isoform-specific composition of the aggregates found in the brain and by structurally distinct tau strains. Although tau oligomers have been implicated as important neurotoxic species, little is known about how the primary structures of the six human tau isoforms affect tau oligomerization because the oligomers are metastable and difficult to analyze. To address this knowledge gap, here, we analyzed the initial oligomers formed by the six tau isoforms in the absence of posttranslational modifications or other manipulations using dot blots probed by an oligomer-specific antibody, native-PAGE/western blots, photo-induced cross-linking of unmodified proteins, mass-spectrometry, and ion-mobility spectroscopy. We found that under these conditions, three-repeat (3R) isoforms are more prone than four-repeat (4R) isoforms to form oligomers. In this study, we also tested whether known inhibitors of tau aggregation affect its oligomerization using three small molecules representing different classes of tau aggregation inhibitors, Methylene Blue (MB), the molecular tweezer CLR01, and the all-D peptide TLKIVW, for their ability to inhibit or modulate the oligomerization of the six tau isoforms. Unlike their reported inhibitory effect on tau fibrillation, the inhibitors had little or no effect on the initial oligomerization. Our study provides novel insight into the primary–quaternary structure relationship of human tau and suggests that 3R-tau oligomers may be an important target for future development of compounds targeting pathological tau assemblies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural studies of intrinsically disordered MLL -fusion protein AF9 in complex with peptidomimetic inhibitors

AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL -rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP–AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1–2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein–inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

Here we present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70–75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70–80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

protein complexes↗
DOE OSTI2020

Hall Effect Characterization of α ‐Irradiated p‐Type 4H‐SiC

Most electrical characterization of radiation damage to semiconductors is conducted on full devices or on low‐doped material. However, evaluating the radiation hardness is challenging in less mature semiconductor systems where low‐doped material is unavailable and full devices are difficult to realize. Herein, temperature‐dependent Hall effect measurements are used to demonstrate α particle‐induced radiation effects in p‐type 4H‐SiC with a room temperature hole concentration of . The 4H‐SiC is irradiated by α particles from a 210 Po source over a fluence of –. Modeling the hole concentration as a function of temperature shows that α radiation causes hole compensation through the introduction of hole traps. The radiation also induces a reduction in hole mobility due to an increase in defect‐related scattering centers. At low temperatures and increasingly higher fluences, the conduction mechanism changes from band conduction to another mechanism.

Frye, Clint D.↗
DOE OSTI2021

Influence of Protection Layers on Thermal Stability of Nitride Thin Films

Nitrides are commonly studied for their properties relevant to numerous coating applications, and have been recently used to synthesize newly predicted materials in thin film form. However, thermodynamic stability of such nitride materials is difficult to experimentally evaluate, due to limited thermal budget of thin films. Here we show that thermal stability of nitride films can be extended using protection layers. Specifically, we find that zirconium nitride (ZrN) thin films are stable up to at least 1200°C annealing temperature in N2 atmosphere, if aluminum nitride (AlN) diffusion barriers and capping layers are used. X-ray diffraction (XRD) measurements show the expected thermodynamically stable rocksalt structure of ZrN, and scanning electron microscopy (SEM) confirms compact microstructure of these ZrN films. Without such protection layers, transient bixbyite Zr2ON2 phase and high-temperature ZrSi2 phase are observed after annealing by XRD, SEM, and auger electron spectroscopy (AES), due to side reaction with native surface oxide (ZrOx) and substrate (Si) respectively. These results demonstrate that protection layers are beneficial to increase the thermal budget of nitride thin films, for evaluating thermodynamic stability of new nitride materials, for capturing transient metastable phases during crystallization, and for using functional nitride coatings in extreme environments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Sensitivity of Cloud-Radiative Effects to Cloud Fraction Parametrizations in Tropical, Mid-Latitude and Arctic Kilometre-Scale Simulations

The Regional Atmosphere (RA) configuration of the Met Office Unified Model currently requires different cloud fraction parametrizations (CFP) for tropical and midlatitude simulations. To explore the scope for unification of these two RA configurations, this paper presents a detailed evaluation of simulations over tropical, midlatitude and arctic domains, with two different diagnostic CFPs, a prognostic CFP, and no CFP at all. Furthermore, a novel, hybrid approach was used that treats liquid cloud diagnostically and ice cloud prognostically. Using observations from three U.S. Department of Energy Atmospheric Radiation Measurement supersites, it is shown that none of these CFPs stands out as superior over all domains. Over the frequently overcast Arctic, the all-or-nothing approach best captures the cloud radiative properties. Conversely, CFPs are of benefit in regions with frequent partial cloudiness, such as the midlatitudes and the tropics. However, their improved cloud radiative properties often hide an error compensation. All models underestimate overcast, low-base cloud with small water paths in convective environments. In addition, mid-latitude overcast, low-base, optically thick clouds in the morning, possibly associated with overnight convection, are frequently too broken. Diagnostic schemes compensate for these errors by producing spurious, scattered afternoon cloud, which could be due to a correct cloud response to too eager convective initiation. Winter clouds over the midlatitudes are improved when liquid cloud is represented diagnostically with a bimodal saturation-departure PDF, without error compensation. While it is difficult to unify the RA across the globe around a single CFP scheme, the newly proposed Hybrid scheme performs reasonably well for cloud cover across all regions. It also exhibits SW biases that are smaller than most other configurations and is less affected by excessive liquid water paths and compensating errors than fully diagnostic schemes. Surface precipitation is fairly insensitive to the CFP in the simulations shown here.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Probing eddy size and its effective mixing length in stably stratified roughness sublayer flows

Stably stratified roughness sublayer flows are ubiquitous yet remain difficult to represent in models and to interpret using field experiments. Here, continuous high-frequency potential temperature profiles from the forest floor up to 6.5 times the canopy height observed with distributed temperature sensing (DTS) are used to link eddy topology to roughness sublayer stability correction functions and coupling between air layers within and above the canopy. The experiments are conducted at two forest stands classified as hydrodynamically sparse and dense. Near-continuous profiles of eddy sizes (length scales) and effective mixing lengths for heat are derived from the observed profiles using a novel conditional sampling approach. The approach utilizes potential temperature isoline fluctuations from a statically stable background state. The transport of potential temperature by an observed eddy is assumed to be conserved (adiabatic movement) and we assume that irreversible heat exchange between the eddy and the surrounding background occurs along the (vertical) periphery of the eddy. This assumption is analogous to Prandtl's mixing-length concept, where momentum is transported rapidly vertically and then equilibrated with the local mean velocity gradient. A distinct dependence of the derived length scales on background stratification, height above ground, and canopy characteristics emerges from the observed profiles. Implications of these findings for (1) the failure of Monin–Obukhov similarity in the roughness sublayer and (2) above-canopy flow coupling to the forest floor are examined. The findings have practical applications in terms of analysing similar DTS data sets with the proposed approach, modelling roughness sublayer flows, and interpreting nocturnal eddy covariance measurements above tall forested canopies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Distributed Quantum Computing with Photons and Atomic Memories

The promise of universal quantum computing requires scalable single- and inter-qubit control interactions. Currently, three of the leading candidate platforms for quantum computing are based on superconducting circuits, trapped ions, and neutral atom arrays. However, these systems have strong interaction with environmental and control noises that introduce decoherence of qubit states and gate operations. Alternatively, photons are well decoupled from the environment and have advantages of speed and timing for quantum computing. Photonic systems have already demonstrated capability for solving specific intractable problems like Boson sampling, but face challenges for practically scalable universal quantum computing solutions because it is extremely difficult for a single photon to “talk” to another deterministically. Here, a universal distributed quantum computing scheme based on photons and atomic-ensemble-based quantum memories is proposed. Taking the established photonic advantages, two-qubit nonlinear interaction is mediated by converting photonic qubits into quantum memory states and employing Rydberg blockade for the controlled gate operation. Spatial and temporal scalability of this scheme is demonstrated further. Furthermore, these results show photon-atom network hybrid approach can be a potential solution to universal distributed quantum computing.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Using transparent fish to observe barotrauma associated with downstream passage through hydropower turbines

During downstream passage of hydroelectric facilities, fish can be injured by rapid decompression; this is especially noted during hydroturbine passage. The rapid decrease in pressure can cause barotrauma as undissolved gas expands according to Boyle’s law. However, it is difficult to see barotrauma occurring within the body of the fish in real time. In order to determine if transparent fish could provide greater insight into barotrauma, five species of transparent tropical fish were exposed to rapid decompressions so internal injuries could be viewed noninvasively. Before and after photos were taken to review the injuries and high speed video allowed observations of barotrauma pathways in vivo. High speed video recordings show the expansion of the swim bladder and subsequent release of gas through the mouth and gills, and into the body cavity when the swim bladder ruptured. Post-decompression photographs show that many internal injuries were visible and included hemorrhaging and the presence of emphysema within the body cavity and tissues. These observations provide new opportunities to understand the pathways and effects of barotrauma.

13 HYDRO ENERGY↗
DOE OSTI2023

Surface Analysis Insight Note: Observations relating to photoemission peak shapes, oxidation state, and chemistry of titanium oxide films

It is common practice to describe the coordination of metal atoms in a binding configuration with their nearest neighbors in terms of oxidation state, a measure by which the number of electrons redistributed between atoms forming chemical bonds. In XPS terms, change to an oxidation state is commonly inferred by correlating photoemission signal with binding energy. The assumption, when classifying photoemission signals into distinct spectral shapes, is that a distribution of intensities shifted to lower binding energy is evidence of a reduction in oxidation state. In this Insight note, we raise the prospect that changes in photoemission peak shape may occur without obvious changes, determined by XPS in stoichiometry for a material. It is well known that TiO 2 measured by XPS yields reproducible Ti 2p photoemission peaks. However, on exposing TiO 2 to ion beams, Ti 2p photoemission evolves to complex distributions in intensity, which are particularly difficult to analyze by traditional fitting of bell-shaped curves to these data. For these reasons, in this Insight note, a thin film of TiO 2 deposited on a silicon substrate is chosen for analysis by XPS and linear algebraic techniques. Alterations in spectral shapes created from modified TiO 2 , which might be interpreted as the change in oxidation state, are assessed in terms of relative proportions of titanium to oxygen. It is found through detailed analysis of spectra that quantification by XPS, using procedures routinely used in practice, is not in accord with the typical interpretations of photoemission shapes. The data processing methods used and results presented in this work are of particular relevance to elucidating fundamental phenomena governing the surface evolution of materials-enabled energy processes where cyclic/non-steady usage changes the nature of bonding, especially in the presence of contaminants.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗