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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Wireworm (Coleoptera: Elateridae) genomic analysis reveals putative cryptic species, population structure, and adaptation to pest control

The larvae of click beetles (Coleoptera: Elateridae), known as “wireworms,” are agricultural pests that pose a substantial economic threat worldwide. We produced one of the first wireworm genome assemblies (Limonius californicus), and investigated population structure and phylogenetic relationships of three species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of multiple genetically distinct groups that diverged in the Pleistocene but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. We also found within-species population structure across relatively short geographic distances. Genome scans for selection provided preliminary evidence for signatures of adaptation associated with different pesticide treatments in an agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in developing effective wireworm control strategies.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cross-species analysis of FcγRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque

Introduction Antibodies play a critical role in immunity in part by mediating clearance of pathogens and infected cells by antibody-dependent cellular phagocytosis (ADCP) through engagement of Fc gamma receptors (FcγRs) on innate immune cells. Among these, FcγRIIa (CD32a) is a key activating receptor expressed on macrophages, dendritic cells, and other antigen-presenting cells. Its affinity for IgG and ability to mediate ADCP is influenced by allelic polymorphisms. In humans, a single amino acid polymorphism at position 131, where histidine (H) is substituted with arginine (R), leads to decreased IgG1 and IgG2 subclass binding affinity and, consequently, lower efficiency of phagocytic responses. Rhesus macaques ( Macaca mulatta ), which are widely used as nonhuman primate models, exhibit a similar polymorphism at position 131 of FcγRIIa, but with arginine replaced by proline (P). Here, we investigated structure-function relationships associated with the FcγRIIa polymorphism at position 131 in both species, specifically with respect to IgG1 and IgG2. Methods We determined the structures of complexes formed by each variant with IgG1 Fc and those formed by the higher affinity variant with IgG2 Fc for both species by x-ray crystallography and linked these structures to affinity and activity using SPR and an ADCP assay. We also determined the structure of human inhibitory FcγRIIb (CD32b) in complex with IgG1 Fc by x-ray crystallography. Results Through analysis of these structures, our studies reveal that FcγRIIa engagement is minimally influenced by Fc glycan composition, distinguishing it from FcγRIIIa whose affinity is strongly influenced by glycan-composition. Comparative structures of human and macaque FcγRIIa variants demonstrate species- and allele-specific differences in Fc binding, but our functional assays showed only minimal allele-specific effects in humans. In contrast, allele-specific effects in macaques were highly significant; the macaque P 131 variant showing uniformly reduced IgG affinity. Conclusion These insights highlight fundamental interspecies and allelic distinctions that are critical for interpreting FcγRIIa-mediated effector functions in macaque models and for optimizing translational antibody and vaccine design.

Tolbert, William D.↗
DOE OSTI2026

Exploring Resonance Structures in the Partial-Wave Analysis of ¿p0 Photoproduction at GlueX

This thesis studies what happens when a photon (¿) collides with a proton (p) and produces a neutral omega (¿) and pion (p0) pair, with a recoiling proton (p'), expressed as ¿p ¿ ¿p0p'. We study this and other reactions to better understand the strong nuclear force; one of the four fundamental forces that govern all the physics of the universe. This force is specifically responsible for the binding and decay of subatomic particles, such as the ones here. While we understand the ¿ and p0, what we are actually interested in is a short-lived unknown particle X that decays via X ¿ ¿p0. There are a multitude of possible particles X can be, and so our focus in this work is to find out what X is by determining its properties from the particles we measure. We do this via an intricate analysis procedure known as “partial-wave analysis”. By analogy, one can think of our particle detector as a buoy, and the particles we want to analyze (X) as pebbles hitting a pond. The waves created by the pebble will move our buoy, giving us information about the pebble that produced the wave. However, when multiple pebbles hit our pond, the waves overlap and interfere with each other. Our buoy only can measure the complicated interfering result of all the waves. To disentangle this, our partial-wave analysis works by modeling this interference pattern so that we may infer the properties of the pebbles (particles) we produced. In this thesis, we review the relevant experimental history in photoproduction and related production mechanisms, as well as the theoretical foundations that motivate our measurement. We describe the methods used to collect our data at the GlueX experiment stationed at the Jefferson Lab accelerator facility in Newport News, Virginia. We then detail the selections we apply to ensure our events are almost exclusively ¿p ¿ ¿p0p'. We cover the intensity model, how we verify its capabilities, and finally present our results together with systematic studies. Our primary result is the detection of a b1(1235) meson interfering with a wide JPC = 1-- vector state, measured via a mass-independent partial-wave analysis. It provides precise experimental results that can be used as input for theoretical models of the reaction, yielding conclusions about the procedures responsible for how our universe behaves at its most basic level.

Scheuer, Kevin [College of William and Mary, Willi↗
DOE OSTI2022

Towards understanding the magnetic properties of the breathing pyrochlore compound Ba3Yb2Zn5O11through single-crystal studies

Abstract Ba 3 Yb 2 Zn 5 O 11 is exceptional among breathing pyrochlore compounds for being in the nearly-decoupled limit where inter-tetrahedron interactions are weak, hosting isolated clusters or molecular magnet-like tetrahedra of magnetic ytterbium (Yb 3+ ) ions. In this work, we present the study carried out on single-crystal samples of the breathing pyrochlore Ba 3 Yb 2 Zn 5 O 11 , using a variety of magnetometry and neutron scattering techniques along with theoretical modeling. We employ inelastic neutron scattering to investigate the magnetic dynamics as a function of applied field (with respect to both magnitude and direction) down to a temperature of 70 mK, where inelastic scattering reveals dispersionless bands of excitations as found in earlier powder sample studies, in good agreement with a single-tetrahedron model. However, diffuse neutron scattering at zero field and dc-susceptibility at finite field exhibit features suggesting the presence of excitations at low-energy that are not captured by the single tetrahedron model. Analysis of the local structure down to 2 K via pair distribution function analysis finds no evidence of structural disorder. We conclude that effects beyond the single tetrahedron model are important in describing the low-energy, low-temperature physics of Ba 3 Yb 2 Zn 5 O 11 , but their nature remains undetermined.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Experimental Measurements of the Wake of a Sphere at Subcritical Reynolds Numbers

This work experimentally investigated the flow phenomena and vortex structures in the wake of a sphere located in a water loop at Reynolds numbers of Re = 850, 1,250, and 1,700. Velocity fields in the wake region were obtained by applying the time-resolved stereoscopic particle image velocimetry (TR-SPIV) technique. From the acquired TR-SPIV velocity vector fields, the statistical values of mean and fluctuating velocities were computed. Spectral analysis, two-point velocity–velocity cross-correlation, proper orthogonal decomposition (POD) and vortex identification analyses were also performed. The velocity fields show a recirculation region that decreases in length with an increase of Reynolds numbers. The power spectra from the spectral analysis had peaks corresponding to a Strouhal number of St = 0.2, which is a value commonly found in the literature studies of flow over a sphere. The two-point cross-correlation analysis revealed elliptical structures in the wake, with estimated integral length scales ranging between 12% and 63% of the sphere diameter. The POD analysis revealed the statistically dominant flow structures that captured the most flow kinetic energy. It is seen that the flow kinetic energy captured in the smaller scale flow structures increased as Reynolds number increased. The POD modes contained smaller structure as the Reynolds number increased and as mode order increased. In addition, spectral analysis performed on the POD temporal coefficients revealed peaks corresponding to St = 0.2, similar to the spectral analysis on the fluctuating velocity. The ability of POD to produce low-order reconstructions of the flow was also utilized to facilitate vortex identification analysis, which identified average vortex sizes of 0.41D for Re1, 0.33D for Re2, and 0.32D for Re3.

Engineering↗
DOE OSTI2020

Dinuclear Gold(I) Complexes Bearing Alkyl-Bridged Bis(N-heterocyclic carbene) Ligands as Catalysts for Carboxylative Cyclization of Propargylamine: Synthesis, Structure, and Kinetic and Mechanistic Comparison to the Mononuclear Complex [Au(IPr)Cl]

Eight new dinuclear gold(I) complexes, [Au 2 (L)X 2 ] (1–8), were synthesized using a straightforward synthetic procedure under very mild conditions. The complexes have been characterized by NMR spectroscopy, elemental analysis, and single-crystal X-ray structure analysis. Their catalytic activity was investigated in the carboxylative cyclization of propargylamine (PPA). A superior performance in comparison to [Au(IPr)Cl] (9) was obtained for complexes 1 and 2 having an eight-methylene bridge connecting two NHCs with an arene bearing an isopropyl substituent for X = Cl, Br. This prompted more detailed kinetic and mechanistic studies by FTIR comparing dinuclear complex 2 of X = Cl to complex 9. Fortuitously the FTIR studies allowed monitoring of the formation of the products carbamic acid (CA) and carbamate salt (CS), as well as a key cyclized intermediate first discovered by Ikariya. These data allow additional insight into the mechanism as well as the central role which may be played by Au(I) carbamate formation as a higher energy resting state present in the catalytic cycle. In conclusion, the crystal structures of four of the new complexes and a detailed computational study relevant to the role of carbamic acid (CA) and carbamates in the catalytic cycle are also reported.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Risk-Informed Mechanistic Source Term Calculation (Final CRADA Report)

As part of an FY18 U.S. Department of Energy (DOE) Gateway for Accelerated Innovation in Nuclear (GAIN) award, a CRADA agreement was established between Argonne National Laboratory (Argonne) and Oklo. The CRADA focused on the following three tasks to assist Oklo with the regulatory licensing of their innovative nuclear reactor design: • Task 1 – Coupling and Demonstration Analysis using The Nek5000, Diablo, and OpenMC Codes: Establishing a coupling between the neutronic, structural, and thermohydraulic analysis codes and utilizing the code package for a high-fidelity demonstration analysis of radial core expansion due to temperature changes and its impact on core reactivity. • Task 2 – Mechanistic Source Term Analysis: Performing a realistic evaluation of the potential release of radionuclides to the environment during postulated transient event sequences. • Task 3 – Data in Support of Metal Fuel Qualification: An assessment of past postirradiation examination data of metal fuel utilized in the Argonne EBR-II reactor to assist in the potential qualification of the fuel typer for regulatory licensing. The details regarding each analysis and the associated conclusions were provided to Oklo in three separate project reports. Due to the utilization of proprietary and export controlled information, the current summary report was created, which provides an uncontrolled overview of each of the three tasks.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2024

Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties

KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a’s thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably,KRAS4aexhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approachingKRAS4bin the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.

Science & Technology - Other Topics↗
DOE OSTI2020

Origin of Capacity Degradation of High-Voltage KVPO 4 F Cathode

Potassium vanadium fluorophosphate (KVPO 4 F) is one of the most promising cathode candidates for K-ion batteries because of its high specific capacity, voltage, and energy density. However, reducing its capacity fade remains an important challenge. This work leverages structure and electrochemical analysis to understand the capacity degradation mechanism of the KVPO 4 F cathode. Interestingly, no structural degradation of the KVPO4F cathode is detected after 200 cycles in the wide voltage window of 5.0-2.5 V (vs K/K + ). Instead, the capacity degradation is attributed to electrolyte decomposition at high voltage ( > 4.5 V vs K/K + ), which causes drying of the electrolyte and the formation of insulating layers on the cathode surface, significantly increasing the polarization. The properties of four KPF 6 - A nd carbonate-based K electrolytes are compared, and 0.7 M KPF 6 in ethylene carbonate/propylene carbonate exhibits the highest oxidation stability and results in the best cycling stability for the KVPO 4 cathode. These findings suggest that the key to improving the cycling stability of KVPO 4 F is to develop novel K electrolytes with even higher oxidation stability.

25 ENERGY STORAGE↗
DOE OSTI2026

Process-level cost analysis of hybrid manufacturing pathways for aerospace structural components

Hybrid manufacturing is a promising route for producing complex aerospace components, yet systematic cost benchmarking across multiple additive-subtractive pathways remains limited. This study presents a comprehensive process-based cost analysis of seven hybrid manufacturing routes, including laser powder bed fusion (L-PBF), powder- and wire-directed energy deposition (DED), wire arc additive manufacturing (WAAM), additive friction stir deposition (AFSD), metal binder jetting (MBJ), and agility forging, followed by scanning and finish machining. Parametric cost models incorporating direct material, labor, and energy costs were developed. L-PBF results are discussed in detail for a pickle fork component and directly compared with commercial pricing. Across all hybrid routes, labor emerged as the dominant cost driver, contributing more than 70% of total manufacturing cost in some cases. AFSD exhibited the lowest cost for aluminum components, with MBJ being its 316 L stainless steel counterpart, after accounting for geometric scaling. Benchmarking against industrial quotes suggests that hybrid manufacturing can achieve cost levels comparable to those of commercial services, although labor-intensive processes exhibit greater deviation. The analysis highlights automation of material handling, setup, and supervision as key opportunities for improving economic competitiveness. Overall, the proposed framework provides a quantitative basis for evaluating and optimizing hybrid manufacturing pathways for aerospace applications.

Baruah, Sweta [ORNL] (ORCID:0009000174256207)↗
DOE OSTI2024

Evaluation of flow-induced plate deflection for University of Missouri research reactor low-enriched uranium fuel element

The University of Missouri Research Reactor (MURR), located on the campus of the University of Missouri in Columbia, Missouri, is one of the six United States (U.S.) High Performance Research Reactors (USHPRR), including one critical facility, that are actively collaborating with the U.S. Department of Energy (DOE) National Nuclear Security Administration (NNSA) Office of Material Management and Minimization (M3) Reactor Conversion Program to convert from highly enriched uranium (HEU, ≥20 wt% U-235) fuel to low-enriched uranium (LEU, <20 wt% U-235) fuel. A new type of very high-density LEU fuel based on a monolithic alloy of uranium and 10 wt% molybdenum (U-10Mo) is expected to allow conversion of some USHPRR, including MURR. In the design of its fuel elements, MURR is using thin parallel curved fuel plates separated by coolant channels. In this work, fluid-structure interaction (FSI) analysis of the MURR LEU fuel element is performed at the element level (as compared to the plate level analysis), which models all components of the LEU fuel element, including fuel plates and the supporting structures. Therefore, the effect of supporting structures on the flow distribution within the element and the fuel plate deflection are evaluated. In addition to the element nominal flow rate and dimensions, the tolerances in the geometry of the coolant channel and plate thickness, the effect of a comb on plate deflection, and the uncertainty of the flow rate per element are evaluated. For the LEU fuel plates, which are thinner than the current HEU plates, the predicted plate deflection is found to be small compared to the fabrication and assembly tolerances. Thus, the FSI-induced deflections are not expected to noticeably reduce the coolant flow rate or predicted safety margins in the limiting channels for the MURR LEU fuel element. In addition to the simulation work, a hydraulic performance test of the MURR LEU fuel element is currently being planned to support conversion to the use of LEU fuel.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. We present the predicted structural proteome (25,134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Singleton Sieving: Overcoming the Memory/Speed Trade-Off in Exascale k-mer Analysis

Traditional filter data structures, such as Bloom filters, do not offer necessary features that modern high-performance data analytics applications need in order to efficiently perform complex data analysis tasks. For example, MetaHipMer, a de novo metagenome assembler, can use filters to weed out singleton k-mers and reduce memory usage by 30%-70%. However, the filter needs the ability to associate values with k-mers in order to perform the analysis in a single communication pass. Bloom filters do not support value associations and cause the application to perform an extra communication pass, thereby increasing the run time. Therefore, MetaHipMer faces a trade off between memory and speed due to the limited capabilities of traditional filters. In this paper, we overcome the memory and speed trade off in MetaHipMer by integrating a GPU-based feature-rich filter, the Two-Choice filter (TCF), in the MetaHipMer pipeline. The TCF uses key-value association to approximately store k-mers with extensions. This allows MetaHipMer to perform k-mer analysis on the GPUs in a single communication pass. Our empirical analysis shows a 50% reduction in memory usage in k-mer analysis on each node in MetaHipMer without any effect on the overall run time or assembly quality. The memory reduction in turn results in a 43% reduction in the number of nodes required to assemble datasets and enables MetaHipMer to scale to much larger datasets.

McCoy, Hunter↗