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At least 649 records · Page 36

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DOE OSTI2025

Site A5 - NREL Scanning Lidar (Halo Allsky SN235) / Reviewed Data

This dataset contains lidar data that have been standardized and quality-controlled through NREL/FIEXTA/LiDARGO (https://github.com/NREL/FIEXTA/tree/main/lidargo). Standardization rearranges the lidar data into convenient range vs beamID vs scanID coordinates that facilitates data analysis. The scan geometry (i.e., azimuth, elevation) is shifted on a regular grid based on the most likely angles within the scan file. Quality control of radial wind speed is performed through a generalized version of the dynamic lidar filter (Beck and Kuhn, 2017).

17 WIND ENERGY↗

DOE OSTI2025

Site A1 - ARM Scanning Lidar (Halo XR) / Reviewed Data

17 WIND ENERGY↗

DOE OSTI2026

FC Site 4.0 - NLR Scanning Lidar (Halo XR+ 235) / Standardized and Quality-Controlled Data

This dataset contains lidar data that have been standardized and quality-controlled through NatLabRockies/FIEXTA/LiDARGO (https://github.com/NatLabRockies/FIEXTA/tree/main/lidargo). Standardization rearranges the lidar data into convenient range vs beamID vs scanID coordinates that facilitate data analysis. The scan geometry (i.e., azimuth, elevation) is shifted on a regular grid based on the most likely angles within the scan file. Quality control of radial wind speed is performed through a generalized version of the dynamic lidar filter (Beck and Kuhn, 2017).

17 WIND ENERGY↗

DOE OSTI2026

FC Site 4.2 - NLR Scanning Lidar (Halo XR+ 199) / Standardized and Quality-Controlled Data

17 WIND ENERGY↗

DOE OSTI2026

FC Site 1.9 - NLR Scanning Lidar (Halo XR+ 200) / Standardized and Quality-Controlled Data

17 WIND ENERGY↗

DOE OSTI2023

FPGA Acceleration of GCN in Light of the Symmetry of Graph Adjacency Matrix

Graph Convolutional Neural Networks (GCNs) are widely used to process large-scale graph data. Different from deep neural networks (DNNs), GCNs are sparse, irregular, and unstructured, posing unique challenges to hardware acceleration with regular processing elements (PEs). In particular, the adjacency matrix of a GCN is extremely sparse, leading to frequent but irregular memory access, low spatial/temporal data locality and poor data reuse. Furthermore, a realistic graph usually consists of unstructured data (e.g., unbalanced distributions), creating significantly different processing times and imbalanced workload for each node in GCN acceleration. To overcome these challenges, we propose an end-to-end hardware-software co-design to accelerate GCNs on resource-constrained FPGAs with the features including: (1) A custom dataflow that leverages symmetry along the diagonal of the adjacency matrix to accelerate feature aggregation for undirected graphs. We utilize either the upper or the lower triangular matrix of the adjacency matrix to perform aggregation in GCN to improve data reuse. (2) Unified compute cores for both aggregation and transform phases, with full support to the symmetry-based dataflow. These cores can be dynamically reconfigured to the systolic mode for transformation or as individual accumulators for aggregation in GCN processing. (3) Preprocessing of the graph in software to rearrange the edges and features to match the custom dataflow. This step improves the regularity in memory access and data reuse in the aggregation phase. Moreover, we quantize the GCN precision from FP32 to INT8 to reduce the memory footprint without losing the inference accuracy. We implement our accelerator design in Intel Stratix10 MX FPGA board with HBM2, and demonstrate 1.3x-110.5x improvement in end-to-end GCN latency as compared to the state-of the-art FPGA implementations, on the graph datasets of Cora, Pubmed, Citeseer and Reddit.

Nair, Gopikrishnan R.↗

DOE OSTI2023

Comparative genomics of the Liberibacter genus reveals widespread diversity in genomic content and positive selection history

‘Candidatus Liberibacter’ is a group of bacterial species that are obligate intracellular plant pathogens and cause Huanglongbing disease of citrus trees and Zebra Chip in potatoes. Here, we examined the extent of intra- and interspecific genetic diversity across the genus using comparative genomics. Our approach examined a wide set of Liberibacter genome sequences including five pathogenic species and one species not known to cause disease. By performing comparative genomics analyses, we sought to understand the evolutionary history of this genus and to identify genes or genome regions that may affect pathogenicity. With a set of 52 genomes, we performed comparative genomics, measured genome rearrangement, and completed statistical tests of positive selection. We explored markers of genetic diversity across the genus, such as average nucleotide identity across the whole genome. These analyses revealed the highest intraspecific diversity amongst the ‘Ca. Liberibacter solanacearum’ species, which also has the largest plant host range. We identified sets of core and accessory genes across the genus and within each species and measured the ratio of nonsynonymous to synonymous mutations (dN/dS) across genes. We identified ten genes with evidence of a history of positive selection in the Liberibacter genus, including genes in the Tad complex, which have been previously implicated as being highly divergent in the ‘Ca. L. capsica’ species based on high values of dN.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Charge-lattice coupling and the dynamic structure of the U–O distribution in UO 2+x

The different structures and behaviors of UO 2+x observed in crystallographic and local structure measurements were examined by extended X-ray absorption fine structure (EXAFS) measurements of pristine UO 2.0 , p + and He 2+ irradiated UO 2.0 , and, at multiple temperatures, bulk U 4 O 9 and U 3 O 7 and thin film U 4 O 9-δ on an epitaxial substrate. The disorder caused by irradiation is mostly limited to increased widths of the existing U–O/U pair distributions, with any new neighbor shells being minor. As has been previously reported, the disorder caused by oxidative addition to U 4 O 9 and U 3 O 7 is much more extensive, resulting in multisite U–O distributions and greater reduction of the U–U amplitude with different distributions in bulk and thin-film U 4 O 9 . This includes the significant spectral feature near R = 1.2 Å for all U 4 O 9 and U 3 O 7 samples fit with a U-oxo type moiety with a U–O distance around 1.7 Å. In addition to indicating that these anomalies only occur in mixed valence materials, this work confirms the continuous rearrangement of the U–O distributions from 10 to 250 K. Although these variations of the structure are not observed in crystallography, their prominence in the EXAFS indicates that the dynamic structure underlying these effects is an essential factor of these materials.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

Solid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall Polymers

Efficient separation of the plant cell wall polymers during lignocellulose processing has been historically challenging due to insolubility of the polymers and their propensity for recalcitrant reassembly. Methods, such as “lignin first” extraction techniques, have advanced efficient biomass use, but the molecular mechanisms for recalcitrance remain enigmatic. Here, we discuss how solid-state Nuclear Magnetic Resonance (NMR) approaches report on the 3D organization of cellulose, xylan, and lignin in the plant cell wall. Recent results illustrate that the organization of these polymers varies across biomass sources and sample preparation methods, with even minimal physical processing causing significant effects. These structural differences contribute to variable extraction efficiencies for bioproducts after downstream processing. We propose that solid-state NMR methods can be applied to follow biomass processing, providing an understanding of the polymer rearrangements that can lead to poor yields for the desired bioproducts. The utility of the technique is illustrated for mechanical processing using lab-scale vibratory ball milling of Sorghum bicolor .

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Two major chromosome evolution events with unrivaled conserved gene content in pomegranate

Pomegranate has a unique evolutionary history given that different cultivars have eight or nine bivalent chromosomes with possible crossability between the two classes. Therefore, it is important to study chromosome evolution in pomegranate to understand the dynamics of its population. Here, we de novo assembled the Azerbaijani cultivar “Azerbaijan guloyshasi” (AG2017; 2n = 16) and re-sequenced six cultivars to track the evolution of pomegranate and to compare it with previously published de novo assembled and re-sequenced cultivars. High synteny was observed between AG2017, Bhagawa (2n = 16), Tunisia (2n = 16), and Dabenzi (2n = 18), but these four cultivars diverged from the cultivar Taishanhong (2n = 18) with several rearrangements indicating the presence of two major chromosome evolution events. Major presence/absence variations were not observed as >99% of the five genomes aligned across the cultivars, while >99% of the pan-genic content was represented by Tunisia and Taishanhong only. We also revisited the divergence between soft- and hard-seeded cultivars with less structured population genomic data, compared to previous studies, to refine the selected genomic regions and detect global migration routes for pomegranate. We reported a unique admixture between soft- and hard-seeded cultivars that can be exploited to improve the diversity, quality, and adaptability of local pomegranate varieties around the world. Our study adds body knowledge to understanding the evolution of the pomegranate genome and its implications for the population structure of global pomegranate diversity, as well as planning breeding programs aiming to develop improved cultivars.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural insights into binding of polyglutamylated tetrahydrofolate by serine hydroxymethyltransferase 8 from soybean

Tetrahydrofolate and its derivatives participate in one-carbon transfer reactions in all organisms. The cellular form of tetrahydrofolate (THF) is modified by multiple glutamate residues and polyglutamylation plays a key role in organellar and cellular folate homeostasis. In addition, polyglutamylation of THF is known to increase the binding affinity to enzymes in the folate cycle, many of which can utilize polyglutamylated THF as a substrate. Here, we use X-ray crystallography to provide a high-resolution view of interactions between the enzyme serine hydroxymethyltransferase (SHMT), which provides one carbon precursors for the folate cycle, and a polyglutamylated form of THF. Our 1.7 Å crystal structure of soybean SHMT8 in complex with diglutamylated 5-formyl-THF reveals, for the first time, a structural rearrangement of a loop at the entrance to the folate binding site accompanied by the formation of novel specific interactions between the enzyme and the diglutamyl tail of the ligand. Biochemical assays show that additional glutamate moieties on the folate ligand increase both enzyme stability and binding affinity. Together these studies provide new information on SHMT structure and function and inform the design of anti-folate agents.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Mechanistic Insights Revealed by YbtPQ in the Occluded State

Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of “alternating access” like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic Escherichia coli in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the “screwdriver” action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Flipped Quartification: Product Group Unification with Leptoquarks

The quartification model is an SU(3) 4 extension with a bi-fundamental fermion sector of the well-known SU(3) 3 bi-fundamentalfication model. An alternative “flipped” version of the quartification model is obtained by rearrangement of the particle assignments. The flipped model has two standard (bi-fundamentalfication) families and one flipped quartification family. In contrast to traditional product group unification models, flipped quartification stands out by featuring leptoquarks and thus allows for new mechanisms to explain the generation of neutrino masses and possible hints of lepton-flavor non-universality.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

A New Modeling Framework for Multi-Scale Simulation of Hydraulic Fracturing and Production from Unconventional Reservoirs

This paper describes a new modeling framework for microscopic to reservoir-scale simulations of hydraulic fracturing and production. The approach builds upon a fusion of two existing high-performance simulators for reservoir-scale behavior: the GEOS code for hydromechanical evolution during stimulation and the TOUGH+ code for multi-phase flow during production. The reservoir-scale simulations are informed by experimental and modeling studies at the laboratory scale to incorporate important micro-scale mechanical processes and chemical reactions occurring within the fractures, the shale matrix, and at the fracture-fluid interfaces. These processes include, among others, changes in stimulated fracture permeability as a result of proppant behavior rearrangement or embedment, or mineral scale precipitation within pores and microfractures, at µm to cm scales. In our new modeling framework, such micro-scale testing and modeling provides upscaled hydromechanical parameters for the reservoir scale models. We are currently testing the new modeling framework using field data and core samples from the Hydraulic Fracturing Field Test (HFTS), a recent field-based joint research experiment with intense monitoring of hydraulic fracturing and shale production in the Wolfcamp Formation in the Permian Basin (USA). Below, we present our approach coupling the reservoir simulators GEOS and TOUGH+ informed by upscaled parameters from micro-scale experiments and modeling. We provide a brief overview of the HFTS and the available field data, and then discuss the ongoing application of our new workflow to the HFTS data set.

58 GEOSCIENCES↗

DOE OSTI2022

Comparison of Auxenochlorella protothecoides and Chlorella spp. Chloroplast Genomes: Evidence for Endosymbiosis and Horizontal Virus-like Gene Transfer

Resequencing of the chloroplast genome (cpDNA) of Auxenochlorella protothecoides UTEX 25 was completed (GenBank Accession no. KC631634.1), revealing a genome size of 84,576 base pairs and 30.8% GC content, consistent with features reported for the previously sequenced A. protothecoides 0710, (GenBank Accession no. KC843975). The A. protothecoides UTEX 25 cpDNA encoded 78 predicted open reading frames, 32 tRNAs, and 4 rRNAs, making it smaller and more compact than the cpDNA genome of C. variabilis (124,579 bp) and C. vulgaris (150,613 bp). By comparison, the compact genome size of A. protothecoides was attributable primarily to a lower intergenic sequence content. The cpDNA coding regions of all known Chlorella species were found to be organized in conserved colinear blocks, with some rearrangements. The Auxenochlorella and Chlorella species genome structure and composition were similar, and of particular interest were genes influencing photosynthetic efficiency, i.e., chlorophyll synthesis and photosystem subunit I and II genes, consistent with other biofuel species of interest. Phylogenetic analysis revealed that Prototheca cutis is the closest known A. protothecoides relative, followed by members of the genus Chlorella. The cpDNA of A. protothecoides encodes 37 genes that are highly homologous to representative cyanobacteria species, including rrn16, rrn23, and psbA, corroborating a well-recognized symbiosis. Several putative coding regions were identified that shared high nucleotide sequence identity with virus-like sequences, suggestive of horizontal gene transfer. Despite these predictions, no corresponding transcripts were obtained by RT-PCR amplification, indicating they are unlikely to be expressed in the extant lineage.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Recent Developments in High-Performance Membranes for CO 2 Separation

In this perspective article, we provide a detailed outlook on recent developments of high-performance membranes used in CO 2 separation applications. A wide range of membrane materials including polymers of intrinsic microporosity, thermally rearranged polymers, metal–organic framework membranes, poly ionic liquid membranes, and facilitated transport membranes were surveyed from the recent literature. In addition, mixed matrix and polymer blend membranes were covered. The CO 2 separation performance, as well as other membrane properties such as film flexibility, processibility, aging, and plasticization, were analyzed.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Engineering Atomic-to-Nano Scale Structural Homogeneity towards High Corrosion Resistance of Amorphous Magnesium-Based Alloys

Magnesium-based amorphous alloys have aroused broad interest in being applied in marine use due to their merits of lightweight and high strength. Yet, the poor corrosion resistance to chloride-containing seawater has hindered their practical applications. Herein, we propose a new strategy to improve the chloride corrosion resistance of amorphous Mg 65 Cu 15 Ag 10 Gd 10 alloys by engineering atomic-to-nano scale structural homogeneity, which is implemented by heating the material to the critical temperature of the liquid–liquid transition. By using various electrochemical, microscopic, and spectroscopic characterization methods, we reveal that the liquid–liquid transition can rearrange the local structural units in the amorphous structure, slightly decreasing the alloy structure’s homogeneity, accelerate the formation of protective passivation film, and, therefore, increase the corrosion resistance. Our study has demonstrated the strong coupling between an amorphous structure and corrosion behavior, which is available for optimizing corrosion-resistant alloys.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Effect of Foot-and-Mouth Disease Virus 2B Viroporin on Expression and Extraction of Mammalian Cell Culture Produced Foot-and-Mouth Disease Virus-like Particles

To improve the production of foot-and-mouth disease (FMD) molecular vaccines, we sought to understand the effects of the FMD virus (FMDV) 2B viroporin in an experimental, plasmid-based, virus-like particle (VLP) vaccine. Inclusion of the FMDV viroporin 2B into the human Adenovirus 5 vectored FMD vaccine enhanced transgene expression despite independent 2B expression negatively affecting cell viability. Evaluating both wildtype 2B and mutants with disrupted viroporin activity, we confirmed that viroporin activity is detrimental to overall transgene expression when expressed independently. However, the incorporation of 2B into an FMD molecular vaccine construct containing a wildtype FMDV 3C protease, a viral encoded protease responsible for processing structural proteins, resulted in enhancement of transgene expression, validating previous observations. This benefit to transgene expression was negated when using the FMDV 3CL127P mutant, which has reduced processing of host cellular proteins, a reversion resulting from 2B viroporin activity. Inclusion of 2B into VLP production constructs also adversely impacted antigen extraction, a possible side effect of 2B-dependent rearrangement of cellular membranes. These results demonstrate that inclusion of 2B enhanced transgene expression when a wildtype 3C protease is present but was detrimental to transgene expression with the 3CL127P mutant. This has implications for future molecular FMD vaccine constructs, which may utilize mutant FMDV 3C proteases.

2B↗