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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Genome resources for three modern cotton lines guide future breeding efforts

Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A sorghum pangenome reference improves global crop trait discovery

Although the green revolution adapted a handful of crops to homogeneous and high-input industrialized agriculture, much of the global population still relies on the local production of variable crop cultivars by low-input smallholder farms. This diversity of unhomogenized crops, like that of the grain and bioenergy crop sorghum, offers raw materials for genetic gain and cultivar improvement. However, breeding efforts can be constrained by highly specialized traits and breeding targets Here, to bridge this diversity, we constructed a 33-member pangenome reference and a diversity panel across 1,984 cultivars and landraces. We leveraged these resources to explore the complex interplay among historical contingency, ongoing adaptation and previously uncharacterized structural diversity. Specifically, our analyses conclusively demonstrated multiple nested and deeply diverged structural variants in the domestication gene SHATTERING1, which distinguish the previously established multicentric origin of sorghum. We then applied landscape genomics to reveal how gene flow and secondary contact created the complex genetic mosaic in contemporary breeding networks. As proof of concept for pangenome-accelerated trait discovery, we connected biosynthetic gene cluster structural variation to phenotypic leaf concentration of the cyanogenic glucoside dhurrin. Combined, these approaches will accelerate breeding and trait discovery and provide a framework for similar applications in other crops.

agricultural genetics↗
DOE OSTI2020

Synthesis and molecular structure of perhalogenated rhenium-oxo corroles

Abstract As part of our efforts to develop rhenium-oxo corroles as photosensitizers for oxygen sensing and photodynamic therapy, we investigated the potential β -perhalogenation of five ReO meso -tris( para -X-phenyl)corroles, Re[T p XPC](O) (X = CF 3 , H, F, CH 3 , and OCH 3 ), with elemental chlorine and bromine. With Cl 2 , β -octachlorinated products Re[Cl 8 T p XPC](O) were rapidly obtained for X = CF 3 , H, and CH 3 , but X = OCH 3 resulted in overchlorination on the meso -aryl groups. Full β -octabromination proved slower relative to Cu and Ir corroles, but the desired Re[Br 8 T p XPC](O) products were finally obtained for X = H and F after a week at room temperature. For X = CH 3 and OCH 3 , these conditions led to undecabrominated products Re[Br 11 T p XPC](O). Compared to the β -unsubstituted starting materials, the β -octahalogenated products were found to exhibit sharp 1 H NMR signals at room temperature, indicating that the aryl groups are locked in place by the β -halogens, and substantially redshifted Soret and Q bands. Single-crystal X-ray structures of Re[Cl 8 T p CF 3 PC](O), Re[Cl 8 T p CH 3 PC](O), and Re[Br 8 T p FPC](O) revealed mild saddling for one Cl 8 structure and the Br 8 structure. These structural variations, however, appear too insignificant to explain the slowness of the β -octabromination protocols, which seems best attributed to the deactivating influence of the high-valent Re center.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Neutrons reveal the dynamics of leaf thylakoids in living plants

The study is the first known exploration of photosynthetic membranes dynamics in living plants by high resolution quasielastic neutron scattering spectroscopy. We investigated the mobility and flexibility of thylakoid membranes in common duckweed (Landoltia punctata) and identified dynamics across various length scales corresponding to individual membranes and membranes stack. We employed classical models typically used to study lipid bilayers to characterize the undulation modes and rigidity of the membranes and reveal how structural variations influence the observed complex dynamics. Our findings show that the stacks of thylakoids in duckweed behave as rigid systems, exhibiting an effective bending coefficient in the lower range associated with surfactant membranes. In contrast, the single thylakoid leaflets display greater apparent flexibility and are well situated within the bi-continuous surfactant phase dynamics. While our observations enhance the understanding of the intricate architecture and mobility of photosynthetic cellular machinery, they also highlight the limitations of applying ideal lipid membranes models to describe complex biological systems. This work opens more questions and the need for further investigations across extended length and time scales, as well as the importance of rigorous sample preparation and experimental control.

Applied physics↗
DOE OSTI2022

The solution structures and relative stability constants of lanthanide–EDTA complexes predicted from computation

Ligand selectivity to specific lanthanide (Ln) ions is key to the separation of rare earth elements from each other. Ligand selectivity can be quantified with relative stability constants (measured experimentally) or relative binding energies (calculated computationally). The relative stability constants of EDTA (ethylenediaminetetraacetic acid) with La 3+ , Eu 3+ , Gd 3+ , and Lu 3+ were predicted from relative binding energies, which were quantified using electronic structure calculations with relativistic effects and based on the molecular structures of Ln–EDTA complexes in solution from density functional theory molecular dynamics simulations. The protonation state of an EDTA amine group was varied to study pH ~7 and ~11 conditions. Further, simulations at 25 °C and 90 °C were performed to elucidate how structures of Ln–EDTA complexes varying with temperature are related to complex stabilities at different pH conditions. Relative stability trends are predicted from computation for varying Ln 3+ ions (La, Eu, Gd, Lu) with a single ligand (EDTA at pH ~11), as well as for a single Ln 3+ ion (La) with varying ligands (EDTA at pH ~7 and ~11). Changing the protonation state of an EDTA amine site significantly changes the solution structure of the Ln–EDTA complex resulting in a reduction of the complex stability. As a result, increased Ln–ligand complex stability is correlated to reduced structural variations in solution upon an increase in temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Investigating PVC polymer–plasticizer interactions with atomistic MD simulations and potential of mean force calculations

For this work, atomistic molecular dynamics (MD) simulations coupled with potential of mean force (PMF) calculations were employed to investigate the interactions between PVC polymer chains containing 6–20 repeating units and various plasticizers, with the goal of identifying potential replacements for the toxic plasticizer di(2-ethylhexyl)phthalate (DEHP) used in blood bags. The selected plasticizers belong to various chemical families, such as orthophthalates, citrates, adipates, and the terephthalate DEHT. Both the polymer and the plasticizers lack ionizable groups, and their interactions are primarily governed by van der Waals and electrostatic forces. A model correlating PMF profiles with interaction forces was developed and validated across polyvinyl chloride (PVC) polymers of different lengths and all investigated plasticizers. This model provides insight into how structural variations in plasticizers influence their respective PMF values. The study ranks the investigated plasticizers based on binding affinity, identifying TOTM (tris(2-ethylhexyl) trimellitate, TEHTM), BTHC (butyryl trihexyl citrate, Citroflex B-6), ATHC (acetyl trihexyl citrate, Citroflex A-6, CA-6), and DEHT (bis(2-ethylhexyl)terephthalate, DOTP/DEHTP) as promising alternatives for further investigation. This comprehensive study encompasses PVC polymers of four different lengths and 14 plasticizers, with all data averaged over 30 independent simulations. The approach provides a deeper understanding of molecular interactions, enabling the tailoring of polymer–plasticizer systems for diverse applications, including extractables and leachables, with relevance spanning materials science to biomedical engineering, and also serves as a basis for developing coarse-grained simulation protocols. Overall, this study provides valuable insights for designing safer and more efficient plasticizer substitutes and is well supported by other studies.

Shet, Sai Athmeeya G. [Sri Sathya Sai Institute of↗
DOE OSTI2020

Introduction to special issue: Colloidal quantum dots

The quantum confinement effect has driven the development and exploration of colloidal semiconductor nanocrystals over approximately the past three decades. These semiconductor nanostructures are typically synthesized as stable colloidal dispersions in solution-phase chemical batch reactions at relatively low temperatures. Researchers have developed a wide range of reaction conditions to produce a variety of shapes, compositions, and structures with well-controlled sizes and low polydispersities. The shape can be controlled to produce confinement in one, two, or all three spatial dimensions, the latter defining a “quantum dot.” Combining two or more semiconductors within the various nanostructures produces additional optical and electronic degrees of freedom. These mixed compositional nanostructures have properties not accessible in bulk semiconductor systems. Further, researchers have fabricated novel nanoheterostructures, such as “dot-in-rods,” quantum wells, core/shell structures, giant-core/shell tetrapods where the core is one material and the arm is another, Janus structures that consist of spherical structures with well-defined internal heterostructures, nano-dumbbells, hollow-core structures, and many other novel and interesting structures. The structural variations are seemingly only limited by the creativity of the various researchers engaged in these endeavors.

36 MATERIALS SCIENCE↗
DOE OSTI2026

XRISM high-resolution X-ray spectroscopy of Cygnus X-1: Orbital and short-term variability of iron absorption

We present the first high-resolution spectroscopy of the black hole high-mass X-ray binary Cygnus X-1 with XRISM, including orbital-phase-resolved analyses and tentative evidence of short-term variability in the Fe K band on second timescales. Using data from the Performance Verification phase in 2024 April, we analyzed spectral variability across orbital phases with the Resolve microcalorimeter and the Xtend CCD imager. The unprecedented resolution of Resolve reveals variability in highly ionized Fe absorption lines. The absorption features show orbital-phase-dependent variability in column density, ionization state, and blueshifted velocity, suggesting structural variations in the focused stellar wind along the line of sight. We also find indications of subtle broadening of the neutral Fe emission profile. In addition, intensity-sorted spectroscopy during dip phases suggests possible variability on timescales of a few seconds in the absorption features, consistent with cooler, denser, and lower-ionized gas clumps. Although the statistical significance is limited, these results hint that the stellar wind and the X-rays from the accretion disk around the black hole may interact on timescales as short as a few seconds. These XRISM results constrain wind-fed accretion in Cyg X-1 and highlight Resolve’s capability to probe plasma environments in high-mass X-ray binaries.

Astronomy and AstroPhysics↗
DOE OSTI2023

Ultrathin epitaxial MgB 2 on SiC: Substrate surface-polarity-dependent properties

High-quality, ultrathin superconducting films are required for advanced devices such as hot-electron bolometers, superconducting nanowire single-photon detectors, and quantum applications. Using hybrid physical-chemical vapor deposition, we show that MgB 2 films as thin as 4 nm can be fabricated on the carbon-terminated 6⁢H-SiC (0001) surface with a superconducting transition temperature above 33 K and a rms roughness of 0.7 nm. Remarkably, the film quality is a function of the SiC surface termination, with the C-terminated surface preferred to the Si-terminated surface. To understand the MgB 2 thin film/SiC substrate interactions giving rise to this difference, we characterized the interfacial structures using Rutherford backscattering spectroscopy/channeling, electron-energy-loss spectroscopy, and x-ray photoemission spectroscopy. The MgB 2 /SiC interface structure is complex and different for the two terminations. Both terminations incorporate substantial unintentional oxide layers influencing MgB 2 growth and morphology, but with a different extent, intermixing, and interface chemistry. In this paper, we report measurements of transport, resistivity, and the critical superconducting temperature of MgB 2 /SiC that are different for the two terminations, and they link interfacial structure variations to observed differences. The result shows that the C face of SiC is a preferred substrate for the deposition of ultrathin superconducting MgB 2 films.

36 MATERIALS SCIENCE↗
DOE OSTI2021

AutoAtlas: Neural Network for 3D Unsupervised Partitioning and Representation Learning

Here we present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one neural network to perform multi-label partitioning based on local texture in the volume, and a second neural network to compress the information contained within each partition. We train both of these components simultaneously by optimizing a loss function that is designed to promote accurate reconstruction of each partition, while encouraging spatially smooth and contiguous partitioning, and discouraging relatively small partitions. We show that the partitions adapt to the subject specific structural variations of brain tissue while consistently appearing at similar spatial locations across subjects. AutoAtlas also produces very low dimensional features that represent local texture of each partition. We demonstrate prediction of metadata associated with each subject using the derived feature representations and compare the results to prediction using features derived from FreeSurfer anatomical parcellation. Since our features are intrinsically linked to distinct partitions, we can then map values of interest, such as partition-specific feature importance scores onto the brain for visualization.

42 ENGINEERING↗
DOE OSTI2024

Altering the substitution and cross‐linking of glucuronoarabinoxylans affects cell wall architecture in Brachypodium distachyon

Summary The Poaceae family of plants provides cereal crops that are critical for human and animal nutrition, and also, they are an important source of biomass. Interacting plant cell wall components give rise to recalcitrance to digestion; thus, understanding the wall molecular architecture is important to improve biomass properties. Xylan is the main hemicellulose in grass cell walls. Recently, we reported structural variation in grass xylans, suggesting functional specialisation and distinct interactions with cellulose and lignin. Here, we investigated the functions of these xylans by perturbing the biosynthesis of specific xylan types. We generated CRISPR/Cas9 knockout mutants in Brachypodium distachyon XAX1 and GUX2 genes involved in xylan substitution. Using carbohydrate gel electrophoresis, we identified biochemical changes in different xylan types. Saccharification, cryo‐SEM, subcritical water extraction and ssNMR were used to study wall architecture. Bd XAX1A and Bd GUX2 enzymes modify different types of grass xylan. Brachypodium mutant walls are likely more porous, suggesting the xylan substitutions directed by both Bd XAX1A and GUX2 enzymes influence xylan‐xylan and/or xylan–lignin interactions. Since xylan substitutions influence wall architecture and digestibility, our findings open new avenues to improve cereals for food and to use grass biomass for feed and the production of bioenergy and biomaterials.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Reaction Diffusion Modelling of 3D Pillar Electrodes in Single-Catalyst CO 2 Reduction Cascades

Effective electrochemical CO 2 reduction to liquid fuels requires that the local catalytic environment facilitates the desired reactivity, yet a microscopic understanding of this environment is difficult to achieve from experiment alone. In this work, a 3D reaction-diffusion model was developed to explore the effects of electrode surface area and local geometry on the performance of a heterogeneous catalyst that performs a two-step CO 2 reduction cascade reaction to CO and then CH 3 OH under aqueous conditions. Kinetic parameters for the model were inspired by experimental results using a cobalt phthalocyanine (CoPc) catalyst. Three-dimensional architectures composed of arrays of square pillars with varying dimensions and either smooth or periodically modulated surfaces were tested, revealing the extent to which geometry modulates the performance of the cascade reactions. Although structural variations modulate local concentration gradients, we find that electrochemically active surface area predominantly governs the overall cascade reaction. Moreover, the results suggest that supersaturation of CO, with concentrations up to ten-fold higher than the equilibrium solubility limit, might be critical for more efficient conversion to CH 3 OH. For any given geometry, the spatially averaged ratio of [CO] to [CO 2 ] is dictated by the electrochemically active surface area and determines the yield of CH 3 OH. For a fixed surface area, geometries that spatially confine the electrolyte yield moderate local [CO] to [CO 2 ] ratios within small volumes. In contrast, less confining geometries result in a broader distribution of local ratios spread over larger volumes, with both configurations yielding the same spatially averaged [CO] to [CO 2 ] ratio. These insights provide valuable design principles—highlighting the critical importance of surface area and possibly CO supersaturation—for engineering advanced electrode architectures that leverage intermediate trapping and CO supersaturation to enhance overall performance in tandem CO 2 reduction systems.

COMSOL↗
DOE OSTI2021

Optimal Decision Making in High-Throughput Virtual Screening Pipelines

ABSTRACT Effective selection of the potential candidates that meet certain conditions in a tremendously large search space has been one of the major concerns in many real-world applications. In addition to the nearly infinitely large search space, rigorous evaluation of a sample based on the reliable experimental or computational platform is often prohibitively expensive, making the screening problem more challenging. In such a case, constructing a high-throughput screening (HTS) pipeline that pre-sifts the samples expected to be potential candidates through the efficient earlier stages, results in a significant amount of savings in resources. However, to the best of our knowledge, despite many successful applications, no one has studied optimal pipeline design or optimal pipeline operations. In this study, we propose two optimization frameworks, applying to most (if not all) screening campaigns involving experimental or/and computational evaluations, for optimally determining the screening thresholds of an HTS pipeline. We validate the proposed frameworks on both analytic and practical scenarios. In particular, we consider the optimal computational campaign for the long non-coding RNA (lncRNA) classification as a practical example. To accomplish this, we built the high-throughput virtual screening (HTVS) pipeline for classifying the lncRNA. The simulation results demonstrate that the proposed frameworks significantly reduce the effective selection cost per potential candidate and make the HTS pipelines less sensitive to their structural variations. In addition to the validation, we provide insights on constructing a better HTS pipeline based on the simulation results.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Failure prediction and estimation of failure parameters

Machine-learning methods and apparatus are disclosed to determine frictional state or other parameters in an earthquake zone or other failing medium, using acoustic emission, seismic waves, or other detectable indicators of microscopic processes. Predictions of future failures are demonstrated in different regimes. A classifier is trained using time series of acoustic emission data along with historic data of frictional state or failure events. In disclosed examples, random forests and gradient boost trees are used, and grid-search or EGO procedures are used for hyperparameter tuning. Once trained, the classifier can be applied to testing or live data in order to assess a frictional state, assess seismic hazard, or make predictions regarding a future failure event. The technology has been developed in a double direct shear apparatus, but can be widely applied to seismic faults, other terrestrial failures, or failures in man-made structures. Variations are disclosed.

Johnson, Paul Allan↗
DOE OSTI2025

Fine-scale vegetation composition and structure shape spatiotemporal variation in surface albedo across a low Arctic tundra landscape

The unprecedented rate of warming in the Arctic is driving changes in the structure and composition of tundra vegetation. Increases in deciduous tall shrub cover, height, and density are of particular concern, as these changes alter local surface albedo in ways that could amplify effects on the regional surface energy budget (SEB). Despite this importance, significant uncertainties remain in understanding the interplay between fine-scale vegetation patterns and emergent albedo dynamics across space and time. Here, we address these uncertainties by (1) quantifying spatiotemporal variation in surface shortwave albedo and (2) determining the relative influence of fine-scale vegetation composition, structure, and environmental conditions on albedo across a representative low-Arctic tundra landscape on Alaska’s Seward Peninsula. To do this, we synthesized multi-scale, multi-platform remote sensing observations, including a novel Landsat-derived albedo time series, a fine-scale map of Arctic plant functional type (PFT) fractional cover, and airborne LiDAR estimates of canopy height and topography. We show that there are substantial reductions in winter albedo for pixels dominated by tall, woody PFTs (28.13%) relative to pixels dominated by non-woody vegetation, but almost no change in summer albedo (3% increase). Further, we identified a unimodal trend in the relationship between canopy height and the timing of the springtime transition from high (snowy) to low (leafy) albedo (peak at 5.5 m), possibly because of competing ‘snow-fence’ and ‘protrusion’ snow-shrub interactions. To explore the primary drivers of albedo, we constructed a random forest model and found that canopy height and the fractional cover of woody PFTs were as- or more important predictors of winter albedo than topographic features. These findings provide strong evidence for the impacts of local vegetation characteristics on regional surface albedo, highlighting the need for better quantification of snow-shrub interactions to accurately predict the Arctic’s SEB under future environmental change.

Arctic↗
DOE OSTI2023

Transitional Structures with Continuous Variations in Atomic Positions from Anatase to Rutile Improve Photocatalytic Activity

Abstract TiO 2 polymorphs have distinct properties that are widely employed in various applications. However, mechanisms of transformations between these polymorphs are not fully understood, especially at atomic scale, inhibiting advancing the design and application of the transitional phases. Here, based on results from semi‐in situ transmission electron microscopy, density functional theory, and X‐ray photoemission experiments, a physical picture of transitional structures is discovered, in which continuous variations in atomic positions form along a previously unreported anatase‐to‐rutile phase transformation path of [010] A –to–[] R and (004) A –to– (011) R . These gradient structures give rise to continuous band bending, which promotes electron‐hole separation and inhibits their recombination across the bulk of the particles, leading to a large functionally active volume fraction and resulting in high photoactivity. These findings suggest that interphase matter based on extended gradient structures can be designed to advance new functions not achievable using abrupt interfaces.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electricity consumption variation versus economic structure during COVID-19 on metropolitan statistical areas in the US

The outbreak of novel coronavirus disease (COVID-19) has resulted in changes in productivity and daily life patterns, and as a result electricity consumption (EC) has also shifted. In this paper, we construct estimates of EC changes at the metropolitan level across the continental U.S., including total EC and residential EC during the initial two months of the pandemic. The total and residential data on the state level were broken down into the county level, and then metropolitan level EC estimates were aggregated from the counties included in each metropolitan statistical area (MSA). This work shows that the reduction in total EC is related to the shares of certain industries in an MSA, whereas regardless of the incidence level or economic structure, the residential sector shows a trend of increasing EC across the continental U.S. Since the MSAs account for 86% of the total population and 87% of the total EC of the continental U.S., the analytical result in this paper can provide important guidelines for future social-economic crises.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2024

Understanding Processes Controlling the Temporal and Spatial Variations of PBL Structures Over the ARM SGP Site

The surface heat, moisture, and momentum fluxes are transferred to the atmosphere above through the planetary boundary layer (PBL), where vertical mixing due to turbulent eddies of different sizes plays critical roles. Therefore, reliably representing PBL processes in numerical models is critical for weather, climate, and air quality prediction. Currently, there are over ten PBL schemes that are selectable within the advanced research version of the Weather Research and Forecasting (WRF) model, indicative of the challenges in capturing the impacts of turbulence within the PBL in models. Further improvements in PBL parameterizations are needed for both weather and climate models, as emphasized in many recent national reports, but require an advanced understanding of the underlying boundary layer processes from observations. This project takes advantage of Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) investments in the atmospheric boundary layer observations and Large-Eddy Simulation (LES) ARM Symbiotic Simulation and Observation (LASSO) simulations to characterize PBL structures, understand key physical processes controlling the mixed layer development, and to evaluate PBL parameterization.

54 ENVIRONMENTAL SCIENCES↗