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At least 883 records · Page 49
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

OzDES Reverberation Mapping Program: Stacking analysis with Hβ, Mg ii , and C iv

ABSTRACT Reverberation mapping is the leading technique used to measure direct black hole masses outside of the local Universe. Additionally, reverberation measurements calibrate secondary mass-scaling relations used to estimate single-epoch virial black hole masses. The Australian Dark Energy Survey (OzDES) conducted one of the first multi-object reverberation mapping surveys, monitoring 735 AGN up to z ∼ 4, over 6 years. The limited temporal coverage of the OzDES data has hindered recovery of individual measurements for some classes of sources, particularly those with shorter reverberation lags or lags that fall within campaign season gaps. To alleviate this limitation, we perform a stacking analysis of the cross-correlation functions of sources with similar intrinsic properties to recover average composite reverberation lags. This analysis leads to the recovery of average lags in each redshift-luminosity bin across our sample. We present the average lags recovered for the Hβ, Mg ii, and C iv samples, as well as multiline measurements for redshift bins where two lines are accessible. The stacking analysis is consistent with the Radius–Luminosity relations for each line. Our results for the Hβ sample demonstrate that stacking has the potential to improve upon constraints on the R–L relation, which have been derived only from individual source measurements until now.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Gene family expansions and transcriptome signatures uncover fungal adaptations to wood decay

Because they comprise some of the most efficient wood-decayers, Polyporales fungi impact carbon cycling in forest environment. Despite continuous discoveries on the enzymatic machinery involved in wood decomposition, the vision on their evolutionary adaptation to wood decay and genome diversity remains incomplete. We combined the genome sequence information from 50 Polyporales species, including 26 newly sequenced genomes and sought for genomic and functional adaptations to wood decay through the analysis of genome composition and transcriptome responses to different carbon sources. The genomes of Polyporales from different phylogenetic clades showed poor conservation in macrosynteny, indicative of genome rearrangements. We observed different gene family expansion/contraction histories for plant cell wall degrading enzymes in core polyporoids and phlebioids and captured expansions for genes involved in signalling and regulation in the lineages of white rotters. Furthermore, we identified conserved cupredoxins, thaumatin-like proteins and lytic polysaccharide monooxygenases with a yet uncharacterized appended module as new candidate players in wood decomposition. Given the current need for enzymatic toolkits dedicated to the transformation of renewable carbon sources, the observed genomic diversity among Polyporales strengthens the relevance of mining Polyporales biodiversity to understand the molecular mechanisms of wood decay.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

A Role for the Plastidial GPT2 Translocator in the Modulation of Lignin Biosynthesis

ABSTRACT Engineering plants with reduced lignin content can result in pleiotropic growth defects. In stems of Arabidopsis plants with reduced expression of hydroxycinnamoyl CoA: shikimate hydroxycinnamoyl transferase (HCT), the plastidial glucose 6‐phosphate: phosphate co‐transporter GPT2 is highly overexpressed, and this coincides with reduced lignin levels and extensive transcriptional and metabolic reprogramming. To explore the potential relationship between GPT2 expression and lignin accumulation, GPT2 transcript levels were evaluated in a suite ofArabidopsis thalianaandMedicago truncatulalignin‐defective lines. We also examined lignin levels and composition, and transcriptomic and metabolic profiles in GPT2 loss‐of‐function, GPT2 overexpression, and wild‐type Arabidopsis plants. Loss of GPT2 had no effect on lignin, but its overexpression caused a decrease in stem lignin levels due to reduced accumulation of both guaiacyl and syringyl lignins and their associated monolignol pools.HCTtranscript levels were diminished in 35S‐GPT2 lines, indicating a potential transcriptional regulatory connection between lignin biosynthesis and GPT2. Based on our transcriptomic and metabolomic analyses, we suggest that GPT2 operates to balance the flux between the biosynthesis of lignin and light‐protective phenylpropanoid derivatives.

Plant Sciences↗
DOE OSTI2020

Microbiomes Reduce Their Host’s Sensitivity to Interspecific Interactions

Description of the Earth’s microbiota has recently undergone a phenomenal expansion that has challenged basic assumptions in many areas of biology, including hominid evolution, human gastrointestinal and neurodevelopmental disorders, and plant adaptation to climate change. By using the classic model system of freshwater phytoplankton that has been drawn upon for numerous foundational theories in ecology, we show that microbiomes, by facilitating their host population, can also influence between-species interactions among their eukaryotic hosts. Between-species interactions, including competition for resources, has been a central tenet in the field of ecology because of its implications for the diversity and composition of communities and how this in turn shapes ecosystem functioning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Multi-Scale Modeling Framework for Mercury Biogeochemistry

Multi-Scale modeling of mercury (Hg) geochemical speciation and reactions has been performed by integrating atomistic quantum chemical calculations with continuum scale speciation models. Major progress has been made in the improvement of quantum chemical models to calculate critical thermodynamic data for Hg complexes in aquatic environments. Rapid and reliable quantum chemical approaches have been developed for calculating acid dissociation constants (pK a ) and stability constants (log K), with calculated mean unsigned errors of 0.5 and 1.5 log units, respectively for ligand molecules and Hg complexes. At the continuum scale, systematic analysis of uncertainty propagation in mercury (Hg) speciation modeling has been conducted and was used to identify environmental conditions under which thermodynamic constant uncertainties are significant and recommended to be accounted for. The integrated framework for multi-scale modeling of mercury geochemistry is open to the research community through the web-based multiscale modeling aqueous speciation resource, AQUA-MER. The improved quantum chemical approaches for thermodynamic constant calculations are accessible through AQUA-MER and can be used to provide the missing constants in the continuum scale speciation calculations. In addition to low molecular mass Hg complex speciation, modeling natural aquatic environments also involve the transport of high molecular weight dissolved organic matter (DOM) in reactive flows simultaneously with equilibrium and kinetic reactions. To this end, atomistic MD simulations were performed to capture the details of aggregation, mechanisms and distribution of functional groups in DOM at the molecular level. The elemental composition and calculated bulk properties of the DOM models are in close agreement with experimental measurements. A travel-time based reactive transport model in the hyporheic zone of stream corridors was established for the multicomponent Hg-DOM-S system and implemented through PFLOTRAN.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Models to Incorporate Reaction Mechanisms into DG-OSPREY: Fixed-Bed Simulations for Organic Iodides Capture Using Ag 0 Z

As one of the most potent radioisotopes released during spent nuclear fuel reprocessing, 129 I is strictly regulated and must be removed before discharge. Organic iodides (primarily alkyl iodides with different chain lengths, i.e., CH 3 I, C 4 H 9 I, and C 12 H 25 I) comprise ~2% of the total iodine in the reprocessing off-gases and are primarily present in vessel off-gas (VOG). Reduced silver mordenite (Ag 0 Z) is predominantly considered for the removal of radioiodine; however, its capture performance and underlying interaction processes with long-chain organic iodides are not fully understood. Two major tasks were accomplished in this study. First, to improve upon the previous experimental studies where Ag 0 Z was used to capture CH 3 I, C 4 H 9 I, and C 12 H 25 I at different concentrations, we comprehensively investigated the corresponding capture mechanisms by characterizing fully loaded Ag 0 Z samples. Second, computational codes were implemented to perform fixed-bed simulations that account for transport and reaction mechanisms. Scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX), powder X-ray diffraction (PXRD), UV-visible diffuse reflectance spectroscopy (UV-vis DRS), and thermogravimetric analysis (TGA) were conducted on Ag 0 Z samples that are saturated with I 2 , CH 3 I, C 4 H 9 I, and C 12 H 25 I), respectively. Results indicate that AgI is the predominant adsorption product regardless of the adsorbed iodine species, yet alkyl iodides with different carbon chain lengths may have different compositions of α- and γ-AgI. Synchrotron pair distribution function (PDF) measurements and TGA coupled with a Fourier transformed infrared detector (TGA FTIR) have been performed, and experimental data are currently analyzed. Results are expected to provide further insights into the adsorption mechanisms. The fixed-bed capture performance for CH 3 I was successfully simulated by solving mathematical equations that describe the underlying transport processes and adsorption reactions. The computational framework, Catalytic After Treatment System (CATS), that was originated in our research group, was used to solve the governing equations. Kinetic parameters, including the pore diffusivity and reaction rate constant were obtained by optimization techniques using data from thin-bed experiments performed at Oak Ridge National Laboratory. The performance of a deep bed predicted using the optimized parameters showed promising agreement with the experimental data.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2023

FRAM Isotopic Analysis of High-Resolution CZT Data

H3D Inc. has introduced a new type of CZT detectors that has resolution several times better than that of a typical, single crystal CZT detector. The better resolution has made it easier for software codes to analyze its spectra for isotopic composition of nuclear materials. The Fixed-energy Response-function Analysis with multiple efficiency (FRAM) is one of such software codes. The good peak resolution of the H3D CZT detectors allows the current FRAM v.6.1 and earlier to successfully analyze uranium spectra with minimal modification of the parameter sets and get reasonable results. (A parameter set governs how an analysis is performed.) The exceptionally large high-energy tail of the peaks makes it difficult to achieve good uranium results and impossible to successfully analyze plutonium spectra. The FRAM code needed to be modified to better fit the high-energy tail of the peaks in order to analyze plutonium data and to get better uranium analysis results. Results of this modification, encoded in beta version FRAM v.7.0i, are reported herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

A novel nonperturbative renormalization scheme for local operators

The gradient flow exponentially suppresses ultraviolet field fluctuations and removes ultraviolet divergences (up to a multiplicative fermionic wavefunction renormalization). It can be used to describe real-space Wilsonian renormalization group transformations and determine the corresponding beta function. We propose a new nonperturbative renormalization scheme for local composite fermionic operators that uses the gradient flow and is amenable to lattice QCD calculations. We present preliminary nonperturbative results for the running of quark bilinear operators in this scheme and outline the calculation of perturbative matching to the MS-bar scheme.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Pulse Electrodeposition for Carbonate-Rich Deposits from Seawater

Seawater electrodeposition is gaining renewed interest in the context of sustainable development, both to build climate-resilient coastal infrastructure and for ocean-based decarbonization applications. Most of the applications benefit from CaCO 3 -rich deposits, but constant-voltage electrodeposition results in a mixture of CaCO 3 and Mg(OH) 2 , especially at higher voltages where precipitation rates are more desirable. The use of pulse voltages can help control interfacial pH that dictates the precipitation reactions. Here, we explore the use of pulse electrodeposition as a function of pulse frequency and duty cycle to control deposit composition. The most CaCO 3 -rich deposits were obtained under 10 Hz frequency and 10% duty cycle conditions for the voltage window investigated (-0.8 V to -1.2 V vs. SCE). While pulsing the voltage increases the amount of CaCO 3 deposited, the energy required per gram of CaCO 3 is significantly higher (14.5×) when compared to the base case of applying a constant voltage of -0.8 V vs. SCE. Further optimization of pulse conditions, electrode materials, and system configuration could lead to finding parameters that result in exclusively carbonate deposits without compromising precipitation rates, which may prove to be more useful for corrosion protection, coastal infrastructure, and other applications in sustainable development.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Shrub Seedling Experiment: Environmental Conditions, Vegetation Composition, and Seedling Recruitment, Seward Peninsula, Alaska, 2018-2019

In June 2018, a manipulative seed-addition experiment was established at the Council Mile Marker 71 (CN_MM71), Quartz Creek Burn Area (Kougarok Mile Marker 86), and Quartz Creek Unburned (Kougarok Mile Marker 80) sites on the Seward Peninsula, Alaska. At each site, 5 replicate blocks were established in disturbed and intact upland tussock tundra (a total of 40 plots). Disturbed plots at Council were located on thermo-erosional (thermokarst) slopes, while disturbed plots in Quartz Creek were in burned areas affected by the Mingvk Lake fire in 2015. Using a split-plot design, an additional manual disturbance treatment (scraping to remove the surface bryophyte layer) was implemented across all blocks in June 2018. Seeds of five erect, deciduous shrubs were broadcast seeded into each plot in June 2018, and seedlings were censused in August 2018 and August 2019. The dataset includes ancillary measurements of plot-level environmental conditions (soil temperature, moisture, chemistry, thaw depth, microtopography, substrate thickness) and vegetation composition (NDVI and estimated percent cover by species and plant functional type). Dataset contains 10 csv data files (five data files with corresponding data dictionaries and one file-level metadata file) and one pdf user guide. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

CRISPR protein inhibitors

The embodiments disclosed herein utilize fluorescence polarization based preliminary screen to identify a putative set of Cas inhibitors from an initial set of candidate inhibitors. The primary screening assay is followed by secondary screening assay to validate the putative set of inhibitors selected by the preliminary screen. In some embodiments, the present disclosure includes compositions and methods are provided for the inhibition of the function of RNA guided endonucleases, including the identification and use of such inhibitors.

Choudhary, Amit↗
DOE OSTI2021

Chemical and structural characterization of EUV photoresists as a function of depth by standing-wave x-ray photoelectron spectroscopy

The success in the miniaturization of the electronic device constituents depends mostly on the photolithographic techniques. Recently, to achieve patterning at the sub-10-nm node, extreme ultraviolet (EUV) lithography has been introduced into high volume production. Continued scaling of EUV via increased numerical aperture to achieve nodes at 3-nm and below requires the development of fundamentally new patterning materials and new characterization methods. Current EUV-resist film thicknesses are in the 20- to 40-nm range, and further thickness reduction is required for the next generation. Therefore, interfaces become exceedingly important, and the properties of the resist film would be dominated by top and bottom interfacial effects. X-ray photoelectron spectroscopy (XPS) combined with standing-wave excitation (SW-XPS), a fairly new method in the EUV lithography field, previously had been largely applied in multilayers and superlattices for characterizing the composition and electronic structure of buried layers and interfaces as a function of depth. We applied the SW-XPS method to organic/inorganic photoresists to provide depth-selective information on their structural and chemical conditions of as a function of temperature, EUV exposure, different underlayers, and other fundamental parameters. As a first attempt, we perform an SW-XPS feasibility study on self-assembled monolayer (SAM) films after exposure to an electron beam. By SW-XPS, we determined that the interface between the Al 2 O 3 underlayer and the SAMs is smooth, with a mean roughness of about 0.2 nm. Moreover, we determined that the SAM chains are, on average, tilted by 1/430 deg off the sample normal. The SW-XPS results also suggest that the SAM is not a perfectly aligned and uniform monolayer, with some areas having thickness higher than a single monolayer. We demonstrated that SW-XPS can provide useful information on ultrathin materials with high potential for being used as a characterization method of organic/inorganic photoresists.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Interactions between microbial diversity and substrate chemistry determine the fate of carbon in soil.

Microbial decomposition drives the transformation of plant-derived substrates into microbial products that form stable soil organic matter (SOM). Recent theories have posited that decomposition depends on an interaction between SOM chemistry with microbial diversity and resulting function. Here, we explicitly test these theories by coupling quantitative stable isotope probing and metabolomics to track the fate of 13C enriched substrates that vary in chemical composition as they are assimilated by microbes and transformed into new metabolic products in soil. We found that mycorrhizal-driven differences in forest nutrient economies (e.g., nutrient cycling, microbial competition) led to arbuscular mycorrhizal (AM) soils harboring greater micro8ial diversity than ectomycorrhizal (ECM) soils. When incubated with 13C enriched substrates, substrate type drove shifts in the identity of active decomposers and their metabolic products in the highly diverse AM soils. The decomposition pathways were more static in the less diverse, ECM soil. Importantly, the majority of these shifts were driven by taxa only present in the AM soil suggesting a strong link between microbial identity and specialized function. Collectively, these results highlight an important interaction between ecosystem-level processes and microbial diversity; whereby the identity and function of active decomposers impacts the composition of decomposition products that can form stable SOM.

Raczka, Nanette↗
DOE OSTI2025

Expanding the interlayer spacing of MXene through nanoarchitecture design

MXenes, a diverse class of two-dimensional transition metal carbides and nitrides with distinct surface chem istries, offer remarkable electrochemical and physicochemical properties. Yet, their performance can be hindered by the intrinsic restacking of layers, which restricts surface activity. This review outlines recent advances in interlayer spacing modulation strategies designed to overcome this limitation. A wide range of guest spe cies–including mono- and polyatomic ions, small molecules, low-dimensional nanomaterials, and polymers–are discussed with respect to their intercalation mechanisms, structural effects, and capacity to introduce functional enhancements. These intercalating species interact with MXene via electrostatic forces, hydrogen bonding, redox reactions, or covalent linkages, resulting in stable, expanded nanoarchitectures. The influence of expanded spacing on capacitive behavior is briefly highlighted to illustrate its practical relevance. Although Ti 3 C 2 T x is currently the most extensively investigated MXene, applying these interlayer engineering strategies to other MXene compositions will be essential for accessing a wider range of properties and functionalities.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Effect of Thermal Oxidation on the Structure, Surface Texturing, and Microstructure Evolution in Nanocrystalline Ga-O-N Films

An extensive examination of the nanoscale, crystallographic growth dynamics of the system, which is impacted by the thermal energy given to the GaN, is carried out to derive a deeper understanding of the growth kinetics, morphology and microstructure evolution, chemical bonding, and optical properties of Ga-O-N films. Thermal annealing of GaN films is performed in the temperature range of 900–1200 °C. Crystal structure, phase formation, chemical composition, surface morphology, and microstructure evolution of Ga-O-N films are investigated as a function of temperature. Increasing temperature induces surface oxidation, which results in the formation of stable β-Ga2O3 phase in the GaN matrix, where the overall film composition evolves from nitride (GaN) to oxynitride (Ga-O-N). While GaN surfaces are smooth, planar, and featureless, oxidation induced granular-to-rod shaped morphology evolution is seen with increasing temperature to 1200 °C. The considerable texturing and stability of the nanocrystalline Ga-O-N on Si substrates can be attributed to the surface and interface driven modification because of thermal treatment. Corroborating with structure and chemical changes, Raman spectroscopic analyses also indicate that the chemical bonding evolution progresses from fully Ga-N bonds to Ga-O-N. While the GaN oxidation process starts with the formation of β-Ga 2 O 3 at an annealing temperature of 1000 °C, higher annealing temperatures induce structural distortion with the potential formation of Ga-O-N bonds. The structure-phase-chemical composition correlation, which will be useful for nanocrystalline materials for selective optoelectronic applications, is established in Ga-O-N films made by thermal treatment of GaN.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Tunable structure and reinforcement of polyvinyl alcohol (PVA) hydrogels using fungal chitin particles

Polysaccharides, including chitin, are one of the most abundant biopolymers in nature and are increasingly recognized as a sustainable alternative to petroleum-derived plastics and synthetic fillers in polymer composites. Traditionally sourced from crustacean shells, chitin offers mechanical strength and biocompatibility with limitations also in processability and functionality. Fungal-derived chitin material represents a promising alternative, with advantages including scalable fermentation on low-cost substrates, absence of shellfish allergens, and tunable molecular architectures that vary by species, developmental stage, and growth environment. Here, in this study, we systematically examined chitinous materials obtained from taxonomically and functionally distinct fungi, Laccaria bicolor, Trichoderma reesei and Rhizopus oryzae, to assess their structural, chemical, and morphological properties as reinforcement agents in polymer composites. Mild alkaline pretreatment was employed to obtain mycelium chitin particles, thereby improving accessibility to chitin and co-occurring β-D-glucans while maintaining microparticle integrity. Comprehensive FTIR and solid-state NMR analyses revealed species-specific differences in chemical composition and microstructure, with R. oryzae exhibiting a unique spectral signature. These fungal-derived chitin were then incorporated into poly(vinyl alcohol) (PVA) hydrogels, where they acted as reinforcing fillers without the need for additional chemical crosslinkers. Comparative evaluation of hydrogel properties demonstrated that fungal chitin significantly enhanced mechanical performance, with all mycelium fillers mitigating the water weakening in PVA hydrogels. R. oryzae-derived composites tripled the hydrogel tensile strength while the submicron fibrous morphology in L. bicolor contributes to over 45 % tensile improvement in dry PVA composites. Our findings highlight the potential of fungal biomass as a tunable, sustainable platform for producing chitin-based reinforcing agents.

Chitin↗
DOE OSTI2026

Microfibril orientation and compositional heterogeneity in fiber and vessel cell walls of poplar xylem studied by AFM-IR and SFG spectroscopy

Understanding the structural organization of cellulose microfibrils (CMFs) within individual plant cell walls is essential for connecting cell wall architecture to its mechanical and physiological functions. However, due to the complex hierarchical structure and nanoscale heterogeneity of cell walls, it remains technically challenging to resolve detailed compositional and orientational information at subcellular levels of individual cell walls. This study investigates the internal 3D structure, chemical composition, and sublayer organization of fiber and vessel cell walls in the xylem tissue of a two-year-old field-grown hybrid poplar tree (Populus alba × P. glandulosa) using photothermal atomic force microscopy coupled with infrared spectroscopy (AFM-IR) and sum frequency generation (SFG) hyperspectral microscopy. AFM-IR provided nanoscale chemical imaging, revealing localized compositional heterogeneity, including variations between adjacent cell walls and transitional layers beyond the traditional S1, S2, and S3 sublayers. SFG microscopy revealed that CMFs in fiber walls are highly aligned along the stem axis, consistent with their role in mechanical support, while vessel cell walls exhibited slightly tilted CMFs, reflecting their function in hydraulic transport. Together, these results offer new insights into cell-type-specific CMF organization and compositional gradients in hybrid poplar xylem. These findings highlight the structural and chemical complexity of secondary cell walls in woody plants and demonstrate the value of AFM-IR and SFG spectroscopy in elucidating plant cell wall architecture.

60 APPLIED LIFE SCIENCES↗