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At least 1,765 records · Page 98
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Evolution of zygomycete secretomes and the origins of terrestrial fungal ecologies

Fungi survive in diverse ecological niches by secreting proteins and other molecules into the environment to acquire food and interact with various biotic and abiotic stressors. Fungal secretome content is, therefore, believed to be tightly linked to fungal ecologies. We sampled 132 genomes from the early-diverging terrestrial fungal lineage zygomycetes (Mucoromycota and Zoopagomycota) and characterized their secretome composition. Our analyses revealed that phylogeny played an important role in shaping the secretome composition of zygomycete fungi with trophic mode contributing a smaller amount. Reconstruction of the evolution of secreted digestive enzymes revealed lineage-specific expansions, indicating that Mucoromycota and Zoopagomycota followed different trajectories early in their evolutionary history. We identified the presence of multiple pathogenicity-related proteins in the lineages known as saprotrophs, suggesting that either the ecologies of these fungi are incompletely known, and/or that these pathogenicity-related proteins have important functions associated with saprotrophic ecologies, both of which invite further investigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Direct Measurement of Terahertz Conductivity in a Gated Monolayer Semiconductor

Two-dimensional semiconductors and their moiré superlattices have emerged as important platforms for investigating correlated electrons. However, many key properties of these systems, such as the frequency-dependent conductivity, remain experimentally inaccessible because of the mesoscopic sample size. Here we report a technique to directly measure the complex conductivity of electrostatically gated two-dimensional semiconductors in the terahertz frequency range. Applying this technique to a WSe2 monolayer encapsulated in hBN, we observe a clear Drude-like response between 0.1 and 1 THz, in a density range challenging to access even in DC transport. Our work opens a new avenue for studying tunable van der Waals heterostructures using terahertz spectroscopy.

2D semiconductors↗
DOE OSTI2024

Characterization and Optimization of Skipper CCDs for the SOAR Integral Field Spectrograph

We present results from the characterization and optimization of Skipper charge-coupled devices (CCDs) for use in a focal plane prototype for the Southern Astrophysical Research Integral Field Spectrograph (SIFS). We tested eight Skipper CCDs and selected six for SIFS based on performance results. The Skipper CCDs are 6k × 1k, 15 μm pixels, thick, fully depleted, p-channel devices that have been thinned to ~250 μm, backside processed, and treated with an anti-reflective coating. We demonstrate a single-sample readout noise of <4.3 e - rms pixel -1 in all amplifiers. We optimize the readout sequence timing to achieve a readout noise of 0.5 e - rms pixel -1 after 74 non-destructive measurements, which can be accomplished in a region covering 5% of the detector area in a readout time of <4 minutes. We demonstrate single-photon-counting in all 24 amplifiers (four amplifiers per detector) with a readnoise of σ N ~ 0.18 e - rms pixel -1 after N samp = 400 samples, and we constrain the degree of nonlinearity to be ≲1% at low signal levels (0 e - to 50 e - ). Clock-induced charge (CIC) remains an important issue when the Skipper CCD is configured to provide a large full-well capacity. We achieve a CIC rate of <1.45 × 10 -3 e - pixel -1 frame -1 for a full-well capacity of ~900 e - , which increases to a CIC rate of ~3 e - pixel -1 frame -1 for full-well capacities ~40,000-65,000 e - . We also perform conventional CCD characterization measurements such as charge transfer inefficiency (3.44 × 10 -7 on average), dark current (~2 × 10 -4 e - pixel -1 s -1 ), photon transfer curves, cosmetic defects (<0.45% “bad” pixels), and charge diffusion (point-spread function < 7.5 μm) to verify that these properties are consistent with expectations from conventional p-channel CCDs used for astronomy. Furthermore, we provide the first measurements of the brighter-fatter effect and absolute quantum efficiency (≳80% between 450 and 980 nm; ≳90% between 600 and 900 nm) using Skipper CCDs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2024

Learning new physics from data: A symmetrized approach

Thousands of person years have been invested in searches for new physics (NP), the majority of them motivated by theoretical considerations. Yet, no evidence of beyond the Standard Model physics has been found. This suggests that model-agnostic searches might be an important key to explore NP, and help discover unexpected phenomena which can inspire future theoretical developments. A possible strategy for such searches is identifying asymmetries between data samples that are expected to be symmetric within the Standard Model. We propose exploiting neural networks (NNs) to quickly fit and statistically test the differences between two samples. Our method is based on an earlier work, originally designed for inferring the deviations of an observed dataset from that of a much larger reference dataset. We present a symmetric formalism, generalizing the original one, avoiding fine-tuning of the NN parameters and any constraints on the relative sizes of the samples. Our formalism could be used to detect small symmetry violations, extending the discovery potential of current and future particle physics experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

In-house synthesized poly(ether ether ketone) ionenes. I. ToF-SIMS spectra in the positive ion mode

Static time-of-flight secondary ion mass spectrometry (ToF-SIMS) was performed for acquiring the high-resolution surface spectra of four types of synthesized imidazolium ionene membranes. These novel membranes have aromatic ether–ketone–ether linkages inspired by poly(ether ether ketone) (PEEK). The PEEK-ionenes synthesized for this study have imidazolium cations placed in the polymeric backbone with bistriflimide [Tf 2 N]- counterions. The attention given to synthetically modified PEEK derivatives, such as PEEK-ionenes, is considerable due to their ability to selectively capture CO 2 molecules and other light gases. Therefore, it is important to characterize the surface of these synthesized novel PEEK-ionenes. In this work, characteristic and unique peaks were identified in the positive spectra of each sample. The differences in mass spectra among the samples provide insights for optimizing or fine-tuning the PEEK-ionenes synthesis to achieve a high-performance CO 2 separation membrane with enhanced permeability, selectivity, and mechanical stability. The SIMS spectra and identified characteristic peaks of these synthesized ionenes will serve as a reference in the positive mode, complementing the corresponding spectra reported in the negative ion mode (Paper II).

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

Spatiotemporal characterization of the field-induced insulator-to-metal transition

Watching a metal filament grow Resistive switching is a process in which the electrical resistance of a sample changes abruptly in response to a voltage pulse, often by orders of magnitude. This process is at the heart of many neuromorphic computing approaches but visualizing it in both space and time is tricky. del Valle et al . monitored the resistive switching in three different vanadium oxide compounds by measuring time- and space-resolved optical reflectivity (see the Perspective by Hilgenkamp and Gao). A characteristic conducting filament was quickly nucleated on the inhomogeneities in the sample and then propagated due to Joule heating. —JS

Science & Technology - Other Topics↗
DOE OSTI2021

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota

Cervical microbiota (CM) are considered an important factor affecting the progression of cervical intraepithelial neoplasia (CIN) and are implicated in the persistence of human papillomavirus (HPV). Collection of liquid-based cytology (LBC) samples is routine for cervical cancer screening and HPV genotyping and can be used for long-term cytological biobanking. We sought to determine whether it is possible to access microbial DNA from LBC specimens, and compared the performance of four different extraction protocols: (ZymoBIOMICS DNA Miniprep Kit; QIAamp PowerFecal Pro DNA Kit; QIAamp DNA Mini Kit; and IndiSpin Pathogen Kit) and their ability to capture the diversity of CM from LBC specimens. LBC specimens from 20 patients (stored for 716 ± 105 days) with CIN values of 2 or 3 were each aliquoted for each of the four kits. Loss of microbial diversity due to long-term LBC storage could not be assessed due to lack of fresh LBC samples. Comparisons with other types of cervical sampling were not performed. We observed that all DNA extraction kits provided equivalent accessibility to the cervical microbial DNA within stored LBC samples. Approximately 80% microbial genera were shared among all DNA extraction protocols. Potential kit contaminants were observed as well. Variation between individuals was a significantly greater influence on the observed microbial composition than was the method of DNA extraction. We also observed that HPV16 was significantly associated with community types that were not dominated by Lactobacillus iners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fundamentals of Scalable Nanoparticle Assembly in Engineering Polymres

Systematically improving the properties of polymer nanocomposites is contingent on effectively controlling nanoparticle (NP) dispersion; further, it is necessary to attain this at scale if these methods are to impact practical applications. While most past work has focused on amorphous polymers, ≈ 70% of all polymers sold annually are semicrystalline. Inspired by this apparent disconnect, our work in the current DOE funded grant and this renewal proposal employs a novel handle, polymer crystallization, to organize NPs into the various amorphous zones of the lamellar semicrystalline morphology (interlamellar, interfibrillar and interspherulitic domains) of stereoregular polymers. We hypothesize that the isothermal crystallization rate of a polymer host, G, and NP diffusivity, are the two relevant control parameters in this context. In the case where the NPs are miscible in the melt, they remain spatially well-dispersed when the polymer is crystallized at a rate that is fast relative to NP diffusion. In contrast, monolayer-thick NP sheets with intersheet spacing of ~10-100nm form in slowly crystallized samples. This sheet stacking is remarkably similar to that seen in natural materials, e.g., Nacre. There is also ordering of the NPs at the larger interfibrillar scale. Importantly, the relative fraction of engulfed, interlamellar and interfibrillar NPs is determined by G. Further, the modulus of these materials can increase by a factor of 2-3 due to the organization state of the NPs, while leaving fracture toughness unaffected. We have established the broad applicability of this approach in two polymers, polyethylene (PE) and polyethyleneoxide (PEO). To achieve this goal we developed a method for grafting long PE chains from NPs with controlled graft density and molecular weight, giving us the ability to tailor their dispersion in the PE melt prior to crystallization. In this renewal proposal, we will develop the fundamental, quantitative understanding that will allow us to independently tailor polymer crystallization rate, NP diffusivity and NP agglomeration state in semicrystalline polymers so as to facilely control NP ordering and hence properties. A program that tightly integrates experiment and theory is proposed, and a key outcome of this research will be a three-dimensional design map for different regimes of NP organization (and hence properties) that can be achieved by polymer crystallization. A second independent outcome is the role of directional solidification and how it competes with the rates of polymer crystallization and NP mobility to affect the organization of the NP.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Accelerating the identification of novel secondary metabolites in bioenergy plant root exudates using MicroED

Small molecule metabolites drive inter- and intraspecies communication and dependencies in diverse biological systems, yet a large proportion of these important chemical compounds remain uncharacterized in plants and microbes. Approximately 90% of the metabolites in root exudate profiles are unknown compounds, despite the importance of root exudate composition in plant-microbe interactions. We need advanced analytical capabilities that will support rapid discovery and structural elucidation of metabolites from biological samples that may be limited in quantity and high in complexity. To fill this gap, this project aimed to develop an integrated workflow involving metabolite extraction, separation, and crystallization from plant root exudates followed by characterization using nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and microcrystal electron diffraction (MicroED). Using crude root exudates from sorghum, this project successfully developed higher throughput exudate fractionation strategies to obtain pure compounds for crystallization and identified crystals in multiple fractions that diffracted. Additional efforts to increase the throughput of high-quality crystal generation for MicroED, such as crystallization screening and crystallization chaperone exploration, will be needed to further advance root exudate metabolite identification. The overall optimized sample preparation process can then be integrated with the existing data collection and data analysis pipelines for MicroED at PNNL to facilitate more rapid natural product discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Illuminating the Material World: Autonomous Microscopy to Understand Order, Disorder, and Everything In Between

Artificial intelligence (AI) holds immense promise for revolutionizing microscopy, yet its widespread adoption has been hindered by challenges ranging from user inexperience to limited model transferability and difficulties in operationalizing machine learning. This presentation showcases our approach to developing practical autonomy for materials discovery, aiming to accelerate the integration of AI into everyday microscopy workflows. As shown in Fig. 1, I will focus on three key areas: understanding order-disorder transitions, quantifying point defects, and achieving truly device-scale microscopy. First, I will demonstrate the power of multi-modal knowledge graphs for integrating diverse microscopy data. By combining imaging, spectroscopy, and diffraction data, these graphs provide a holistic view of material behavior, capturing the intricate relationships between different modalities [1,2]. I will present a case study on how these models illuminate the structural and chemical changes associated with irradiation in oxide thin films, revealing critical insights for designing materials for extreme environments like spaceflight and nuclear energy. Specifically, I will show how multi-modal analysis clarifies the evolution of order-disorder transitions under irradiation, a key factor influencing material performance in these applications. Next, I will address the challenge of quantifying point defects in 2D materials. We demonstrate the application of computer vision and transfer learning to accurately identify and classify various defect types, such as vacancies and substitutional atoms, and to quantify their concentrations. This information is crucial for understanding and tailoring the properties of 2D materials for applications in electronics, optoelectronics, and catalysis. For example, I will show how our models can characterize the topological distribution of point defects in MXene transition metal carbides, providing valuable insights for optimizing their performance in energy storage and separation science. Finally, I will discuss our progress toward autonomous device-scale microscopy [3,4]. We are fundamentally redesigning electron microscopes around the principles of machine reasoning, enabling automation beyond basic tasks like sample navigation and data acquisition to include sophisticated experimental design. This approach paves the way for truly reproducible and massively scaled analysis campaigns. I will emphasize the importance of autonomous microscopy platforms for high-throughput materials discovery and characterization, facilitating the rapid screening of materials for a broad range of applications and accelerating the development of next-generation technologies.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Carbon Isotope Composition and the NDVI as Phenotyping Approaches for Drought Adaptation in Durum Wheat: Beyond Trait Selection

High-throughput phenotyping platforms provide valuable opportunities to investigate biomass and drought-adaptive traits. We explored the capacity of traits associated with drought adaptation such as aerial measurements of the Normalized Difference Vegetation Index (NDVI) and carbon isotope composition (δ13C) determined at the leaf level to predict genetic variation in biomass. A panel of 248 elite durum wheat accessions was grown at the Maricopa Phenotyping platform (US) under well-watered conditions until anthesis, and then irrigation was stopped and plot biomass was harvested about three weeks later. Globally, the δ13C values increased from the first to the second sampling date, in keeping with the imposition of progressive water stress. Additionally, δ13C was negatively correlated with final biomass, and the correlation increased at the second sampling, suggesting that accessions with lower water-use efficiency maintained better water status and, thus, performed better. Flowering time affected NDVI predictions of biomass, revealing the importance of developmental stage when measuring the NDVI and the effect that phenology has on its accuracy when monitoring genotypic adaptation to specific environments. The results indicate that in addition to choosing the optimal phenotypic traits, the time at which they are assessed, and avoiding a wide genotypic range in phenology is crucial.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Impacts of Different Operation Conditions and Geological Formation Characteristics on CO2 Sequestration in Citronelle Dome, Alabama

Major concerns of carbon dioxide (CO2) sequestration in subsurface formations are knowledge of the well injectivity and gas storage capacity of the formation, the CO2 pressure and saturation plume extensions during and after injection, and the risks associated with CO2 leakage and fault reactivation. Saline reservoirs are considered as one of the target formations for CO2 sequestration through structural, residual, dissolution, and mineral trapping mechanisms. The boundary condition of the saline reservoir dictates the pressure and saturation plume extension of the injected supercritical CO2 that could expand over large distances. This can lead to sources of risk, e.g., leakage and/or fault reactivation due to presence of wells, thief zones, and geological discontinuities. Therefore, there is a critical need to develop a model that describes how risk-related performance metrics (i.e., the CO2 saturation plume size, the pressure differential plume area, and the pressure differential at specific locations) vary as a function of the size of injection, time following injection, injection operations, and geologic environment. In this study, a systematic reservoir modeling studies of anthropogenic CO2 sequestration in Citronelle dome, Alabama, was performed where all relevant scenarios and conditions to address the questions of the saturation and pressure plume size in the area of review (AoR) and post-injection site care (PISC) are considered. The objective for this study was firstly to systematically simulate CO2 sequestration, i.e., saturation dynamics, and pressure behavior over a range of operational and geological conditions and to derive conclusions about the factors influencing saturation and pressure plume size, post-injection behavior, and the risk associated with them, by developing third-generation reduced order models (ROMs) for reservoir behavior. Finally, to assess the uncertainty associated with our studies, Latin Hypercube Sampling (LHS) together with an experimental design technique, i.e., Plackett–Burman design, was used. Application of Pareto charts and respond surfaces enabled us to determine the most important parameters impacting saturation and pressure plume sizes and to quantify the auto- and cross-correlation among different parameters in both history-matched and upscaled models.

58 GEOSCIENCES↗
NASA NTRS1974

Auger electron spectroscopy of lunar samples

Auger spectroscopy has been employed to study the surface composition of a number of grains from the submillimeter lunar fines. Some of the problems associated with using this technique for lunar sample analyses are discussed in terms of relevant physical principles. The use of inert gas sputtering to obtain thickness profiles of surface films is shown to be important in this type of investigation. Four anorthite grains from the Apollo 17 fines have been examined for evidence of vapor-deposited surface coatings of micrometeorite impact origin. The results indicate that the thickness of surface deposits, if they exist at all, are orders of magnitude less than expected. Auger analysis of orange glass balls form the 74220,107 fines have established sulfur-rich surface coatings on the order of 30 A in thickness.

Grant, R. W.↗
NASA NTRS1979

Molecular phylogenetic trees - On the validity of the Goodman-Moore augmentation algorithm

A response is made to the reply of Nei and Tateno (1979) to the letter of Holmquist (1978) supporting the validity of the augmentation algorithm of Moore (1977) in reconstructions of nucleotide substitutions by means of the maximum parsimony principle. It is argued that the overestimation of the augmented numbers of nucleotide substitutions (augmented distances) found by Tateno and Nei (1978) is due to an unrepresentative data sample and that it is only necessary that evolution be stochastically uniform in different regions of the phylogenetic network for the augmentation method to be useful. The importance of the average value of the true distance over all links is explained, and the relative variances of the true and augmented distances are calculated to be almost identical. The effects of topological changes in the phylogenetic tree on the augmented distance and the question of the correctness of ancestral sequences inferred by the method of parsimony are also clarified.

Holmquist, R.↗
NASA NTRS1983

Design and implementation of a multigrid code for the Euler equations

The steady-state equations of inviscid fluid flow, the Euler equations, are a nonlinear nonelliptic system of equations admitting solutions with discontinuities (for example, shocks). The efficient numerical solution of these equations poses a strenuous challenge to multigrid methods. A multigrid code has been developed for the numerical solution of the Euler equations. In this paper some of the factors that had to be taken into account in the design and development of the code are reviewed. These factors include the importance of choosing an appropriate difference scheme, the usefulness of local mode analysis as a design tool, and the crucial question of how to treat the nonlinearity. Sample calculations of transonic flow about airfoils will be presented. No claim is made that the particular algorithm presented is optimal.

Jespersen, D. C.↗
NASA NTRS1988

Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions

Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30 deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing 3 dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally samples data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.

Kussoy, M. I.↗
NASA NTRS1988

Carbon dioxide catastrophes: Past and future menace

Carbon dioxide is important in its role as coupler of the terrestrial biosphere to inorganic chemical processes and as the principal greenhouse gas controlling Earth's surface temperature. The hypothesis that atmospheric CO2 levels have diminished with time, with the resulting cooling effect offsetting an increase in the solar constant, seems firmly established, and it is shown that feedback mechanisms exist which can maintain the terrestrial surface in a relatively narrow temperature range over geological time. Of the factors involved in such CO2 variation, the oceanic reservoir appears the most important. Surface waters are probably in approximate equilibrium with regard to CO2 exchange with the ambient atmosphere in most regions, but data from deep-ocean water sampling indicates that such waters are somewhat undersaturated in the sense that they would tend to absorb CO2 from the atmosphere if brought to the surface without change in composition or temperature. If major impacts into the ocean can result in loss of a substantial portion of the atmospheric CO2 reservoir, then any such future event could imperil the continuation of most higher forms of life on Earth. The most likely candidate for an inverse Nyos global event in previous Earth history is the Cretaceous-Tertiary terminal extinction event. The Cretaceous was characterized by warm, equable temperatures presumably indicative of relatively high CO2 levels and an intense greenhouse heating. Cooling of the oceans in absence of massive transfer of CO2 to the oceanic reservoir in itself would promote a condition of CO2 undersaturation in abyssal waters, and this is made even more extreme by the pattern of ocean water circulation. It is possible to envision a situation in which deep ocean waters were at least occasionally profoundly undersaturated with regard to CO2. Turnover of a major fraction of such an ocean would then remove, on a very short time scale, as much as 90 percent of the atmospheric CO2 inventory.

Baur, Mario E.↗
NASA NTRS1988

Fluctuations and massive separation in three-dimensional shock-wave/boundary-layer interactions

Shock-wave unsteadiness was observed in rapidly compressed supersonic turbulent boundary layer flows with significant separation. A Mach 2.85 shock-wave/turbulent boundary layer flow was set up over a series of cylinder-flare bodies in the High Reynolds Number Channel 1. The transition from fully attached to fully separated flow was studied using axisymmetric flares with increasing compression angles. In the second phase, the 30-deg flare was inclined relative to the cylinder axis, so that the effect on a separated flow of increasing three-dimensionality could be observed. Two 3-D separated cases are examined. A simple conditional sampling technique is applied to the data to group them according to an associated shock position. Mean velocities and turbulent kinetic energies, computed from the conditionally sampled data, are compared to those from the unsorted data and to computed values. Three basic questions were addressed: can conditional sampling be used to provide snapshots of the flow; are averaged turbulence quantities dominated by the bimodal nature of the interaction; and is the shock unsteadiness really important to computational accuracy.

Kussoy, M. I.↗