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At least 271 records · Page 15

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DOE OSTI2021

Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics

Background Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context. Results. Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition. Conclusions The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Data for "Event Horizon Telescope Pattern Speeds in the Visibility Domain”

Visibility Amplitude Pattern Speeds from the v3 Sgr A* Library. Data for "Event Horizon Telescope Pattern Speeds in the Visibility Domain” (Conroy et al.). Data are provided in 2 file formats: a TXT table which is a standard format for the Astrophysical Journal (ApJ) where the paper is submitted and the original NPY format.

Conroy, Nicholas S. [University of Illinois] (ORCI↗

DOE OSTI2021

Numerical Modeling of CO2 Sequestration within a Five-Spot Well Pattern in the Morrow B Sandstone of the Farnsworth Hydrocarbon Field: Comparison of the TOUGHREACT, STOMP-EOR, and GEM Simulators

The objectives of this study were (1) to assess the fate and impact of CO2 injected into the Morrow B Sandstone in the Farnsworth Unit (FWU) through numerical non-isothermal reactive transport modeling, and (2) to compare the performance of three major reactive solute transport simulators, TOUGHREACT, STOMP-EOR, and GEM, under the same input conditions. The models were based on a quarter of a five-spot well pattern where CO2 was injected on a water-alternating-gas schedule for the first 25 years of the 1000 year simulation. The reservoir pore fluid consisted of water with or without petroleum. The results of the models have numerous broad similarities, such as the pattern of reservoir cooling caused by the injected fluids, a large initial pH drop followed by gradual pH neutralization, the long-term persistence of an immiscible CO2 gas phase, the continuous dissolution of calcite, very small decreases in porosity, and the increasing importance over time of carbonate mineral CO2 sequestration. The models differed in their predicted fluid pressure evolutions; amounts of mineral precipitation and dissolution; and distribution of CO2 among immiscible gas, petroleum, formation water, and carbonate minerals. The results of the study show the usefulness of numerical simulations in identifying broad patterns of behavior associated with CO2 injection, but also point to significant uncertainties in the numerical values of many model output parameters.

STOMP↗

DOE OSTI2023

Pangeo-Enabled ESM Pattern Scaling (PEEPS): A customizable dataset of emulated Earth System Model output

Emulation through pattern scaling is a well-established method of rapidly producing climate fields (like temperature or precipitation) from existing Earth System Model (ESM) output that, while inaccurate, is often useful for a variety of downstream purposes. Conducting pattern scaling has historically been a laborious process, in large part due to the increasing volume of ESM output data that has often required downloading and storing locally to train on. Here we describe the Pangeo-Enabled ESM Pattern Scaling (PEEPS) dataset, a repository of trained annual and monthly patterns from CMIP6 outputs. This manuscript describes and validates these updated patterns so that users can save effort calculating and reporting error statistics in manuscripts focused on the use of patterns. The trained patterns are available as NetCDF files on Zenodo for ease of use in the impact community, and are reproducible with the code provided via GitHub in both Jupyter notebook and Python script formats. Because all training data for the PEEPS data set is cloud-based, users do not need to download and house the ESM output data to reproduce the patterns in the zenodo archive, should that be more efficient. Validating the PEEPS data set on the CMIP6 archive for annual and monthly temperature, precipitation, and near-surface relative humidity, pattern scaling performs well over a variety of future scenarios except for regions in which there are strong, potentially nonlinear climate feedbacks. Although pattern scaling is normally conducted on annual mean ESM output data, it works equally well on monthly mean ESM output data. We identify several downstream applications of the PEEPS data set, including impacts assessment and evaluating certain types of Earth system uncertainties.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Domain patterns and super-elasticity of freestanding BiFeO 3 membranes via phase-field simulations

Super-elasticity of functional ferroelectric oxides offers promises for integrating ferroelectric films into flexible electronics. However, super-elastic deformation is a complex phenomenon related to possibly multiple concurrent mechanisms. Fundamentally understanding how multiple mechanisms contribute to the super-elasticity of ferroelectric oxides is crucial to realizing their potential flexible electronic applications. In this study, we employ phase-field simulations to model the dynamics of ferroelectric domain patterns of freestanding BiFeO 3 membranes to understand the origin of their super-elasticity under substantial bending deformation (5% strain). It is demonstrated that both a reversible Rhombohedral-Tetragonal (R-T) phase transition and a nearly reversible domain evolution of BiFeO 3 membranes contribute to accommodating the large deformation and thus their super-elasticity. The dynamics of domain evolution also reveal the formation of an exotic ferroelectric vortex and polarization rotation before the phase transition. We constructed a diagram of phases and domain patterns as a function of the membrane thickness and bending angle, which allows one to readily predict the emergence of T phase and ferroelectric vortex in bent BFO membranes. These results not only provide fundamental understanding of mesoscale super-elastic mechanisms but also reveal exotic domain states of ferroelectric membranes.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Cold shock induces novel nuclear bodies in Xenopus oocytes

Here we describe novel spherical structures that are induced by cold shock on the lampbrush chromosomes (LBCs) of Xenopus laevis oocytes. We call these structures cold bodies or C-bodies. C-bodies are distributed symmetrically on homologous LBCs, with a pattern similar to that of 5S rDNA. Neither active transcription nor translation is necessary for their formation. Similar protrusions occur on the edges of some nucleoli. Endogenous LBCs as well as those derived from injected sperm form C-bodies under cold shock conditions. The function of C-bodies is unknown.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

Probing orientation-specific charge-dipole interactions between hexafluoroisopropanol and halides: A joint photoelectron spectroscopy and theoretical study

The interactions between hexafluoroisopropanol (HFIP) and halogen anions X? (F?, Cl?, Br?, and I?) have been investigated by negative ion photoelectron spectroscopy (NIPES) and ab initio calculations. The measured NIPE spectrum of each [HFIP·X]? (X = Cl, Br, and I) complex shows the identical pattern to the corresponding X? by shifting to the high electron binding energy side, indicative of formation of [HFIP···X?] structure, in which X? interacts with HFIP via charge-dipole interactions. However, the spectrum of [HFIP·F]? appears completely different from that of F?, and is more similar to the spectrum of the deprotonated HFIP anion (HFIP?H?). The geometry and electron density calculations indicate that a neutral HF molecule is formed upon HFIP interacting with F? via proton transfer, rendering a stable structure of [HFIP?H···HF]?. Two conformers of [HFIP?H·HF]? with HFIP being in synperiplanar and antiperiplanar configurations, respectively, are observed, providing direct experimental evidences to show the distinctly different and orientation-specific interactions between HFIP and halide anions.

Wang, Lei↗

DOE OSTI2022

Symmetry-breaking in patch formation on triangular gold nanoparticles by asymmetric polymer grafting

Synthesizing patchy particles with predictive control over patch size, shape, placement and number has been highly sought-after for nanoparticle assembly research, but is fraught with challenges. Here we show that polymers can be designed to selectively adsorb onto nanoparticle surfaces already partially coated by other chains to drive the formation of patchy nanoparticles with broken symmetry. In our model system of triangular gold nanoparticles and polystyrene-b-polyacrylic acid patch, single- and double-patch nanoparticles are produced at high yield. These asymmetric single-patch nanoparticles are shown to assemble into self-limited patch-patch connected bowties exhibiting intriguing plasmonic properties. To unveil the mechanism of symmetry-breaking patch formation, we develop a theory that accurately predicts our experimental observations at all scales—from patch patterning on nanoparticles, to the size/shape of the patches, to the particle assemblies driven by patch-patch interactions. Both the experimental strategy and theoretical prediction extend to nanoparticles of other shapes such as octahedra and bipyramids. Our work provides an approach to leverage polymer interactions with nanoscale curved surfaces for asymmetric grafting in nanomaterials engineering.

42 ENGINEERING↗

DOE OSTI2024

Unlocking the potential: machine learning applications in electrocatalyst design for electrochemical hydrogen energy transformation

Machine learning (ML) is rapidly emerging as a pivotal tool in the hydrogen energy industry for the creation and optimization of electrocatalysts, which enhance key electrochemical reactions like the hydrogen evolution reaction (HER), the oxygen evolution reaction (OER), the hydrogen oxidation reaction (HOR), and the oxygen reduction reaction (ORR). This comprehensive review demonstrates how cutting-edge ML techniques are being leveraged in electrocatalyst design to overcome the time-consuming limitations of traditional approaches. ML methods, using experimental data from high-throughput experiments and computational data from simulations such as density functional theory (DFT), readily identify complex correlations between electrocatalyst performance and key material descriptors. Leveraging its unparalleled speed and accuracy, ML has facilitated the discovery of novel candidates and the improvement of known products through its pattern recognition capabilities. This review aims to provide a tailored breakdown of ML applications in a format that is readily accessible to materials scientists. Hence, we comprehensively organize ML-driven research by commonly studied material types for different electrochemical reactions to illustrate how ML adeptly navigates the complex landscape of descriptors for these scenarios. We further highlight ML's critical role in the future discovery and development of electrocatalysts for hydrogen energy transformation. Potential challenges and gaps to fill within this focused domain are also discussed. As a practical guide, we hope this work will bridge the gap between communities and encourage novel paradigms in electrocatalysis research, aiming for more effective and sustainable energy solutions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A microfluidic spore chamber for long-term imaging of single-spore hyphal development.

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device's capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, and stress-associated phenomena such as microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research.

Antifungal screening↗

DOE OSTI2025

Dataset for "A Microfluidic Spore Chamber for Long-Term Imaging of Single-Spore Hyphal Development"

Understanding the life cycle of fungal spores is essential for elucidating their roles in pathogenesis, dispersal, and survival. However, studying spore development under controlled, spatially defined conditions remains challenging. Here, we present the Spore Chamber, a custom-built microfluidic platform engineered for parallel trapping and long-term imaging of individual spores under defined media conditions, enabling real-time visualization of hyphal development. Using Aspergillus fumigatus as a model organism, we demonstrate that sparse trapping of individual spores within size-matched trap geometries enables long-term time-lapse imaging of key developmental stages, including germination, polarized hyphal elongation, branching, and conidiophore formation. To assess the device’s capacity to resolve morphogenetic responses to exogenous signals, we introduced lipochitooligosaccharides (LCOs) and short-chain chitooligosaccharides (COs). Rhizobium-derived, non-sulfated LCO (nsLCO) mixtures induced enhanced secondary branching (hyperbranching), a response not previously reported in A. fumigatus under these signal conditions, to our knowledge, whereas sulfated LCOs and CO4 did not significantly alter branching patterns. In addition, long-term confinement and imaging revealed rare developmental morphologies previously described primarily in mutant strains, including split conidiophore formation, elongated phialides, microcyclic conidiation, and chlamydospore development. Together, these results establish the Spore Chamber as a targeted microfluidic platform for single-spore phenotyping and long-term developmental analysis, with applications in fungal biology, chemical signaling studies, and host–microbe interaction research. Videos of the observed phenomena are included in this data set.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

The geology, geochemistry, and geographic distribution of southern Idaho obsidian

The Snake River Plain Volcanic Province of Southern Idaho is host to an abundance of pyroclastic obsidian deposits that constitute the principal lithic raw material utilized by Native Americans of the region throughout the Precontact Period. Archaeologists have long looked to obsidian as a source of information on past patterns of raw material selection, landscape use, and mobility through geochemical analysis of obsidian artifacts and lithic raw materials. Formation of the Snake River Plain through cataclysmic “super-eruptions” of the Yellowstone hotspot, however, presents one of the most complex and poorly understood obsidian source-scapes of North America. To clarify the geographic distribution of Southern Idaho obsidian source groups, the INL CRMO has compiled a comprehensive reference library of geologic obsidian from 138 source locales distributed across the southern half of the state. In this report, we define 28 geochemically distinct obsidian source groups that occur at these deposits through X-ray Fluorescence spectrometry and contextualize the geographic distribution of each source group relative to the history of silicic magmatism on the Snake River Plain. This research facilitates ongoing investigations at the INL CRMO into patterns of obsidian procurement, conveyance, and exchange in Southern Idaho throughout the Precontact Period.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Insights into the Biomimetic Synthesis of 2D ZnO Nanomaterials through Peptoid Engineering

Achieving predictable biomimetic crystallization using sequence-defined synthetic molecules in mild conditions represents a long-standing challenge in materials synthesis. Herein we report a peptoid-based approach for biomimetic control over the formation of nanostructured ZnO materials in ambient aqueous conditions. A series of two-dimensional (2D) ZnO nanomaterials have been successfully obtained using amphiphilic peptoids with different numbers, ratios, and patterns of various hydrophilic and hydrophobic side chains. By investigating the relationship between peptoid hydrophobicity and the thickness of the resultant ZnO nanomaterials, we found the critical role of peptoid hydrophobicity in the peptoid-controlled ZnO formation. Our results suggest that tuning the hydrophobicity of peptoids can be used to moderate peptoid–ZnO surface interactions, thus controlling the formation of ultrathin (<2.5 nm) 2D ZnO nanomaterials. Here, the peptoid-controlled formation of ZnO nanomaterials was further investigated using ultrasmall-angle X-ray scattering (USAXS). Our work suggests a new approach to synthesizing 2D metal oxide nanomaterials using sequence-defined synthetic molecules.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Formation of antireflective surfaces

Technologies are described for methods and systems effective for etching nanostructures in a substrate. The methods may comprise depositing a patterned block copolymer on the substrate. The patterned block copolymer may include first and second polymer block domains. The methods may comprise applying a precursor to the patterned block copolymer to generate an infiltrated block copolymer. The precursor may infiltrate into the first polymer block domain and generate a material in the first polymer block domain. The methods may comprise applying a removal agent to the infiltrated block copolymer to generate a patterned material. The removal agent may be effective to remove the first and second polymer block domains from the substrate. The methods may comprise etching the substrate. The patterned material on the substrate may mask the substrate to pattern the etching. The etching may be performed under conditions to produce nanostructures in the substrate.

Black, Charles T.↗

DOE OSTI2022

Formation of antireflective surfaces

Black, Charles T.↗

DOE OSTI2022

Assessment of chemo-mechanical impacts of CO 2 sequestration on the caprock formation in Farnsworth oil field, Texas

This study evaluates the chemo-mechanical influence of injected CO 2 on the Morrow B sandstone reservoir and the upper Morrow shale caprock utilizing data from the inverted 5-spot pattern centered on Well 13-10A within the Farnsworth unit (FWU). This study also seeks to evaluate the integrity of the caprock and the long-term CO 2 storage capability of the FWU. The inverted 5-spot pattern was extracted from the field-scale model and tuned with the available field observed data before the modeling work. Two coupled numerical simulation models were utilized to continue the study. First, a coupled hydro-geochemical model was constructed to simulate the dissolution and precipitation of formation minerals by modeling three intra-aqueous and six mineral reactions. In addition, a coupled hydro-geomechanical model was constructed and employed to study the effects of stress changes on the caprock’s porosity, permeability, and ground displacement. The Mohr–Coulomb circle and failure envelope were used to determine caprock failure. In this work, the CO 2 -WAG injection is followed by the historical field-observed strategy. During the forecasting period, a Water Alternating Gas (WAG) injection ratio of 1:3 was utilized with a baseline bottom-hole pressure constraint of 5500 psi for 20 years. A post-injection period of 1000 years was simulated to monitor the CO 2 plume and its effects on the CO 2 storage reservoir and caprock integrity. The simulation results indicated that the impacts of the geochemical reactions on the porosity of the caprock were insignificant as it experienced a decrease of about 0.0003% at the end of the 1000-year post-injection monitoring. On the other hand, the maximum stress-induced porosity change was about a 1.4% increase, resulting in about 4% in permeability change. It was estimated that about 3.3% of the sequestered CO 2 in the formation interacted with the caprock. Despite these petrophysical property alterations and CO 2 interactions in the caprock, the caprock still maintained its elastic properties and was determined to be far from its failure.

04 OIL SHALES AND TAR SANDS↗

DOE OSTI2023

Zinc‐Imidazolate Films as an All‐Dry Resist Technology

Here, motivated by the drawbacks of solution phase processing, an all‐dry resist formation process is presented that utilizes amorphous zinc‐imidazolate (aZnMIm) films deposited by atomic/molecular layer deposition (ALD/MLD), patterned with electron beam lithography (EBL), and developed by novel low temperature (120 °C) gas phase etching using 1,1,1,5,5,5‐hexafluoroacetylacetone (hfacH) to achieve well‐resolved 22 nm lines with a pitch of 30 nm. The effects of electron beam irradiation on the chemical structure and hfacH etch resistance of aZnMIm films are investigated, and it is found that electron irradiation degrades the 2‐methylimidazolate ligands and transforms aZnMIm into a more dense material that is resistant to etching by hfacH and has a C:N:Zn ratio effectively identical to that of unmodified aZnMIm. These findings showcase the potential for aZnMIm films to function in a dry resist technology. Sensitivity, contrast, and critical dimensions of the patterns are determined to be 37 mC cm −2 , 0.87, and 29 nm, respectively, for aZnMIm deposited on silicon substrates and patterned at 30 keV. This work introduces a new direction for solvent‐free resist processing, offering the prospect of scalable, high‐resolution patterning techniques for advanced semiconductor fabrication processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2026

Decoding α-MoC 1− x Nanoparticle Formation in Continuous Flow via Machine Learning

Molybdenum carbide nanoparticles (α-MoC 1−x NPs) are promising catalysts that offer noble-metal-like performance at lower cost. We report a mild continuous-flow synthesis of α-MoC 1−x NPs from Mo(CO) 6 , coupled with in-line spectroscopic monitoring and machine learning (ML)-based analysis to quantify precursor conversion and product formation in real time. A multilayer perceptron ML model was found to accurately deconvolute complex, nonlinear spectral patterns, enabling identification of a two-step reaction pathway, involving precursor conversion to an amorphous intermediate followed by intraparticle crystallization to α-MoC 1−x NPs, with the first step being rate limiting. Ex situ small angle X-ray scattering (SAXS) and X-ray diffraction (XRD) validation confirm the predicted concentration profiles and crystallization behavior. This integrated approach showcases how ML can empower insights into NP nucleation and growth, paving the way for self-driving, flow-based platforms for NP synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗