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At least 1,549 records · Page 86
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

A traditional evolutionary history of foot-and-mouth disease viruses in Southeast Asia challenged by analyses of non-structural protein coding sequences

Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversifcation, spread, and emergence of new variants with enhanced ftness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specifc viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages’ divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at diferent breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Computational screening of organic polymer dielectrics for novel accelerator technologies

The use of infrared lasers to power accelerating dielectric structures is a developing area of research. Within this technology, the choice of the dielectric material forming the accelerating structures, such as the photonic band gap (PBG) structures, is dictated by a range of interrelated factors including their dielectric and optical properties, amenability to photo-polymerization, thermochemical stability and other target performance metrics of the particle accelerator. In this direction, electronic structure theory aided computational screening and design of dielectric materials can play a key role in identifying potential candidate materials with the targeted functionalities to guide experimental synthetic efforts. In an attempt to systematically understand the role of chemistry in controlling the electronic structure and dielectric properties of organic polymeric materials, here we employ empirical screening and density functional theory (DFT) computations, as a part of our multi-step hierarchal screening strategy. Our DFT based analysis focused on the bandgap, dielectric permittivity, and frequency-dependent dielectric losses due to lattice absorption as key properties to down-select promising polymer motifs. In addition to the specific application of dielectric laser acceleration, the general methodology presented here is deemed to be valuable in the design of new insulators with an attractive combination of dielectric properties.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

Assessing the impact of human mobility to predict regional excess death in Ecuador

Abstract COVID-19 outbreaks have had high mortality in low- and middle-income countries such as Ecuador. Human mobility is an important factor influencing the spread of diseases possibly leading to a high burden of disease at the country level. Drastic control measures, such as complete lockdown, are effective epidemic controls, yet in practice one hopes that a partial shutdown would suffice. It is an open problem to determine how much mobility can be allowed while controlling an outbreak. In this paper, we use statistical models to relate human mobility to the excess death in Ecuador while controlling for demographic factors. The mobility index provided by GRANDATA, based on mobile phone users, represents the change of number of out-of-home events with respect to a benchmark date (March 2nd, 2020). The study confirms the global trend that more men are dying than expected compared to women, and that people under 30 show less deaths than expected, particularly individuals younger than 20 with a death rate reduction between 22 and 27%. The weekly median mobility time series shows a sharp decrease in human mobility immediately after a national lockdown was declared on March 17, 2020 and a progressive increase towards the pre-lockdown level within two months. Relating median mobility to excess deaths shows a lag in its effect: first, a decrease in mobility in the previous two to three weeks decreases excess death and, more novel, we found an increase of mobility variability four weeks prior increases the number of excess deaths.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Field trials reveal the complexities of deploying and evaluating the impacts of yeast-baited ovitraps on Aedes mosquito densities in Trinidad, West Indies

The use of lure-and-kill, large-volume ovitraps to control Aedes aegypti and Aedes albopictus populations has shown promise across multiple designs that target gravid females (adulticidal) or larvae post-oviposition (larvicidal). Here we report on a pilot trial to deploy 10 L yeast-baited ovitraps at select sites in Curepe, Trinidad, West Indies during July to December, 2019. Oviposition rates among ovitraps placed in three Treatment sites were compared to a limited number of traps placed in three Control areas (no Aedes management performed), and three Vector areas (subjected to standard Ministry of Health, Insect Vector Control efforts). Our goal was to gain baseline information on efforts to saturate the Treatment sites with ovitraps within 20–25 m of each other and compare oviposition rates at these sites with background oviposition rates in Control and Vector Areas. Although yeast-baited ovitraps were highly attractive to gravid Aedes females, a primary limitation encountered within the Treatment sites was the inability to gain access to residential compounds for trap placement, primarily due to residents being absent during the day. This severely limited our intent to saturate these areas with ovitraps, indicating that future studies must include plans to account for these inaccessible zones during trap placement.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Permeability scaling relationships of volcanic tuff from core to field scale measurements

A recent chemical explosive test in P-Tunnel at the Nevada National Security Site, Nevada, USA, was conducted to better understand how signals propagate from explosions in the subsurface. A primary signal of interest is the migration of gases that can be used to differentiate chemical from nuclear explosions. Gas migration is highly dependent on the rock permeability which is notoriously difficult to determine experimentally in the field due to a potentially large dependence on the scale over which measurements are made. Here, we present pre-explosion permeability estimates to characterize the geologic units surrounding the recent test. Permeability measurements were made at three scales of increasing size: core samples (≈2 cm), borehole packer system tests (≈1 m), and a pre-shot cavity pressurization test (> 10 m) across ten tuff units. Permeability estimates based on core measurements showed little difference from borehole packer tests. However, permeability in most rock units calibrated from cavity pressurization tests resulted in higher permeability estimates by up to two orders of magnitude. Here, we demonstrate that the scale of the measurement significantly impacts the characterization efforts of hydraulic properties in volcanic tuff, and that local-scale measurements (< 10 m scale) do not incorporate enough heterogeneity to accurately predict field-scale flow and mass transport.

Environmental sciences↗
DOE OSTI2026

Predicting multiphase flow and tracer transport for an underground chemical explosive test

Detecting radionuclide gas seepage from clandestine underground nuclear tests is central to nonproliferation explosion monitoring research. Yet, early-time (<6 day) gas transport driven by the explosive pressure wave remains poorly constrained due to scarcity of field data. We simulate multi-phase gas transport in the vadose zone using pre-shot data from a recent chemical explosion in P-Tunnel at the Nevada National Security Site, USA. Despite using a simplified 2D-radial model, predictions of tracer arrival matched observations within one order-of-magnitude. Our results show how transient blast forcing rapidly mobilizes gases from the cavity into surrounding rock – critical for optimizing sensor placement and test planning. This unique integration of field data and modeling represents a significant improvement in our ability to predict gas migration from underground explosions. More broadly, it offers insights into the coupled dynamics of pressure waves and contaminant transport in the vadose zone, with implications for monitoring and hazard assessment.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli

Escherichia coli CusCBAF represents an important class of bacterial efflux pump exhibiting selectivity towards Cu(I) and Ag(I). The complex is comprised of three proteins: the CusA transmembrane pump, the CusB soluble adaptor protein, and the CusC outer-membrane pore, and additionally requires the periplasmic metallochaperone CusF. Here we used spectroscopic and kinetic tools to probe the mechanism of copper transfer between CusF and CusB using selenomethionine labeling of the metal-binding Met residues coupled to RFQ-XAS at the Se and Cu edges. The results indicate fast formation of a protein–protein complex followed by slower intra-complex metal transfer. An intermediate coordinated by ligands from each protein forms in 100 ms. Stopped-flow fluorescence of the capping CusF-W44 tryptophan that is quenched by metal transfer also supports this mechanism. The rate constants validate a process in which shared-ligand complex formation assists protein association, providing a driving force that raises the rate into the diffusion-limited regime.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Phylogenetic and ecological drivers of the avian lung mycobiome and its potentially pathogenic component

Vertebrate lungs contain diverse microbial communities, but little is known about the drivers of community composition or consequences for health. Microbiome assembly by processes such as dispersal, coevolution, and host-switching can be probed with comparative surveys; however, few studies exist for lung microbiomes, particularly for the fungal component, the mycobiome. Distinguishing among fungal taxa that are generalist or specialist symbionts, potential pathogens, or incidentally inhaled spores is urgent because of potential for emerging diseases. Here, we characterize the avian lung mycobiome and test the relative influences of environment, phylogeny, and functional traits. We used metabarcoding and culturing from 195 lung samples representing 32 bird species across 20 families. We identified 526 fungal taxa as estimated by distinct sequence types (zOTUs) including many opportunistic pathogens. These were predominantly from the phylum Ascomycota (79%) followed by Basidiomycota (16%) and Mucoromycota (5%). Yeast and yeast-like taxa (Malassezia, Filobasidium, Saccharomyces, Meyerozyma, and Aureobasidium) and filamentous fungi (Cladosporium, Alternaria, Neurospora, Fusarium, and Aspergillus) were abundant. Lung mycobiomes were strongly shaped by environmental exposure, and further modulated by host identity, traits, and phylogenetic affinities. Our results implicate migratory bird species as potential vectors for long-distance dispersal of opportunistically pathogenic fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Resonant inelastic x-ray scattering in warm-dense Fe compounds beyond the SASE FEL resolution limit

Resonant inelastic x-ray scattering (RIXS) is a widely used spectroscopic technique, providing access to the electronic structure and dynamics of atoms, molecules, and solids. However, RIXS requires a narrow bandwidth x-ray probe to achieve high spectral resolution. The challenges in delivering an energetic monochromated beam from an x-ray free electron laser (XFEL) thus limit its use in few-shot experiments, including for the study of high energy density systems. Here we demonstrate that by correlating the measurements of the self-amplified spontaneous emission (SASE) spectrum of an XFEL with the RIXS signal, using a dynamic kernel deconvolution with a neural surrogate, we can achieve electronic structure resolutions substantially higher than those normally afforded by the bandwidth of the incoming x-ray beam. We further show how this technique allows us to discriminate between the valence structures of Fe and Fe2O3, and provides access to temperature measurements as well as M-shell binding energies estimates in warm-dense Fe compounds.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Digital Twin for Chemical Science: a case study on water interactions on the Ag(111) surface

Directly visualizing chemical trajectories offers insights into catalysis, gas-phase reactions and photoinduced dynamics. Tracking the transformation of chemical species is best achieved by coupling theory and experiment. Here we developed Digital Twin for Chemical Science (DTCS) v.01, which integrates theory, experiment and their bidirectional feedback loops into a unified platform for chemical characterization. DTCS addresses a core question: given a set of experimental conditions, what is the expected outcome and why? It consists of a forward solver that takes a chemical reaction network and predicts spectra under experimental conditions, and an inverse solver that infers kinetics from measured spectra. We applied DTCS to ambient-pressure X-ray photoelectron spectroscopy measurements of the Ag–H2O interface as an example. This approach enables real-time knowledge extraction and guides experiments until a stopping condition is met based on accuracy and degeneracy. As a step toward autonomous chemical characterization, DTCS provides mechanistic knowledge in a verified, standardized manner.

Chemistry↗
DOE OSTI2024

Ni-catalysed dicarbofunctionalization for the synthesis of sequence-encoded cyclooctene monomers

The properties of polymeric materials can be modulated by factors such as sequence control or functional group modifications. However, the synthesis of new macromolecular scaffolds is limited by the accessibility of structurally diverse monomers. This work describes a one-step, nickel-catalysed synthesis of 5,6-diaryl cyclooctene monomers from the feedstock chemical 1,5-cyclooctadiene. The reaction proceeds in a modular, regio- and diastereoselective fashion, granting access to both homo- and hetero-diaryl cyclooctene monomers that smoothly undergo ring-opening metathesis polymerization (ROMP). The resulting 1,2-diaryl-substituted polymers possess sequences with head-to-head styrene dyads that have not been previously explored, giving rise to unique and tunable properties. Density functional theory calculations highlight mechanistic aspects of the nickel-catalysed diarylation reaction and the ruthenium-catalysed ROMP process, revealing a previously unappreciated role of the boronic ester in promoting migratory insertion, which was leveraged to provide enantioinduction.

Catalytic mechanisms↗
DOE OSTI2012

In Situ Ambient Pressure X-ray Photoelectron Spectroscopy Studies of Lithium-Oxygen Redox Reactions

The lack of fundamental understanding of the oxygen reduction and oxygen evolution in nonaqueous electrolytes significantly hinders the development of rechargeable lithium-air batteries. Here we employ a solid-state Li4+xTi5O12/LiPON/LixV2O5 cell and examine in situ the chemistry of Li-O2 reaction products on LixV2O5 as a function of applied voltage under ultra high vacuum (UHV) and near ambient-pressure of oxygen using X-ray photoelectron spectroscopy (APXPS). Oxygen reduction and evolution reactions take place on the surface of the mixed electronic and Li+ ionic conductor, LixV2O5, which eliminate parasitic reactions between oxygen reduction/evolution reaction intermediates and aprotic electrolytes used in Li-O2 batteries reported to date. Under UHV, reversible lithium intercalation and de-intercalation from LixV2O5 was noted, where the changes in the vanadium valence state revealed from XPS in this study were comparable to that reported previously from Li/LixV2O5 thin film batteries. In presence of oxygen near ambient pressure, the LixV2O5 surface was covered gradually by the reaction product of oxygen reduction, namely lithium peroxide (Li2O2) (approximately 1-2 unit cells) upon discharge. Interestingly, the LixV2O5 surface became re-exposed upon charging, and the oxidation of Li2O2 began at much lower overpotentials (~240 mV) than the charge overpotentials of Li-O2 cells (~1000 mV) with aprotic electrolytes, which can be attributed to subnanometer-thick Li2O2 with surfaces free of contaminants such as carbonate species. Our study provides first evidence of reversible lithium peroxide formation and decomposition in situ on an oxide surface using a solid-state cell, and new insights into the reaction mechanism of Li-O2 chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Using “Tender” x-ray ambient pressure x-Ray photoelectron spectroscopy as a direct probe of solid-liquid interface

We report a new method to probe the solid-liquid interface through the use of a thin liquid layer on a solid surface. An ambient pressure XPS (AP-XPS) endstation that is capable of detecting high kinetic energy photoelectrons (7 keV) at a pressure up to 110 Torr has been constructed and commissioned. Additionally, we have deployed a “dip & pull” method to create a stable nanometers-thick aqueous electrolyte on platinum working electrode surface. Combining the newly constructed AP-XPS system, “dip & pull” approach, with a “tender” X-ray synchrotron source (2 keV–7 keV), we are able to access the interface between liquid and solid dense phases with photoelectrons and directly probe important phenomena occurring at the narrow solid-liquid interface region in an electrochemical system. Using this approach, we have performed electrochemical oxidation of the Pt electrode at an oxygen evolution reaction (OER) potential. Under this potential, we observe the formation of both Pt²⁺ and Pt⁴⁺ interfacial species on the Pt working electrode in situ . We believe this thin-film approach and the use of “tender” AP-XPS highlighted in this study is an innovative new approach to probe this key solid-liquid interface region of electrochemistry.

25 ENERGY STORAGE↗
DOE OSTI2015

Independently tunable dual-band perfect absorber based on graphene at mid-infrared frequencies

We design a dual-band absorber formed by combining two cross-shaped metallic resonators of different sizes within a super-unit-cell arranged in mirror symmetry. Simulations indicate that absorption efficiencies greater than 99% can be achieved at two different frequencies under normal incidence. We also employ a design scheme with graphene integration, which allows independent tuning of individual absorption frequencies by electrostatically changing the Fermi energy of the graphene layer. High absorbance is maintained over a wide incident angle range up to 50 degrees for both TE and TM polarizations. Thus, it enables a promising way to design electrically tunable absorbers, which may contribute toward the realization of frequency selective detectors for sensing applications.

36 MATERIALS SCIENCE↗
DOE OSTI2014

The Local Atomic Structure and Chemical Bonding in Sodium Tin Phases

To understand these electrochemically-derived materials we have reinvestigated the formation of Na-Sn alloys to identify all the phases which form when x ≥ 1 (NaxSn) and characterized the local bonding around the Sn atoms with X-ray diffraction, 119 Sn M ssbauer spectroscopy, and X-ray absorption spectroscopies. The results from the well-defined crystallographic materials were compared to the spectroscopic measurements of the local Sn structures in the electrochemically prepared materials. The reinvestigation of the Na-Sn compounds yields a number of new results: (i) Na 7 Sn 3 is a new thermodynamically-stable phase with a rhombohedral structure and R-3m space group; (ii) orthorhombic Na 9 Sn 4 (Cmcm) has relatively slow formation kinetics suggesting why it does not form at room temperature during the electrochemical reaction; (iii) orthorhombic Na 14.78 Sn 4 (Pnma), better described as Na 16-x Sn 4 , is Na-richer than cubic Na 15 Sn 4 (I-43d). Characterization of electrochemically prepared Na-Sn alloys indicate that, at the exception of Na 7 Sn 3 and Na 15 Sn 4 , different crystal structures than similar Na-Sn compositions prepared via classic solid state reactions are formed. These phases are composed of disordered structures characteristic of kinetic-driven solid-state amorphization reactions. In these structures, Sn coordinates in asymmetric environments, which differ significantly from the environments present in Na-Sn model compounds.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Electrochemical impedance analysis of perovskite–electrolyte interfaces

Here, the flat band potentials and carrier densities of spin coated and sprayed MAPbI 3 , FA 0.85 Cs 0.15 PbI 3 , and MAPbBr 3 perovskite films were determined using the Mott-Schottky relation. The films developed a space charge layer and exhibited p-type conduction with carrier concentration ~ 10 16 cm -3 for spin coated films. Electrochemical impedance spectra showed typical space charge impedance at frequencies > 1 kHz with increasing capacitance < 1 kHz owing to an ion diffusion component.

14 SOLAR ENERGY↗
DOE OSTI2016

Ambient pressure XPS and IRRAS investigation of ethanol steam reforming on Ni–CeO 2 (111) catalysts: An in situ study of C–C and O–H bond scission

Ambient-Pressure X-ray Photoelectron Spectroscopy (AP-XPS) and Infrared Reflection Absorption Spectroscopy (AP-IRRAS) have been used to elucidate the active sites and mechanistic steps associated with the ethanol steam reforming reaction (ESR) over Ni–CeO 2 (111) model catalysts. Our results reveal that surface layers of the ceria substrate are both highly reduced and hydroxylated under reaction conditions while the small supported Ni nanoparticles are present as Ni 0 /NixC. A multifunctional, synergistic role is highlighted in which Ni, CeO x and the interface provide an ensemble effect in the active chemistry that leads to H 2 . Ni 0 is the active phase leading to both C–C and C–H bond cleavage in ethanol and it is also responsible for carbon accumulation. On the other hand, CeO x is important for the deprotonation of ethanol/water to ethoxy and OH intermediates. The active state of CeO x is a Ce 3+ (OH) x compound that results from extensive reduction by ethanol and the efficient dissociation of water. Additionally, we gain an important insight into the stability and selectivity of the catalyst by its effective water dissociation, where the accumulation of surface carbon can be mitigated by the increased presence of surface OH groups. As a result, the co-existence and cooperative interplay of Ni 0 and Ce 3+ (OH) x through a metal–support interaction facilitate oxygen transfer, activation of ethanol/water as well as the removal of coke.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗