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NASA NTRS1992

Extracellular vesicles of calcifying turkey leg tendon characterized by immunocytochemistry and high voltage electron microscopic tomography and 3-D graphic image reconstruction

To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.

NASA Discipline Musculoskeletal↗

DOE OSTI2023

Recent Developments in Revealing the Impact of Complex Metal Oxide Reconstruction on Catalysis

Surface reconstruction of complex metal oxides refers to the alterations of the topmost catalyst surface, relative to the bulk structure, following exposure to pretreatment or reaction conditions during heterogeneous catalysis. (1) This structural and electronic transformation may involve (1) changes of the exposed crystallographic facets, (2) changes in chemical composition, such as the enrichment of specific elements, and, (3) morphological variations, including surface roughness and defects (Scheme 1). Beyond relaxation, surface reconstruction here also encompasses disruptions to the periodicity of the sublayers and changes to its stoichiometry. This change significantly influences the chemical properties of the catalyst surface, such as redox sites, (2) acid/base pairs, hydroxyl groups, (3) and surface defects. Surface reconstruction occurs due to the thermodynamic drive to lower the surface energy of the catalyst under the surrounding environment (e.g., temperature, chemical potential of species present). In addition to the treatment or reaction conditions, the extent of reconstruction also depends on the elements in the metal oxide structure. For instance, annealing ABO 3 perovskites (SrTiO 3 , BaTiO 3 , and BaZrO 3 ) at high temperatures (500 °C) in O 2 has a very different impact on the A/B ratio at the surface (ranging from 0.9 to 2.5), depending on the identity of A and B. (4) Metal oxide surface reconstruction under an electric field and exposure to acidic and alkaline media has recently gained increased attention in electrocatalysis, such as in the oxygen evolution reaction (OER); (5,6) however, in this Viewpoint we focus on the impact of surface reconstruction on thermal catalysis, a critical enduring research theme with ongoing challenges. Here, we start showcasing approaches to characterize surface reconstruction at the topmost surface layer, such as low-energy ion scattering (LEIS), discussing advantages and limitations. Next, we connect characterization of surface reconstruction to site-specific kinetic analysis, enabled via steady-state isotopic transient kinetic analysis (SSITKA), and we express our viewpoint on building structure–performance relationships by deeply understanding reconstructed surfaces. Later, we comment on the potential of tuning surface reconstruction to enhance catalytic performance. Finally, we explore the interplay between surface reconstruction and the “intelligent behavior”.

alcohol conversion↗

DOE OSTI2021

Visualizing defects and pore connectivity within metal–organic frameworks by X-ray transmission tomography

Metal–Organic Frameworks (MOFs) have the potential to change the landscape of molecular separations in chemical processes owing to their ability of selectively binding molecules. Their molecular sorting properties generally rely on the micro- and meso-pore structure, as well as on the presence of coordinatively unsaturated sites that interact with the different chemical species present in the feed. In this work, we show a first-of-its-kind tomographic imaging of the crystal morphology of a metal– organic framework by means of transmission X-ray microscopy (TXM), including a detailed data reconstruction and processing approach. Corroboration with Focused Ion Beam-Scanning Electron Microscopy (FIB-SEM) images shows the potential of this strategy for further (non-destructively) assessing the inner architecture of MOF crystals. By doing this, we have unraveled the presence of large voids in the internal structure of a MIL-47(V) crystal, which are typically thought of as rather homogeneous lattices. This challenges the established opinion that hydrothermal syntheses yield relatively defect-free material and sheds further light on the internal morphology of crystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

In Situ Reconstructed Mo–doped Amorphous FeOOH Boosts the Oxygen Evolution Reaction

Developing a fast and highly active oxygen evolution reaction (OER) catalyst to change energy kinetics technology is essential for making clean energy. Herein, we prepare three-dimensional (3D) hollow Mo-doped amorphous FeOOH (Mo-FeOOH) based on the precatalyst MoS 2 /FeC 2 O 4 via in situ reconstruction strategy. Mo-FeOOH exhibits promising OER performance. Specifically, it has an overpotential of 285 mV and a durability of 15 h at 10 mA cm –2 . Characterizations indicate that Mo was included inside the FeOOH lattice, and it not only modifies the electronic energy levels of FeOOH but also effectively raises the inherent activity of FeOOH for OER. Additionally, in situ Raman analysis indicates that FeC 2 O 4 gradually transforms into the FeOOH active site throughout the OER process. Finally, this study provides ideas for designing in situ reconstruction strategies to prepare heteroatom doping catalysts for high electrochemical activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Revealing the interplay between “intelligent behavior” and surface reconstruction of non-precious metal doped SrTiO 3 catalysts during methane combustion

The impact of surface reconstruction of a model perovskite, SrTiO 3 (STO), on CH 4 activation for combustion and oxidative coupling was previously revealed that the reaction rate was proportional to the creation of Srterminated step sites. Doped perovskites (SrTi 1-x M x O 3 , M=metal dopant) present yet another form of reconstruction throughout the surface and the bulk, where the metal dopant can migrate in and out of the perovskite lattice, also known as "intelligent behavior". In this work, understanding the interplay between perovskite surface reconstruction (surface termination) and the "intelligent behavior" is tackled for the first time, and the catalytic consequences are probed with CH 4 combustion as a model reaction. A set of experimental techniques, including XRD, Raman spectroscopy, X-ray adsorption spectroscopy, kinetic measurements, as well as DFT calculations were used to understand the catalytic behavior of the reconstructed surfaces of Ni and Cu-doped STO for methane combustion. Here, we found that during methane oxidation, the diffusion of Ni and Cu into the lattice due to the "intelligent behavior" is accompanied by Sr enrichment on the surface of the perovskite. This Srenrichment process is reversible when Cu or Ni species exsolute as clusters/nanoparticles upon H 2 treatment. Such a surface reconstruction is found to greatly impact the catalytic activity of doped perovskites towards methane combustion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Edge-Confined Excitons in Monolayer Black Phosphorus

Quantum confinement of two-dimensional excitons in van der Waals materials via electrostatic trapping, lithographic patterning, Moiré potentials, and chemical implantation has enabled significant advances in tailoring light emission from nanostructures. While such approaches rely on complex preparation of materials, natural edges are a ubiquitous feature in layered materials and provide a different approach for investigating quantum-confined excitons. Here, we observe that certain edge sites of monolayer black phosphorus (BP) strongly localize the intrinsic quasi-one-dimensional excitons, yielding sharp spectral lines in photoluminescence, with nearly an order of magnitude line width reduction. Through structural characterization of BP edges using transmission electron microscopy and first-principles GW plus Bethe–Salpeter equation (GW-BSE) calculations of exemplary BP nanoribbons, we find that certain atomic reconstructions can strongly quantum-confine excitons resulting in distinct emission features, mediated by local strain and screening. Here we observe linearly polarized luminescence emission from edge reconstructions that preserve the mirror symmetry of the parent BP lattice, in agreement with calculations. Furthermore, we demonstrate efficient electrical switching of localized edge excitonic luminescence, whose sites act as excitonic transistors for emission. Localized emission from BP edges motivates exploration of nanoribbons and quantum dots as hosts for tunable narrowband light generation, with future potential to create atomic-like structures for quantum information processing applications as well as exploration of exotic phases that may reside in atomic edge structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

A Many-Body Perturbation Theory Approach to Energy Band Alignment at the Crystalline Tetracene–Silicon Interface

Hybrid inorganic–organic semiconductor (HIOS) interfaces are of interest for new photovoltaic devices operating above the Shockley–Queisser limit. Predicting energy band alignment at the interfaces is crucial for their design, but represents a challenging problem due to the large scales of the system, the energy precision required and a wide range of physical phenomena that occur at the interface. To tackle this problem, many-body perturbation theory in the non-self-consistent GW approximation, orbital relaxation corrections for organic semiconductors, and line-up potential method for inorganic semiconductors which allows for tractable and accurate computing of energy band alignment in crystalline van-der-Waals hybrid inorganic–organic semiconductor interfaces are used. In this work, crystalline tetracene physisorbed on the clean hydrogen-passivated 1 × 2 reconstructed (100) silicon surface is studied. Using this computational approach, it is found that the energy band alignment is determined by an interplay of the mutual dynamic dielectric screening of two materials and the formation of a dipole layer due to a weak hybridization of atomic/molecular orbitals at the interface. The significant role of the exchange-correlation effects in predicting band offsets for the hybrid inorganic–organic semiconductor interfaces is also emphasized.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2021

Pulse Radiolysis Investigation of Radicals Derived from Water-Soluble Cyanine Dyes: Implications for Super-resolution Microscopy

Light-induced blinking, an inherent feature of many forms of super-resolution microscopy, has been linked to transient reduction of the fluorescent cyanine dye used as an imaging agent. There is, however, only scant literature information related to one-electron reduced cyanine dyes, especially in an aqueous environment. Here, we examine a small series of cyanine dyes, possessing disparate π-conjugation lengths, under selective reducing or oxidizing conditions. The experiment allows recording of both differential absorption spectra and decay kinetics of the resultant one-electron reduced or oxidized transient species in water. Relative to the ground state, absorption transitions for the various radicals are weak and somewhat broadened but do allow correlation with the π-conjugation length. In all cases, absorption maxima lie to the blue of the main ground-state transition. Under anaerobic conditions, the transient species decay on the microsecond to millisecond time scale, with the mean lifetime depending on molecular structure, radiation dose, and dye concentration. The experimental absorption spectra recorded for the one-electron reduced radicals and the presumed dimer cation radical compare well to spectra obtained from time-dependent density functional theory calculations. Furthermore, the results allow conclusions to be drawn regarding the plausibility of the reduced species being responsible for light-induced blinking in direct stochastic optical reconstruction microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Design and calibration of an optically segmented single volume scatter camera for neutron imaging

The Optically Segmented Single Volume Scatter Camera (OS-SVSC) aims to image neutron sources for non-proliferation applications using the kinematic reconstruction of elastic double-scatter events. Our prototype system consists of 64 EJ-204 organic plastic scintillator bars, each measuring 5mm × 5mm × 200mm and individually wrapped in Teflon tape. The scintillator array is optically coupled to two silicon photomultiplier ArrayJ-60035 64P-PCB arrays, each comprised of 64 individual 6x6mm J-Series sensors arranged in an 8 × 8 array. We report on the design details, including component selections, mechanical design and assembly, and the electronics system. The described design leveraged existing off-the-shelf solutions to support the rapid development of a phase 1 prototype. Several valuable lessons were learned from component and system testing, including those related to the detector's mechanical structure and electrical crosstalk that we conclude originates in the commercial photodetector arrays and the associated custom breakout cards. We detail our calibration efforts, beginning with calibrations for the electronics, based on the IRS3D application-specific integrated circuits, and their associated timing resolutions, ranging from 3090ps. With electronics calibrations applied, energy and position calibrations were performed for a set of edge bars using 22 Na and 90 Sr, respectively, reporting an average resolution of 12.07±0.03mm for energy depositions between 900keVee and 1000keVee. We further demonstrate a position calibration method for the internal bars of the matrix using cosmic-ray muons as an alternative to emission sources that cannot easily access these bars, with an average measured resolution of 14.86+-0.29mm for depositions between 900keVee and 1000keVee. The coincident time resolution reported between pairs of bars measured up to 400ps from muon acquisitions. Energy and position calibration values measured with muons are consistent with those obtained using particle emission sources.

47 OTHER INSTRUMENTATION↗

DOE OSTI2023

Power Density Distributions in Electron Beams

Measuring and controlling the power density distribution of electron beams used for welding is critical for producing repeatable welds and for transferring welding parameters between different machines. On any given machine, the power density distribution is controlled by defocusing the beam relative to its sharpest focused condition. However, measuring the power density distribution can be difficult due to the intense nature of welding beams and is further complicated by imperfect electron optics that can distort the beam, making it difficult to quantify. The enhanced modified Faraday cup (EMFC) diagnostic method was used here for beam analysis that utilizes computed tomography to reconstruct the beam’s power density distribution. These results were compared to the International Standards Organization (ISO) method for characterizing laser beams using a second-moment D4σ calculation. For ideal Gaussian-shaped beams, both methods would give the same result. However, for imperfect beams, the calculated D4σ diameter was shown to be about 25% larger relative to the FWe2 diameter measured by the EMFC due to the heavier weighting of data in the tails of the beam by D4σ. Finally, although both methods produce repeatable welds, it is important to understand the differences in the reported beam diameters, divergence angles, and beam parameter products when transferring parameters between machines.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Reconstructing Oxygen-Deficient Zirconia with Ruthenium Catalyst on Atomic-Scale Interfaces toward Hydrogen Production

Downsizing a catalyst nanoparticle (NP) to a single atom (SA) has proven to be highly effective in increasing catalytic activity and decreasing the amount of catalyst required for various electrochemical reactions. However, insufficient stability of the single-atom site catalysts (SACs) is still a significant challenge for their practical application. Here, SACs firmly bound to stable metal oxide NPs are proposed to dramatically increase the electrochemical activity and stability of SA-based catalysts for hydrogen evolution reaction (HER). Starting from a Ru-infiltrated, Zr-based metal-organic framework (MOF), the tetragonal zirconium oxide (ZrO 2-x ) NPs-embedded carbon matrix is fabricated as support through facile pyrolysis. Simultaneously, Ru SAs as active sites are well dispersed on the surface of ZrO 2-x NPs due to the generation of oxygen vacancies in the tetragonal ZrO 2-x . Finally, the Ru-ZrO 2-x SAC exhibits a 4–5 times higher mass activity than commercial Pt and Ru catalysts and superior durability due to strong metal-support interaction (SMSI) between Ru atoms and ZrO 2-x substrate.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

maslov-group/FUN-PROSE

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Liu, Simon↗

DOE OSTI2023

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1988

Morphological evidence for parallel processing of information in rat macula

Study of montages, tracings and reconstructions prepared from a series of 570 consecutive ultrathin sections shows that rat maculas are morphologically organized for parallel processing of linear acceleratory information. Type II cells of one terminal field distribute information to neighboring terminals as well. The findings are examined in light of physiological data which indicate that macular receptor fields have a preferred directional vector, and are interpreted by analogy to a computer technology known as an information network.

Saccule and Utricle/ultrastructure↗

DOE OSTI2022

Grazing-Incidence Texture Tomography and Diffuse Reflectivity Tomography of an Organic Semiconductor Device Array

The use of grazing-incidence scattering methods for the characterization of 2D patterned organic thin films is limited due to the elongated 1D footprint of the X-ray beam on the sample. However, this characteristic feature can be turned into an advantage, when combined with tomographic reconstruction. In this pilot study we show, how the use of a chosen texture reflection and a diffuse reflectivity signal can each provide 2D images of the deposits, simultaneously revealing the organic film's crystal orientation and the location of the metal electrodes in a field-effect transistor structure from a single sequence of diffraction images.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Fossil Corals With Various Degrees of Preservation Can Retain Information About Biomineralization-Related Organic Material

Scleractinian corals typically form a robust calcium carbonate skeleton beneath their living tissue. This skeleton, through its trace element composition and isotope ratios, may record environmental conditions of water surrounding the coral animal. While bulk unrecrystallized aragonite coral skeletons can be used to reconstruct past ocean conditions, corals that have undergone significant diagenesis have altered geochemical signatures and are typically assumed to retain insufficient meaningful information for bulk or macrostructural analysis. However, partially recrystallized skeletons may retain organic molecular components of the skeletal organic matrix (SOM), which is secreted by the animal and directs aspects of the biomineralization process. Some SOM proteins can be retained in fossil corals and can potentially provide past oceanographic, ecological, and indirect genetic information. Here, we describe a dataset of scleractinian coral skeletons, aged from modern to Cretaceous plus a Carboniferous rugosan, characterized for their crystallography, trace element composition, and amino acid compositions. We show that some specimens that are partially recrystallized to calcite yield potentially useful biochemical information whereas complete recrystalization or silicification leads to significant alteration or loss of the SOM fraction. Our analysis is informative to biochemical-paleoceanographers as it suggests that previously discounted partially recrystallized coral skeletons may indeed still be useful at the microstructural level.

58 GEOSCIENCES↗

DOE OSTI2025

Neutrino interaction vertex reconstruction in DUNE with Pandora deep learning

The Pandora Software Development Kit and algorithm libraries perform reconstruction of neutrino interactions in liquid argon time projection chamber detectors. Pandora is the primary event reconstruction software used at the Deep Underground Neutrino Experiment, which will operate four large-scale liquid argon time projection chambers at the far detector site in South Dakota, producing high-resolution images of charged particles emerging from neutrino interactions. While these high-resolution images provide excellent opportunities for physics, the complex topologies require sophisticated pattern recognition capabilities to interpret signals from the detectors as physically meaningful objects that form the inputs to physics analyses. A critical component is the identification of the neutrino interaction vertex. Subsequent reconstruction algorithms use this location to identify the individual primary particles and ensure they each result in a separate reconstructed particle. A new vertex-finding procedure described in this article integrates a U-ResNet neural network performing hit-level classification into the multi-algorithm approach used by Pandora to identify the neutrino interaction vertex. The machine learning solution is seamlessly integrated into a chain of pattern-recognition algorithms. The technique substantially outperforms the previous BDT-based solution, with a more than 20% increase in the efficiency of sub-1 cm vertex reconstruction across all neutrino flavours.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Dose Coefficient Calculation for Use in Dosimetry Assessment of a Fission-Based Weapon

In the event of a fission-based weapon or improvised nuclear device (IND) detonation, dose coefficients can be harnessed to provide dose assessments for defense, emergency preparedness, and consequence management, as well as to prospectively inform the assessment of radiation biomarkers and development of medical prophylaxis countermeasures for defense and homeland security stakeholders and decision-makers. Although dose coefficients have previously been calculated for this group, they would apply specifically to the studied population, the 1945 Japanese cohort, after which their anthropomorphic computational phantoms were modeled. For this reason, applications to other populations may be limited, and instead, an assessment of a more standardized population is desired. We employed a series of computational human phantoms representing international reference individuals: UF/NCI voxel phantom series containing newborn, 1-, 5-, 10-, 15-, and 35-year-old males and females. Irradiation of the phantoms was simulated using the Monte Carlo N-Particle transport code to determine organ dose coefficients under four idealized irradiation geometries at three distances from the detonation hypocenter at Hiroshima and Nagasaki using DS02 free-in-air prompt neutron and photon fluence spectra. Through these simulations, age-specific dose coefficients were determined for individual organs. Various articulated PIMAL stylized phantoms were simulated as well to estimate the effect of body posture on dose coefficients and determine the effect of posture on dosimetric estimation and reconstruction. Results additionally demonstrate that 137 Cs and the Watt fission spectra are not ideal general surrogate sources for fission weapons, which may be considered for experimental testing of medical countermeasures. Supplementary data provided tabulates the compilation of organ dose-rate coefficients in this study.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗