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DOE OSTI2022

PDBspheres: a method for finding 3D similarities in local regions in proteins

Abstract We present a structure-based method for finding and evaluating structural similarities in protein regions relevant to ligand binding. PDBspheres comprises an exhaustive library of protein structure regions (‘spheres’) adjacent to complexed ligands derived from the Protein Data Bank (PDB), along with methods to find and evaluate structural matches between a protein of interest and spheres in the library. PDBspheres uses the LGA (Local–Global Alignment) structure alignment algorithm as the main engine for detecting structural similarities between the protein of interest and template spheres from the library, which currently contains >2 million spheres. To assess confidence in structural matches, an all-atom-based similarity metric takes side chain placement into account. Here, we describe the PDBspheres method, demonstrate its ability to detect and characterize binding sites in protein structures, show how PDBspheres—a strictly structure-based method—performs on a curated dataset of 2528 ligand-bound and ligand-free crystal structures, and use PDBspheres to cluster pockets and assess structural similarities among protein binding sites of 4876 structures in the ‘refined set’ of the PDBbind 2019 dataset.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Bulk and Short-Circuit Anion Diffusion in Epitaxial Fe 2 O 3 Films Quantified Using Buried Isotopic Tracer Layers

Self-diffusion is a fundamental physical process that, in solid materials, is intimately correlated with both microstructure and functional properties. In this work, a universal approach is presented to precisely characterize self-diffusion in ionic solids by isotopically enriching anions and/or cations at specific locations within an epitaxial film stack, and characterize their redistribution at high spatial resolution with atom probe tomography. Nanoscale anion diffusivity is quantified in epitaxial α-Fe 2 O 3 thin films deposited by molecular beam epitaxy with a thin (10 nm) buried layer highly enriched in 18 O. The isotopic sensitivity of the atom probe allows precise measurement of 18 O distribution across the sharp interfaces between this layer and the surrounding Fe 2 O 3 after annealing. Short-circuit anion diffusion through 1D and 2D structural defects in Fe 2 O 3 are also directly visualized in 3D. This versatile approach to study precisely tailored thin film samples at high spatial and mass fidelity will facilitate a deeper understanding of atomic-scale diffusion phenomena.

36 MATERIALS SCIENCE↗

DOE OSTI2022

High‐Resolution Electron Tomography of Ultrathin Boerdijk–Coxeter–Bernal Nanowire Enabled by Superthin Metal Surface Coating

Abstract The rapid advancement of transmission electron microscopy has resulted in revolutions in a variety of fields, including physics, chemistry, and materials science. With single‐atom resolution, 3D information of each atom in nanoparticles is revealed, while 4D electron tomography is shown to capture the atomic structural kinetics in metal nanoparticles after phase transformation. Quantitative measurements of physical and chemical properties such as chemical coordination, defects, dislocation, and local strain have been made. However, due to the incompatibility of high dose rate with other ultrathin morphologies, such as nanowires, atomic electron tomography has been primarily limited to quasi‐spherical nanoparticles. Herein, the 3D atomic structure of a complex core–shell nanowire composed of an ultrathin Boerdijk–Coxeter–Bernal (BCB) core nanowire and a noble metal thin layer shell deposited on the BCB nanowire surface is discovered. Furthermore, it is demonstrated that a new superthin noble metal layer deposition on an ultrathin BCB nanowire could mitigate electron beam damage using an in situ transmission electron microscope and atomic resolution electron tomography. The colloidal coating method developed for electron tomography can be broadly applied to protect the ultrathin nanomaterials from electron beam damage, benefiting both the advanced material characterizations and enabling fundamental in situ mechanistic studies.

Song, Xiaohui↗

DOE OSTI2022

Chromium-coated cladding analysis under simulated LOCA burst conditions

Of the near-term accident-tolerant fuel concepts identified, chromium coatings have been shown to slow cladding oxidation without altering fuel system geometry or greatly affecting neutronic performance. To identify how coated cladding tubes perform under high-temperature accident conditions, pressurized-tube burst tests were conducted in the Severe Accident Test Station at Oak Ridge National Laboratory. To analyze how the coating affects cladding behavior, coated and uncoated cladding burst tests were simulated by using the BISON fuel performance code. Thermocouple data from these tests were fit into axial and azimuthal profiles and combined to generate 3D cladding surface temperatures, and pressure transducer data were compared until cladding failure. Additionally, the cladding temperatures at failure and the internal gas pressure evolution show relatively good agreement between the simulation and experiment results. Simulations were then extrapolated to demonstrate the coatings effectiveness to increasing the cladding burst temperature by using a parametric evaluation of the initial tube gas pressure. This work demonstrates the possibility of an increased cladding failure margin under transient conditions due to the addition of chromium coating, and more pertinently, an increased cladding failure margin from more accurate experimental characterization.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2025

Nanoscale Magnetic Ordering Dynamics in a High Curie Temperature Ferromagnet

Thermally driven transitions between ferromagnetic and paramagnetic phases are characterized by critical behavior with divergent susceptibilities, long-range correlations, and spin dynamics that can span kHz to GHz scales as the material approaches the critical temperature T c , but it has proven technically challenging to probe the relevant length and time scales with most conventional measurement techniques. In this study, we employ scanning nitrogen-vacancy center based magnetometry and relaxometry to reveal the critical behavior of a high-T c ferromagnetic oxide near its Curie temperature. Cluster analysis of the measured temperature-dependent nanoscale magnetic textures points to a 3D universality class with a correlation length that diverges near T c . Meanwhile, the temperature-dependent spin dynamics, measured through all optical relaxometry suggest that the phase transition is in the XY universality class. In conclusion, our results capture both static and dynamic aspects of critical behavior, providing insights into universal properties that govern phase transitions in magnetic materials.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Characterization of Uranium Foil Irradiations at the WSU TRIGA Reactor Using a New Reactor Model in Scale

A new reactor model of the Washington State University TRIGA was developed in the SCALE neutron transport code, and its fidelity was verified by comparison to MCNP and available data for several reactor parameters. The model was used to characterize irradiations designed to produce the short-lived actinides 237 U and 239 U, two key isotopes for nuclear forensics. These short-lived actinides, their decay daughters 237Np and 239Pu, and total fissions (via 99 Mo) were measured in irradiated foils at Los Alamos National Laboratory and other labs with good agreement among parent/daughter pairs and among labs. The laboratory-measured isotope ratios were used as a benchmark for the model determination of reaction rates. The flux distribution in the foils was also determined. Finally, using the continuous energy TSUNAMI-3D module of SCALE, a sensitivity/uncertainty analysis was performed to determine the effects on foil reactions caused by other system-wide reactions and by uncertainties in the known cross-sections.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2026

Additive Manufacturing Evaporative Casting

Traditional lost foam casting has been around for decades. The process uses foam forms blown by an injection molding like process or CNC milled into the desired shape, then pouring molten metal over the foam pattern to create a metallic object. Additive Manufacturing Evaporative Casting (AMEC) is a new process that eliminates foam forms by using additive manufacturing to 3D print the desired cast geometry. This not only saves time and money but allows for more advanced and complex designs that can’t be achieved by carving foam. Additionally, AMEC doesn’t require molds and tooling like other casting and foundry options. Because the AMEC process is new, extensive testing is needed to develop a better understanding of the process to minimize defects, quantify material properties, and start computer modeling for the process. This CRADA (collaborative research and development agreement) between ORNL and Skuld seeks to improve the process, develop a computational model, characterize material properties, and explore new applications.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Uncovering the three-dimensional structure of upconverting core–shell nanoparticles with multislice electron ptychography

In photon upconverting core–shell nanoparticles, structure strongly dictates performance. Typical imaging in scanning transmission electron microscopy has sufficient resolution to probe the atomic structure of these nanoparticles, but contrast, dose, and projection limitations make conventional methods insufficient for fully characterizing these structures. Phase retrieval techniques provide a promising alternative imaging mode, and, in particular, multislice electron ptychography can recover depth-dependent information. Here, we study beam-sensitive photon upconverting core–shell nanoparticles with a multislice ptychography approach using a low electron dose to avoid damage. Large strain fields arise in these heterostructures due to the mismatch in lattice parameter between the core and the shell. We reconstruct both a nanoparticle that appears defect-free and one that has a large break in the side and map the distribution of strain in 3D by computing distortion fields from high-resolution potential images of each slice. In the defect-free nanoparticle, we observe twisting of the shell, while in the broken nanoparticle, we measure the 3D position of the crack, the core, and dislocations. These results highlight the advantage of multislice electron ptychography to recover 3D information from a single scan, even under strict electron dose requirements from beam-sensitive samples.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Deep Learning Based Workflow for Accelerated Industrial X-Ray Computed Tomography

X-ray computed tomography (XCT) is an important tool for high-resolution non-destructive characterization of additively-manufactured metal components. XCT reconstructions of metal components may have beam hardening artifacts such as cupping and streaking which makes reliable detection of flaws and defects challenging. Furthermore, traditional workflows based on using analytic reconstruction algorithms require a large number of projections for accurate characterization - leading to longer measurement times and hindering the adoption of XCT for in-line inspections. In this paper, we introduce a new workflow based on the use of two neural networks to obtain high-quality accelerated reconstructions from sparse-view XCT scans of single material metal parts. The first network, implemented using fully-connected layers, helps reduce the impact of BH in the projection data without the need of any calibration or knowledge of the component material. The second network, a convolutional neural network, maps a low-quality analytic 3D reconstruction to a high-quality reconstruction. Using experimental data, we demonstrate that our method robustly generalizes across several alloys, and for a range of sparsity levels without any need for retraining the networks thereby enabling accurate and fast industrial XCT inspections.

Rahman, Obaid↗

DOE OSTI2023

Isolation of phosphorus-hyperaccumulating microalgae from revolving algal biofilm (RAB) wastewater treatment systems

Excess phosphorus (P) in wastewater effluent poses a serious threat to aquatic ecosystems and can spur harmful algal blooms. Revolving algal biofilm (RAB) systems are an emerging technology to recover P from wastewater before discharge into aquatic ecosystems. In RAB systems, a community of microalgae take up and store wastewater P as polyphosphate as they grow in a partially submerged revolving biofilm, which may then be harvested and dried for use as fertilizer in lieu of mined phosphate rock. In this work, we isolated and characterized a total of 101 microalgae strains from active RAB systems across the US Midwest, including 82 green algae, 9 diatoms, and 10 cyanobacteria. Strains were identified by microscopy and 16S/18S ribosomal DNA sequencing, cryopreserved, and screened for elevated P content (as polyphosphate). Seven isolated strains possessed at least 50% more polyphosphate by cell dry weight than a microalgae consortium from a RAB system, with the top strain accumulating nearly threefold more polyphosphate. These top P-hyperaccumulating strains include the green alga Chlamydomonas pulvinata TCF-48 g and the diatoms Eolimna minima TCF-3d and Craticula molestiformis TCF-8d, possessing 11.4, 12.7, and 14.0% polyphosphate by cell dry weight, respectively. As a preliminary test of strain application for recovering P, Chlamydomonas pulvinata TCF-48 g was reinoculated into a bench-scale RAB system containing Bold basal medium. The strain successfully recolonized the system and recovered twofold more P from the medium than a microalgae consortium from a RAB system treating municipal wastewater. These isolated P-hyperaccumulating microalgae may have broad applications in resource recovery from various waste streams, including improving P removal from wastewater.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1992

Low energy CMOS for space applications

The current focus of NASA's space flight programs reflects a new thrust towards smaller, less costly, and more frequent space missions, when compared to missions such as Galileo, Magellan, or Cassini. Recently, the concept of a microspacecraft was proposed. In this concept, a small, compact spacecraft that weighs tens of kilograms performs focused scientific objectives such as imaging. Similarly, a Mars Lander micro-rover project is under study that will allow miniature robots weighing less than seven kilograms to explore the Martian surface. To bring the microspacecraft and microrover ideas to fruition, one will have to leverage compact 3D multi-chip module-based multiprocessors (MCM) technologies. Low energy CMOS will become increasingly important because of the thermodynamic considerations in cooling compact 3D MCM implementations and also from considerations of the power budget for space applications. In this paper, we show how the operating voltage is related to the threshold voltage of the CMOS transistors for accomplishing a task in VLSI with minimal energy. We also derive expressions for the noise margins at the optimal operating point. We then look at a low voltage CMOS (LVCMOS) technology developed at Stanford University which improves the power consumption over conventional CMOS by a couple of orders of magnitude and consider the suitability of the technology for space applications by characterizing its SEU immunity.

Panwar, Ramesh↗

DOE OSTI2024

Comprehensive characterization of the structure of Zr-based metallic glasses

Structure of metallic glasses fascinates as the generic amorphous structural template for ubiquitous systems. Its specification necessitates determination of the complete hierarchical structure, starting from short-range-order (SRO) → medium-range-order (MRO) → bulk structure and free volume (FV) distribution. This link has largely remained elusive since previous investigations adopted one-technique-at-a-time approach, focusing on limited aspects of any one domain. Reconstruction of structure from experimental data inversion is non-unique for many of these techniques. As a result, complete and precise structural understanding of glass has not emerged yet. In this work, we demonstrate the first experimental pathway for reconstruction of the integrated structure, for and glasses. Our strategy engages diverse (×7) multi-scale techniques [XAFS, 3D-APT, ABED/NBED, FEM, XRD, PAS, FHREM] on the same glass. This strategy complemented mutual limitations of techniques and corroborated common parameters to generate complete, self-consistent and precise parameters. Further, MRO domain size and inter-void separation were correlated to identify the presence of FV at MRO boundaries. This enabled the first experimental reconstruction of hierarchical subset: SRO → MRO → FV → bulk structure. The first ever image of intermediate region between MRO domains emerged from this link. We clarify that determination of all subsets is not our objective; the essence and novelty of this work lies in directing the pathway towards finite solution, in the most logical and unambiguous way.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Hydrous Transition Metal Oxides for Electrochemical Energy and Environmental Applications

Hydrous transition metal oxides (TMOs) are redox-active materials that confine structural water within their bulk, organized in 1D, 2D, or 3D networks. In an electrochemical cell, hydrous TMOs can interact with electrolyte species not only via their outer surface but also via their hydrous inner surface, which can transport electrolyte species to the interior of the material. Many TMOs operating in an aqueous electrochemical environment transform to hydrous TMOs, which then serve as the electrochemically active phase. This review summarizes the physicochemical properties of hydrous TMOs and recent mechanistic insights into their behavior in electrochemical reactions of interest for energy storage, conversion, and environmental applications. Particular focus is placed on first-principles calculations and operando characterization to obtain an atomistic view of their electrochemical mechanisms. Hydrous TMOs represent an important class of energy and environmental materials in aqueous and nonaqueous environments. Further understanding of their interaction with electrolyte species is likely to yield advancements in electrochemical reactivity and kinetics for energy and environmental applications.

36 MATERIALS SCIENCE↗

NASA NTRS2014

Microorganisms in the Stratosphere (MIST): In-flight Sterilization with UVC Leds

The stratosphere (10 km to 50 km above sea level) is a unique place on Earth for astrobiological studies of microbes in extreme environments due to the combination of harsh conditions (high ultraviolet radiation, low pressure, desiccation, and low temperatures). Microorganisms in the Stratosphere (MIST) will attempt to characterize the diversity of microbes at these altitudes using a balloon collection device on a meteorological weather balloon. A major challenge of such an aerobiology study is the potential for ground contamination that makes it difficult to distinguish between collected microbes and contaminants. One solution is to use germicidal ultraviolet light emitting diodes (UV LEDs) to sterilize the collection strip. To use this solution, an optimal spatial arrangement of the lights had to be determined to ensure the greatest chance of complete sterilization within the 30 to 60 minute time of balloon ascent. A novel, 3D-printed test stand was developed to experimentally determine viable Bacillus pumilus SAFR-032 spore reduction after exposure to ultraviolet radiation at various times, angles, and distances. Taken together, the experimental simulations suggested that the UV LEDs on the MIST flight hardware should be active for at least 15 minutes and mounted within 4 cm of the illuminated surface at any angle to achieve optimal sterilization. These findings will aid in the production of the balloon collection device to ensure pristine stratospheric microbial samples are collected. Flight hardware capable of in-flight self-sterilization will enable future life detection missions to minimize both forward contamination and false positives.

Exobiology↗

NASA NTRS2025

Magnetic Resonance Imaging (MRI) to Assess Changes to Trabecular Microarchitecture (Trb µArch) of the Hip

BACKGROUND . Calculated loss rates in trabecular (Trb) volumetric bone mineral density (vBMD), in astronauts after return from 6-month long-duration (LD) spaceflight, are rapid relative to menopause-induced loss rates and could contribute to the observed lack of recovery. Perforations in the Trb bony struts, skeletal fragility and fractures [5] have been associated with the rapid rate of bone loss in women due to menopause. The more rapid loss rate observed in astronauts could be inducing similar, irreversible losses of trabecular connectivity as seen in cadaver studies of female skeletons. These changes are not detectable by DXA technology and would not be discovered in astronauts during scheduled, triennial DXA testing for primary osteoporosis. High-resolution-peripheral quantitative computed tomography (HR-pQCT) of the lower leg have detected losses in Trb vBMD (vBMD) and changes in Trb microarchitecture (µArch) in astronauts immediately following routine 6-month spaceflights and continuing in some individuals for 1 or more years postflight with no signs of recovery. Resolution of these microarchitectural changes by whole body QCT, especially in the deeply embedded hip bone, is prohibitive due to excessive and unsafe radiation exposures. While HR-pQCT has sufficient resolution to study Trb µArch at safe and lower radiation exposure testing is restricted only to the lower leg and wrist. Hence, a technology to detect detrimental changes to Trb µArch in astronauts, especially of the hip, is needed to inform type and timing of countermeasures to irreversible deficits (preflight, inflight and postflight). METHODS . This HRP-funded study (2023-2027) will verify the sensitivity of a protocol for MRI scanning (on a 3T Siemens Vida) to detect changes to hip Trb µArch in persons following spinal cord injury (SCI); skeletal immobilization below the spinal lesion will serve as an analog for non-weight-bearing during spaceflight. The study period has been extended by 1 yr due to delayed Richmond IRB approval in Y1. A 3T MRI protocol will characterize serial changes in hip Trb µArch in SCI patients from time of admission at the Richmond VA Medical Center to their scheduled annual exam 12-months later. SCI patients with age, sex, and physical characteristics like ISS astronauts will be consented. The ability of 3T MRI hip scan to discriminate loss of trabecular connectivity subjects with SCI will be compared to age- and sex-matched ambulatory controls. A comparison between HR-pQCT and MRI measurements at the ankle (distal tibia) of study subjects will also be performed. A modified DXA scan analysis (3D-Shaper) will also be verified as a potential method for monitoring concurrent changes in hip Trb bone over 12-month. SIGNIFICANCE . Deliverables: a surveillance method for assessing for irreversible losses of connectivity and how skeletal changes after LD spaceflight(s) would modify the terrestrial risk of primary osteoporosis.

Spinal Cord Injury↗

NASA NTRS2025

Magnetic Resonance Imaging (MRI) to Assess Changes to Trabecular Microarchitecture (Trb µArch) of the Hip

Risk Surveillance↗

DOE OSTI2024

Understanding Formation of Irradiation-Induced Defects through 4D-STEM, Electron Tomography, and WBDF-STEM

A major challenge in advancing nuclear materials for next-generation fission and proposed fusion reactors is to comprehensively understand the formation of irradiation-induced defects. Here it is essential to correlate the evolution of irradiation-induced defects and the degradation of mechanical properties, as they collectively dictate the material's lifespan and ensure nuclear safety. Scanning transmission electron microscopy (STEM) based techniques have emerged as indispensable tools for irradiation-induced defect characterization, offering high spatial resolution imaging and chemical analysis, such as electron energy loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDXS). These techniques have been effectively used to obtain an atomic-scale view of the defect structure. Recent advances in electron microscopy, particularly in 4D-STEM, offer detailed insight into microstructural evolution by capturing full 2D diffraction patterns at every pixel position. Using high-speed direct electron detectors, this technology generates a four-dimensional dataset, overcoming the limitations of traditional STEM imaging.

36 MATERIALS SCIENCE↗

NASA NTRS2016

Summary Report for the Technical Interchange Meeting on Development of Baseline Material Properties and Design Guidelines for In-Space Manufacturing Activities

NASA Marshall Space Flight Center (MSFC) and the Agency as a whole are currently engaged in a number of in-space manufacturing (ISM) activities that have the potential to reduce launch costs, enhance crew safety, and provide the capabilities needed to undertake long-duration spaceflight. The recent 3D Printing in Zero-G experiment conducted on board the International Space Station (ISS) demonstrated that parts of acrylonitrile butadiene styrene (ABS) plastic can be manufactured in microgravity using fused deposition modeling (FDM). This project represents the beginning of the development of a capability that is critical to future NASA missions. Current and future ISM activities will require the development of baseline material properties to facilitate design, analysis, and certification of materials manufactured using in-space techniques. The purpose of this technical interchange meeting (TIM) was to bring together MSFC practitioners and experts in materials characterization and development of baseline material properties for emerging technologies to advise the ISM team as we progress toward the development of material design values, standards, and acceptance criteria for materials manufactured in space. The overall objective of the TIM was to leverage MSFC's shared experiences and collective knowledge in advanced manufacturing and materials development to construct a path forward for the establishment of baseline material properties, standards development, and certification activities related to ISM. Participants were asked to help identify research and development activities that will (1) accelerate acceptance and adoption of ISM techniques among the aerospace design community; (2) benefit future NASA programs, commercial technology developments, and national needs; and (3) provide opportunities and avenues for further collaboration.

Prater, T. J.↗