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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4

Shock tube experiments on the three-layer Richtmyer–Meshkov instability

Here, a vertical shock tube is used for experiments on the three-layer Richtmyer–Meshkov instability. Two closely spaced membrane-less interfaces are formed by the flow of two different sects of three gases: one with air above CO 2 above SF 6 and the other with helium above air above SF 6 . The lightest of the three gases enters the shock tube at the top of the driven section and flows downward. Conversely, the heaviest gas enters at the bottom of the shock tube and flows upward while the intermediate density gas enters at the middle through porous plates. All three gases are allowed to escape through holes at the layer location, leaving an approximately 30-mm layer of intermediate-density gas suspended between the lightest gas from above and the heaviest gas from below. A single-mode, two-dimensional initial perturbation is then imposed on the lower interface by oscillating the shock tube in the horizontal direction. The flow is visualized by seeding the intermediate gas with particles and illuminating it with a pulsed laser. Image sequences are then captured using high-speed video cameras. Perturbation amplitude measurements are made from the three-layer system and compared with measurements from 2, two-layer systems. It is observed that the presence of the upper, initially flat interface produces a decrease in growth of instability amplitude in the nonlinear phase over an equivalent single-interface configuration.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NEAMS Workbench MOOSE Integration Update

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench is a graphical user interface (GUI) that provides a common analysis environment for the accelerated use of the NEAMS toolkit. To improve design and analysis of current and future nuclear energy systems, the NEAMS Workbench provides an integrated development environment for model creation, review, execution, output review, and visualization for integrated tools. In addition to a GUI, the NEAMS Workbench provides the Workbench Analysis Sequence Processor, an open-source tool set that facilitates input-content assistance for supported domain-specific input languages and user-friendly syntaxes. These supported syntaxes enable accelerated development and deployment of enhanced user inputs and workflows. The Multiphysics Object-Oriented Simulation Environment (MOOSE) has been supported in the NEAMS Workbench since 2016 and receives continuous updates. Efforts to improve MOOSE-based tool integration in the NEAMS Workbench are ongoing. This document details the current and planned enhancements of the NEAMS Workbench and the MOOSE framework to improve integration and usability of MOOSE-based applications within the NEAMS Workbench.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Multiscale dynamic experiments on fiber-reinforced composites with damage assessment using high-speed synchrotron X-ray phase-contrast imaging

We report fiber-reinforced composites (FRCs) have been widely used as protection materials to replace heavier metals. However, predictive capabilities for the impact-induced failure of FRCs have not been well-developed. In this work, we introduced an integrated technique to visualize the dynamic failure of FRCs, with the modified Kolsky bar loading and the high-speed synchrotron X-ray phase-contrast imaging (PCI). We summarize our experimental studies across the FRCs’ structural levels by using this integrated technique, including single-fiber tensile experiments, fiber/matrix debonding experiments, and single-edge notched bending experiments on composite laminates. It is revealed that the high-speed synchrotron X-ray PCI technique possesses sufficient spatial resolution to identify the failure behavior of a single fiber in the 10-μm scale level, as well as temporal resolution to identify the time sequence of internal dynamic damage evolution. The technique can penetrate through the opaque composite sample and provide real-time visualization of small-scale damaging mechanisms such as the embedded fiber’s sliding in the matrix and the fiber’s transverse debonding with the matrix. At an expanding scale, the technique can identify the crack initiation and track the cracking behavior inside a single ply or between different plies of a composite laminate. High-speed visualization inside the material by this integrated technique provides critical deformation and failure information to develop physical understanding of the damage inside composites under impact.

47 OTHER INSTRUMENTATION↗

Genetic control of morphological transitions in a coacervating protein template

Nature routinely exploits liquid–liquid phase separation (LLPS) of proteins to control the assembly and mineralization of hybrid materials. Here, we show that fusion of the Car9 silica-binding peptide to an elastin-like polypeptide (ELP) yields temperature- and sequence-programmable soft matter templates for the synthesis of silicified architectures ranging in size from nanometers to micrometers. Specifically, we demonstrate unprecedented control over the diameter of silica nanoparticles (SiNP) in the 30–60 nm range with 4 nm precision, show that a single arginine residue (R4) in the Car9 sequence underpins the transition from micelles to proteinosomes, and find that substitutions in other basic residues modulate electrostatic repulsion and solvation to enable access to kinetically trapped species. These structures, which include interconnected micelles, small (∼200 nm) and large (>5 µm) vesicles, are readily visualized by SEM imaging following silicification. Molecular dynamics (MD) simulations and AlphaFold predictions reveal that mutations in positively charged residues alter interfacial packing, hydration, and conformational freedom of the silica-binding segments. Overall, our results establish sequence and thermal energy as synergistic levers for morphological control across length scales using solid-binding ELPs and establish mineralization as a powerful tool to visualize the structure of dynamic soft matter assemblies.

hierarchy↗

Nanocrystal Geometry Governs Phase Transformation Pathways in Palladium Hydride

Pathways and structural dynamics of phase transformations impact performance of materials in energy and information storage technologies. Palladium hydride (PdH x ) nanocrystals are an ideal model system for studying solute-induced phase transformations, where elastic energy from lattice mismatch between α-PdH x and β-PdH x phases is often considered a key to determining the transformation pathways. α/β-PdH x interfacial elastic energy is affected by the confined geometry of a nanocrystal. However, how nanocrystal geometry influences phase transformation pathways is largely unknown. Using in situ liquid phase transmission electron microscopy, we directly visualize hydrogenation in Pd nanocrystals with two geometries, a nanocube and a hexagonal nanoplate. Both follow similar sequences of an initially curved nucleus, interface flattening, and reverse-stage nucleation; however, their evolving α/β-PdH x interfaces exhibit geometry-dependent crystallographic alignments. In nanocubes, {100}-aligned configurations conform to static elastic energy ordering, representing a pathway that maintains a local mechanical equilibrium, whereas nanoplates display both {110}- and {211}-aligned interfaces. Theoretical simulations show that geometry determines the accessibility of alternative phase transformation pathways as the system is driven far from equilibrium during hydrogenation. In conclusion, these findings identify geometry as a fundamental parameter for directing phase transformation pathways, offering design principles for accessing atypical configurations and improving properties of intercalation-based devices.

Lee, Daewon [Lawrence Berkeley National Laboratory↗

High-Resolution Comonomer Sequencing of Blocky Brominated Syndiotactic Polystyrene Copolymers Using 13C NMR Spectroscopy and Computer Simulations

This work demonstrates the first high-resolution comonomer sequencing of Blocky brominated syndiotactic polystyrene (sPS-co-sPS-Br) copolymers based on pentad assign- ments of the quaternary carbon region of the nuclear magnetic resonance spectrum. Copolymers containing p-bromostyrene (Br-Sty) units were prepared in matched sets using postpolymerization bromination methods carried out in the heterogeneous gel state (Blocky) and homogeneous solution state (Random). Quantitative information from the quaternary carbon spectra, heteronuclear multiple bond correlation spectroscopy, electronic structure calculations, and simulated statistically random copolymers was correlated to confirm the carbon resonance assignments for all 20 possible pentad comonomer sequences. Using the experimental pentad sequence prevalences, a computer code was developed to simulate chains with microstructures typical of each sample as a means to visually represent the copolymer blockiness with quantitative precision. Based on the microstructure and distribution of run lengths in these chains, the simulations revealed that the Blocky copolymers contain a high degree of blockiness. By comparing the run lengths in the simulated chains to the average number of styrene units in a crystalline segment of sPS (found by small-angle X-ray scattering), copolymer crystallizability was predicted. For the simulated Blocky B-21% (21 mol % Br-Sty) chain, the probability of randomly selecting a styrene unit in a crystallizable block was 25.8%, while that in the simulated Random R-18% was zero, in excellent agreement with the experimental crystallization behavior measured by differential scanning calorimetry. Additionally, these predictions confirmed that the simulated chains accurately represent the ensemble of chains in their respective copolymer samples. Furthermore, each simulated Blocky chain contained one or more long sPS blocks that paralleled the measured 38-40 styrene units spanning a crystalline segment within the sPS/CCl4 gel. This finding affirmed that the long sPS segments originated from the precise lamellar structure within the heterogeneous gel morphology (i.e., block length is correlated with lamellar thickness). Overall, the ability to tailor the copolymer microstructure through control of the semicrystalline gel morphology opens the door to synthesizing ordered copolymers by postpolymerization functionalization processes with unprecedented levels of compositional control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Spatial distribution of marker gene activity in the mouse lung during alveolarization

Here, this data is a curated collection of visual images of gene expression patterns from the pre- and post-natal mouse lung, accompanied by associated mRNA probe sequences and RNA-Seq expression profiles. Mammalian lungs undergo significant growth and cellular differentiation before and after the transition to breathing air. Documenting normal lung development is an important step in understanding abnormal lung development, as well as the challenges faced during a preterm birth. Images in this dataset indicate the spatial distribution of mRNA transcripts for over 500 different genes that are active during lung development, as initially determined via RNA-Seq. Images were systematically acquired using high-throughput in situ hybridization with non-radioactive digoxigenin-labeled mRNA probes across mouse lungs from developmental time points E16.5, E18.5, P7, and P28.

59 BASIC BIOLOGICAL SCIENCES↗

UEMtomaton: A Source-Available Platform to Aid in Start-up of Ultrafast Electron Microscopy Labs

The steady rise in the number of ultrafast electron microscopy (UEM) labs, in addition to the opacity and lack of detailed descriptions of current approaches that would enable point-by-point construction, has created an opportunity for sharing common methods and instrumentation for (for example) automating data acquisition to assist in efficient lab start-up and to learn about common and robust protocols. In the spirit of open sharing of methods, we provide here a description of an entry-level method and user interface (UI) for automating UEM experiments, and we provide access to the source code and scripts (source-available) for ease of implementation or as a starting reference point for those entering or seeking to enter the field (https://github.com/CEMSFlannigan/UEMtomaton/releases/tag/v1.0). Core instrumentation and physical connections in the UEM lab at Minnesota are described. Interface communication schemes consisting of duo server-client pairs between critical components – the optical delay stage and the UEM digital camera – are presented, with emphasis placed on describing the logic and communications sequence designed to conduct automated series acquisitions. An application designed and programmed with C++/CLI as Windows Forms in Microsoft Visual Studio – dubbed UEMtomaton – is also presented. Key to the UI layout is centralization of the automation tasks and establishment of communication within the software rather than by interfacing with each individual workstation. It is our hope that this note provides useful insight for current and future UEM researchers, particularly with respect to generalizability and portability of the approach to emerging labs. Here, we note that while this basic, entry-level approach is certainly not the most sophisticated or comprehensive of those currently in use, we feel there is nevertheless value in clearly communicating a proven straightforward method to hopefully lower the barrier to entry into the field.

47 OTHER INSTRUMENTATION↗

CYPminer: an automated cytochrome P450 identification, classification, and data analysis tool for genome data sets across kingdoms

Background: Cytochrome P450 monooxygenases (termed CYPs or P450s) are hemoproteins ubiquitously found across all kingdoms, playing a central role in intracellular metabolism, especially in metabolism of drugs and xenobiotics. The explosive growth of genome sequencing brings a new set of challenges and issues for researchers, such as a systematic investigation of CYPs across all kingdoms in terms of identification, classification, and pan-CYPome analyses. Such investigation requires an automated tool that can handle an enormous amount of sequencing data in a timely manner. Results: CYPminer was developed in the Python language to facilitate rapid, comprehensive analysis of CYPs from genomes of all kingdoms. CYPminer consists of two procedures i) to generate the Genome-CYP Matrix (GCM) that lists all occurrences of CYPs across the genomes, and ii) to perform analyses and visualization of the GCM, including pan-CYPomes (pan- and core-CYPome), CYP co-occurrence networks, CYP clouds, and genome clustering data. The performance of CYPminer was evaluated with three datasets from fungal and bacterial genome sequences. Conclusions: CYPminer completes CYP analyses for large-scale genomes from all kingdoms, which allows systematic genome annotation and comparative insights for CYPs. CYPminer also can be extended and adapted easily for broader usage.

59 BASIC BIOLOGICAL SCIENCES↗

tSFM 1.0: tRNA Structure–Function Mapper

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

59 BASIC BIOLOGICAL SCIENCES↗

Nanoscale wetting controls reactive Pd ensembles in synthesis of dilute PdAu alloy catalysts

The performance of bimetallic dilute alloy catalysts is largely determined by the size of minority metal ensembles on the nanoparticle surface. By analyzing the synthesis of catalysts comprising Pd 8 Au 92 nanoparticles supported on silica using surface-sensitive techniques, we report that whether Pd overgrowth occurs before or after Au nanoparticle deposition onto the support controls the surface Pd ensemble size and abundance. These differences in Pd ensembles influence catalytic reactivity in H 2 –D 2 isotope exchange and benzaldehyde hydrogenation, which, in correlation with theoretical calculations, is used to elucidate the active site(s) in each reaction. To clarify how the synthetic sequence controls the formation of Pd ensembles, we combine numerical wetting calculations and molecular dynamics simulations (with a machine-learned force field) to visualize Pd deposition and migration on the nanoparticle surface, respectively. Our results suggest that the nanoparticle–support interface restricts nanoparticle accessibility to Pd deposition, which consequently controls the Pd ensemble size, illustrating the critical role of nanoscale wetting phenomena during bimetallic catalyst preparation.

36 MATERIALS SCIENCE↗

Voltage decay and redox asymmetry mitigation by reversible cation migration in lithium-rich layered oxide electrodes

Despite the high energy density of lithium-rich layered-oxide electrodes, their real-world implementation in batteries is hindered by the substantial voltage decay on cycling. This voltage decay is widely accepted to mainly originate from progressive structural rearrangements involving irreversible transition-metal migration. As prevention of this spontaneous cation migration has proven difficult, a paradigm shift toward management of its reversibility is needed. Herein, we demonstrate that the reversibility of the cation migration of lithium-rich nickel manganese oxides can be remarkably improved by altering the oxygen stacking sequences in the layered structure and thereby dramatically reducing the voltage decay. The preeminent intra-cycle reversibility of the cation migration is experimentally visualized, and first-principles calculations reveal that an O2-type structure restricts the movements of transition metals within the Li layer, which effectively streamlines the returning migration path of the transition metals. Furthermore, we propose that the enhanced reversibility mitigates the asymmetry of the anionic redox in conventional lithium-rich electrodes, promoting the high-potential anionic reduction, thereby reducing the subsequent voltage hysteresis. Our findings demonstrate that regulating the reversibility of the cation migration is a practical strategy to reduce voltage decay and hysteresis in lithium-rich layered materials.

25 ENERGY STORAGE↗

Genome expansion by a CRISPR trimmer-integrase

CRISPR–Cas adaptive immune systems capture DNA fragments from invading mobile genetic elements and integrate them into the host genome to provide a template for RNA-guided immunity. CRISPR systems maintain genome integrity and avoid autoimmunity by distinguishing between self and non-self, a process for which the CRISPR/Cas1–Cas2 integrase is necessary but not sufficient. In some microorganisms, the Cas4 endonuclease assists CRISPR adaptation, but many CRISPR–Cas systems lack Cas4. Here we show here that an elegant alternative pathway in a type I-E system uses an internal DnaQ-like exonuclease (DEDDh) to select and process DNA for integration using the protospacer adjacent motif (PAM). The natural Cas1–Cas2/exonuclease fusion (trimmer-integrase) catalyses coordinated DNA capture, trimming and integration. Five cryo-electron microscopy structures of the CRISPR trimmer-integrase, visualized both before and during DNA integration, show how asymmetric processing generates size-defined, PAM-containing substrates. Before genome integration, the PAM sequence is released by Cas1 and cleaved by the exonuclease, marking inserted DNA as self and preventing aberrant CRISPR targeting of the host. Together, these data support a model in which CRISPR systems lacking Cas4 use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

59 BASIC BIOLOGICAL SCIENCES↗

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

Host-associated microbial communities (microbiomes) play critical roles in human, animal, and plant health and development. However, interactions between the host, members of the microbiome, and invading pathogens are in most cases still poorly understood. Such interactions are multidimensional and can alter the taxonomic composition and/or the functional metabolic activities of the microbiome in response to disease or treatment conditions. For example, after 2 days of antibiotic treatment, the mouse gut microbiome is altered and more susceptible to invasion by the pathogen Clostridioides difficile. Studies of these multidimensional interactions have been fueled by the ability to use high-throughput sequencing of phylogenetic marker genes to profile microbial community composition and shotgun metagenomics to profile functional potential. However, many protein-coding genes predicted from metagenomes are not necessarily expressed under a given condition, and thus, it is difficult to assess the activities and functional interactions in microbial communities based on DNA sequencing data alone. The physiological and pathological processes expressed in these communities under specific conditions are better reflected by the abundances of transcripts or proteins. In this Pearl, we provide a brief introduction to metaproteomics, which is a tool for the large-scale analysis of proteins in microbiomes that allows researchers to address a diversity of questions related to functions and interactions in microbiomes. The term “metaproteomics” was first used in 2004 for “the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time”, and since then, a large array of metaproteomics approaches have been developed. Our objective in this Pearl is to highlight what we feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.

59 BASIC BIOLOGICAL SCIENCES↗

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗

SynopFrame: Multiscale time-dependent visual abstraction framework for analyzing DNA nanotechnology simulations

We present an open-source framework, SynopFrame, that allows DNA nanotechnology (DNA-nano) experts to analyze and understand molecular dynamics simulation trajectories of their designs. We use a multiscale multi-dimensional abstraction space, connect the representations to a projected conformational space plot of the structure’s temporal sequence, and thus enable experts to analyze the dynamics of their structural designs and, specifically, failure cases of the assembly. In addition, our time-dependent abstraction representation allows the biologists, for the first time in a smooth and structurally clear way, to identify and observe temporal transitions of a DNA-nano design from one configuration to another, and to highlight important periods of the simulation for further analysis. We realize SynopFrame as a dashboard of the different synchronized 3D spatial and 2D schematic visual representations, with a color overlay to show essential properties such as the status of hydrogen bonds. The linking of the spatial, schematic, and abstract views ensures that users can effectively analyze the high-frequency motion. We also categorize the status of the hydrogen bonds into a new format to allow us to color-encode it and overlay it on the representations. To demonstrate the utility of SynopFrame, we describe example usage scenarios and report user feedback.

Abstraction space↗

High-speed synchrotron X-ray phase-contrast imaging for evaluating microscale damage mechanisms and tracking cracking behaviors inside cross-ply GFRCs

In this study, we integrated the high-speed synchrotron X-ray phase-contrast imaging (PCI) with a modified Kolsky compression bar loading platform to visualize the dynamic failure processes of cross-ply glass fiber reinforced composites (GFRCs). Four S-2 glass/SC-15 composite specimens were prepared, having similar thicknesses but different stacking sequences, namely as [0 12 /90 12 ], [90 12 /0 12 ], [0 8 /90 8 /0 8 ], and [90 8 /0 8 /90 8 ]. Three-dimensional synchrotron X-ray computed tomography and scanning electron microscopy (SEM) were employed to examine the microstructures and quantify the fiber volume fractions. Each specimen was notched and subjected to a dynamic three-point flexural loading. The onset of cracking close to the notch tip, crack propagation in 0° or 90° plies and their interface, crack opening, and ultimately failure of the specimen were captured by high-speed synchrotron X-ray PCI. Additional dynamic experiments were performed to determine the average time when the stress wave propagated through the specimen and correlate the X-ray images with the specimen's force-deflection response. Finally, the surface morphology of each specimen after the dynamic loading was imaged by SEM. Comparison between real-time X-ray images and post-fracture SEM images demonstrated the capability of the X-ray method to record damage evolution inside composites. Furthermore, the high spatial and temporal resolutions of the X-ray setup and edge enhancement by PCI enabled the identification of microscale damage features within 1 μs. Two damaging processes were identified, crack growth was quantified, and fracture toughness of the composites was evaluated. The method is deemed useful to reveal microscale damage mechanisms and track cracking behaviors inside cross-ply GFRCs under dynamic loading in real time.

42 ENGINEERING↗

A deep learning approach to programmable RNA switches

Engineered RNA elements are programmable tools capable of detecting small molecules, proteins, and nucleic acids. Predicting the behavior of these synthetic biology components remains a challenge, a situation that could be addressed through enhanced pattern recognition from deep learning. Here, we investigate Deep Neural Networks (DNN) to predict toehold switch function as a canonical riboswitch model in synthetic biology. To facilitate DNN training, we synthesize and characterize in vivo a dataset of 91,534 toehold switches spanning 23 viral genomes and 906 human transcription factors. DNNs trained on nucleotide sequences outperform (R 2 = 0.43–0.70) previous state-of-the-art thermodynamic and kinetic models (R 2 = 0.04–0.15) and allow for human-understandable attention-visualizations (VIS4Map) to identify success and failure modes. This work shows that deep learning approaches can be used for functionality predictions and insight generation in RNA synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗