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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 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Development of low temperature fuel cell holders for Operando x-ray micro and nano computed tomography to visualize water distribution

Abstract Synchrotron x-ray imaging techniques, like x-ray computed tomography (CT) and radiography have proven instrumental in expanding the communities knowledge of complex transport and reaction kinetics in electrochemical devices such as fuel cells and electrolyzers. This work presents the development of novel x-ray CT imaging techniques for operando visualization of water within low temperature fuel cells at spatial resolutions spanning the micro and nano scales. The design of operando sample holders, for both micro x-ray CT and nano CT experiments is described in depth, and prototypes of these sample holders were evaluated across a set of requirements, the most important of which are x-ray transmissibility, electrical conductivity and mechanical stability. Water segmentation from micro x-ray CT data was enabled by an image subtraction method, where the image without water is subtracted from the one with water. Through iterative experimentations, the operando nano CT cell was developed to optimize mechanical compression, electric conductivity and gas flow. While three-dimensional fuel cell reconstructions were shown possible, there remain challenges to overcome at typical lower energies (8 keV) due to beam damage, whereas it is not as significant for higher energies (>17.5 keV).

Kulkarni, Devashish↗
DOE OSTI2013

SPOCS: Software for Predicting and Visualizing Orthology/Paralogy Relationships Among Genomes

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. AVAILABILITY AND IMPLEMENTATION: A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

comparative genomics↗
DOE OSTI2016

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Galaxy Zoo DECaLS: Detailed visual morphology measurements from volunteers and deep learning for 314,000 galaxies

We present Galaxy Zoo DECaLS: detailed visual morphological classifications for Dark Energy Camera Legacy Survey images of galaxies within the SDSS DR8 footprint. Deeper DECaLS images (r = 23.6 versus r = 22.2 from SDSS) reveal spiral arms, weak bars, and tidal features not previously visible in SDSS imaging. To best exploit the greater depth of DECaLS images, volunteers select from a new set of answers designed to improve our sensitivity to mergers and bars. Galaxy Zoo volunteers provide 7.5 million individual classifications over 314 000 galaxies. 140 000 galaxies receive at least 30 classifications, sufficient to accurately measure detailed morphology like bars, and the remainder receive approximately 5. All classifications are used to train an ensemble of Bayesian convolutional neural networks (a state-of-the-art deep learning method) to predict posteriors for the detailed morphology of all 314 000 galaxies. We use active learning to focus our volunteer effort on the galaxies which, if labelled, would be most informative for training our ensemble. When measured against confident volunteer classifications, the trained networks are approximately 99 per cent accurate on every question. Morphology is a fundamental feature of every galaxy; our human and machine classifications are an accurate and detailed resource for understanding how galaxies evolve.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

VIBES: a workflow for annotating and visualizing viral sequences integrated into bacterial genomes

Abstract Bacteriophages are viruses that infect bacteria. Many bacteriophages integrate their genomes into the bacterial chromosome and become prophages. Prophages may substantially burden or benefit host bacteria fitness, acting in some cases as parasites and in others as mutualists. Some prophages have been demonstrated to increase host virulence. The increasing ease of bacterial genome sequencing provides an opportunity to deeply explore prophage prevalence and insertion sites. Here we present VIBES (Viral Integrations in Bacterial genomES), a workflow intended to automate prophage annotation in complete bacterial genome sequences. VIBES provides additional context to prophage annotations by annotating bacterial genes and viral proteins in user-provided bacterial and viral genomes. The VIBES pipeline is implemented as a Nextflow-driven workflow, providing a simple, unified interface for execution on local, cluster and cloud computing environments. For each step of the pipeline, a container including all necessary software dependencies is provided. VIBES produces results in simple tab-separated format and generates intuitive and interactive visualizations for data exploration. Despite VIBES’s primary emphasis on prophage annotation, its generic alignment-based design allows it to be deployed as a general-purpose sequence similarity search manager. We demonstrate the utility of the VIBES prophage annotation workflow by searching for 178 Pf phage genomes across 1072 Pseudomonas spp. genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Expansion of the tmRNA sequence database and new tools for search and visualization

Abstract Transfer–messenger RNA (tmRNA) contributes essential tRNA-like and mRNA-like functions during the process of trans-translation, a mechanism of quality control for the translating bacterial ribosome. Proper tmRNA identification benefits the study of trans-translation and also the study of genomic islands, which frequently use the tmRNA gene as an integration site. Automated tmRNA gene identification tools are available, but manual inspection is still important for eliminating false positives. We have increased our database of precisely mapped tmRNA sequences over 50-fold to 97 179 unique sequences. Group I introns had previously been found integrated within a single subsite within the TψC-loop; they have now been identified at four distinct subsites, suggesting multiple founding events of invasion of tmRNA genes by group I introns, all in the same vicinity. tmRNA genes were found in metagenomic archaeal genomes, perhaps a result of misbinning of bacterial sequences during genome assembly. With the expanded database, we have produced new covariance models for improved tmRNA sequence search and new secondary structure visualization tools.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Knocksideways in plants: an inducible system for in planta visualization of protein interactions

Understanding protein-protein interactions (PPIs) is key to unlocking the secrets of various cellular processes. While many tools have been developed to detect PPIs, such as the yeast two-hybrid assay, bimolecular fluorescence complementation, and affinity purification, there is great demand for additional methods to complement existing ones. As all approaches have limitations, evidence from at least two independent assays is required to validate PPIs. In a Breakthrough Report, Joanna Winkler and colleagues present here a promising method, named “knocksideways in plants” (KSP), for inducible visualization of PPIs in planta.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Bats flying through a Y-maze are visually attracted to wind turbine surfaces

Wind energy’s rapid expansion has led to unintended consequences for wildlife, with migratory bats among the species most at risk. The behavioural mechanisms underlying collisions remain poorly understood, but one hypothesis is that bats are attracted to wind turbine structures. Vision is important to bat orientation and obstacle avoidance, yet it has been relatively understudied in the context of bat–turbine interactions. We hypothesize that light reflected off turbine surfaces could attract bats, acting as a sensory pollutant that may increase collision risk. To test whether reflective turbine surfaces elicit attraction, we flew 242 Lasiurus cinereus and 154 Lasionycteris noctivagans through Y-maze assays. Bats were at least twice as likely to fly towards white turbine blade sections compared to less reflective black ones. This attraction intensified when the alternative exit was a dark, empty flyway, with 74% of L. cinereus and 97% of L. noctivagans flying towards the white turbine blade. These findings provide evidence that visual sensory pollutants could underlie bat–turbine interactions, and if so, wind turbines could be ecological traps.

17 WIND ENERGY↗
DOE OSTI2025

Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC

AbstractThe folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

Zhao, Yanyan (ORCID:0000000323021763)↗
DOE OSTI2021

Photoporomechanics: An Experimental Method to Visualize the Effective Stress Field in Fluid-Filled Granular Media

Effective stress governs the mechanical behavior of porous media. In this study, we use photoelasticimetry to visualize the evolving effective stress field in fluid-filled granular media in processes that couple fluid flow and mechanical deformation. We refer to this experimental method as photoporomechanics. We develop a fabrication process to produce millimeter-scale residual-stress-free photoelastic spheres with high geometric accuracy. We use color to quantify the forces acting on the particles over a wide range of forces, while using light intensity for a small range of forces. We then provide an application of photoporomechanics to illustrate the evolution of effective stress during one-dimensional consolidation: a process by which the stresses caused by a sudden load are gradually transmitted through a fluid-filled granular pack as the fluid drains and excess pore pressures dissipate. We report our technique provides a powerful experimental model system to study the grain-scale underpinning of coupled solid-fluid processes in granular media.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Direct visualization and control of antiferromagnetic domains and spin reorientation in a parent cuprate

Here, we report magnetic optical second-harmonic generation (SHG) polarimetry and imaging on Sr 2 Cu 3 O 4 Cl 2 , which allows direct visualization of the mesoscopic antiferromagnetic (AFM) structure of a parent cuprate. Temperature- and magnetic-field-dependent SHG reveals large domains with 90° relative orientations that are stabilized by a combination of uniaxial magnetic anisotropy and the Earth's magnetic field. Below a temperature T R ~ 97 K, we observe an unusual 90° spin reorientation transition, possibly driven by competing magnetic anisotropies of the two copper sublattices, which swaps the AFM domain states while preserving the domain structure. This allows deterministic switching of the AFM states by thermal or laser heating. Near T R , the domain walls become exceptionally responsive to an applied magnetic field, with the Earth's field sufficient to completely expel them from the crystal. Our findings unlock opportunities to study the mesoscopic AFM behavior of parent cuprates and explore their potential for AFM technologies.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

Visualization of atomic-scale phenomena in superconductors: application to FeSe

Here we propose a simple method of calculating inhomogeneous, atomic-scale phenomena in superconductors which makes use of the wave function information traditionally discarded in the construction of tight-binding models used in the Bogoliubov-de Gennes equations. The method uses symmetry- based first principles Wannier functions to visualize the effects of superconducting pairing on the distribution of electronic states over atoms within a crystal unit cell. Local symmetries lower than the global lattice symmetry can thus be exhibited as well, rendering theoretical comparisons with scanning tunneling spectroscopy data much more useful. As a simple example, we discuss the geometric dimer states observed near defects in superconducting FeSe.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Visualizing topological edge states of single and double bilayer Bi supported on multibilayer Bi(111) films

Freestanding single bilayer Bi(111) is a two-dimensional topological insulator with edge states propagating along its perimeter. Given the interlayer coupling experimentally, the topological nature of Bi(111) thin films and the impact of the supporting substrate on the topmost Bi bilayer are still under debate. Combined with scanning tunneling microscopy and first-principles calculations, we systematically study the electronic properties of Bi(111) thin films grown on a $\mathrm{NbS}{\mathrm{e}}_{2}$ substrate. Two types of nonmagnetic edge structures, i.e., a conventional zigzag edge and a 2 x 1 reconstructed edge, coexist alternately at the boundaries of single bilayer islands, the topological edge states of which exhibit remarkably different energy and spatial distributions. Prominent edge states are persistently visualized at the edges of both single and double bilayer Bi islands, regardless of the underlying thickness of Bi(111) thin films. We provide an explanation for the topological origin of the observed edge states that is verified with first-principles calculations. Our paper clarifies the long-standing controversy regarding the topology of Bi(111) thin films and reveals the tunability of topological edge states via edge modifications.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Visualizing the Coupling between Red and Blue Stark States Using Photoionization Microscopy

In nonhydrogenic atoms in a dc electric field, the finite size of the ionic core introduces a coupling between quasibound Stark states that leads to avoided crossings between states that would otherwise cross. Near an avoided crossing, the interacting states may have decay amplitudes that cancel each other, decoupling one of the states from the ionization continuum. This well-known interference narrowing effect, observed as a strongly electric field-dependent decrease in the ionization rate, was previously observed in several atoms. Here we use photoionization microscopy to visualize interference narrowing in helium atoms, thereby explicitly revealing the mechanism by which Stark states decay. As a result, the interference narrowing allows measurements of the nodal patterns of red Stark states, which are otherwise not observable due to their intrinsic short lifetime.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2016

Atomic-Scale Visualization of Quasiparticle Interference on a Type-II Weyl Semimetal Surface

Here we combine quasiparticle interference simulation (theory) and atomic resolution scanning tunneling spectromicroscopy (experiment) to visualize the interference patterns on a type-II Weyl semimetal Mo x W 1-x Te 2 for the first time. Our simulation based on first-principles band topology theoretically reveals the surface electron scattering behavior. We identify the topological Fermi arc states and reveal the scattering properties of the surface states in Mo 0.66 W 0.34 Te 2 . In addition, our result reveals an experimental signature of the topology via the interconnectivity of bulk and surface states, which is essential for understanding the unusual nature of this material.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Visualizing Anisotropic Oxygen Diffusion in Ceria under Activated Conditions

Oxygen reactivity plays a key role in the performance of ceria-based catalysts. Aberration-corrected transmission electron microscopy and molecular dynamics simulations were used to study the oxygen atom diffusion in ceria under activated conditions. Reactive oxygen atom and its real-time diffusion were visualized. Additionally, the interplay between cerium and oxygen atoms originating from a Coulomb interaction was revealed by the out-of-plane buckling of cerium atoms associated with oxygen transport. Anisotropic oxygen atom diffusion that depends on crystal orientations was discovered, demonstrating a preferential [001] crystallographic diffusion pathway. These findings reveal prospects for applications of anisotropic orientation-relevant fluorite-structured oxides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Visualization of Chiral Electronic Structure and Anomalous Optical Response in a Material with Chiral Charge Density Waves

Chiral materials have attracted significant research interests as they exhibit intriguing physical properties, such as chiral optical response, spin-momentum locking, and chiral induced spin selectivity. Recently, layered transition metal dichalcogenide 1T–TaS 2 has been found to host a chiral charge density wave (CDW) order. Nevertheless, the physical consequences of the chiral order, for example, in electronic structures and the optical properties, are yet to be explored. Here, we report the spectroscopic visualization of an emergent chiral electronic band structure in the CDW phase, characterized by windmill-shaped Fermi surfaces. Further, we uncover a remarkable chirality-dependent circularly polarized Raman response due to the salient in-plane chiral symmetry of CDW, although the ordinary circular dichroism vanishes. Chiral Fermi surfaces and anomalous Raman responses coincide with the CDW transition, proving their lattice origin. Our Letter paves a path to manipulate the chiral electronic and optical properties in two-dimensional materials and explore applications in polarization optics and spintronics.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Ultrafast electron diffraction: Visualizing dynamic states of matter

Since the discovery of electron-wave duality, electron scattering instrumentation has developed into a powerful array of techniques for revealing the atomic structure of matter. Beyond detecting local lattice variations in equilibrium structures with the highest possible spatial resolution, recent research efforts have been directed toward the long-sought-after dream of visualizing the dynamic evolution of matter in real time. The atomic behavior at ultrafast timescales carries critical information on phase transition and chemical reaction dynamics, the coupling of electronic and nuclear degrees of freedom in materials and molecules, and the correlation among structure, function, and previously hidden metastable or nonequilibrium states of matter. Ultrafast electron pulses play an essential role in this scientific endeavor, and their generation has been facilitated by rapid technical advances in both ultrafast laser and particle accelerator technologies. Here this review presents a summary of the noteworthy developments in this field in the last few decades. The physics and technology of ultrafast electron beams is presented with an emphasis on the figures of merit most relevant for ultrafast electron diffraction experiments. Recent developments in the generation, manipulation, and characterization of ultrashort electron beams aimed at improving the combined spatiotemporal resolution of these measurements are discussed. The fundamentals of electron scattering from atomic matter and the theoretical frameworks for retrieving dynamic structural information from solid-state and gas-phase samples is described. Essential experimental techniques and several landmark works that have applied these approaches are also highlighted to demonstrate the widening applicability of these methods. Ultrafast electron probes with ever-improving capabilities, combined with other complementary photon-based or spectroscopic approaches, hold tremendous potential for revolutionizing our ability to observe and understand energy and matter at atomic scales.

43 PARTICLE ACCELERATORS↗