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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 847 records · Page 47
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs

Research is communicated more effectively and reproducibly when articles depict genetic designs consistently and fully disclose the complete sequences of all reported constructs. Now, ACS Synthetic Biology is providing authors with updated guidance and piloting a new tool and publication workflow that facilitate compliance with these recommended practices and standards for visual representation and data exchange.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Visualizing Millisecond Atomic Dynamics of Nanocrystals in Liquid

Atomic structures of nanomaterials are inherently dynamic and continuously reshaped through interactions with chemical species and external stimuli. Such dynamics are further amplified as the size and dimensionality of nanomaterials decrease. Despite advances in analytical methods, it remains challenging to capture the structural dynamics of nanomaterials in reactive environments with both atomic spatial resolution and commensurate temporal resolution. Here, in this study, we directly visualize atomic-scale dynamics of gold (Au) nanocrystals in reactive liquid environments with millisecond-speed liquid-cell electron microscopy (EM) and deep-learning denoising. We uncover reversible fluctuations in the local crystallinity of Au nanocrystals dependent on the surrounding chemical environment. These transient fluctuations, driven by interactions at nanocrystal–liquid interfaces, critically influence the dissolution kinetics and grain boundary relaxation. By overcoming the spatiotemporal limitations in conventional liquid-cell EM, our findings provide insights into how transient nanoscale structures dictate the stability and reactivity of nanomaterials.

Kang, Sungsu [University of Chicago, IL (United St↗
DOE OSTI2018

Pore‐Scale Visualization of Methane Hydrate‐Bearing Sediments With Micro‐CT

Abstract X‐ray computed tomography (CT) has become a critical technique in the study of porous media. It has attracted growing attention for analyzing hydrate‐bearing sediment, but this has been done using surrogates (Xe/Kr) only due to difficulties in distinguishing methane hydrate from water. This study presents the successful imaging of methane hydrate coexisting with pore liquid, gas, and sediments. We used potassium iodide (KI) solutions and in‐line propagation‐based phase‐contrast CT analysis of X‐ray attenuation and diffraction to distinguish the four materials. Thus, consideration for CT‐related X‐ray physics was necessary to optimize KI concentrations, improve material separation with X‐ray propagation, and properly interpret artifacts within the images. The images clearly show methane hydrate in the pore space of sand (~250 μm) coexisting with KI solution and gas. Following this, X‐ray CT can now be used to visualize pore habits of natural methane hydrate in sediment cores.

Lei, Liang↗
DOE OSTI2023

nmrrr : A Reproducible Workflow for Binning and Visualizing NMR Spectra From Environmental Samples

Nuclear magnetic resonance (NMR) spectroscopy is a useful tool for detection and identification of molecular structural information, with increasing applications in environmental sciences. NMR instrument outputs are however heterogeneous and require extensive post-processing, creating barriers to their use and application by non-specialists. Here, we report on a new open-source R package, nmrrr, that processes and visualizes spectral data obtained from one-dimensional solution-state and solid-state NMR experiments; the package also performs relevant calculations commonly applied in natural organic matter communities, such as computing the relative abundance of various functional groups. We document the package's installation, dependencies, and functions; and provide a standard workflow for processing NMR data. This package is currently available on CRAN and GitHub, and community contributions are welcome.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Cooperative Singlet and Triplet Exciton Transport in Tetracene Crystals Visualized by Ultrafast Microscopys

Singlet fission presents an attractive solution to overcome the Shockley–Queisser limit by generating two triplet excitons from one singlet exciton. Although triplet excitons are long-lived, their transport occurs through a Dexter transfer, making them slower than singlet excitons, which travel by means of a Förster mechanism. A thorough understanding of the interplay between singlet fission and exciton transport is therefore necessary to assess the potential and challenges of singlet-fission utilization. We report a direct visualization of exciton transport in single tetracene crystals using transient absorption microscopy with 200 fs time resolution and 50 nm spatial precision. Moreover, these measurements reveal a new singlet-mediated transport mechanism for triplets, which leads to an enhancement in effective triplet exciton diffusion of more than one order of magnitude on picosecond to nanosecond timescales. These results establish that there are optimal energetics of singlet and triplet excitons that benefit both singlet fission and exciton diffusion.

14 SOLAR ENERGY↗
DOE OSTI2017

Visualization of lithium-ion transport and phase evolution within and between manganese oxide nanorods

Multiple lithium-ion transport pathways and local phase changes upon lithiation in silver hollandite are revealed via in situ microscopy including electron diffraction, imaging and spectroscopy, coupled with density functional theory and phase field calculations. Here, we report unexpected inter-nanorod lithium-ion transport, where the reaction fronts and kinetics are maintained within the neighbouring nanorod. Notably, this is the first time-resolved visualization of lithium-ion transport within and between individual nanorods, where the impact of oxygen deficiencies is delineated. Initially, fast lithium-ion transport is observed along the long axis with small net volume change, resulting in two lithiated silver hollandite phases distinguishable by orthorhombic distortion. As a result, a slower reaction front is observed, with formation of polyphase lithiated silver hollandite and face-centred-cubic silver metal with substantial volume expansion. Our results indicate lithium-ion transport is not confined within a single nanorod and may provide a paradigm shift for one-dimensional tunnelled materials, particularly towards achieving high-rate capability.

25 ENERGY STORAGE↗
DOE OSTI2015

Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses

Ultrafast photoinduced electron transfer preceding energy equilibration still poses many experimental and conceptual challenges to the optimization of photoconversion since an atomic-scale description has so far been beyond reach. Here we combine femtosecond transient optical absorption spectroscopy with ultrafast X-ray emission spectroscopy and diffuse X-ray scattering at the SACLA facility to track the non-equilibrated electronic and structural dynamics within a bimetallic donor–acceptor complex that contains an optically dark centre. Exploiting the 100-fold increase in temporal resolution as compared with storage ring facilities, these measurements constitute the first X-ray-based visualization of a non-equilibrated intramolecular electron transfer process over large interatomic distances. Thus experimental and theoretical results establish that mediation through electronically excited molecular states is a key mechanistic feature. The present study demonstrates the extensive potential of femtosecond X-ray techniques as diagnostics of non-adiabatic electron transfer processes in synthetic and biological systems, and some directions for future studies, are outlined.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Multi-resolution 3D visualization of the early stages of cellular uptake of peptide-coated nanoparticles

A detailed understanding of the cellular uptake process is essential to the development of cellular delivery strategies and to the study of viral trafficking. However, visualization of the entire process, encompassing the fast dynamics (local to the freely diffusing nanoparticle) as well the state of the larger-scale cellular environment, remains challenging. Here, we introduce a three-dimensional multi-resolution method to capture, in real time, the transient events leading to cellular binding and uptake of peptide (HIV1-Tat)-modified nanoparticles. Applying this new method to observe the landing of nanoparticles on the cellular contour in three dimensions revealed long-range deceleration of the delivery particle, possibly due to interactions with cellular receptors. Furthermore, by using the nanoparticle as a nanoscale ‘dynamics pen’, we discovered an unexpected correlation between small membrane terrain structures and local nanoparticle dynamics. This approach could help to reveal the hidden mechanistic steps in a variety of multiscale processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Direct visualization of critical hydrogen atoms in a pyridoxal 5'-phosphate enzyme

Enzymes dependent on pyridoxal 5'-phosphate (PLP, the active form of vitamin B6) perform a myriad of diverse chemical transformations. They promote various reactions by modulating the electronic states of PLP through weak interactions in the active site. Neutron crystallography has the unique ability of visualizing the nuclear positions of hydrogen atoms in macromolecules. Here we present a room-temperature neutron structure of a homodimeric PLP-dependent enzyme, aspartate aminotransferase, which was reacted in situ with α-methylaspartate. In one monomer, the PLP remained as an internal aldimine with a deprotonated Schiff base. In the second monomer, the external aldimine formed with the substrate analog. We observe a deuterium equidistant between the Schiff base and the C-terminal carboxylate of the substrate, a position indicative of a low-barrier hydrogen bond. As a result, quantum chemical calculations and a low-pH room-temperature X-ray structure provide insight into the physical phenomena that control the electronic modulation in aspartate aminotransferase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

A browser-based tool for visualization and analysis of diffusion MRI data

Human neuroscience research faces several challenges with regards to reproducibility. While scientists are generally aware that data sharing is important, it is not always clear how to share data in a manner that allows other labs to understand and reproduce published findings. Here we report a new open source tool, AFQ-Browser, that builds an interactive website as a companion to a diffusion MRI study. Because AFQ-Browser is portable—it runs in any web-browser—it can facilitate transparency and data sharing. Moreover, by leveraging new web-visualization technologies to create linked views between different dimensions of the dataset (anatomy, diffusion metrics, subject metadata), AFQ-Browser facilitates exploratory data analysis, fueling new discoveries based on previously published datasets. In an era where Big Data is playing an increasingly prominent role in scientific discovery, so will browser-based tools for exploring high-dimensional datasets, communicating scientific discoveries, aggregating data across labs, and publishing data alongside manuscripts.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Operando and three-dimensional visualization of anion depletion and lithium growth by stimulated Raman scattering microscopy

Visualization of ion transport in electrolytes provides fundamental understandings of electrolyte dynamics and electrolyte-electrode interactions. However, this is challenging because existing techniques are hard to capture low ionic concentrations and fast electrolyte dynamics. Here we show that stimulated Raman scattering microscopy offers required resolutions to address a long-lasting question: how does the lithium-ion concentration correlate to uneven lithium deposition? In this study, anions are used to represent lithium ions since their concentrations should not deviate for more than 0.1 mM, even near nanoelectrodes. A three-stage lithium deposition process is uncovered, corresponding to no depletion, partial depletion, and full depletion of lithium ions. Further analysis reveals a feedback mechanism between the lithium dendrite growth and heterogeneity of local ionic concentration, which can be suppressed by artificial solid electrolyte interphase. This report shows that stimulated Raman scattering microscopy is a powerful tool for the materials and energy field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase

Mevalonate diphosphate decarboxylases (MDDs) catalyze the ATP-dependent-Mg 2+ -decarboxylation of mevalonate-5-diphosphate (MVAPP) to produce isopentenyl diphosphate (IPP), which is essential in both eukaryotes and prokaryotes for polyisoprenoid synthesis. The substrates, MVAPP and ATP, have been shown to bind sequentially to MDD. Here we report crystals in which the enzyme remains active, allowing the visualization of conformational changes in Enterococcus faecalis MDD that describe sequential steps in an induced fit enzymatic reaction. Initial binding of MVAPP modulates the ATP binding pocket with a large loop movement. Upon ATP binding, a phosphate binding loop bends over the active site to recognize ATP and bring the molecules to their catalytically favored configuration. Positioned substrates then can chelate two Mg 2+ ions for the two steps of the reaction. Closure of the active site entrance brings a conserved lysine to trigger dissociative phosphoryl transfer of γ-phosphate from ATP to MVAPP, followed by the production of IPP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ultrafast coherent motion and helix rearrangement of homodimeric hemoglobin visualized with femtosecond X-ray solution scattering

Ultrafast motion of molecules, particularly the coherent motion, has been intensively investigated as a key factor guiding the reaction pathways. Recently, X-ray free-electron lasers (XFELs) have been utilized to elucidate the ultrafast motion of molecules. However, the studies on proteins using XFELs have been typically limited to the crystalline phase, and proteins in solution have rarely been investigated. Here we applied femtosecond time-resolved X-ray solution scattering (fs-TRXSS) and a structure refinement method to visualize the ultrafast motion of a protein. We succeeded in revealing detailed ultrafast structural changes of homodimeric hemoglobin involving the coherent motion. In addition to the motion of the protein itself, the time-dependent change of electron density of the hydration shell was tracked. Besides, the analysis on the fs-TRXSS data of myoglobin allows for observing the effect of the oligomeric state on the ultrafast coherent motion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Visualization and validation of twin nucleation and early-stage growth in magnesium

The abrupt occurrence of twinning when Mg is deformed leads to a highly anisotropic response, making it too unreliable for structural use and too unpredictable for observation. Here, we describe an in-situ transmission electron microscopy experiment on Mg crystals with strategically designed geometries for visualization of a long-proposed but unverified twinning mechanism. Combining with atomistic simulations and topological analysis, we conclude that twin nucleation occurs through a pure-shuffle mechanism that requires prismatic-basal transformations. Also, we verified a crystal geometry dependent twin growth mechanism, that is the early-stage growth associated with instability of plasticity flow, which can be dominated either by slower movement of prismatic-basal boundary steps, or by faster glide-shuffle along the twinning plane. The fundamental understanding of twinning provides a pathway to understand deformation from a scientific standpoint and the microstructure design principles to engineer metals with enhanced behavior from a technological standpoint.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Ultrafast visualization of incipient plasticity in dynamically compressed matter

Plasticity is ubiquitous and plays a critical role in material deformation and damage; it inherently involves the atomistic length scale and picosecond time scale. A fundamental understanding of the elastic-plastic deformation transition, in particular, incipient plasticity, has been a grand challenge in high-pressure and high-strain-rate environments, impeded largely by experimental limitations on spatial and temporal resolution. Here, we report femtosecond MeV electron diffraction measurements visualizing the three-dimensional (3D) response of single-crystal aluminum to the ultrafast laser-induced compression. We capture lattice transitioning from a purely elastic to a plastically relaxed state within 5 ps, after reaching an elastic limit of ~25 GPa. Our results allow the direct determination of dislocation nucleation and transport that constitute the underlying defect kinetics of incipient plasticity. Large-scale molecular dynamics simulations show good agreement with the experiment and provide an atomic-level description of the dislocation-mediated plasticity.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV’s complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein’s post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Visualizing moiré ferroelectricity via plasmons and nano-photocurrent in graphene/twisted-WSe2 structures

Abstract Ferroelectricity, a spontaneous and reversible electric polarization, is found in certain classes of van der Waals (vdW) materials. The discovery of ferroelectricity in twisted vdW layers provides new opportunities to engineer spatially dependent electric and optical properties associated with the configuration of moiré superlattice domains and the network of domain walls. Here, we employ near-field infrared nano-imaging and nano-photocurrent measurements to study ferroelectricity in minimally twisted WSe 2 . The ferroelectric domains are visualized through the imaging of the plasmonic response in a graphene monolayer adjacent to the moiré WSe 2 bilayers. Specifically, we find that the ferroelectric polarization in moiré domains is imprinted on the plasmonic response of the graphene. Complementary nano-photocurrent measurements demonstrate that the optoelectronic properties of graphene are also modulated by the proximal ferroelectric domains. Our approach represents an alternative strategy for studying moiré ferroelectricity at native length scales and opens promising prospects for (opto)electronic devices.

42 ENGINEERING↗
DOE OSTI2020

Seeing is believing: visualization of antiferromagnetic domains

Abstract Understanding and utilizing novel antiferromagnetic (AFM) materials has been recently one of the central issues in condensed matter physics, as well as in materials science and engineering. The relevant contemporary topics include multiferroicity, topological magnetism and AFM spintronics. The ability to image magnetic domains in AFM materials is of key importance for the success of these exciting fields. While imaging techniques of magnetic domains on the surfaces of ferro-(ferri)magnetic materials with, for example, magneto-optical Kerr microscopy and magnetic force microscopy have been available for a number of decades, AFM domain imaging is a relatively new development. We review various experimental techniques utilizing scanning, optical, and synchrotron X-ray probes to visualize AFM domains and domain walls, and to unveil their physical properties. We also discuss the existing challenges and opportunities in these techniques, especially with further increase of spatial and temporal resolution.

36 MATERIALS SCIENCE↗