Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “molecular imaging”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A study of real-world micrograph data quality and machine learning model robustness

Abstract Machine-learning (ML) techniques hold the potential of enabling efficient quantitative micrograph analysis, but the robustness of ML models with respect to real-world micrograph quality variations has not been carefully evaluated. We collected thousands of scanning electron microscopy (SEM) micrographs for molecular solid materials, in which image pixel intensities vary due to both the microstructure content and microscope instrument conditions. We then built ML models to predict the ultimate compressive strength (UCS) of consolidated molecular solids, by encoding micrographs with different image feature descriptors and training a random forest regressor, and by training an end-to-end deep-learning (DL) model. Results show that instrument-induced pixel intensity signals can affect ML model predictions in a consistently negative way. As a remedy, we explored intensity normalization techniques. It is seen that intensity normalization helps to improve micrograph data quality and ML model robustness, but microscope-induced intensity variations can be difficult to eliminate.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Evaluating Cryo–TEM Reconstruction Accuracy of Self–Assembled Polymer Nanostructures

Cryogenic transmission electron microscopy (cryo–TEM) combined with single particle analysis (SPA) is an emerging imaging approach for soft materials. However, the accuracy of SPA–reconstructed nanostructures, particularly those formed by synthetic polymers, remains uncertain due to potential packing heterogeneity of the nanostructures. In this study, the combination of molecular dynamics (MD) simulations and image simulations is utilized to validate the accuracy of cryo–TEM 3D reconstructions of self–assembled polypeptoid fibril nanostructures. Using CryoSPARC software, image simulations, 2D classifications, ab initio reconstructions, and homogenous refinements are performed. By comparing the results with atomic models, the recovery of molecular details is assessed, heterogeneous structures are identified, and the influence of extraction location on the reconstructions is evaluated. In conclusion, these findings confirm the fidelity of single particle analysis in accurately resolving complex structural characteristics and heterogeneous structures, exhibiting its potential as a valuable tool for detailed structural analysis of synthetic polymers and soft materials.

36 MATERIALS SCIENCE↗
NASA NTRS2026

The Evolution in Coma Molecular Composition of Comet C/2017 K2 (PanSTARRS) Across the H 2 O Sublimation Zone: ALMA Imaging of an H 2 O-Dominated Coma

We report a survey of molecular emission from cometary volatiles using the Atacama Large Millimeter/Submillimeter Array (ALMA) toward comet C/2017 K2 (PanSTARRS) carried out on UT 2022 September 21, 22, and 23 at a heliocentric distance r H 3 OH, and H 2 CO (along with continuum emission from dust) sampled molecular chemistry in C/2017 K2 at the inner edge of the H 2 O sublimation zone, the region from r H 2 O begins vigorously subliming and increasingly dominating comet activity, discerning parent from daughter or extended source species. This work presents spectrally integrated flux maps, production rates, and parent scale lengths for each molecule. CH 3 OH, CO, and HCN were produced within ~250 km of the nucleus, potentially including contributions from sublimation of icy grains. CS was consistent with production from CS 2 photolysis, and H 2 CO required production from extended sources in the coma. An ortho-to-para ratio of 2.9 ± 0.4 for H 2 CO was derived from simultaneously measured transitions of each spin species. The continuum was extended and spatially resolved, consistent with thermal emission from dust in the coma. Analysis of the continuum visibilities provided an upper limit on the nucleus diameter d <6.6 km and coma dust masses of (1.2-2.4) times10 11 kg.

Nathan X Roth↗
NASA NTRS1993

A new near-infrared imaging study of AFGL 2688

The object AFGL 2688 is a bipolar nebula surrounding a post-asymptotic giant branch star and is in transition toward becoming a planetary nebula. We present new NIR images in the I, J, H, and K bandpasses. These images reveal a wealth of structure in the nebula not previously seen. We find that the northern lobe is not smooth, but clumpy. There is evidence in the I-band image for periodic variations in mass-loss rate. In addition, we present narrowband images centered on the V = 1 - 0 S(1) line of molecular hydrogen and nearby continuum. The narrowband images reveal that broadband flux found in the equatorial region is dominated by line emission from vibrationally excited molecular hydrogen. H2 emission is also present in the lobes. Our K-band images show the equatorial emission to be in the form of a ring or torus extending around the object at a distance R about 7 x 10 exp 16 (D/1 kpc) cm. Mechanisms for exciting the equatorial H2 emission are discussed; we conclude that shocks are the only plausible source. We have analyzed the broadband images using models which assume single scattering of photons from the central star. We find that the bipolar axis is inclined to the plane of the sky by i about 5 deg. The images are best reproduced by models in which the density of scattering dust decreases fairly rapidly with increasing stellar latitude, with little or no dust near the poles. Furthermore, the optical depth is found to have very little wavelength dependence, which implies that the dust in AFGL 2688 is different from that in the interstellar medium.

Latter, William B.↗
DOE OSTI2024

An integrated atom array-nanophotonic chip platform with background-free imaging

Arrays of neutral atoms trapped in optical tweezers have emerged as a leading platform for quantum information processing and quantum simulation due to their scalability, reconfigurable connectivity, and high-fidelity operations. Individual atoms are promising candidates for quantum networking due to their capability to emit indistinguishable photons that are entangled with their internal atomic states. Integrating atom arrays with photonic interfaces would enable distributed architectures in which nodes hosting many processing qubits could be efficiently linked together via the distribution of remote entanglement. However, many atom array techniques cease to work in close proximity to photonic interfaces, with atom detection via standard fluorescence imaging presenting a major challenge due to scattering from nearby photonic devices. Here, we demonstrate an architecture that combines atom arrays with up to 64 optical tweezers and a millimeter-scale photonic chip hosting more than 100 nanophotonic cavities. We achieve high-fidelity ( ~ 99.2%), background-free imaging in close proximity to nanofabricated cavities using a multichromatic excitation and detection scheme. The atoms can be imaged while trapped a few hundred nanometers above the dielectric surface, which we verify using Stark shift measurements of the modified trapping potential. Finally, we rearrange atoms into defect-free arrays and load them simultaneously onto the same or multiple devices.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Correlative chemical and elemental nano-imaging of morphology and disorder at the nacre-prismatic region interface in Pinctada margaritifera

Abstract Understanding biomineralization relies on imaging chemically heterogeneous organic–inorganic interfaces across a hierarchy of spatial scales. Further, organic minority phases are often responsible for emergent inorganic structures from the atomic arrangement of different polymorphs, to nano- and micrometer crystal dimensions, up to meter size mollusk shells. The desired simultaneous chemical and elemental imaging to identify sparse organic moieties across a large field-of-view with nanometer spatial resolution has not yet been achieved. Here, we combine nanoscale secondary ion mass spectroscopy (NanoSIMS) with spectroscopic IR s -SNOM imaging for simultaneous chemical, molecular, and elemental nanoimaging. At the example of Pinctada margaritifera mollusk shells we identify and resolve ~ 50 nm interlamellar protein sheets periodically arranged in regular ~ 600 nm intervals. The striations typically appear ~ 15 µm from the nacre-prism boundary at the interface between disordered neonacre to mature nacre. Using the polymorph distinctive IR-vibrational carbonate resonance, the nacre and prismatic regions are consistently identified as aragonite ( $${\overline{\nu }}_{a}=860$$ ν ¯ a = 860 cm −1 ) and calcite ( $${\overline{\nu }}_{c}=880$$ ν ¯ c = 880 cm −1 ), respectively. We observe previously unreported morphological features including aragonite subdomains encapsulated in extensions of the prism-covering organic membrane and regions of irregular nacre tablet formation coincident with dispersed organics. We also identify a ~ 200 nm region in the incipient nacre region with less well-defined crystal structure and integrated organics. These results show with the identification of the interlamellar protein layer how correlative nano-IR chemical and NanoSIMS elemental imaging can help distinguish different models proposed for shell growth in particular, and how organic function may relate to inorganic structure in other biomineralized systems in general.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Single-Filament Imaging Mass Spectrometry Lipidomics in Arthrospira platensis

Elucidating intra-organismal biochemical and lipid organization in photosynthetic biological cell factories of filamentous cyanobacteria, i.e., Arthrospira platensis (Spirulina), is important to track physiological response mechanisms during growth. Little is known about the filaments' biochemical organization and cellular structure and no label-free imaging techniques exist that provide molecular mapping. We applied ultra-high resolution mass spectrometry (7T FT-ICR-MS) matrix-assisted laser desorption ionization (MALDI) imaging to immobilized Spirulina filaments to investigate the localization of lipids across distinct physiological regions. We optimized matrix selection and deposition methods with the goal of facilitating high spatial, and intra-filament, resolution using untargeted multivariate statistical spectral deconvolution across MS pixels. Our results demonstrate an improved two step application with an optimized procedure for intra-organismal lipid profiling to improve analyte sensitivity and achieve higher spatial resolution, whereby we evaluate three conventional matrices 2,5-dihydroxybenzoic acid (DHB), a 9:1 ratio of DHB:superDHB (sDHB), 1,5- diaminonaphthalene (DAN) and a 50:50 mix of DHB:sDHB and compare delineation and pixel-based elucidation of intra-filament lipidomics. We identified a total of 1,626 features that could be putatively assigned a lipid-like formula based on database query and 46 unique features, with associated lipid assignments that were significantly distinct in their intra-filament location. MALDI- imaging MS with untargeted statistical spectral deconvolution was used to visualize intra-filament lipidomics organization in Spirulina filaments. Improvements in matrix deposition, including sequential sublimation and pneumatic spraying, increased signal abundance at high spatial resolution and allowed for identification of distinct lipid composition regions. Here in this work outlines a methodology that may be used for micro-ecological untargeted molecular phenotyping.

09 BIOMASS FUELS↗
DOE OSTI2022

X-ray multiphoton-induced Coulomb explosion images complex single molecules

Following structural dynamics in real time is a fundamental goal towards a better understanding of chemical reactions. Recording snapshots of individual molecules with ultrashort exposure times is a key ingredient towards this goal, as atoms move on femtosecond (10 -15 s) timescales. For condensed-phase samples, ultrafast, atomically resolved structure determination has been demonstrated using X-ray and electron diffraction. Pioneering experiments have also started addressing gaseous samples. However, they face the problem of low target densities, low scattering cross sections and random spatial orientation of the molecules. Therefore, obtaining images of entire, isolated molecules capturing all constituents, including hydrogen atoms, remains challenging. Here we demonstrate that intense femtosecond pulses from an X-ray free-electron laser trigger rapid and complete Coulomb explosions of 2-iodopyridine and 2-iodopyrazine molecules. We obtain intriguingly clear momentum images depicting ten or eleven atoms, including all the hydrogens, and thus overcome a so-far impregnable barrier for complete Coulomb explosion imaging—its limitation on molecules consisting of three to five atoms. In combination with state-of-the-art multi-coincidence techniques and elaborate theoretical modelling, this allows tracing ultrafast hydrogen emission and obtaining information on the result of intramolecular electron rearrangement. Our work represents an important step towards imaging femtosecond chemistry via Coulomb explosion.

74 ATOMIC AND MOLECULAR PHYSICS↗
NASA NTRS2017

ALMA Mapping of Rapid Gas and Dust Variations in Comet C/2012 S1 (ISON): New Insights into the Origin of Cometary HNC

Observations of the sungrazing comet C/2012 S1 (ISON) were carried out using the Atacama Large Millimeter/submillimeter Array at a heliocentric distance of 0.58-0.54 AU (Astronomical Units) (pre-perihelion) on 2013 November 16-17. Temporally resolved measurements of the coma distributions of HNC, CH3OH, H2CO, and dust were obtained over the course of about an hour on each day. During the period UT 10:10-11:00 on November 16, the comet displayed a remarkable drop in activity, manifested as a greater than 42 percent decline in the molecular line and continuum fluxes. The H2CO observations are consistent with an abrupt, approximately 50 percent reduction in the cometary gas production rate soon after the start of our observations. On November 17, the total observed fluxes remained relatively constant during a similar period, but strong variations in the morphology of the HNC distribution were detected as a function of time, indicative of a clumpy, intermittent outflow for this species. Our observations suggest that at least part of the detected HNC originated from degradation of nitrogen-rich organic refractory material, released intermittently from confined regions of the nucleus. By contrast, the distributions of CH3OH and H2CO during the November 17 observations were relatively uniform, consistent with isotropic outflow and stable activity levels for these species. These results highlight a large degree of variability in the production of gas and dust from comet ISON during its pre-perihelion outburst, consistent with repeated disruption of the nucleus interspersed with periods of relative quiescence.

techniques: interferometric↗
DOE OSTI2021

Quantitative phase microscopy monitors subcellular dynamics in single cells exposed to nanosecond pulsed electric fields

A substantial body of literature exists to study the dynamics of single cells exposed to short duration (<1 μs), high peak power (~1 MV/m) transient electric fields. Much of this research is limited to traditional fluorescence-based microscopy techniques, which introduce exogenous agents to the culture and are only sensitive to a single molecular target. Quantitative phase imaging (QPI) is a coherent imaging modality which uses optical path length as a label-free contrast mechanism, and has proven highly effective for the study of single-cell dynamics. In this work, we introduce QPI as a useful imaging tool for the study of cells undergoing cytoskeletal remodeling after nanosecond pulsed electric field (nsPEF) exposure. In particular, we use cell swelling, dry mass and disorder strength measurements derived from QPI phase images to monitor the cellular response to nsPEFs. We hope this demonstration of QPI's utility will lead to a further adoption of the technique for the study

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Ambient Tip-Enhanced Two Photon Photoluminescence from CdSe/ZnS Quantum Dots

Nonlinear nano-optical measurements that combine ultrafast spectroscopy with tools of scanning probe microscopy are scarce. This is particularly the case when high spatial resolution on the order of a few nanometers is sought after in experiments performed under ambient laboratory conditions. In this work, we demonstrate the latter through measurements that track two-photon photoluminescence from aggregates of CdSe/ZnS quantum dots with sub-5 nm spatial resolution. We report our proof-of-principle measurements that only take advantage of a plasmonic probe (as opposed to a gap mode) pave the way for nonlinear photoluminescence-based spectral nano-imaging of realistic/heterogeneous (bio)molecular and (bio)material systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

An Activity-Based Sensing Approach to Monitor Nanomaterial-Promoted Changes in Labile Metal Pools in Living Systems

Metal-based nanoparticles are a promising class of materials for diagnosis and treatment of cancer and other diseases. However, mechanisms of action of these nanomedicines remain insufficiently understood due in large part to our limited understanding of the dynamic equilibria between solid metal nanoparticles and labile metal ions generated from these nanoparticles within complex biological milieus. Here, we apply activitybased sensing to directly identify and investigate the fate of labile copper pools with metal and oxidation state-specificity generated by anticancer copper nanomedicines. We found that treatment of cells with copper-releasing nanoparticles alter labile Cu(I)/Cu(II) ratios through an increase in labile Cu(II), while overall labile copper levels decrease. Labile copper release triggers compensatory responses in two major antioxidant pathways, glutathione (GSH) and nuclear factor erythroid 2-related factor 2 (NRF2), as well as in metal homeostasis to limit copper availability via regulation of copper export (ATP7B) and copper import (CTR1) proteins. These findings establish the value of activity-based sensing as a generalizable approach for labile metal imaging to help decipher molecular mechanisms of bioactive metal nanoparticles and guide the development of more effective nanomedicine diagnostics and therapies to target metal-dependent disease vulnerabilities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Prolonging All-Optical Molecular Electron Spin Coherence in the Tissue Transparency Window

Coherent electron spin states within paramagnetic molecules hold significant potential for microscopic quantum sensing. However, all-optical coherence measurements amenable to high spatial and temporal resolution under ambient conditions remain a significant challenge. Here we conduct room-temperature, picosecond time-resolved Faraday ellipticity/rotation (TRFE/R) measurements of the electron spin decoherence time T 2 * in [IrBr 6 ] 2- . Decoherence is strongly sensitive to solution phase viscosity, pointing to molecular tumbling as an important decoherence mechanism. Accordingly, immobilization of [IrBr 6 ] 2- molecules in thin polymer films results in an order-of-magnitude increase in coherence lifetime and significantly greater magnetic field sensitivity. Here, by tuning energies of ligand-to-metal charge transfer (LMCT) states, TRFE/R enables spin initialization and readout in the tissue transparency window, paving the way toward all-optical, ultrafast molecular electron spin coherence imaging in biological systems.

Electron paramagnetic resonance spectroscopy↗
DOE OSTI2026

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗
DOE OSTI2025

Octo-diamond crystal of nanoscale tetrahedra with interchanging chiral motifs

Despite their simplicity, tetrahedra can assemble into diverse high- and low-density structures. Here we report a low-density ‘octo-diamond’ structure formed by nanoscale solid tetrahedra with a 64-tetrahedron unit cell containing 8 cubic-diamond subcells. The formed crystal is achiral, but is composed of chiral bilayers with alternating handedness. The left- and right-handed chirality of the bilayers, combined with the plasmonic nature of the gold tetrahedra, produces chiroptical responses at the crystal surface. We uncover that the hydrophobic substrate facilitates the arrangement of tetrahedra into irregular ring-like patterns, creating a critical, uneven topography to stabilize the observed octo-diamond structure. This study reveals a potent way to affect colloidal crystallization through particle–substrate interactions, expanding the nanoparticle self-assembly toolbox.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Windowed Fourier transform and cross-correlation algorithms for molecular tagging velocimetry

In this study, simulated and experimental molecular tagging velocimetry (MTV) images have been analyzed with a technique commonly used to process grid images on surfaces, the windowed Fourier transform with local spectrum analysis (WFT-LSA). A systematic synthetic image study of the modulation transfer function (MTF) and error tendencies of the WFT-LSA was performed and compared with a PIV-style cross-correlation algorithm to see if advanced strategies such as iterative image deformation can improve analysis of gridded images with high noise levels. Testing of single-pass algorithms showed that in typical MTV images, the WFT-LSA yields significantly lower bias errors than cross-correlation (CC) at displacements greater than 1 pixel but slightly higher random error at all displacements and image conditions. Analysis of the MTF shows that CC provided better resolution of spatial fluctuations than the WFT-LSA in many combinations of grid size and interrogation window. Tests of image deformation algorithms showed that the gap in performance between CC and WFT-LSA is maintained even as both methods improve. Additionally, WFT-LSA and CC methods are applied to real MTV experiments in high-speed gas jet flows. A preliminary analysis of phosphorescence lifetime provided by acetone vapor excited at 266 nm is used for assessing the required gas speeds for making MTV application feasible. The application of WFT-LSA to real MTV images demonstrates the ability of the algorithm to handle further real-world effects that could not be considered in the synthetic image analysis, like reduced signal-to-noise ratio and non-uniform intensity of the tagging grid across the image introduced by the actual laser beam energy distribution. With experimental images, CC is more accurate with shear flows but less robust to high noise levels than WFT-LSA, as predicted by the synthetic image analysis.

42 ENGINEERING↗
DOE OSTI2024

Roadmap on nanoscale magnetic resonance imaging

Abstract The field of nanoscale magnetic resonance imaging (NanoMRI) was started 30 years ago. It was motivated by the desire to image single molecules and molecular assemblies, such as proteins and virus particles, with near-atomic spatial resolution and on a length scale of 100 nm. Over the years, the NanoMRI field has also expanded to include the goal of useful high-resolution nuclear magnetic resonance (NMR) spectroscopy of molecules under ambient conditions, including samples up to the micron-scale. The realization of these goals requires the development of spin detection techniques that are many orders of magnitude more sensitive than conventional NMR and MRI, capable of detecting and controlling nanoscale ensembles of spins. Over the years, a number of different technical approaches to NanoMRI have emerged, each possessing a distinct set of capabilities for basic and applied areas of science. The goal of this roadmap article is to report the current state of the art in NanoMRI technologies, outline the areas where they are poised to have impact, identify the challenges that lie ahead, and propose methods to meet these challenges. This roadmap also shows how developments in NanoMRI techniques can lead to breakthroughs in emerging quantum science and technology applications.

Budakian, Raffi↗