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.

SourceResearch connectionFrom yearThrough year

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

At least 289 records · Page 16

All sources NASA NTRS DOE OSTI

DOE OSTI2020

Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter

Superresolution fluorescence microscopy and cryogenic electron tomography (CET) are powerful imaging methods for exploring the subcellular organization of biomolecules. Superresolution fluorescence microscopy based on covalent labeling highlights specific proteins and has sufficient sensitivity to observe single fluorescent molecules, but the reconstructions lack detailed cellular context. CET has molecular-scale resolution but lacks specific and nonperturbative intracellular labeling techniques. Here, we describe an imaging scheme that correlates cryogenic single-molecule fluorescence localizations with CET reconstructions. Our approach achieves single-molecule localizations with an average lateral precision of 9 nm, and a relative registration error between the set of localizations and CET reconstruction of ∼30 nm. We illustrate the workflow by annotating the positions of three proteins in the bacterium Caulobacter crescentus : McpA, PopZ, and SpmX. McpA, which forms a part of the chemoreceptor array, acts as a validation structure by being visible under both imaging modalities. In contrast, PopZ and SpmX cannot be directly identified in CET. While not directly discernable, PopZ fills a region at the cell poles that is devoid of electron-dense ribosomes. We annotate the position of PopZ with single-molecule localizations and confirm its position within the ribosome excluded region. We further use the locations of PopZ to provide context for localizations of SpmX, a low-copy integral membrane protein sequestered by PopZ as part of a signaling pathway that leads to an asymmetric cell division. Our correlative approach reveals that SpmX localizes along one side of the cell pole and its extent closely matches that of the PopZ region.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Ultrafast nano-imaging and nano-spectroscopy

Ultrafast pump–probe nano-imaging combines scanning probe-based optical near-field microscopy with ultrafast spectroscopy to enable imaging with deep sub-wavelength spatial resolution, femtosecond temporal resolution and simultaneous spectral resolution. Ultrafast nano-imaging has gained increased attention for its ability to provide far-from-equilibrium excitation and excited-state contrast. With coherent and nonlinear probing, coupled electron, spin and lattice dynamics on elementary timescale and length scale can be resolved. Through nano-movies, ultrafast nano-imaging visualizes correlated quantum dynamics underlying the properties of solid-state materials, semiconductors, molecular electronic, photonic, photovoltaic and other functional materials. With nanometre spatial resolution, this method probes elementary dynamic processes across multiple length scales that are otherwise obscured in conventional ultrafast spectroscopy in which heterogeneities are spatially averaged. Furthermore, this Primer describes the theoretical background and experimental implementation of ultrafast nano-imaging; signal interpretation and modelling; representative examples and a perspective for the future development of the field.

Microscopy↗

DOE OSTI2024

Chemical Insights into the Molecular Composition of Organic Aerosols in the Urban Region of Houston, Texas

Molecular functional groups, such as organosulfates (CHOS) and organonitrates (CHNO) are important tracers for field observations of secondary organic aerosols (SOA). While CHOS and CHNO are prevalent in the atmosphere, there is a lack of knowledge regarding daily and day- and night-time variations in these species in the urban atmosphere. Meteorological factors such as wind speed/direction, relative humidity (RH), and temperature can influence the formation of CHOS/CHNO. To investigate these trends, we utilized multimodal chemical imaging and advanced high resolution mass spectrometry techniques to acquire particle speciation and molecular formulas (MFs) associated with day and night sampling periods. Back trajectory analyses revealed the oceanic influence of southern wind airmasses in later June sampling periods with organic fractions <10%. Conversely, northern winds in early June sampling periods contributed to the episodic emergence of extremely low volatile organics (ELVOCs) and organic factions up to 41%. The observed unique MFs to June 3 (223 MFs) and to June 4 (144 MFs) were largely found to be of biogenic rather than anthropogenic origin. Finally, our findings reveal episodic prevalence and temporal distribution of SOA constituents across the urban region of Houston, Texas.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

AFM Slip Length Measurements for Water at Selected Phyllosilicate Surfaces

Most reported slip length measurements have been made at the surfaces of synthetic materials and modified synthetic materials. In contrast, few slip length measurements at the surface of unmodified natural mineral surfaces have been reported. In this regard, flow at the silica face surfaces of the phyllosilicate minerals, talc and mica, was considered. A slip boundary condition was expected at the nonpolar hydrophobic silica surface of talc leading to enhanced flow, and a no-slip boundary condition was expected at the hydrophilic silica surface of mica. Atomic force microscopy (AFM) slip length measurements were made at the talc and mica surfaces. The slip length results for the hydrophobic silica surface of talc were contrasted to the results for the hydrophilic silica surface of mica (no-slip flow). The results are discussed based on molecular dynamics simulations (MDS), as reported in the literature, and AFM images of surface nanobubbles. For nonpolar hydrophobic surfaces (such as talc), it is doubtful that the MDS interfacial water structure and the water exclusion zone (3.2 Å) account for the AFM slip flow with slip lengths as great as 95 nm. Rather, a better explanation for the AFM slip flow condition is based on reduced interfacial viscosity due to the presence of dissolved gas and the accommodation of pancake nanobubbles at the talc surface having a height dimension of magnitude similar to the slip length.

42 ENGINEERING↗

DOE OSTI2023

Unsupervised machine learning discovery of structural units and transformation pathways from imaging data

We show that unsupervised machine learning can be used to learn chemical transformation pathways from observational Scanning Transmission Electron Microscopy (STEM) data. To enable this analysis, we assumed the existence of atoms, a discreteness of atomic classes, and the presence of an explicit relationship between the observed STEM contrast and the presence of atomic units. With only these postulates, we developed a machine learning method leveraging a rotationally invariant variational autoencoder (VAE) that can identify the existing molecular fragments observed within a material. The approach encodes the information contained in STEM image sequences using a small number of latent variables, allowing the exploration of chemical transformation pathways by tracing the evolution of atoms in the latent space of the system. The results suggest that atomically resolved STEM data can be used to derive fundamental physical and chemical mechanisms involved, by providing encodings of the observed structures that act as bottom-up equivalents of structural order parameters. The approach also demonstrates the potential of variational (i.e., Bayesian) methods in the physical sciences and will stimulate the development of more sophisticated ways to encode physical constraints in the encoder–decoder architectures and generative physical laws and causal relationships in the latent space of VAEs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Super-resolution and segmentation deep learning for breast cancer histopathology image analysis

Traditionally, a high-performance microscope with a large numerical aperture is required to acquire high-resolution images. However, the images’ size is typically tremendous. Therefore, they are not conveniently managed and transferred across a computer network or stored in a limited computer storage system. As a result, image compression is commonly used to reduce image size resulting in poor image resolution. Here, we demonstrate custom convolution neural networks (CNNs) for both super-resolution image enhancement from low-resolution images and characterization of both cells and nuclei from hematoxylin and eosin (H&E) stained breast cancer histopathological images by using a combination of generator and discriminator networks so-called super-resolution generative adversarial network-based on aggregated residual transformation (SRGAN-ResNeXt) to facilitate cancer diagnosis in low resource settings. The results provide high enhancement in image quality where the peak signal-to-noise ratio and structural similarity of our network results are over 30 dB and 0.93, respectively. The derived performance is superior to the results obtained from both the bicubic interpolation and the well-known SRGAN deep-learning methods. In addition, another custom CNN is used to perform image segmentation from the generated high-resolution breast cancer images derived with our model with an average Intersection over Union of 0.869 and an average dice similarity coefficient of 0.893 for the H&E image segmentation results. Finally, we propose the jointly trained SRGAN-ResNeXt and Inception U-net Models, which applied the weights from the individually trained SRGAN-ResNeXt and inception U-net models as the pre-trained weights for transfer learning. The jointly trained model’s results are progressively improved and promising. We anticipate these custom CNNs can help resolve the inaccessibility of advanced microscopes or whole slide imaging (WSI) systems to acquire high-resolution images from low-performance microscopes located in remote-constraint settings.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Single-Molecule Tracking Measurements Reveal the Detailed Mechanisms of Molecular Diffusion in Solvent Mixtures under Nanoconfinement

Understanding mass transport mechanisms in nanopores is important for developing advanced materials for chemical separations, chemical sensing, and energy storage. This paper reports a novel imaging platform that is employed for the first time to investigate the detailed diffusion dynamics of single rhodamine B (RhB) dye molecules confined within solution-filled cylindrical anodic aluminum oxide (AAO) nanopores. The imaging platform relies on illumination of horizontally-oriented AAO nanopores in a highly inclined and laminated optical (HILO) light sheet microscopy geometry. The method was used to investigate the translational and orientational dynamics of single rhodamine B (RhB) molecules within horizontally-oriented 5- and 10-nm diameter AAO nanopores filled with water–ethanol mixtures. The established platform enabled the observation of one-dimensional motion along the pore axis involving occasional short- or long-term immobilization at the single-molecule level. Analysis of cumulative squared-displacement distributions revealed fast (5 – 30 µm²/s), intermediate (1 – 5 µm²/s), and slow (< 1 µm²/s) diffusion components. From the effects of mixture composition and pore size on the contributions of these three components, we inferred that the fast, intermediate, and slow components could be assigned to desorption-mediated hopping, crawling, and wiggling motions, respectively. The platform based on the horizontally-oriented AAO nanopores also permitted single-molecule emission polarization measurements that revealed the negligible steric confinement of individual diffusing RhB molecules within the AAO nanopores. The imaging platform based on AAO membranes and HILO microscopy provided a unique means to investigate how solvation-mediated surface interactions and nanoconfinement govern molecular transport in nanoporous environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Molecular-Level Insights into the NMR Relaxivity of Gadobutrol Using Quantum and Classical Molecular Simulations

MRI is an indispensable diagnostic tool in modern medicine; however, understanding the molecular-level processes governing NMR relaxation of water in the presence of MRI contrast agents remains a challenge, hindering the molecular-guided development of more effective contrast agents. By using quantum-based polarizable force fields, the first-of-its-kind molecular dynamics (MD) simulations of Gadobutrol are reported where the 1 H NMR longitudinal relaxivity r 1 of the aqueous phase is determined without any adjustable parameters. The MD simulations of r 1 dispersion (i.e., frequency dependence) show good agreement with measurements at frequencies of interest in clinical MRI. Importantly, the simulations reveal key insights into the molecular level processes leading to r 1 dispersion by decomposing the NMR dipole–dipole autocorrelation function G(t) into a discrete set of molecular modes, analogous to the eigenmodes of a quantum harmonic oscillator. The molecular modes reveal important aspects of the underlying mechanisms governing r 1 , such as its multiexponential nature and the importance of the second eigenmodal decay. By simply analyzing the MD trajectories on a parameter-free approach, the Gadobutrol simulations show that the outer-shell water contributes ∼50% of the total relaxivity r 1 compared to the inner-shell water, in contrast to simulations of (nonchelated) gadolinium-aqua where the outer shell contributes only ∼15% of r 1 . The deviation between simulations and measurements of r 1 below clinical MRI frequencies is used to determine the low-frequency electron-spin relaxation time for Gadobutrol, in good agreement with independent studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Solvent–Solvent Correlations across Graphene: The Effect of Image Charges

Wetting experiments show pure graphene to be weakly hydrophilic, but its contact angle (CA) also reflects the character of the supporting material. Measurements and Molecular Dynamics simulations on suspended and supported graphene often reveal a CA reduction due to the presence of the supporting substrate. A similar reduction is consistently observed when graphene is wetted from both sides. The effect has been attributed to transparency to molecular interactions across the graphene sheet, however, the possibility of substrate-induced graphene polarization has also been considered. Computer simulations of CA on graphene have so far been determined by ignoring the material’s conducting properties. We improve the graphene model by incorporating its conductivity according to the Constant Applied Potential Molecular Dynamics. Using this method, we compare the wettabilities of suspended graphene and graphene supported by water by measuring the CA of cylindrical water drops on the sheets. The inclusion of graphene conductivity and concomitant polarization effects lead to a lower CA on suspended graphene but the CA reduction is significantly bigger when the sheets are also wetted from the opposite side. The stronger adhesion is accompanied by a profound change in the correlations among water molecules across the sheet. While partial charges on water molecules interacting across an insulator sheet attract charges of the opposite sign, apparent attraction among like charges is manifested across the conducting graphene. The change is associated with graphene polarization, as the image charges inside the conductor attract equally signed partial charges of water molecules on both sides of the sheet. Additionally, by using a non-polar liquid (diiodomethane), we affirm a detectable wetting translucency when liquid-liquid forces are dominated by dispersive interactions. Furthermore, our findings are important for predictive modeling toward a variety of applications including sensors, fuel cell membranes, water filtration, and graphene-based electrode materials in high-performance supercapacitors.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2023

Magnetic imaging of topological phases of matter (Final Report)

This project presents a detailed understanding of the local electronic transport in two different types of conductors. The experimental tools are a combination of local magnetic probes and electronic transport measurements. The first set of samples were superconducting microstructures that exhibited unusual transport behavior. Magnetic imaging revealed the presence of a strain field in the microstructures, which spatially modulated the superconducting properties. This strain field can be controlled through a variety of design parameters opening opportunities for a broad range of quantum materials including topological phases of matter. The second set of samples was fabricated from Cr-doped (Bi,Sb) 2 Te 3 heterostructures that exhibited the quantum anomalous Hall effect (QAHE). Magnetic imaging visualized the current flow in these devices, while simultaneous transport measurements verified that the devices exhibit the QAHE. Surprisingly, the current flowed in the interior of the sample even when exhibiting a high level of quantization.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Super-resolution imaging reveals resistance to mass transfer in functionalized stationary phases

Chemical separations are costly in terms of energy, time, and money. Separation methods are optimized with inefficient trial-and-error approaches that lack insight into the molecular dynamics that lead to the success or failure of a separation and, hence, ways to improve the process. We perform super-resolution imaging of fluorescent analytes in five different commercial liquid chromatography materials. Unexpectedly, we observe that chemical functionalization can block more than 50% of the material’s porous interior, rendering it inaccessible to small-molecule analytes. Only in situ imaging unveils the inaccessibility when compared to the industry-accepted ex situ characterization methods. Selectively removing some of the functionalization with solvent restores pore access without substantially altering the single-molecule kinetics that underlie the separation and agree with bulk chromatography measurements. Our molecular results determine that commercial “fully porous” stationary phases are over-functionalized and provide an alternative avenue to characterize and direct separation material design from the bottom-up.

Science & Technology - Other Topics↗

DOE OSTI2022

Trace Impurities Identified as Forensic Signatures in CMX-5 Fuel Pellets Using X-ray Spectroscopic Techniques

We report that small-particle analysis is a highly promising emerging forensic tool for analysis of interdicted special nuclear materials. Integration of microstructural, morphological, compositional, and molecular impurity signatures could provide significant advancements in forensic capabilities. We have applied rapid, high-sensitivity, hard X-ray synchrotron chemical imaging to analyze impurity signatures in two differently fabricated fuel pellets from the 5th Collaborative Materials Exercise (CMX5) of the IAEA Nuclear Forensics International Working Group. The spatial distributions, chemical compositions, and morphological and molecular characteristics of impurities were evaluated using X-ray absorption near-edge structure (XANES) and X-ray fluorescence chemical imaging to discover principal impurities, their granularity, particle sizes, modes of occurrence (distinct grains vs incorporation in the UO 2 lattice), and sources and mechanisms of incorporation. Differences in UO 2+x stoichiometry were detected at the microscale in nominally identical UO 2 ceramics (CMX5-A and CMX5-B), implying the presence of multiple UO 2 host phases with characteristic microstructures and feedstock compositions. Al, Fe, Ni, W, and Zr impurities and integrated impurity signature analysis identified distinctly different pellet synthesis and processing methods. For example, two different Al, W, and Zr populations in the CMX5-B sample indicated a more complex processing history than the CMX5-A sample. K-edge XANES measurements reveal both metallic and oxide forms of Fe and Ni but with different proportions between each sample. Altogether, these observations suggest multiple sources of impurities, including fabrication (e.g., force-sieving) and feedstock (mineral oxides). This study demonstrates the potential of synchrotron techniques to integrate different signatures across length scales (angstrom to micrometer) to detect and differentiate between contrasting UO 2 fuel fabrication techniques.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. Here we describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Lattice Symmetry-Guided Charge Transport in 2D Supramolecular Polymers Promotes Triplet Formation

Singlet-to-triplet intersystem crossing (ISC) in organic molecules is intimately connected with their geometries: by modifying the molecular shape, symmetry selection rules pertaining to spin-orbit coupling can be partially relieved, leading to extra matrix elements for increased ISC. As an analog to this molecular design concept, the study finds that the lattice symmetry of supramolecular polymers also defines their triplet formation efficiencies. A supramolecular polymer self-assembled from weakly interacting molecules is considered. Its 2D oblique unit cell effectively renders it as a coplanar array of 1D molecular columns weakly bound to each other. Using momentum-resolved photoluminescence imaging in combination with Monte Carlo simulations, the study found that photogenerated charge carriers in the supramolecular polymer predominantly recombine as spin-uncorrelated carrier pairs through inter-column charge transfer states. This lattice-defined recombination pathway leads to a substantial triplet formation efficiency (≈60%) in the supramolecular polymer. These findings suggest that lattice symmetry of micro-/macroscopic structures relying on intermolecular interactions can be strategized for controlled triplet formation.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Atomistic Mechanics of Torn Back Folded Edges of Triangular Voids in Monolayer WS 2

Triangular nanovoids in 2D materials transition metal dichalcogenides have vertex points that cause stress concentration and lead to sharp crack propagation and failure. Here, the atomistic mechanics of back folding around triangular nanovoids in monolayer WS 2 sheets is examined. Combining atomic-resolution images from annular dark-field scanning transmission electron microscopy with reactive molecular modelling, it is revealed that the folding edge formation has statistical preferences under geometric conditions based on the orientation mismatch. It is further investigated how loading directions and strong interlayer friction, interplay with WS 2 lattice's crack preference, govern the deformation and fracture pattern around folding edges. Finally, these results provide fundamental insights into the combination of fracture and folding in flexible monolayer crystals and the resultant Moiré lattices.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Understanding the local structure of disordered carbons from cellulose and lignin

An electron microscopy investigation was performed to understand the relationship between the microstructure and properties of carbonized cellulose and lignin (softwood kraft lignin) relative to the structure of the original biomass components. Structure details at micro- and molecular levels were investigated by scanning transmission electron microscopy. Atomic-resolution images revealed the presence of random disordered carbon in carbonized cellulose (C-CNC) and of large domains of well-ordered carbon with graphite sheet structure in carbonized lignin (C-Lignin). These structural differences explain why C-CNC exhibits higher surface area and porosity than C-Lignin. The presence of certain well-ordered carbon in carbonized lignin indicates some of the carbon in lignin are graphitized with heat treatment temperature up to 950 °C. This result is encouraging for future endeavors of attaining acceptable modulus of carbon fiber from lignin given suitable modifications to the chemistry and structure of lignin. The results of this research contribute to an improved understanding of the carbonization mechanism of the key cellulose and lignin components of biomass materials.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Strain-Induced asymmetry and on-site dynamics of silicon defects in graphene

In the last decade, the atomically-focused electron beams utilized in scanning transmission electron microscopes (STEMs) have been shown to induce a broad set of local structural transformations in materials, opening pathways for directing material synthesis and modification atom-by-atom. The mechanisms underlying these transformations remain largely unknown, due to the intractability of modeling the myriad of reaction pathways that can be accessed through high-energy electron scattering. The information on materials’ structure and dynamics that can be extracted from STEM images is similarly left underexplored. Here, we report the observation of anomalous on-site dynamics of individual silicon impurity atoms in graphene during STEM imaging. Density functional theory-based structural optimizations of anisotropically-strained molecular nanographenes reveal two distinct (but nearly degenerate) stable structures for four-fold coordinated silicon impurities, where interconversion between the two structures manifests slight changes of the silicon position within the lattice site. Implications for defect-based strain engineering in graphene are discussed.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Spatiotemporal characterization of cerium monoxide in laser ablation plasmas using spectrally-resolved fast-gated imaging

The impact of oxidation chemistry on the emission characteristics and spatial structure of laser-produced Ce metal plasmas was investigated using laser-induced breakdown spectroscopy (LIBS) and time-resolved fast-gated imaging employing narrowband optical filters. Images of the plasma emission show that CeO coexists with atomic species in the periphery and vortex ring of the plasma plume. Image processing was also applied to combine independent monochromatic images of the plasma emission into a single merged image, culminating in a timelapse on the spatiotemporal evolution of atomic and molecular species within the plasma plume. The formation of CeO species was observed to proceed faster for plasmas generated in atmospheres containing larger concentrations of oxygen based on ratios of CeO-to-atomic emission intensities. Furthermore, these same ratios were shown to plateau and decrease at later times (≥25 μs), potentially indicating the depletion of CeO number densities in the plasma as the monoxide undergoes reactions to form higher polyatomic oxides. Altogether, these results provide fundamental insights into the chemical dynamics and intermixing between plasma-gas species in laser ablation cerium plasmas, advancing our understanding on optical signatures of nuclear-relevant materials to enable in-field measurement capabilities.

47 OTHER INSTRUMENTATION↗