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DOE OSTI2023

Multimodal Few-Shot Segmentation of Electron Micrographs

Scanning transmission electron microscopy (STEM) is one of the most used methods of analyzing the chemistry and composition of materials. By analyzing microstructures, these microscopes can help scientists better understand the molecular underpinnings of microelectronics, batteries, and more. However, STEM data can be difficult to interpret, so recent developments have been made in applications of machine learning to analyze these images. The PNNL-developed pyCHIP Classifier has achieved results in segmenting STEM these images via few-shot learning, a method which requires little data and human input, perfect for quickly analysis. In my internship I (Eli Meyers) investigated a multimodal improvement of this classifier by incorporating energy dispersive x-ray spectroscopy (EDS) data into the classification process for a more accurate segmentation. Furthermore, I encoded the spectral data by training a mass spectrometry encoder on the EDS data to extract a more meaningful representation of the data.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Chemical abrasion: the mechanics of zircon dissolution

Chemical abrasion is a technique that combines thermal annealing and partial dissolution in hydrofluoric acid (HF) to selectively remove radiation-damaged portions of zircon crystals prior to U–Pb isotopic analysis, and it is applied ubiquitously to zircon prior to U–Pb isotope dilution thermal ionization mass spectrometry (ID-TIMS). The mechanics of zircon dissolution in HF and the impact of different leaching conditions on the zircon structure, however, are poorly resolved. We present a microstructural investigation that integrates microscale X-ray computed tomography (µCT), scanning electron microscopy, and Raman spectroscopy to evaluate zircon dissolution in HF. We show that µCT is an effective tool for imaging metamictization and complex dissolution networks in three dimensions. Acid frequently reaches crystal interiors via fractures spatially associated with radiation damage zoning and inclusions to dissolve soluble high-U zones, some inclusions, and material around fractures, leaving behind a more crystalline zircon residue. Other acid paths to crystal cores include the dissolution of surface-reaching inclusions and the percolation of acid across zones with high defect densities. In highly crystalline samples dissolution is crystallographically controlled with dissolution proceeding almost exclusively along the c axis. Increasing the leaching temperature from 180 to 210 °C results in deeper etching textures, wider acid paths, more complex internal dissolution networks, and greater volume losses. How a grain dissolves strongly depends on its initial radiation damage content and defect distribution as well as the size and position of inclusions. As such, the effectiveness of any chemical abrasion protocol for ID-TIMS U–Pb geochronology is likely sample-dependent. We also briefly discuss the implications of our findings for deep-time (U-Th)/He thermochronology.

58 GEOSCIENCES↗

NASA NTRS1995

Transmission electron microscope studies of extraterrestrial materials

Transmission Electron Microscopy, X-Ray spectrometry and electron-energy-loss spectroscopy are used to analyse carbon in interplanetary dust particles. Optical micrographs are shown depicting cross sections of the dust particles embedded in sulphur. Selected-area electron diffraction patterns are shown. Transmission Electron Microscope specimens of lunar soil were prepared using two methods: ion-milling and ultramicrotomy. A combination of high resolution TEM imaging and electron diffraction is used to characterize the opaque assemblages. The opaque assemblages analyzed in this study are dominated by ilmenite with lesser rutile and spinel exsolutions, and traces of Fe metal.

Keller, Lindsay P.↗

NASA NTRS2023

Direct Analyses of Aqueous Fluids from C-Class Asteroid 162173 Ryugu

Imaging using X-ray absorption contrast by synchrotron nano-computed tomography (47.4 nm/voxel, 7keV) of a Ryugu pyrrhotite crystal revealed probable fluid inclusions. The inclusions were completely encapsuled in pyrrhotite, suggesting the fluids were trapped in the early stages of crystal growth, and filled with low-Z material. We performed Time-of Flight-Secondary Ion Mass Spectrometry (TOF-SIMS) depth profiling and high-resolution mapping at -120°C to exposure and measure the composition of the trapped fluids in a frozen state. These measurements revealed that the ancient, trapped fluids on Ryugu’s parent asteroid were saline aqueous solutions containing H2O, CO2, sulfur species, and nitrogen- and chlorine-bearing organic compounds identified by representative secondary ion species including O(-), OH(-), CO(-), S(-), Cl(-), C2(-), C2H(-), and CN(-). The inferred presence of CO2 indicates formation of the sulfides, and by implication the Ryugu parent body, beyond the H2O and CO2 snow lines of the early solar system, i.e. > 3-4 au from the Sun.

M Zolensky↗

DOE OSTI2023

Revealing the Bacterial Quorum-Sensing Effect on the Biofilm Formation of Diatom Cylindrotheca sp. Using Multimodal Imaging

Diatoms contribute to carbon fixation in the oceans by photosynthesis and always form biofouling organized by extracellular polymeric substances (EPS) in the marine environment. Bacteria-produced quorum-sensing signal molecules N-acyl homoserine lactones (AHLs) were found to play an important role in the development of Cylindrotheca sp. in previous studies, but the EPS composition change was unclear. This study used the technology of alcian blue staining and scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) to directly observe the biofilm formation process. The results showed that AHLs promote the growth rates of diatoms and the EPS secretion of biofilm components. AHLs facilitated the diatom-biofilm formation by a forming process dependent on the length of carbon chains. AHLs increased the biofilm thickness and the fluorescence intensity and then altered the three-dimensional (3D) structures of the diatom-biofilm. In addition, the enhanced EPS content in the diatom-biofilm testified that AHLs aided biofilm formation. This study provides a collection of new experimental evidence of the interaction between bacteria and microalgae in fouling biofilms.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2010

NASA Tech Briefs, November 2010

Topics covered include: Portable Handheld Optical Window Inspection Device; Salience Assignment for Multiple-Instance Data and Its Application to Crop Yield Prediction; Speech Acquisition and Automatic Speech Recognition for Integrated Spacesuit Audio Systems ; Predicting Long-Range Traversability from Short-Range Stereo-Derived Geometry; Browser-Based Application for Telemetry Monitoring of Robotic Assets; Miniature Low-Noise G-Band I-Q Receiver; Methods of Using a Magnetic Field Response Sensor Within Closed, Electrically Conductive Containers; Differential Resonant Ring YIG Tuned Oscillator; Microfabricated Segmented-Involute-Foil Regenerator for Stirling Engines; Reducing Seal Adhesion in Low Impact Docking Systems; Optimal Flow Control Design; Corrosion-Resistant Container for Molten-Material Processing; Reusable Hot-Wire Cable Cutter; Deployment of a Curved Truss; High-Volume Airborne Fluids Handling Technologies to Fight Wildfires; Modeling of Alkane Oxidation Using Constituents and Species; Fabrication of Lanthanum Telluride 14-1-11 Zintl High-Temperature Thermoelectric Couple; A Computer Model for Analyzing Volatile Removal Assembly; Analysis of Nozzle Jet Plume Effects on Sonic Boom Signature; Optical Sidebands Multiplier; Single Spatial-Mode Room-Temperature-Operated 3.0 to 3.4 micrometer Diode Lasers; Self-Nulling Beam Combiner Using No External Phase Inverter; Portable Dew Point Mass Spectrometry System for Real-Time Gas and Moisture Analysis; Maximum Likelihood Time-of-Arrival Estimation of Optical Pulses via Photon-Counting Photodetectors; Handheld White Light Interferometer for Measuring Defect Depth in Windows; Decomposition Algorithm for Global Reachability on a Time-Varying Graph; Autonomous GN and C for Spacecraft Exploration of Comets and Asteroids; Efficient Web Services Policy Combination; Using CTX Image Features to Predict HiRISE-Equivalent Rock Density; Isolation of the Paenibacillus phoenicis, a Spore-Forming Bacterium; Monolithically Integrated, Mechanically Resilient Carbon-Based Probes for Scanning Probe Microscopy; Cell Radiation Experiment System; Process to Produce Iron Nanoparticle Lunar Dust Simulant Composite; Inversion Method for Early Detection of ARES-1 Case Breach Failure; Use of ILTV Control Laws for LaNCETS Flight Research;and Evaluating Descent and Ascent Trajectories Near Non-Spherical Bodies.

Source record↗

NASA NTRS2016

Overview of LBTI: A Multipurpose Facility for High Spatial Resolution Observations

The Large Binocular Telescope Interferometer (LBTI) is a high spatial resolution instrument developed for coherent imaging and nulling interferometry using the 14.4 m baseline of the 2x8.4 m LBT. The unique telescope design, comprising of the dual apertures on a common elevation-azimuth mount, enables a broad use of observing modes. The full system is comprised of dual adaptive optics systems, a near-infrared phasing camera, a 1-5 micrometer camera (called LMIRCam), and an 8-13 micrometer camera (called NOMIC). The key program for LBTI is the Hunt for Observable Signatures of Terrestrial planetary Systems (HOSTS), a survey using nulling interferometry to constrain the typical brightness from exozodiacal dust around nearby stars. Additional observations focus on the detection and characterization of giant planets in the thermal infrared, high spatial resolution imaging of complex scenes such as Jupiter's moon, Io, planets forming in transition disks, and the structure of active Galactic Nuclei (AGN). Several instrumental upgrades are currently underway to improve and expand the capabilities of LBTI. These include: Improving the performance and limiting magnitude of the parallel adaptive optics systems; quadrupling the field of view of LMIRcam (increasing to 20"x20"); adding an integral field spectrometry mode; and implementing a new algorithm for path length correction that accounts for dispersion due to atmospheric water vapor. We present the current architecture and performance of LBTI, as well as an overview of the upgrades.

The Large Binocular Telescope Interferometer (LBTI↗

NASA NTRS2018

Investigating Variations in Water Abundances in Lunar Felsite Clasts Using Coordinated Field-Emission STEM and NanoSIMS Analyses

As representatives of petrochemically-evolved igneous rocks on the Moon, the granitic felsite clasts in lunar breccias have come under renewed focus as part of new efforts to use feldspars for assessing the inventory of lunar water and other volatiles. Previous petrologic studies of these clasts were tilted towards finding those assemblages and relationships most likely to be direct products of magmatic processes. In support of our on-going NanoSIMS (Nanoscale Secondary Ion Mass Spectrometry) measurements of trace water contents in the feldspars in these clasts, we are using coordinated analytical SEM (Scanning Electron Microscopy), electron probe microanalyzer (EPMA) and analytical field emission scanning transmission electron microscopy (FE-STEM) techniques to re-evaluate the full diversity of processes under which the feldspar-bearing assemblages in these clasts formed. Here we report a comparison of FE-STEM imaging and microanalysis results obtained on focused ion beam (FIB) sections extracted from felsite (alkali feldspar plus SiO2 plus or minus plagioclase) clasts in lunar breccias 15405 and 12013. The feldspars in these clasts have water contents which, although relatively low (7-18 ppm) by terrestrial standards, still show values significantly higher than measurements (approximately 0.5 ppm) of nominally anhydrous NanoSIMS standards.

Christoffersen, Roy↗

DOE OSTI2023

Array-Based Machine Learning for Functional Group Detection in Electron Ionization Mass Spectrometry

Mass spectrometry is a ubiquitous technique capable of complex chemical analysis. The fragmentation patterns that appear in mass spectrometry are an excellent target for artificial intelligence methods to automate and expedite the analysis of data to identify targets such as functional groups. To develop this approach, we trained models on electron ionization (a reproducible hard fragmentation technique) mass spectra so that not only the final model accuracies but also the reasoning behind model assignments could be evaluated. The convolutional neural network (CNN) models were trained on 2D images of the spectra using transfer learning of Inception V3, and the logistic regression models were trained using array-based data and Scikit Learn implementation in Python. Our training dataset consisted of 21,166 mass spectra from the United States’ National Institute of Standards and Technology (NIST) Webbook. The data was used to train models to identify functional groups, both specific (e.g., amines, esters) and generalized classifications (aromatics, oxygen-containing functional groups, and nitrogen-containing functional groups). We found that the highest final accuracies on identifying new data were observed using logistic regression rather than transfer learning on CNN models. It was also determined that the mass range most beneficial for functional group analysis is 0–100 m/z. We also found success in correctly identifying functional groups of example molecules selected from both the NIST database and experimental data. Beyond functional group analysis, we also have developed a methodology to identify impactful fragments for the accurate detection of the models’ targets. The results demonstrate a potential pathway for analyzing and screening substantial amounts of mass spectral data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Enhanced Spatial Mapping of Histone Proteoforms in Human Kidney Through MALDI-MSI by High-Field UHMR-Orbitrap Detection

Core histones including H2A, H2B, H3, and H4 are key modulators of cellular repair, transcription, and replication within eukaryotic cells, playing vital roles within the pathogenesis of disease and cellular responses to environmental stimuli. Traditional mass spectrometry (MS) based bottom-up and top-down proteomics allows for the comprehensive identification of proteins and of post-translational modification (PTM) harboring proteoforms. However, these methodologies have difficulties preserving near cellular spatial distributions because they typically require laser capture microdissection (LCM) and advanced sample preparation techniques. Herein, we coupled matrix-assisted laser desorption/ionization (MALDI) source with a Thermo Scientific Q-Exactive HF Orbitrap MS upgraded with ultra-high mass range (UHMR) boards for the first demonstration of complementary high-resolution accurate mass measurements of proteoforms directly from tissue using this benchtop mass spectrometer. The platform achieved isotopic resolution throughout the detected mass range, providing confident assignments of proteoforms with low ppm mass error and a vastly improved duty cycle over other Fourier transform mass analyzers. Proteoform mapping of core histones was demonstrated on sections of human kidney at near-cellular spatial resolution, with several key distributions of histone and other proteoforms noted within both healthy biopsy and a section from a renal cell carcinoma (RCC) containing nephrectomy. Further, the use of MALDI-MS imaging (MSI) for proteoform mapping demonstrates several steps towards high-throughput accurate identification of proteoforms and provides a new tool for mapping biomolecule distributions throughout tissue sections in extended mass ranges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Multi-modal chemical characterization of highly viscous submicrometer organic particles

Distinguishing highly viscous organic particles within complex mixtures of atmospheric aerosol and accurate descriptions of their composition, size distributions, and mixing states are challenges at the forefront of aerosol measurement science and technology. Here, we present results obtained from complementary single-particle measurement techniques employed for the in-depth characterization of highly viscous particles. In this study, we demonstrate advantages and synergy of this multi-modal particle characterization approach based on the analysis of individual viscous particles formed in the air-discharged waste produced by a common sewer pipe rehabilitation technology. Using oil immersion flow microscopy, we investigate particle size distributions and morphology of colloidal components present in field-collected aqueous waste condensates. We compare these results with corresponding measurements of viscous particles formed in drying droplets of the aerosolized discharged waste. The colloidal components and viscous particles were found to be approximately 10 µm and 0.5 µm, respectively. The aerosolized viscous particles exhibited a spherical morphology, while the colloidal particles appeared noticeably fractal, resembling fragments of a cured composite material. Chemical imaging of the viscous particles collected on substrates was performed using scanning electron microscopy and soft X-ray spectro-microscopy techniques. Through these methods, comprehensive description of these particles emerged, confirming their high solid-like viscosity, wide-ranging sizes, diverse carbon speciation with high degrees of oxygenation, and high organic volume fractions. The aerosolized viscous particles were further characterized using high-throughput single particle mass spectrometry. This technique provides real-time measurements of composition, size, and morphological metrics for large numbers of individual particles, enabling the identification of their distinct mass spectrometric signatures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Solid‐State Reaction Heterogeneity During Calcination of Lithium‐Ion Battery Cathode

Abstract During solid‐state calcination, with increasing temperature, materials undergo complex phase transitions with heterogeneous solid‐state reactions and mass transport. Precise control of the calcination chemistry is therefore crucial for synthesizing state‐of‐the‐art Ni‐rich layered oxides (LiNi 1‐x‐y Co x Mn y O 2 , NRNCM) as cathode materials for lithium‐ion batteries. Although the battery performance depends on the chemical heterogeneity during NRNCM calcination, it has not yet been elucidated. Herein, through synchrotron‐based X‐ray, mass spectrometry microscopy, and structural analyses, it is revealed that the temperature‐dependent reaction kinetics, the diffusivity of solid‐state lithium sources, and the ambient oxygen control the local chemical compositions of the reaction intermediates within a calcined particle. Additionally, it is found that the variations in the reducing power of the transition metals (i.e., Ni, Co, and Mn) determine the local structures at the nanoscale. The investigation of the reaction mechanism via imaging analysis provides valuable information for tuning the calcination chemistry and developing high‐energy/power density lithium‐ion batteries.

Chemistry↗

DOE OSTI2021

Saccharide analysis of onion outer epidermal walls

Abstract Background Epidermal cell walls have special structural and biological roles in the life of the plant. Typically they are multi-ply structures encrusted with waxes and cutin which protect the plant from dehydration and pathogen attack. These characteristics may also reduce chemical and enzymatic deconstruction of the wall for sugar analysis and conversion to biofuels. We have assessed the saccharide composition of the outer epidermal wall of onion scales with different analytical methods. This wall is a particularly useful model for cell wall imaging and mechanics. Results Epidermal walls were depolymerized by acidic methanolysis combined with 2M trifluoracetic acid hydrolysis and the resultant sugars were analyzed by high-performance anion-exchange chromatography with pulsed amperometric detection (HPAEC-PAD). Total sugar yields based on wall dry weight were low (53%). Removal of waxes with chloroform increased the sugar yields to 73% and enzymatic digestion did not improve these yields. Analysis by gas chromatography/mass spectrometry (GC/MS) of per- O -trimethylsilyl (TMS) derivatives of the sugar methyl glycosides produced by acidic methanolysis gave a high yield for galacturonic acid (GalA) but glucose (Glc) was severely reduced. In a complementary fashion, GC/MS analysis of methyl alditols produced by permethylation gave substantial yields for glucose and other neutral sugars, but GalA was severely reduced. Analysis of the walls by 13 C solid-state NMR confirmed and extended these results and revealed 15% lipid content after chloroform extraction (potentially cutin and unextractable waxes). Conclusions Although exact values vary with the analytical method, our best estimate is that polysaccharide in the outer epidermal wall of onion scales is comprised of homogalacturonan (~ 50%), cellulose (~ 20%), galactan (~ 10%), xyloglucan (~ 10%) and smaller amounts of other polysaccharides. Low yields of specific monosaccharides by some methods may be exaggerated in epidermal walls impregnated with waxes and cutin and call for cautious interpretation of the results.

09 BIOMASS FUELS↗

DOE OSTI2023

Hyperspectral Light Sheet Raman Imaging of Leaf Metabolism (Final Report)

This final technical report details the accomplishment and findings of a project that developed technology related to imaging metabolic processes in plants. The report gives technical details of the design, construction and characterization of a Raman microscope system capable of identifying chemical species using the wavelength shifts of scattered excitation light. Some of the unique aspects of the design include: use of a Bessel beam excitation source, which allow long excitation lines that are resistant to scattering in complex media such as plants; excitation at 785 nm to avoid fluorescence emission that can occur in photosynthetic organisms; and a flat optical design that makes construction and alignment significantly simpler. This project also used stable isotope labeling to look at photorespiratory flux in the leaves of three different types of plants that have different photosynthesis pathways. Gas chromatography–mass spectrometry was used to look at which metabolites and amino acids had altered oxygen, carbon and hydrogen uptake under various conditions of environmental oxygen. This generated a rich data set that is being further analyzed to understand metabolic pathways in plants. This project also used the natural fluorescence in sorghum and rice to conduct an extensive experiment across different developmental stages. Spectral differences were identified at most of the developmental stages and these can be attributed to differential pigment and pigment-protein complexes present in different relative abundances as the plant develops.

09 BIOMASS FUELS↗

DOE OSTI2022

Ultrafast disruptive probing: Simultaneously keeping track of tens of reaction pathways

Ultrafast science depends on different implementations of the well-known pump–probe method. Here, we provide a formal description of ultrafast disruptive probing, a method in which the probe pulse disrupts a transient species that may be a metastable ion or a transient state of matter. Disruptive probing has the advantage of allowing for simultaneous tracking of the yield of tens of different processes. Our presentation includes a numerical model and experimental data on multiple products resulting from the strong-field ionization of two different molecules, partially deuterated methanol and norbornene. The correlated enhancement and depletion signals between all the different fragmentation channels offer comprehensive information on photochemical reaction pathways. In combination with ion imaging and/or coincidence momentum imaging or as complementary to atom-specific probing or ultrafast diffraction methods, disruptive probing is a particularly powerful tool for the study of strong-field laser–matter interactions.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

Ion fluxes and memory effects in an Ar–O 2 modulated radiofrequency-driven atmospheric pressure plasma jet

In this work we used molecular beam mass spectrometry to characterize ion fluxes produced by a modulated radiofrequency (RF)-driven atmospheric pressure plasma jet operating in a homogeneous gas environment (Ar + 1% O 2 ). The influence of the RF modulation frequency (100 Hz to 20 kHz) on the ion fluxes was investigated by time-resolved measurements, and the lifetimes of the dominant ions, O 2 + , NO + , O − , O 2 − and O 3 − , were found to be 28 ± 2, 117 ± 8, 7.3 ± 0.4, 17 ± 1 and 23 ± 2 μs, respectively. The absolute ion densities in the near afterglow region were found to be of the order of 1011 cm−3. Significant differences in the dynamics of the positive and negative ions were found; these are explained by the presence of electrons at similar densities in the afterglow produced by electron detachment reactions from negative ions due to the large concentrations of atomic oxygen and singlet delta oxygen. Transitions in ion flux dynamics for different modulation frequencies and at the startup of the plasma were analyzed together with intensified charge coupled device images recording the plasma propagation in order to assess the dynamics of plasma plume propagation and how it is impacted by ‘memory effects’. Quantitative measurements of the ion densities enabling these memory effects are reported. The results in this paper highlight the tremendous impact of memory effects on plasma propagation and the corresponding pre-ionization.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRSDate not supplied

Update on Measurement of the Composition of Ryugu Fluid Inclusions

Imaging using X-ray absorption contrast by synchrotron nano-computed tomography of a Ryugu pyrrhotite crystal (C0002-FC012 - from the second Hayabusa2 spacecraft touch-down site) revealed probable fluid inclusions in the center of a crystal of pyrrhotite, suggesting the parent fluids were trapped in the early stages of crystal growth on Ryugu’s parent asteroid. We previously described the performance of Time-of Flight-Secondary Ion Mass Spectrometry (TOF-SIMS) depth profiling and high-resolution mapping at -120°C to expose and measure the composition of the trapped fluids in a frozen state in two Ryugu inclusions [1,2]. Here we report results from follow-on measurements of additional inclusions in the same pyrrhotite crystal, and the initial results of measurement of standards. The ultimate goal is to reveal the quantitative composition of the fluids that caused aqueous alteration, in particular the H2O:CO2 ratio, which will also facilitate cosmochemical modeling of the alteration process.

M Zolensky↗

NASA NTRS2005

Neutral Mass Spectrometry for Venus Atmosphere and Surface

The assignment is to make precise (better than 1 %) measurements of isotope ratios and accurate (5-10%) measurements of abundances of noble gas and to obtain vertical profiles of trace chemically active gases from above the clouds all the way down to the surface. Science measurement objectives are as follows: 1) Determine the composition of Venus atmosphere, including trace gas species and light stable isotopes; 2) Accurately measure noble-gas isotopic abundance in the atmosphere; 3) Provide descent, surface, and ascent meteorological data; 4) Measure zonal cloud-level winds over several Earth days; 5) Obtain near-IR descent images of the surface from 10-km altitude to the surface; 6) Accurately measure elemental abundances & mineralogy of a core from the surface; and 7) Evaluate the texture of surface materials to constrain weathering environment.

Mahaffy, Paul↗