XRD and STEM Analysis of Structural Variation in Nanocrystalline Cu-Ag Thin Films
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Dorman, Kyle Rhys [Sandia National Laboratories (S↗
SEARCH · Engineering Papers
Results for “STEM”
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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Visualization of lignification in flax stem cell walls with novel click-compatible monolignol analogs
As an essential part of plant cell walls, lignin provides mechanical support for plant growth, enhances water transport, and helps to defend against pathogens. As the most abundant natural aromatic-based renewable resource on earth, its biosynthesis has always been a research focus, and it is still currently under study. In this study, the p-coumaryl alcohol analog (H ALK ) and the coniferyl alcohol analog (G ALK ) containing an alkyne group at the ortho position were synthesized and applied to lignification in vivo and in vitro. The incorporation of these novel lignin monomers was observed via fluorescence imaging. It was found that the two monolignol analogs could be incorporated in dehydrogenated polymers (DHPs) in vitro and in flax cell walls in vivo. The results showed that as the cultivation time and precursor concentration varied, the deposition of H and G-type lignin exhibited differences in deposition mode. At the subcellular scale, the deposited lignin first appears in the cell corner and the middle lamella, and then gradually appears on the cell walls. Furthermore, lignin was also found in bast fiber. It was demonstrated that these new molecules could provide high-resolution localization of lignin during polymerization.
59 BASIC BIOLOGICAL SCIENCES↗
Automated STEM Distortion Correction for Arbitrary Scan Patterns
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36 MATERIALS SCIENCE↗
MORAL JUDGEMENT IN STEM STUDENTS AND PROFESSIONALS: DEVELOPMENT AND VALIDATION OF THE GENERAL ENGINEERING ETHICS REASONING INSTRUMENT (GEERI)
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Odom, Peter Wesley [Sandia National Laboratories (↗
Data for Development of Vegetative Oil Sorghum: From Lab-to-Field
Biomass crops engineered to accumulate energy-dense triacylglycerols (TAG or ‘vegetable oils’) in their vegetative tissues have emerged as potential feedstocks to meet the growing demand for renewable diesel and sustainable aviation fuel (SAF). Unlike oil palm and oilseed crops, the current commercial sources of TAG, vegetative tissues, such as leaves and stems, only transiently accumulate TAG. In this report, we used grain (Texas430 or TX430) and sugar-accumulating ‘sweet’ (Ramada) genotypes of sorghum, a high-yielding, environmentally resilient biomass crop, to accumulate TAG in leaves and stems. We initially tested several gene combinations for a ‘push-pull-protect’ strategy. The top TAG-yielding constructs contained five oil transgenes for a sorghum WRINKLED1 transcription factor (‘push’), a Cuphea viscosissima diacylglycerol acyltransferase (DGAT; ‘pull’), a modified sesame oleosin (‘protect’) and two combinations of specialized Cuphea lysophosphatidic acid acyltransferases and medium-chain acyl-acyl carrier protein thioesterases. Though intended to generate oils with medium-chain fatty acids, engineered lines accumulated oleic acid-rich oil to amounts of up to 2.5% DW in leaves and 2.0% DW in stems in the greenhouse, 36-fold and 49-fold increases relative to wild-type (WT) plants, respectively. Under field conditions, the top-performing event accumulated TAG to amount to 5.5% DW in leaves and 3.5% DW in stems, 78-fold and 58-fold increases, respectively, relative to WT TX430. Transcriptomic and fluxomic analyses revealed potential bottlenecks for increased TAG accumulation. Overall, our studies highlight the utility of a lab-to-field pipeline coupled with systems biology studies to deliver high vegetative oil sorghum for SAF and renewable diesel production.
Biofuels↗
Structural characterization of influenza group 1 chimeric hemagglutinins as broad vaccine immunogens
Chimeric hemagglutinins (cHA) appear to be promising for the design and development of universal influenza vaccines. Influenza A group 1 cHAs, cH5/1, cH8/1, and cH11/1, comprising an H1 stem attached to either an H5, H8, or H11 globular head, have been used sequentially as vaccine immunogens in human clinical trials and induced high levels of broadly protective antibodies. Using X-ray crystallography and negative-stain electron microscopy, we determined structures of cH5/1, cH8/1, and cH11/1 HAs in their apo (unliganded) and antibody Fab-bound states. Stem-reactive antibodies 3E1 and 31.b.09 recognize their cognate epitopes in cH5/1, cH8/1, and cH11/1 HAs. However, with cH5/1, the head domains are rotated by 35 to 45° around the threefold axis of the HA trimer compared to native HA with a more splayed-open conformation at the stem base. cH11/1 with 3E1 is structurally more native-like but resembles cH5/1 with 31.b.09, whereas cH8/1 with 31.b.09 exhibited a range of closed-to-open stem configurations with some separation of head and stem domains. Furthermore, all of these group 1 cHAs effectively bound a broad head trimer interface antibody and other broad stem antibodies. Thus, the cHAs exhibit structural plasticity without compromising the stem and head trimer interface epitopes for elicitation of influenza A group 1 cross-reactive antibodies.
Science & Technology - Other Topics↗
Data for Yield from Iowa’s first commercial miscanthus fields: implications of spatial variability for productivity and sustainability beyond research plots
This dataset contains biomass yield measurements and associated vegetation index data collected from commercial Miscanthus × giganteus fields in eastern Iowa during the 2022–2023 growing seasons. The data support the analyses presented in the article: “Yield From Iowa's First Commercial Miscanthus Fields: Implications of Spatial Variability for Productivity and Sustainability Beyond Research Plots.” We collected 105 ground-truth biomass samples from four mature commercial fields (>4 years old) covering 92.81 ha. Samples were taken from 3 m² quadrats that were hand-harvested in alignment with commercial harvest timing. Stem biomass (excluding leaves) was weighed, moisture-corrected, and converted to dry-matter yield expressed in Mg DM ha⁻¹. Sampling locations were selected to capture spatial variability visible in aerial imagery and were recorded using RTK GPS. Each biomass observation was paired with vegetation indices derived from high-resolution PlanetScope satellite imagery (3 m resolution). Images were acquired throughout the growing season, and indices were calculated to evaluate their ability to predict end-of-season biomass yield. Statistical and machine learning approaches were used to identify key predictors, and a linear regression model based on end-of-July Green Normalized Difference Vegetation Index (GNDVI) was developed and evaluated. This repository includes the data used in that modeling workflow. Management practices, economic data, full imagery time series, and additional methodological details are described in the associated publication and are not included here. The dataset consists of three comma-separated value (CSV) files: 1. Combine_Groundtruth_Yield_VI_22_23.csv This file contains ground-truth biomass yield measurements and associated key vegetation index values collected during the 2022 and 2023 growing seasons. Rows: 105 observations Columns: Year — Year of observation (2022 or 2023) Field — Field location identifier Sample_number — Unique sample identifier GNDVI_End_Jul — Green Normalized Difference Vegetation Index calculated at end of July GNDVI_End_Aug — Green Normalized Difference Vegetation Index calculated at end of August NDRE_End_Aug — Normalized Difference Red Edge index calculated at end of August Biomass_Stem_Yield_MgDM/ha — Measured stem biomass yield (megagrams dry matter per hectare) 2. trainData_GNDVI.csv This file contains the subset of observations used to train the predictive relationship between July GNDVI and biomass yield. Rows: 76 observations Columns: Unnamed: 0 — Row index retained from the original data processing workflow GNDVI_End_Jul — GNDVI at end of July Stem_Yield_MgDM/ha — Observed stem biomass yield (Mg DM ha⁻¹) 3. testData_GNDVI.csv This file contains the test dataset used to evaluate model performance. Rows: 29 observations Columns: Unnamed: 0 — Row index retained from the original data processing workflow GNDVI_End_Jul — GNDVI at end of July Predicted_Yield_MgDM/ha — Model-predicted stem biomass yield (Mg DM ha⁻¹) Observed_Yield_MgDM/ha — Measured stem biomass yield (Mg DM ha⁻¹)
Potential yield, yield gap, in-field management, y↗
Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis
Bioenergy sorghum’s large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop’s resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7 th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17 th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation (WOX4), auxin transport (LAX2, PIN4), meristem activation (NGAL2), and genes involved in cell proliferation. Expression of WOX11 and WOX5, genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5, SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO, a gene involved in root cap formation, and GATA19, BBM, LBD29 and RITF1/RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.
09 BIOMASS FUELS↗
Investigation of the thermal decomposition of Pu(IV) oxalate: a transmission electron microscopy study
The degradation of the internal structure of plutonium (IV) oxalate during calcination was investigated with Transmission Electron Microscopy (TEM), electron diffraction, Electron Energy-Loss Spectroscopy (EELS), and 4D Scanning TEM (STEM). TEM lift-outs were prepared from samples that had been calcined at 300°C, 450°C, 650°C and 950°C. The resulting phase at all calcination temperatures was identified as PuO 2 with electron diffraction. The grain size range was obtained with high-resolution TEM. In addition, 4D STEM images were analyzed to provide grain size distributions. In the 300°C calcined sample, the grains were <10 nm in diameter, at 650°C, the grains ranged from 10 to 20 nm, and by 950°C, the grains were 95–175 nm across. Using the Kolmogorov-Smirnov (K-S) two sample test, it was shown that morphological measurements obtained from 4D-STEM provided statistically significant distributions to distinguish samples at the different calcination conditions. Using STEM-EELS, carbon was shown to be present in the low temperature calcined samples associated with oxalate but had formed carbon (possibly graphite) deposits in the 950°C calcined sample. This work highlights the new methods of STEM-EELS and 4D-STEM for studying the internal structure of special nuclear materials (SNM).
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Synergistic Combination of Living Ring-Opening Metathesis Polymerization and Atom Transfer Radical Polymerization to Synthesize Structurally Tailored and Engineered Macromolecular Networks
Structurally tailored and engineered macromolecular (STEM) networks are attractive materials for soft robotics, stretchable electronics, tissue engineering, and 3D printing due to their tunable properties. To date, STEM networks have been synthesized by atom transfer radical polymerization (ATRP) or the combination of reversible addition–fragmentation chain-transfer (RAFT) polymerization and ATRP. RAFT polymerization could have limited selectivity with ATRP inimer sites that can participate in radical-transfer processes. On the other hand, living ring-opening metathesis polymerization (ROMP) can produce a polymeric network with latent ATRP initiator sites in high selectivity. Herein, for the first time, we report the syntheses of STEM zero-generation (STEM-0) networks using a monomer, a cross-linker, and an ATRP/ROMP inimer via living ROMP, followed by their modification using a second monomer via ATRP to synthesize STEM first-generation (STEM-1) networks. The mechanical property and swelling capacity analyses of these networks were carried out. A change in mechanical properties and swelling capacity of these networks was observed due to their structural modification.
Absorption↗
The ABCs of phase retrieval: Connecting the acronyms of scanning transmission electron microscopy
High-resolution scanning transmission electron microscopy (S/TEM) is an indispensable tool for characterizing the structure and properties of materials down to the atomic scale. Conventional S/TEM imaging, however, is limited by the phase problem, whereby the phase of the electron exit wave is lost upon detection. Recent advances in diffractive imaging and 4D-STEM have enabled a range of phase-retrieval techniques that computationally reconstruct the missing information encoded in the phase of the transmission function. These approaches offer improved dose efficiency and enhanced sensitivity to weakly scattering signals, extending quantitative imaging to beam-sensitive materials composed of light elements. In this work, we introduce the phase problem in electron microscopy and survey the diverse landscape of phase-retrieval techniques used in the field. Despite their many acronyms and algorithmic variations, these techniques share a common physical and mathematical foundation. We present a unified framework that connects these seemingly distinct methods, from parallax imaging and tilt-corrected bright-field (tcBF-STEM), to aberration-corrected bright-field (acBF-STEM), optimum bright-field (OBF-STEM) and single-sideband (SSB) ptychography, as well as first-moment integrated center of mass techniques (iCOM) and iterative ptychographic algorithms. Based on these insights, we discuss the opportunities and practical limitations of applying these methods across different materials systems, detector designs, and microscope configurations.Graphical abstractRepresentative electron microscopy configurations used for phase retrieval and diffractive imaging in S/TEM: (a) Zernike phase-contrast transmission electron microscopy (TEM), (b) small-convergence-angle four-dimensional scanning transmission electron microscopy (4D-STEM) for nanobeam-based phase reconstruction methods, and (c) large-convergence-angle 4D-STEM for ptychographic and related diffractive imaging techniques reviewed in this work.
36 MATERIALS SCIENCE↗
Atomic resolution scanning transmission electron microscopy at liquid helium temperatures for quantum materials
Fundamental quantum phenomena in condensed matter, ranging from correlated electron systems to quantum information processors, manifest their emergent characteristics and behaviors predominantly at low temperatures. This necessitates the use of liquid helium (LHe) cooling for experimental observation. Atomic resolution scanning transmission electron microscopy combined with LHe cooling (cryo-STEM) provides a powerful characterization technique to probe local atomic structural modulations and their coupling with charge, spin and orbital degrees-of-freedom in quantum materials. However, achieving atomic resolution in cryo-STEM is exceptionally challenging, primarily due to sample drifts arising from temperature changes and noises associated with LHe bubbling, turbulent gas flow, etc. In this work, we demonstrate atomic resolution cryo-STEM imaging at LHe temperatures using a commercial side-entry LHe cooling holder. Firstly, we examine STEM imaging performance as a function of He gas flow rate, identifying two primary noise sources: He-gas pulsing and He-gas bubbling. Secondly, we propose two strategies to achieve low noise conditions for atomic resolution STEM imaging: either by temporarily suppressing He gas flow rate using the needle valve or by acquiring images during the natural warming process. Lastly, we show the applications of image acquisition methods and image processing techniques in investigating structural phase transitions in Cr 2 Ge 2 Te 6 , CuIr 2 S 4 , and CrCl 3 . In conclusion, our findings represent an advance in the field of atomic resolution electron microscopy imaging for quantum materials and devices at LHe temperatures, which can be applied to other commercial side-entry LHe cooling TEM holders.
36 MATERIALS SCIENCE↗
End-to-End Automated Segmentation Framework for Four-Dimensional Scanning Transmission Electron Microscopy Data
Four-dimensional scanning transmission electron microscopy (4D-STEM) is powerful for rapidly characterizing arrays of nanoparticles produced via high-throughput synthesis. However, such 4D-STEM datasets typically contain thousands of nanoparticles, each characterized by thousands of diffraction patterns spatially distributed across the nanoparticle, necessitating efficient and comprehensive analysis. We propose an end-to-end segmentation framework to automatically segment each nanoparticle into regions with distinct composition/orientation of crystal grains, using only the 4D-STEM data. Bragg disk information is extracted in a physics-informed manner from the diffraction patterns at each spatial location and combined with the real space coordinates to form feature vectors. These feature vectors are then used as inputs to a Gaussian mixture model (GMM) to segment the nanoparticle into distinct regions. We also develop two visualization tools based on the GMM outputs to infer the interface transition and the degree of superposition. Our framework comprehensively integrates machine learning tools and physics knowledge, and provides a basis for substantially compressing enormous 4D-STEM datasets, e.g., by replacing the full 4D-STEM dataset for each nanoparticle with only a single set of Bragg disk features for each distinct crystal grain identified in the nanoparticle. In this article, we demonstrate the power of our framework by presenting results for real, complex datasets.
47 OTHER INSTRUMENTATION↗
Soil nutrients affect biomass allocation at the individual tree level in Populus_deltoides
The allocation of carbon (C) to tree roots has implication for forest productivity and soil C storage. Here, we elucidated the factors affecting absolute and relative production of resource-acquiring absorptive fine roots (AFR) and other tree organs. We assessed soil properties, leaf (Leaves), stem and branch (Stem-Br), coarse root (CR), transport fine root (TFR), and AFR biomass, production, and allocation and leaf litterfall and AFR and TFR turnover for 12 trees in a youngPopulus deltoides plantation. On a biomass basis, standing crop of AFRs was significantly related to that of TFRs, but both were independent of biomass of leaves, CRs and Stem-Brs. Production (standing crop + turnover) as a proportion of total biomass (allocation) highlighted significant relationships between AFR%, TFR%, and tree and soil characteristics. AFR% and TFR% were negatively correlated with Stem-Br%, Leaf%, and total tree production. Spatial variation in soil nutrient gradients altered allocation withinP. deltoides.AFR% and TFR% were negatively correlated with CEC, N, and Ca but positively correlated with soil P, Fe, and Na. Stem-Br% was positively correlated with CEC and soil N but negatively correlated with P. AFR and TFR growth and death are tightly coupled at the individual tree level. AFR allocation, but not standing biomass, is highly correlated with allocation to leaves, suggesting tight regulation of the growth of these two resource-acquiring organs. Lower soil N and Ca increased allocation to AFRs at the cost of leaves, whereas allocation to AFRs and leaves increased with soil P. Such changes in response to soil P may control whole-tree production in the current study.
Biomass allocation↗
Experimental study of energy-dependent angular broadening of MeV electron beams for high-resolution imaging in thick samples
In scanning transmission electron microscopy (STEM), spatial resolution is primarily influenced by the projected size of the electron probe within the specimen. In thin samples, a large semi-convergence angle enables a tightly focused beam and sub-nanometer resolution. However, in thick specimens, resolution is fundamentally limited by transverse beam broadening from multiple large-angle scattering events—for example, a probe with 10 mrad angular divergence can broaden by ∼100 nm over a 10 μm path. Since this broadening scales inversely with beam energy, MeV-STEM offers a promising route for high-resolution imaging in thick materials. To quantitatively assess this effect, we performed high-precision measurements at UCLA’s PEGASUS beamline, characterizing beam divergence and intensity profiles for 3–8 MeV electrons transmitted through a wedged-silicon sample of varying thickness. Our results reconcile discrepancies among analytical models and validate Monte Carlo simulations. Here, we find that increasing beam energy from 3.0 to 5.8 MeV reduces angular broadening by a factor of 2.6, with diminishing returns observed at 7.6 MeV. These findings provide a quantitative framework for optimizing MeV-STEM parameters in high-resolution imaging of thick biological and microelectronic specimens, and for guiding beam energy selection in other advanced imaging modes beyond STEM.
36 MATERIALS SCIENCE↗
Approximately 15% of Miscanthus yield is lost at current commercial cutting heights in Iowa
Various works have quantitatively characterized the effects of environmental and management factors on Miscanthus x giganteus Greef et Deu (mxg) yield and, therefore, anticipated land requirement per unit production. However, little work has addressed the effects of cutting height, which may significantly contribute to the difference between the standing aboveground biomass at harvest (i.e., biological yield) and harvested yield. This study quantitatively characterized the effect of cutting height using a replicated nitrogen trial of a 5-year-old mxg stand in southeast Iowa and related this information to observations of cutting height in nearby commercial fields. Nitrogen fertilizer did not significantly change the relationship of the stem segment mass to length, and overall, a 1-cm stem segment contributes 0.5% of the total stem biomass within the bottom 44 cm of the stem. This results in an average harvest loss of 15% of the aboveground standing biomass when cutting at 30 cm, typically seen in commercial mxg fields in eastern Iowa. Cutting height should be considered when accurately predicting commercial mxg harvest yields and changes in soil organic carbon in a commercial mxg agroecosystem.
60 APPLIED LIFE SCIENCES↗
Dynamic changes in evapotranspiration, canopy photosynthesis and expansive growth in open field under rapid fluctuating radiation
Abstract In open fields, plants experience dynamic changes in environment, particularly radiation, temperature, wind, and humidity but their short-term responses have not been adequately characterized under natural conditions. In this study, we assessed causal effects of rapid radiation fluctuation on seven plant parameters in open fields of cotton and sweet corn canopies. The parameters are evapotranspiration ( ET ), canopy photosynthesis indicated by CO2 flux from air to canopy ( FCO2 ), sensible heat energy flux ( H ), canopy conductance for water vapor ( gcw ), canopy surface temperature ( Ts ), shoot and leaf elongation rate, and stem diameter change. The energy and CO2 fluxes were measured with Bowen ratio/energy balance/CO2 gradient (BREB+) technique, using averaging time of 5 min. Shoot + leaf elongation and stem diameter change were monitored with position transducers using averaging time of 1 min. All parameters were all found to respond to change in radiation and transpiration within minutes or sooner. While radiation effects on canopy gas exchanges are expected, illuminating are the indirect but immediate effects on shoot + leaf growth and stem diameter change through radiation effects on transpiration and plant water status. A novel finding is that gcw also responded within minutes or sooner to radiation fluctuations and that FCO2 was related almost linearly to gcw . Results are discussed in terms of soil-plant-atmosphere continuum, and interpreted in terms of dynamic interactions between transpiration and plant water status. The clear inverse relationship between ET and elongation rate or stem diameter changes provides additional evidence supporting the validity of 5-min averaging for the BREB + technique.
Hsiao, Theodore C.↗
Scanning Transmission Electron Microscopy–Atom Probe Tomography Correlative Analysis for the Characterization of Solute-defect Interactions
Atom probe tomography (APT) and (scanning) transmission electron microscopy ((S)TEM) are complementary techniques that provide spatially resolved chemical and structural information at the atomic scale. Here, in this study, we employ two different STEM/APT correlative analysis methods to investigate Cr segregation at dislocation loops in ultra-high purity Fe–Cr alloys. APT needles for the correlative analysis were extracted either from bulk material or from thinned TEM lamellae. STEM analysis was used to determine the Burgers vectors of ion-irradiation-induced dislocation loops, while APT reconstruction of the same region revealed the Cr segregation to these loops. We extended the g•b = 0 invisibility criterion of dislocation loops from TEM mode in a lamella to STEM mode in a needle-shaped specimen. STEM and APT analysis on the same needle provide straightforward correlative analysis, although it is limited by a small observation volume. In contrast, iterative STEM analysis of TEM lamellae, followed by the selective extraction of specific regions of interest for APT analysis, expands the observation area by up to 100 times but requires additional time-consuming steps for APT needle extraction from the lamellae.
47 OTHER INSTRUMENTATION↗