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At least 397 records · Page 22

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structures of biological macromolecular complexes. Picking single-protein particles from cryo-EM micrographs is a crucial step in reconstructing protein structures. However, the widely used template-based particle picking process is labor-intensive and time-consuming. Though machine learning and artificial intelligence (AI) based particle picking can potentially automate the process, its development is hindered by lack of large, high-quality labelled training data. To address this bottleneck, we present CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for protein particle picking and analysis. It consists of labelled cryo-EM micrographs (images) of 34 representative protein datasets selected from the Electron Microscopy Public Image Archive (EMPIAR). The dataset is 2.6 terabytes and includes 9,893 high-resolution micrographs with labelled protein particle coordinates. The labelling process was rigorously validated through 2D particle class validation and 3D density map validation with the gold standard. The dataset is expected to greatly facilitate the development of both AI and classical methods for automated cryo-EM protein particle picking.

42 ENGINEERING↗

Convective flow effects on protein crystal growth

A high-resolution microscopic interferometric setup for the monitoring of protein morphologies has been developed. Growth or dissolution of a crystal can be resolved with a long-term depth resolution of 200 A and a lateral resolution of 2 microns. This capability of simultaneously monitoring the interfacial displacement with high local depth resolution has yielded several novel results. We have found with lysozyme that (1) the normal growth rate is oscillatory, and (2) depending on the impurity content of the solution, the growth step density is either greater or lower at the periphery of a facet than in its center. The repartitioning of Na plus and Cl minus ions between lysozyme solutions and crystals was studied for a wide range of crystallization conditions. A nucleation-growth-repartitioning model was developed, to interpret the large body of data in unified way. The results strongly suggest that (1) the ion to lysozyne ratio in the crystal depends mostly on kinetic rather than crystallographic parameters, and (2) lysozyme crystals possess a salt-rich core with a diameter electron microscopy results appear to confirm this finding, which could have far-reaching consequences for x-ray diffraction studies. A computational model for diffusive-convective transport in protein crystallization has been applied to a realistic growth cell geometry, taking into account the findings of the above repartitioning studies and our kinetics data for the growth of lysozyme. The results show that even in the small cell employed, protein concentration nonuniformities and gravity-driven solutal convection can be significant. The calculated convection velocities are of the same order to magnitude as those found in earlier experiments. As expected, convective transport, i.e., at Og, lysozyme crystal growth remains kinetically limited. The salt distribution in the crystal is predicted to be non-uniform at both 1g and 0g, as a consequence of protein depletion in the solution. Static and dynamic light scattering studies in undersaturated and supersaturated solutions have been performed. Diffusivities in undersaturated solutions, were found to vary with lysozyme concentrations. Depending on the salt concentration, the diffusivities either increase or decrease. Interestingly, the corresponding static scattering intensities behave oppositely, Our current analysis indicates that these changes are inconsistent with aggregation in undersaturated solutions. However, the data are compatible with concentration-dependent changes of the interactions between protein and salt.

Rosenberger, Franz↗

Liquid Interfacial Electron Microscopy Identifies Nanogalvanic Corrosion in Pearlitic Steel

The nanoscale mechanisms of localized corrosion in low carbon steels have remained elusive due to the complexity of studying the degradative material behavior at nanoscale solid-liquid interfaces. We identified various steps in the nanogalvanic corrosion processes using in-situ liquid-cell scanning transmission electron microscopy (STEM) using a microfluidic holder by Hummingbird Scientific. Initial work, performed at low magnification, identified the initiation point on a 1018 low-carbon steel surface. This initiation point was determined to be a triple junction of two ferrite grains bridging a cementite grain in contact with a baseline electrolyte of 6 uM CO2 dissolved in a buffered (2.78 uM Na2SO4) aqueous solution, pH 6.1. The pre-etched low-carbon steel surface was prepared using focused ion beam lift-out procedures to extract a cross-section of the low-carbon steel surface, which then was thinned to about 150 nm and transferred to a SiN membrane microfluidic window. The transfer was made using a lift-out needle to attach the low-carbon steel lamella to the corner of the SiN window, and then Pt/C deposition held the lamella in contact with the window while it was released from the lift out needle. To identify the triple point on the low carbon steel lamella, prior to attachment on the SiN window, the sample was characterized for compositional variations with energy dispersive x-ray spectroscopy mapping, grain orientation and phase mapping with precession electron diffraction, and thickness mapping with energy filtered transmission electron microscopy. This pre-characterization prior to the in-situ experiment provided a map of the multiphase and multigrain structure, where the in-situ liquid cell imaging provided a clear understanding of the initiation point on the sample. These data were cross-correlated to paint a holistic picture of the triple junction site, enabling low electron-fluence in-situ snapshot imaging to avoid dominating the native corrosion reactions with effects from the incident electron beam. This initial result identified that localized, nanogalvanic corrosion at the phase interface was the dominant corrosion process in the low-carbon steel, so we next targeted the observation of an array of these nanogalvanic features phase boundaries in a pearlite grain. Near-surface ferrite/cementite phase interfaces that typify pearlitic low-carbon steel were extracted, pre-characterized, and imaged for the in-situ corrosion processes. The sample was a cross-section from a pearlite grain, with alternating ferrite and cementite grains that extended microns down from the pre-etched low-carbon steel pipe surface. After contact with a buffered aqueous solution, the phase boundaries between the ferrite and cementite began to dissolve, with observable material loss and thickness changes in the dark-field and bright-field STEM images. Within minutes, the corrosion front proceeded deeper into the material, claiming a thin layer of ferrite around all exposed phase boundaries before progressing laterally into the ferrite matrix, converting the ferrite to corrosion product normal to each buried cementite grain. Formation of the corrosion product causes a volumetric expansion, creating a lateral wedging force that mechanically ejects the cementite grains from their grooves and leaves behind percolation channels into the steel substructure. Rapid and deleterious, this nanogalvanic corrosion pathway represents an important target for understanding and preventing run-away degradation in this common building material. Observation of this corrosion mechanism was enabled by the combination of pre-characterization using standard structural, grain, and compositional analysis in the TEM, which provides maps for understanding the reaction propagation captured in low-dose, in-situ, liquid-cell STEM.

corrosion↗

Release of somatic embryogenic potential from excised zygotic embryos of carrot and maintenance of proembryonic cultures in hormone-free medium

Excised zygotic embryos, mericarps ("seeds") and hypocotyls of seedlings of cultivated carrot Daucus carota cv. Scarlet Nantes were evaluated for their ability to generate somatic embryos on a semisolid hormone-free nutrient medium. Neither intact zygotic embryos nor hypocotyls ever produced somatic embryos. However, mericarps and broken zygotic embryos were excellent sources for somatic embryo production (response levels as high as 86%). Somatic embryo formation was highest from cotyledons, but was also observed on isolated hypocotyls and root tips of mature zygotic embryos. On media containing unreduced nitrogen, somatic embryo formation led to the generation of vigorous cultures comprised entirely of somatic embryos at various stages of development which in turn proliferated still other somatic embryos. However, a medium was devised which when 1-5 mM NH4+ was the sole nitrogen source, led only to a proliferation of globular proembryos. Sustained subculturing of these proembryos at 2-3 week intervals enabled establishment of highly uniform cultures in which no further development into more mature stages of embryonic development occurred. These have been maintained, without decline, as morphogenetically competent proembryonic globules for over ten months. A basal medium containing from 1-5 mM NH4+ as the sole nitrogen source appears not to be inductive to somatic proembryo formation. Instead, such a medium is best thought of as permissive to the expression of embryogenically determined cells within zygotic embryos. By excising and breaking or wounding zygotic embryos, constituent cells are probably released from positional or chemical restraints and thus are able to express their innate embryogenic potential. Once a proembryonic culture is established, this medium containing 1-5 mM NH4+ as the sole nitrogen source provides a nonpermissive environment to the development and growth of later embryonic stages, but it does allow the continued formation and multiplication of globular somatic proembryos. The sequence of events leading from excised broken zygotic embryos to the formation of somatic embryos and the maintenance of somatic proembryos are demonstrated by scanning electron microscopy and histological preparations. Germination levels from intact zygotic embryos on media with varying levels and ratios of unreduced vs. reduced inorganic nitrogen were determined as well and provided baseline or control data on the type of response obtained from nonwounded material.

Non-NASA Center↗

Tribochemical changes of alloy 800HT under sliding contact at elevated temperature in impure helium environment

This work investigates the chemical changes of the surface of Alloy 800HT during sliding contact under helium atmosphere in the presence of impurities at 750 °C, which is of interest for the nuclear industry. The alloy samples are exposed to helium (He) atmosphere at high temperature for long duration of 500 h to identify the chemical and topographical changes of the alloy surface. The oxidation rate constant is reported based on the weight change data. For the tribo-experimental samples, the surfaces inside and outside the wear track are studied thoroughly using techniques such as secondary electron microscopy, energy dispersive spectroscopy, x-ray diffraction, Raman spectroscopy and secondary ion mass spectroscopy. The formation and evolution of surface oxides are discussed in He atmosphere, compared with air. The presence of Fe-rich thin layer of oxide on top of a thicker Cr-rich oxide and a mixed spinel-based inner layer on the bulk is found. The persistent presence of thicker Fe3O4 in the wear track in high temperature air proved to be the reason of lower friction property. Pre-oxidation of the samples in air or He does not improve but worsen the tribological behavior in He atmosphere.

36 MATERIALS SCIENCE↗

Mapping nanocrystal orientations via scanning Laue diffraction microscopy for multi-peak Bragg coherent diffraction imaging

The recent commissioning of a movable monochromator at the 34-ID-C endstation of the Advanced Photon Source has vastly simplified the collection of Bragg coherent diffraction imaging (BCDI) data from multiple Bragg peaks of sub-micrometre scale samples. Laue patterns arising from the scattering of a polychromatic beam by arbitrarily oriented nanocrystals permit their crystal orientations to be computed, which are then used for locating and collecting several non-co-linear Bragg reflections. The volumetric six-component strain tensor is then constructed by combining the projected displacement fields that are imaged using each of the measured reflections via iterative phase retrieval algorithms. Complications arise when the sample is heterogeneous in composition and/or when multiple grains of a given lattice structure are simultaneously illuminated by the polychromatic beam. Here, a workflow is established for orienting and mapping nanocrystals on a substrate of a different material using scanning Laue diffraction microscopy. The capabilities of the developed algorithms and procedures with both synthetic and experimental data are demonstrated. The robustness is verified by comparing experimental texture maps obtained with Laue diffraction microscopy at the beamline with maps obtained from electron back-scattering diffraction measurements on the same patch of gold nanocrystals. Such tools provide reliable indexing for both isolated and densely distributed nanocrystals, which are challenging to image in three dimensions with other techniques.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Summary of the Initial Post-Irradiation Characterization of HFIR-Irradiated Low-N and High-N HT-9 Steel

Reference cladding systems for sodium fast reactors are based on the historical steel, HT-9. HT-9 is a Fe12Cr ferritic/martensitic steel with additions of Mo, W, V, and other minor elements and demonstrates low irradiation swelling and adequate mechanical properties. Extensive irradiation literature exists on the use of HT-9 as cladding for metal fuel, primarily irradiation on the U-Zr/HT-9 system from the Experimental Breeder Reactor-II (EBR-II) and Fast Flux Test Facility (FFTF) sodium fast reactor, and as a structural material from experiments in the FFTF. The large amount of historical data makes the U-Zr/HT-9 system the reference fuel specification for many nuclear reactor vendors that seek to license modern sodium-cooled fast reactors in the United States. However, it is yet unclear how variations in impurity content within HT-9 fundamentally affect irradiation performance at various irradiation temperatures. Recent work suggests that impurity content may noticeably alter the production of helium through nuclear transmutation. For these reasons, High-Flux Isotope Reactor (HFIR) irradiation of HT-9 steels with known variations in the impurity content is particularly timely to generate data to enable more accurate refinement of the chemical specification for nuclear-grade HT-9 material. This report summarizes the initial transmission electron microscopy characterization of HFIR-irradiated HT-9 steels following mechanical property measurements by the Advanced Fuels Campaign (AFC). This report includes qualitative results of the cavity, dislocation loop and cluster/precipitate microstructures as well as radiation-induced segregation. Quantitative results are being shared with partner institutions and will be included in more detail in a future report in FY2026.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Analytical electron microscopy of a hydrated interplanetary dust particle

Properties of a hydrated interplanetary dust particle (IDP), Ames-Dec86-11, were investigated using TEM and analytical electron microscopy. The particle was found to have mineralogy and chondritic composition indicating an absence of direct kinship with known carbonaceous chondrites. The available data on the Ames-Dec86-11 suggest that at least one aqueous alteration event took place in this hydrated IDP, during which fine-grained material, possibly glass, was transformed to smectite. This event appears to be unique to hydrated IDPs.

Blake, David F.↗

Spatially resolved ballistic electron spectroscopy of subsurface interfaces

Buried interfaces have traditionally been inaccessible to direct investigation by surface-sensitive techniques. A unique and novel electronic probe, which is sensitive to subsurface electronic structure, has been utilized to probe Schottky barrier interfaces. The method, ballistic electron emission microscopy (BEEM), is based on scanning tunnelling microscopy (STM) techniques. A theoretical treatment has been developed to describe the ballistic electron spectra obtained by BEEM and this treatment is applied to data obtained on the Au-Si Schottky barrier interface system. Excellent agreement between experiment and theory is obtained. In addition, the treatment predicts nanometer spatial resolution for interface imaging by BEEM.

Bell, L. D.↗

Textural variability of ordinary chondrite chondrules: Implications of their formation

Scanning electron microscopy (SEM) and microprobe examination of the Raguli H3-4, Saratov L3, and Fucbin L5-6 ordinary chondrites and the analysis of preexisted data on other meteorites have shown that the variety of textural types of chondrules depends on the chemical composition of the chondrules. The comparison of bulk-rock chemistries of the chondrules by major components demonstrates that they apparently fall, like basic-ultrabasic rock, into groups of dunitic and pyroxenitic composition. This separation is further validated by the character of zoning in chondrules of the intermediate, peridotitic type. The effect is vividly demonstrated by the 'chondrule-in-chondrule' structure.

Zinovieva, N. G.↗

Solutocapillary Convection Effects on Polymeric Membrane Morphology

Macro voids are undesirable large pores in membranes used for purification. They form when membranes are cast as thin films on a smooth surface by evaporating solvent (acetone) from a polymer solution. There are two un-tested hypotheses explaining the growth of macro voids. One states that diffusion of the non-solvent (water) is solely responsible, while the other states that solutocapillary convection is the primary cause of macro void growth. Solutocapillary convection is flow-caused by a concentration induced surface-tension gradient. Macrovoid growth in the former hypothesis is gravity independent, while in the latter it is opposed by gravity. To distinguish between these two hypotheses, experiments were designed to cast membranes in zero-gravity. A semi-automated apparatus was designed and built for casting membranes during the 20 secs of zero-g time available in parabolic aircraft flight such as NASA's KC-135. The phase changes were monitored optically, and membrane morphology was evaluated by scanning electron microscopy (SEM). These studies appear to be the first quantitative studies of membrane casting in micro-gravity which incorporate real-time data acquisition. Morphological studies of membranes cast at 0, 1, and 1.8 g revealed the presence of numerous, sparse and no macrovoids respectively. These results are consistent with the predictions of the solutocapillary hypothesis of macrovoid growth.

Krantz, William B.↗

Soot Formation in Laminar Premixed Ethylene/Air Flames at Atmospheric Pressure

Soot formation was studied within laminar premixed ethylene/air flames (C/O ratios of 0.78-0.98) stabilized on a flat-flame burner operating at atmospheric pressure. Measurements included soot volume fractions by both laser extinction and gravimetric methods, temperatures by multiline emission, soot structure by thermophoretic sampling and transmission electron microscopy, major gas species concentrations by sampling and gas chromatography, concentrations of condensable hydrocarbons by gravimetric sampling. and velocities by laser velocimetry. These data were used to find soot surface growth rates and primary soot particle nucleation rates along the axes of the flames. Present measurements of soot surface growth rates were correlated successfully by predictions based on typical hydrogen-abstraction/carbon-addition (HACA) mechanisms of Frenklach and co-workers and Colket and Hall. These results suavest that reduced soot surface growth rates with increasing residence time seen in the present and other similar flames were mainly caused by reduced rates of surface activation due to reduced H atom concentrations as temperatures decrease as a result of radiative heat losses. Primary soot particle nucleation rates exhibited variations with temperature and acetylene concentrations that were similar to recent observations for diffusion flames; however, nucleation rates in the premixed flames were significantly lower than in, the diffusion flames for reasons that still must be explained. Finally, predictions of yields of major gas species based on mechanisms from both Frenklach and co-workers and Leung and Lindstedt were in good agreement with present measurements and suggest that H atom concentrations (relevant to HACA mechanisms) approximate estimates based on local thermodynamic equilibrium in the present flames.

Xu, F.↗

Characterization and Glass Formation of JSC-1 Lunar and Martian Soil Simulants

The space exploration mission of NASA requires long duration presence of human being beyond the low earth orbit (LEO), especially on Moon and Mars. Developing a human habitat or colony on these planets would require a diverse range of materials, whose applications would range from structural foundations, (human) life support, (electric) power generation to components for scientific instrumentation. A reasonable and cost-effective approach for fabricating the materials needed for establishing a self-sufficient human outpost would be to primarily use local (in situ) resources on these planets. Since ancient times, glass and ceramics have been playing a vital role on human civilization. A long term project on studying the feasibility of developing glass and ceramic materials using Lunar and Martian soil simulants (JSC-1) as developed by Johnson Space Center has been undertaken. The first step in this on-going project requires developing a data base on results that fully characterize the simulants to be used for further investigations. The present paper reports characterization data of both JSC-1 Lunar and JSC Mars-1 simulants obtained up to this time via x-ray diffraction analysis, scanning electron microscopy, thermal analysis (DTA, TGA) and chemical analysis. The critical cooling rate for glass formation for the melts of the simulants was also measured in order to quantitatively assess the glass forming tendency of these melts. The importance of the glasses and ceramics developed using in-situ resources for constructing human habitats on Moon or Mars is discussed.

Sen, Subhayu↗

Influence of Thin-Film Adhesives in Pullout Tests Between Nickel-Titanium Shape Memory Alloy and Carbon Fiber-Reinforced Polymer Matrix Composites

Strips of nickel-titanium (NiTi) shape memory alloy (SMA) and carbon fiber-reinforced polymer matrix composite (PMC) were bonded together using multiple thin film adhesives and their mechanical strengths were evaluated under pullout test configuration. Tensile and lap shear tests were conducted to confirm the deformation of SMAs at room temperature and to evaluate the adhesive strength between the NiTi strips and the PMC. Optical and scanning electron microscopy techniques were used to examine the interfacial bonding after failure. Simple equations on composite tensile elongation were used to fit the experimental data on tensile properties. ABAQUS models were generated to show the effects of enhanced bond strength and the distribution of stress in SMA and PMC. The results revealed that the addition of thin film adhesives increased the average adhesive strength between SMA and PMC while halting the room temperature shape memory effect within the pullout specimen.

Polymer Matrix Composites↗

Interpreting nanovoids in atom probe tomography data for accurate local compositional measurements

Quantifying chemical compositions around nanovoids is a fundamental task for research and development of various materials. Atom probe tomography (APT) and scanning transmission electron microscopy (STEM) are currently the most suitable tools because of their ability to probe materials at the nanoscale. Both techniques have limitations, particularly APT, because of insufficient understanding of void imaging. Here, we employ a correlative APT and STEM approach to investigate the APT imaging process and reveal that voids can lead to either an increase or a decrease in local atomic densities in the APT reconstruction. Simulated APT experiments demonstrate the local density variations near voids are controlled by the unique ring structures as voids open and the different evaporation fields of the surrounding atoms. We provide a general approach for quantifying chemical segregations near voids within an APT dataset, in which the composition can be directly determined with a higher accuracy than STEM-based techniques.

36 MATERIALS SCIENCE↗

Cryo-EM sample preparation for high-resolution structure studies

High-resolution structures of biomolecules can be obtained using single-particle cryo-electron microscopy (SPA cryo-EM), and the rapidly growing number of structures solved by this method is encouraging more researchers to utilize this technique. As with other structural biology methods, sample preparation for an SPA cryo-EM data collection requires some expertise and an understanding of the strengths and limitations of the technique in order to make sensible decisions in the sample-preparation process. Here, in this article, common strategies and pitfalls are described and practical advice is given to increase the chances of success when starting an SPA cryo-EM project.

36 MATERIALS SCIENCE↗

Bayesian Active Learning for Scanning Probe Microscopy: From Gaussian Processes to Hypothesis Learning

Recent progress in machine learning methods and the emerging availability of programmable interfaces for scanning probe microscopes (SPMs) have propelled automated and autonomous microscopies to the forefront of attention of the scientific community. However, enabling automated microscopy requires the development of task-specific machine learning methods, understanding the interplay between physics discovery and machine learning, and fully defined discovery workflows. This, in turn, requires balancing the physical intuition and prior knowledge of the domain scientist with rewards that define experimental goals and machine learning algorithms that can translate these to specific experimental protocols. Here, we discuss the basic principles of Bayesian active learning and illustrate its applications for SPM. We progress from the Gaussian process as a simple data-driven method and Bayesian inference for physical models as an extension of physics-based functional fits to more complex deep kernel learning methods, structured Gaussian processes, and hypothesis learning. These frameworks allow for the use of prior data, the discovery of specific functionalities as encoded in spectral data, and exploration of physical laws manifesting during the experiment. Here, the discussed framework can be universally applied to all techniques combining imaging and spectroscopy, SPM methods, nanoindentation, electron microscopy and spectroscopy, and chemical imaging methods and can be particularly impactful for destructive or irreversible measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Microstructural dependence of defect formation in iron-oxide thin films

In this report passivating iron-oxide films are grown atop iron films simulating the corrosion process in a nuclear reactor environment. Two oxide films grown via physical vapor deposition at 600 °C and room temperature exhibited dense-epitactic and columnar-polycrystalline, microstructures respectively. A third oxide film grown in open air at 600 °C exhibited an eqiuaxed, porous morphology. Cubic maghemite and magnetite phases in each oxide film were identified via grazing incidence X-ray diffraction. Positron annihilation spectroscopy was used to characterize point defects and measure their depth and size distributions in each oxide layer and showed a range of average positron lifetimes from 0.23 ns in the high temperature, vapor deposited film, 0.35 ns in the room temperature-grown film, and 0.31 ns in the thermally grown oxide. These data indicate that the film morphology, which varies greatly in these films, leads to very different defect content. Finally, four-dimensional scanning transmission electron microscopy was used to measure the internal stress of each film and was correlated to the strain state presented in the X-ray diffraction spectra. The defect formation in each film is reasoned through using a thin film growth model.

36 MATERIALS SCIENCE↗