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At least 757 records · Page 42

Automating STEM Aberration Correction via Bayesian Optimization

Multipole aberration correctors have given scanning transmission electron microscopes (STEM) the ability to produce high-quality, atomic-resolution images, enabling STEM to be a key tool in material sciences for characterizing the structure and composition of materials. However, the process of correcting these aberrations typically requires human input and is accomplished using scanned STEM or Ronchigram images at different focii and beam tilts. In this work, we demonstrate an automated on-sample aberration correction system using Bayesian Optimization. We have developed a Python-based server able to communicate with the CEOS DCOR aberration corrector and the Thermo Fischer microscope scripting interface. This server allows us to change aberrations, acquire images and perform basic image analysis.

47 OTHER INSTRUMENTATION↗

Stomata in-sight: Integrating live confocal microscopy with leaf gas exchange and environmental control

Stomatal anatomy (aperture area, length, and width) influences leaf-level physiology traits including conductance to water vapor. Stomatal anatomy can be visualized in situ by microscopy, but the difficulty of regulating the atmospheric environment of a microscope stage means that the conditions under which imaging is done are rarely physiologically relevant. Alternatively, leaf gas exchange instruments that measure gas fluxes reflect stomatal anatomical characteristics in aggregate, but the relative strengths of anatomical traits to control water use (e.g. size vs density) cannot be firmly established. To reconcile the microscopic stomatal characteristics with leaf-level gas exchange, we describe a tool that combines laser scanning confocal microscopy, gas exchange instruments, and machine-learning image analysis to simultaneously observe anatomical characteristics of many (>40) stomata alongside leaf-level traits like photosynthesis, transpiration, and stomatal conductance. We demonstrate how the tool has the resolution capable of quantifying aperture sizes and variability in maize (Zea mays) leaves under 5 steady-state light/pCO 2 treatments while tightly controlling other environmental variables like relative humidity and temperature. A model used to calculate stomatal conductance from measured apertures and stomatal density accurately matched stomatal conductance measured by gas exchange. This technical advancement will provide insight on how stomatal anatomy and function trade off to influence stomatal conductance and leaf-level water use efficiency.

59 BASIC BIOLOGICAL SCIENCES↗

In Situ Transmission Electron Microscopy: Signal processing challenges and examples

Transmission electron microscopy (TEM) is a powerful tool for imaging material structure and characterizing material chemistry. Recent advances in data collection technology for TEM have enabled high-volume and high-resolution data collection at a microsecond frame rate. Here, taking advantage of these advances in data collection rates requires the development and application of data processing tools, including image analysis, feature extraction, and streaming data processing techniques. In this article, we highlight a few areas in materials science that have benefited from combining signal processing and statistical analysis with data collection capabilities in TEM and present a future outlook on opportunities of integrating signal processing with automated TEM data analysis.

36 MATERIALS SCIENCE↗

OSCA1 is an osmotic specific sensor: a method to distinguish Ca 2+ -mediated osmotic and ionic perception

Genetic mutants defective in stimulus-induced Ca 2+ increases have been gradually isolated, allowing the identification of cell-surface sensors/receptors, such as the osmosensor OSCA1. However, determining the Ca 2+ -signaling specificity to various stimuli in these mutants remains a challenge. For instance, less is known about the exact selectivity between osmotic and ionic stresses in the osca1 mutant. Here, we have developed a method to distinguish the osmotic and ionic effects by analyzing Ca 2+ increases, and demonstrated that osca1 is impaired primarily in Ca 2+ increases induced by the osmotic but not ionic stress. We recorded Ca 2+ increases induced by sorbitol (osmotic effect, OE) and NaCl/CaCl 2 (OE + ionic effect, IE) in Arabidopsis wild-type and osca1 seedlings. Here we assumed the NaCl/CaCl 2 total effect (TE) = OE + IE, then developed procedures for Ca 2+ imaging, image analysis and mathematic fitting/modeling, and found osca1 defects mainly in OE. The osmotic specificity of osca1 suggests that osmotic and ionic perceptions are independent. The precise estimation of these two stress effects is applicable not only to new Ca 2+ -signaling mutants with distinct stimulus specificity but also the complex Ca 2+ signaling crosstalk among multiple concurrent stresses that occur naturally, and will enable us to specifically fine tune multiple signal pathways to improve crop yields.

Arabidopsis↗

A Versatile Fiber Coating Process for Efficient Fabrication of Multifunctional Composites

The objective of this research is to demonstrate the versatility of a dip coating process for the efficient integration of piezoelectric barium titanate (BaTiO3) microparticles on a wide variety of fibers to design passive self-sensing composites. The microparticles were deposited on glass, aramid, and basalt fiber weaves through the proposed dip coating technique. A computational framework is established to predict the deposition thickness on the fiber surfaces from the given microparticle concentration, size, coating velocity, and coating fluid viscosity. The deposition quality assessment was performed through scanning electron microscope imaging and subsequent image analysis. BaTiO3-coated fibers were directly used in composite preparation. After fabrication, the BaTiO3-enhanced composites were subjected to high-voltage poling. Finally, their passive self-sensing properties were characterized through experimental studies. The results show the adaptability of the proposed coating process to integrate BaTiO3 microparticles within different types of fiber-reinforced composites enabling passive self-sensing to attain subsurface damage characterization.

Gupta, Sumit↗

Protorheology

We all instinctively poke, bounce, scoop, and observe materials to understand rheological properties quickly. Yet, these observations are rarely analyzed quantitatively. To address this, here we introduce the paradigm of protorheology: approximate quantitative inference from simple observations. Several case studies demonstrate how protorheology is an inclusive entry to rheology for a broad range of practitioners and strengthens the confidence and interpretation of accurate laboratory measurements. We survey a range of creative tests according to which rheological phenomenon is revealed. Some new working equations are derived, and all working equations are summarized for convenient reference and comparison across different methods. Finally, this establishes a framework to enable increased use of photos, videos, and quantitative inference and to support the increasing interest in digital image analysis, inverse methods, and high-throughput characterization being applied to rheological properties.

42 ENGINEERING↗

Installation and imaging of thousands of minirhizotrons to phenotype root systems of field-grown plants

Roots are vital to plant performance because they acquire resources from the soil and provide anchorage. However, it remains difficult to assess root system size and distribution because roots are inaccessible in the soil. Existing methods to phenotype entire root systems range from slow, often destructive, methods applied to relatively small numbers of plants in the field to rapid methods that can be applied to large numbers of plants in controlled environment conditions. Much has been learned recently by extensive sampling of the root crown portion of field-grown plants. But, information on large-scale genetic and environmental variation in the size and distribution of root systems in the field remains a key knowledge gap. Minirhizotrons are the only established, non-destructive technology that can address this need in a standard field trial. Prior experiments have used only modest numbers of minirhizotrons, which has limited testing to small numbers of genotypes or environmental conditions. This study addressed the need for methods to install and collect images from thousands of minirhizotrons and thereby help break the phenotyping bottleneck in the field. Over three growing seasons, methods were developed and refined to install and collect images from up to 3038 minirhizotrons per experiment. Modifications were made to four tractors and hydraulic soil corers mounted to them. High quality installation was achieved at an average rate of up to 84.4 minirhizotron tubes per tractor per day. A set of four commercially available minirhizotron camera systems were each transported by wheelbarrow to allow collection of images of mature maize root systems at an average rate of up to 65.3 tubes per day per camera. This resulted in over 300,000 images being collected in as little as 11 days for a single experiment. The scale of minirhizotron installation was increased by two orders of magnitude by simultaneously using four tractor-mounted, hydraulic soil corers with modifications to ensure high quality, rapid operation. Image collection can be achieved at the corresponding scale using commercially available minirhizotron camera systems. Along with recent advances in image analysis, these advances will allow use of minirhizotrons at unprecedented scale to address key knowledge gaps regarding genetic and environmental effects on root system size and distribution in the field.

54 ENVIRONMENTAL SCIENCES↗

PyCMG-based Simulation of Volumetric Concrete Microstructure

Concrete is a complex, heterogeneous material with a microstructure composed of aggregates, cement paste, and pores spanning multiple length scales. Understanding this microstructure is critical for advancing the performance, durability, and modeling of concrete-based systems. While experimental imaging such as X-ray computed tomography (XCT) provides valuable insights, generating large datasets with detailed ground truth annotations is both costly and labor-intensive due to challenges in segmenting similar phases, such as aggregates and cement paste, that often share similar attenuation properties. To address this, we developed a pipeline to simulate realistic 3D concrete microstructures using the open-source Python package PyCMG. This simulation effort focuses on generating high-fidelity, annotated microstructures that can serve as training or benchmarking datasets for image analysis, segmentation algorithms, and machine learning models, particularly in scenarios where experimental data is scarce.

Ziabari, Amir [Oak Ridge National Laboratory; ORNL↗

Non-destructive identification of absorptive damage sites by photoluminescence brightening

We present a non-destructive photoluminescence (PL) imaging strategy for probing damage growth behavior in fused silica under laser irradiation. Transient wide-field PL image measurements were conducted at varying excitation intensities to investigate the dynamics of radiative defect generation and annihilation in laser-induced damage sites. Our results reveal that, while low excitation intensities predominantly induce PL quenching due to defect annihilation, high-intensity excitation (>0.3 GW/cm 2 at 532 nm) triggers pronounced PL brightening (PLB), indicative of radiative defect generation. Image analysis demonstrates that PLB events are strongly correlated with subsequent damage growth (10 J/cm 2 at 351 nm), whereas overall PL intensity is not. No optically detectable morphological changes were observed during PLB, confirming the non-destructive nature of the technique. We propose that PLB arises from defect-assisted absorption of multiple photons at pre-existing absorptive centers, which enhances local absorptivity and initiates further defect formation. These findings establish PLB monitoring as a sensitive diagnostic tool for identifying damage sites with elevated absorptivity, enabling targeted maintenance and improved laser damage management in optical materials.

Materials science↗

Monitoring the impact of confinement on hyphal penetration and fungal behavior

Through their expansive mycelium network, soil fungi alter the physical arrangement and chemical composition of their local environment. This can significantly impact bacterial distribution and nutrient transport and can play a dramatic role in shaping the rhizosphere around a developing plant. However, direct observation and quantitation of such behaviors is extremely difficult due to the opacity and complex porosity of the soil microenvironment. In this study, we demonstrate the development and use of an engineered microhabitat to visualize fungal growth in response to varied levels of confinement. Microfluidics were fabricated using photolithography and conventional soft lithography, assembled onto glass slides, and prepared to accommodate fungal cultures. Selected fungal strains across three phyla (Ascomycota: Morchella sextalata , Fusarium falciforme ; Mucoromycota: Linnemannia elongata , Podila minutissima , Benniella ; Basidiomycota: Laccaria bicolor , and Serendipita sp.) were cultured within microhabitats and imaged using time-lapse microscopy to visualize development at the mycelial level. Fungal hyphae of each strain were imaged as they penetrated through microchannels with well-defined pore dimensions. The hyphal penetration rates through the microchannels were quantified via image analysis. Other behaviors, including differences in the degree of branching, peer movement, and tip strength were also recorded for each strain. Our results provide a repeatable and easy-to-use approach for culturing fungi within a microfluidics platform and for visualizing the impact of confinement on hyphal growth and other fungal behaviors pertinent to their remodeling of the underground environment.

Guo, Yi-Syuan (ORCID:0000000340142225)↗

Assessment of Different Approaches for Measuring Shear Fracture Appearance in Charpy Tests

In this work, different approaches for establishing shear fracture appearance (SFA) on tested Charpy specimens were assessed and compared, namely (in order of increasing expected accuracy) estimates based on characteristic forces from instrumented Charpy tests, optical measurements using image analysis software, and measurements performed with the aid of a scanning electron microscope. Comparisons between different SFA values for 129 instrumented Charpy tests currently included in the National Institute of Standards and Technology database allowed us to establish the relationships between the different available approaches and formulate recommendations for the revision of the standards ASTM E2298-18, Standard Test Method for Instrumented Impact Testing of Metallic Materials, and ISO 14556:2015, Metallic Materials — Charpy V-Notch Pendulum Impact Test — Instrumented Test Method, which currently provide four empirical correlations that can be used to estimate SFA.

36 MATERIALS SCIENCE↗

"Sintering" Models and In-Situ Experiments: Data Assimilation for Microstructure Prediction in SLS Additive Manufacturing of Nylon Components

Selective laser sintering methods are workhorses for additively manufacturing polymer-based components. The ease of rapid prototyping also means it is easy to produce illicit components. It is necessary to have a data-calibrated in-situ physical model of the build process in order to predict expected and defective microstructure characteristics that inform component provenance. Toward this end, sintering models are calibrated and characteristics such as component defects are explored. This is accomplished by assimilating multiple data streams, imaging analysis, and computational model predictions in an adaptive Bayesian parameter estimation algorithm. From these data sources, along with a phase-field model, bulk porosity distributions are inferred. Model parameters are constrained to physically-relevant search directions by sensitivity analysis, and then matched to predictions using adaptive sampling. Using this feedback loop, data-constrained estimates of sintering model parameters along with uncertainty bounds are obtained.

3D printing, Additive Manufacturing, polymer, sint↗

Feedback, physics, and forecasts: The emerging paradigm of machine learning-driven battery research

Machine learning (ML) is reshaping how we understand, predict, and optimize electrochemical systems. In batteries, ML accelerates discovery across chemistry, design, and operation by transforming massive experimental and simulated datasets into predictive, interpretable models. This review consolidates a decade of progress in ML-driven battery innovation, from early-cycle feature extraction to operando image analysis and physics-informed modeling. We categorize approaches by data domain and physical fidelity, emphasizing interpretable ML for diagnostics, reinforcement learning for control, and multi-objective optimization for lifetime extension strategies. Additionally, we demonstrate how integrated models accelerate discovery, reduce testing time, and guide sustainable design. Economic analyses furthermore illustrate how these advances can lower cost per cycle and improve circularity. Together, these developments chart a path toward self-optimizing, sustainable battery technologies.

artificial intelligence↗

Slide Test FY 2019 Report

At Los Alamos, the Slide Test was developed in 2019 to investigate whether the mass of a main charge of explosive sliding on a gritty surface, in the absence of impact, is sufficient to heat grit to ignition temperatures in PBX 9501. This is a practical test to address frictional ignition during assembly/disassembly operations at the Pantex Plant. Twenty-seven Slide Tests were performed in total, testing PBX 9501 at various slide velocities, grit diameters, grit patterns, and charge masses. Time-resolved velocimetry of the slide event (from PDV) and spot area of the explosive charge (obtained from image analysis) is reported. High-speed videography is used to diagnose explosive reaction. Eighteen of these tests were performed with a charge mass of 30 lbs at velocities ≤ 4 m s-1 and grit diameters between 75 and 1000 µm. Nine Slide Tests were performed with a 15 lb charge mass at similar parameters. No ignition was observed in any of the tests. These data provide evidence that the mass of a main charge, caused to slide on a surface at the low velocities achievable during routine handling, is insufficient stimulus to heat grit to ignition temperatures. These findings are relevant to risk assessment for explosive handling operations and provide evidence that PBX 9501 is safe within the constraints that were tested. However, because ignitions were not observed in any of the tests, we cannot determine which variables (mass or velocity) dominate the explosive response and to what extent. The absence of observed ignition also precludes the determination of a safety margin. To identify this safety margin, further research would be necessary to define the velocity and/or mass threshold at which ignition occurs.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

X-ray Computed Tomography on UNESE Core: FY2020 Data Report to Support Fracture and Multiphase Fluid Flow Studies

Natural and induced fractures are potential preferential pathways for migration of radioactive gases to earths surface from underground nuclear explosions (UNEs). This report documents X-ray computed tomography (XRCT) imaging on 26 samples of rock core that was collected to support the Underground Nuclear Explosion Signatures Experiment (UNESE) program. The XRCT datasets are intended to help fill a data gap on the three-dimensional (3D) characteristics of natural and/or induced fractures at the centimeter and smaller scale, which may strongly influence multiphase fluid flow and transport properties of preferential flow paths and interaction with the matrix of the surrounding host rock. Pre- and post-UNE rock samples were carefully chosen to enable comparison of fractures as a function of lithologic and petrophysical properties, as well as distance to the past UNEs. This report serves as documentation for the data, including an introduction with the research motivation, a methods and materials section, descriptions of the XRCT datasets without post-processing, and recommendations for 3D quantification via image analysis and digital rock physics.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Understanding the dynamics of vacuole trafficking and secretion for enhanced plant storage reserves

Vacuoles are essential in plants and serve roles in both protein and organelle degradation for reutilization and storage of high energy molecules such as storage proteins which are critical for seed germination under normal and stress conditions and impact biomass production and nutrition. In addition, plants secrete many different molecules such as cell wall components, lipids, waxes and others that are important for plant protection, structure and biomass. Vacuole accumulation and secretion are closely linked and highly regulated pathways within the endomembrane trafficking network. We have discovered many drug-like synthetic small molecules that can suppress vacuole trafficking and enhance secretion; other chemicals can enhance vacuole trafficking and suppress secretion. The ability of our compounds to modulate these pathways indicates that these pathways are tightly coupled and highly regulated. Thus, to achieve the goals of enhanced energy reserves or enhanced secretion it is essential to understand how this dynamic is controlled. Bioactive chemicals have provided us unique insight into natural mechanisms controlling the dynamics of vacuole trafficking and secretion that was not possible previously. One such compound, ES2, negatively modulates secretion while enhancing vacuole trafficking. This is the first compound discovered that targets an essential secretory complex known as the exocyst and will reveal important regulatory domains controlling secretion and vacuole trafficking. During the current funding period, we determined the structure of the EXO70A1 in plants and identifying its binding site. To understand the dynamics of vacuole trafficking it is key to have compounds that inhibit vacuole trafficking as well as enhancing it (ES2). We have used sophisticated image analysis to identify another novel compound ES17 that enhances secretion while negatively modulating vacuole trafficking (opposite of ES2). We have already made rapid progress. Our preliminary data indicates that ES17 very specifically targets a late stage of vesicle fusion with the tonoplast which is highly regulated. Thus, ES17 is an ideal compound to dissect the regulation of vacuole targeting dynamics. In addition, we have now synthesized a biotinylated version of ES17 that is fully functional, permitting the use of chemical proteomics to identify the cognate target with a high probability of success. We propose to investigate the ES17 target which can negatively modulate vacuole trafficking and combine this with knowledge of the ES2 target which can promote vacuole trafficking. Dissecting the mechanisms controlling the dynamics of secretion vs vacuole accumulation and the use of synthetic modulators will permit us to understand and regulate trafficking to enhance secretion to the plasma membrane and cell wall or the accumulation of biological energy reserves for increased biomass, nutritional value, stress resistance, and the secretion of specialized plant products.

59 BASIC BIOLOGICAL SCIENCES↗

Assessing the Consistency of Estimated Ground Cover Fractions between the BLM AIM Method and Optical Remote Sensing Method

Since 2012, Argonne National Laboratory (Argonne) has supported the Bureau of Land Management (BLM) in developing remote sensing methodologies for long-term environmental monitoring of Palo Verde Mesa in eastern Riverside County, California, including methods for: detailed mapping of ephemeral streams, estimating fractional cover of desert-land surface components (e.g., trees, shrubs, litters, and bare ground), evaluating erosion risk or land stability, and characterizing vegetation alliances using spatial structure and geostatistical approaches. These studies showed the promise of remote sensing for monitoring changes in desert landscapes by providing information that would be difficult to obtain through field surveys. During this time the BLM has also worked to establish long-term monitoring protocols and compiled field-observation data collected using standardized protocols from the Assessment, Inventory, and Monitoring (AIM) strategy. The AIM data can be compared to data derived from remote sensing methods to evaluate their relative operational utility in monitoring landscape change. If ground cover estimated using remotely sensed imagery is comparable to AIM ground cover estimates, then remote sensing can be used to monitor whether any land cover change in desert landscapes may be related to solar energy development. Therefore, the goal of this study was to determine the consistency in ground cover estimates between AIM data and those derived from publicly- available remotely sensed imagery, such as that available through the U.S. Department of Agriculture, National Agricultural Imagery Program (NAIP), to examine feasibility of a remote sensing method for complementing AIM monitoring. Based on the image analysis in this study, we also provide recommendations for how small unmanned aerial system (sUAS) data may be used to complement BLM’s AIM data and NAIP imagery for future vegetation monitoring. The ground cover types we originally planned to investigate were trees, shrubs, and bare ground. However, the small sample size and a limited range of cover fraction of trees and shrubs in the AIM dataset (e.g., 33 samples with a maximum shrub cover of 18%, 14 samples with a maximum tree cover of 17%) did not allow for performing a meaningful evaluation for the remote sensing approach. Therefore, we conducted the study focusing on bare ground, foliar, and rock cover, all of which are indicators reported in the AIM remote sensing dataset.

47 OTHER INSTRUMENTATION↗

Unified Language Frontend for Physic-Informed AI/ML

Artificial intelligence and machine learning (AI/ML) are becoming important tools for scientific modeling and simulation as in several other fields such as image analysis and natural language processing. ML techniques can leverage the computing power available in modern systems and reduce the human effort needed to configure experiments, interpret and visualize results, draw conclusions from huge quantities of raw data, and build surrogates for physics based models. Domain scientists in fields like fluid dynamics, microelectronics and chemistry can automate many of their most difficult and repetitive tasks or improve the design times by use of the faster ML-surrogates. However, modern ML and traditional scientific highperformance computing (HPC) tend to use completely different software ecosystems. While ML frameworks like PyTorch and TensorFlow provide Python APIs, most HPC applications and libraries are written in C++. Direct interoperability between the two languages is possible but is tedious and error-prone. In this work, we show that a compiler-based approach can bridge the gap between ML frameworks and scientific software with less developer effort and better efficiency. We use the MLIR (multi-level intermediate representation) ecosystem to compile a pre-trained convolutional neural network (CNN) in PyTorch to freestanding C++ source code in the Kokkos programming model. Kokkos is a programming model widely used in HPC to write portable, shared-memory parallel code that can natively target a variety of CPU and GPU architectures. Our compiler-generated source code can be directly integrated into any Kokkosbased application with no dependencies on Python or cross-language interfaces.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗