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At least 163 records · Page 9

FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images

The extracellular matrix (ECM) is a complex network of biomolecules that plays an integral role in the structure, processes, and signaling mechanisms of cells and tissues. Identifying and quantifying changes in these matrix components provides insight into the mechanisms behind specific tissue remodeling processes; however, quantifying these changes is challenging due to difficult imaging conditions, complexity of the ECM, and the subtlety of these changes. Current imaging techniques allow us to visualize these critical remodeling events and developments in image analysis have employed a combination of analysis software and machine learning techniques to improve the efficiency and accuracy with which features are measured. Although image analysis has seen much improvement in recent years, there has been no technique developed to address ambiguity in feature edges in electron microscopy images. Presented here is a new machine learning-based workflow for the analysis of microscopy images named FIRM (Feature Identification from Raw Microscopy) that uses a random forest classifier to identify ECM features of interest and generate binary segmentation masks for quantification with ImageJ-FIJI. FIRM performed with an F1 score of 0.794 and greater than 80% accuracy for number and size of features detected. FIRM had similar deviation from the ground truth in the number of identified fibrils, fibril size, and size distributions when compared to human analyses. The results suggest that FIRM performs as well as manual analysis and requires a fraction of the time. This analysis technique is more efficient, eliminates user bias, and can be easily optimized to identify a variety of features, making it useful for any discipline requiring image analysis.

Science & Technology - Other Topics↗

Quantitative investigation of surface structure and interatomic potential with impact-collision ion scattering spectroscopy

Helium ion beam interactions with materials have important implications for magnetic confinement fusion, material modification, and helium ion microscopy. These interactions depend on the precise physics of how helium ions channel into the materials, which can vary greatly based on the local crystalline orientation. Here, we performed a dedicated experiment to investigate helium ion channeling in a well-characterized tungsten single crystal. Time-of-flight impact-collision ion scattering spectroscopy was used to obtain multi-angle maps of the backscattering intensity for 3 keV He + → W(111). We found that the backscattering intensity profile arising from helium ion channeling could be well described by a shadow cone analysis. This analysis revealed that subsurface W atoms as deep as the ninth monolayer contributed to the backscattering intensity profile. Binary collision approximation simulations were performed with MARLOWE to model the experimental maps with sufficient accuracy to allow for quantitative comparisons using reliability factors. These quantitative comparisons were applied to investigate how the W lattice structure and He–W interatomic potential affect the multi-angle maps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Efficient loading of reduced data ensembles produced at ORNL SNS/HFIR neutron time-of-flight facilities

We present algorithmic improvements to the loading operations of certain reduced data ensembles produced from neutron scattering experiments at Oak Ridge National Laboratory (ORNL) facilities. Ensembles from multiple measurements are required to cover a wide range of the phase space of a sample material of interest. They are stored using the standard NeXus schema on individual HDF5 files. This makes it a scalability challenge, as the number of experiments stored increases in a single ensemble file. The present work follows up on our previous efforts on data management algorithms, to address identified input output (I/O) bottlenecks in Mantid, an open-source data analysis framework used across several neutron science facilities around the world. We reuse an in-memory binary-tree metadata index that resembles data access patterns, to provide a scalable search and extraction mechanism. In addition, several memory operations are refactored and optimized for the current common use cases, ranging most frequently from 10 to 180, and up to 360 separate measurement configurations. Results from this work show consistent speed ups in wall-clock time on the Mantid LoadMD routine, ranging from 19% to 23% on average, on ORNL production computing systems. The latter depends on the complexity of the targeted instrument-specific data and the system I/O and compute variability for the shared computational resources available to users of ORNL’s Spallation Neutron Source (SNS) and the High Flux Isotope Reactor (HFIR) instruments. Nevertheless, we continue to highlight the need for more research to address reduction challenges as experimental data volumes, user time and processing costs increase.

Godoy, William↗

Techno-Economic Analysis of Greenfield Geothermal Hybrid Power Plants using a Solar or Natural Gas Steam Topping Cycle

The relatively low generation costs associated with wind, solar PV, and natural gas power plants make it challenging for geothermal power plants to produce and sell the power that has the reliability and sustainability characteristics that are greatly needed in US power markets. This is especially true for geothermal resources with low to medium temperatures, which results in relatively low thermal efficiency and generation costs that are higher than those for wind, solar PV, and natural gas. This analysis evaluates solar thermal- and natural gas combustion waste heat recovery-based topping cycle hybridization of geothermal binary power plants. This approach provides several benefits that may allow geothermal power plants to generate power at more competitive costs. First, the addition of solar thermal energy or natural gas combustion waste heat input to a geothermal power plant provides additional heat input that can be converted to electrical power. Second, the temperature level of the heat obtained from concentrating solar collectors or natural gas combustion exhaust is higher than that of geothermal heat, which provides opportunities for improving the efficiency of the conversion of thermal energy to electrical power. Third, the ease with which solar thermal systems integrate with energy storage and the flexibility of natural gas means power generation can occur during peak demand periods.

14 SOLAR ENERGY↗

Assurance of Reasoning Enabled Systems (ARES)

ARES was in part motivated by the determination of President’s Council of Advisors on Science and Technology (PCAST) on May 13th, 2023 that published a set of inquiries: In an era in which convincing images, audio, and text can be generated with ease on a massive scale, how can we ensure reliable access to verifiable, trustworthy information? How can we be certain that a particular piece of media is genuinely from the claimed source? What technologies, policies, and infrastructure can be developed to detect and counter AI-generated disinformation? In an effort to automatically analyze and patch/optimize code the work in this report describes various neural Machine Learning (ML) analysis engine implementations to assist in situations where source code is deficient or completely lacking to decompile (lift) binary code to ’C’. The goal is to gradually reduce human intervention. To this end, two Large Language Model (LLM) variants (Code LLama 2, LLama 3.1 and Starcoder1, Starcoder 2) where finetuned with ’before/after’ code pairs on the OpenBLAS library. LLama trained on the lowering process, Starcoder trained on the lifting process with National Security Agency’s (NSA) open-source Ghidra decompiler assist. The inferencing test results indicate correctness for only very short sequences for Starcoder 2. Moving forward, the experiments conclude with a set of recommendations of required resources and technologies

97 MATHEMATICS AND COMPUTING↗

Proposed Analytical Methods for Determining Filter Media Properties

High Efficiency Particulate Air (HEPA) filters, commonly used in nuclear filtration applications, are an integral part of the waste management processes in nuclear plants. HEPA filters are 99.97% efficient filtration devices characterized by their high resistance to air flow, or pressure drop. From theoretical models, the initial pressure drop across a clean filter is proven to be a function of the filter media fiber diameters and porosity of the media. These filter properties are relatively difficult to obtain with traditional manual methods; therefore, there is a need to develop analytical methods to find the fiber diameter and porosity to determine the pressure drop. Typically, these values can be found by substituting a calculated representative value based upon measured values, such as equivalent fiber diameter based upon a clean pressure drop. However, these values may also be directly recorded and measured by incorporating Scanning Electron Microscope (SEM) image analysis and other measurement methods to analyze the filter media and determine its physical properties without the need for media testing. DiameterJ, an open source Java plug-in, used with ImageJ, can process images of filter media taken by an SEM to find statistical data such as mean fiber diameter and porosity. To produce the raw data, SEM images of two filter media type samples are taken and segmented in DiameterJ using the traditional and statistical region merging segmentation algorithms. Manual segmentation is necessary after the initial segmentation by the algorithms as the images tend to be too complex for the algorithms to output with the necessary accuracy. However, complications exist in the manual segmentation process as these methods can be time intensive and prone to the individual bias of the user. This in turn can skew the final mean fiber diameter result, and lead to either an over or under prediction of the pressure drop. It was also discovered that the porosity data produced by DiameterJ is inaccurate, as the SEM analyzes the three-dimensional filter media by projecting its geometry onto a plane and analyzing it as a two-dimensional binary image. Thus, the porosity is artificially inflated through the segmentation process, rendering this result incorrect. Alternatively, density determination, gravimetric analysis, and thickness testing of the filter media is collectively used to determine the filter fiber porosity. Together, the SEM image analysis and analytical lab methods produce results through direct measurements which allow for the prediction of the initial pressure drop from clean filter media without the need for prior media testing to collect pressure data. By improving upon this proposed analytical method in the future, there is potential to streamline the process of finding these filter properties into a more direct methodology for determining the pressure drop across HEPA filters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

The Challenges Ahead for Multimessenger Analyses of Gravitational Waves and Kilonova: A Case Study on GW190425

In recent years, there have been significant advances in multimessenger astronomy due to the discovery of the first, and so far only confirmed, gravitational wave event with a simultaneous electromagnetic (EM) counterpart, as well as improvements in numerical simulations, gravitational wave (GW) detectors, and transient astronomy. This has led to the exciting possibility of performing joint analyses of the GW and EM data, providing additional constraints on fundamental properties of the binary progenitor and merger remnant. Here, in this work, we present a new Bayesian framework that allows inference of these properties, while taking into account the systematic modeling uncertainties that arise when mapping from GW binary progenitor properties to photometric light curves. We extend the relative binning method presented in Zackay et al. to include extrinsic GW parameters for fast analysis of the GW signal. The focus of our EM framework is on light curves arising from r-process nucleosynthesis in the ejected material during and after merger, the so-called kilonova, and particularly on black hole–neutron star systems. As a case study, we examine the recent detection of GW190425, where the primary object is consistent with being either a black hole or a neutron star. We show quantitatively how improved mapping between binary progenitor and outflow properties, and/or an increase in EM data quantity and quality are required in order to break degeneracies in the fundamental source parameters.

79 ASTRONOMY AND ASTROPHYSICS↗

Polymer electrolytes based on protic ionic liquids with perfluorinated anions for safe lithium-ion batteries

Here, the quest for safe and high-performance polymer electrolytes in lithium-ion batteries (LIBs) has led researchers to explore protic ionic liquids (PILs) as potential candidates to be entrapped in polymer matrices. In this context, we present an investigation into solid polymeric systems based on poly(methyl methacrylate) (PMMA) as a host for PILs, featuring 1,8-diazabicyclo-[5,4,0]-undec-7-ene (DBU) cation paired with three different anions: bis(trifluoromethanesulfonyl)imide (TFSI – ), trifluoromethanesulfonate (TFO – ), and (trifluoromethanesulfonyl-nonafluorobutylsulfonyl)imide (IM14 – ). Additionally, we explore the lithium-doped IM14-gel-like system to broaden our understanding of these intriguing materials. Through comprehensive thermal analysis, solid-state NMR, and diffusion NMR techniques, we delve into the interactions and structural features of these binary and ternary polymeric systems. Our investigation reveals unique dynamics and ion interactions within the PMMA matrix, shedding light on the potential of these materials for advanced energy storage technologies. Particularly, we highlight the distinctive features of DBUH-IM14 and its specific interaction with the polymeric matrix and the lithium ions, underscoring its significance in advancing safer and more efficient energy storage devices.

25 ENERGY STORAGE↗

Benchmarking Coordination Number Prediction Algorithms on Inorganic Crystal Structures

Coordination numbers and geometries form a theoretical framework for understanding and predicting materials properties. Algorithms to determine coordination numbers automatically are increasingly used for machine learning and automatic structural analysis. In this work, we introduce MaterialsCoord, a benchmark suite containing 56 experimentally-derived crystal structures (spanning elements, binaries, and ternary compounds) and their corresponding coordination environments as described in the research literature. We also describe CrystalNN, a novel algorithm for determining near neighbors. We compare CrystalNN against 7 existing near-neighbor algorithms on the MaterialsCoord benchmark, finding CrystalNN to perform similarly to several well-established algorithms. For each algorithm, we also assess computational demand and sensitivity towards small perturbations that mimic thermal motion. Finally, we investigate the similarity between bonding algorithms when applied to the Materials Project database. Finally, we expect that this work will aid the development of coordination prediction algorithms as well as improve structural descriptors for machine learning and other applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Effect of Solvents on Lignin–Surface Interactions via Molecular Dynamics Simulations

Lignin, an essential building block of lignocellulosic biomass, is a potential abundant source of aromatic monomers for the polymer and chemical industry. Reductive catalytic fractionation (RCF) is one promising process that can produce high yields of phenolic monomers and oligomers from lignin under different catalytic conditions. An important choice in optimizing RCF is the selection of solvent; however, detailed insights into solvent effects on lignin behaviors and interactions remain limited. Here, in this work, we perform all-atom molecular dynamics simulations to study the solvation of lignin, solvent-mediated conformational changes, and the interaction of solvated lignin oligomers with model surfaces. We focus on the behavior of an oligomeric lignin model compound in methanol, ethanol, a binary mixture of ethanol and water, and water at both the RCF reaction temperature (473 K) and room temperature. Analysis of structural features of lignin suggests that these three organic solvent systems favorably solvate lignin, resulting in a more extended conformation suitable for catalytic conversion to valuable chemicals. We further introduce model palladium (Pd) and carbon (C) surfaces to understand how solvent choice impacts adsorption onto a representative catalytic surface and support, and to quantify the competition among the reactant and solvent molecules for the surface. Unbiased simulations suggest strong adsorption of lignin on both Pd and C surfaces at 473 K, with notable solvent-mediated differences in adsorption energies. Additionally, our findings indicate that lignin adsorption is promoted by the entropy change resulting from the displacement of solvent molecules from the surface. This study provides a molecular perspective of adsorption of lignin onto varying surfaces, which is a step towards understanding and optimizing the catalytic conversion of lignin into valuable chemicals.

adsorption↗

An Overview of ARTMIP's Tier 2 Reanalysis Intercomparison: Uncertainty in the Detection of Atmospheric Rivers and Their Associated Precipitation

Atmospheric rivers, or long but narrow regions of enhanced water vapor transport, are an important component of the hydrologic cycle as they are responsible for much of the poleward transport of water vapor and result in precipitation, sometimes extreme in intensity. Despite their importance, much uncertainty remains in the detection of atmospheric rivers in large datasets such as reanalyses and century scale climate simulations. To understand this uncertainty, the Atmospheric River Tracking Method Intercomparison Project (ARTMIP) developed tiered experiments, including the Tier 2 Reanalysis Intercomparison that is presented here. Eleven detection algorithms submitted hourly tags--binary fields indicating the presence or absence of atmospheric rivers--of detected atmospheric rivers in the Modern Era Retrospective Analysis for Research and Applications, version 2 (MERRA-2) and European Centre for Medium-Range Weather Forecasts' Reanalysis Version 5 (ERA5) as well as six-hourly tags in the Japanese 55-year Reanalysis (JRA-55). Due to a higher climatological mean for integrated water vapor transport in MERRA-2, atmospheric rivers were detected more frequently relative to the other two reanalyses, particularly in algorithms that use a fixed threshold for water vapor transport. The finer horizontal resolution of ERA5 resulted in narrower atmospheric rivers and an ability to detect atmospheric rivers along resolved coastlines. We found that the fraction of hemispheric area covered by ARs varies throughout the year in all three reanalyses, with different atmospheric river detection tools having different seasonal cycles.

54 ENVIRONMENTAL SCIENCES↗

Giant magnetic anisotropy of Pb atoms in 3 d -based magnets

Electronic structure analysis is performed to study the properties of several Pb-containing 3⁢ d intermetallics. Our study reveals that binary metastable C⁢o 3 ⁢Pb and F⁡e 3 ⁢Pb intermetallic compounds exhibit very attractive intrinsic magnetic properties. We primarily focus on the magnetic anisotropic properties arising from the high spin-orbit coupling of the Pb atom. Decomposing the total anisotropy into intra- and interatomic contributions reveals a significant deviation from single-ion anisotropy model with strong symmetric anisotropic pair interactions present. Furthermore, we consider magnetic properties of ternary Pb-based 3⁢⁢ d intermetallics, which recently have been reported as stable or metastable. Giant magnetic anisotropy is found on Pb atoms in these systems. The origin of such strong anisotropy in L⁢a 18⁢ C⁢o 28 ⁢P⁢b 3 appears from two sources: spin-orbit and interelectronic Breit couplings. Additionally, the significance of Breit interaction for magnetic anisotropy in bulk systems is reported. It is expected that Breit coupling-induced anisotropy is dominating in magnetic Pb-based magnets with lower dimensionality including thin films.

74 ATOMIC AND MOLECULAR PHYSICS↗

Improvements of pre-emptive identification of particle accelerator failures using binary classifiers and dimensionality reduction

In this paper we look at the properties of the Spallation Neutron Source (SNS) Differential Beam Current Monitor (DCM) data and various methods of data transformation to improve pre-emptive detection of machine trips. In this study, the foundation of the approach is the analysis of new underlying data and understanding various properties with the goal of faster classification, higher precision and higher recall with the aim to reduce false positives as low as required. The result of the research presented in this paper are a binary classifier capable of predicting accelerator failures with millisecond classification time, 96% precision, 58% true positive and 0% false positive rate and optimization techniques enabling real-time implementations.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Composition Quantification of SiGeSn Alloys Through Time-of-Flight Secondary Ion Mass Spectrometry: Calibration Methodologies and Validation With Atom Probe Tomography

Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) is a powerful technique for elemental compositional analysis and depth profiling of materials. However, it encounters the problem of matrix effects that hinder its application. In this work, we introduce a pioneering ToF-SIMS calibration method tailored for SixGeySnz ternary alloys. SixGe1-x and Ge1-zSnz binary alloys with known compositions are used as calibration reference samples. Through a systematic SIMS quantification study of SiGe and GeSn binary alloys, we unveil a linear correlation between secondary ion intensity ratio and composition ratio for both SiGe and GeSn binary alloys, effectively mitigating the matrix effects. Extracted relative sensitivity factor (RSF) value from SixGe1-x (0.07 < x < 0.83) and Ge1-zSnz (0.066 < z < 0.183) binary alloys are subsequently applied to those of SixGeySnz (0.011 < x < 0.113, 0.863 < y < 0.935 and 0.023 < z < 0.103) ternary alloys for elemental compositions quantification. These values are cross-checked by Atom Probe Tomography (APT) analysis, an indication of the great accuracy and reliability of as-developed ToF-SIMS calibration process. Furthermore, the proposed method and its reference sample selection strategy in this work provide a low-cost as well as simple-to-follow calibration route for SiGeSn composition analysis, thus driving the development of next-generation multifunctional SiGeSn-related semiconductor devices.

36 MATERIALS SCIENCE↗

Undercooling minimization in ultrasound coupled DTA measurements of molten salts

Molten salts are ionic liquids that are used for the electrolytic pyroprocessing of metals and as heat transfer fluids in very high temperature processes. Recently, halide-based molten salt reactors (MSR) have gained momentum for high density and environmentally responsible electricity generation. The function of these reactors and their fuel cycle depend on a knowledge of the halide salt’s thermodynamic properties [1]. Therefore, high accuracy phase equilibria of MSR relevant base halide and actinide containing salts are needed. Modern thermal analysis of the phase transitions of halide salts is usually done during heating at relatively high scan rates with commercial devices. Normally such measurements are adequate for pure or pseudo-binary salts. However, as the number of components in the mixture increases, accurately resolving the liquidus becomes increasingly difficult. Reversing the scanning mode greatly increases the sensitivity of phase transition measurements but can decrease accuracy due to undercooling [2] — a common occurrence in molten halide systems [3]. This work presents the development of a differential thermal analysis (DTA) cell intended for use in radiological gloveboxes. Non-contact ultrasonic agitation of the halide salt is implemented to limit kinetic limitations on crystallization during cooling to minimize undercooling [4]. Measurements on halide salts are also presented to elucidate the effect of non-contact mixing on undercooling. Reference [1] S. Boyd and C. Taylor, “3 - Chemical fundamentals and applications of molten salts,” in Molten Salt Reactors and Thorium Energy, T. J. Dolan, Ed., Woodhead Publishing, 2017, pp. 29–91. doi: 10.1016/B978-0-08-101126-3.00003-8. [2] K. Nitsch, A. Cihlár, and M. Rodová, “Molten state and supercooling of lead halides,” J. Cryst. Growth, vol. 264, no. 1, pp. 492–498, Mar. 2004, doi: 10.1016/j.jcrysgro.2004.01.011. [3] L. Rycerz, “Practical remarks concerning phase diagrams determination on the basis of differential scanning calorimetry measurements,” J. Therm. Anal. Calorim., vol. 113, no. 1, pp. 231–238, Jul. 2013, doi: 10.1007/s10973-013-3097-0. [4] Md. H. Zahir, S. A. Mohamed, R. Saidur, and F. A. Al-Sulaiman, “Supercooling of phase-change materials and the techniques used to mitigate the phenomenon,” Appl. Energy, vol. 240, pp. 793–817, Apr. 2019, doi: 10.1016/j.apenergy.2019.02.045.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Barrier-free predictions of short-range ordering/clustering kinetics in binary FCC solid solutions

We present comparisons of kinetic Monte Carlo (kMC) simulations of isothermal short-range ordering (SRO) and clustering (SRC) kinetics in binary FCC alloys with a mean-field concentration wave (CW) model. We find that the CW model is able to give order-of-magnitude agreement with kMC simulations for ordering/clustering relaxation times over a wide range of temperatures and compositions. The advantage of the CW model is that it does not require parameterization of vacancy hopping energy barriers, which, for a concentrated alloy, becomes prohibitive. We assess limits in the accuracy of the model and discuss the effect of cooling rates as well as the extension to multi-component systems. Ultimately, the simplicity and performance of the CW model compared to kMC simulations suggests that it is a useful tool to connect with models of properties dependent on SRO/SRC as well as for designing thermal treatments to control formation of SRO/SRC.

36 MATERIALS SCIENCE↗

Classified channel masks of the East River, Colorado, U.S.A and areas of floodplain erosion and accretion ranging from 1955 to 2015

This dataset provides four sets of geotiffs used for the mapping and analysis an alluvial floodplain reach of the East River, downstream of Gothic, CO, U.S.A near Crested Butte. The files include binary masks of the river channel at five in intervals from 1955 to 2015. Another set of rasters provide a map of the channel centerline pixels of the river for each date. Also included in the dataset are rasters of the areas of channel change due to migration over 8 time intervals. The masks were generated from aerial and satellite imagery collected on seven dates over a sixty-year timespan: 1955, 1973, 1983, 1990, 2001, 2011, and 2015. The masks were analyzed using the Spatially Continuous Riverbank Erosion and Accretion Measurements (SCREAM) software detailed in Rowland et al. 2016 to create the channel centerlines and the change area rasters. The change masks were generated for the following time periods: 1955-1973; 1955-2015; 1973-1983; 1983-1990; 1990-2001; 2001-2011; 2001-2015; and 2011-2015.

54 ENVIRONMENTAL SCIENCES↗

Multimodal Analysis of Spatially Heterogeneous Microstructural Refinement and Softening Mechanisms in Three-Pass Friction Stir Processed Al4Si Alloy

Multiple thermally and thermomechanically induced microstructural refinement mechanisms can be activated in metallic alloys when subjected to solid phase processing methods such as friction stir processing (FSP). In this work, we provide detailed descriptions of the relationship between region-specific microstructural refinement mechanisms and the variation in microhardness, through a systematic and multimodal microstructural characterization of an FSP-processed 75% cold-rolled Al-4 at.% Si model binary alloy. Spatially resolved high-energy synchrotron X-ray diffraction, electron backscattered diffraction, and scanning transmission electron microscopy were used to understand the spatially heterogeneous microstructural evolution due to FSP. Results provide insights into how mechanisms such as static recovery, static recrystallization, dynamic recovery and recrystallization, geometric and continuous dynamic recrystallization, and particle-stimulated static or dynamic grain nucleation may occur heterogeneously in the microstructure as a function of the distance from the stir zone in processed alloys, directly influencing the degree of softening. The systematic analysis of microstructures and hardness in the FSP-processed model binary alloy given in this work highlights the rich microstructural domains that can be uniquely harnessed through solid phase processing of metallic alloys.

Al4Si, Friction Stir Processing, Geometric Dynamic↗