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Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

Data supporting manuscript from L. Sheneman, G. Stephanopoulos, A.E. Vasdekis titled "Deep learning classification of lipid droplets in quantitative phase images" as currently under review at PLOS ONE. This includes: 1) raw and binary labeled Quantitative Phase Images (QPI) of Y. lipolytica cells used in the analyses described within the manuscript. 2) various derived data including classifier scores, etc.

ANN↗

Design of Electrostatic Aberration Correctors for Scanning Transmission Electron Microscopy

Abstract In a scanning transmission electron microscope (STEM), producing a high-resolution image generally requires an electron beam focused to the smallest point possible. However, the magnetic lenses used to focus the beam are unavoidably imperfect, introducing aberrations that limit resolution. Modern STEMs overcome this by using hardware aberration correctors comprised of many multipole elements, but these devices are complex, expensive, and can be difficult to tune. We demonstrate a design for an electrostatic phase plate that can act as an aberration corrector. The corrector is comprised of annular segments, each of which is an independent two-terminal device that can apply a constant or ramped phase shift to a portion of the electron beam. We show the improvement in image resolution using an electrostatic corrector. Engineering criteria impose that much of the beam within the probe-forming aperture be blocked by support bars, leading to large probe tails for the corrected probe that sample the specimen beyond the central lobe. We also show how this device can be used to create other STEM beam profiles such as vortex beams and probes with a high degree of phase diversity, which improve information transfer in ptychographic reconstructions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Mixtures of CO 2 and poly(fluoroacrylate) based on monomers containing only six or four fluorinated carbons: Phase behavior and solution viscosity

In this study, homopolymerization of fluoroacrylate monomers containing a segment with eight fluorinated carbons, (CH 2 CHCOO(CH 2 ) 2 (CF 2 ) 7 CF 3 ), yield poly(fluoroacrylate) (PFA) with remarkably high solubility in CO 2 , but the corresponding ultimate PFA degradation product perfluorooctanoic acid (PFOA) is bio-accumulative. Based on cloud point loci in the 1–4 wt% PFA in CO 2 concentration range at temperatures of 25, 50, 75, 100 and 125°C, it is shown that C 6 F 13 -based and C 4 F 9 -based PFA, with relatively benign degradation products perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA), respectively, retain the same level of CO 2 -solubility as that of C 8 F 17 -based PFA. Further, both C 6 F 13 -based and C 4 F 9 -based PFA can increase the viscosity of single-phase CO 2 -PFA solutions (i.e. thicken CO 2 ) as much as C 8 F 17 -based PFA in the 25–125°C range. Therefore, the design of CO 2 -soluble PFA need not be constrained to monomers containing the C 8 F 17 moiety; fluoroacrylate monomers containing shorter fluoroalkyl segments with only four or six fluorocarbons can be utilized.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Deep learning for lipid droplet recognition in quantitative phase images

This library of Python code is used for performing semantic segmentation of images using 6 different machine learning methods. Five of the methods are implemented entirely within the scikit-learn framework. The Convolutional Neural Network (CNN) method requires Keras with a TensorFlow backend and generally uses a different set of scripts in order to perform the complete training and evaluation.

Sheneman, Lucas↗

Partition between supercooled liquid droplets and ice crystals in mixed-phase clouds based on airborne in situ observations

Abstract. The onset of ice nucleation in mixed-phase clouds determines the lifetime and microphysical properties of ice clouds. In this work, we develop a novel method that differentiates between various phases of mixed-phase clouds, such as clouds dominated by pure liquid or pure ice segments, compared with those having ice crystals surrounded by supercooled liquid water droplets or vice versa. Using this method, we examine the relationship between the macrophysical and microphysical properties of Southern Ocean mixed-phase clouds at −40 to 0 °C (e.g. stratiform and cumuliform clouds) based on the in situ aircraft-based observations during the US National Science Foundation Southern Ocean Clouds, Radiation, Aerosol Transport Experimental Study (SOCRATES) flight campaign. The results show that the exchange between supercooled liquid water and ice crystals from a macrophysical perspective, represented by the increasing spatial ratio of regions containing ice crystals relative to the total in-cloud region (defined as ice spatial ratio), is positively correlated with the phase exchange from a microphysical perspective, represented by the increasing ice water content (IWC), decreasing liquid water content (LWC), increasing ice mass fraction, and increasing ice particle number fraction (IPNF). The mass exchange between liquid and ice becomes more significant during phase 3 when pure ice cloud regions (ICRs) start to appear. Occurrence frequencies of cloud thermodynamic phases show a significant phase change from liquid to ice at a similar temperature (i.e. −17.5 °C) among three types of definitions of mixed-phase clouds based on ice spatial ratio, ice mass fraction, or IPNF. Aerosol indirect effects are quantified for different phases using number concentrations of aerosols greater than 100 or 500 nm (N>100 and N>500, respectively). N>500 shows stronger positive correlations with ice spatial ratios compared with N>100. This result indicates that larger aerosols potentially contain ice-nucleating particles (INPs), which facilitate the formation of ice crystals in mixed-phase clouds. The impact of N>500 is also more significant in phase 2 when ice crystals just start to appear in the mixed phase compared with phase 3 when pure ICRs have formed, possibly due to the competing aerosol indirect effects on primary and secondary ice production in phase 3. The thermodynamic and dynamic conditions are quantified for each phase. The results show stronger in-cloud turbulence and higher updraughts in phases 2 and 3 when liquid and ice coexist compared with pure liquid or ice (phases 1 and 4, respectively). The highest updraughts and turbulence are seen in phase 3 when supercooled liquid droplets are surrounded by ice crystals. These results indicate both updraughts and turbulence support the maintenance of supercooled liquid water amongst ice crystals. Overall, these results illustrate the varying effects of aerosols, thermodynamics, and dynamics through various stages of mixed-phase cloud evolution based on this new method that categorizes cloud phases.

54 ENVIRONMENTAL SCIENCES↗

Multi deep learning-based stochastic microstructure reconstruction and high-fidelity micromechanics simulation of time-dependent ceramic matrix composite response

A multi deep learning-based framework is developed for efficient, automated microstructure reconstruction and generation of stochastic representative volume elements (SRVEs) with periodic boundary conditions (PBCs) for accurate modeling of ceramic matrix composite (CMC) response. The methodology comprises a convolutional neural network coupled with regression layers to act as a vanilla regression network for semantic segmentation of the microstructure, allowing accurate characterization of the phases and their distributions at the microscale. Scanning electron microscope and confocal microscope are used to obtain C/SiNC and SiC/SiNC CMCs micrographs for vanilla regression testing. Microstructure variability in terms of fiber volume fraction and porosity are quantified through the output regression layer, ensuring accurate representation of material variability in SRVE construction. Generative adversarial network (GAN) and its variants are designed to produce high-fidelity SRVE, spanning CMCs microstructure variability space. A circular padding algorithm is developed to generate SRVEs with PBCs during training of GANs. The accuracy of the generated SRVEs is established through micromechanics simulations, where an efficient formulation of the high-fidelity generalized methods of cells (HFGMC) approach is used to compute the effective mechanical properties. Furthermore, an iterative algorithm is implemented in the HFGMC solver to simulate time-dependent deformation of SiC/SiNC subjected to creep loading conditions.

36 MATERIALS SCIENCE↗

ANDRA's Underground Research Laboratory in Bure: Major Role in the Cigeo Development - 20005

The Industrial Center for Geological Disposal, also called Cigeo, is the deep geological disposal facility project developed by Andra since 1991. It is intended for the final disposal of High-Level Waste (HLW) and Intermediate Level Waste-Long Lived (ILW-LL) generated in France by the nuclear industry. Cigeo is located in the east of France (Meuse/Haute-Marne site). The disposal will be implemented in a 140 to 160 m thick clay layer at about 500 m depth. The license application file will be submitted in 2020. If the license is granted, the construction of the pilot phase of Cigeo (ramp, shafts, drifts, initial disposal vaults) could start in 2025 at the earliest. Since 2000, the development of the safety case of Cigeo for post closure has been supported by a three-stage construction, design, and scientific and technological experiment program performed in the French Underground Research Laboratory (URL) in Bure. These stages of the URL activities supported the iterative interactions between the knowledge acquired by scientific and technological R and D program, the design process and the safety assessment. The stages focused on assessing the suitability of the disposal concept, providing the basis for safety options and construction design, and preparing for licensing using large scale demonstrations. Recently, Andra launched the fourth development stage of the URL to implement a new set of technological experiments aiming at consolidating the design options of disposal cells and galleries for the pilot phase of Cigeo and at assessing monitoring technologies. Recently, Andra launched the fourth development stage of the URL to implement a new set of technological experiments aiming at consolidating the design of the pilot phase of Cigeo and at assessing design options and monitoring technologies. Removal of a segment ring, construction of an X drift crossing, improved construction techniques for HLW vaults, and construction of an ILW-LL prototype disposal vault are example activities during the fourth phase. In the future, the URL in Bure will remain a unique location to carry out research on promising technical solutions, to reduce Cigeo's construction and operation risks and strengthen the long-term safety assessment. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Geometrical-Based Generative Adversarial Network to Enhance Digital Rock Image Quality

X-ray microcomputed tomography (micro-CT) is a common tool for the study of porous media structures and properties. High-quality micro-CT data are required to accurately capture pore structures. Acquiring high-quality micro-CT data, however, is not always possible, owing to application limitations and experimental constraints. Therefore, we propose a geometrical-based generative adversarial network (GAN) to rapidly restore noisy micro-CT images to their clean counterparts. The training data and related ground-truth (GT) data are scanned for 7 min and 9.5 h, respectively. To evaluate the performance of the geometrical-based GAN, a 6003 voxel image that has never been used for training is reconstructed and compared with the corresponding GT image. Histogram matching and linear normalization are implemented to adjust the histogram of the reconstructed image to that of the GT image. A watershed-based segmentation method is then applied to delineate pore and solid phases. Lastly, we measure the Minkowski functionals and petrophysical properties, including absolute permeability, pore size distribution, drainage capillary pressure-saturation curve, and imbibition relative permeability, to estimate the physical accuracy of the denoised image. The results show that the proposed geometrical-based GAN can accurately restore noisy micro-CT data. By reducing the scanning time from 9.5 h to 7 min, the expenditure of collecting micro-CT can be decreased significantly. This is particularly important for applications where time-lapse images of a dynamic process are required, high-throughput imaging is necessary for real-time data analysis, or where the quantification of large sample volumes is required.

58 GEOSCIENCES↗

Grain2mesh: A Python and cubit mesh generator from unprocessed mesoscale images

Predicting bulk behavior from microscale features constitutes a key objective in multiscale modeling research, often involving numerical models composed of finite elements that capture the diversity of constituent phases, shapes, and orientations within the material. The Grain2mesh toolbox allows the user to input unprocessed mesoscopic images for automatic segmentation, pre-processing, quality control, and numerical mesh generation. The numerical mesh generation incorporates Cubit routines to generate robust multi-phase mesh structure for use in computational mechanics solvers. The python classes developed contain detailed documentation and examples to support standard usage and case-specific alternative options.

58 GEOSCIENCES↗

Structural insights into plasmalemma vesicle-associated protein (PLVAP): Implications for vascular endothelial diaphragms and fenestrae

In many organs, small openings across capillary endothelial cells (ECs) allow the diffusion of low–molecular weight compounds and small proteins between the blood and tissue spaces. These openings contain a diaphragm composed of radially arranged fibers, and current evidence suggests that a single-span type II transmembrane protein, plasmalemma vesicle-associated protein-1 (PLVAP), constitutes these fibers. Here, we present the three-dimensional crystal structure of an 89-amino acid segment of the PLVAP extracellular domain (ECD) and show that it adopts a parallel dimeric alpha-helical coiled-coil configuration with five interchain disulfide bonds. The structure was solved using single-wavelength anomalous diffraction from sulfur-containing residues (sulfur SAD) to generate phase information. Biochemical and circular dichroism (CD) experiments show that a second PLVAP ECD segment also has a parallel dimeric alpha-helical configuration—presumably a coiled coil—held together with interchain disulfide bonds. Overall, ~2/3 of the ~390 amino acids within the PLVAP ECD adopt a helical configuration, as determined by CD. We also determined the sequence and epitope of MECA-32, an anti-PLVAP antibody. Taken together, these data lend strong support to the model of capillary diaphragms formulated by Tse and Stan in which approximately ten PLVAP dimers are arranged within each 60- to 80-nm-diameter opening like the spokes of a bicycle wheel. Passage of molecules through the wedge-shaped pores is presumably determined both by the length of PLVAP—i.e., the long dimension of the pore—and by the chemical properties of amino acid side chains and N-linked glycans on the solvent-accessible faces of PLVAP.

59 BASIC BIOLOGICAL SCIENCES↗

Data-Efficient Methods for Determining Flory–Huggins χ Parameters in Multicomponent Polymer Formulations

Polymer formulations are essential in diverse applications including personal care products, coatings, paints, adhesives, and plastic materials. Designing these formulations requires navigating large, complex design spaces, where phase and self-assembly behavior critically impact performance. The Flory–Huggins χ parameter, which quantifies segmental miscibility, is widely used to parametrize the excess free energy of mixing in formulation models. In this work, we introduce two data-efficient, top-down methods for estimating χ parameters using the Random Phase Approximation (RPA): (i) Boundary Nonlinear Regression (Boundary-NLR), which fits theoretical spinodal boundaries to experimental phase boundaries, and (ii) Surrogate Model Inverse Parameter Estimation (SMIPE), which uses a Gaussian Process Classifier to fit sparse phase maps via a surrogate model. Both methods allow rapid parametrization of polymer field-theoretic models without the need for additional experiments. We evaluate these approaches on data sets involving polymer–solvent–nonsolvent ternary mixtures and block copolymer–solvent systems, demonstrating their robustness to experimental noise and their relevance for real-world formulation design.

copolymers↗

Deep learning-based segmentation of lithium-ion battery microstructures enhanced by artificially generated electrodes

Accurate 3D representations of lithium-ion battery electrodes, in which the active particles, binder and pore phases are distinguished and labeled, can assist in understanding and ultimately improving battery performance. Here, we demonstrate a methodology for using deep-learning tools to achieve reliable segmentations of volumetric images of electrodes on which standard segmentation approaches fail due to insufficient contrast. We implement the 3D U-Net architecture for segmentation, and, to overcome the limitations of training data obtained experimentally through imaging, we show how synthetic learning data, consisting of realistic artificial electrode structures and their tomographic reconstructions, can be generated and used to enhance network performance. We apply our method to segment x-ray tomographic microscopy images of graphite-silicon composite electrodes and show it is accurate across standard metrics. We then apply it to obtain a statistically meaningful analysis of the microstructural evolution of the carbon-black and binder domain during battery operation.

25 ENERGY STORAGE↗

Influence of fixed charge concentration and water uptake on ion sorption in AMPS/PEGDA membranes

Water content and charge density strongly influence ion sorption in charged membranes. However, isolating the individual effect of each parameter on ion sorption can be difficult due to experimental challenges associated with independently controlling these two variables during membrane synthesis. This frustrates development and validation of fundamental models and structure/property relationships. In this study, three series of uncharged and negatively charged hydrogel membranes were prepared using poly(ethylene glycol) diacrylate (PEGDA) as a cross-linker and 2-acrylamido-2-methylpropanesulfonic acid (AMPS) as an ionic monomer. Here, water content and charge density were controlled by varying AMPS content and PEGDA chain length. Ion sorption in these materials was measured using aqueous NaCl solutions at concentrations ranging from 0.01 to 1.0 M. At constant charge density, salt sorption increased as water content increased. At fixed water content, salt sorption decreased as charge density increased. Salt sorption in membranes with the highest water content and charge density was predicted using the Donnan/Manning model, which accounts for solution and membrane phase thermodynamic non-idealities. However, this approach could not predict sorption in weakly charged and uncharged membranes, presumably due to additional membrane phase thermodynamic non-idealities associated with ion solvation and uncharged polymer segments.

36 MATERIALS SCIENCE↗

Vibro-impact analysis and characterization of pipeline conveying fluids with multi-segmented motion-limiting constraints

Previous studies of the cantilevered pipeline conveying fluid system have included motion-limiting constraints in the form of trilinear springs. While this is desirable in experimental scenarios, it may not be representative of real-world applications. Therefore, here, this study focuses on multi-segmented motion-limiting constraints. As this type of motion-limiting constraint has not been investigated with a cantilevered pipeline system, a wide variety of outer and inner constraint stiffness and constraint gap sizes are investigated in this study to gain a comprehensive understanding of how the multi-segmented constraints affect the dynamics of the cantilevered pipeline. In this effort, bifurcation diagrams, phase portraits, Poincare maps, time histories, and power spectra are used to investigate the dynamics of the system, and the fluid flow speeds where dynamic characteristics are considered. In general, it is found that critical flow speeds like when the pipe sticks in the constraints are reduced as the constraint stiffnesses are increased. Additionally, the sticking flow speed occurred at lower flow speeds as the gap sizes of the inner and outer constraints decrease, and a larger constraint offset results in a smaller inner gap size leading to critical behaviors occurring at earlier flow speeds.

97 MATHEMATICS AND COMPUTING↗

Nanopore networks in colloidal silica assemblies characterized by XCT for confined fluid flow modeling

Fluid flow through nanopore structures has exhibited different behavior than that described by Darcy's law, derived from pore networks of micrometer scale. Here, pressure assemblies of colloidal silica spheres of specified diameters from 94 to 620 nanometers were prepared as model nano-porous media. The smaller silica spheres tended to form random packing, but some substantial ordering was found in the packing of the larger silica spheres. X-ray computed tomography (XCT), with a voxel resolution of 16 nm, was used to characterize the nanopore networks. The porosity of the Nano-XCT pore network (34%) was less than the total porosity of the assemblies as determined by X-ray attenuation (52%), possibly due to the limits of voxel resolution during segmentation. Fluid flow in the nanopore networks was simulated using the single-phase Lattice Boltzmann Method, and the simulated permeability was compared with the empirical and experimental values. Based on our characterization, although a well-ordered packing of silica spheres was not achieved, it was found that the nanopore networks in the colloidal silica assemblies had pore size distributions corresponding to the particle sizes. The simulated permeability was less than the experimental measurement for water flow, but the complex packing of silica spheres and surface chemistry issues need to be considered in future research.

02 PETROLEUM↗

Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils

The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP’s propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development.

60 APPLIED LIFE SCIENCES↗

Correlated X‐Ray and Electron Microscopies of a Single Biphasic GaAs Nanowire

Engineering the properties of semiconductors by changing their crystalline phase is a technologically and economically relevant alternative to doping using foreign elements, with strong potential for photonic and electronic applications. Although major advances have been reported recently for crystal‐phase engineering of III‐V and group IV semiconductor nanowires, interfacing two mismatched crystalline phases in a nanostructure induces several deformation mechanisms, which remain largely unexplored. Here, using state‐of‐the‐art synchrotron X‐ray nanobeam diffraction and transmission electron microscopy, subtle twisting and bending is unveiled within an individual GaAs nanowire containing cubic and hexagonal segments. Their role is discussed in accommodating the inter‐reticular spacing fluctuations, and their variations are correlated to the nanoscale phase distribution and to the effect of the NW support. This study brings direct evidence of a complex combination of deformation mechanisms in biphasic nanowires, which opens a new path to tune the nanowire properties with appealing perspectives for device engineering in nanophotonics and nanomechanics.

III-V semiconductors↗

Sister Rod Destructive Examinations (FY23) Appendix E2: Four-Point Bend Fractured Specimen Images

This report documents work performed under the Spent Fuel and Waste Disposition’s Spent Fuel and Waste Science and Technology program for the US Department of Energy (DOE) Office of Nuclear Energy (NE). This work was performed to fulfill Level 2 Milestone M2SF-24OR010201024, “FY23 ORNL Testing on Sibling Pins,” within work package SF-24OR01020102 and is an update to the work reported in M2SF-23OR010201024, M2SF-22OR010201047, M2SF-21OR010201032, M2SF-19ORO010201026, and M2SF-19OR010201028. As a part of the DOE NE High Burnup Spent Fuel Data Project, Oak Ridge National Laboratory (ORNL) is performing destructive examinations (DEs) of high burnup (HBU) (>45 GWd/MTU) spent nuclear fuel (SNF) rods from the North Anna Nuclear Power Station operated by Dominion Energy. The SNF rods, called sister rods or sibling rods, are all HBU and include four different kinds of fuel rod cladding: standard Zircaloy-4 (Zirc-4), low-tin Zirc-4, ZIRLO, and M5. The DEs are being conducted to obtain a baseline of the HBU rods’ condition before they are sent to dry storage and are focused on gaining an understanding of overall SNF rod strength and durability. Composite fuel and defueled cladding will be tested to derive material properties. Although the data generated can be used for multiple purposes, one primary goal for obtaining the post-irradiation examination data and the associated measured mechanical properties is to support SNF dry storage licensing and relicensing activities by (1) addressing identified knowledge gaps and (2) enhancing the technical basis for post-storage transportation, handling, and subsequent disposition. This report documents the status of the ORNL Phase 1 DE activities related to the mechanical testing of selected sister rods in Phase 1 of the sister rod test program. This appendix provides images of the segments broken in four-point bending (4PB).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗