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At least 757 records · Page 42

Generative diffusion model surrogates for mechanistic agent-based biological models

Mechanistic, multicellular, agent-based models are commonly used to investigate tissue, organ, and organism-scale biology at single-cell resolution. The Cellular-Potts Model (CPM) is a powerful and popular framework for developing and interrogating these models. CPMs become computationally expensive at large space- and time- scales making application and investigation of developed models difficult. Surrogate models may allow for the accelerated evaluation of CPMs of complex biological systems. However, the stochastic nature of these models means each set of parameters may give rise to different model configurations, complicating surrogate model development. In this work, we leverage denoising diffusion probabilistic models (DDPMs) to train a generative AI surrogate of a CPM used to investigate in vitro vasculogenesis. We describe the use of an image classifier to learn the characteristics that define unique areas of a 2-dimensional parameter space. We then apply this classifier to aid in surrogate model selection and verification. Our CPM model surrogate generates model configurations 20,000 timesteps ahead of a reference configuration and demonstrates approximately a 22x reduction in computational time as compared to native code execution. Our work represents a step towards the implementation of DDPMs to develop digital twins of stochastic biological systems.

97 MATHEMATICS AND COMPUTING↗

High average-flux laser-driven neutron source

Laser-driven neutron generation is an attractive alternative to more established methods for compact, short-pulse-duration neutron sources with applications in medical science, material science and imaging. Despite extensive investigation of various techniques, achieving performance comparable to nuclear reactors or conventional accelerators remains challenging. In this work, we generate a stable, high-repetition-rate laser-driven neutron source reaching a record average flux of 7.8 × 10 7 n/sr/s, improving on other existing laser-based sources by more than one order of magnitude. Our approach is based on a two-step process where electrons are accelerated to relativistic energies via laser wakefield acceleration (LWFA), and subsequently generate neutrons through Bremsstrahlung emission followed by photonuclear reactions in a tungsten converter. Experimental results, supported by Monte Carlo simulations, show a neutron flux of 3.0 × 10 7 n/cm 2 /s near the target, on par with some compact accelerator-based neutron sources. Additionally, a direct comparison with the target-normal sheath acceleration (TNSA) pitcher-catcher scheme, performed on the same laser system, reveals a significantly higher total neutron yield of 3.9 × 10 8 neutrons per shot, outperforming the TNSA scheme by several orders of magnitude. These findings represent a significant advancement towards the development of practical laser-driven neutron sources and highlight the advantages of LWFA-based neutron generation for future applications.

Vallières, Simon [Institut National de la Recherch↗

High-Energy Coherent X-Ray Dffraction Microscopy of Polycrystal Grains: First Steps Towards a Multi-Scale Approach

Here, we present proof-of-concept imaging measurements of a polycrystalline material that integrate the elements of conventional high-energy x-ray diffraction microscopy with coherent diffraction-imaging techniques, and that can enable in situ strain-sensitive imaging of lattice structure in ensembles of deeply embedded crystals over five decades of length scale upon full realization. We demonstrate that the combination of these two characterization methods enables a more complete picture of the crystal-lattice strain than either method is capable of providing individually. Such complementary imaging capabilities are critical to addressing questions in a variety of research areas such as materials science and engineering, chemistry, and solid-state physics. Towards this eventual goal, the following key aspects are demonstrated: (1) high-energy Bragg coherent diffraction imaging (HE BCDI) of submicron-scale crystallites at 52 keV at current third-generation synchrotron light sources, (2) HE BCDI performed in conjunction with far-field high-energy diffraction microscopy (FF HEDM) on the grains of a polycrystalline sample in a smoothly integrated manner, and (3) the orientation information of an ensemble of grains obtained via FF HEDM used to perform complementary HE BCDI on multiple Bragg reflections of a single targeted grain. The imaged structures are seen to be 477 ± 50 nm or smaller in size, with an estimated strain resolution of 2.5 x 10 -4 . These steps lay the foundation for integration of HE BCDI, which typically provides a spatial resolution tens of nanometers, into a broad suite of well-established HEDM methods, extending HEDM beyond the few-micrometer resolution bound and into the nanoscale, and positioning the approach to take full advantage of the orders-of-magnitude improvement of x-ray coherence expected at fourth-generation light sources presently being built and commissioned worldwide.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Measurement of Deformation Heterogeneity During Shale Swelling Using Digital Image Correlation

Abstract Rock-fluid interactions in shale formations are one of the main sources of wellbore instability issues and inadequate stimulation performance. For better planning of fracturing operations and optimizing production from these reservoirs, it is important to understand the mechanisms behind these interactions. These issues are especially prevalent in clay-rich shales, such as Tuscaloosa Marine Shale, which is the subject of this study. Conventional techniques to quantify these shale-fluid interactions comprise of measuring swelling in powdered rock grains or measurement of deformation in the whole pieces of the core using a linear variable differential transformer and strain gages. However, the contribution from individual laminae to overall deformation cannot be evaluated using these methods. In this study, we developed an experimental setup to evaluate the spatial deformation in shale during interaction with water using digital image correlation (DIC). Deformation of two shale samples, with 34 wt% to 51 wt% clay content, was studied. White paint was used to generate a random speckle pattern on the specimen and then immersed in deionized water. The deformation process was captured using a digital camera and images were analyzed using DIC to quantify the deformation. The implementation of the DIC technique enables the visualization and quantification of spatial deformation in the specimen during interacting with water. The results show the localization of large strains in select laminations. The results provide a better understanding of shale deformation when interacting with water in comparison to traditional measurements that can provide only an average strain value.

Energy & Fuels↗

Nanoscale Three-Dimensional Imaging of Degradation in Composite Si-Containing Anodes

The use of silicon (Si) in next-generation lithium-ion battery (LIB) anodes has the potential to dramatically improve electrochemical performance over current LIB graphite (Gr) anodes, due to silicon’s higher specific capacity.1 However, widespread implementation of Si-containing anodes is inhibited by issues such as significant Si volume expansion during lithiation and an unstable solid-electrolyte interphase (SEI), resulting in unreliable performance and poor cycle life. Currently, composite anodes with both Si and graphite active materials are used to increase capacity and mitigate some of the limitations associated with Si. In composite electrodes with a heterogeneous distribution of components with varying electrical properties (including Si, Gr, conductive carbon additive, and binder), it is important to understand the local distribution of each component to correlate with electrochemical processes, particularly localized degradation and heterogeneous aging, and to optimize performance. To investigate Si-containing composite anodes in the nanoscale, we use scanning spreading resistance microscopy (SSRM), a form of scanning probe microscopy (SPM) that probes local electronic resistivity. By examining the intrinsic electronic resistivity contrast between the anode components, separate phases can be distinguished and understood within the composite structure.2 This work studies the effect of electrochemical cycling in two different electrolytes on component distribution and aging by comparing the electrical and structural evolution of composite Si-graphite electrodes and SEI before and after charge-discharge cycling. 1. W. J. Zhang. A review of the electrochemical performance of alloy anodes for lithium-ion batteries J. Power Sources 196 13–24 (2011). 2. C. Stetson, Z. Huey, A. Downard, Z. Li, B. To, A. Zakutayev, C.-S. Jiang, M. Al-Jassim, D. Finegan, S.-D. Han and S. DeCaluwe: Three-Dimensional Mapping of Resistivity and Microstructure of Composite Electrodes for Lithium-Ion Batteries. ACS Nano Letters Accepted (2020).

ADVANCED PROPULSION SYSTEMS↗

Hexamethyldisiloxane pyrolysis: probing H-atom initiation by femtosecond two-photon LIF

Previous experiments have led to the hypothesis that pyrolysis of silica nanoparticle precursors carried in an inert central gas jet surrounded by a laminar flame is initiated not by thermal decomposition (the measured jet temperatures are too low for pyrolysis), but by reactions with H-atoms diffusing from the surrounding flame into the jet. The current work tests this hypothesis using femtosecond two-photon laser-induced fluorescence (fs-TPLIF) to image H-atom concentrations in the same flame configuration as the previous experiments. Methane flames (ϕ = 0.83, 1.01 and 1.13) were generated using a multi-element diffusion (Hencken) burner equipped with a central tube through which the N2 jet was introduced. The fs-TPLIF line imaging showed significant concentrations of H-atoms in the nitrogen jets at heights above the burner (HAB) close to the methane flame front. The measurements indicate radial diffusion of the H atoms from the flame to the jet is significant. The H-atom concentrations in the jet increased with increasing stoichiometry of the methane flame. Additional experiments were performed with hexamethyldisiloxane entrained in the central jet flow. In each case, a diffusion flame producing silica nanoparticles was established at the boundaries between the central jet and the methane flames. The 2D H-atom images showed a transition from over-ventilated diffusion flames to under-ventilated diffusion flames with increasing equivalence ratio. Furthermore, the fs-TPLIF profiles show a significant production of H-atoms within the jet when the surrounding flame is lean. This knowledge contributes to a deeper understanding of the underlying mechanisms governing these synthesis flame systems and opens avenues for advancing silica nanoparticle synthesis techniques.

Kim, Keunsoo↗

Moly 99 Reactor Case Study

Molybdenum-99 (Moly 99) is a critical raw material for Technetium (Tc) 99m, a radioactive isotope most widely used in nuclear medicine procedures. Moly 99 has a short half-life of about six hours, which means it cannot be stockpiled. When Moly 99 decays, it turns into Tc 99m, which has a half-life of 214,000 years. The photon energy emitted from the decay of Moly 99 is used in a variety of nuclear imaging technologies such as gamma cameras. Furthermore, radiopharmaceutical manufacturers use the photon energy emitted from the decay of Moly 99 to produce generators for hospitals, clinics, and radiopharmacies. Once Moly 99 decays to Tc 99m, it is used to make individual patient doses for a variety of diagnostic imaging procedures. The Moly 99 Reactor Design is a conceptual blueprint for Moly 99 production that does not use weapon-grade uranium; instead, the reactor has a target core of low-enriched uranium. The reactor design is small, reaching a foot-and-a-half in height and diameter and consumes less than two megawatts of power. The reactor's only purpose is for medical isotope production and with every fission, Moly 99 is produced.

07 ISOTOPE AND RADIATION SOURCES↗

Comparison of the spatial statistics of random and defined-sequence photoresist films

The resolution-line edge roughness-sensitivity tradeoff has motivated the exploration of potential improvements using defined sequence polymers and polymer-bound photoacid generators and quenchers. We characterize the internal structures of positive tone photoresist polymer films formed from defined sequence polymers and compare them with random copolymers of the same composition. We model their imaging to connect initially to developable film structures. We use a polymer packing algorithm to simulate films of diverse compositions and locations of photoacid generators and quenchers, using the composition of an ESCAP photoresist. We use a simple extreme ultraviolet exposure-deprotection algorithm to model developable image formation within them. In all cases, the spatial distribution of chemical moieties in the film for defined sequence polymers is nearly indistinguishable from random copolymers. We evaluate several exposure-deprotection scenarios and find that a defined sequence copolymer has a distinctive developable image under certain circumstances. The use of defined sequence polymers within a photoresist layer does not automatically result in improved imaging; however, they do have some characteristics different from random polymers of the same composition. Further study of these characteristics may provide a route to improved control over the nanoscale imaging process.

36 MATERIALS SCIENCE↗

Photon Entanglement Spectroscopy and Imaging in Actinide Research

Quantumly entangled particles are capable of affecting the quantum state of their entangled counterpart instantaneously once one particle has changed. Herein, quantumly entangled photons are generated by spontaneous parametric down conversion through a temperature controlled non-linear crystals. This process generates two pairs of photons of lower energy of which the sum of energy equals the energy of the pump photons. These entangled photons can be separated and provide imaging capabilities by using one set of photons for imaging and the other set of photons for detection.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A tabletop X-ray tomography instrument for nanometer-scale imaging: reconstructions

Abstract We show three-dimensional reconstructions of a region of an integrated circuit from a 130 nm copper process. The reconstructions employ x-ray computed tomography, measured with a new and innovative high-magnification x-ray microscope. The instrument uses a focused electron beam to generate x-rays in a 100 nm spot and energy-resolving x-ray detectors that minimize backgrounds and hold promise for the identification of materials within the sample. The x-ray generation target, a layer of platinum, is fabricated on the circuit wafer itself. A region of interest is imaged from a limited range of angles and without physically removing the region from the larger circuit. The reconstruction is consistent with the circuit’s design file.

47 OTHER INSTRUMENTATION↗

Design of a graphical user interface for few-shot machine learning classification of electron microscopy data

The recent growth in data generation by modern electron microscopes requires rapid, scalable, and flexible approaches to image segmentation and analysis. Few-shot machine learning, which can richly classify images from a handful of user-provided examples, is a promising route to high-throughput analysis. However, current command-line implementations of such approaches can be slow and unintuitive to use, lacking the real-time feedback necessary to perform effective classification. Here we report on the development of a Python-based graphical user interface that enables end users to easily conduct and visualize the output of few-shot learning models. This interface is portable and can be hosted locally or on the web, providing the opportunity to reproducibly conduct, share, and crowd-source few-shot analyses.

97 MATHEMATICS AND COMPUTING↗

Using X-ray spectrum imaging to quantify fission gas in high-burnup UO2 fuel

Analysis of fission gas bubbles (FGBs) in light-water reactor (LWR) fuel is needed to improve the understanding and predictive capability of fuel evolution under normal- and transient conditions. One of the most important parameters of a FGB is the pressure of the gas, primarily Xe, inside it. Bubble volume and location (inter- vs. intragranular) are important considerations as well. However, experimental analysis of such bubbles is challenging due to their small size and embedded nature, and usefulness of the data requires large numbers be analyzed. This paper proposes a method to measure the pressure of Xe bubbles using X-ray spectrum imaging (XSI) in scanning transmission electron microscopy (STEM). From X-ray generation and instrumental parameters, the number of Xe atoms yielding a given number of Xe L-series X-ray counts is estimated, and then from the estimated volume of the bubble the Xe density is estimated, which can then be converted to pressure via an equation-of-state. We apply the method to XSI datasets from high burnup (HBu) fuel from North Anna 1 reactor in as-irradiated and post-LOCA-test conditions and find Xe pressures in the FGBs clustered around 1 GPa.

Parish, Chad [ORNL] (ORCID:0000000312097439)↗

Measurement of flow properties coupled to experimental and numerical analyses of dense, granular flows for solar thermal energy storage

Granular flows of sintered bauxite proppants were researched along an inclined plane for solar thermal energy storage applications. Granular flow properties needed to drive numeric granular models were measured for improved numerical model predictions for Carbobead CP 50/140, 40/100, and 30/60 particles. Particle shape and size distributions were determined by coupling optical microscopy to an in-house image processing algorithm. The impulse excitation technique was used to measure elastic and shear moduli, and compute Poisson’s ratio. The coefficient of static sliding friction was measured using the slip-stick method, and the static rolling friction was determined from measured shear on particles positioned between two hot-pressed plates. The coefficient of restitution was measured by dropping particles on a surface and determining the kinetic energy before and after impact with the surface using high resolution particle tracking velocimetry. Particle size did not significantly impact the coefficients of restitution and static rolling friction, however, particle shape distribution resulted in a large variation in measurements. An inclined flow experiment was performed to characterize granular flows of Carbobead CP 30/60 particles using particle image velocimetry. Numerical models of the experiment using discrete element method were generated with the measured mechanical properties as inputs for comparison with experimental results. A constant directional torque rolling friction model best predicted bulk granular flow behavior. Furthermore, good agreement between the model and experiment was achieved at ambient, steady state conditions, with average velocity differences <10%.

14 SOLAR ENERGY↗

Proximity ferroelectricity in wurtzite heterostructures

Proximity ferroelectricity is an interface-associated phenomenon in electric-field-driven polarization reversal in a non-ferroelectric polar material induced by one or more adjacent ferroelectric materials. Here, in this paper, we report proximity ferroelectricity in wurtzite ferroelectric heterostructures. In the present case, the non-ferroelectric layers are AlN and ZnO, whereas the ferroelectric layers are Al 1−x B x N, Al 1−x Sc x N and Zn 1−x Mg x O. The layered structures include nitride–nitride, oxide–oxide and nitride–oxide stacks that feature two-layer (asymmetric) and three-layer (symmetric) configurations. Ferroelectric switching in both layers is validated by multimodal characterization methods, including polarization hysteresis, anisotropic chemical etching, second harmonic generation, piezo response force microscopy, electromechanical testing and atomic resolution polarization orientation imaging in real space by scanning transmission electron microscopy. We present a physical switching model in which antipolar nuclei originate in the ferroelectric layer and propagate towards the internal non-ferroelectric interface. The domain wall leading edge produces elastic and electric fields that extend beyond the interface at close proximity, reducing the switching barrier in the non-ferroelectric layer, and allowing complete domain propagation without breakdown. Density functional theory calculations of polymorph energies, reversal barriers and domain wall energies support this model. Proximity ferroelectricity enables polarization reversal in wurtzites without the chemical or structural disorder that accompanies elemental substitution, opening new questions and opportunities regarding interface-based ferroelectricity.

36 MATERIALS SCIENCE↗

Multi-campaign ship and aircraft observations of marine cloud condensation nuclei and droplet concentrations

In situ marine cloud droplet number concentrations (CDNCs), cloud condensation nuclei (CCN), and CCN proxies, based on particle sizes and optical properties, are accumulated from seven field campaigns: ACTIVATE; NAAMES; CAMP 2 EX; ORACLES; SOCRATES; MARCUS; and CAPRICORN2. Each campaign involves aircraft measurements, ship-based measurements, or both. Measurements collected over the North and Central Atlantic, Indo-Pacific, and Southern Oceans, represent a range of clean to polluted conditions in various climate regimes. With the extensive range of environmental conditions sampled, this data collection is ideal for testing satellite remote detection methods of CDNC and CCN in marine environments. Remote measurement methods are vital to expanding the available data in these difficult-to-reach regions of the Earth and improving our understanding of aerosol-cloud interactions. The data collection includes particle composition and continental tracers to identify potential contributing CCN sources. Several of these campaigns include High Spectral Resolution Lidar (HSRL) and polarimetric imaging measurements and retrievals that will be the basis for the next generation of space-based remote sensors and, thus, can be utilized as satellite surrogates.

54 ENVIRONMENTAL SCIENCES↗

Deep learning-enabled probing of irradiation-induced defects in time-series micrographs

Modeling time-series data with convolutional neural networks (CNNs) requires building a model to learn in batches as opposed to training sequentially. Coupling CNNs with in situ or operando techniques opens the possibility of accurately segmenting dynamic reactions and mass transport phenomena to understand how materials behave under the conditions in which they are used. In this article, in situ ion irradiation transmission electron microscopy (TEM) images are used as inputs into the CNN to assess the defect generation rate, defect cluster density, and saturation of defects. We then use the output segmentation maps to correlate with conventional TEM micrographs to assess the model’s ability to detail nanoscale interactions. Next, we discuss the implications of preprocessing and hyperparameters on model variability, accuracy when expanded to other datasets, and the role of regularization when controlling model variance. Ultimately, we eliminate human bias when extrapolating physical metrics, speed up analysis time, decouple reactions that happen at 100 ms intervals, and deploy models that are both accurate and transferable to similar experiments.

Burns, Kory (ORCID:0000000158019909)↗

spammR: an R package designed for analysis and integration of spatial multi-omic measurements

Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (spatial analysis of multi-omics measurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.

spammR↗

Simulated Feasibility of 3-D Lightning Mapping From Space

In addition to the awe it inspires, lightning can illuminate the microphysical processes hidden away within deep convection. The current generation of space-based lightning mapping uses mostly 2-D optical imaging to connect overall flash characteristics to their parent storm dynamics, but are missing a dimension’s worth of information. With lightning now classified as an essential climate variable, future spaceborne mappers will need improved capabilities to take advantage of the 3-D structure of lightning flashes to support meteorological and climate modeling. We report here on a study of the feasibility of high-resolution 3-D lightning mapping using a radio frequency (RF)-based network of satellites from low-Earth orbit (LEO). Lightning sources are simulated using existing lightning mapping array (LMA) tools, modified for orbital detection, and spatially reconstructed using a Levenberg–Marquardt geolocation algorithm to assess sources of uncertainty in these solutions. We analyze the benefits and limitations of this approach compared to existing orbital and ground-based methods. Results of this study show that lightning can be mapped in 3-D with a vertical location accuracy better than 2 km using as few as five satellites in LEO capable of measuring the time-of-arrival of impulsive RF signals in the very high-frequency (VHF) band. The consequence of this study is that high-resolution, spaceborne 3-D mapping of lightning is achievable across most of the globe, having crucial implications for our understanding of not only lightning, but also severe weather development, climate science, and more.

47 OTHER INSTRUMENTATION↗