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Tardigrade-examples V0.1.0

Tardigrade-examples is a repository of computational workflows that exercise the Tardigrade software package. The Tardigrade software package is an implementation of Eringen’s micromorphic continuum theory with capabilities to support multiscale material modeling. These capabilities include homogenization through the Micromorphic Filter, calibration of micromorphic material models, and macroscale simulation in Tardigrade-MOOSE. This repository investigates continuum upscaling of various direct numerical simulations (DNS) conducted in Abaqus finite element (FE), Ratel FE, and GEOS material point method (MPM) software. Verification of the upscaling workflow is first investigated by considering DNS of trivial stress states for homogeneous materials, results of which indicate that classical continuum behavior is recovered as expected. DNS of heterogeneous materials are then considered.

Allard, Thomas↗

Penalized ensemble Kalman filters for high dimensional non-linear systems

The ensemble Kalman filter (EnKF) is a data assimilation technique that uses an ensemble of models, updated with data, to track the time evolution of a usually non-linear system. It does so by using an empirical approximation to the well-known Kalman filter. However, its performance can suffer when the ensemble size is smaller than the state space, as is often necessary for computationally burdensome models. This scenario means that the empirical estimate of the state covariance is not full rank and possibly quite noisy. To solve this problem in this high dimensional regime, we propose a computationally fast and easy to implement algorithm called the penalized ensemble Kalman filter (PEnKF). Under certain conditions, it can be theoretically proven that the PEnKF will be accurate (the estimation error will converge to zero) despite having fewer ensemble members than state dimensions. Further, as contrasted to localization methods, the proposed approach learns the covariance structure associated with the dynamical system. These theoretical results are supported with simulations of several non-linear and high dimensional systems.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Reducing Exposures to Airborne Particles Through Improved Filtration: A High-Level Modeling Analysis

Indoor airborne particulates are well-known health hazards and filtration is one common method of reducing exposures. Based on our previously developed Regional Shelter Analysis methodology and parameters that characterize the existing US building stock, we perform a high-level assessment of the potential benefits of upgrading existing filters in furnace and in heating, ventilation, and air conditioning systems using off-the-shelf filters. We use three metrics to assess the improvement: Building Transmission Factor (a measure of protection against outdoor airborne particles), Indoor Normalized Time and Space Integrated Air Concentration (a measure of indoor exposure to indoor-origin airborne particles), and Building Exit Fraction (fraction of indoor airborne particles that are released to the outdoor atmosphere). We also discuss the potential reduction in regional exposures due to particles exiting the building and exposing downwind building occupants. Our modeling indicates that while buildings provide their occupants passive protection against airborne particulate hazards, including but not limited to PM 2.5 , PM 10 , and wildfire smoke; improving particle filtration efficiency may further improve this protection. The degree of improvement varies with particle size and building type. Of the building types studied, apartments are predicted to benefit most, with greater than a factor of 2 improvement (≥50% reduction in exposures) for 1 µm particle exposures when using MERV 7 to 12 rated filters. Non-residential buildings were notably less responsive to improved filtration but had the highest Building Exit Fractions with 30% to 40% of indoor airborne particles released to the outdoor atmosphere (apartment buildings only released 6% to 9%). Improvements predicted for single family homes were intermediate between apartments and non-residential buildings. Improvements in the Regional Exposure metric are larger, ranging from a factor of 2.5x to 10x for residences (when using MERV 7 to 12 rated filters) and up to 25x for large apartments with MERV 14 or 15 rated filters. The results of our modeling analysis are broadly consistent with the limited experimental data and modeling results available in the literature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Tagged DVCS on neutron with the CLAS12 Experiment and the detector BONuS12 at Jefferson Lab (USA)

Hadronic physics studies the properties of the proton and neutron. The theory of Quantum Chromodynamics (QCD) governs the structure of hadrons. Non-perturbative structure functions are used to describe the hadrons? structure. Generalized Parton Distributions (GPDs) are a set of structure functions providing access to a 3D view of the nucleon. GPDs contain information about the longitudinal momentum and transverse position of quarks and their correlation. They are related to the spin structure and play a role in solving the proton spin puzzle. They provide access to the quarks? orbital angular momentum, a crucial puzzle piece. For this, measurements on the proton, already present, and neutron are necessary. This thesis aims to explore Compton scattering on the neutron with a deuterium target by measuring the spectator proton with the CLAS12 detector and the BONuS12 RTPC at Jefferson Lab. This work first describes the implementation, which I carried out, of a Kalman filter to reconstruct spectator protons in the BONuS12 detector. The second part of the manuscript is dedicated to the work on the analysis of DVCS on the neutron with the subtraction of background noises. Two different methods for the subtraction of ?0 will be detailed. Finally, the obtained results are presented and discussed

Ouillon, Mathieu↗

Background cancellation for frequency-selective quantum sensing

A key challenge in quantum sensing is the detection of weak time dependent signals, particularly those that arise as specific frequency perturbations over a background field. Conventional methods usually demand complex dynamical control of the quantum sensor and heavy classical post-processing. We propose a quantum sensor that leverages time independent interactions and entanglement to function as a passive, tunable, thresholded frequency filter. By encoding the frequency selectivity and thresholding behavior directly into the dynamics, the sensor is responsive only to a target frequency of choice whose amplitude is above a threshold. This approach circumvents the need for complex control schemes and reduces the post-processing overhead.

Puig, Ricard [Los Alamos; Ecole Polytechnique, Lau↗

The Binary INformation from Open Clusters Using SEDs (BINOCS) Project: Reliable Photometric Mass Determinations of Binary Star Systems in Clusters

We introduce a new binary detection technique, Binary INformation from Open Clusters using SEDs (binocs), which we show is able to determine reliable stellar multiplicity and masses over a much larger mass range than current approaches. This new technique determines accurate component masses of binary and single systems of the open clusters’ main sequence by comparing observed magnitudes from multiple photometric filters to synthetic star spectral energy distributions (SEDs), allowing us to systematically probe the binary population for low-mass stars in clusters for eight well-studied open clusters. We provide new deep, infrared photometric catalogs (1.2–8.0 μm) for the key open clusters NGC 1960 (M36), NGC 2099 (M37), NGC 2420, and NGC 2682 (M67), using observations from NOAO/NEWFIRM and Spitzer/IRAC. Using these deep multiwavelength catalogs, the binocs method is applied to these clusters to determine accurate component masses for unresolved cluster binaries. We explore binary fractions as a function of cluster age, Galactic location, and metallicity.

47 OTHER INSTRUMENTATION↗

A Stochastic Covariance Shrinkage Approach in Ensemble Transform Kalman Filtering

The Ensemble Kalman Filters (EnKF) employ a Monte-Carlo approach to represent covariance information, and are affected by sampling errors in operational settings where the number of model realizations is much smaller than the model state dimension. To alleviate the effects of these errors EnKF relies on model-specific heuristics such as covariance localization, which takes advantage of the spatial locality of correlations among the model variables. This work proposes an approach to alleviate sampling errors that utilizes a locally averaged-in-time dynamics of the model, described in terms of a climatological covariance of the dynamical system. We use this covariance as the target matrix in covariance shrinkage methods, and develop a stochastic covariance shrinkage approach where synthetic ensemble members are drawn to enrich both the ensemble subspace and the ensemble transformation. We additionally provide for a way in which this methodology can be localized similar to the state-of-the-art LETKF method, and that for a certain model setup, our methodology significantly outperforms it.

54 ENVIRONMENTAL SCIENCES↗

Uncertainty quantification and reliability assessment for intermodal freight transportation

Intermodal freight optimization models support cost-effective, low-emission, and timely goods movement by coordinating trucks, rail, and barges. These models determine optimal flows, routing, and modal switches while respecting infrastructure and operational constraints. However, their real-world utility is often undermined by pervasive uncertainties-such as fluctuating transportation costs and emissions, variable terminal capacities, and uncertain freight demand-that distort key performance outcomes, including total system cost, carbon footprint, and transit time reliability. This study presents a structured framework for quantifying uncertainty in intermodal freight transportation (IFT) optimization. The framework evaluates how input uncertainty affects system performance and reliability, a critical need for ensuring that model-based decisions remain robust under real-world variability, especially amid volatile fuel prices, shifting demand, and growing disruptions. It integrates three complementary methods: (1) Sobol-based global sensitivity analysis to identify influential parameters affecting cost, emissions, and transit time, (2) Monte Carlo-based capacity perturbation analysis to assess robustness under probabilistic facility disruptions, and (3) Monte Carlo filtering with Bayesian inference to detect threshold-based performance vulnerabilities. The results highlight diesel truck unit cost as the dominant driver of variability. To improve system resilience, planners should prioritize uncertainty in fuel-related parameters when designing intermodal strategies.

Intermodal freight transportation↗

Phase-shifted Bragg gratings in a foundry silicon nitride platform

Bragg gratings are key optical elements for applications in communications, sensing, and lasers. Phase-shifted Bragg gratings are a special case where the simple periodic structure is altered to allow a narrow spectral passband within the optical bandgap. Here, we demonstrate phase-shifted silicon nitride gratings fabricated using 193 nm deep ultraviolet lithography (DUV) on the AIM Photonics 300 mm silicon photonics foundry line. We measure the grating properties and verify the results with a transfer-matrix method (TMM) model. The standard grating expressions for extracting the coupling coefficient κ and bandwidth do not apply and are updated to account for the phase shift. These results inform future designs for on-chip grating filters and distributed feedback (DFB) lasers.

Husko, Chad (ORCID:0000000271252518)↗

Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study

Background Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. Objective We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. Methods We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher’s query. Results PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. Conclusions The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.</:p>

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

An Integrated Framework for Memory-Centric Analysis: From Trace Collection to Co-Design

The memory wall phenomenon—where advances in processor performance significantly outpace those in memory subsystems—poses a fundamental challenge for contemporary computing systems. In memory-bound applications, memory subsystem behavior dominates performance, yet existing analysis approaches present significant limitations: detailed microarchitectural simulators require days to weeks to simulate modest workloads; hardware performance counters provide only aggregate statistics that obscure temporal and spatial access patterns; and scaled simulation approaches face challenges in capturing certain behaviors that emerge at larger scales. These limitations reflect a processor-centric design philosophy increasingly misaligned with memory-bound workloads where detailed understanding of memory access patterns, cache hierarchy interactions, and contention is critical for effective optimization. This paper presents an integrated framework for memory-centric analysis that enables effective hardware-software co-design. We describe practical trace collection techniques, including hardware-assisted processor tracing with minimal overhead and portable software-based instrumentation with statistical sampling. We present multi-perspective analysis methods that examine memory behavior from temporal, sequential, spatial, and relational viewpoints, revealing distinct optimization opportunities invisible in aggregate metrics. We detail an architectural modeling framework that uses sampled traces with temporal interpolation and confidence-based filtering to evaluate cache and memory configurations. Evaluation on representative benchmarks demonstrates that this framework achieves practical accuracy (L2 cache errors of 2.64\%, confidence-filtered L3 errors of 9.92\%, bandwidth errors of 7.33\%) while providing substantial speedup (26.8×) over cycle-accurate simulation, enabling rapid design space exploration. We demonstrate how this integrated framework enables systematic identification of both hardware optimizations (memory controller tuning, bank partitioning, NUMA configuration) and software optimizations (data layout restructuring, prefetching strategies, memory-aware scheduling). Through this comprehensive treatment of the memory-centric analysis pipeline—from trace collection through architectural modeling to co-design application—we provide researchers and practitioners with practical techniques for addressing memory bottlenecks in contemporary computing systems.

Gajaria, Dhruv Mayur↗

Technetium-99M generator for enriched molybdenum

A method for separating a parent isotope from a daughter isotope is provided, the method comprising supplying irradiated target; dissolving the irradiated target; treating the dissolved irradiated target to a precipitation step to form a first solid phase of the parent isotope and a first liquid phase of the daughter isotope; filtering the first liquid phase of daughter isotope to create a first purified fraction of the daughter isotope to create a second solid phase of the parent isotope and a second liquid phase of the daughter isotope; and filtering the second liquid phase to create a second liquid fraction of the daughter isotope. The process can be repeated until the 99 Mo is exhausted and the enriched target material 98 Mo or 100 Mo can be easily re-used.

Brown, Michael A.↗

Tomographic detection of photon pairs produced from high-energy X-rays for the monitoring of radiotherapy dosing

Measuring the radiation dose reaching a patient’s body is difficult. Here we report a technique for the tomographic reconstruction of the location of photon pairs originating from the annihilation of positron–electron pairs produced by high-energy X-rays travelling through tissue. We used Monte Carlo simulations on pre-recorded data from tissue-mimicking phantoms and from a patient with a brain tumour to show the feasibility of this imaging modality, which we named ‘pair-production tomography’, for the monitoring of radiotherapy dosing. We simulated three image-reconstruction methods, one applicable to a pencil X-ray beam scanning through a region of interest, and two applicable to the excitation of tissue volumes via broad beams (with temporal resolution sufficient to identify coincident photon pairs via filtered back projection, or with higher temporal resolution sufficient for the estimation of a photon’s time-of-flight). In addition to the monitoring of radiotherapy dosing, we show that image contrast resulting from pair-production tomography is highly proportional to the material’s atomic number. The technique may thus also allow for element mapping and for soft-tissue differentiation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Maximum a posteriori Ly α estimator (MAPLE): band power and covariance estimation of the 3D Ly α forest power spectrum

We present a novel maximum a posteriori estimator to jointly estimate band powers and the covariance of the three-dimensional power spectrum (P3D) of Ly $\alpha$ forest flux fluctuations, called MAPLE. Our Wiener-filter based algorithm reconstructs a window-deconvolved P3D in the presence of complex survey geometries typical for Ly $\alpha$ surveys that are sparsely sampled transverse to and densely sampled along the line of sight. We demonstrate our method on idealized Gaussian random fields with two selection functions: (i) a sparse sampling of 30 background sources per square degree designed to emulate the current Dark Energy Spectroscopic Instrument; (ii) a dense sampling of 900 background sources per square degree emulating the upcoming Prime Focus Spectrograph Galaxy Evolution Survey. Our proof-of-principle shows promise, especially since the algorithm can be extended to marginalize jointly over nuisance parameters and contaminants, i.e. offsets introduced by continuum fitting. Our code is implemented in JAX and is publicly available on GitHub.

79 ASTRONOMY AND ASTROPHYSICS↗

Exploration of Options for Ultra-Fast Mass Spectroscopy for Pulsed Power Applications

Mega-ampere class pulsed power machines drive intense currents into small volumes to study high energy and density environments. Power lost during these events is a difficult and paramount problem to solve. For example, facilities such as Sandia National Laboratories’ Z machine experience meaningful power loss, which can be linked to non-linear ohmic heating at high currents (i.e., 26 MA on Z) leading to thermal desorption of contaminants and subsequent shunt plasma formation. Characterizing and understanding this type of thermal desorption is key to design optimizations necessary to minimize current loss, which will be even more important for next generation pulsed power. This type of characterization requires the ability to identify and determine concentration of analytes with nanosecond resolution given the pulse width of Z is on the order of 100 ns. This report summarizes progress on a small exploratory project focused on investigating options to meet this challenge using mass spectrometry. The main focus of these efforts utilized an Energy and Velocity Analyzer for Distributions of Electric Rockets intending to determine how quickly transient data could be resolved. This probe combines an electrostatic analyzer with a Wien velocity filter (ExB) to obtain ion energy and velocity distributions. Primary results from this exploratory project indicate significant additional work is needed to demonstrate a nanosecond time scale mass spectrometer for this application and also highlight that alternative detection methods such as laser-based diagnostics should be considered to meet the need for ultra-fast detection.

42 ENGINEERING↗

Constraints on Metastable Helium in the Atmospheres of WASP-69b and WASP-52b with Ultranarrowband Photometry

Infrared observations of metastable 2{sup 3}S helium absorption with ground- and space-based spectroscopy are rapidly maturing, as this species is a unique probe of exoplanet atmospheres. Specifically, the transit depth in the triplet feature (with vacuum wavelengths near 1083.3 nm) can be used to constrain the temperature and mass-loss rate of an exoplanet’s upper atmosphere. Here, we present a new photometric technique to measure metastable 2{sup 3}S helium absorption using an ultranarrowband filter (FWHM 0.635 nm) coupled to a beam-shaping diffuser installed in the Wide-field Infrared Camera on the 200 inch Hale Telescope at Palomar Observatory. We use telluric OH lines and a helium arc lamp to characterize refractive effects through the filter and to confirm our understanding of the filter transmission profile. We benchmark our new technique by observing a transit of WASP-69b and detect an excess absorption of 0.498% ± 0.045% (11.1σ), consistent with previous measurements after considering our bandpass. We then use this method to study the inflated gas giant WASP-52b and place a 95th percentile upper limit on excess absorption in our helium bandpass of 0.47%. Using an atmospheric escape model, we constrain the mass-loss rate for WASP-69b to be 5.25{sub −0.46}{sup +0.65}×10{sup −4} M{sub J} Gyr{sup −1} (3.32{sub −0.56}{sup +0.67}×10{sup −3} M{sub J} Gyr{sup −1}) at 7000 K (12,000 K). Additionally, we set an upper limit on the mass-loss rate of WASP-52b at these temperatures of 2.1×10{sup −4} M{sub J} Gyr{sup −1} (2.1×10{sup −3} M{sub J} Gyr{sup −1}). These results show that ultranarrowband photometry can reliably quantify absorption in the metastable helium feature.

79 ASTRONOMY AND ASTROPHYSICS↗

Fourier method for 3-dimensional data fusion of X-ray Computed Tomography and ultrasound

X-ray Computed Tomography (CT) is essential for nondestructive inspection of many manufactured components but is susceptible to various forms of artifacts and noise. In particular, multi-detector row cone-beam CT systems can suffer from so called “cone-beam” artifacts and partial volume effects, particularly on planar edges at the periphery of the field of view in the cone angle dimension. Uni-directional ultrasonic testing methods generally have extremely accurate in-plane depth resolution but poorer lateral resolution due to physical and geometric constraints. This paper presents a novel technique called Computed Tomographic Fusion (CT-F) which uses three-dimensional Fourier filtering to combine x-ray cone-beam CT reconstructions and ultrasound data in the frequency space. The result is a single image with improved accuracy and quality. CT-F mitigates artifacts while allowing for rapid, accurate characterization of large three-dimensional CT volumes. Finally, using simulations and experiments, we demonstrate artifact reduction and edge contrast improvement in volumetric reconstructions.

42 ENGINEERING↗

Development of a deep learning based automated data analysis for step-filter x-ray spectrometers in support of high-repetition rate short-pulse laser-driven acceleration experiments

We present a deep learning based framework for real-time analysis of a differential filter based x-ray spectrometer that is common on short-pulse laser experiments. The analysis framework was trained with a large repository of synthetic data to retrieve key experimental metrics, such as slope temperature. With traditional analysis methods, these quantities would have to be extracted from data using a time-intensive and manual analysis. Furthermore, this framework was developed for a specific diagnostic, but may be applicable to a wide variety of diagnostics common to laser experiments and thus will be especially crucial to the development of high-repetition rate (HRR) diagnostics for HRR laser systems that are coming online.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗