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DOE OSTI2020

Improvements to a class of hybrid methods for radiation transport: Nyström reconstruction and defect correction methods

In this study, two modifications are introduced for improving the accuracy, versatility, and robustness of a class of hybrid methods for radiation transport. In general, such methods are constructed by splitting the radiative flux into collided and uncollided components to which low- and high-resolution angular approximations are applied, respectively. In this work we focus on discrete ordinates discretizations of high and low order. The first modification we introduce changes the way in which the collided component is mapped into the uncollided component at the end of each time step in a simulation. The new mapping is a Nyström-type reconstruction that is applicable to arbitrary discrete ordinates quadratures, is guaranteed to preserve positivity of the solution provided that all ordinate weights are positive, is significantly more accurate than previous methods, and can be readily extended to other discretizations such as moment methods, finite element methods, and diffusion approximations. The second modification leverages integral deferred correction (IDC) to iteratively correct for the splitting error introduced by the inconsistency in angular discretization between the collided and uncollided components, in addition to improving the accuracy of the low-order temporal error that is treated by traditional IDC methods. Numerical tests in one- and two-dimensional geometries are used to demonstrate the increased accuracy and efficiency of the proposed modifications. It is found that the two techniques combined yield methods with solution accuracy and memory requirements comparable to that of monolithic discrete ordinates methods while reducing runtime by as much as a factor of between two and ten, depending on the problem.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Calibration and Performance of the ICARUS Detector at Fermilab

ICARUS is the largest Liquid Argon Time Projection Chamber (LArTPC) in operation and serves as the Far Detector of the Short Baseline Neutrino (SBN) program at Fermilab. Precise detector calibration is essential for reliable energy reconstruction and for maximizing the physics reach of the experiment. In this talk, I will describe the energy and timing calibration procedures developed at ICARUS. Thanks to the abundant flux of cosmic ray muons at the surface, the TPC response to ionization charge has been equalized across the detector, removing non-uniformities and in-transparency effects. A novel data-driven procedure has been used to tune the simulation of ionization signals and electronics noise yielding close agreement between Monte Carlo and data with minimal residual bias in reconstructed charge. In addition, the light detection system has been calibrated to sub-nanosecond timing resolution. This precision enables efficient cosmic background rejection and accurate synchronization of neutrino interactions with the time structure of both the Booster Neutrino Beam (BNB) and Neutrinos at the Main Injector (NuMI) beam. Together, these efforts demonstrate the robust performance of the detector and provide critical experience for future large LArTPCs, such as DUNE.

Vicenzi, Matteo [Brookhaven]↗

DOE OSTI2021

Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data

Genome-scale metabolic models (GEMs) enable the mathematical simulation of the metabolism of archaea, bacteria, and eukaryotic organisms. GEMs quantitatively define a relationship between genotype and phenotype by contextualizing different types of Big Data (e.g., genomics, metabolomics, and transcriptomics). In this review, we analyze the available Big Data useful for metabolic modeling and compile the available GEM reconstruction tools that integrate Big Data. We also discuss recent applications in industry and research that include predicting phenotypes, elucidating metabolic pathways, producing industry-relevant chemicals, identifying drug targets, and generating knowledge to better understand host-associated diseases. In addition to the up-to-date review of GEMs currently available, we assessed a plethora of tools for developing new GEMs that include macromolecular expression and dynamic resolution. Finally, we provide a perspective in emerging areas, such as annotation, data managing, and machine learning, in which GEMs will play a key role in the further utilization of Big Data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

First study of neutrino angle reconstruction using quasielasticlike interactions in MicroBooNE

We investigate the expected precision of the reconstructed neutrino direction using a 𝜈 𝜇 -argon quasielasticlike event topology with one muon and one proton in the final state and the reconstruction capabilities of the MicroBooNE liquid argon time projection chamber. This direction is of importance in the context of DUNE sub-GeV atmospheric oscillation studies. MicroBooNE allows for a data-driven quantification of this resolution by investigating the deviation of the reconstructed muon-proton system orientation with respect to the well-known direction of neutrinos originating from the Booster Neutrino Beam with an exposure of 1.3 ×10 21 protons on target. Using simulation studies, we derive the expected sub-GeV DUNE atmospheric-neutrino reconstructed simulated spectrum by developing a reweighting scheme as a function of the true neutrino energy. We further report flux-integrated single- and double-differential cross section measurements of charged-current 𝜈 𝜇 quasielasticlike scattering on argon as a function of the muon-proton system angle using the full MicroBooNE data sets. We also demonstrate the sensitivity of these results to nuclear effects and final state hadronic reinteraction modeling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Broadband X-ray ptychography using multi-wavelength algorithm

Ptychography is a rapidly developing scanning microscopy which is able to view the internal structures of samples at a high resolution beyond the illumination size. The achieved spatial resolution is theoretically dose-limited. A broadband source can provide much higher flux compared with a monochromatic source; however, it conflicts with the necessary coherence requirements of this coherent diffraction imaging technique. In this paper, a multi-wavelength reconstruction algorithm has been developed to deal with the broad bandwidth in ptychography. Compared with the latest development of mixed-state reconstruction approach, this multi-wavelength approach is more accurate in the physical model, and also considers the spot size variation as a function of energy due to the chromatic focusing optics. Therefore, this method has been proved in both simulation and experiment to significantly improve the reconstruction when the source bandwidth, illumination size and scan step size increase. It is worth mentioning that the accurate and detailed information of the energy spectrum for the incident beam is not required in advance for the proposed method. Further, we combine multi-wavelength and mixed-state approaches to jointly solve temporal and spatial partial coherence in ptychography so that it can handle various disadvantageous experimental effects. The significant relaxation in coherence requirements by our approaches allows the use of high-flux broadband X-ray sources for high-efficient and high-resolution ptychographic imaging.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2025

Simulations of the churning mode: Toroidally symmetric plasma convection and turbulence around the X-points in a snowflake divertor

Using a reduced MHD model, extended to include field-aligned thermal conduction, we present numerical simulations of the churning mode (CM): a toroidally symmetric, non-linear plasma vortex in the vicinity of the null points in a snowflake (SF) divertor [D. D. Ryutov et al., Phys. Scr. 89, 088002 (2014)]. Simulations are carried out across a range of inter-null separations, d xx ⁠, and inter-null orientations, θ⁠, primarily in conditions relevant to the MAST-U tokamak. We find that, when d xx is small, the CM induces additional transport across the X-points when β pm ≳8%, where β pm is the ratio of the plasma pressure in the null region to poloidal magnetic pressure at the midplane. This transport also increases approximately linearly as d xx is reduced. A diffusive model of this transport is shown to predict the total transport across the null points, where diffusion coefficients of up to ∼ 10 2 m 2 s −1 centered on a small region around the X-points are used. However, the CM also results in significant changes to the flux surfaces in the null region, which is not captured by this diffusive model. The changes in magnetic geometry mean the fractional exhaust power delivered to each divertor leg is highly sensitive to β pm ⁠, d xx ⁠, and θ⁠. For small values of θ⁠, the CM can induce a change in topology, redirecting exhaust power from a secondary divertor leg on the high field side to one on the low field side. Similar behavior is found in the fraction of exhaust power going to the inner and outer divertor. Such changes in the flux surfaces may not be captured by Grad–Shafranov solvers and so may be a source of error in the magnetic reconstruction of SF experiments. We consistently find that the fractional exhaust power going to a secondary divertor leg on the high field side is small, consistent with SF experiments.

Computer simulation↗

DOE OSTI2025

Bayesian Gaussian process inference for neutron spin echo measurement

Neutron spin echo (NSE) spectroscopy provides unique access to microscopic dynamics, but its application is often constrained by low neutron flux, long acquisition times, and significant noise. Here, we present a Bayesian inference approach based on Gaussian process regression (GPR) to reconstruct high-quality spin echo signals from sparse and noisy data by exploiting correlations in reciprocal space. Benchmarks on synthetic datasets and validation with experimental NSE measurements of dendrimers show that GPR suppresses noise, interpolates missing intensity values, and accommodates irregular observations. The method improves accuracy, shortens acquisition times, and enables high-throughput and real-time studies. Beyond NSE, the framework is broadly applicable to other low signal-to-noise ratio scattering techniques, thereby extending the scope of neutron spectroscopy.

Tung, Chi-Huan [Oak Ridge National Laboratory (ORN↗

DOE OSTI2026

Estimation of Fission Product Transport Parameters for Cesium in the AGR-3/4 TRISO Fuel Experiment

A one-dimensional (1D) finite-element model of fission product transport in the AGR-3/4 experiment has been developed using the Multiphysics Object Oriented Simulation Environment (MOOSE) framework and implemented in the fuel performance code, BISON. The model resolves capsule-specific geometries, materials, and temperature histories and simulates radial migration of fission products from the fuel compact through the inner ring, outer ring, and into the sink ring. Model parameters governing diffusion and sorption were estimated for key fission products – cesium (Cs), and europium (Eu) – by simultaneously fitting modeled isotopic concentration profiles and total ring inventories to a post-irradiation experimental measurement. These data include gamma scanning, liquid scintillation for Sr-90, radial deconsolidation leach-burn-leach analysis, tomographic reconstructions, and destructive physical sampling. A mortar-based interfacial sorption framework was implemented to enforce physically consistent mass transfer and flux conservation across gas gaps. Two classes of parameter sets were derived: a least-squares best-fit, and a safety-oriented conservative-fit, what applies strong penalties for underprediction of sink inventories. Across all twelve capsules, the model successfully reproduces the dominant radial transport trends for Cs, Sr, with decreasing concentrations from the compact outward through successive rings. Cs behavior is captured most consistently, while strontium predictions reveal systematic trade-offs between compact accuracy and conservative sink-ring bounding. The results demonstrate that sink ring weighted calibration provides conservative, safety relevant bounds on low temperature fission product transport, but at the cost of underpredicting compact inventories for Sr isotopes. These discrepancies highlight the need for additional physics, including fast-slow diffusion model, incorporating trapping mechanism in the transport behavior. Overall, this work establishes a robust, capsule-specific modeling framework for AGR-3/4 fission product transport and provides a defensible basis for parameter selection in source-term and fuel performance analyses for high temperature gas-cooled reactors.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2020

Medium Energy Electron Flux in Earth's Outer Radiation Belt (MERLIN): A Machine Learning Model

The radiation belts of the Earth, filled with energetic electrons, comprise complex and dynamic systems that pose a significant threat to satellite operation. While various models of electron flux both for low and relativistic energies have been developed, the behavior of medium energy (120–600 keV) electrons, especially in the MEO region, remains poorly quantified. At these energies, electrons are driven by both convective and diffusive transport, and their prediction usually requires sophisticated 4D modeling codes. In this paper, we present an alternative approach using the Light Gradient Boosting (LightGBM) machine learning algorithm. The Medium Energy electRon fLux In Earth's outer radiatioN belt (MERLIN) model takes as input the satellite position, a combination of geomagnetic indices and solar wind parameters including the time history of velocity, and does not use persistence. MERLIN is trained on >15 years of the GPS electron flux data and tested on more than 1.5 years of measurements. Tenfold cross validation yields that the model predicts the MEO radiation environment well, both in terms of dynamics and amplitudes o f flux. Evaluation on the test set shows high correlation between the predicted and observed electron flux (0.8) and low values of absolute error. The MERLIN model can have wide space weather applications, providing information for the scientific community in the form of radiation belts reconstructions, as well as industry for satellite mission design, nowcast of the MEO environment, and surface charging analysis.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Multi-omics profiling of the cold tolerant Monoraphidium minutum 26B-AM in response to abiotic stress

Microalgae that are of interest for biofuel production must be able to tolerate environmental changes that occur in outdoor cultivation systems. While algal cultures may experience daily temperature fluctuations and seasonal environmental changes, the underlying mechanisms that control and regulate physiological responses and adaptation to environmental pressures are largely unknown. Systems-level characterization enabled by functional genomics can help identify biochemical pathways that promote stability and productivity of algae in various environmental conditions. Monoraphidium minutum 26B-AM, a freshwater green microalga, was identified as a top performer in biomass production in winter season screens. We sequenced the genome of M. minutum 26B-AM and applied our multi-omics pipeline to profile this high potential strain under high salt and cold temperature perturbations. Through comparative analysis, including other green algae in the class Chlorophyceae, we identified gene families unique to the genus Monoraphidium, including a desaturase that has been linked to cold tolerance in plants. We observed that osmolytes, such as trehalose, proline and betaine, accumulate under salt stress, coinciding with upregulation of genes involved in biosynthesis of these metabolites. From the genome annotation, we reconstructed a metabolic model to provide a detailed map of the metabolic pathways and can be used to simulate growth and reaction fluxes. This multi-omics analysis provides a foundation to explore algal strain potential for biofuel applications, guides strain engineering, and expands our understanding of metabolic and regulatory mechanisms of algae in applied systems.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Unlocking hidden information in sparse small-angle neutron scattering measurements

Hypothesis Small-Angle Neutron Scattering (SANS) is a powerful technique for studying soft matter systems such as colloids, polymers, and lyotropic phases, providing nanoscale structural insights. However, its effectiveness is limited by low neutron flux, leading to long acquisition times and noisy data. Here, we hypothesize that Bayesian statistical inference using Gaussian Process Regression (GPR) can reconstruct high-fidelity scattering data from sparse measurements by leveraging intensity smoothness and continuity. Experiments and Simulations The method was benchmarked computationally and validated through SANS experiments on various soft matter systems, including wormlike micelles, colloidal suspensions, polymeric structures, and lyotropic phases. GPR-based inference was applied to both experimental and synthetic data to evaluate its effectiveness in noise reduction and intensity reconstruction. Findings GPR significantly enhances SANS data quality and therefore reducing measurement times by up to two orders of magnitude. This cost-effective approach maximizes experimental efficiency, enabling high-throughput studies and real-time monitoring of dynamic systems. It is particularly beneficial for weakly scattering and time-sensitive studies. Beyond SANS, this framework applies to other low-SNR techniques, including laboratory-based small-angle X-ray scattering and various dynamical scattering methods. Furthermore, it offers transformative potential for compact neutron sources, enhancing their viability for structural analysis in resource-limited settings.

Small angle neutron scattering↗

DOE OSTI2020

Two-fluid and kinetic transport physics of Kelvin–Helmholtz instabilities in nonuniform low-beta plasmas

Hall-magnetohydrodynamic (Hall-MHD) theory, two-fluid simulations, and kinetic simulations are used in this work to investigate the cross-field transport properties of Kelvin–Helmholtz instabilities in nonuniform low-beta collisionless plasmas. Hall-MHD analysis shows how the linear properties of the instability are modified by density gradients and magnetization. High-order accurate two-fluid and kinetic simulations, with complete dynamics of finite-mass electrons and ions, are applied to a suite of parameter cases to systematically assess the effects of diamagnetic drift, magnetization, charge separation, and finite Larmor motion. Initialization of exact two-species kinetic equilibria facilitates the study of isolated physical effects and enables detailed cross-comparisons between two-fluid and kinetic simulations, including for cases where ion gyroradii are comparable to gradient scale lengths. For nonuniform plasmas with significant space charge, the results of two-fluid and kinetic simulations are found to disagree with Hall-MHD predictions. Kelvin–Helmholtz instability growth rates, per unit shear, are shown to be smaller when ion diamagnetic drift and $E \times B$ drift are parallel and larger when the two drifts are antiparallel. The effect is attributed to polarization drift in the shear layer, which leads to redistribution of charge, alters the electric field that drives plasma advection, and consequently modifies growth rates. Instability-induced mass transport for different parameters is characterized in terms of the flux across the shear layer and a simplified diffusion model. Distribution functions from kinetic simulations are shown to deviate substantially from Maxwellian reconstructions, indicating the importance of kinetic physics during the nonlinear phase of the instability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2022

AmeriFlux FLUXNET-1F US-Myb Mayberry Wetland

This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Myb Mayberry Wetland. This is the FLUXNET version of the carbon flux data for the site US-Myb Mayberry Wetland produced by applying the standard ONEFlux (1F) software. Site Description - The Mayberry Wetland site is a 300-acre restored wetland on Sherman Island, north of Mayberry Slough, that is on the property of Mayberry Farms and managed by the California Department of Water Resources and Ducks Unlimited. During Summer 2010, the site was restored from a pepperweed and annual grassland pasture to a wetland through a project managed by Bryan Brock (bpbrock@water.ca.gov). A flux tower equipped to analyze energy, H2O, CO2, and CH4 fluxes was installed on October 14, 2010. At the time of installation, flooding of the site had only recently begun after extensive reconstruction of the wetland bathymetry conducted during the summer. Although some small patches of tules remain within the site, the site is a patchwork of deep and shallow open water with some remaining vegetation. Currently, there is an intention to flood-to-kill the current pepperweed and upland grasses and let the wetland plants propagate naturally, so no additional plant manipulation will occur.

Matthes, Jaclyn Hatala↗

DOE OSTI2026

AI-driven neutrino diagnostics and radiation-hard beam instrumentation for next-generation neutrino experiments

The Long Baseline Neutrino Facility (LBNF) at Fermilab will deliver a high-intensity, multi-megawatt neutrino beam to the Deep Underground Neutrino Experiment (DUNE), enabling precision tests of the three-neutrino paradigm, CP violation searches, neutrino mass ordering determination, and supernova neutrino studies. To accelerate DUNE’s physics reach and ensure robust beam operations, we propose an integrated AI-driven framework with real-time diagnostics and radiation-hardened instrumentation. At its core is a Real-Time Beam Integrity Monitor using a physics-informed Digital Twin. By reconstructing pion phase space from muon profiles and exploiting magnetic horn optic linearity, it enables spill-by-spill beam correction and flux stabilization. By using this approach, flux-related systematics could be reduced from 5% to 1%, potentially accelerating the discovery of CP violations by four to six years. Complementing this, a US–Japan R&D effort will deploy a LAPPD-based muon monitor in the NuMI beamline. ToF measurements can be acquired with picosecond precision using this radiation-hard system, enhancing sensitivity to horn chromatic effects. Simulations confirm strong response to these effects. ML models predict beam quality and horn current to sub-percent accuracy from muon data, enhancing anomaly detection and stability. This scalable, AI-enabled strategy improves beam fidelity, reduces systematics, and sets a new standard for high-power accelerator operations.

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

DOE OSTI2025

AI-driven neutrino diagnostics and radiation-hard beam instrumentation for next-generation neutrino experiments

Ganguly, Sudeshna [Fermilab] (ORCID:00000003163482↗

DOE OSTI2020

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org and KBase.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Measurements of the z > 5 Lyman-α forest flux autocorrelation functions from the extended XQR-30 data set

We present the first observational measurements of the Lyman-α (Ly α) forest flux autocorrelation functions in ten redshift bins from 5.1 ≤ z ≤ 6.0. We use a sample of 35 quasar sightlines at z > 5.7 from the extended XQR-30 data set; these data have signal-to-noise ratios of >20 per spectral pixel. We carefully account for systematic errors in continuum reconstruction, instrumentation, and contamination by damped Ly α systems. With these measurements, we introduce software tools to generate autocorrelation function measurements from any simulation. Our measurements of the smallest bin of the autocorrelation function increase with redshift when normalizing by the mean flux, $\langle{F}\rangle$. This increase may come from decreasing $\langle{F}\rangle$ or increasing mean free path of hydrogen-ionizing photons, λmfp. Recent work has shown that the autocorrelation function from simulations at z > 5 is sensitive to λmfp, a quantity that contains vital information on the ending of reionization. For an initial comparison, we show our autocorrelation measurements with simulation models for recently measured λmfp values and find good agreements. Further work in modelling and understanding the covariance matrices of the data is necessary to get robust measurements of λmfp from this data.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Updates on MURAVES Project at Mt. Vesuvius

The MUon RAdiography of VESuvius (MURAVES) project aims to employ muography imaging techniques to investigate the internal structure of the summit of Mount Vesuvius, an active volcano located near Naples, Italy. This paper reports recent advancements in data analysis and simulation tools that significantly improve the quality and reliability of the experiment’s results. A new track selection method, referred to as the Golden Selection, has been developed to identify high-quality muon tracks by applying an improved χ 2 -based criterion. This method enhances the signal-to-background ratio and improves the resolution of the resulting muographic images. Moreover, the simulation framework has been upgraded through the integration of the MULDER (MUon simuLation for DEnsity Reconstruction) library, which consolidates the functionalities of previously used libraries into a single, unified platform. MULDER enables efficient and accurate modeling of muon flux variations induced by topographical features. A good agreement is observed between the simulated and measured muon flux maps, validating the effectiveness of the new analysis and simulation approaches.

Cosmic rays↗