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At least 37 records · Page 2

Enhancing Cluster Identification in Atom Probe Tomography Data Using Transfer Learning

Atom Probe Tomography (APT) is a powerful technique for visualizing the atomic-scale distribution of solutes in materials, but quantitative cluster analysis of APT datasets remains a challenge due to the need for subjective parameter selection in clustering algorithms. While distance-based and density-based methods such as HDBSCAN are widely used, their performance is highly sensitive to user-defined parameters, which undermines reproducibility and accuracy. This study proposes an image-based, deep learning-aided workflow for automating parameter selection and cluster detection in APT data analysis. By projecting 3D APT point clouds onto 2D planes, we leverage pretrained convolutional neural networks (ConvNeXt-Tiny and ResNet-50) through transfer learning to predict the number of clusters present in synthetic datasets. The output is used to guide K-means clustering and estimate HDBSCAN parameters, specifically minimum cluster size and minimum sample points. This approach reduces reliance on manual parameter tuning, improving consistency and scalability. The methodology demonstrates the feasibility of using image-based deep learning for interpreting complex spatial patterns in APT data, enabling faster and more objective analysis. The complete workflow and code are made publicly available to support reproducibility and future research.

Density-based clustering

Plant Reload Optimization (prlo)

The PRLO framework is built on a modular and extensible architecture that tightly couples advanced evolutionary optimization algorithms with nuclear fuel depletion solvers (i.e., nuclear physics neutronics code). It supports exploring complex, high-dimensional design spaces constrained by user-specified operational, safety, and economic constraints. Objectives such as minimizing fresh fuel enrichment, flattening radial and axial power distributions, and maximizing discharge burnup are evaluated. PRLO’s equilibrium cycle optimization capability enables the identification of core configurations that maintain fuel cycle sustainability over extended planning horizons. Its integration with the RAVEN platform facilitates optimization of loading patterns or fuel shuffling schemes across multiple cycles. The interface with SIMULATE, a licensed industry-standard nodal code developed by Studsvik, ensures accurate neutronic and thermal-hydraulic feedback for reactor core design. PRLO’s automated workflow engine supports iterative design refinement, enabling utilities to streamline core design processes and meet evolving performance and regulatory targets.

Kim, Junyung [Idaho National Laboratory] (00090005

Thermonuclear Burn in a Multiphysics Code on GPUs

Multiphysics codes links to a library called SINGE for the calculation of thermonuclear (TN) burn rates, but some current multiphysics codes do not attempt to leverage the support for parallel operation that SINGE provides. Our goal is to investigate implementations of the SINGE workflow and analyze how the use of a performance portability layer could reduce run time on CPU archi tectures while also supporting GPU architectures without requiring code modifications. We looked to the Kokkos C++ Performance Portability Ecosystem to implement hardware agnostic parallel patterns.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS

Comparative mitogenomics of kingdom Fungi – evolutionary insights and metagenomic applications

Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.

Ahrendt, Steven R. [USDOE Joint Genome Institute (

Code Description for "Brief Communication: Monitoring snow depth using small, cheap, and easy-to-deploy ground surface temperature sensors"

Temporally continuous snow depth estimates are vital for understanding changing snow patterns and impacts on permafrost in the Arctic. We train a random forest machine learning model to predict snow depth from variability in ground surface temperature. To our knowledge, this is the first time that small ground surface temperature sensors have been used to estimate snow depth. The model performs well at sites where the model was trained and at pan-arctic evaluation sites (RMSE <= 0.15 m). Small temperature sensors are cheap and easy-to-deploy, so this technique enables spatially distributed and temporally continuous snowpack monitoring to an extent previously infeasible. The model is flexible and can be applied to datasets retroactively to retrieve snow depth estimates at additional sites. This code package includes a *.joblib file of the trained random forest model and a *.ipynb file showing how to clean input data, train the random forest model, and apply the model.

Bachand, Claire

Challenges in Rotor Aerodynamic Modeling for Non-Uniform Inflow Conditions

Within an international collaboration framework, the accuracy of rotor aerodynamic models used for design load calculations of wind turbines is being assessed. Where the use of high-fidelity computation fluid dynamics (CFD) and mid-fidelity free-vortex wake (FVW) models has become commonplace within the wind energy community, these still fail to meet the requirements in terms of execution time and computational cost needed for design load calculations. The fast but engineering fidelity blade-element/momentum (BEM) method can therefore still be considered the industry workhorse for design load simulations. At the same time, upscaling of wind turbine rotors makes inflow non-uniformities (e.g. shear, veer, turbulence) more important. The objective of this work is to assess model accuracy in non-uniform inflow conditions, which violate several BEM assumptions. Thereto a comparison in turbulent inflow has been executed including a wide variety of codes, focusing on the DanAero field measurements, where a 2.3-MW turbine was equipped with, among other sensors, a pressure measurement apparatus. The results indicate that, although average load patterns are in good agreement, this does not hold for the unsteady loads that drive fatigue damage and aero-elastic stability. A simplified comparison round in vertical shear was initiated to investigate the observed differences in a more controlled manner. A consistent offset in load amplitude was observed between CFD and free-vortex codes on the one hand and BEM-type codes on the other hand. To shed more light on the observations, dedicated efforts are ongoing to pinpoint the cause for these differences, in the end leading to guidelines for an improved BEM implementation.

17 WIND ENERGY

A new synthetic correlation electron cyclotron emission diagnostic for validating nonlinear gyrokinetic simulations of electron temperature turbulence

To validate nonlinear gyrokinetic simulations of electron temperature turbulence, the experimental correlation electron cyclotron emission (CECE) measurements are to be compared using a synthetic CECE diagnostic, which generates modeled CECE measurement quantities by implementing realistic measurement parameters (e.g., spatial and wavenumber resolutions, radial location, etc.) to nonlinear gyrokinetic simulations. In this work, we calculate the radial and vertical spatial and wavenumber transfer functions, which are defined by the electron cyclotron emission emissivity radial profile and vertical probing antenna pattern, respectively. These transfer functions are applied to nonlinear gyrokinetic simulations of electron temperature turbulence using the continuum gyrokinetic code. A simultaneous comparison of the experimental electron temperature turbulence power spectrum and root-mean-square (RMS) level, as well as the radial correlation length with the new synthetic CECE diagnostic at a core location ρ ∼ 0.75 in an L-mode DIII-D tokamak plasma, is presented. Here, the preliminary result shows that the synthetic CECE output underestimates the RMS level by ∼42% and overestimates the radial correlation length by ∼40%.

Cyclotron radiation

The R -Process Alliance: Exploring the cosmic scatter among ten r -process sites with stellar abundances

Context. The astrophysical origin of the rapid neutron-capture process (r-process), responsible for producing roughly half of the elements heavier than iron, remains uncertain. Detailed chemical signatures from the oldest, most metal-poor stars, which act as fossil records of the earliest nucleosynthesis events, can be used to identify the dominant r-process sites. Aims. We present a homogeneous chemical abundance analysis of ten r-process element-enhanced stars. These old and metal-poor stars are strongly enriched in r-process elements with minimal contamination from other nucleosynthetic sources. By focusing on this chemically pure sample, we aim to investigate intrinsic variations in the r-process abundance patterns and explore their implications for the nature and potential diversity of r-process sites. Methods. We performed a detailed chemical abundance analysis of high-resolution, high-signal-to-noise spectra. For each star, we inspected over 1400 individual absorption lines using a combination of equivalent width measurements and spectral synthesis. The analysis was conducted under the assumption of 1D local thermodynamic equilibrium and employing the MOOG radiative transfer code. Results. We derived abundances for 54 chemical species, including 29 neutron-capture (n-capture) elements, covering the full mass range of the r-process abundance pattern. A kinematic analysis reveals that stars likely originated from ten kinematically distinct systems. Based on this assumption, we used the sample to probe the maximum variation expected from ten independent r-process nucleosynthesis events and computed the intrinsic dispersion of each element relative to Zr and Eu for the light and heavy r-process elements, respectively. This exercise resulted in a remarkably low cosmic scatter across the ten r-process sites enriching these stars; for the rare earth and third peak elements, for example, we find σ [La/Eu] = 0.08 and σ [Os/Eu] = 0.11 dex, while the scatter between light and heavy elements, σ [Zr/Eu] , is slightly higher at 0.18 dex. Conclusions. The elemental abundance patterns across the ten independent r-process sites show remarkably small cosmic dispersions. This minimal dispersion suggests a high degree of uniformity in r-process yields across diverse astrophysical environments.

Astronomy and AstroPhysics

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

While a rich set of putative cis-regulatory sequences involved in mouse fetal development have been annotated recently on the basis of chromatin accessibility and histone modification patterns, delineating their role in developmentally regulated gene expression continues to be challenging. To fill this gap, here we mapped chromatin contacts between gene promoters and distal sequences across the genome in seven mouse fetal tissues and across six developmental stages of the forebrain. We identified 248,620 long-range chromatin interactions centered at 14,138 protein-coding genes and characterized their tissue-to-tissue variations and developmental dynamics. Integrative analysis of the interactome with previous epigenome and transcriptome datasets from the same tissues revealed a strong correlation between the chromatin contacts and chromatin state at distal enhancers, as well as gene expression patterns at predicted target genes. We predicted target genes of 15,098 candidate enhancers and used them to annotate target genes of homologous candidate enhancers in the human genome that harbor risk variants of human diseases. We present evidence that schizophrenia and other adult disease risk variants are frequently found in fetal enhancers, providing support for the hypothesis of fetal origins of adult diseases.

59 BASIC BIOLOGICAL SCIENCES

Integrated modeling of boron powder injection for real-time plasma-facing component conditioning

An integrated modeling framework for investigating the application of solid boron (B) powder injection for real-time surface conditioning of plasma-facing components (PFCs) in tokamak environments is presented. Utilizing the DIII-D impurity powder dropper (IPD) setup, this study simulates B powder injection scenarios ranging from milligrams to tens of milligrams per second, corresponding to boron flux rates of 10 20 –10 21 B/s in standard L-mode conditions. The comprehensive modeling approach combines EMC3-EIRENE for simulating the deuterium plasma background and the Dust Injection Simulator (DIS) for the ablation and transport of the boron powder particles. EMC3 trace impurity fluid modeling results show substantial boron transport to the inboard lower divertor, predominantly influenced by the main ion plasma flow. The dependency on powder particle size (5-250 µm) was found to be insignificant for the scenario considered. The effects of erosion and redeposition were considered to reconcile the discrepancies with experimental observations, which saw substantial deposition on the outer divertor plasma-facing components. For this purpose, the WallDYN3D code was updated to include boron sources within the plasma domain and integrated into the modeling framework. The mixed-material migration modeling shows evolving boron deposition patterns, suggesting the formation of mixed B-C layers or predominantly B coverage depending on the powder mass flow rate. While the modeling outcomes at lower B injection rates tend to align with DIII-D experimental observations, the prediction of near-pure boron layers at higher rates has yet to be experimentally verified in the carbon environment of the DIII-D tokamak. The extensive reach of boron layers found in the modeling suggests the need for modeling that encompasses the entire wall geometry for more accurate experimental correlations. This integrated approach sets a precedent for analyzing and applying real-time in-situ boron coating techniques in advanced tokamak scenarios, potentially extendable to ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability: Supporting Data and Code

This repository contains R code and associated datasets for reproducing the analysis described in the manuscript titled “Disentangling the Impacts of Microtopography and Shrub Distribution on Snow Depth in a Subarctic Watershed: Toward a Predictive Understanding of Snow Spatial Variability” (DOI: 10.1029/2024JG008604). The provided scripts facilitate a comprehensive analysis of snow depth variability influenced by microtopography and vegetation distribution in a subarctic watershed. Included datasets are high-resolution spatial maps of snow depth, terrain elevation, vegetation height, and distance from shrubs taller than 1 meter, all formatted as text files (.txt). These data are fully describe in doi:10.15485/2316038. Users can adapt the provided R scripts to accommodate different data formats or larger spatial domains, noting that some output files may require modification due to their size.The code includes implementations for boosted regression tree analysis adapted from methods outlined in Elith et al. (2008). Users interested in understanding or modeling landscape-scale snow distribution patterns, particularly in Arctic or subarctic ecosystems, will find this package useful. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES

Detailed Characterization of CZT Detector Response for Improved Coded-Aperture Imaging Performance

Gamma-ray imaging is a powerful method for locating and quantifying sources of radiation. The coded-aperture technique demonstrates superior angular resolution in comparison to other methods (e.g., Compton reconstruction). In this method, a mask constructed of highly attenuating material encodes the scene as a shadow pattern on a position-sensitive detector; this pattern can then be used to recreate the origin(s) of incident radiation. This is typically done through convolution of the mask and shadow patterns. Iterative methods which attempt to reconstruct the observed shadow pattern using a weighted combination of simulated patterns may also be employed. In either case, errors in event position reconstruction due to detector imperfections alter the shadow pattern and will therefore degrade system performance and may introduce imaging artifacts. These effects can be mitigated with a detailed understanding of such errors – allowing for the generation of representative simulations that include the errors and/or correction of raw imager data to remove the errors. We present a calibration process for a commercially available cadmium zinc telluride (CZT) gamma imager which provides a comprehensive characterization of the spatial and energy dependence of event reconstruction. By illuminating a mask featuring a regular grid of pinholes with a calibration source, the localized response of the detector can be measured with fine granularity. These local responses are combined to generate a full detector response map which can be used to distort simulations in a manner that is representative of the observed detector data. Details of the calibration procedure and an assessment of the impact of its end products on the performance of iterative imaging methods will be presented.

Ziock, Klaus-Peter

Thermonuclear 28 P(p, γ ) 29 S reaction rate and astrophysical implication in ONe nova explosion

An accurate 28 P(p, γ) 29 S reaction rate is crucial to defining the nucleosynthesis products of explosive hydrogen burning in ONe novae. Using the recently released nuclear mass of 29 S, together with a shell model and a direct capture calculation, we reanalyzed the 28 P(p, γ) 29 S thermonuclear reaction rate and its astrophysical implication. We focus on improving the astrophysical rate for 28 P(p, γ) 29 S based on the newest nuclear mass data. Our goal is to explore the impact of the new rate and associated uncertainties on the nova nucleosynthesis. We evaluated this reaction rate via the sum of the isolated resonance contribution instead of the previously used Hauser-Feshbach statistical model. The corresponding rate uncertainty at different energies was derived using a Monte Carlo method. Nova nucleosynthesis is computed with the 1D hydrodynamic code SHIVA. The contribution from the capture on the first excited state at 105.64 keV in 28 P is taken into account for the first time. We find that the capture rate on the first excited state in 28 P is up to more than 12 times larger than the ground-state capture rate in the temperature region of 2.5 × 10 7 K to 4 × 10 8 K, resulting in the total 28 P(p, γ) 29 S reaction rate being enhanced by a factor of up to 1.4 at ~1 × 10 9 K. In addition, the rate uncertainty has been quantified for the first time. It is found that the new rate is smaller than the previous statistical model rates, but it still agrees with them within uncertainties for nova temperatures. The statistical model appears to be roughly valid for the rate estimation of this reaction in the nova nucleosynthesis scenario. Using the 1D hydrodynamic code SHIVA, we performed the nucleosynthesis calculations in a nova explosion to investigate the impact of the new rates of 28 P(p, γ) 29 S. Our calculations show that the nova abundance pattern is only marginally affected if we use our new rates with respect to the same simulations but statistical model rates. Finally, the isotopes whose abundance is most influenced by the present 28 P(p, γ) 29 S uncertainty are 28 Si, 33,34 S, 35,37 Cl, and 36 Ar, with relative abundance changes at the level of only 3% to 4%.

Astronomy & Astrophysics

Amorphization and siliconization of silicon carbide as a first wall material

The understanding and prediction of silicon carbide (SiC) material evolution exposed to SOL plasma conditions is of prime interest because SiC represents a promising main chamber wall plasma-facing material for next-step fusion devices (low hydrogenic diffusion, good mechanical and thermal properties under neutron irradiation). Gross and net Si erosion rates from SiC surfaces in contact with a well-diagnosed L-mode plasma in the DIII-D tokamak have been simulated and the surface concentrations of impurities have been tracked as a function of time. Coupled simulation of surface model and impurity transport demonstrates amorphization of crystalline SiC exposed to L-mode plasma due to the accumulation of displacement damages under ion irradiation. This affects the lifetime of SiC plasma facing components. Surface evolution is tightly coupled to impurity transport in the plasma and therefore needs to be integrated with impurity transport simulations to effectively predict Si erosion rates and sub-surface concentrations as a function of time. The simulation workflow couples a semi-analytical surface model to the impurity transport code GITR. The surface model is a homogeneous mixed-material model that tracks physical & chemical sputtering and reflection of impurities. Gross erosion is primarily influenced by the background plasma parameters and redeposition patterns are mainly influenced by the prompt redeposition due to the gyro-orbits of impurity ions. Although crystalline form of SiC is preferable for fusion wall applications because of resistance to neutron irradiation, this work indicates that crystalline SiC will undergo amorphization under D plasma contact with implications of higher sputtering and fuel retention. These results direct us to explore the effects of amorphization on crystalline SiC and further the physics basis of SiC usage as first wall material for fusion environments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

MODE: A Web Application for Interactive Visualization and Exploration of Omics Data

Studies generating transcriptomics, proteomics, lipidomics, and metabolomics (colloquially referred to as “omics”) data allow researchers to find biomarkers or molecular targets, or understand complex biological structures and functions by identifying changes in biomolecule abundance and expression between experimental conditions. Omics data is multi-dimensional and oftentimes summarization techniques such as principal component analysis (PCA) are used to identify high-level patterns in data. Though useful, these summaries don’t allow exploration of detailed patterns in omics data that may have biological relevance. The use of interactive HTML displays with plots allows researchers to interact with omics data at a detailed level, but building these displays requires significant coding expertise. To overcome this barrier, the software MODE was built to empower users to build their own interactive HTML displays to support scientific discovery. These displays are easily shareable, do not depend on a specific operating system, and allow users to effortlessly sort and filter plots by categorical or numerical variables. MODE allows users to build and share these displays with several options for plot design and meta selection. In conclusion, the MODE web application and its capabilities are presented and then demonstrated on lipidomics data from a leaf wounding study.

lipidomics

Enabling Efficient Sparse Computations using Linear Algebra Aware Compilers

This project developed the LAPIS compiler framework, built on the Multilevel Intermediate Representation (MLIR), to optimize sparse linear algebra operations and support performance portability across diverse architectures. The main innovation of LAPIS is the Kokkos dialect, which allows for lowering codes from a high productivity language to different architectures in an elegant way. The dialect also allows the conversion of lower-level MLIR code to C++ Kokkos code, facilitating the integration of scientific machine learning (SciML) models into applications. To extend LAPIS for distributed memory architectures, a new partition dialect was created to manage the distribution of sparse tensors and express communication patterns for sparse linear algebra operations. This dialect also supports the distributed execution of operators and includes algorithmic optimizations to minimize communication to improve performance. The project also demonstrates that MLIR can enable effective linear algebra-level optimizations, improving performance on different GPUs for both sparse and dense linear algebra kernels. Key applications of LAPIS include sparse linear algebra and graph kernels, TenSQL, a relational database management solution built on GraphBLAS, and the development of subgraph isomorphism and monomorphism kernels, showcasing performance portability. In summary, the LAPIS framework supports productivity, performance, portability, and distributed memory execution, while also enabling linear algebra-level optimizations that are challenging in traditional programming languages, with successful applications ranging from simple sparse linear algebra to complex graph kernels.

97 MATHEMATICS AND COMPUTING

PPI DataHub Project Data Package: S. elongatus PCC 7942 Circadian Control Bioproduction Metabolomics (PB-DP5)

The purpose of this experiment was to evaluate how circadian clock regulation impacts carbon partitioning between storage, growth, and product synthesis in Synechococcus elongatus PCC 7942 in providing insights to strategies for enhanced bioproduction. Culture samples were collected at 0, 0.5, 1, 2, 4, 6, and 8 hours for extracellular sucrose analysis. Circadian metabolomics data was acquired using a Agilent single quadrupole gas chromatography-mass spectrometer and processed using Agilent Mass Hunter for targeted sucrose quantification. Metabolomic analysis of PCC 7942 light-dark cycle cultures transitioned to constant light revealed distinct temporal patterns in sucrose production. Processed metabolomic datasets are openly accessible from the PNNL DataHub project dataset download page and contain secondary processed GC-MS results files and supporting metadata materials linked to relevant source code information supporting data transparency and reuse.

59 BASIC BIOLOGICAL SCIENCES

A methodology for domain overlapping coupling of thermal-hydraulic systems

Multi-scale coupling has increasingly drawn attention as a promising approach for modeling thermal systems. Traditional system codes provide fast and robust predictions at the plant scale, while high-fidelity computational fluid dynamics (CFD)-based tools resolve localized flow and heat transfer phenomena with greater accuracy. By combining these complementary strengths, co-simulations enable multi-scale analysis that would otherwise be computationally prohibitive for a standalone CFD code. Here, this work introduces a robust and problem-agnostic domain overlapping (DO) coupling between the system thermal-hydraulic (STH) code System Analysis Module (SAM) and the coarse-mesh CFD code Pronghorn. Both applications belong to the Comprehensive Reactor Analysis Bundle (BlueCRAB) code suite, a code suite in active development at the Idaho National Laboratory (INL), tailored for multi-physics analysis of advanced reactors. Unlike previous approaches, BlueCRAB supports an agnostic interface between codes based on different fidelity, while its coupling formulation can address arbitrary flow geometries with multiple inlets and outlets in coupled components. The implemented method leads to consistent pressure drops, enthalpies, and scalar concentrations between coupled SAM and Pronghorn simulations. The methodology is demonstrated through two verification tests, which ensure the numerical consistency and conservation across the codes, and through one validation test against experimental data. The proposed problems explore different physical aspects inherent to thermal systems, with particular attention given to nuclear reactor analysis. These include buoyancy-driven flows, complex flow patterns, and setups with multiple inlets and outlets, representing challenges in advanced reactor applications.

22 - GENERAL STUDIES OF NUCLEAR REACTORS