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All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Quantitative Performance Assessment of Proxy Apps and Parents (ECP Proxy App Project Milestone ADCD-504-9)

This report presents highlights of these efforts. Section 2 describes work that has been done to compare the performance of proxy applications on AMD MI60 vs. Nvidia V100 GPUs. So far only a small set of ECP proxies are running on AMD GPUs, but we will continue to expand this analysis as additional proxies become available. We find that although the MI60 and V100 have nearly the same measured memory bandwidth, memory bound proxy app kernels perform 20-30% worse on the MI60. Further work is needed to refine these comparisons to determine whether the root cause is due to differences in the hardware, software stack, platform specific optimization, or some combination of the three. Section 3 describes our continuing effort to find methods to accurately assess the similarity of proxies and parents. We have recently seen very encouraging results using a cosine similarity metric. This technique uses the angle between two vectors of hardware performance counters to characterize the similarity (or difference) between two applications or proxies. We show not only that several widely used proxies are highly similar to their parents, but also that they differ from non-related codes. We also show that cosine similarity can be used to identify gaps and redundancies in suites and even to gain insight into the effects of architectural differences between platforms. Our work on assessing the Exascale toolchain is ongoing. Our successes with performance measurement tools are evident from the data provided in this report. However, our assessments across the broader tool chain are still too incomplete to provide a meaningful report at this time. We will continue to assess tools and work with vendors and third party developers as issues are identified.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A Comprehensive Review of Latent Space Dynamics Identification Algorithms for Intrusive and Non-Intrusive Reduced-Order-Modeling

Numerical solvers of partial differential equations (PDEs) have been widely employed for simulating physical systems. However, the computational cost remains a major bottleneck in various scientific and engineering applications, which has motivated the development of reduced-order models (ROMs). Recently, machine-learning-based ROMs have gained significant popularity and are promising for addressing some limitations of traditional ROM methods, especially for advection dominated systems. In this chapter, we focus on a particular framework known as Latent Space Dynamics Identification (LaSDI), which transforms the high-fidelity data, governed by a PDE, to simpler and low-dimensional latent-space data, governed by ordinary differential equations (ODEs). These ODEs can be learned and subsequently interpolated to make ROM predictions. Each building block of LaSDI can be easily modulated depending on the application, which makes the LaSDI framework highly flexible. In particular, we present strategies to enforce the laws of thermodynamics into LaSDI models (tLaSDI), enhance robustness in the presence of noise through the weak form (WLaSDI), select high-fidelity training data efficiently through active learning (gLaSDI, GPLaSDI), and quantify the ROM prediction uncertainty through Gaussian processes (GPLaSDI). We demonstrate the performance of different LaSDI approaches on Burgers equation, a non-linear heat conduction problem, and a plasma physics problem, showing that LaSDI algorithms can achieve relative errors of less than a few percent and up to thousands of times speed-ups.

Computational Engineering, Finance, and Science (c↗
DOE OSTI2026

CHESS 2025: Leaf Area Index (LAI) for meadow, shrub, tree, and understory vegetation

This dataset contains Leaf Area Index (LAI) measurements made as part of the Colorado Headwaters Ecological Spectroscopy Study (CHESS) during June and July of 2025. Data were collected in the Upper Gunnison Basin, Colorado, across three study domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). Field observations of LAI were collected within 72 hours of airborne data collection by the National Ecological Observatory Network’s Aerial Observation Platform (NEON AOP). The NEON AOP collected waveform LiDAR (Light Detection and Ranging) and imaging spectrometer data in 426 spectral bands from the visible to shortwave infrared. LAI measurements were collected using the LICOR LAI-2200C Plant Canopy Analyzer following protocols outlined in the instrument manual (LI-COR 2019). Sampling targeted four distinct vegetation types: meadows, shrubs, trees, and aspen forest understory. We have archived data separately by site type because different field methods were used for each. At meadow sites, measurements were made at the four corners of 1m x 1m plots, with the instrument moving inward toward the center of the plot. At shrub sites, we measured the canopies of individual shrubs. At tree sites, we made measurements within a 10m x 10m subplot centered around a focal tree, with 30 observations taken on a regular grid. At aspen understory sites, we measured overstory trees following the tree protocol and understory herbaceous vegetation following the meadow protocol. All measurements included above-canopy (A) and below-canopy (B) readings, with specific protocols for scattering correction measurements in direct-sun conditions. Data were processed using the R package `rlai` (Worsham 2025). This package includes functions to calculate LAI, gap fraction, apparent clumping factor (Ω), scattering correction, and other canopy metrics. Package contents: Full file descriptions appear in ‘flmd.csv’. Files named according to the convention ‘lai_*_summary_data_cleaned.csv’ contain summary values of LAI, apparent clumping factor (Ωapp), and scattering correction factors for each site. These are the analysis-ready products that most data users will work with. Files named ‘lai_*_metadata_cleaned.csv’ contain additional site-level observations made during field collection. We have also archived intermediate and supplementary data for users who wish to check our processing approach or apply alternative methods. ‘raw_lai_2200C.zip’ contains the raw files as read from the LI-COR instrument, with no processing applied, in TXT format. The zip archive contains subdirectories by site type, which are further subdivided by sampling area. Filenames correspond to the sampling site number. ‘intermediate_results.zip’ contains detailed output from the processing routines, in JSON format. The zip archive contains subdirectories by site type; filenames correspond to the sampling site number. ‘scattering_correction_logs.zip’ contains logfiles from the implementation of Kobayashi et al.'s (2013) scattering correction algorithm. The logfiles report values of several parameters at each iteration of the algorithm, as the model converges toward a stable solution. They are intended for users who want to verify scattering correction performance. The zip archive contains subdirectories by site type; filenames correspond to the sampling site number. ‘spot_checks.csv’ reports LAI and other values for a small number of files processed with LI-COR FV2200 software (LI-COR 2013) using the same control parameters as in our R-based approach. Additional metadata are provided in a data dictionary describing column names and definitions (dd.csv), and in a file-level metadata file (flmd.csv). All zip files can be expanded with common archive utilities. TXT, CSV, and JSON files can be ingested into R or Python computing environments or read in common text editor utilities. Geospatial information: Geospatial data for mapping measurement site locations are in the files CHESS_polygons_lai_UTM.geojson, CHESS_polygons_shrub_UTM.geojson, and CHESS_polygons_meadow_UTM.geojson in the companion geospatial package for the 2025 CHESS campaign, ‘CHESS 2025: Location data for field observations and sampling’ (Henderson et al., 2026). CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. * Todorov and Worsham are co–first authors.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2022

$\mathrm{D}$ark$\mathrm{F}$lux: A new tool to analyze indirect-detection spectra of next-generation dark matter models

Here we present DarkFlux, a software tool designed to analyze indirect-detection signatures for next-generation models of dark matter (DM) with multiple annihilation channels. Version 1.0 of this tool accepts user-generated models with 2→2 tree-level dark matter annihilation to pairs of Standard Model (SM) particles and analyzes DM annihilation to γ rays. The tool consists of three modules, which can be run in a loop in order to scan over DM mass if desired: The annihilation fraction module calls an internal installation of MadDM, a dark matter phenomenology plugin for the Monte Carlo event generator MadGraph5 _ aMC@NLO, to compute the thermally averaged cross section $\langle σv\rangle_i$ for each annihilation channel $χχ$ ($\bar{χ}$,$χ^†$)→ i $\∈{SM, SM}. . The module then computes the fractional annihilation rate (annihilation fraction) into each channel. The flux module combines the flux spectrum from each annihilation channel, weighted by the appropriate annihilation fractions, to compute the total flux at Earth due to DM annihilation. In DarkFlux v1.0, this module specifically computes the γ-ray flux for each channel using the publicly available PPPC4DMID tables. The analysis module compares the total flux to observational data and computes the upper limit at 95% confidence level (CL) on the total thermally averaged DM annihilation cross section. In DarkFlux v1.0, this module compares the total γ-ray flux to a joint-likelihood analysis of fifteen dwarf spheroidal galaxies (dSphs) analyzed by the Fermi-LAT collaboration. DarkFlux v1.0 automatically provides data tables and can plot the output of these three modules. In this manual, we briefly motivate this indirect-detection computer tool and review the essential DM physics. We then describe the several modules of DarkFlux in greater detail. Finally, we show how to install and run DarkFlux and provide two worked examples demonstrating its capabilities.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Opportunities in AI/ML for the Rubin LSST Dark Energy Science Collaboration

The Vera C. Rubin Observatory's Legacy Survey of Space and Time (LSST) will produce unprecedented volumes of heterogeneous astronomical data (images, catalogs, and alerts) that challenge traditional analysis pipelines. The LSST Dark Energy Science Collaboration (DESC) aims to derive robust constraints on dark energy and dark matter from these data, requiring methods that are statistically powerful, scalable, and operationally reliable. Artificial intelligence and machine learning (AI/ML) are already embedded across DESC science workflows, from photometric redshifts and transient classification to weak lensing inference and cosmological simulations. Yet their utility for precision cosmology hinges on trustworthy uncertainty quantification, robustness to covariate shift and model misspecification, and reproducible integration within scientific pipelines. This white paper surveys the current landscape of AI/ML across DESC's primary cosmological probes and cross-cutting analyses, revealing that the same core methodologies and fundamental challenges recur across disparate science cases. Since progress on these cross-cutting challenges would benefit multiple probes simultaneously, we identify key methodological research priorities, including Bayesian inference at scale, physics-informed methods, validation frameworks, and active learning for discovery. With an eye on emerging techniques, we also explore the potential of the latest foundation model methodologies and LLM-driven agentic AI systems to reshape DESC workflows, provided their deployment is coupled with rigorous evaluation and governance. Finally, we discuss critical software, computing, data infrastructure, and human capital requirements for the successful deployment of these new methodologies, and consider associated risks and opportunities for broader coordination with external actors.

Aubourg, Eric [APC, Paris] (ORCID:000000025592023X↗
DOE OSTI2025

Data from: 'Abiotic influences on continuous conifer forest structure across a subalpine watershed'

This package archives the core data used for analysis and inference in 'Abiotic influences on continuous conifer forest structure across a subalpine watershed' (Worsham et al., 2025). All data were collected in the East River, Washington Gulch, Slate River, and Coal Creek watersheds of Colorado. In the paper, we quantified the relative influence of climate, topographic, edaphic, and geologic factors on conifer stand structure and composition, and their functional relationships, at the watershed scale. We used waveform LiDAR data to derive spatially continuous stand structure metrics. We fused these with a species-level classification map to estimate tree species abundance. We applied generalized additive and generalized boosted models to evaluate the covariability of structural and compositional metrics with abiotic variables. The package contains the essential products required for reproducing our analysis and the tables and figures reported in the publication. The products comprise four classes: (1) geospatial data, (2) tabular data used for inferential analysis, (3) tabular data describing analytical results and performance statistics, and (4) a data user guide. (1) includes discretized waveform LiDAR data, locations and attributes of individual tree crowns, sampling locations and domain boundaries, a canopy height model, and raster files of estimated forest structural and compositional metrics at 100 m grid scale. (2) includes all response and explanatory variable values applied in inferential models. Response variables include conifer forest stand density, basal area, 95th percentile height, quadratic mean diameter, and others. Explanatory variables include climatic water deficit, actual evapotranspiration, elevation, heat load, soil available water content, and others. (3) includes results of training and testing several individual tree detection (ITD) algorithms, as well as inferential modeling results. (4) is a PDF user guide for this data package, including detailed descriptions and data dictionaries for all files. The data package root contains 17 assets: 8 compressed tape archive (.tar.gz) files, 5 comma-separated values (.csv) files, 3 Geographic Tagged Image File Format (GeoTIFF) (.tif) files, and 1 Portable Document Format (.pdf) file. The compressed .tar.gz archives contain ESRI shapefiles (.shp) .tif, compressed LASer (.laz), and .csv files. The archives must first be decompressed using the widely distributed command-line software utility TAR. All other files, including constituent files within the .tar.gz archives, can be opened in the open-source R statistical computing environment. Alternatively, .csv files may also be read in any simple text editor software or Microsoft Excel. Geospatial files including .shp and .tif files can also be opened in GIS software, such as QGIS (open-source) or ESRI ArcGIS (proprietary). The .pdf Data User Guide can be read with Adobe Acrobat Reader or other compatible readers.

2018 NEON and 2025 CHESS Campaigns↗
DOE OSTI2023

MatLib-1.2: Nuclear Material Properties Library

The U.S. Nuclear Regulatory Commission (NRC) uses the computer code Fuel Analysis under Steady-state and Transients (FAST) to model steady-state and transient fuel behavior to support regulatory decisions. FAST relies on a material properties library (MatLib) that contains the thermal and mechanical properties of the nuclear materials and coolants of interest to support the US commercial nuclear industry. MatLib contains properties for a variety of nuclear fuels, cladding and other structural materials, gases, and coolants. In this document, material property correlations for the materials contained within MatLib are presented and discussed. When available, comparisons are made between the material property correlations and available data. Additionally, uncertainties are quantified on the material proper- ties, which is then used by the NRC to support uncertainty quantification for best-estimate plus uncertainty safety evaluation reviews. This document describes MatLib-1.2, which was updated from MatLib-1.1 to include cleanup of the code for streamlined calls to MatLib from the main FAST source code, and to enable easier readability of the code by developers that maintain and enhance the FAST code. The results of MatLib did not change between MatLib-1.1 and MatLib-1.2; however, the source code changes warranted incrementing the minor numbering of the software version number. The changes may result in faster execution times of FAST-1.2 as compared to FAST-1.1. This document is one of a series of documents on FAST; the other documents detail the models used by FAST as well as its integral assessment to experiments and commercial data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Opportunities for enhancing MLCommons efforts while leveraging insights from educational MLCommons earthquake benchmarks efforts

MLCommons is an effort to develop and improve the artificial intelligence (AI) ecosystem through benchmarks, public data sets, and research. It consists of members from start-ups, leading companies, academics, and non-profits from around the world. The goal is to make machine learning better for everyone. In order to increase participation by others, educational institutions provide valuable opportunities for engagement. In this article, we identify numerous insights obtained from different viewpoints as part of efforts to utilize high-performance computing (HPC) big data systems in existing education while developing and conducting science benchmarks for earthquake prediction. As this activity was conducted across multiple educational efforts, we project if and how it is possible to make such efforts available on a wider scale. This includes the integration of sophisticated benchmarks into courses and research activities at universities, exposing the students and researchers to topics that are otherwise typically not sufficiently covered in current course curricula as we witnessed from our practical experience across multiple organizations. As such, we have outlined the many lessons we learned throughout these efforts, culminating in the need for benchmark carpentry for scientists using advanced computational resources. The article also presents the analysis of an earthquake prediction code benchmark while focusing on the accuracy of the results and not only on the runtime; notedly, this benchmark was created as a result of our lessons learned. Energy traces were produced throughout these benchmarks, which are vital to analyzing the power expenditure within HPC environments. Additionally, one of the insights is that in the short time of the project with limited student availability, the activity was only possible by utilizing a benchmark runtime pipeline while developing and using software to generate jobs from the permutation of hyperparameters automatically. It integrates a templated job management framework for executing tasks and experiments based on hyperparameters while leveraging hybrid compute resources available at different institutions. The software is part of a collection called cloudmesh with its newly developed components, cloudmesh-ee (experiment executor) and cloudmesh-cc (compute coordinator).

58 GEOSCIENCES↗
DOE OSTI2024

Economic and Jobs Impacts of Point-Source Carbon Capture in Cement Industry – Case Study

The cement industry accounts for an estimated 8% of global CO2 emissions, which surpasses that of the entire aviation sector. In contrast with other industries, where CO2 emissions can be drastically reduced via electrification or fuels substitution, cement production releases CO2 as part of its process, during the calcination of carbonates to yield oxides. Thus, point-source carbon capture has become a key technology in the cement industry’s decarbonization. Apart from the expected environmental benefits, point-source carbon capture in the cement industry can yield important economic benefits and create jobs. The objective of this study was to perform a preliminary assessment of the economic and workforce impacts associated with the construction and operation of a point-source carbon capture retrofit of an existing cement production facility, using as a basis the data from a front-end engineering design (FEED) study to install a 3.9 million metric tons per year (Mtpy) CO2 capture facility at Holcim Ste Genevieve cement plant in Missouri, United States of America. The advanced carbon capture technology used in this FEED study was Air Liquide’s Cryocap™ FG carbon capture technology. The study evaluated the direct, indirect, and induced economic impacts of the construction, operation, and maintenance activities of the project over its lifespan. It also covered how the project will generate new jobs, their nature, and quantity, along with strategies to prepare the workforce. To perform this study, construction, operation, and maintenance cost estimates, as well as construction and operation staffing plans from the FEED study were input into IMPLAN version 7.5 software, licensed by IMPLAN Group LLC (Huntersville, VC), to predict the direct, indirect and induced economic impacts of the project using industry multipliers from the software. Additionally, recruitment strategies were developed for hiring individuals who belong to groups that are historically underserved or underrepresented, as well as anticipated recruitment of workers from the local community (whether training will be required or if the skills are associated with an existing labor force). The analysis estimated that the construction and operation of the carbon capture at Holcim Ste. Genevive will result in over 24 thousand work-years of job opportunities, close to USD 10 billion of economic impacts, including over USD 460 million of tax revenue. These results encompass the direct, indirect, and induced effects. A strategy to maximize hiring from the project and neighboring counties was developed, leveraging training agreements with local trade groups and universities. The result of this study can be used for a strategic preliminary assessment of the potential regional economic and job impacts of retrofitting existing cement plants with point source carbon systems, and its methodology can be replicated to individual projects to aid in planning and workforce development.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2021

On the Limits of EM Based Detection of Control Logic Injection Attacks In Noisy Environments

The difficulty in applying traditional security mechanisms in Industrial Control System (ICS) environments makes a large portion of these mission-critical assets vulnerable to cyber attacks. Therefore, there is a dire need for the development of novel security mechanisms specifically designed to protect such critical systems. Recently a lot of attention has been given to mechanisms that exploit the EM emanations of devices for defense purposes. Such practices may lead to the development of robust external and non-intrusive anomaly detection systems. Nevertheless, the majority of current work in the area neglects to consider the implications of real-life environments, particularly environmental noise. In this work, we explore the limits of EM-based anomaly detection towards identifying injection attacks in control logic software in noisy environments. Our study conducted upon both synthetically generated and real signals identified that indeed environmental noise might significantly degrade the accuracy of the anomaly detection process. Experiments done upon synthetic data indicated that assuming that signals are captured with high sampling rates, even minor code injections can be detected with above-90% accuracy in noisy environments where SNR is up to -2dB. This is true even if naive detection methods are considered. Moreover, experiments done using a real-life testbed attest that even single-instruction injections can be detected with near-perfect accuracy in relatively clean environments. Finally, noise-elimination techniques can drastically improve the reliability of the detection mechanism even in noisy environments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Snekmer: a scalable pipeline for protein sequence fingerprinting based on amino acid recoding

Abstract Motivation The vast expansion of sequence data generated from single organisms and microbiomes has precipitated the need for faster and more sensitive methods to assess evolutionary and functional relationships between proteins. Representing proteins as sets of short peptide sequences (kmers) has been used for rapid, accurate classification of proteins into functional categories; however, this approach employs an exact-match methodology and thus may be limited in terms of sensitivity and coverage. We have previously used similarity groupings, based on the chemical properties of amino acids, to form reduced character sets and recode proteins. This amino acid recoding (AAR) approach simplifies the construction of protein representations in the form of kmer vectors, which can link sequences with distant sequence similarity and provide accurate classification of problematic protein families. Results Here, we describe Snekmer, a software tool for recoding proteins into AAR kmer vectors and performing either (i) construction of supervised classification models trained on input protein families or (ii) clustering for de novo determination of protein families. We provide examples of the operation of the tool against a set of nitrogen cycling families originally collected using both standard hidden Markov models and a larger set of proteins from Uniprot and demonstrate that our method accurately differentiates these sequences in both operation modes. Availability and implementation Snekmer is written in Python using Snakemake. Code and data used in this article, along with tutorial notebooks, are available at http://github.com/PNNL-CompBio/Snekmer under an open-source BSD-3 license. Supplementary information Supplementary data are available at Bioinformatics Advances online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

BraggNN : fast X-ray Bragg peak analysis using deep learning

X-ray diffraction based microscopy techniques such as high-energy diffraction microscopy (HEDM) rely on knowledge of the position of diffraction peaks with high precision. These positions are typically computed by fitting the observed intensities in detector data to a theoretical peak shape such as pseudo-Voigt. As experiments become more complex and detector technologies evolve, the computational cost of such peak-shape fitting becomes the biggest hurdle to the rapid analysis required for real-time feedback in experiments. To this end, we propose BraggNN, a deep-learning based method that can determine peak positions much more rapidly than conventional pseudo-Voigt peak fitting. When applied to a test dataset, peak center-of-mass positions obtained from BraggNN deviate less than 0.29 and 0.57 pixels for 75 and 95% of the peaks, respectively, from positions obtained using conventional pseudo-Voigt fitting (Euclidean distance). When applied to a real experimental dataset and using grain positions from near-field HEDM reconstruction as ground-truth, grain positions using BraggNN result in 15% smaller errors compared with those calculated using pseudo-Voigt. Recent advances in deep-learning method implementations and special-purpose model inference accelerators allow BraggNN to deliver enormous performance improvements relative to the conventional method, running, for example, more than 200 times faster on a consumer-class GPU card with out-of-the-box software.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Data for The Stem Cell-Type Transcriptome of Bioenergy Sorghum Reveals the Spatial Regulation of Secondary Cell Wall Networks

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum’s 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about stem cell-type gene expression and regulation was available to enable engineering. To obtain this information, Laser Capture Microdissection (LCM) was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type specific gene regulatory networks (GRNs) revealed that unique TF families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with a stem developmental transcriptome dataset to identify the GRN that differentially activates the secondary cell wall (SCW) formation in stem xylem sclerenchyma and epidermal cells. The cell-type transcriptomic dataset provides a valuable source of information about the function of sorghum stem cell types and GRNs that will enable the engineering of bioenergy sorghum stems.

Software↗
DOE OSTI2022

Statistical characterization of twin transmission across grain boundaries in magnesium

Here, a detailed statistical analysis of twin transmission (TT) across grain boundaries is performed in rolled, commercial purity magnesium compressed along the rolling direction. EBSD images are acquired from two different cuts: a section containing the rolling (RD) and normal (ND) directions; and a section at 35° to the ND which contains transverse direction (TD). An automated twinning analysis software, METIS, is used to obtain the statistical correlations between deformation twins and other microstructural features by analyzing EBSD microstructures comprising thousands of grains and twins. This detailed statistical analysis reveals that the TT propensity is sensitive to the grain boundary (GB) misorientation angle but not to the GB misorientation axis. Specifically, TT propensity decreases with increasing GB misorientation angle; however, the decreasing trend is not monotonic. Further, the detailed analysis of TT events combining macroscopic Schmid factor and the geometric measures (m’: accounts for the alignment of both twin plane normal and shear directions; m”: accounts for the alignment of only twin shear directions; and m”’: accounts for the alignment of only twin plane normal) helps in understanding and identifying the process of twin-pair formation, i.e., co-nucleation versus transmission, also to identify the role of local stresses at GBs induced by inter-grain interaction versus twinning shear transformation processes. In addition, Bayesian inference is used to draw statistically meaningful conclusions as to the likelihood of transmission given misorientation angles. Lastly, twin chain frequency as a function of chain length is predicted using the probability distribution obtained from the Bayesian inference and compared with the actual data from the EBSD microstructures.

36 MATERIALS SCIENCE↗
DOE OSTI2023

POWTEX visits POWGEN

The high-intensity time-of-flight (TOF) neutron diffractometer POWTEX for powder and texture analysis is currently being built prior to operation in the eastern guide hall of the research reactor FRM II at Garching close to Munich, Germany. Because of the world-wide 3 He crisis in 2009, the authors promptly initiated the development of 3 He-free detector alternatives that are tailor-made for the requirements of large-area diffractometers. Herein is reported the 2017 enterprise to operate one mounting unit of the final POWTEX detector on the neutron powder diffractometer POWGEN at the Spallation Neutron Source located at Oak Ridge National Laboratory, USA. As a result, presented here are the first angular- and wavelength-dependent data from the POWTEX detector, unfortunately damaged by a 50 g shock but still operating, as well as the efforts made both to characterize the transport damage and to successfully recalibrate the voxel positions in order to yield nonetheless reliable measurements. Also described is the current data reduction process using the PowderReduceP2D algorithm implemented in Mantid [Arnold et al. (2014). Nucl. Instrum. Methods Phys. Res. A , 764 , 156–166]. The final part of the data treatment chain, namely a novel multi-dimensional refinement using a modified version of the GSAS-II software suite [Toby & Von Dreele (2013). J. Appl. Cryst. 46 , 544–549], is compared with a standard data treatment of the same event data conventionally reduced as TOF diffraction patterns and refined with the unmodified version of GSAS-II . This involves both determining the instrumental resolution parameters using POWGEN's powdered diamond standard sample and the refinement of a friendly-user sample, BaZn(NCN) 2 . Although each structural parameter on its own looks similar upon comparing the conventional (1D) and multi-dimensional (2D) treatments, also in terms of precision, a closer view shows small but possibly significant differences. For example, the somewhat suspicious proximity of the a and b lattice parameters of BaZn(NCN) 2 crystallizing in Pbca as resulting from the 1D refinement (0.008 Å) is five times less pronounced in the 2D refinement (0.038 Å). Similar features are found when comparing bond lengths and bond angles, e.g. the two N—C—N units are less differently bent in the 1D results (173 and 175°) than in the 2D results (167 and 173°). The results are of importance not only for POWTEX but also for other neutron TOF diffractometers with large-area detectors, like POWGEN at the SNS or the future DREAM beamline at the European Spallation Source.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Time-Gated Raman Spectroscopy (Intern Final Report)

Time-gated Raman spectroscopy is a powerful tool for rapid non-destructive analysis of chemical compounds, particularly when combined with other investigative methods. Time-gating the signal obtained from a sample during Raman spectroscopy allows for the removal of background emission and black body radiation, improving clarity and accuracy of scans. The main objectives of this project were to prove the lab’s time-gated Raman spectroscopy system works as proof of concept and to make select improvements to the in-house LabVIEW software used to run the time-gated system. This time-gated system will be added to the CTK’s TAP reactors in the future, but this is out of the scope of this internship project. This research is important, as understanding the mechanisms behind catalysts leads to designing better systems/materials and the perfection of catalysts, and energy-efficient chemical manufacturing is key when designing a greener future. The research for this project was done with samples at both ambient conditions in sample holders and at operando conditions (i.e., high temperature, unsteady-state) inside a small-volume chemical reactor. Numerous spectro-kinetic scans of the catalysts were obtained, but the advanced dynamics of these systems are still being interpreted. There is data that demonstrates that the time-gated system is correctly rejecting emission from samples, and one can observe real-time changes in the signal from the sample, due to coking or changes induced by redox chemistry. Chemical manufacturers and the planet are the main beneficiaries of catalysis research, as better catalysts will reduce carbon emissions.

36 MATERIALS SCIENCE↗
DOE OSTI2026

NanoPSD: A software for automatic detection of Nano-Particle Shape Distribution in electron microscopy images

Accurate quantification of the size and morphology of nanoparticles from electron microscopy (EM) images is essential to understand growth mechanisms, surface reactivity, and functional behavior in nanoscale materials. Manual analysis remains slow, subjective, and difficult to reproduce in large datasets. We introduce NanoPSD (Nano-Particle Shape Distribution), an open-source and fully automated framework for quantitative particle detection and morphology analysis from EM images. NanoPSD integrates adaptive contrast enhancement, polarity-agnostic scale-bar detection, Optical Character Recognition (OCR)-based calibration, and classical segmentation via Otsu thresholding with morphological refinement. Particle contours are used to extract geometric descriptors, including equivalent circular diameter, aspect ratio, circularity, and solidity, enabling automated classification into spherical, rod-like, and aggregate morphologies. The framework supports both single-image and batch processing, generating publication-quality visualizations, LaTeX-ready tables, and structured comma-separated values (CSV) datasets. As a demonstration, we applied NanoPSD to plasma-synthesized nanoparticle samples diagnosed via transmission electron microscopy (TEM). The code produced statistically robust size and morphology distributions spanning a few to tens of nanometers with minimal user supervision. The pipeline demonstrates high reproducibility and scalability, processing large image collections with consistent calibration and output formatting. Its modular design enables seamless integration of future deep-learning-based segmentation models, providing a pathway toward intelligent, data-driven electron microscopy analysis.

36 MATERIALS SCIENCE↗