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DOE OSTI2024

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

The folding and unfolding of RNA stem-loops are critical biological processes; however, their computational studies are often hampered by the ruggedness of their folding landscape, necessitating long simulation times at the atomistic scale. Here, we adapted DeepDriveMD (DDMD), an advanced deep learning-driven sampling technique originally developed for protein folding, to address the challenges of RNA stem-loop folding. Although tempering- and order parameter-based techniques are commonly used for similar rare-event problems, the computational costs or the need for a priori knowledge about the system often present a challenge in their effective use. DDMD overcomes these challenges by adaptively learning from an ensemble of running MD simulations using generic contact maps as the raw input. DeepDriveMD enables on-the-fly learning of a low-dimensional latent representation and guides the simulation toward the undersampled regions while optimizing the resources to explore the relevant parts of the phase space. We showed that DDMD estimates the free energy landscape of the RNA stem-loop reasonably well at room temperature. Our simulation framework runs at a constant temperature without external biasing potential, hence preserving the information on transition rates, with a computational cost much lower than that of the simulations performed with external biasing potentials. Here, we also introduced a reweighting strategy for obtaining unbiased free energy surfaces and presented a qualitative analysis of the latent space. This analysis showed that the latent space captures the relevant slow degrees of freedom for the RNA folding problem of interest. Finally, throughout the manuscript, we outlined how different parameters are selected and optimized to adapt DDMD for this system. We believe this compendium of decision-making processes will help new users adapt this technique for the rare-event sampling problems of their interest.

Gupta, Ayush↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Trail Creek in Taylor River Watershed, Colorado 2024-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors near Trail Creek. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format TR-X-Y, where TR refers to Trail Creek, X is the treatment block identifier, and Y is the location identifier. Specifically, TR-ASCC1 is the control treatment block under the Adaptive Silviculture for Climate Change (ASCC) project, and TR-ASCC2 is the clear-cut treatment block. TR-ASCC-EHSn is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and TR-ASCC-ERTn (upslope n=1) are ecohydrology sites along the electrical resistivity tomography transects. The sample and location information can be found in metadata.csv, and the data from the soil sensors will be included in a future data version when the observation period becomes sufficiently long for data analysis. Sampling and Measurements Each sample falls into one of the two sampling methods – (1) intact cores or (2) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. The intact cores were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was 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.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Snodgrass Mountain in East River Watershed, Colorado 2020-2025

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors at Snodgrass Mountain. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format SG-X-Y, where SG refers to Snodgrass Mountain, X is the location identifier, and Y is the depth identifier at the same X (shallow Y=1). Specifically, SG-EHS is associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and SG-ERTn (upslope n=1) are points along the Snodgrass electrical resistivity tomography transect not associated with the existing site names in the directory. The sample and location information can be found in metadata.csv. Sampling and Measurements Each sample falls into one of the three sampling methods – (1) intact cores, (2) repacked samples, or (3) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. Both intact cores and repacked samples were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores and in-situ soil sensors could be prioritized because these sampling methods are less destructive. While the repacked samples were packed to the target bulk density (estimated post-sampling, when sample volume was known), these samples had altered pore structures. Nevertheless, intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method also has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was 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.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2026

Haze processing of atmospheric particles during wintertime in the Indo-Gangetic Plains

The impacts of haze on visibility, air quality, and climate are not well quantified due to a lack of understanding of the evolution of the mixing state and phase state of atmospheric particles during haze processing. The variability of the mixing state of atmospheric particles contributes significantly to uncertainties associated with the estimated aerosol radiative forcing. We collected particle samples in January 2018 from the highly polluted Indo-Gangetic plain during hazy conditions to study haze-processed particles. Single particle analysis using multi-modal micro-spectroscopy techniques revealed an abundance (40–70% by number) of potassium-rich sulfate particles from biomass-burning influenced smoke. Tilted view imaging showed that most of the organic particles that had inorganic potassium and sulfate inclusions were liquid-like while those without inclusions were more semi-solid. High-resolution mass spectrometry analysis revealed a significant presence of organosulfates and nitroxy-organosulfates in the morning samples (24%) compared to the afternoon samples (9%), despite higher relative humidity in the afternoon. Overall, our results highlight the significant contribution of both organic and inorganic sulfate to the total particulate sulfur budget during haze processing in winter, when anthropogenic emissions such as household burning, agricultural burning, and vehicular emissions are major contributors to particle mass.

Mathai, Susan [Pacific Northwest National Laborato↗
DOE OSTI2025

Optical vibrational spectroscopic signatures of ammonium diuranate process parameters

Ammonium diuranate (ADU) is commonly encountered in the nuclear fuel cycle; however, previous investigations have shown that ADU is a complex mixture of distinct compounds. Moreover, production parameters are known to heavily influence the composition of the resulting ADU. Here, we examine four samples of ADU prepared at Oak Ridge National Laboratory (ORNL), and one sample of ADU made at Pacific Northwest National Laboratory (PNNL), with the goal of further characterizing and elucidating the effect of processing parameters such as stir rate, strike direction, and temperature on material composition. Process parameters during ADU precipitation at ORNL and PNNL were well documented, and we relate process variables to optical vibrational spectroscopic signatures observed using Raman and infrared (IR) spectroscopy. In addition, powder X-ray diffraction (PXRD) reveals differences in the solid-phase composition of ADU precipitates, but we find that the primary phase is similar to the uranyl oxyhydroxyhydrate mineral metaschoepite. Despite the significant phase contributions of a metaschoepite-like phase, spectroscopic evidence of both nitrate and ammonium are observed for all samples. To gain a more holistic understanding of spectroscopic features of process parameters in ADU, principal component analysis (PCA) is employed and results in observable signatures that relate to the stir rate used during synthesis. These results provide further information about the process-dependence of ADU precipitate composition.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Autonomous organic synthesis for redox flow batteries via flexible batch Bayesian optimization

Traditional trial-and-error methods for materials discovery are inefficient to meet the urgent demands posed by the rapid progression of climate change. This urgency has driven the increasing interest in integrating robotics and machine learning into materials research to accelerate experimental learning. However, idealized decision-making frameworks to achieve maximum sampling efficiency are not always compatible with high-throughput experimental workflows inside a laboratory. For multi-step chemical processes, differences in hardware capacities can complicate the digital framework by introducing constraints on the maximum number of samples in each step of the experiment, hence causing varying batch sizes in variable selection within the same batch. Therefore, designing flexible sampling algorithms is necessary to accommodate the multi-step synthesis with practical constraints unique to each high-throughput workflow. In this work, we designed and employed three strategies on a high-throughput robotic platform to optimize the sulfonation reaction of redox-active molecules used in flow batteries. Our strategies adapt to the multi-step experimental workflow, where their formulation and heating steps are separate, causing varying batch size requirements. By strategically sampling using clustering and mixed-variable batch Bayesian optimization, we were able to iteratively identify optimal conditions that maximize the yields. Our work presents a flexible approach that allows tailoring the machine learning decision-making to suit the practical constraints in individual high-throughput experimental platforms, followed by performing resource-efficient yield optimization using available open-source Python libraries.

Tamura, Clara [Univ. of Washington, Seattle, WA (U↗
DOE OSTI2025

Performance Evaluation of LPBF Manufactured 316H Components

This work represents the continuation of a benchmark study that includes modeling, fabrication and characterization as demonstration to support industry’s adoption of advanced manufacturing processes in a variety of structures. This comprehensive study investigated the feasibility of using additive manufacturing (AM) technologies, specifically Laser Powder Direct Energy Deposition (LP-DED) and Laser Powder Bed Fusion (LPBF), to produce complex nuclear microreactor components using 316H stainless steel. The research focused on manufacturing an expanded elbow pipe component with transitioning sections, which are traditionally difficult and costly to produce through conventional manufacturing methods. The overall study’s primary objectives are therefore demonstrating AM viability for nuclear applications, optimizing process parameters, developing comprehensive material characterization protocols, validating computational modeling approaches, and establishing manufacturing guidelines for complex geometries. Although the initial work included the phased approach of cubical, upscaled cylindrical components, it is to enable to obtain more knowledge for the printing of the expanded elbow structure. The project achieved significant progress in process development by successfully optimizing LP-DED parameters to achieve 99.16-99.97% relative density in 316H stainless steel components. Through systematic evaluation of sixteen cube samples with varied laser powers (400-700W) and scan speeds (600-900 mm/min), optimal processing windows were identified at 500-550W with 600-700 mm/min or 650-700W with 650-900 mm/min scan speeds. The DED manufactured 316H demonstrated mechanical properties comparable or superior to wrought materials, with Young's modulus ranging from 153-208 GPa and controlled microstructural characteristics including greater than 95% face-centered cubic (FCC) phases and engineered cellular structures with sizes between 3.23-6.17 µm.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Additive Manufacturing of Fe-based Alloys for Nuclear Reactor Environments

This report is a Milestone 2 deliverable in FY2025, under work package MT-25AN090211 to support research and qualification activities supported by the Advanced Materials and Manufacturing Technologies (AMMT) program. It provides an update on the work done on the laser based additive manufacturing of steels for nuclear applications, conducted collaboratively by Argonne National Laboratory and Pacific Northwestern National Laboratory. Building upon FY23 and FY24 efforts, the focus of FY25 includes continued optimization of process parameters for the alloys: A709 & G92. The work package also includes fabricating test samples to conduct a thorough microstructural analysis and perform preliminary mechanical testing. The major accomplishments of this work package are summarized below, applicable to both Laser Powder Bed Fusion (LPBF) processes conducted at Argonne National Laboratory and Laser Powder Directed Energy Deposition (LP-DED) processes conducted at Pacific Northwest National Laboratory.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2024

Determination of Reportable Radionuclides for Defense Waste Processing Facility (DWPF) Sludge Batch 10 (Macrobatch 12)

Savannah River National Laboratory (SRNL) was tasked with the radionuclide characterization of the Sludge Batch 10 (SB10) Tank 40 sample (HTF-40-23-24) in accordance with requirements for reporting the Waste Acceptance Product Specifications (WAPS). The Defense Waste Processing Facility (DWPF) is required to report all radionuclides with half-lives greater than ten years and which comprise greater than 0.05% of the total activity inventory for a given waste form at certain specified “index years”. DWPF complies with the requirements by considering the half-life requirement (t1/2 > 10 years) and radionuclides with concentrations greater than 0.01% of the total inventory from the approximate time of production through 1,100 years.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Selective laser sintering and spark plasma sintering of (Zr,Nb,Ta,Ti,W)C compositionally complex carbide ceramics

Abstract Two advanced manufacturing processes, spark plasma sintering (SPS) and selective laser sintering (SLS), have been developed for synthesis of (Zr,Nb,Ta,Ti,W)C compositionally complex carbide (CCC) via reactive sintering of a powder mixture of constitute monocarbides. X‐ray diffraction analysis confirmed that the single‐phase CCC can be formed by both SPS and SLS. While a homogenous microstructure with uniform metal element distributions was developed during SPS, three‐layer microstructures with a thin TiC‐rich layer and two TaC‐rich layers along with a TiO 2 ‐rich surface layer containing W nanoparticles were formed during SLS. In addition, cellular structures with W, Zr, and Ti element segregation and dislocations on cell boundaries were observed in the SLS‐CCC sample, indicating the effect of nonequilibrium conditions on microstructure formation during laser melting followed by rapid cooling and solidification process. Compared to the SPS‐CCC sample, the SLS‐CCC showed enhanced hardness and reduced thermal conductivity, which may be related to their unique cellular structures.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Divide and conquer: using RhizoVision Explorer to aggregate data from multiple root scans using image concatenation and statistical methods

Roots are important in agricultural and natural systems for determining plant productivity and soil carbon inputs. Sometimes, the amount of roots in a sample is too much to fit into a single scanned image, so the sample is divided among several scans, and there is no standard method to aggregate the data. Here, we describe and validate two methods for standardizing measurements across multiple scans: image concatenation and statistical aggregation. We developed a Python script that identifies which images belong to the same sample and returns a single, larger concatenated image. These concatenated images and the original images were processed with RhizoVision Explorer, a free and open-source software. An R script was developed, which identifies rows of data belonging to the same sample and applies correct statistical methods to return a single data row for each sample. These two methods were compared using example images from switchgrass, poplar, and various tree and ericaceous shrub species from a northern peatland and the Arctic. Most root measurements were nearly identical between the two methods except median diameter, which cannot be accurately computed by statistical aggregation. We believe the availability of these methods will be useful to the root biology community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Enabling dynamic 3D coherent diffraction imaging via adaptive latent space tuning of generative autoencoders

Abstract Coherent diffraction imaging (CDI) is an advanced non-destructive 3D X-ray imaging technique for measuring a sample’s electron density. The main challenge of CDI is loss of phase information in diffraction intensity measurements, resulting in lengthy iterative reconstruction processes that can return non-unique solutions, which pose challenges for experiments attempting to track dynamic sample evolution through multiple states. As the increased brightness of fourth-generation light sources enables faster sample measurements and drives operando experiments with Bragg CDI, there is a growing need for faster reconstruction techniques that can keep pace. We have developed an adaptive generative autoencoder approach for uniquely tracking a sample’s electron density as it dynamically evolves. Our approach adaptively tunes the low-dimensional latent embedding of a generative autoencoder, enabling a computationally efficient manner to account for time-varying shifting distributions in real-time. Analytic proof of convergence is provided as well as numerical demonstration of sample tracking with noisy measurements.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Soil Water Retention and Hydraulic Conductivity Data and Model at Pump House in East River Watershed, Colorado 2019-2024

This data package includes soil water retention and hydraulic conductivity data and model fitting results from measurements of ex-situ soil samples and in-situ soil sensors near Pump House at Mount Crested Butte in the East River Watershed. Soil water retention curves (SWRC) characterize soil water content as a function of soil water potential. SWRC depends on soil texture and pore structure and can be used to describe the constraints on biogeochemical processes in terms of soil water availability. In this data package, the sample identification follows the format ER-X-Y, where ER refers to East River, X is the location identifier, and Y is the depth identifier at the same X (shallow Y=1). Specifically, ER-PHS, ER-LMC, ER-LMF, and ER-SMN are associated with ecohydrology sites under the East-Taylor Watershed Community Observatory Sites directory, and ER-RBTn (upslope n=1) are sampling transects during the 2019 Rootball Campaign. The sample and location information can be found in metadata.csv. Sampling and Measurements Each sample falls into one of the three sampling methods – (1) intact cores, (2) repacked samples, or (3) soil sensors – and one of the two measurement methods – (a) laboratory or (b) in-situ. Both intact cores and repacked samples were measured using the laboratory methods, which include measurements of soil water potential (HYPROP & WP4C, METER), saturated (KSAT, METER) and unsaturated hydraulic conductivity (HYPROP). The in-situ method uses a pair of co-located soil sensors to measure volumetric water content (TEROS12, METER) and soil water potential (TEROS21, METER), and the hydraulic conductivity was not measured. In comparison, the laboratory methods progress from full saturation to dry conditions, and the in-situ method includes both dry-to-wet and wet-to-dry cycles. The sampling and measurement methods for each sample can be found in metadata.csv, and more information about the measurements is detailed in the Methods section below. Models Retention and hydraulic conductivity data were fitted with four van-Genuchten-type models (specified by “model_name” column in the files): (1) traditional constrained van Genuchten model (“vG_constrained”), (2) traditional unconstrained van Genuchten model (“vG_unconstrained”), (3) PDI-variant of the constrained van Genuchten model (“vG_constrained_PDI”), and (4) PDI-variant of the unconstrained van Genuchten model (“vG_unconstrained_PDI”). The difference between the constrained (1: n) and the unconstrained (2: n, m) van Genuchten models is the number of pore-size distribution parameters in the model equations, giving the unconstrained model more degrees of freedom when fitting the data. Between the traditional and the PDI-variant models, model fitting differs the most at the dry end of the measurements. The traditional models allow infinite suction at the residual water content (water content does not drop below residual water content), and the PDI-variant models enforce a soil water potential value of pF=6.8 (~ -630 MPa) at oven-dryness (water content reaches 0). The inclusion of the van-Genuchten-type models is due to their common application. If other retention models are required, users can access the data in data.csv for further data fitting. More information about the models can be found in the Methods section below. Fitting Tasks The model fitting can be categorized into three levels of tasks (specified by “fitting_task” column in the files). Level 1 (“fit_retention”) only includes retention data fitting (the only level available for the in-situ method). Level 2 (“fit_retention_conductivity”) includes both retention and hydraulic conductivity data fitting, and the saturated hydraulic conductivity (Ks, a parameter of the hydraulic conductivity functions) is fixed by the measurements from KSAT. Level 3 (“fit_retention_conductivity_Ks”) also includes both retention and hydraulic conductivity data fitting, but Ks is a fitted parameter without the constraints from KSAT measurements. Among the same retention models (e.g. vG_constrained models of the same sample), level 1 should produce the best retention data fitting. Level 2 should have the highest misfit of the retention and hydraulic conductivity data, because the retention and hydraulic conductivity functions share common model parameters, and the unsaturated hydraulic conductivity (HYPROP) data fitting is subject to Ks measured independently by KSAT. Level 3 should have mid-level misfits of the retention and hydraulic conductivity data. While level 3 fits the hydraulic conductivity data better than level 2, the fitted Ks value might be unreasonable due to the lack of constraints at the wet end of the measurements. General recommendation when using this data package: (1) Choice of sampling methods: Intact cores and in-situ soil sensors could be prioritized because these sampling methods are less destructive. While the repacked samples were packed to the target bulk density (estimated post-sampling, when sample volume was known), these samples had altered pore structures. Nevertheless, intact cores might suffer from sample gaps that would lead to overestimation of Ks (sample gaps can be inferred from the “soil_sample_volume” column in metadata.csv when the value is < 249). In-situ method also has higher uncertainty in characterizing the wet end of the SWRC because of sensor limitations and the difficulty in reaching full saturation under natural conditions. (2) Choice of fitting tasks: When only retention data is needed, level 1 (“fit_retention”) should be prioritized. When both retention and hydraulic conductivity data are needed, level 2 (“fit_retention_conductivity”) could be prioritized. (3) Choice of models: This could depend on what the downstream models call for. If no specific model is required, model misfit could be used as a ranking criterion. Model misfit values in terms of RMSE can be found in model_parameters.csv. The following files are included in this data package: (1) metadata.csv – This file includes the general information of each sample, including location (description, geocoordinates, elevation), sampling and measurements details (method, depth, time or period, volume, instruments), and soil physical properties (bulk density, saturated hydraulic conductivity, only applicable to physical soil samples). (2) data.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity data of each sample. Column “instrument” specifies the instrument (HYPROP, WP4C, or TEROS) used to perform the measurements. (3) model_fit.csv – This file includes soil water potential, volumetric water content, and unsaturated hydraulic conductivity fitted from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the variable does not apply to that fitting task. (4) model_parameters.csv – This file includes the fitted model parameters, model misfits, and conventional water content thresholds (field capacity and wilting point) from the four models and three fitting tasks. Column “model_name” specifies the retention model used, and “fitting_task” specifies the level of data fitting. Missing values indicate that the parameter does not apply to that model and/or that fitting task. (5) data_Ks.csv – This file includes the saturated hydraulic conductivity measurements from KSAT. (6) /figure/*.png – This folder includes three quick visualizations of the data, retention model fitting results and misfits, and hydraulic conductivity model fitting results, misfits, and parameters. The model fitting results are separated by samples and fitting tasks and colored by models. Zoom-in required. (7) /hyprop/*.bdhx – This folder includes proprietary hyprop files that require the free Labros SoilView-Analysis (METER) to open. Users can explore data fitting using other retention models (i.e. Brooks-Corey, Fredlund-Xing, Kosugi, bimodal models). Be aware that Ks value is pre-entered under “Fitting tab, Conductivity functions parameters” for level 2 fitting. If the value is lost, please refer to metadata.csv under “Ks” column. (8) Six file-level metadata that summarize file, header, column, and variable information of all files. This work was 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.

EARTH SCIENCE > LAND SURFACE > SOILS↗
DOE OSTI2025

Amorphous complexion-aided sintering enables scalable processing of bulk nanocrystalline Cu-Zr with high strength and compressive plasticity

Nanocrystalline alloys can have exceptional strengths, yet due to limited microstructural stability it is difficult to fabricate bulk pieces through traditional processing routes that retain nanosized grains. In this study, centimeter-sized Cu-Zr alloy pellets were fabricated via a simple and improved powder metallurgy processing route. Different consolidation temperatures and times were employed to investigate the effect of amorphous grain boundary complexions on densification and the resulting mechanical properties. Bulk compression tests were carried out, with the samples that were hot pressed at 900 °C for 10 h exhibiting an excellent combination of average yield strength of 722 ± 45 MPa and average failure strain of 25.3 ± 2.4 %. Furthermore, we find that a powder processing route which enables amorphous complexion-assisted sintering leads to samples that (1) reach full density without requiring quenching treatments or other complex processing, (2) demonstrate appreciable plasticity, and (3) have strength that competes with commercially available high-strength Cu alloys.

Bulk nanocrystalline alloy↗
DOE OSTI2026

Transient uncertainty quantification and Global Sensitivity Analysis of the open-source Molten Chloride Reactor Experiment (MCRE) using GP-PCA surrogate models

Uncertainties in the thermophysical properties of molten salts impact both the steady-state and transient behavior of Molten Salt Reactors (MSRs). In this work, we aim to quantify the influence of such uncertainties on the transient operation of the Molten Chloride Reactor Experiment (MCRE), utilizing the open-source specifications provided for this reactor. Seven representative transient scenarios are considered. For each scenario, we evaluate the impact of thermophysical property uncertainties on four key multiphysics model output variables of interest (VoIs): maximum power density, maximum fuel temperature, maximum reflector temperature, and average fuel velocity magnitude. In addition, we perform a Global Sensitivity Analysis (GSA) by computing Sobol’ indices for the uncertain input parameters to determine their contribution to the variability of each VoI. Conducting GSA is computationally intensive due to the large number of required evaluations of the high-fidelity multiphysics model. To mitigate this cost, we develop a surrogate modeling framework that combines Gaussian Process (GP) regression with Principal Component Analysis (PCA), enabling efficient sample generation for the GSA. Our results show that for energy-related VoIs, thermal conductivity is the dominant contributor to uncertainty. In contrast, for flow-related VoIs, density and dynamic viscosity are the primary sources of uncertainty. The specific heat of the fuel salt was found to play a secondary role in the transient analyses.

42 - ENGINEERING↗
DOE OSTI2026

CO 2 Sorption in Moisture Swing Anion Exchange Resins for Direct Air Capture: Experimental Isotherm Determination and Modeling

Moisture swing (MS) sorption is a promising direct air capture (DAC) technology to achieve negative CO 2 emissions and counter global warming. Here, in this study, MS CO 2 sorption in a model MS sorbent, IRA900, was investigated. IRA900 is a macroporous commercial strong-base anion exchange resin (AER) with quaternary ammonium functional groups. A rigorous CO 2 desorption process was developed to desorb all CO 2 from the sample and obtain CO 2 sorption isotherms as a function of relative humidity, CO 2 partial pressure, and temperature. CO 2 sorption increased with decreasing relative humidity, decreasing temperature, and increasing CO 2 partial pressure. Remarkably, the total CO 2 uptake from the sorption isotherms matched the ion exchange capacity (IEC) of the material, suggesting a stoichiometry of one CO 2 molecule reacting per active site. An isotherm model for CO 2 sorption starting with empty sorption sites (i.e., with the AER in the OH – form) described the experimental data well, supporting the hypothesis that the bicarbonate-loaded AER fully unloaded to the OH – state following rigorous CO 2 desorption. CO 2 sorption kinetics were studied, and carbon diffusion coefficients were estimated as a function of %RH and CO 2 partial pressure. Overall, this study provides a roadmap for the systematic evaluation of MS CO 2 DAC materials.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Thermochemical Properties of a Water-Soluble Zr(IV)-Flavonolate Complex for Fluoride Sensing

Detection of fluoride in water samples is critical for monitoring many chemical, environmental, and biological processes, however, these measurements often rely on costly instrumentation. Here, this situation has motivated the design of simple to use, fieldable fluoride sensors. Previously, a fluorometric sensor based on (EDTA)­Zr­(H 2 O) 2 (EDTA = ethylenediamine-N,N,N′,N′-tetraacetate) and 3-hydroxyflavone (FlvH) was reported for fluoride detection in ethanol-H 2 O mixtures. Herein, we report the synthesis and characterization of the previously proposed Zr­(IV)-flavonolate complex as the dimethylammonium salt, [(EDTA)­Zr­(Flv)]­[NMe 2 H 2 ] (Flv = 3-hydroxyflavonolate), and detail its utility for aqueous fluoride sensing. This species exhibits an intense blue fluorescence upon excitation with near-UV light (λ ex = 390 nm; λ em = 460 nm) that is quenched in the presence of NaF (100 mM acetate buffer, pH = 5) with good sensitivity (LOD = 20.9 nM; [F – ] from 10 –8 to 10 –4 M) under neat aqueous conditions. The equilibrium constant (K eq = 1.26 ± 0.00184 × 10 8 M –2 ) and free energy (Δ$G^°_{\textrm{rxn}}$ = –11.0 kcal mol –1 ) were determined under the conditions used for fluoride sensing, indicating a highly favorable reaction with F – in water. Finally, we developed paper-based sensing strips for qualitative fluoride sensing by immobilizing the sensor in a deposited gel enabling good selectivity and reduced interference due to slower ion diffusion.

aqueous chemistry↗
DOE OSTI2026

A Field Guide to Corralling the Chaos: A Conceptual Framework for Using Models to Guide Opportunistic Field Studies of Natural Disturbances

Watersheds regulate biogeochemical processes and provide ecosystem services to human societies, but disturbances can fundamentally alter these processes across space and time. Determining when and where to sample to capture disturbance impacts in watersheds remains a central challenge. Manipulation studies and long-term monitoring are often constrained by scope, and opportunistic studies often lack pre-disturbance data needed to statistically determine disturbance impacts. We identify a persistent knowledge gap: the absence of a clear, transferable framework to guide opportunistic disturbance research where pre-disturbance data collection is not a feasible option. To address this gap, we present a conceptual framework that intentionally integrates modeling and empirical observation in an iterative, stepwise model–experiment workflow. We demonstrate its application through two contrasting case studies: wildfire impacts on headwater streams using a pre-disturbance preparedness approach, and saltwater flooding impacts on coastal forests using an ‘ex-post-facto’ approach. From these applications, we assess strengths, limitations, and the critical role of team science for transferability across disturbance types and study designs. Broadly, this framework offers a scalable path towards more rigorous, timely, and actionable disturbance science that can inform watershed management, hazard risk reduction, and ecosystem resilience.

Coastal Biogeochemistry↗