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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Melting and Re-Freezing Leads to Irreversible Changes in the Morphology and Molecular-Level Dynamics of Pfizer-BioNTech COVID-19 Vaccine

As an mRNA-based vaccine, the Pfizer-BioNTech COVID-19 vaccine has stringent cold storage requirements to preserve functionality of the mRNA active ingredient. To this end, lipid components of the vaccine formulation play an important role in stabilizing and protecting the mRNA molecule for long-term storage. The purpose of the current study was to measure molecular-level dynamics as a function of temperature in the Pfizer-BioNTech COVID-19 vaccine to gain microscopic insight into its thermal stability. Materials and Methods: We used quasielastic and inelastic neutron scattering to probe (1) the vaccine extracted from the manufacturer-supplied vials and (2) unperturbed vaccine in the original manufacturer-supplied vials. The latter measurement was possible due to the high penetrative power of neutrons. Upon warming from the low-temperature frozen state, the vaccine in its original form exhibits two-step melting, indicative of a two-phase morphology. Once the melting is completed (above 0 °C), vaccine re-freezing cannot restore its original two-phase state. This observation is corroborated by the changes in the molecular vibrational spectra. The molecular-level mobility measured in the resulting single-phase state of the re-frozen vaccine greatly exceeds the mobility measured in the original vaccine. Even a brief melting (above 0 °C) leads to an irreversible alteration of the two-phase morphology of the original vaccine formulation. Re-freezing of the vaccine results in a one-phase morphology with much increased molecular-level mobility compared to that in the original vaccine, suggesting irreversible deterioration of the vaccine’s in-storage stability. Neutron scattering can be used to distinguish between the vibrational spectra characteristic of the original and deteriorated vaccines contained in the unperturbed original manufacturer-supplied vials.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Aggregation of Leslie matrix models with application to ten diverse animal species

Some grouping is necessary when constructing a Leslie matrix model because it involves discretizing a continuous process of births and deaths. Here, the level of grouping is determined by the number of age classes and frequency of sampling. It is largely unknown what is lost or gained by using fewer age classes, and I address this question using aggregation theory. I derive an aggregator for a Leslie matrix model using weighted least squares, determine what properties an aggregated matrix inherits from the original matrix, evaluate aggregation error, and measure the influence of aggregation on asymptotic and transient behaviors. To gauge transient dynamics, I employ reactivity of the standardized Leslie matrix. I apply the aggregator to 10 Leslie models developed for animal populations drawn from a diverse set of species. Several properties are inherited by the aggregated matrix: (a) it is a Leslie matrix; (b) it is irreducible whenever the original matrix is irreducible; (c) it is primitive whenever the original matrix is primitive; and (d) its stable population growth rate and stable age distribution are consistent with those of the original matrix if the least squares weights are equal to the original stable age distribution. In the application, depending on the population modeled, when the least squares weights do not follow the stable age distribution, the stable population growth rate of the aggregated matrix may or may not be approximately consistent with that of the original matrix. Transient behavior is lost with high aggregation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Evaluating performance of different generative adversarial networks for large-scale building power demand prediction

We report as an unsupervised-learning data-driven model, Generative Adversarial Networks (GANs) have recently attracted a lot of attention for various applications. There is potential to apply GANs for large-scale building power demand prediction, which is needed for power grid operation. However, there are many GAN variations and it is unclear which GAN is suitable for this application. To answer this question, this paper identifies five promising GANs (Original GAN, cGAN, SGAN, InfoGAN, and ACGAN) and evaluates their performance for predicting building power demand at a large scale. Physics-based building energy models are developed to generate training and reference data. A new evaluation indicator that combines accuracy and reproducibility is proposed to evaluate the performance of different GANs in predicting building power demand. The results show that SGAN and InfoGAN are not suitable because they cannot control the number of generated building samples for different building types. The prediction performance among the Original GAN, cGAN, and ACGAN can vary depending on training sample sizes and number of building types. If the training sample size is sufficiently large, Original GAN and cGAN can predict building power demand more accurately than ACGAN with the same number of samples. If training samples are limited, Original GAN provides better accuracy than cGAN and ACGAN. When the number of building types increase, the prediction accuracy increases for cGAN, decreases for ACGAN, and remains the same for Original GAN. As a result, cGAN and Original GAN are recommended for large-scale building power demand prediction.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

The chemical compositions of accreted and in situ galactic globular clusters according to SDSS/APOGEE

ABSTRACT Studies of the kinematics and chemical compositions of Galactic globular clusters (GCs) enable the reconstruction of the history of star formation, chemical evolution, and mass assembly of the Galaxy. Using the latest data release (DR16) of the SDSS/APOGEE survey, we identify 3090 stars associated with 46 GCs. Using a previously defined kinematic association, we break the sample down into eight separate groups and examine how the kinematics-based classification maps into chemical composition space, considering only α (mostly Si and Mg) elements and Fe. Our results show that (i) the loci of both in situ and accreted subgroups in chemical space match those of their field counterparts; (ii) GCs from different individual accreted subgroups occupy the same locus in chemical space. This could either mean that they share a similar origin or that they are associated with distinct satellites which underwent similar chemical enrichment histories; (iii) the chemical compositions of the GCs associated with the low orbital energy subgroup defined by Massari and collaborators is broadly consistent with an in situ origin. However, at the low-metallicity end, the distinction between accreted and in situ populations is blurred; (iv) regarding the status of GCs whose origin is ambiguous, we conclude the following: the position in Si–Fe plane suggests an in situ origin for Liller 1 and a likely accreted origin for NGC 5904 and NGC 6388. The case of NGC 288 is unclear, as its orbital properties suggest an accretion origin, its chemical composition suggests it may have formed in situ.

Horta, Danny↗
DOE OSTI2023

Carbon Organisms Rhizosphere and Protection in Soil Environment model script and input data for soil moisture-respiration responses in tropical forests

Objectives: Climatic drying is predicted for many tropical forests, yet models remain poorly parameterized for tropical forests, hampering predictions of forest-climate feedbacks. We applied an integrated model–experiment approach, parameterizing an ecosystem model Carbon Organisms Rhizosphere and Protection in the Soil Environment (CORPSE) with tropical forest observational data, and comparing model predictions with a field drying manipulation. We hypothesized that drying would suppress soil CO2 fluxes (i.e., respiration) in already-drier tropical forests, but increases CO2 fluxes in wetter tropical forests by alleviating anaerobiosis. We measured soil CO2 fluxes, soil moisture, soil temperature, and forest floor biomass during wet-dry cycles (2015 – 2022) in four Panamanian forests that vary in rainfall and soil fertility. We used the field data to parameterize and run tests in the model.Results: Measured CO2 fluxes declined in the dry season and peaked in the early wet season ahead of peak soil moisture, resulting in a lower soil moisture optimum for respiration than previously modeled. We used this data to parameterize the model, which then predicted increased soil CO2 fluxes in wetter and fertile forests with drying, and decreased fluxes in drier, infertile forests. In contrast to model predictions, a chronic throughfall exclusion experiment in the forests initially suppressed soil CO2 fluxes across forests, with sustained suppression after four years in the wettest forest only (-28 ± 4% during the dry season), but elevated soil CO2 fluxes in a fertile forest after four years (+75 ± 28% during the late wet season), as predicted by the model. The unexpected negative drying effect in the wettest, most infertile forest could have resulted from reduced vertical flushing of nutrients into soils. Including hydro-nutrient interactions in ecosystem models could improve predictions of tropical forest-climate feedbacks (results presented in Cusack et al. 2023). Datasets included: Code files:CORPSE_array.py: Defines the equations of the CORPSE modelCORPSE_solvers: Functions for running the CORPSE model using either iterative or ordinary differential equation (ODE) solversrun_Panama_sims.py: Read in datasets and run the model simulations for this studyInput data:PanamaGradientEcosystemChem_BT_CPools_20152016CO2_DC_20190615.xlsx: Plot characteristics used in running model simulationsLiCor compiled surface flux only to 2020_03 DC_20200825.xlsx: Surface gas exchange fluxes used in model-data comparisonsPARCHED litterfall data for Ben Sulman LD 20200902.xlsx: Litterfall data used to drive model simulationsInitialization data:state_500y_20190823.csv: Initial state of model pools based on previous spinup runsOutput data:Outputs/prev_moisture_response.csv: Simulations of multiple sites using original model moisture response function.Outputs/updated_moisture_response.csv: Simulations of multiple sites using updated model moisture response function.Outputs/dry15_prev_moisture_response.csv: Simulations with soil moisture reduced by 15%, using original moisture response function.Outputs/dry15_updated_moisture_response.csv: Simulations with soil moisture reduced by 15%, using updated moisture response function.Outputs/dry30_prev_moisture_response.csv: Simulations with soil moisture reduced by 30%, using original moisture response function.Outputs/dry30_updated_moisture_response.csv: Simulations with soil moisture reduced by 30%, using updated moisture response function.Outputs/latestart_prev_moisture_response.csv: Simulations with extended dry season, using original moisture response function.Outputs/latestart_updated_moisture_response.csv: Simulations with extended dry season, using updated moisture response function.Outputs/[site name]_oneyear.csv: One-year simulation for each site in expanded site list using original moisture response function.Outputs/[site name]_oneyear_dried.csv: One-year simulation for each site in expanded site list using original moisture response function, with soil moisture reduced by 25%.Outputs/[site name]_oneyear_updated_moisture_response.csv: One-year simulation for each site in expanded site list using updated moisture response function.Outputs/[site name]_oneyear_updated_moisture_response_dried.csv: One-year simulation for each site in expanded site list using updated moisture response function, with soil moisture reduced by 25%.Field plot location data:There is also a .kml file that includes coordinates for all 32 plots included in the study of four forests (n = 4 throughfall reduction and n = 4 control plots per site).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Literature Review on Next Generation Solvent Isopar ® L Vapor Pressure Curve and the Partitioning of its Modifier and Extractant

The Next Generation Solvent (NGS) is set to replace the Original Caustic Side Solvent Extractant (CSSX) at the Salt Waste Processing Facility (SWPF). The Savannah River National Laboratory (SRNL) was requested by Savannah River Mission Completion (SRMC), formerly Savannah River Remediation (SRR), to perform a literature review on the following topics to address flammability concerns with the current solvent: Isopar ® L vapor pressure curve for NGS, partitioning ratio for the extractant MaxCalix and the modifier Cs-7SB, and high cesium concentration impacts on NGS radiolysis and potential solvent degradation rates in high cesium concentrations. The following conclusions and recommendations are made based on previous experimental work and literature: (1) Current SWPF flammable gas generation calculations use an Isopar ® L vapor pressure curve based on experimental testing with the Original CSSX solvent. No such testing to date has been performed with NGS. It is suggested that the decrease in Cs-7SB concentration for NGS compared to the Original CSSX solvent would lead to a slightly higher vapor pressure at all temperatures in SWPF vessels. A bounding NGS vapor pressure curve has been provided; it is recommended to see if these values would challenge current flammability controls and to perform testing if needed.(2) The partitioning ratio for Cs-7SB is known in the Original CSSX solvent with dilute nitric acid and caustic solutions. No tests could be found for the partitioning of Cs-7SB to dilute boric acid solutions; however, a similar partitioning ratio is expected. Due to the lipophilic alkyl chains on MaxCalix, it is expected to be even less soluble than BOBCalixC6 in the aqueous phase and should not be considered a significant contributor to the f organic term. Additionally, the reaction rate of N,N’,N’’-Tris(3,7-dimethyloctyl)guanidine (TiDG) or its degradation products with a hydrogen radical should be estimated/determined if they are found to be significant contributors to the f organic term. (3) NGS is expected to see much higher Cs concentrations at SWPF in comparison to its use at the Modular CSSX Unit (MCU). These higher Cs concentrations could influence radiolytic degradation rates of the solvent. NGS appears to be fairly stable to radiolytic degradation based on previous testing and its use at MCU. However, there has not been radiolytic flammable gas generation testing with NGS to date. There is a risk that the continued use of G-values obtained for flammable gases produced from the irradiation of the Original CSSX solvent is not bounding for NGS, but this is considered a very low risk due to the similarities in the composition of the solvents, as well as the conservatisms in the experimental design of the Original CSSX testing.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2021

Grid Service Values of Generic Marginal Building Flexibility in Modeled 2030 U.S. Power Systems

The datasets include the capacity, energy, and ancillary service values of a marginal kilowatt-hour (kWh) of generic, daily, shiftable building flexibility as a presumed market entrant in the 2030 U.S. power systems. The results should be interpreted along with the caveats listed in "Valuation of Building Flexibility: Grid Service Value for Initial Market Entrants in Projected 2030 United States Power Systems", which also documents the methods used for the study. The factors examined in the study include: grid scenario, region, original usage hour in the day (local time), and building flexibility parameters - efficiency, dissipation, and shifting window include max pre-shift and max post-shift. Filenames in the datasets: The filenames contain information on the grid scenario, and the building flexibility efficiency and dissipation. For example: MidCase_2030_efficiency1.25_dissipation0.05_value.csv contains all results under Mid RE 2020, efficiency = 1.25, and dissipation = 0.05. * MidCase = Mid RE Each .csv file contains: region: The location of the building flexibility, aligned with U.S. Energy Information Administration (EIA) National Energy Modeling System (NEMS) Electricity Market Module regions. max_pre_shift: Part of building flexibility shifting window parameter, indicates the max number of hours the building flexibility can shift earlier. max_post_shift: Part of building flexibility shifting window parameter, indicates the max number of hours the building flexibility can shift later. local_datetime: Original datetime of 1kWh of building energy consumption. local_orig_h: Original usage hour (1-24) of building energy consumption, ignores daylight saving. local_shift_to: The datetime to when building energy consumption shifts, if shifting happens. If no shifting occurs, this cell is left blank. energy: Net energy value of energy shifting. capacity: Net capacity value of energy shifting. shifting_value: Net energy plus capacity value of energy shifting. spin: Spin reserve value at the original datetime of consumption. flex: Flexible reserve value at the original datetime of consumption. reg: Regulation reserve value at the original datetime of consumption. total_profit: Assuming the building flexibility is capable of providing energy, capacity, and ancillary services, total profit is the maximum value of energy shifting value, spin reserve value, flexible reserve value, and regulation reserve value - one of the four choices at any given hour - because we do not allow its value to be double-counted.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2020

Annotation of images based on a 3D model of objects

An annotation system for providing annotations for original images is provided. In some embodiments, the annotation system accesses an annotation associated with an object of a 3D model. The annotation system also accesses and displays an original image. The annotation system renders a model image of the 3D model based on the view from which the original image was collected. When the model image contains the annotated object, the annotation system provides an indication that an annotation is associated with the object of the original image. The annotation system can provide indications of the annotation for other original images that include the annotated object irrespective of the view from which the other original images are collected.

42 ENGINEERING↗
DOE OSTI2021

Grandparent Inference from Genetic Data: The Potential for Parentage-Based Tagging Programs to Identify Offspring of Hatchery Strays

Abstract Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent–grandchild trios by using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false-positive and false-negative error rates and showed that genetic panels containing 500–700 single-nucleotide polymorphisms or 200–300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

Delomas, Thomas A. (ORCID:000000015154759X)↗
DOE OSTI2023

Genetic monitoring of steelhead in the Klickitat River to estimate productivity, straying, and migration timing

Abstract Objective Salmonids with a complex life history variation present challenges for conservation management, but genetic approaches alongside fisheries monitoring can address questions regarding the viability of the natural populations. Methods We genotyped adult (n = 3108) and juvenile (n = 2624) samples of steelhead Oncorhynchus mykiss that were collected in the Klickitat River, Washington, USA at traps in the lower drainage to examine tributary level productivity, straying from outside sources, and variation in adult migration timing. Result Genetic assignment of steelhead from this system indicated that the majority were produced within or near tributaries of the middle Klickitat River (juvenile mean = 72.8%; adult mean = 87.3%). Analyses with parentage-based tagging identified that most hatchery-origin adults were assigned to the Skamania Hatchery (80.8%), as expected, since this has been the release stock for decades within the Klickitat River drainage. Hatchery-origin adults were also identified from programs operating outside the Klickitat River, which were primarily strays from Snake River hatcheries. Most natural-origin steelhead were assigned to the Klickitat River, but there were also natural-origin fish identified as strays from other regions of the Columbia River (22.3% of natural returns). We also examined genes known to be associated with migration timing in adult steelhead observed at the trap and observed a strong relationship between migration date and alleles for early and late migration, but individual outliers were detected across seasons. Conclusion Our results indicate that genetic variation of steelhead in the Klickitat River has been influenced by hatchery programs as well as natural-origin straying from other subbasins, but genetic diversity remains high throughout the subbasin, and both early and late migration alleles are maintained. The genetic diversity present in Klickitat River steelhead may enable this Endangered Species Act listed (threatened) species to better adapt to stochastic environmental conditions compared to less diverse populations.

Collins, Erin E. (ORCID:0000000260978479)↗
DOE OSTI2023

Demographic and genetic consequences of a steelhead supplementation program

Abstract Objective Supplementation of naturally spawning populations by the addition of hatchery-spawned individuals is commonly conducted for recovery of threatened and endangered populations and to support harvest opportunities. Our objective was to evaluate whether the use of a juvenile captive broodstock and an integrated paradigm could increase returns of steelhead, the anadromous form of Rainbow Trout Oncorhynchus mykiss, while avoiding negative genetic impacts commonly associated with hatchery propagation. Methods We analyzed 291 genetic markers in adult steelhead returning to an integrated population in southwest Washington over the course of 15 years. Reproductive success (RS) of fish spawning in the natural environment was evaluated by origin (hatchery versus natural) and return year. Data were then pooled over years to maximize sample sizes for comparing RS estimates among groups (i.e., estimation of relative reproductive success [RRS]). Result We observed a weak relationship between RS and origin (male p = 0.347; female p = 0.066), but a significant relationship between RS and return year (male p < 0.001, η2 = 0.896; female p ⟨ 0.001, η2 = 0.867) (i.e., hatchery- and natural-origin fish did well or poorly together each year). Estimates of RRS for fish spawned in the hatchery ranged from 2.4 to 6.4, indicating that fish spawned in the hatchery produced more returning adult progeny than did fish allowed to spawn in the natural environment. Estimates of RRS were ⟨1.0 for hatchery-origin fish spawning in the natural environment, but the difference was nonsignificant for males and marginally significant for females. Hatchery-origin fish exhibited reduced genetic diversity as well as evidence of increased temporal population structure. Conclusion We conclude that the program was successful in achieving an increase in adult returns but not in avoiding negative genetic effects on the population and that any lasting impacts of supplementation remain to be determined.

Smith, Christian T. (ORCID:0000000240522669)↗
DOE OSTI2022

A time‐varying formulation of the curled wake model within the FAST.Farm framework

Abstract In this article, we present a time‐varying formulation of the curled wake model that we implemented in FAST.Farm. The curled wake model, originally developed for steady‐state conditions, is used to produce realistic wake profiles behind a wind turbine in yawed (or skewed) conditions. We begin by introducing the key elements of the FAST.Farm framework. Then, after briefly summarizing the original wake dynamics formulation of FAST.Farm based on a polar wake profile, we present the new time‐varying formulation of the curled wake model, compare the two, and highlight the differences with the original curled wake model. After discussing some implementation details, we present different applications with increasing levels of complexity: single turbine with uniform and turbulent inflow, fixed and transient yaw, and multiple turbines. We verify our results using the original FAST.Farm implementation and large‐eddy simulations. The results with the new curled wake model are improved compared to the original implementation, as they include cross‐flow velocities and wake asymmetry. Yet, large‐eddy simulation results show a more pronounced lateral convection of the wake and a stronger concentration of vorticity at the top vortex. The new curled wake implementation in FAST.Farm should enable the calculation of not only generator power but also wind turbine structural loads for applications involving intentional or unintentional skewed flow and wind‐farm control involving wake steering.

17 WIND ENERGY↗
DOE OSTI2025

Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks

Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance

baseflow↗
DOE OSTI2026

Global metagenomics reveals plastid diversity and unexplored algal lineages

Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A dendritic strontium river isoscape for fisheries applications in the Sacramento River basin, California, USA

Objective Understanding the origins and movements of fish is fundamental to effective conservation and fisheries management. Strontium isotope ratios ( 87 Sr/ 86 Sr) in otoliths provide a powerful tracer of natal origin and migratory pathways. However, existing 87 Sr/ 86 Sr isoscapes for the Sacramento River basin, an ecosystem that supports ecologically and economically important salmon populations, rely on discrete classification approaches that overlook unsampled habitats and do not incorporate spatial uncertainty. Our objective was to develop a continuous, network-explicit 87 Sr/ 86 Sr isoscape with quantified uncertainty to fill in data gaps and enable probabilistic assignments of fish origin and movement. Methods We used river water 87 Sr/ 86 Sr data from 106 sites (1997–2021) to develop spatial stream network models that use dendritic connectivity and watershed characteristics (lithology, bedrock age, and land cover) to predict river water 87 Sr/ 86 Sr throughout the basin. Models were fitted using maximum and restricted likelihood and were evaluated via Akaike’s information criterion and leave-one-out cross validation. We produced both historical (pre-dam) and present-day (below-dam) isoscapes, delineated uncertainty-informed isotopic ranges using k -means clustering, and applied a proof-of-concept Bayesian assignment to estimate natal origins and early rearing habitats for two endangered winter-run Chinook Salmon Oncorhynchus tshawytscha. Results Cross validation indicated strong performance of the 87 Sr/ 86 Sr model (leave-one-out cross validation: R 2 = 0.91; root mean square error = 0.0005). Uncertainty-informed clustering identified 19 isotopic “suites” (reaches with indistinguishable 87 Sr/ 86 Sr values) in present-day anadromous habitats and 25 suites in the historical network. Example natal and early rearing assignments included predictions that challenged expectations for juvenile salmon migration based on predicted river 87 Sr/ 86 Sr compositions. Conclusions This study developed a continuous, network-explicit 87 Sr/ 86 Sr isoscape that integrates existing river data to predict 87 Sr/ 86 Sr in unsampled reaches and the likely achievable range and resolution of otolith-based origin and life history inference. The resulting river isoscape provides a valuable tool to predict salmon movements and identify habitats supporting their survival and growth that otherwise might remain undetected. Coupling these predictions with complementary approaches that ground-truth juvenile presence (e.g., targeted fish surveys) represents an important step toward science-informed restoration and management of critical habitats throughout the Sacramento River basin.

Environmental sciences↗
DOE OSTI2020

Learning in Modal Space: Solving Time-Dependent Stochastic PDEs Using Physics-Informed Neural Networks

One of the open problems in scientific computing is the long-time integration of nonlinear stochastic partial differential equations (SPDEs), especially with arbitrary initial data. We address this problem by taking advantage of recent advances in scientific machine learning and the spectral dynamically orthogonal (DO) and borthogonal (BO) methods for representing stochastic processes. The recently introduced DO/BO methods reduce the SPDE to solving a system of deterministic PDEs and a system of stochastic ordinary differential equations. Specifically, we propose two new physics-informed neural networks (PINNs) for solving time-dependent SPDEs, namely the neural network (NN)-DO/BO methods. The proposed methods incorporate the DO/BO constraints into the loss function (along with the modal decomposition of the SPDE) with an implicit form instead of generating explicit expressions for the temporal derivatives of the DO/BO modes. Hence, the NN-DO/BO methods can overcome some of the drawbacks of the original DO/BO methods. For example, we do not need the assumption that the covariance matrix of the random coefficients is invertible as in the original DO method, and we can remove the assumption of no eigenvalue crossing as in the original BO method. Moreover, the NN-DO/BO methods can be used to solve time-dependent stochastic inverse problems with the same formulation and same computational complexity as for forward problems. Furthermore, we demonstrate the capability of the proposed methods via several numerical examples, namely: (1) A linear stochastic advection equation with deterministic initial condition: we obtain good results with the proposed methods, while the original DO/BO methods cannot be applied directly in this case. (2) Long-time integration of the stochastic Burgers' equation: we show the good performance of NN-DO/BO methods, especially the effectiveness of the NN-BO approach for such problems with many eigenvalue crossings during the whole time evolution, while the original BO method fails. (3) Nonlinear reaction diffusion equation: we consider both the forward problem and the inverse problems, including very noisy initial point values, to investigate the flexibility of the NN-DO/BO methods in handling inverse and mixed type problems. Taken together, these simulation results demonstrate that the NN-DO/BO methods can be employed to effectively quantify uncertainty propagation in a wide range of physical problems, but future work should address the efficiency issue of PINNs for forward problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2022

Next Generation Solvent Vapor Pressure Testing

Previous work by Savannah River National Laboratory (SRNL) indicated that the actual Next Generation Solvent vapor pressure would be higher than the Original Caustic Side Solvent Extraction (CSSX) solvent vapor pressure, but below a bounding vapor pressure using Raoult’s Law. Since solvent vapor pressure has a significant impact on Composite Lower Flammability Limits (CLFL) and attendant accident analyses, obtaining an additional margin from the bounding NGS vapor pressure would be valuable. In order to quantify how much margin might be gained from the NGS bounding solvent, SRNL researchers were requested to perform vapor pressure testing with the Next Generation Solvent (NGS) by Savannah River Mission Completion (SRMC). The vapor pressure curve for the NGS formulation set to be deployed at the Salt Waste Processing Facility (SWPF) has been determined by SRNL up to 55°C (131°F) using headspace Gas Chromatography (GC). It was expected that NGS would have a higher vapor pressure than the Original CSSX solvent; however, experimental results indicate a lower vapor pressure. At this time, it is uncertain if this difference is due to the 7x increase in concentration of the large calixarene in the solvent (0.007M BOBCalix in Original CSSX solvent vs. 0.05M MaxCalix in NGS) or to minor batch-to-batch variations in Isopar-L constituents. The NGS and the Original CSSX solvent vapor pressure data were fitted to the Antoine Equation. The Antoine equation gives a more accurate representation of the expected vapor pressure of the solvents outside of the temperature range tested. The Antoine equation fitting for NGS is given below: $P=10^{6.364⁻\frac{1788.4}{T+219.3}}$. Where, p is the vapor pressure (partial pressure) of NGS in mmHg and T is the temperature in °C. It is recommended that SRMC either continue using the more conservative Isopar-L vapor pressure calculations at SWPF with the equation developed for the Original CSSX solvent, or the equation presented above for the NGS solvent. Additionally, it is recommended to study the variability in Isopar-L vapor pressure between lots.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗