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At least 199 records · Page 11

metabCombiner 2.0: Disparate Multi-Dataset Feature Alignment for LC-MS Metabolomics

Liquid chromatography–high-resolution mass spectrometry (LC-HRMS), as applied to untargeted metabolomics, enables the simultaneous detection of thousands of small molecules, generating complex datasets. Alignment is a crucial step in data processing pipelines, whereby LC-MS features derived from common ions are assembled into a unified matrix amenable to further analysis. Variability in the analytical factors that influence liquid chromatography separations complicates data alignment. This is prominent when aligning data acquired in different laboratories, generated using non-identical instruments, or between batches from large-scale studies. Previously, we developed metabCombiner for aligning disparately acquired LC-MS metabolomics datasets. Here, we report significant upgrades to metabCombiner that enable the stepwise alignment of multiple untargeted LC-MS metabolomics datasets, facilitating inter-laboratory reproducibility studies. To accomplish this, a “primary” feature list is used as a template for matching compounds in “target” feature lists. We demonstrate this workflow by aligning four lipidomics datasets from core laboratories generated using each institution’s in-house LC-MS instrumentation and methods. We also introduce batchCombine, an application of the metabCombiner framework for aligning experiments composed of multiple batches. metabCombiner is available as an R package on Github and Bioconductor, along with a new online version implemented as an R Shiny App.

97 MATHEMATICS AND COMPUTING↗

Design of Multi-Stage Solvent Extraction Process for Separation of Rare Earth Elements

Flowsheet design and stage determination for the separation of rare earth elements (REEs) using solvent extraction (SX) is a challenging task because of the chemical similarity of the REEs. Low separation factors between the elements and complex equilibrium chemistry provide unique challenges to designing an efficient flowsheet for the separation of elements. The multi-stage nature of the SX process adds further complexity, making the assessment of products for a proposed design and stage combination difficult. Therefore, to develop a SX flowsheet, it is essential to quantify the performance for various design and separation conditions. This paper attempts to address the challenge by utilizing an equilibrium and process modeling approach. Results from a bench-scale study performed on a 10 g/L rare earth salt mixture were used in studying the extraction/stripping behavior and developing equilibrium models. DEHPA with TBP as a phase modifier was used as an extractant, while hydrochloric acid was utilized as a stripping agent. The results obtained were used in developing extraction/stripping models, which were integrated into a process framework of a SX train in a Matlab/Simulink environment. The models were programmed as a function block routine and used for developing a flowsheet, which was simulated for differing separation and design conditions. To identify optimum stage combinations, a particle swarm optimization (PSO) routine was developed and implemented for each SX train. Recovery and purity of elements of interest were used as objective function criteria. The stage combination leading to the minimization of the objective function was used to identify the optimum stage combination for a series of SX trains to attempt a balance of purity and recovery. The models and optimization method were implemented to separate a feed mixture containing REEs, which indicated that 99.52 and 85.41 percent purity is achievable for Yttrium and Lanthanum separation using 8-12-3 and 10-3-5 stage combination for loading, scrubbing, and striping. The model also indicated difficult separability between neodymium, praseodymium, and cerium.

Srivastava, Vaibhav (ORCID:0000000212645987)↗

Stellar Rotation of T Tauri Stars in the Orion Star-forming Complex

We present a large-scale study of stellar rotation for T Tauri stars in the Orion star-forming complex. We use the projected rotational velocity ($v\sin (i)$) estimations reported by the APOGEE-2 collaboration as well as individual masses and ages derived from the position of the stars in the HR diagram, considering Gaia-EDR3 parallaxes and photometry plus diverse evolutionary models. We find an empirical trend for $v\sin (i)$ decreasing with age for low-mass stars (0.4M ⊙ < M $\star$ < 1.2M ⊙ ). Our results support the existence of a mechanism linking $v\sin (i)$ to the presence of accreting protoplanetary disks, responsible for regulating stellar rotation on timescales of about 6 Myr, which is the timescale in which most of the T Tauri stars lose their inner disk. Our results provide important constraints to models of rotation in the early phases of evolution of young stars and their disks.

79 ASTRONOMY AND ASTROPHYSICS↗

Exploring the Neutron Substructure with Advanced Polarized Helium-3 Targets (Or: How I Learned to Stop Worrying and Love Spectroscopy)

As we seek to understand the smallest, physical aspects of our universe, we cannot simply rely on our senses to probe the world around us as we did in the past. The smallest physical elements of our universe behave in strange, probabilistic ways and are completely invisible to the naked eye/ear/etc. So, we design clever experiments (such as scattering experiments) to probe these minute realms. Then, just as with the larger, observable world, we devise models and equations to describe what we think is happening. Due to the nature of the physical universe at the quantum scale and with the aid of symmetries such as Lorentz invariance, we can write down equations that describe the scattering, but the expressions contain functions, which we call ?form factors? and ?structure functions?, that we cannot compute from first principles. We can, however, formulate models that make predictions for these functions. By comparing our predictions with the observed data, we can gain insight into the validity of our models and thus a better physical understanding of what is happening at these minuscule scales. Studying the constituents inside of the nucleus of an atom adds another layer of difficulty if we can?t remove those components from the nucleus. This is the case with the neutron. When not bound in the nucleus with protons and other neutrons, the neutron will decay into a proton after about 15 minutes. So, we?re forced to study the neutron while it is still bound in the nucleus of an atom such as helium-3 (3He). For the last 1,000 years (rounding up), our group has developed high quality, polarized 3He targets made of an aluminosilicate glass. These targets are made in order to perform experiments at Jefferson Lab (JLab), experiments which let us determine the form factors and structure functions of the neutron by scattering polarized electrons from polarized neutrons (or rather polarized 3He). The specific experiments reported on in this thesis push the bounds of our understanding of the internal structure of the neutron. Good science is often about pushing experimental techniques to a new level. Toward that goal we study our polarized 3He targets both to advance the technology and to choose the best ones for our experiments. We do this using a process called nuclear magnetic resonance (NMR) to gauge the maximum polarization of a target and how fast the polarization decays with time. While these tests primarily provide us information that make analysis of our experimental scattering data possible, they also let us determine whether or not a target-cell is useful or even, dare I say, of spectacular quality. Our latest targets utilize a novel convection design allowing 3He to be polarized and quickly moved in front of the electron-beam, making it possible to use larger targets with higher electron-beam currents than ever before. This means more electrons scatter and we get more data. And by studying our targets in detail prior to using them in our experiments, we have found techniques to take effects which could have been detrimental to target quality and turn them to our advantage! It?s a real case of making lemonade out of lemons. We also use laser spectroscopy to study the absorption lines of alkali-metals in the target (potassium and rubidium, specifically). We add these alkali-metals to our target to facilitate polarizing the 3He. We can use the measurement of these pressure broadened absorption lines to determine the 3He density inside of the target with great precision. Historically, we understood the width of these lines would be dependent on the temperature of the target. Specifically, if I raise the temperature, the width should get bigger. I found that was not the case, which was very confusing at first, though very exciting now that I realize the data are self-consistent and suggestive of unexpected behavior. This thesis details the development of high quality, glass, polarized 3He targets for the 2020 An 1 /dn 2 and 2023 Gn E experiments, which utilized the first 3He convection targets and broke records in target quality. This thesis also covers the initial development of metal windows for the next-generation of 3He target-cells. Finally, this thesis documents the temperature dependence of the width of potassium (K) and rubidium (Rb) absorption lines as measured with laser spectroscopy.

Jantzi, Christopher↗

Development and Preliminary Analysis of a U.S. Geothermal Heat Pump Installation Database

This paper seeks to addresses the significant gap in the literature regarding the installation and adoption of geothermal heat pump (GHP) systems in the United States. While the "2021 U.S. Geothermal Power Production and District Heating Market Report" published by the National Renewable Energy Laboratory (NREL) focused on direct-use geothermal district heating systems, it did not include an analysis of GHP installations (Robins et al. 2021). To bridge this gap, NREL has compiled a novel database currently containing 70,470 records of GHP installations, primarily sourced from state well permits and small-scale studies. Our methodology emphasizes the collection, cleaning, and standardization of data, addressing challenges such as inconsistent reporting formats and privacy concerns. Despite limitations in data on capacity, costs, and performance, our preliminary geospatial analysis reveals insights into the distribution of GHP systems across urban and rural areas and climate zones. The paper highlights the importance of publicly accessible data for advancing GHP technology adoption with a discussion of existing data sources and their limitations, advocating for improved collaboration between NREL and industry stakeholders.

data collection↗

Quality Guidelines for Energy System Studies: Capital Cost Scaling Methodology: Revision 4b Report

The National Energy Technology Laboratory (NETL) regularly updates legacy analysis with new studies and cases as the Department of Energy objectives change, technology performance improves, costs are reduced, regulations change, market drivers are established, fuel prices fluctuate, and any number of other relevant factors vary in the market. As legacy studies are updated by NETL, the underlying performance and cost of the cases presented changes, and as such, the methods for interpreting and scaling the cost estimates change. Therefore, it is important that NETL maintain public guidance documents associated with different sets of cost estimates that delineate how a specific set, based on report vintage and/or year published, should be scaled. This Quality Guidelines for Energy System Studies report, providing guidance on capital cost scaling, should generally be applied to NETL case costs included in the report “Cost and Performance Baseline for Fossil Energy Plants Volume 1: Bituminous Coal and Natural Gas to Electricity Revision 4b,” (NETL, 2025) or any cases derived from the cases presented in the referenced report.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Neural Scaling Laws of Deep ReLU and Deep Operator Network: A Theoretical Study

Neural scaling laws play a pivotal role in the performance of deep neural networks and have been observed in a wide range of tasks. However, a complete theoretical framework for understanding these scaling laws remains underdeveloped. In this paper, we explore the neural scaling laws for deep operator networks, which involve learning mappings between function spaces, with a focus on the Chen and Chen style architecture. These approaches, which include the popular Deep Operator Network (DeepONet), approximate the output functions using a linear combination of learnable basis functions and coefficients that depend on the input functions. We establish a theoretical framework to quantify the neural scaling laws by analyzing its approximation and generalization errors. We articulate the relationship between the approximation and generalization errors of deep operator networks and key factors such as network model size and training data size. Moreover, we address cases where input functions exhibit low-dimensional structures, allowing us to derive tighter error bounds. These results also hold for deep ReLU networks and other similar structures. Our results offer a partial explanation of the neural scaling laws in operator learning and provide a theoretical foundation for their applications.

97 MATHEMATICS AND COMPUTING↗

Lessons Learned from Ecosystem-Scale Experimental Field Studies (Workshop Report)

Efforts to understand and predict ecosystem responses to environmental change require long-term, large-scale, spatially representative experiments and observations that capture natural variability, test predictive models, and generate transferable knowledge. Such studies are indispensable for unraveling the complexities of terrestrial ecosystems and their responses to disturbances and evolving environmental conditions, while generating the data necessary for developing mechanistic models and predictive tools that inform decision-making processes. Having a rich history of designing and executing large-scale ecosystem experiments, the U.S. Department of Energy’s Environmental System Science program convened a workshop in January 2025 that brought together leaders in the field to distill critical lessons from decades of experience in large-scale experiments. The workshop aimed to (1) provide an ecosystem experiment primer for best practices, thus ensuring a high scientific return on investment for funding agencies, and (2) offer a robust framework for the design and management of future research initiatives. This report synthesizes insights and experiences from workshop participants and is structured to capture the entire research life cycle, from goal setting and design to operations, adaptive management, team dynamics, collaborations, and the often overlooked aspect of decommissioning. By synthesizing decision-making and lessons learned across diverse research approaches, the report aims to provide a template of essential factors to consider when designing successful long-term, large-scale ecosystem experiments.

54 ENVIRONMENTAL SCIENCES↗

OrthoPhyl—streamlining large-scale, orthology-based phylogenomic studies of bacteria at broad evolutionary scales

Abstract There are a staggering number of publicly available bacterial genome sequences (at writing, 2.0 million assemblies in NCBI's GenBank alone), and the deposition rate continues to increase. This wealth of data begs for phylogenetic analyses to place these sequences within an evolutionary context. A phylogenetic placement not only aids in taxonomic classification but informs the evolution of novel phenotypes, targets of selection, and horizontal gene transfer. Building trees from multi-gene codon alignments is a laborious task that requires bioinformatic expertise, rigorous curation of orthologs, and heavy computation. Compounding the problem is the lack of tools that can streamline these processes for building trees from large-scale genomic data. Here we present OrthoPhyl, which takes bacterial genome assemblies and reconstructs trees from whole genome codon alignments. The analysis pipeline can analyze an arbitrarily large number of input genomes (>1200 tested here) by identifying a diversity-spanning subset of assemblies and using these genomes to build gene models to infer orthologs in the full dataset. To illustrate the versatility of OrthoPhyl, we show three use cases: E. coli/Shigella, Brucella/Ochrobactrum and the order Rickettsiales. We compare trees generated with OrthoPhyl to trees generated with kSNP3 and GToTree along with published trees using alternative methods. We show that OrthoPhyl trees are consistent with other methods while incorporating more data, allowing for greater numbers of input genomes, and more flexibility of analysis.

59 BASIC BIOLOGICAL SCIENCES↗

A nuclear-hydrogen hybrid energy system with large-scale storage: A study in optimal dispatch and economic performance in a real-world market

Here a study in optimal dispatch and economic analysis of a novel nuclear hybrid energy system (NHES) with large-scale hydrogen storage and a novel control scheme is conducted. The control scheme makes charge and discharge decisions by using the real-time electricity price relative to the historical price distribution. The pricing data is taken from the ERCOT Houston and West load zones with different price oscillations. Six case control studies with different levels of aggressiveness were chosen for each load zone for a total of 12 case studies. It is found that in a high price volatility load zone, a more aggressive control strategy maximizes revenue, while in a less oscillatory load zone, a moderate control strategy performs better. The NHES can store energy when the price is low and sell additional electricity when the price is high, as well as participate in the ancillary services market. Due to these advantages, the NHES can generate 10–40 million USD more revenue annually than a stand-alone nuclear plant. Due to higher costs, the NHES has a higher LCOE (81.36 USD/MWh) than a stand-alone plant (68.66 USD/MWh); however, the LCOE of the NHES is still comparable to other new forms of electricity generation. It is found that both the NHES and the stand-alone plant are not economical in the existing electricity market. Due to the extra revenue generated, the hybrid system has a positive annual cashflow whereas the stand-alone plant does not. It is found that the hybrid plant needs less cost subsidy than a stand-alone plant to become economical.

08 HYDROGEN↗

The Challenges of Modeling Defect Behavior and Plasticity across Spatial and Temporal Scales: A Case Study of Metal Bilayer Impact

Atomistic molecular dynamics (MD) and a microstructural dislocation density-based crystalline plasticity (DCP) framework were used together across time scales varying from picoseconds to nanoseconds and length scales spanning from angstroms to micrometers to model a buried copper–nickel interface subjected to high strain rates. The nucleation and evolution of defects, such as dislocations and stacking faults, as well as large inelastic strain accumulations and wave-induced stress reflections were physically represented in both approaches. Both methods showed similar qualitative behavior, such as defects originating along the impactor edges, a dominance of Shockley partial dislocations, and non-continuous dislocation distributions across the buried interface. The favorable comparison between methods justifies assumptions used in both, to model phenomena, such as the nucleation and interactions of single defects and partials with reflected tensile waves, based on MD predictions, which are consistent with the evolution of perfect and partial dislocation densities as predicted by DCP. This substantiates how the nanoscale as modeled by MD is representative of microstructural behavior as modeled by DCP.

36 MATERIALS SCIENCE↗

Valuation of pollination services from habitat management: a case study of utility scale solar energy facilities in the United States

Creating and maintaining pollinator habitats following the ecological infrastructure concept in degraded or unutilized land, such as solar energy facilities, is a practical way to synergistically advance the food, energy, and ecology nexus. Given the large land-use requirements for solar farming—the fastest growing renewable energy technology–considerable attention has been focused on strategies to maximize multiple ecosystem services. In this study, we coupled the principles of agronomy and ecology with economics and integrated national-scale data on crops, pollinators, and solar facilities to identify locations for creating pollinator habitats and estimating the economic value of pollination from the habitats. We examined opportunities for pollination services from pollinator-friendly utility-scale solar facilities adjacent to 42 million hectares of pollination-dependent crops in the conterminous United States at high resolution of 1 ha. We used the net income method to estimate the potential economic value of creating habitat in the land adjacent to solar facilities in the eight states with the greatest number of solar installations. Creating pollinator habitats at the 217 utility-scale solar facilities in these states could support adjacent 80,000 hectares of high pollinator dependent crops, which could potentially generate a pollination value of $\$$120 to $\$$264 million USD. The location-specific information and high-resolution maps generated for the United States demonstrate integration of grey and green infrastructure to support the food, energy, and environment nexus.

14 SOLAR ENERGY↗

Breaking the Window of Detection: Using Multi-Scale Solute Tracer Studies to Assess Mass Recovery at the Detection Limit

Stream solute tracers are commonly injected to assess transport and transformation in study reaches, but results are biased toward the shortest and fastest storage locations. While this bias has been understood for decades, the impact of an experimental constraint on our understanding has yet to be considered. Here, we ask how different our understanding of reach- and segment-scale transport would be if our empirical limits were extended. We demonstrate a novel approach to manipulate experimental conditions and observe mass that is stored at timescales beyond the traditional reach-scale window of detection. We are able to explain the fate of an average of 26% of solute tracer mass that would have been considered as “lost” in a traditional study design across our 14 replicates, extending our detection limits to characterize flowpaths that would have been previously unmeasured. We demonstrate how this formerly lost mass leads to predicting lower magnitudes of gross gains and losses in individual reaches, and ultimately show that the network turnover we infer from solute tracers represents an upper limit on actual, expected behavior. Finally, we review the evolution of tracer studies and their interpretation including this approach and provide a proposed future direction to extend empirical studies to not-before-seen timescales.

54 ENVIRONMENTAL SCIENCES↗

Aggregation bias and its drivers in large‐scale flood loss estimation: A Massachusetts case study

Abstract Large‐scale estimations of flood losses are often based on spatially aggregated inputs. This makes risk assessments vulnerable to aggregation bias, a well‐studied, sometimes substantial outcome in analyses that model fine‐grained spatial phenomena at coarse spatial units. To evaluate this potential in the context of large‐scale flood risk assessments, we use data from a high‐resolution flood hazard model and structure inventory for over 1.3 million properties in Massachusetts and examine how prominent data aggregation approaches affect the magnitude and spatial distribution of flood loss estimates. All considered aggregation approaches rely on aggregate structure inventories but differ in whether flood hazard is also aggregated. We find that aggregating only structure inventories slightly underestimates overall losses (−10% bias), and when flood hazard data is spatially aggregated to even relatively small spatial units (census block), statewide aggregation bias can reach +366%. All aggregation‐based procedures fail to capture the spatial covariation of inputs distributions in the upper tails that disproportionately generate total expected losses. Our findings are robust to several key assumptions, add important context to published risk assessments and highlight opportunities to improve flood loss estimation uncertainty quantification.

54 ENVIRONMENTAL SCIENCES↗

A Generalizable Evaluated Approach, Applying Advanced Geospatial Statistical Methods, to Identify High Lead Exposure Locations at Census Tract Scale: Michigan Case Study

BACKGROUND: Despite great progress in reducing environmental lead (Pb) levels, many children in the United States are still being exposed. OBJECTIVE: Our aim was to develop a generalizable approach for systematically identifying, verifying, and analyzing locations with high prevalence of children’s elevated blood Pb levels (EBLLs) and to assess available Pb models/indices as surrogates, using a Michigan case study. METHODS: We obtained ~1:9 million BLL test results of children <6 years of age in Michigan from 2006–2016; we then evaluated them for data representativeness by comparing two percentage EBLL (%EBLL) rates (number of children tested with EBLL divided by both number of children tested and total population). We analyzed %EBLLs across census tracts over three time periods and between two EBLL reference values (≥5 vs. ≥10 μg/dL) to evaluate consistency. Locations with high %EBLLs were identified by a top 20 percentile method and a Getis-Ord Gi* geospatial cluster “hotspot” analysis. For the locations identified, we analyzed convergences with three available Pb exposure models/indices based on old housing and sociodemographics. RESULTS: Analyses of 2014–2016 %EBLL data identified 11 Michigan locations via cluster analysis and 80 additional locations via the top 20 percentile method and their associated census tracts. Data representativeness and consistency were supported by a 0.93 correlation coefficient between the two EBLL rates over 11 y, and a Kappa score of ~0:8 of %EBLL hotspots across the time periods (2014–2016) and reference values. Many EBLL hotspot locations converge with current Pb exposure models/indices; others diverge, suggesting additional Pb sources for targeted interventions. DISCUSSION: This analysis confirmed known Pb hotspot locations and revealed new ones at a finer geographic resolution than previously available, using advanced geospatial statistical methods and mapping/visualization. It also assessed the utility of surrogates in the absence of blood Pb data. This approach could be applied to other states to inform Pb mitigation and prevention efforts. https://doi.org/10.1289/EHP9705

54 ENVIRONMENTAL SCIENCES↗

Quality Guidelines for Energy System Studies - Capital Cost Scaling Methodology: Revision 4a Report

Costs are frequently required as part of systems analysis work at NETL. Many of the cost results provided as part of systems analysis work were created with the use of scaling, since obtaining new vendor-supplied cost quotes for each category developed by NETL would be prohibitively time consuming and costly. Additionally, many of the technologies being investigated by NETL have not progressed far enough to have quotable costs. The costs are scaled from a quote for a similar plant configuration by use of various equations that typically employ at least one process parameter (e.g., coal-feed rate, oxidant-feed rate) and often an exponent. The primary purpose of the exponent is to account for economies of scale (i.e., as equipment size gets larger, it gets progressively cheaper to add additional capacity). The purpose of this section of the QGESS report is to provide a standard basis for scaling costs, with specific emphasis on scaling exponents. The intention of having a standardized document is to provide guidelines for proper procedures to reduce the potential of errors and increase credibility through consistency.

99 GENERAL AND MISCELLANEOUS↗