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At least 163 records · Page 9

Surface soil temperature and water content from warming experiment located at the Rocky Mountain Biological Laboratory, Colorado, 2015 to 2019

This data package consists of soil temperature and soil water content sensor data from the warming experiment near the Rocky Mountain Biological Laboratory. Data range is from summer 2015 to summer 2019, when the warming manipulation was terminated. The location of the warming experiment is in the upper montane life zone and consists of meadow vegetation with a mixture of sagebrush (Artemisia tridentata), forb species (Erigeron speciosus, Helianthella quinquenervis, Lathyrus lanszwertii), and graminoid species (Festuca thurberi, Carex spps). Early studies showed that the heating treatment led to earlier snowmelt as well as warmer and drier surface soils, and changes in the functional composition of aboveground biomass favoring sagebrush over forb species (Harte and Shaw, 1995). These changes were mainly observed in the upper, naturally drier zone for the experimental plots. More recent observations of aboveground biomass, soil carbon, and microbial composition require concurrent information about the abiotic environment for interpretation and extrapolation to process-based models. This data package provides the plot- and zone-level abiotic context for the final years of the experiment and consists of csv files with hourly soil temperature (WM_ST.csv) and soil water content (WM_SWC.csv).

54 ENVIRONMENTAL SCIENCES↗

Dimensional Control over Metal Halide Perovskite Crystallization Guided by Active Learning

Metal halide perovskite (MHP) derivatives, a promising class of optoelectronic materials, have been synthesized with a range of dimensionalities that govern their optoelectronic properties and determine their applications. We demonstrate a data-driven approach combining active learning and high-throughput experimentation to discover, control, and understand the formation of phases with different dimensionalities in the morpholinium (morph) lead iodide system. Using a robot-assisted workflow, we synthesized and characterized two novel MHP derivatives that have distinct optical properties: a one-dimensional (1D) morphPbI 3 phase ([C 4 H 10 NO][PbI 3 ]) and a two-dimensional (2D) (morph) 2 PbI 4 phase ([C 4 H 10 NO] 2 [PbI 4 ]). To efficiently acquire the data needed to construct a machine learning (ML) model of the reaction conditions where the 1D and 2D phases are formed, data acquisition was guided by a diverse-mini-batch-sampling active learning algorithm, using prediction confidence as a stopping criterion. Querying the ML model uncovered the reaction parameters that have the most significant effects on dimensionality control. Based on these insights, we discuss possible reaction schemes that may selectively promote the formation of morph-Pb-I phases with different dimensionalities. The data-driven approach presented here, including the use of additives to manipulate dimensionality, will be valuable for controlling the crystallization of a range of materials over large reaction-composition spaces.

36 MATERIALS SCIENCE↗

A Synoptic System for Capturing Ecosystem Control Points Across Terrestrial‐Aquatic Interfaces

Interconnected landscape features such as terrestrial‐aquatic interfaces play an outsized role in biogeochemical cycles as ecosystem control points, but it is notoriously challenging to characterize these. Here, we document a synoptic sensor network design that is (a) flexible to accommodate diverse ecosystem interfaces and gradients, (b) adaptable to monitoring and modeling needs of small and large projects alike, (c) standardized for intercomparability across sites and field experiments, and (d) adequately replicated to capture heterogeneity of each parameter monitored. This real‐time monitoring of surface water, groundwater, soil, and vegetation supports configuration and evaluation of models that span upland, wetland, open water strata, and transitions between them. We established the network at seven sites along the Chesapeake Bay and Lake Erie coastlines, including large‐scale flood manipulation experiments in both regions. A central design element is “one data logger program to rule them all”—a collection of sensor‐specific modules deployed on 40 loggers controlling ∼2,000 sensors, with the goal of streamlining maintenance, debugging, and reproducible data processing. The network generates ∼6 M observations per month, capturing system dynamics at the broad spatial and fine temporal scales needed to initialize and benchmark models; measurement frequency can be modified remotely to capture events. This network design has also revealed behaviors not represented in Earth system models, such as transient groundwater oxygen pulses. Completely documented and open source, this standardized, flexible, and efficient sensor network design can reduce barriers to understanding environmental changes and ecosystem responses across systems and scales.

Ward, Nicholas D. [Pacific Northwest National Labo↗

PandAna: A Python Analysis Framework for Scalable High Performance Computing in High Energy Physics

Modern experiments in high energy physics analyze millions of events recorded in particle detectors to select the events of interest and make measurements of physics parameters. These data can often be stored as tabular data in files with detector information and reconstructed quantities. Current techniques for event selection in these files lack the scalability needed for high performance computing environments. We describe our work to develop a high energy physics analysis framework suitable for high performance computing. This new framework utilizes modern tools for reading files and implicit data parallelism. Framework users analyze tabular data using standard, easy-to-use data analysis techniques in Python while the framework handles the file manipulations and parallelism without the user needing advanced experience in parallel programming. In future versions, we hope to provide a framework that can be utilized on a personal computer or a high performance computing cluster with little change to the user code.

Groh, Micah↗

Water isotope data for the TEMPEST study site, 2023-2026

This dataset contains water isotope (deuterium (dD) and oxygen (d18O)) data from porewater, experimental source water, and aquifer sources from the Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experimental field site in Edgewater, MD. Samples were taken from 2023-2026 and included in file "TEMPEST_Water_Isotope_LANL_2023-2026.csv". Porewater samples were taken from 15cm depth at multiple locations in each experimental plot (i.e., control, freshwater, and saltwater). Water samples were stored in 2 ml amber glass vials with septum caps under refrigeration until analysis. A L2140-i Picarro cavity ringdown spectrometer connected to an A0211 Picarro vaporization module was used to run water samples. Standards (United States Geological Survey (USGS) 47 and 48) were used to check instrument accuracy during each run of samples. Post-processing codes were run to calculate isotopic values from raw data. Reported isotope data is post-processed. Raw data CSV files from the Picarro were processed using a Python script and output as excel files containing data calibrated to Vienna Standard Mean Ocean Water (VSMOW). Standardization is based on USGS47 and USGS48 standards that are measured before and after every 5-10 unknowns. Every measurement is comprised of 10 injections. Processing involved discarding the first 4 injections due to a known memory effect. Raw means of the last 6 injections are taken for each measurement and then corrected from the linear calibration relationship of the USGS standards expected vs measured values to obtain corrected compositions relative to VSMOW. Reported isotope data are corrected mean results.

Aquifer↗

Dynamic time-warping correction for shifts in ultrahigh resolving power ion mobility spectrometry and structures for lossless ion manipulations

Detection of arrival time shifts between ion mobility spectrometry (IMS) separations can limit achievable resolving power (Rp), particularly when multiple separations are summed or averaged, as commonly practiced. Such variations are more apparent in higher Rp measurements, and are particularly evident in long path length traveling wave structures for lossless ion manipulations (SLIM) IMS due to their typically much longer separation times. Here we explore the utility of a data processing approaches employing linear alignment (LA) and nonlinear dynamic time warping (DTW) of IMS separations to correct for variations between separations, such as due to pressure fluctuations. For multipass SLIM IMS separations, where narrow mobility range measurements have arrival times that can extend to several seconds, the LA approach effectively corrected for such variations, and significantly improvement Rp for summed separations. However, LA was much less effective for high Rp broad mobility range separations, such as obtained with multilevel SLIM IMS. Changes in IMS arrival times ions were observed to be correlated with small pressure changes, with approximately 0.6% relative arrival time shifts being common, sufficient to result in a loss of Rp for summed separations. Comparison of the approaches showed DTW alignment performed similarly to LA when used over a narrow mobility range, but was significantly better (providing narrower peaks and higher signal intensities) for wide mobility range data. We found the DTW approach increased Rp by as much as 115% for measurements in which 50 IMS separations over 2 seconds were summed, and leading to a large improvement in effective Rp. We conclude that DTW is superior to LA for ultrahigh resolution broad mobility range SLIM IMS separations, correcting for ion arrival time shifts regardless of the cause. Our tool is publicly available for use with universal ion mobility format (.UIMF) and text (.txt) files.

Data alignment, dynamic time warping, ion mobility↗

EVALUATING NUCLEAR SECURITY IMPLICATIONS OF THE SPLINTERNET

The internet, which for years has been viewed as a global online commons with standardized protocols but few regulations is, according to some experts, starting to mirror the contentious political and commercial contours of the physical world. Contributing to this is the rise in data breaches, cyber-enabled attacks on critical infrastructure, government surveillance operations, theft of intellectual property, manipulation of electoral processes, and perceived erosion of privacy, all of which are resulting in a growing skepticism that an open internet will naturally serve the best interests of users, communities, countries, and the global economy. In addition, the rapidly emerging and increasingly lucrative power of data has global superpowers scrambling to protect their informational sovereignty as an urgent matter of national security. Underscoring this urgency is the fact that, despite its global reach and cosmopolitan contributor base, internet infrastructure and governance of the World Wide Web remain largely under U.S. corporate auspices, which reinforces the perception of U.S. control. Whether fragmentation is politically, economically, or socially motivated, there appears to be a growing appetite for an internet that is partitioned and controlled at the national level. From “the Great Firewall of China” to the “Halal” internet of Iran, the trend towards a “Splinternet” has courts and governments embarking on what some call a "legal arms race" to impose a maze of national or regional rules, often conflicting, in the digital realm. The paper explores the emerging Splinternet phenomenon, analyses the implications of this trend on nuclear security, and identifies questions that present opportunities for future research.

Internet, Data Security, Cyber Security, Nuclear S↗

Data from: "Responses of alpine plant communities to climate warming"

The Alpine Treeline Warming Experiment (ATWE) was a common garden-climate manipulation experiment set up across an elevation gradient in Niwot Ridge, in the Front Range of the Colorado Rocky Mountains, USA. The project sought to learn more about the effects of climate change on alpine and subalpine ecosystems, namely tree species ranges and alpine plant communities. Plots were experimentally manipulated using infrared heaters set up to warm plots to temperatures comparable to those projected for the year 2100. Other treatments include watering, and a combination of watering and heating. Three sites were set up at different elevations to study three tree species, with the highest-elevation “Alpine” site ( ~3540 m) containing twenty additional plots to study alpine plant communities. Data in this package originate from these unseeded alpine plots. To evaluate soil nitrogen availability given site treatments, resin bags were deployed, removed, and extracted annually to produce ammonium and nitrate/nitrite readings.--------------------------------------------------Data files within this archive are in comma-separated-values (.csv) and Microsoft Excel (.xlsx) formats. .csvs can be read and opened by Microsoft Excel, R, or any other simple text-editing software, and .xlsx files can be opened using Microsoft Excel. Geospatial data associated with this package are in .kml and ESRI shapefile (.shp) formats. .kml files can be read using Google Earth or Google Maps, and shapefiles can be read with any software compatible with the file type, such as QGIS or ESRI’s ArcMap suite.Data files in this package - excluding “Winkler_2019_ALPO_inorganic_N_allyears.csv” - are provided in both Microsoft Excel and .csv formats, for added accessibility and flexibility in workflows. File contents are identical.

54 ENVIRONMENTAL SCIENCES↗

A guide to the BRAIN Initiative Cell Census Network data ecosystem

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

59 BASIC BIOLOGICAL SCIENCES↗

COMPASS-FME Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) Soil Greenhouse Gas Fluxes 04/2020-06/2024

Both raw and processed data measured using a LI-COR 7810 Greenhouse Gas Analyzer in the TEMPEST experiment, part of COMPASS-FME (https://compass.pnnl.gov/FME/COMPASSFME), at Smithsonian Environmental Research Center. This ecosystem-scale experiment probes the effects of saltwater versus freshwater flooding in a coastal deciduous forest.The data consist of both concentrations and fluxes of carbon dioxide and methane measured using static chambers on the soil surface, approximately every two weeks from early 2020 to mid 2024. Some of the measurement points are controls, and some subject to root-exclusion techniques; all measurements are embedded in the TEMPEST control, freshwater, and saltwater plots (see Hopple et al. 2023). These data were generated to understand changing soil greenhouse gas (CO2 and CH4) production and consumption. File types are comma-separated value (.csv) for data, and markdown (.md) for supplementary information.

54 ENVIRONMENTAL SCIENCES↗

CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations

CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of sgRNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Lastly, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.

59 BASIC BIOLOGICAL SCIENCES↗

Driving magnetic domains at the nanoscale by interfacial strain-induced proximity

Here, we investigate the local nanoscale changes of the magnetic anisotropy of a Ni film subject to an inverse magnetostrictive effect by proximity to a V 2 O 3 layer. Using temperature-dependent photoemission electron microscopy (PEEM) combined with X-ray magnetic circular dichroism (XMCD), direct images of the Ni spin alignment across the first-order structural phase transition (SPT) of V 2 O 3 were obtained. We find an abrupt temperature-driven reorientation of the Ni magnetic domains across the SPT, which is associated with a large increase of the coercive field. Moreover, angular dependent ferromagnetic resonance (FMR) shows a remarkable change in the magnetic anisotropy of the Ni film across the SPT of V 2 O 3 . Micromagnetic simulations based on these results are in quantitative agreement with the PEEM data. Direct measurements of the lateral correlation length of the Ni domains from XMCD images show an increase of almost one order of magnitude at the SPT compared to room temperature, as well as a broad spatial distribution of the local transition temperatures, thus corroborating the phase coexistence of Ni anisotropies caused by the V 2 O 3 SPT. We show that the rearrangement of the Ni domains is due to strain induced by the oxide layers’ structural domains across the SPT. Our results illustrate the use of alternative hybrid systems to manipulate magnetic domains at the nanoscale, which allows for engineering of coercive fields for novel data storage architectures.

36 MATERIALS SCIENCE↗

Non-Equilibrium Effects in Quantum Magnets

While most often the state of a material will tend toward an equilibrium determined by its environment, there are many cases of scientific and technological interest where materials are manipulated to be or are found in non-equilibrium configurations. For example, data can be stored in hard drives by deliberately altering the magnetic orientation in a material to store information in non-equilibrium pattern. In this project, the main goals were studies of non-equilibrium properties of quantum magnets using neutron scattering as the primary experimental method. Neutron scattering allows characterization of magnetic correlation lengths sensitive to the presence of defects. It can also be used to distinguish equilibrium from non-equilibrium states via energy transfer rates. Typical bulk state magnetization relaxation times are too short to perform many neutron scattering measurements of interest. To enable the study of non-equilibrium conditions, materials with longer magnetic relaxation times were targeted. CoNb 2 O 6 was used in two experiments related to non-equilibrium physics. In the first, evidence for defects created via the Kibble-Zurek mechanism (KZM) was sought by quenching across a magnetic field-dependent phase transition. Somewhat unexpectedly, clear evidence for KZM-induced defects was absent. Additional measurements of CoNb 2 O 6 were made to better characterize its crystal field and other properties to provide a better theoretical understanding to enable more effective non-equilibrium physics measurements. In another project, LiHo 0.45 Y 0.55 F 4 was used to compare a quantum annealing protocol to a thermal annealing one since magnetic fields can be used to control the thermal fluctuations in LiHo 0.45 Y 0.55 F 4 . In addition, a new pulsed magnet power supply and new techniques were developed suitable for neutron scattering experimental environments to enable faster magnetic field changes for producing non-equilibrium conditions. The power supply developed for this project has wider technological applications in addition to faster magnetic field ramps.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Response patterns of simulated corn yield and soil nitrous oxide emission to precipitation change

Abstract Background Precipitation plays an important role in crop production and soil greenhouse gas emissions. However, how crop yield and soil nitrous oxide (N 2 O) emission respond to precipitation change, particularly with different background precipitations (dry, normal, and wet years), has not been well investigated. In this study, we examined the impacts of precipitation changes on corn yield and soil N 2 O emission using a long-term (1981–2020, 40 years) climate dataset as well as seven manipulated precipitation treatments with different background precipitations using the DeNitrification-DeComposition (DNDC) model. Results Results showed large variations of corn yield and precipitation but small variation of soil N 2 O emission among 40 years. Both corn yield and soil N 2 O emission showed near linear relationships with precipitation based on the long-term precipitation data, but with different response patters of corn yield and soil N 2 O emission to precipitation manipulations. Corn yield showed a positive linear response to precipitation manipulations in the dry year, but no response to increases in precipitation in the normal year, and a trend of decrease in the wet year. The extreme drought treatments reduced corn yield sharply in both normal and wet years. In contrast, soil N 2 O emission mostly responded linearly to precipitation manipulations. Decreases in precipitation in the dry year reduced more soil N 2 O emission than those in the normal and wet years, while increases in precipitation increased more soil N 2 O emission in the normal and wet years than in the dry year. Conclusions This study revealed different response patterns of corn yield and soil N 2 O emission to precipitation and highlights that mitigation strategy for soil N 2 O emission reduction should consider different background climate conditions.

54 ENVIRONMENTAL SCIENCES↗

Fungal and bacterial growth variation due to drought and nitrogen addition experimental treatments. Loma Ridge Experimental Project. 2010-2012

Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities. This data package includes ten csv files (five data files and their corresponding data dictionaries) and one file-level metadata excel file. Data files contains information about which plots were exposed to treatments related to drought and nitrogen, information about litter bags reciprocal transplants manipulation for water input and nitrogen, detail information about water addition, precipitation records, and litter variables collected. Data dictionary files include detail explanation for each column in the data files. The file-level metadata file describes each file mentioned above. All the analyses were done using the R software.

54 ENVIRONMENTAL SCIENCES↗

2025 Workshop on Envisioning Frontiers in AI and Computing for Biological Research: Position Papers

This workshop aims to identify key research directions for transforming biology using artificial intelligence (AI), machine learning (ML) and computational methods to facilitate the discovery of new behaviors, mechanisms, and designs of biological processes relevant to DOE missions, underpinning a broader U.S. bioeconomy. By developing novel AI/ML technologies to analyze and interpret complex biological data, researchers can organize and simulate biological processes at various scales as well as advance predictive understanding and manipulation of biological systems. This integration of computation, experimentation, and next-generation experimental technologies can lead to discoveries in new biological behaviors and mechanisms relevant to DOE missions. The focus is on how advanced computational and mathematical methods can impact this mission by exploring digital twins, foundation models, automated laboratory experiments, modeling of complex living systems, and data-driven approaches for the biodesign of plants and microbial systems. While data management is important, it is not the primary focus of this workshop, which will assess the current state, trends, and AI/ML challenges at the interface between biology and computational science to identify opportunities for high-impact research at their intersection. The goal is to define research needs and opportunities that align with biological sciences, computational sciences, and applied mathematics research.

59 BASIC BIOLOGICAL SCIENCES↗

Probing Electron Beam Induced Transformations on a Single-Defect Level via Automated Scanning Transmission Electron Microscopy

A robust approach for real-time analysis of the scanning transmission electron microscopy (STEM) data streams, based on ensemble learning and iterative training (ELIT) of deep convolutional neural networks, is implemented on an operational microscope, enabling the exploration of the dynamics of specific atomic configurations under electron beam irradiation via an automated experiment in STEM. Combined with beam control, this approach allows studying beam effects on selected atomic groups and chemical bonds in a fully automated mode. Here, in this study, we demonstrate atomically precise engineering of single vacancy lines in transition metal dichalcogenides and the creation and identification of topological defects in graphene. The ELIT-based approach facilitates direct on-the-fly analysis of the STEM data and engenders real-time feedback schemes for probing electron beam chemistry, atomic manipulation, and atom by atom assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Pseudogap and Fermi arc induced by Fermi surface nesting in a centrosymmetric skyrmion magnet

Skyrmions in noncentrosymmetric materials are believed to occur due to the Dzyaloshinskii-Moriya interaction. By contrast, the skyrmion formation mechanism in centrosymmetric materials remains elusive. Here, in this work, we reveal the intrinsic electronic structure of the centrosymmetric GdRu 2 Si 2 by selectively measuring magnetic domains using angle-resolved photoemission spectroscopy (ARPES). We found robust Fermi surface (FS) nesting, consistent with the magnetic modulation q -vector detected by the previous resonant x-ray scattering measurements. The pseudogap opens at the nested FS portions, which vary for different magnetic domains. The anomalous pseudogap disconnects the FS to generate Fermi arcs with twofold symmetry. These results indicate that the Ruderman-Kittel-Kasuya-Yosida (RKKY) interaction plays a decisive role in generating the screw spin modulation responsible for the skyrmion formation in GdRu 2 Si 2 . Furthermore, we demonstrate the flexible nature of magnetism in GdRu 2 Si 2 by manipulating magnetic domains with magnetic field and temperature cyclings, providing potential future applications for data storage and processing devices.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗