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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 451 records · Page 25

Geochemistry, RNA radiocarbon signature, and metatranscriptome data from Rifle, Colorado groundwater well

Understanding the different sources of carbon subsurface microbes use is highly informative yet remains challenging. The goal of this work was to develop and test a cultivation-independent method that analyzes both the radiocarbon and ribosomal RNA (rRNA) signature of unamplified RNA from the same environmental sample, and that collectively characterizes community carbon utilization under in situ conditions. The method was applied to a filtered groundwater sample from a geochemically reduced zone of a shallow alluvial aquifer near Rife, Colorado (CO), where multiple potential carbon sources co-occur. The radiocarbon and RNA-Seq results, while addressing diverse sample properties, indicated a strikingly similar conclusion about the quantitative role of autotrophy in the subsurface microbial community.This data package provides (1) ribosomal RNA (rRNA) sequences for groundwater microbial populations, (2) the taxonomic identity and relative abundance of groundwater microbial populations based on these rRNA sequences, (3) radiocarbon signatures of the rRNA indicating the source of carbon used by the groundwater microbial populations (provided in both Word docx file and pdf file), (4) geochemical measurements for the monitoring well corresponding to these measurements.

54 ENVIRONMENTAL SCIENCES↗

Biogeochemistry of Pond B (Savannah River Site, South Carolina, USA): Water column and Sediments

Pond B at Savannah River Site (SRS, South Carolina) is a monomictic reservoir that received SRS R reactor cooling water from 1961–1964. Previous studies conducted between the 1980s–1990s on the water column and sediments of Pond B measured trace amounts of Pu (33 MBq 238Pu and 430 MBq 239,240Pu), 241Am, and 137Cs. Since then, the pond has been relatively isolated and the radionuclide concentrations have not been monitored over time. Herein, about 30 years after the last publication on Pond B, we are re-evaluating the geochemistry and radionuclide distribution within Pond B at five locations along a horizontal transect from the inlet to outlet. In addition, we are conducting the first analysis of the microbial community composition. This data package consists of water column measurements (1) using a multi-probe sonde, (2) plutonium isotopes and total concentrations, (3) total organic/inorganic carbon concentrations, (4) trace metals and major ions concentrations, and (6) microbial community composition. Sediment measurements include (1) plutonium isotopes and total concentrations and (2) microbial community composition.For sediment core and porewater, please see other Pond B data package (ess-dive-60d2352a4495472-20200615T203925174).The data in this package will be submitted for peer review in 2023.

54 ENVIRONMENTAL SCIENCES↗

Lightshow: a Python package for generating computational x-ray absorption spectroscopy input files

First-principles computational spectroscopy is a critical tool for interpreting experiment, per- forming structure refinement, and developing new physical understanding. Systematically setting up input files for different simulation codes and a diverse class of materials is a challeng- ing task with a very high barrier-to-entry, given the complexities and nuances of each individual simulation package. This task is non-trivial even for experts in the electronic structure field and nearly formidable for non-expert researchers. Lightshow solves this problem by providing a uniform abstraction for writing computational x-ray spectroscopy input files for multiple popular codes, including FEFF, VASP, OCEAN, exciting and XSpectra. Its extendable framework will also allow the community to easily add new functions and to incorporate new simulation codes.

36 MATERIALS SCIENCE↗

The AGORA High-resolution Galaxy Simulations Comparison Project. III. Cosmological Zoom-in Simulation of a Milky Way–mass Halo

In this work, we present a suite of high-resolution cosmological zoom-in simulations to z = 4 of a 10 12 M⊙ halo at z = 0, obtained using seven contemporary astrophysical simulation codes (Art-I, Enzo, Ramses, Changa, Gadget-3, Gear, and Gizmo) widely used in the numerical galaxy formation community. The physics prescriptions for gas cooling and heating and star formation are the same as the ones used in our previous Assembling Galaxies of Resolved Anatomy (AGORA) disk comparison but now account for the effects of cosmological processes such as the expansion of the universe, intergalactic gas inflow, and the cosmic ultraviolet background radiation emitted by massive stars and quasars. In this work, we introduce the most careful comparison yet of galaxy formation simulations run by different code groups, together with a series of four calibration steps each of which is designed to reduce the number of tunable simulation parameters adopted in the final run. In the first two steps, we methodically calibrate the gas physics, such as cooling and heating, in simulations without star formation. In the third step, we seek agreement on the total stellar mass produced with the common star formation prescription used in the AGORA disk comparison, in stellar-feedback-free simulations. In the last calibration step, we activate stellar feedback, where each code group is asked to set the feedback prescription to as close to the most widely used one in its code community as possible, while aiming for convergence in the stellar mass at z = 4 to the values predicted by semiempirical models. After all the participating code groups successfully complete the calibration steps, we achieve a suite of cosmological simulations with similar mass assembly histories down to z = 4. With numerical accuracy that resolves the internal structure of a target halo (≲100 physical pc at z = 4), we find that the codes overall agree well with one another, e.g., in gas and stellar properties, but also show differences, e.g., in circumgalactic medium (CGM) properties. We argue that, if adequately tested in accordance with our proposed calibration steps and common parameters, high-resolution cosmological zoom-in simulations can have robust and reproducible results. New code groups are invited to join and enrich this comparison by generating equivalent models or to test the code's compatibility on their own, by adopting the common initial conditions, the common easy-to-implement physics package, and the proposed calibration steps. Further analyses of the zoom-in simulations presented here will be presented in forthcoming reports from the AGORA Collaboration, including studies of the CGM, simulations by additional codes, and results at lower redshift.

79 ASTRONOMY AND ASTROPHYSICS↗

Accurate determination of solvation free energies of neutral organic compounds from first principles

The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Geospatial Data from the Alpine Treeline Warming Experiment (ATWE) on Niwot Ridge, Colorado, USA

This is a collection of all GPS- and computer-generated geospatial data specific to the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, Colorado, USA. The experiment ran between 2008 and 2016, and consisted of three sites spread across an elevation gradient. Geospatial data for all three experimental sites and cone/seed collection locations are included in this package. –––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––Geospatial files include cone collection, experimental site, seed trap, and other GPS location/terrain data. File types include ESRI shapefiles, ESRI grid files or Arc/Info binary grids, TIFFs (.tif), and keyhole markup language (.kml) files. Trimble-imported data include plain text files (.txt), Trimble COR (CorelDRAW) files, and Trimble SSF (Standard Storage Format) files. Microsoft Excel (.xlsx) and comma-separated values (.csv) files corresponding to the attribute tables of many files within this package are also included. A complete list of files can be found in this document in the “Data File Organization” section in the included Data User's Guide. Maps are also included in this data package for reference and use. These maps are separated into two categories, 2021 maps and legacy maps, which were made in 2010. Each 2021 map has one copy in portable network graphics (.png) format, and the other in .pdf format. All legacy maps are in .pdf format. .png image files can be opened with any compatible programs, such as Preview (Mac OS) and Photos (Windows). All GIS files were imported into geopackages (.gpkg) using QGIS, and double-checked for compatibility and data/attribute integrity using ESRI ArcGIS Pro. Note that files packaged within geopackages will open in ArcGIS Pro with “main.” preceding each file name, and an extra column named “geom” defining geometry type in the attribute table. The contents of each geospatial file remain intact, unless otherwise stated in “niwot_geospatial_data_list_07012021.pdf/.xlsx”. This list of files can be found as an .xlsx and a .pdf in this archive.As an open-source file format, files within gpkgs (TIFF, shapefiles, ESRI grid or “Arc/Info Binary”) can be read using both QGIS and ArcGIS Pro, and any other geospatial softwares. Text and .csv files can be read using TextEdit/Notepad/any simple text-editing software; .csv’s can also be opened using Microsoft Excel and R. .kml files can be opened using Google Maps or Google Earth, and Trimble files are most compatible with Trimble’s GPS Pathfinder Office software. .xlsx files can be opened using Microsoft Excel. PDFs can be opened using Adobe Acrobat Reader, and any other compatible programs. A selection of original shapefiles within this archive were generated using ArcMap with associated FGDC-standardized metadata (xml file format). We are including these original files because they contain metadata only accessible using ESRI programs at this time, and so that the relationship between shapefiles and xml files is maintained. Individual xml files can be opened (without a GIS-specific program) using TextEdit or Notepad. Since ESRI’s compatibility with FGDC metadata has changed since the generation of these files, many shapefiles will require upgrading to be compatible with ESRI’s latest versions of geospatial software. These details are also noted in the “niwot_geospatial_data_list_07012021” file.

54 ENVIRONMENTAL SCIENCES↗

GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics

Data package for Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon This data is published under a CC0 license. The authors encourage data reuse and request attribution by referencing the below citations for the data packages and associated manuscript. Please cite as: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. GLBRC Soil Yearlong Incubation 13C-SIP-Lipidomics. [Data Set] PNNL DataHub. doi: Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. MSV000097435: GLBRC soil yearlong incubation 13C-SIP-Lipidomics [Data Set] MassIVE. doi:10.25345/C57659T3K Rempfert KR, Bell SL, Kasanke CP, Kyle JE, Hofmockel KS. 2025. Lipids represent a dynamic, yet stable pool of microbially-derived soil carbon. In Prep This data package consists of compound-specific 13C SIP-lipidomics data from a yearlong tracer incubation experiment designed to investigate microbial lipid persistence in switchgrass bioenergy crop soils. In order to explore how lipid structure may modulate the persistence of C in soil lipids, we leveraged soils from two sites (Michigan - sandy texture, Wisconsin - silty texture) operated by the U.S. Department of Energy-funded Great Lakes Bioenergy Research Center (GLBRC). These sites had comparable climates, identical management practices, but contrasting soil textures, allowing us to assess the variability of lipid accrual or degradation in soils as well as provide insight regarding the degree to which edaphic properties may regulate the retention of soil lipids. Untargeted lipidomics analyses were performed to identify 13C-labeled lipids in the soil microbiome after long-term incubation. Soils were supplemented with 100 micrograms glucose per gram dry soil (99 atom % 13C or natural abundance for paired control) and incubated; samples were collected two months and one year after glucose addition. Lipid extracts (MPLEx) were analyzed by LC-MS/MS and identified using LIQUID. Calculation of isotopic enrichment of lipids was performed by targeted approach using TarMet to quantify lipid isotopologues and IsoCorrectoR to correct for natural abundance isotopes. Contents: Data package contents reported here are the first version and contain downstream analysis files for the raw LC-MS mass spectrometry files (.mzXML) deposited at the MassIVE database repository under accession MSV000097435 (80 experimental runs; 5.85 GB) | MassIVE DOI: 10.25345/C57659T3K. Support files include the additional data download 'Read Me' file containing data descriptor information. Reported data download contents are structured for compliance with project data sharing guidelines, community standards initiatives, and sponsor stakeholder policies supporting FAIR data principles. Data processing software, analysis tools, and data workflows are listed below corresponding to the host repository long-term location. Available Data Downloads (0.3 GB): "GLBRC soil yearlong incubation 13C-SIP-Lipidomics_readme.txt" - 'Read Me' data package content file (txt) "GLBRC_DataPackage_analysis files" - Data processing files (Rmd) and saved intermediate data processing outputs (rds, csv, xlsx) "GLBRC_13C_lipidomics_dataset.xlsx" - processed data in tabular format (xlsx) Linked Software: LIQUID LC-MS Analysis Software | 10.5281/zenodo.6459462 Lipid Mini-On Software Tools | 10.5281/zenodo.1492803 pmartR Omics Statistical Software | 10.5281/zenodo.6108667 xcms (v4.3.3) TarMet (v1.1.1) IsoCorrectoR (1.24.0) Funding Acknowledgments: This research was supported by an Early Career Research Program award funded by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research (OBER) Genomic Science program under FWP 68292, FWP 07880 and EMSL Exploratory Research Project 51095. A portion of this work was performed in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by OBER and located at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the DOE under Contract DE-AC05-76RLO1830.

Rempfert, Kaitlin R [Pacific Northwest National La↗

Integration and Packaging

Vertically integrated (3D) combinations of sensors and electronics provide the ability to fabricate small, fine pitch pixels with very small total capacitance monolithically integrated with complex circuitry. The small capacitance, enabled by the fine pixel pitch and low interconnect capacitance available in 3D hybrid bonding, provides excellent signal/noise with moderate power. This combination enables fabrication of integrated sensors and electronics with both excellent position and time resolution. In this white paper a discussion will be presented on 3D integration advantages, ongoing projects and prospects in high energy physics and beyond.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterizing PuO 2 Powder at Oak Ridge National Laboratory for the Multi-Lab Plutonium Process Signatures Campaign FY 2022

This report highlights the development of advanced analytical capabilities at Oak Ridge National Laboratory to characterize PuO 2 powder to support the Multi-Lab Plutonium Process Signatures Campaign in FY 2022. Two samples from a batch of 76 statistical precipitation runs were packaged and shipped from Pacific Northwest National Laboratory to Oak Ridge National Laboratory at the beginning of FY 2022. Techniques were used to characterize the sample, including powder X-ray diffraction, Raman spectroscopy, and diffuse reflectance spectroscopy. A brief description of each technique, the results and discussion, and future work are described in this report. Opportunities to expand current capabilities and include additional analytical capabilities for the next campaign will also be discussed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Data associated with “Different methods of estimating riverbed sediment grain size diverge at the basin scale ” (v2)

This data package is associated with the publication “Different methods of estimating riverbed sediment grain size diverge at the basin scale” published in Frontiers in Earth Science (Regier et al., 2025). The distribution of sediment grain size in streams and rivers is often quantified by the median grain size (d50), a key metric for understanding and predicting hydrologic and biogeochemical function of streams and rivers. Manual methods to measure d50 are time-consuming and ignore larger grains, while model-based methods to estimate d50 often over-generalize basin characteristics, and therefore cannot accurately represent site-scale heterogeneity. Here, we apply a machine learning-enabled photogrammetry methodology (You Only Look Once, or YOLO) for estimating d50 for grains > 2 mm based on images collected from streams and rivers throughout the Yakima River Basin (YRB). To understand how such methods may help bridge the gaps in resolution and accuracy between manual and catchment characteristics model-based d50 estimates, we compared YOLO d50 values to manual and model-based estimates across the YRB. We found distinct differences among methods for d50 averages and variability, and relationships between d50 estimates and basin characteristics. Source images can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1892052. This data package was originally published in May 2023. It was updated August 2025 (v2; new and modified files). File and folder names were not revised to indicate changes. See the change history section in the readme for more details. In addition to the readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) readme; (4) and subfolders containing data, figures, and scripts. The data folder contains datasets used for the analyses in the manuscript in image, text-delimited or geospatially-referenced formats. The figures folder contains the figures from the manuscript in different formats. The scripts folder contains all of the scripts used to complete the analyses in the manuscript. All files are .csv, .rds, .dbf, .prj, .shp, .shx, .jpg, .png, .R, .Rproj, or .pdf. We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected some of these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

Design and Manufacturing of High Performance, Reduced Charge Heat Exchangers

Air-to-fluid heat exchangers (HXs) play a critical role as the main heat transfer component in Heating, Ventilation, Air-Conditioning, and Refrigeration (HVAC&R) systems. However, their airside thermal resistance significantly inhibits their overall performance. Furthermore, these HXs must be continually more compact to meet the latest refrigerant charge limits to reduce emissions. Recent literature suggests that traditional HX geometries (e.g., round or flat tubes with fins), have reached their limits, and more sophisticated shape- and topology-optimized designs are required to achieve the next jump in performance. This research sheds light on the next generation of air-to-refrigerant HXs and aims to address several practical issues to commercialization such as novelty challenges (improved performance for significant charge reduction; modeling expertise & time investment), manufacturing challenges (non-round tube manufacturing; tube-header integration; product qualification, e.g., burst pressure testing, extreme operational environment, etc.), and operational challenges (flow maldistribution, fouling & wetting, noise & vibration). For example, a >20% improvement on one (or more) HX-level performance metrics (e.g., envelope volume, airside pressure drop, face area, capacity, refrigerant charge, weight, cost, etc.) must be achieved before a HX design is considered for commercialization. We present a new, comprehensive and experimentally validated air-to-refrigerant HX optimization framework with simultaneous thermal-hydraulic performance and mechanical strength considerations for novel, non-round, shape- and topology-optimized tubes capable of optimizing single and two-phase HX designs for any refrigerant choice and performance requirement with significant engineering time savings compared to conventional design practices. The framework was exercised for a wide range of applications and refrigerants, resulting in HXs which achieved greater than 20% improved performance, 20% reductions in size, and 25% reductions in refrigerant charge. To enable non-round tube bundle use in next generation HVAC&R equipment, novel manufacturing techniques were investigated, including the development of conventional manufacturing methods for small diameter, non-round tubes and novel tube-header integration strategies. In total, ten HX prototypes were manufactured, nine using conventional methods directly attributed to this project and one using advanced additive manufacturing methods. The five-year manufacturing feasibility of the proposed HXs was found to have a good outlook. The non-round tube HX simulated performance was validated through comprehensive experimental testing, including nine in-house component-level tests, one independent component-level test at an industry partner laboratory, and in-house system-level tests of using a commercially-available, residential packaged A/C unit which was retrofitted with a non-round tube prototype HX. It was found that HX designs proposed by the new framework can successfully predict experimental thermal-hydraulic performance within ±10-20% the first time with no manual design changes, eliminating the need for time-consuming and expensive prototyping efforts. This work will accelerate design and time to market for next generation HXs while simultaneously facilitating industry transition to new refrigerants at lower charge.

42 ENGINEERING↗

Data for Photosynthetic responses to temperature across the tropics: a meta-analytic approach

This data package contains raw data, data output, and code of photosynthetic temperature response curves from tropical forests. Data are used in "Photosynthetic responses to temperature across the tropics: a meta-analytic approach". The research investigates how photosynthetic optimum temperatures and shapes of photosynthetic temperature response curves varies across tropical forest climates and growth conditions. Growth climate variables include mean annual temperature, max and max temperature, diurnal temperature range, and aridity index. Meta-analysis combines 18 datasets with representation from Africa, Oceana, North American, and South America. Growth conditions analyzed considers deciduousness, successional status, light conditions, and whether plants are grown in situ or ex situ. All files, except for the raw datafile (Tropical_MetaAnalysis_Master_3.8.22_Edit.csv), have been processed using R code, which is provided.

54 ENVIRONMENTAL SCIENCES↗

FATES size- and age-dependent mortality simulation output analysis scripts

This dataset contains python scripts to analyse outputs from the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) and accompanies the paper “Needham, J.F., Chambers, J., Fisher, R., Knox, R., and Koven, C. D., Forest responses to simulated elevated CO2 under alternate hypotheses of size- and age-dependent mortality, 2020, Global Change Biology”. These scripts process FATES outputs from size- and age-dependent mortality simulations which were run to test the effect of different mechanisms of mortality on forest response to elevated CO2 (eCO2). Specifically, these scripts will process single plant functional type (PFT) simulations in which mortality is either a constant background rate, size-dependent or age-dependent. In each case, a simulation with constant woody NPP is compared to a simulation in which woody NPP increases by 25% to simulate the growth response of forests to eCO2. In addition, the data package contains scripts to analyse ensemble simulations with size- and age-dependent mortality and two PFTs, that were run to test the impact of different demographic rates on coexistence and the forest response to eCO2. Finally, the dataset includes scripts for processing simulations testing the sensitivity of results to allometry and to the recruitment scheme.

54 ENVIRONMENTAL SCIENCES↗

IDAES-PSE 2.4.0 Release

The Institute for the Design of Advanced Energy Systems (IDAES) Integrated Platform is a versatile computational environment offering extensive process systems engineering (PSE) capabilities for optimizing the design and operation of complex, interacting technologies and systems. IDAES enables users to efficiently search vast, complex design spaces to discover the lowest cost, most environmentally sustainable solutions while supporting the full process modeling lifecycle, from conceptual design to dynamic optimization and control. The extensible, open platform empowers users to create models of novel processes and rapidly develop custom analyses, workflows, and end-user applications.. Deprecations • Convergence Analysis tool (idaes/core/util/convergence): deprecated in favor of new Parameter Sweep tools. To be removed in v3.0.0. New Beta Capabilities • Parameter Sweep Tool (idaes.core.util.parameter_sweep) o A new API for defining and performing parameter sweep studies on IDAES models has been developed • Diagnostics Tools (idaes.core.util.model_diagnostics) o New methods for identifying duplicate variables and constraints have been added to the diagnostics toolbox o New tools for detecting ill conditioning in Jacobians have been developed and are available in the model_diagnostics module. These provide alternatives to the existing DegeneracyHunter toolbox, and will eventually be merged with this capability, but initial working versions have been provided as beta capabilities for interested users o IpoptConvergenceAnalysis (replaces deprecated Convergence Analysis tool):  A new tool for performing convergence analysis studies that leverages the new Parameter Sweep tools has been developed. This tool allows users to define the input parameters to their model and sampling methods for these (leveraging Pysmo's sampling tools) and to then solve their model across the sampled domains and return a summary of the solver performance (IPOPT only) Improved Models • Thickener model (idaes.models.unit_models.solid_liquid.thickener) o Improved model to include predictive correlations for unit sizing based on settling velocity measurements (steady-state only) • Modular Property Packages o Added general support for calculating critical properties of mixtures using defined Equation of State modules. New API defined for Equation of State modules in order to define the necessary constraints for calculating critical properties (most EoS modules DO NOT support calculation of critical properties (yet)) o Added new methods to Cubic Equation of State module to support calculation of critical properties

DiagnosticsToolbox↗

The Simons Observatory: Magnetic Shielding Measurements for the Universal Multiplexing Module

The Simons Observatory (SO) includes four telescopes that will measure the temperature and polarization of the cosmic microwave background using over 60,000 highly sensitive transition-edge bolometers (TES). These multichroic TES bolometers are read out by a microwave RF SQUID multiplexing system with a multiplexing factor of 910. Given that both TESes and SQUIDs are susceptible to magnetic field pickup and that it is hard to predict how they will respond to such fields, it is important to characterize the magnetic response of these systems empirically. This information can then be used to limit spurious signals by informing magnetic shielding designs for the detectors and readout. This paper focuses on measurements of magnetic pickup with different magnetic shielding configurations for the SO universal multiplexing module (UMM), which contains the SQUIDs, associated resonators, and TES bias circuit. The magnetic pickup of a prototype UMM was tested under three shielding configurations: no shielding (copper packaging), aluminum packaging for the UMM, and a tin/lead-plated shield surrounding the entire dilution refrigerator 100 mK cold stage. We also present measurements of the pickup in the UMM when aluminum feedhorns are installed. The measurements show that the aluminum packaging outperforms the copper packaging by a shielding factor of 8-10, and adding the tin/lead-plated 1K shield further increases the relative shielding factor in the aluminum configuration by 1-2 orders of magnitude. Furthermore, the addition of feedhorns provides a factor of 30 improvement when the tin/lead shield is not installed and a factor of 5 improvement when it is.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NCAP: Noncanonical Amino Acid Parameterization Software for CHARMM Potentials

Noncanonical Amino Acids (NCAAs) provide numerous avenues for introduction of novel functionality to peptides and proteins. NCAAs can be incorporated through solid phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis, wide chemical space and lack of empirically resolved structures modeling the effects of NCAA mutation is critical for rational protein design. To evaluate the structural and functional perturbations NCAAs introduce we utilize molecular potentials that describe the forces in protein structure. Most potentials such as CHARMM are designed to model canonical residues but can be parameterized in include novel NCAAs. Here, in this work, we introduce NCAP a software package to generate CHARMM compatible parameters from quantum chemical calculation. Unlike currently available tools NCAP is designed to recognize NCAA structure and automatically bridge the gap between DFT calculations and potential parameters. For our software we discuss workflow, validation against canonical parameter sets and comparison to published NCAA-protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

Data from: "Warming and provenance limit tree recruitment across and beyond the elevation range of subalpine forest"

This data package contains data used to support conclusions drawn in “Warming and provenance limit tree recruitment across and beyond the elevation range of subalpine forest”, by Kueppers et al. 2017. Data were collected in field sites within the Alpine Treeline Warming Experiment (ATWE), located on Niwot Ridge, on the eastern slope of the Colorado Rocky Mountains, USA. Files containing geospatial data are also included, to provide additional locational context.There are four document formats associated with this archive: three comma-separated values (.csv) files, three Microsoft Excel (.xlsx) files, one .pdf data user’s guide, four keyhole markup language (.kml) files, and a compressed folder containing seven ESRI shapefiles (.shp). The .csv files can be opened using any simple text-editor software, R, or Microsoft Excel. The .xlsx files can only be opened using Microsoft Excel. The .kml file can be opened by Google Earth and Google Maps, and the shapefiles can be opened with any GIS application compatible with the file type, such as ESRI’s ArcGIS, and QGIS.We provide two versions of the seedling data file: “PIEN_PIFLseedlings20150522_20150525rev12222020.csv/.xlsx” (hereafter PIEN_PIFLseedlings2015) and “PIEN_PIFLseedlings20160408rev12222020.csv/.xlsx” (hereafter PIEN_PIFLseedlings2016). PIEN_PIFLseedlings2015 contains the data we used in the paper. PIEN_PIFLseedlings2016 contains an updated version of these data that includes sampling from later years. The main differences between the two files lie in the columns titled “k[YEAR],” which describe the number of seedlings that were killed in a particular year. In PIEN_PIFLseedlings2016, there also is an additional year of data for k2015, and k2014 also has additional data input for the 2014 cohort. Additionally, in years 2010-2014, there are minor differences in the number of seedlings killed -- in as few as 0 plots (in 2011) to as many as 5 plots (in 2014) -- due to errors in data input that were rectified in later years.------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Upslope range shifts by subalpine tree species are a widely anticipated effect of climate change. Climate niche models predict subalpine forests to expand upslope, given more suitable growing conditions for adult trees. However, these models do not take into account climates required for successful seedling recruitment and establishment, an essential element for expansion. Further, localized upper treeline populations are hypothesized to contain favorable traits for colonizing the alpine. To test these expectations and to expand our knowledge of seedling recruitment under climate change, we designed a common garden, climate-warming experiment spread across an elevation gradient at Niwot Ridge in the Colorado Rocky Mountains. We focus on two widespread Western North American species, Engelmann spruce (Picea engelmannii Parry ex. Engelm) and limber pine (Pinus flexilis James), which occur at treeline. While the former is considered a late-seral species more tolerant of shade, limber pine is a shade-intolerant pioneer species able to establish on infertile sites.Every autumn, seeds of the two species were collected from high- (3370 m–3570 m) and low-provenance (2910–3240 m) sources close to the experimental sites and sown in our plots. A subset of plots were heated and another subset watered over the summer months to offset the effects of warming. Across five years, we found that seeds originating from low elevation recruited more strongly for both species, although this provenance difference diminished by the fourth year for Engelmann spruce, likely due to small sample sizes. Despite the recruitment of low-provenance seed, warming treatments decreased recruitment at all elevations. Combining this with the likeliness and availability of lower-quality, high provenance seed moving upslope at the treeline, tree migration into the alpine may be slowed. Overall, our findings suggest that the hardier limber pine is likely to become a more significant species in subalpine forest communities in the future, while the more sensitive Engelmann spruce may experience range contraction.

54 ENVIRONMENTAL SCIENCES↗

BMX: Biological modelling and interface exchange

Abstract High performance computing has a great potential to provide a range of significant benefits for investigating biological systems. These systems often present large modelling problems with many coupled subsystems, such as when studying colonies of bacteria cells. The aim to understand cell colonies has generated substantial interest as they can have strong economic and societal impacts through their roles in in industrial bioreactors and complex community structures, called biofilms, found in clinical settings. Investigating these communities through realistic models can rapidly exceed the capabilities of current serial software. Here, we introduce BMX, a software system developed for the high performance modelling of large cell communities by utilising GPU acceleration. BMX builds upon the AMRex adaptive mesh refinement package to efficiently model cell colony formation under realistic laboratory conditions. Using simple test scenarios with varying nutrient availability, we show that BMX is capable of correctly reproducing observed behavior of bacterial colonies on realistic time scales demonstrating a potential application of high performance computing to colony modelling. The open source software is available from the zenodo repository https://doi.org/10.5281/zenodo.8084270 under the BSD-2-Clause licence.

97 MATHEMATICS AND COMPUTING↗