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At least 253 records · Page 14

Boat-Dragged Riverbed and Mid-Column Water Quality along the Hanford Reach in the Columbia River Shorelines

This dataset contains water quality measurements used to identify sites of hydrologic exchange (i.e.hydrologic exchange flows; HEFs) in the Columbia River near Richland, WA by looking for anomalies in temperature and electrical conductivity (EC) along the bed of the river in February, June, July, August, and November 2017. These are ultimately the ‘ends’ of HEFs as they are locations of subsurface inflow to the river. This dataset contains dissolved oxygen (DO) measurements at 1-min intervals; temperature, EC, depth, and GPS coordinates at 1-second intervals; and N-NO3 at 2-min intervals along the river bed and mid-column water. DO measurements are included in this dataset for completeness but were not used in the analysis of HEFs due to the relatively long time interval of collection.

54 ENVIRONMENTAL SCIENCES↗

Multifrequency radar observations of clouds and precipitation including the G-band

Abstract. Observations collected during the 25 February 2020 deployment of the Vapor In-Cloud Profiling Radar at the Stony Brook Radar Observatory clearly demonstrate the potential of G-band radars for cloud and precipitation research, something that until now was only discussed in theory. The field experiment, which coordinated an X-, Ka-, W- and G-band radar, revealed that the Ka–G pairing can generate differential reflectivity signal several decibels larger than the traditional Ka–W pairing underpinning an increased sensitivity to smaller amounts of liquid and ice water mass and sizes. The observations also showed that G-band signals experience non-Rayleigh scattering in regions where Ka- and W-band signal do not, thus demonstrating the potential of G-band radars for sizing sub-millimeter ice crystals and droplets. Observed peculiar radar reflectivity patterns also suggest that G-band radars could be used to gain insight into the melting behavior of small ice crystals. G-band signal interpretation is challenging, because attenuation and non-Rayleigh effects are typically intertwined. An ideal liquid-free period allowed us to use triple-frequency Ka–W–G observations to test existing ice scattering libraries, and the results raise questions on their comprehensiveness. Overall, this work reinforces the importance of deploying radars (1) with sensitivity sufficient enough to detect small Rayleigh scatters at cloud top in order to derive estimates of path-integrated hydrometeor attenuation, a key constraint for microphysical retrievals; (2) with sensitivity sufficient enough to overcome liquid attenuation, to reveal the larger differential signals generated from using the G-band as part of a multifrequency deployment; and (3) capable of monitoring atmospheric gases to reduce related uncertainty.

54 ENVIRONMENTAL SCIENCES↗

Resilience Design Patterns: A Structured Approach to Resilience at Extreme Scale (V.2.0)

Reliability is a serious concern for future extreme-scale high-performance computing (HPC) systems. Projections based on the current generation of HPC systems and technology roadmaps suggest the prevalence of very high fault rates in future systems. The errors resulting from these faults will propagate and generate various kinds of failures, which may result in outcomes ranging from result corruptions to catastrophic application crashes. Therefore, the resilience challenge for extreme-scale HPC systems requires coordination between various hardware and software technologies that are capable of handling a broad set of fault models at accelerated fault rates. Also, due to practical limits on power consumption in future HPC systems, they are likely to embrace innovative architectures, increasing the levels of hardware and software complexities. Therefore, the techniques that seek to improve resilience must navigate the complex trade-off space between resilience and the overheads to power consumption and performance. While the HPC community has developed various resilience solutions, application-level techniques as well as system-based solutions, the solution space of HPC resilience techniques remains fragmented. There are no formal methods to integrate the various HPC resilience techniques into composite solutions, nor are there methods to holistically evaluate the adequacy and efficacy of such solutions in terms of their protection coverage, and their performance & power efficiency characteristics. Additionally, few implementations of current resilience solutions are portable to newer architectures and software environments that will be deployed on future systems. We developed a new structured approach to the management of HPC resilience using the concept of resilience-based design patterns. In general, a design pattern is a repeatable solution to a commonly occurring problem. We identified the well-known solutions that are commonly used to deal with faults, errors and failures in HPC systems. In the initial design patterns specification (version 1.0), we described the various solutions, which address specific problems in the design of resilient HPC environments, in the form of patterns. Each pattern describes a problem caused by a fault, error or failure event in an HPC environment, and then describes the core of the solution of the problem in such a way that this solution may be adapted to different systems and implemented at different layers of the system stack. The catalog of these resilience design patterns provides designers with a collection of design elements. To construct complete resilience solutions using combinations of various patterns, we defined a framework that enhances HPC designers' understanding of the important constraints and the opportunities for the design patterns to be implemented and deployed at various layers of the system stack. The design framework is also useful for establishing interfaces and mechanisms to coordinate flexible fault management across hardware and software components, as well as to consider the trade-off between performance, resilience, and power consumption when constructing a solution. The resilience design patterns specification version 1.1 included more detailed explanations of the pattern solutions, the context in which the patterns are applicable, and the implications for hardware or software design. It also provided several additional examples and detailed case studies to demonstrate the use of patterns to build realistic solutions. In version 1.2 of the specification document, we have improved the pattern descriptions, including graphical representations of the pattern components. These improvements are largely based on critical comments, feedback and suggestions received from pattern experts and readers of the previous versions of the specification. The pattern classification has been modified to further clarify the relationships between pattern categories. This version of the specification also introduces a pattern language for resilience design patterns. The pattern language presents the patterns in the catalog as a network, revealing the relations among the resilience patterns. The language provides designers with the means to explore alternative techniques for handling a specific fault model that may have different efficiency and complexity characteristics. Using the pattern language also enables the design and implementation of comprehensive resilience solutions as a set of interconnected resilience patterns that can be instantiated across layers of the system stack. The overall goal of this work is to provide hardware and software designers, as well as the users and operators of HPC systems, a systematic methodology for the design and evaluation of resilience technologies in HPC systems that keep scientific applications running to a correct solution in a timely and cost-efficient manner despite frequent faults, errors, and failures of various types. Version 2.0 expands the resilience design pattern classification and catalog to include self-stabilization patterns and reliability, availability and performance models for each structural pattern.

97 MATHEMATICS AND COMPUTING↗

A soft departure from jamming: the compaction of deformable granular matter under high pressures

Here, the high-pressure compaction of three-dimensional granular packings is simulated using a bonded particle model (BPM) to capture linear elastic deformation. In the model, grains are represented by a collection of point particles connected by bonds. A simple multibody interaction is introduced to control Poisson's ratio and the arrangement of particles on the surface of a grain is varied to model both high- and low-frictional grains. At low pressures, the growth in packing fraction and coordination number follows the expected behavior near jamming and exhibit friction dependence. As the pressure increases, deviations from the low-pressure power-law scaling emerge after the packing fraction grows by approximately 0.1 and results from simulations with different friction coefficients converge. These results are compared to predictions from traditional discrete element method simulations which, depending on the definition of packing fraction and coordination number, may only differ by a factor of two. As grains deform under compaction, the average volumetric strain and asphericity, a measure of the change in the shape of grains, are found to grow as power laws and depend heavily on the Poisson's ratio of the constituent solid. Larger Poisson's ratios are associated with less volumetric strain and more asphericity and the apparent power-law exponent of the asphericity may vary. The elastic properties of the packed grains are also calculated as a function of packing fraction. In particular, we find the Poisson's ratio near jamming is 1/2 but decreases to around 1/4 before rising again as systems densify.

36 MATERIALS SCIENCE↗

Translator Plan: A Coordinated Vision for Fiscal Years 2023-2025

Translators serve a unique role in the U.S. Department of Energy (DOE)’s Atmospheric Radiation Measurement (ARM) user facility, offering scientific input through various leadership and service roles. The Translators direct the creation of value-added products (VAPs) and analysis tools that make ARM measurements more accessible to the scientific community. Translators also serve as liaisons between users and the ARM infrastructure, collecting information about priorities and communicating ARM data and services. A key group focus is supporting the DOE Atmospheric System Research (ASR) program scientists and ASR’s efforts towards a process-level understanding of cloud-aerosol interactions, and in reducing uncertainty in global climate model projections. The ARM Translator Group (Table 1) consists of the five Translators, a representative of software development, and one from the Data Quality Office (DQO). Additionally, the ARM Engineering and Process Manager participates in this group and provides input and direction from ARM and its programmatic priorities.

54 ENVIRONMENTAL SCIENCES↗

Virulence and Genetic Diversity of Puccinia spp., Causal Agents of Rust on Switchgrass (Panicum virgatum L.) in the USA

Switchgrass (Panicum virgatum L.) is an important cellulosic biofuel grass native to North America. Rust, caused by Puccinia spp. is the most predominant disease of switchgrass and has the potential to impact biomass conversion. In this study, virulence patterns were determined on a set of 38 switchgrass genotypes for 14 single-spore rust isolates from 14 field samples collected in seven states. Single nucleotide polymorphism (SNP) variation was also assessed in 720 sequenced cloned amplicons representing 654 base pairs of the elongation factor 1-α gene from the field samples. Five major haplotypes were identified differing by 11 out of the 39 SNP positions identified. STRUCTURE, Principal Coordinate Analysis, and phylogenetic analyses divided the rust population into two genetic clusters. Virginia and Georgia had the highest and lowest rust genetic diversity, respectively. Only nine accessions showed a differential disease response between the 14 isolates, allowing the identification of eight races, differing by 1–3 virulence factors. Overall, the results suggested clonal reproduction of the pathogen and a North–South differentiation via local adaptation. However, similar haplotypes and races were also recovered from several states, suggesting migration events, and highlighting the need to further investigate the switchgrass rust population structure and evolution in the USA.

Bahri, Bochra A. (ORCID:0000000159055880)↗

HarDWR - Harmonized Water Rights Records

For a detailed description of the database of which this record is only one part, please see the HarDWR meta-record. Here we present a new dataset of western U.S. water rights records. This dataset provides consistent unique identifiers for each spatial unit of water management across the domain, unique identifiers for each water right record, and a consistent categorization scheme that puts each water right record into one of 7 broad use categories. These data were instrumental in conducting a study of the multi-sector dynamics of intersectoral water allocation changes through water markets (Grogan et al., in review). Specifically, the data were formatted for use as input to a process-based hydrologic model, WBM, with a water rights module (Grogan et al., in review). While this specific study motivated the development of the database presented here, U.S. west water management is a rich area of study (e.g., Anderson and Woosly, 2005; Tidwell, 2014; Null and Prudencio, 2016; Carney et al, 2021) so releasing this database publicly with documentation and usage notes will enable other researchers to do further work on water management in the U.S. west. The raw downloaded data for each state is described in Lisk et al. (in review), as well as here. The dataset is a series of various files organized by state sub-directories. The first two characters of each file name is the abbreviation for the state the in which the file contains data for. After the abbreviation is the text which describes the contents of the file. Here is each file type described in detail: XXFullHarmonizedRights.csv: A file of the combined groundwater and surface water records for each state. Essentially, this file is the merging of XXGroundwaterHarmonizedRights.csv and XXSurfaceWaterHarmonizedRights.csv by state. The column headers for each of this type of file are: state - The name of the state the data comes from. FIPS - The two digit numeric state ID code. waterRightID - The unique identifying ID of the water right, the same identifier as its state uses. priorityDate - The priority date associated with the right. origWaterUse - The original stated water use from the state. waterUse - The water use category under the unified use categories established here. source - Whether the right is for surface water or groundwater. basinNum - The alpha-numeric identifier of the WMA the record belongs to. CFS - The maximum flow of the allocation in cubic feet per second (ft3s-1). Arizona is unique among the states, as its surface and groundwater resources are managed with two different sets of boundaries. So, for Arizona, the basinNum column is missing and instead there are two columns: surBasinNum - The alpha-numeric identifier of the surface water WMA the record belongs to. grdBasinNum - The alpha-numeric identifier of the groundwater WMA the record belongs to. XXStatePOD.shp: A shapefile which identifies the location of the Points of Diversion for the state's water rights. It should be noted that not all water right records in XXFullHarmonizedRights.csv have coordinates, and therefore may be missing from this file. XXStatePOU.shp: A shapefile which contains the area(s) in which each water right is claimed to be used. Currently, only Idaho and Washington provided valid data to included within this file. XXGroundwaterHarmonizedRights.csv: A file which contains only harmonized groundwater rights collected from each state. See XXFullHarmonizedRights.csv for more details on how the data is formatted. XXSurfaceWaterHarmonizedRights.csv: A file which contains only harmonized surface water rights collected from each state. See XXFullHarmonizedRights.csv for more details on how the data is formatted. Additionally, one file, stateWMALabels.csv, is not stored within a sub-directory. While we have referred to the spatial boundaries that each state uses to manage its water resources as WMAs, this term is not shared across all states. This file lists the proper name for each boundary set, by state.

Economics↗

Spectroscopic and computational investigations of organometallic complexation of group 12 transition metals by methanobactins from Methylocystis sp. SB2

Methanotrophic bacteria catalyze the aerobic oxidation of methane to methanol using Cu-containing enzymes, thereby exerting a modulating influence on the global methane cycle. To facilitate the acquisition of Cu ions, some methanotrophic bacteria secrete small modified peptides known as “methanobactins,” which strongly bind Cu and function as an extracellular Cu recruitment relay, analogous to siderophores and Fe. In addition to Cu, methanobactins form complexes with other late transition metals, including the Group 12 transition metals Zn, Cd, and Hg, although the interplay among solution-phase configurations, metal interactions, and the spectroscopic signatures of methanobactin-metal complexes remains ambiguous. In this study, the complexation of Zn, Cd, and Hg by methanobactin from Methylocystis sp. strain SB2 was studied using a combination of absorbance, fluorescence, extended x-ray absorption fine structure (EXAFS) spectroscopy, and time-dependent density functional theory (TD-DFT) calculations. We report changes in sample absorbance and fluorescence spectral dynamics, which occur on a wide range of experimental timescales and characterize a clear stoichiometric complexation dependence. Mercury L3-edge EXAFS and TD-DFT calculations suggest a linear model for Hg--S coordination, and TD-DFT suggests a tetrahedral model for Zn 2+ and Cd 2+ . We observed an enhancement in the fluorescence of methanobactin upon interaction with transition metals and propose a mechanism of complexation-hindered isomerization drawing inspiration from the wild-type Green Fluorescent Protein active site. Collectively, our results represent the first combined computational and experimental spectroscopy study of methanobactins and shed new light on molecular interactions and dynamics that characterize complexes of methanobactins with Group 12 transition metals.

59 BASIC BIOLOGICAL SCIENCES↗

Aerosol Particle Mixing State and Composition at AMF3 (Interim Field Campaign Report)

The campaign is designed to support deployment of aerosol sampling equipment at the U.S. Department of Energy Atmospheric Radiation Measurement (ARM) user facility’s third ARM Mobile Facility (AMF3) to enable both singe-particle and bulk characterization of the aerosol particles at the field site in Bankhead National Forest, northern Alabama. We are proposing to do this work as part of our proposal “Generalizing aerosol mixing state: synthesis from observations and connection to models,” which has the pre-proposal tracking number PRE-0000035878. The full proposal has Dr. Rachel O’Brien as the Principal Investigator (PI) and Dr. Andy Ault and Dr. Nicole Riemer as Co-PIs. We sought to deploy instruments in winter 2025 and summer 2025 to obtain samples in different seasons, but were delayed by AMF3 set-up and availability of students and PIs. We just completed our first deployment this summer (2025) and we are interested in obtaining samples during this upcoming fall and winter to see the seasonal trends in aerosol mixing state at the site. This will provide a comparison of the impact of biogenic emissions on the mixing state and the chemical composition of the aerosol particles. Overall, the proposed study will provide key information regarding the mixing state of aerosol particles at AMF3 with direct ties to impacts of the particles on cloud formation and light scattering/absorption. From our deployment that ended las week we have some visible observations from our samples. We are observing a regular amount of black carbon on stage 6 of our Micro-Orifice Uniform Deposit Impactor (MOUDI) and we have also observed some short, large increases in aerosol loading. We hope to continue observations of these two features to determine the sources/aging for the black carbon and the physical mixing state as well as the sources for the short (a few minutes) increases in the aerosol loading and determine if the source for these is dust or sea salt or another source. We are also interested in comparing the black carbon we see here to samples collected during the agriculture burns in January/February and in comparing the larger particles to bioaerosols in the spring. To obtain these comparisons, we will need to collect more samples in the other seasons. Finally, we have some size-resolved particle collectors that can be deployed at the same time as the tethered balloon launches. We have discussed with Swarup China about trying to get the timing to work in August and we are interested in coordinating again later, if possible. This will give us ground-level and vertical aerosol mixing state sample sets that will be very exciting to analyze.

54 ENVIRONMENTAL SCIENCES↗

A network of soil moisture, soil temperature, air temperature, net radiation, ground heat flux and ground water for Chicago, Illinois

This dataset contains environmental monitoring data collected using solar-powered Multi-Function Research (MFR) Long Range Wide Area (LoRaWAN)-enabled nodes at 11 sites in Chicago, Illinois, as part of the DOE Urban Integrated Field Lab CROCUS project. The MFR node system consists of an Input/Output Digital Input Module (IB8) interface box (ICT International) providing wired connections for environmental sensors and an MFR-Node-L data logger that manages power, data processing, and LoRaWAN communication. The wireless data are ingested via Sage network (https://sagecontinuum.org/) nodes that contain LoRaWAN antennae. Measurements were collected from 11 MFR nodes deployed across Chicago State University (CSU), Northeastern Illinois University (NEIU), Northwestern University (NU), University of Illinois Chicago (UIC), West Woodlawn "Blacks in Green" (BIG), and Indian Boundary Prairies (IBP). Each MFR node supports a consistent suite of sensors measuring atmospheric, soil, and hydrological variables. Atmospheric measurements include 2m air temperature (°C), 2m vapor pressure deficit (kPa), and 2m shortwave/longwave radiation (incoming and outgoing, W/m²) measured using ATH-VPD and Apogee SN500 sensors. Soil measurements include volumetric water content (VWC, %) and temperature (°C) at four depths (15, 30, 45, and 60 cm below surface) using Meter Teros54 sensors, and heat flux (W/m²) at 10 cm depth using Huske HFP01-05 sensors. At selected locations, Meter Hydros21 sensors measure groundwater depth (mm), specific conductivity (dS/m), and temperature (°C). The dataset includes timestamps, site identifiers with location names, device IDs, Global Positioning System (GPS) coordinates, variable names with units, measurement depths, values, sensor names, and Sage node identifiers. All timestamps are in local Chicago time (CDT/CST). Quality control flags are provided using a 6-bit binary system indicating physical range violations, step spikes, 24-hour flat-line conditions, 6-hour jitter, 7-day ultra-low variance, and persistent high offset. Data is provided in CSV and CF-compliant NetCDF formats. This dataset is part of a larger collection of CROCUS environmental monitoring data, including linked datasets from Air Quality Transmitter (AQT) sensors, Weather Transmitter (WXT) sensors, and Sap Flow Meter (SFM1x) sensors.

Chicago↗

CHESS 2025: Discrete-return LiDAR point clouds from NEON AOP surveys

This dataset provides Level 1 (L1) discrete-return light detection and ranging (LiDAR) point cloud data collected for the 2025 Colorado Headwaters Ecological Spectroscopy Study (CHESS). These data were acquired to enable characterization of vegetation structure and other three-dimensional features of the land surface, and to evaluate structural changes that may have occurred between a prior LiDAR acquisition in 2018 and the 2025 overflight. The data were acquired over three study domains in the Upper Gunnison river basin: the upper East River watershed (CRBU); Almont Triangle and Taylor Canyon (ALMO); and Upper Taylor River watershed (UPTA) between 2025-06-13 and 2025-07-15. LiDAR data were acquired using the Optech Galaxy Prime Airborne LiDAR Terrain Mapper onboard the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP). These are the primary unclassified discrete-return LiDAR data delivered by NEON and are provided per flightline as LASzip (LAZ) 1.4 Format 6 files. Data were processed following the workflow described in the NEON L0-to-L1 Discrete Return LiDAR Algorithm Theoretical Basis Document (Krause and Goulden 2022). Each record in the unclassified point clouds represents a geolocated laser target/return recorded by the LiDAR system, with values for X, Y, Z position and return intensity. All point coordinates are provided in meters. Horizontal coordinates are referenced in Universal Transverse Mercator (UTM) zone 13N and the World Geodetic System (WGS) 1984 ensemble datum. Elevations are referenced to Geoid12A. Flight metadata describing flightline boundaries and positional uncertainty by point are also included. CHESS Project Description: The Colorado Headwaters Ecological Spectroscopy Study (CHESS) comprised a multi-week airborne remote sensing and field observation campaign in the Upper Gunnison Basin, Colorado, conducted in June and July of 2025. Airborne remote sensing was conducted by the National Ecological Observatory Network Airborne Observation Platform (NEON AOP), concurrent with a field campaign run by the Rocky Mountain Biological Laboratory (RMBL), the Lawrence Berkeley National Laboratory (LBNL) and SLAC National Accelerator Laboratory Watershed Function Science Focus Area (SFA), and NASA-JPL (Jet Propulsion Laboratory) Earth Surface Mineral Dust Source Investigation (EMIT) program. Between June 10 and July 18, 2025, the NEON AOP flight team collected high-resolution aerial imaging spectroscopy and Light Detection and Ranging (LiDAR) data over three domains: the Upper East River (CRBU), Almont Triangle (ALMO), and the Upper Taylor Basin (UPTA). In coordination with the flights, a field campaign acquired ground-truth observations, including observations of vegetation composition, foliar traits, forest demography, and subsurface properties in 18 core sampling areas within the domains. Additional surface water observations were taken at over 380 point locations. All CHESS campaign datasets can be found within the CHESS ESS-DIVE data portal: https://data.ess-dive.lbl.gov/portals/chess. Funding Acknowledgement: Field and remote-sensing data acquisition was performed under a grant from the National Aeronautics and Space Administration (80NSSC24K1005). This work was also supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231.

2018 NEON and 2025 CHESS Campaigns↗

Accelerating Biological Insight for Understudied Genes

Synopsis The rapid expansion of genome sequence data is increasing the discovery of protein-coding genes across all domains of life. Annotating these genes with reliable functional information is necessary to understand evolution, to define the full biochemical space accessed by nature, and to identify target genes for biotechnology improvements. The majority of proteins are annotated based on sequence conservation with no specific biological, biochemical, genetic, or cellular function identified. Recent technical advances throughout the biological sciences enable experimental research on these understudied protein-coding genes in a broader collection of species. However, scientists have incentives and biases to continue focusing on well documented genes within their preferred model organism. This perspective suggests a research model that seeks to break historic silos of research bias by enabling interdisciplinary teams to accelerate biological functional annotation. We propose an initiative to develop coordinated projects of collaborating evolutionary biologists, cell biologists, geneticists, and biochemists that will focus on subsets of target genes in multiple model organisms. Concurrent analysis in multiple organisms takes advantage of evolutionary divergence and selection, which causes individual species to be better suited as experimental models for specific genes. Most importantly, multisystem approaches would encourage transdisciplinary critical thinking and hypothesis testing that is inherently slow in current biological research.

Zoology↗

General approaches for shear-correcting coordinate transformations in Bragg coherent diffraction imaging. Part II

X-ray Bragg coherent diffraction imaging (BCDI) has been demonstrated as a powerful 3D microscopy approach for the investigation of sub-micrometre-scale crystalline particles. The approach is based on the measurement of a series of coherent Bragg diffraction intensity patterns that are numerically inverted to retrieve an image of the spatial distribution of the relative phase and amplitude of the Bragg structure factor of the diffracting sample. This 3D information, which is collected through an angular rotation of the sample, is necessarily obtained in a non-orthogonal frame in Fourier space that must be eventually reconciled. To deal with this, the approach currently favored by practitioners (detailed in Part I) is to perform the entire inversion in conjugate non-orthogonal real- and Fourier-space frames, and to transform the 3D sample image into an orthogonal frame as a post-processing step for result analysis. In this article, which is a direct follow-up of Part I, two different transformation strategies are demonstrated, which enable the entire inversion procedure of the measured data set to be performed in an orthogonal frame. The new approaches described here build mathematical and numerical frameworks that apply to the cases of evenly and non-evenly sampled data along the direction of sample rotation ( i.e. the rocking curve). The value of these methods is that they rely on the experimental geometry, and they incorporate significantly more information about that geometry into the design of the phase-retrieval Fourier transformation than the strategy presented in Part I. Finally, two important outcomes are (1) that the resulting sample image is correctly interpreted in a shear-free frame and (2) physically realistic constraints of BCDI phase retrieval that are difficult to implement with current methods are easily incorporated. Computing scripts are also given to aid readers in the implementation of the proposed formalisms.

36 MATERIALS SCIENCE↗

Three-dimensional phenotyping of peach tree-crown architecture utilizing terrestrial laser scanning

Tree training systems for temperate fruit have been developed throughout history by pomologists to improve light interception, fruit yield, and fruit quality. These training systems direct crown and branch growth to specific configurations. Quantifying crown architecture could aid the selection of trees that require less pruning or that naturally excel in specific growing/training system conditions. Regarding peaches [Prunus persica (L.) Batsch], access tools such as branching indices have been developed to characterize tree-crown architecture. However, the required branching data (BD) to develop these indices are difficult to collect. Traditionally, BD have been collected manually, but this process is tedious, time-consuming, and prone to human error. These barriers can be circumnavigated by utilizing terrestrial laser scanning (TLS) to obtain a digital twin of the real tree. TLS generates three-dimensional (3D) point clouds of the tree crown, wherein every point contains 3D coordinates (x, y, z). To facilitate the use of these tools for peach, we selected 16 young peach trees scanned in 2021 and 2022. These 16 trees were then modeled and quantified using the open-source software TreeQSM. As a result, “in silico” branching and biometric data for the young peach trees were calculated to demonstrate the capabilities of TLS phenotyping of peach tree-crown architecture. The comparison and analysis of field measurements (in situ) and in silico BD, biometric data, and quantitative structural model branch uncertainty data were utilized to determine the reconstructive model’s reliability as a source substitute for field measurements. Mean average deviation when comparing young tree (YT) height was approx. 5.93%, with crown volume was approx. 13.26% across both 2021 and 2022. All point clouds of the YTs in 2022 showed residuals lower than 12 mm to cylinders fitted to all branches, and mean surface coverage greater than 40% for both the trunk and primary branching orders.

09 BIOMASS FUELS↗

Effects of high concentrate rations on ruminal fermentation and microbiota of yaks

Ruminal microflora is closely correlated with the ruminant’s diet. However, information regarding the effect of high concentrate diets on rumen microflora in yaks is lacking. In the current study, 24 healthy male yaks were randomly assigned to two groups, each fed with different diets: less concentrate (LC; concentrate: coarse = 40: 60) and high concentrate (HC; concentrate: coarse = 80: 20) diets. Subsequently, a 21-day feeding trial was performed with the yaks, and rumen fluid samples were collected and compared using 16 s rRNA sequencing. The results showed that NH 3 -N, total VFA, acetate, butyrate, isobutyrate, and isovalerate were significantly higher in the HC group than that in the LC group ( p < 0.05), while microbial diversity and richness were significantly lower in the HC group ( p < 0.05). Principal coordinate analysis indicated that rumen microflora was significantly different in LC and HC groups ( p < 0.05). In the rumen, phyla Firmicutes and Bacteroidota were the most abundant bacteria, with Firmicutes being more abundant, and Bacteroidota being less abundant in the HC group than those found in the LC group. Christensenellaceae_R-7_group and Prevotella are the highest abundant ones at the genus level. The relative abundance of Acetitomaculum , Ruminococcus , and Candidatus_Saccharimonas were significantly higher in the HC group than that in the LC group ( p < 0.05), while the relative abundance of Olsenella was significantly lower in the HC group than in the LC group ( p < 0.05). Compared to the LC group, the relative abundance of Prevotella , Ruminococcus , and Candidatus_Saccharimonas was significantly higher in the HC group. The relative abundances of Prevotella , Prevotellaceae_UCG-003 , Olsenella , Ruminococcus , Acetitomaculum , Candidatus_Saccharimonas , and NK4A214_group were correlated with ruminal fermentation parameters ( p < 0.05). Furthermore, PICRUSt 2 estimation indicated that microbial genes associated with valine, leucine, and isoleucine biosynthesis were overexpressed in the rumen microflora of yaks in the HC group ( p < 0.05). Conclusively, our results suggest that high concentrate diets affect the microflora composition and fermentation function in yak rumen. The present findings would provide new insights into the health of yaks under high concentrate feeding conditions and serve as a potent reference for the short-term fattening processes of yaks.

Pang, Kaiyue↗

Estimation of Arrivals on Green at Signalized Intersections Using Stop-Bar Video Detection

Across the world, traffic congestion is increasing with alarming rapidity. Traffic signal control effectiveness, in coordinated networks, is often investigated in relation to the type of vehicle arrivals at the signalized intersections. Recently, several transportation agencies have switched from traditional loop detectors to video detection. When video cameras are accompanied by computer vision, one can extract more information about traffic “dynamics” than by using traditional inductive loop detectors. Collecting arrival times of multiple vehicles after the first arrival at the stop-bar detector might be challenging when using inductive loop detectors (since after the first arrival, detector status is always occupied). However, emerging video detection systems allow tracking of each vehicle’s entrance time in the detection zone, departure time from the detection zone, and the type of vehicle. This information can be used to estimate vehicular arrival and departure times, which then can be fed into machine learning algorithms to estimate arrivals on green (AOG). However, such research ideas have not been documented so far. Thus, this paper presents an estimation model for AOG, which was developed using multigene genetic programming. A robust experimental dataset was collected from a highly calibrated and validated microsimulation model of an 11-intersection corridor in Chattanooga, TN. The results of the model’s performance analysis showed the high accuracy of the training-, testing-, and validation datasets. The practical benefit of this model is that it can be applied to estimate arrival types at intersections where only stop-bar video detection exists.

Engineering↗

U.S. Department of Energy: National Virtual Biotechnology Laboratory (Technical Report)

With funding from the CARES Act, the U.S Department of Energy (DOE) established the National Virtual Biotechnology Laboratory (NVBL) in March 2020 to address key challenges associated with the COVID-19 crisis. The NVBL brought together the broad scientific and technical expertise and resources of DOE’s 17 national laboratories to help tackle medical supply shortages, discover potential drugs to fight the virus, develop and validate COVID-19 testing methods, model disease spread and impact across the nation, and understand virus transport in buildings and the environment. National laboratory resources leveraged for this effort include a suite of world-leading user facilities broadly available to the research community, such as light and neutron sources, nanoscale science research centers, sequencing and biocharacterization facilities, and high-performance computing facilities. As part of the NVBL framework, DOE rapidly assembled five project teams to (1) identify new targets for medical therapeutics; (2) develop innovations in testing capabilities; (3) provide epidemiological and logistical support; (4) understand viral fate and transport in the environment; and (5) address supply chain bottlenecks by harnessing extensive additive manufacturing capabilities. Each research team was charged with defining high-impact projects that could be completed in a 6-month sprint while coordinating their developments with academia, other government agencies, and the private sector. Within months, NVBL teams used DOE’s high-performance computers and light and neutron sources to identify promising candidates for antibodies and antivirals that universities and drug companies are now evaluating. NVBL researchers also developed new diagnostic targets and sample collection approaches, and supported efforts by the U.S. Food and Drug Administration, Centers for Disease Control and Prevention, and U.S. Department of Defense to establish national guidelines used in administering millions of tests. Researchers used artificial intelligence and high-performance computing to produce near-real-time data analysis to forecast disease transmission, stress on public health infrastructure, and economic impact, which supported decision-makers at the local, state, and national levels. To minimize virus uptake and protect human health, NVBL teams studied how to control indoor virus movement. Researchers also produced innovations in materials and advanced manufacturing that mitigated shortages in test kits and personal protective equipment, creating nearly 1,000 new jobs. Through its NVBL framework, DOE has contributed significantly to the nation’s COVID response, demonstrating in only a few months the critical impact of its national laboratories. NVBL’s accomplishments demonstrate not only the powerful resource represented by DOE’s national laboratories working together to meet national needs, but also the effectiveness of the integrated NVBL framework for rapidly responding to emergencies with research and development solutions. Going forward, the NVBL is poised to apply the unique capabilities and expertise of the national laboratory complex to future national and international emergencies, both natural and engineered. Through this framework, DOE will continue to be an integral component of agency-wide efforts to prepare for and respond to biorisks and other crises. This technical report describes the goals, progress, and results of NVBL’s five project teams—Molecular Design for COVID-19 Therapeutics, COVID-19 Testing, Epidemiological Modeling, Viral Fate and Transport, and Materials and Manufacturing of Critical Supplies—and lists each team’s publications and research output.

42 ENGINEERING↗

Hawai‘i Play Fairway (Final Report)

Most of Hawai'i's geothermal resources are blind—their manifestations, such as hot springs and steam vents, do not appear on the ground surface because the heated water flows far below. With the exception of $K\bar{i}lauea East Rift Zone$, in most areas of Hawai'i, high lateral permeability in the first kilometer below ground surface prevents surface thermal features from developing. As a methodology for discovering these blind resources, Play Fairway Analysis (PFA) involves finding potential locations of blind hydrothermal systems and describing potential geothermal sources in rift-zone settings. Using the PFA to find Hawai'i's geothermal resources, the University of Hawai'i (UH) conducted the Hawai‘i Play Fairway Project, Hawai'i's first statewide geothermal resource assessment since 1985. Sponsored by the U.S. Department of Energy, the Hawai'i Play Fairway Project provided an updated resource assessment, a roadmap for additional exploration activities, and the identification of areas for further exploration. Benefitting from UH's core competency in earth sciences and experienced geothermal researchers, the project comprised three phases. During the first phase, the team identified, compiled, and ranked existing geologic, groundwater, and geophysical datasets relevant to subsurface heat, fluid and permeability. Using a Bayesian statistical approach, the team developed a statistical methodology to integrate these data into a resource probability map. The team evaluated the confidence in the probability value and considered development viability of areas with geothermal resources. With these analyses, the team identified 10 locations in the Hawaiian Islands for exploration activities. For the second phase, the team collected new groundwater data in 10 locations across the state and new geophysical data on $L\bar{a}na‘i, Maui$, and central Hawai'i Island and modeled topographically induced stress to better characterize subsurface permeability. Analyzing the subsurface stresses, the team evaluated the potential for fracture-induced permeability. The team inverted the MT and gravity data to produce 3D models of resistivity and density, respectively, on $L\bar{a}na‘i$, across $Haleakal\bar{a}'s$ SW rift (Maui), and surrounding Mauna Kea (Hawai‘i Island). The team developed and applied a new method for incorporating depth information about resistivity, density, and potential for fracture-induced permeability into the statistical method for computing resource probability in these three focus areas. The team incorporated the new groundwater results with the new geophysical results and the calculations of potential for fracture-induced permeability to produce updated maps of resource probability and confidence. Through combining data from the first and second phases, the team determined locations for further exploration during the third phase. For MT and gravity surveys, the team recommended $Kaua'i's$ $L\bar{i}hu'e$ $Basin$, the east rift of $Maui's$ $Haleakal\bar{a}$ volcano, and the southwest rift of Hawai'i Island's Mauna Loa volcano. The MT and gravity surveys aimed to enable improved confidence in the resource potential in these locations. For drilling deep groundwater well(s), the team recommended Southeast Mauna Kea and $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$. During the third phase, further exploration involved drilling a groundwater well in $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$ and performing more geophysical surveys. We deepened an existing water well proximal to our target area on $L\bar{a}na'i$ due to funding constraints that precluded us from spudding a new well that would exceed 1km depth. Drilling was preceded by a number of substantial elements including: writing an Environmental Assessment and the subsequent legal process, performance of deviation logging, lowering a camera down the well, coordinating site preparation with $P\bar{u}lama$ $L\bar{a}na'i$, shipping the UH-owned rig interisland, procuring supplies, and leading 3 community meetings on $L\bar{a}na'i$. Drilling occurred 24/7 the entire month of June 2019 over which time $L\bar{a}na'i$ $Well$ 10 was deepened from 427 m to 1057 m, with continuous core collected. We measured a roughly linear temperature gradient averaging 42°C/km and a maximum bottom hole temperature of 66°C. This gradient is more than twice the background for Hawai'i and within a range of gradients measured in this depth range for some exploration wells within KERZ. We consider these results encouraging for $L\bar{a}na'i's$ resource potential and recommend following with a slim hole within $L\bar{a}na'i's$ caldera (our target zone) to ~ 2 km. Further, the positive implications such results have for the island of O‘ahu are substantial - the shield stage of O'ahu's volcanoes ended 1-2 My earlier. However, O'ahu uses more electricity than the rest of the islands combined, and the utility recently called for 500-700MW of firm, dispatchable renewable electricity on O'ahu by 2033. In Phase 3, we also collected limited new encouraging groundwater data, and updated our thoughts on the probabilities of fluid and permeability at resource depths (Pr F = 1; Pr P = mostly unconstrained). Ultimately, we advocate for using our final probability of heat, and confidence in this probability, to drive the next phase of exploration. We contend further development of geothermal in Hawai‘i will enable the state to achieve its 100% renewable policy objective and Hawai'i to transition off of fossil fuels through geothermal discovery and development. The project not only produced a large amount of data and expanded the existing knowledge of Hawai'i's geothermal resources, but also produced publications, theses, presentations, core photos, datasets, media reports, television interviews, community events, and a blog. Students and new professionals benefitted from the project's hands-on research experiences and educational opportunities and earned awards and recognition.

15 GEOTHERMAL ENERGY↗