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At least 955 records · Page 53

The Applicability of Unit Systems to High-Performance Computing Applications

Dimensional analysis is a key technique used to verify the soundness of scientific models. Most experts agree that engineering and scientific software would be made more reliable by integrating dimensional analysis in their type system. We explored how High Performance Computing (HPC) applications could integrate compile-time dimensional analysis. We started by investigating various implementation of unit systems for C++. Eventually, selecting the latest (and most advanced) one to apply to our test codes. We worked with code of increasing complexity, from a projectile trajectory calculation to the proxy-application Lulesh. This included our code, Springs-3D, which focuses on demonstrating language features while performing simple physic computations. Finally, our main contribution is a source-code analysis which extracts constraints on the dimension of all variables, functions, and constants in an application. This resulting system of equations is solved using the dimensions of a few of these objects. This analysis has the potential to greatly reduce the time spent performing dimensional analysis when refactoring application to use a representation of units.

97 MATHEMATICS AND COMPUTING↗

Electron Beam Irradiation for Water Treatment of Per- and Polyfluoroalkyl Substances (PFAS)

Per- and polyfluoroalkyl substances (PFAS) are widely used but are now considered a water contamination risk. Fermi National Accelerator Laboratory’s IARC group has demonstrated that passing water through electron beam radiation can destroy PFAS. This project aims to develop a process to scale the system for bulk water treatment. The key is efficient radiation usage, ensuring that all water receives only the minimum dose. Software was developed for this purpose, consisting of a computational fluid dynamics model (CFD) in COMSOL, which calculates particle trajectories through the radiation area. A MATLAB script integrates the radiation dose of these particles, and statistical analysis is performed to evaluate the radiation utilization efficiency. These models are validated with a flow test where colored dye is injected and optically tracked. Radiation dose is measured by testing under an e-beam to measure the degradation of a PFAS analog.

Mueller, Scott [Northern Illinois U.]↗

User Manual for the Thermal Hydraulic Code SE2RCT

SE2-ANL is a modified version of SUPERENERGY-2 which interfaces the power distribution in the ANL maintained physics codes for the user. SE2RCT is a special version of SE2-ANL developed for specific use on models of the Experimental Breeder Reactor-II (EBR-II). SE2RCT fulfills a specific role in the calculated results as part of the Fuels Irradiation and Physics Database (FIPD) and is built to connect with the Physics and Analysis DataBase (PADB) for metallic fuel research and development in advanced sodium-cooled fast reactors (SFRs) created for EBR-II. SE2RCT is primarily a thermal analysis code that interfaces with the RCT based pin power details instead of the built-in pin power dehomogenization strategy in SE2-ANL. Beyond the thermal hydraulic calculation, the SE2RCT code provides detailed axial distributions of the RCT calculated results. SE2RCT also calculates the the axial distribution of pin wise DPA for the cladding materials which is part of the FIPD calculated results. This report serves as the user manual for SE2RCT and thus eliminates the QA gap of missing documentation on the SE2RCT software. All of the features and limitations of SE2RCT are documented in this report. The input and output specifications of SE2RCT are discussed in detail, and some unique features of SE2RCT, e.g. accurate pin power and temperature results for problems with non-uniform composition within an assembly, are also demonstrated and tested.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A full-ring variable-aperture cadmium zinc telluride system for whole-body single photon emission computed tomography: realistic simulations with phantoms

Single photon emission computed tomography (SPECT) is an imaging modality that has demonstrated its utility in a number of clinical indications. Despite this progress, a high sensitivity, high spatial resolution, multi-tracer SPECT with a large field of view suitable for whole-body imaging of a broad range of radiotracers for theranostics is not available. Purpose We have designed a cadmium zinc telluride (CZT) variable-aperture full-ring SPECT scanner instrumented with a broad-energy tungsten collimator intended to fill this technological gap. The final purpose is to provide a multi-tracer solution for brain and whole-body imaging. Our static SPECT scanner breaks the paradigm of the standard dual- and triple-head rotational SPECT systems, utilizing a larger detector area in each scan increasing the sensitivity. We provide a demonstration of the performance of our design using a realistic model of our detector with simulated body-sized 99mTc phantoms. Methods We developed a realistic model of our detector by using a combination of a Geant4 Monte Carlo simulation and a CZT detector response model based on a finite element model. Our approach models the characteristic low-energy tail effect in CZT that noticeably affects the sensitivity and the quality of the scatter correction in CZT detectors. We implement a modified dual energy window scatter correction adapted to include the CZT low-energy tail effect. A dedicated correction is also developed to eliminate the undesirable truncation observed in images given the presence of detector edges and gaps between detectors, due to the non-rotational nature of our device. Corrections for the attenuation, detector response and the presence of collimators are also included. The images are reconstructed using the maximum-likelihood expectation-maximization algorithm implemented in the reconstruction open software STIR. Detector and reconstruction performance are characterized with a Derenzo phantom and a body-sized National Electrical Manufacturers Association (NEMA) Image Quality (IQ) phantom containing 99mTc. Results Our SPECT design can resolve 6.4mm rods in a Derenzo phantom and obtain a good image contrast with the IQ phantom. Explicit testing of the gap and edge correction is provided, showing an excellent performance in eliminating the image truncation artifacts. Our modified scatter correction shows no overestimation of the contrast-recovery ratio for our realistic CZT detector model, as opposed to the cases without correction and with a standard dual-energy window scatter correction. Conclusions In this paper, we further demonstrate the performance of our design for whole-body imaging purposes. This adds to our previous demonstration of improved qualitative and quantitative 99mTc imaging for brain perfusion and 123I imaging for dopamine transport with respect to state-of-the-art NaI dual-head cameras. We show that our design performs similarly to the VERITON SPECT from Spectrum Dynamics, a commercial full-ring CZT SPECT camera, with the potential advantage of the broader energy range of application given by our custom-design tungsten collimators. Here, our device combines high sensitivity and image resolution with a broad-energy imaging application for the purpose of clinical imaging and theranostics of emerging radionuclides.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Advanced Laboratory and Field Arrays: Technical Report for Performance Enhancement for Marine Energy Converter (MEC) Arrays (Task 5)

Task 5 consisted of two parts, wave energy converter (WEC) arrays and current energy converter (CEC) arrays. The two parts of the project were executed independently, and this report covers only the work on WECs. In this part of the task, the team characterized the behavior of and developed control schemes for wave energy converter (WEC) arrays that improved performance (i.e., maximized aggregate power generation and reduced the levelized cost of energy) over baseline, non-coordinated control approaches. Specifically, for WEC arrays: the team developed optimal layouts of arrays that considered the effect of WEC placement within an array on coordinated array control with real-time estimation schemes. The numerical codes developed through this task were made available to users for array design. These tools utilized existing commercial software as well as software developed within the project team.

13 HYDRO ENERGY↗

End-to-end AI framework for interpretable prediction of molecular and crystal properties

We introduce an end-to-end computational framework that allows for hyperparameter optimization using the DeepHyper library, accelerated model training, and interpretable AI inference. The framework is based on state-of-the-art AI models including CGCNN, PhysNet, SchNet, MPNN, MPNN-transformer, and TorchMD-NET. We employ these AI models along with the benchmark QM9, hMOF, and MD17 datasets to showcase how the models can predict user-specified material properties within modern computing environments. We demonstrate transferable applications in the modeling of small molecules, inorganic crystals and nanoporous metal organic frameworks with a unified, standalone framework. We have deployed and tested this framework in the ThetaGPU supercomputer at the Argonne Leadership Computing Facility, and in the Delta supercomputer at the National Center for Supercomputing Applications to provide researchers with modern tools to conduct accelerated AI-driven discovery in leadership-class computing environments. We release these digital assets as open source scientific software in GitLab, and ready-to-use Jupyter notebooks in Google Colab.

36 MATERIALS SCIENCE↗

Resonant ultrasound spectroscopy probe for in-situ neutron scattering measurements

Resonant ultrasound spectroscopy (RUS) is an efficient, nondestructive technique to study the elastic properties of solids. A low-temperature (2-300 K) probe has been assembled and tested at the NOMAD beamline at the Spallation Neutron Source at Oak Ridge National Laboratory to assess the probe's neutronic properties, data acquisition system, and compatibility with existing sample environment. A case study on a bulk metallic glass, La 65 Cu 20 Al 10 Co 5, served to benchmark both hardware and software developments. The elastic constants of the metallic glass were determined as a function of temperature between 4 and 300 K and were used to guide neutron diffraction measurements at NOMAD. Tracking of a specific RUS peak center frequency and width enabled live monitoring of the sample temperature evolution that lagged thermometry by upwards of 40 K near room temperature. Assembly of a high-temperature (300-875 K) probe is underway and both probes are scheduled to be available to users by late-2021. Our aim is to provide users with live monitoring of an intrinsic variable at the neutron scattering beamlines, in addition to existing controls, to monitor the state of their samples and its elastic moduli and make informed decisions in real time.

Torres, James↗

Smart Monitoring and Diagnostic System (SMDS) for Packaged Air Conditioners and Heat Pumps for Small/Medium Commercial Buildings: Preparation for Commercialization: CRADA 478 [Abstract only]

This project will enable Pacific Northwest National Laboratory (PNNL) and industry partner, mCloud Technologies, to work collaboratively to ready the Smart Monitoring and Diagnostic System (SMDS) for commercial deployment and validate its performance under real-world conditions at field sites. This project will specifically focus on 1) implementing the SMDS algorithms in a scalable cloud-based software architecture, 2) designing new, innovative, complimentary commercial services based on the SMDS, 3) enhancing the SMDS energy and cost impact algorithms to reduce uncertainty in estimates, 4) determining the lower limits on SMDS performance degradation detection, 5) validating algorithm performance and default values of adjustable thresholds with existing data from controlled physical testing and from customer packaged air conditioners and heat pumps (commonly referred to as rooftop units or RTUs), 6) field testing to validate the system on multiple customer buildings in diverse environments, and 7) expanding field deployment to a larger set of mCloud’s customer buildings. Project results by validating, enhancing, and quantifying the performance of the SMDS will position mCloud, and potential future licensees, to implement the SMDS in commercial offerings that encourage and enable use of condition-based and predictive maintenance, leading to significant reductions in energy use and greenhouse gas emissions associated with space conditioning by RTUs. Furthermore, these enhancements will increase the value of the SMDS for users and increase the potential market for its use and impacts.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗

nautilus : boosting Bayesian importance nested sampling with deep learning

ABSTRACT We introduce a novel approach to boost the efficiency of the importance nested sampling (INS) technique for Bayesian posterior and evidence estimation using deep learning. Unlike rejection-based sampling methods such as vanilla nested sampling (NS) or Markov chain Monte Carlo (MCMC) algorithms, importance sampling techniques can use all likelihood evaluations for posterior and evidence estimation. However, for efficient importance sampling, one needs proposal distributions that closely mimic the posterior distributions. We show how to combine INS with deep learning via neural network regression to accomplish this task. We also introduce nautilus, a reference open-source python implementation of this technique for Bayesian posterior and evidence estimation. We compare nautilus against popular NS and MCMC packages, including emcee, dynesty, ultranest, and pocomc, on a variety of challenging synthetic problems and real-world applications in exoplanet detection, galaxy SED fitting and cosmology. In all applications, the sampling efficiency of nautilus is substantially higher than that of all other samplers, often by more than an order of magnitude. Simultaneously, nautilus delivers highly accurate results and needs fewer likelihood evaluations than all other samplers tested. We also show that nautilus has good scaling with the dimensionality of the likelihood and is easily parallelizable to many CPUs.

97 MATHEMATICS AND COMPUTING↗

New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements

Abstract Integrative genetic elements (IGEs) are mobile multigene DNA units that integrate into and excise from host bacterial genomes. Each IGE usually targets a specific site within a conserved host gene, integrating in a manner that preserves target gene function. However, a small number of bacterial genes are known to be inactivated upon IGE integration and reactivated upon excision, regulating phenotypes of virulence, mutation rate, and terminal differentiation in multicellular bacteria. The list of regulated gene integrity (RGI) cases has been slow-growing because IGEs have been challenging to precisely and comprehensively locate in genomes. We present software (TIGER) that maps IGEs with unprecedented precision and without attB site bias. TIGER uses a comparative genomic, ping-pong BLAST approach, based on the principle that the IGE integration module (i.e. its int-attP region) is cohesive. The resultant IGEs from 2168 genomes, along with integrase phylogenetic analysis and gene inactivation tests, revealed 19 new cases of genes whose integrity is regulated by IGEs (including dut, eccCa1, gntT, hrpB, merA, ompN, prkA, tqsA, traG, yifB, yfaT and ynfE), as well as recovering previously known cases (in sigK, spsM, comK, mlrA and hlb genes). It also recovered known clades of site-promiscuous integrases and identified possible new ones.

59 BASIC BIOLOGICAL SCIENCES↗

DEEPEN 3D PFA Favorability Models and 2D Favorability Maps at Newberry Volcano

DEEPEN stands for DE-risking Exploration of geothermal Plays in magmatic ENvironments. Part of the DEEPEN project involved developing and testing a methodology for a 3D play fairway analysis (PFA) for multiple play types (conventional hydrothermal, superhot EGS, and supercritical). This was tested using new and existing geoscientific exploration datasets at Newberry Volcano. This GDR submission includes images, data, and models related to the 3D favorability and uncertainty models and the 2D favorability and uncertainty maps. The DEEPEN PFA Methodology is based on the method proposed by Poux et al. (2020), which uses the Leapfrog Geothermal software with the Edge extension to conduct PFA in 3D. This method uses all available data to build a 3D geodata model which can be broken down into smaller blocks and analyzed with advanced geostatistical methods. Each data set is imported into a 3D model in Leapfrog and divided into smaller blocks. Conditional queries can then be used to assign each block an index value which conditionally ranks each block's favorability, from 0-5 with 5 being most favorable, for each model (e.g., lithologic, seismic, magnetic, structural). The values between 0-5 assigned to each block are referred to as index values. The final step of the process is to combine all the index models to create a favorability index. This involves multiplying each index model by a given weight and then summing the resulting values. The DEEPEN PFA Methodology follows this approach, but split up by the specific geologic components of each play type. These components are defined as follows for each magmatic play type: 1. Conventional hydrothermal plays in magmatic environments: Heat, fluid, and permeability 2. Superhot EGS plays: Heat, thermal insulation, and producibility (the ability to create and sustain fractures suitable for and EGS reservoir) 3. Supercritical plays: Heat, supercritical fluid, pressure seal, and producibility (the proper permeability and pressure conditions to allow production of supercritical fluid) More information on these components and their development can be found in Kolker et al., 2022. For the purposes of subsurface imaging, it is easier to detect a permeable fluid-filled reservoir than it is to detect separate fluid and permeability components. Therefore, in this analysis, we combine fluid and permeability for conventional hydrothermal plays, and supercritical fluid and producibility for supercritical plays. More information on this process is described in the following sections. We also project the 3D favorability volumes onto 2D surfaces for simplified joint interpretation, and we incorporate an uncertainty component. Uncertainty was modeled using the best approach for the dataset in question, for the datasets where we had enough information to do so. Identifying which subsurface parameters are the least resolved can help qualify current PFA results and focus future efforts in data collection. Where possible, the resulting uncertainty models/indices were weighted using the same weights applied to the respective datasets, and summed, following the PFA methodology above, but for uncertainty. There are two different versions of the Leapfrog model and associated favorability models: - v1.0: The first release in June 2023 - v2.1: The second release, with improvements made to the earthquake catalog (included additional identified events, removed duplicate events), to the temperature model (fixed a deep BHT), and to the index models (updated the seismicity-heat source index models for supercritical and EGS, and the resistivity-insulation index models for all three play types). Also uses the jet color map rather than the magma color map for improved interpretability. - v2.1.1: Updated to include v2.0 uncertainty results (see below for uncertainty model versions) There are two different versions of the associated uncertainty models: - v1.0: The first release in June 2023 - v2.0: The se...

15 GEOTHERMAL ENERGY↗

Prioritizing ICS Beachhead Systems for Cyber Vulnerability Testing

Cyber Testing for Resilient Industrial Control Systems™ (CyTRICS™) is the Department of Energy’s (DOE’s) program for cybersecurity vulnerability testing, digital subcomponent enumeration, and forensic assessment. CyTRICS leverages best-in-class test facilities and analytic capabilities at six DOE National Laboratories and strategic partnerships with key stakeholders including technology developers, manufacturers, asset owners and operators, and interagency partners. During the program’s development, CyTRICS established a unique methodology for prioritizing digital components within operational technology (OT) and industrial control systems (ICS) in the Energy Sector Industrial Base (ESIB) for cyber vulnerability testing. The CyTRICS Prioritization Process leverages multiple characteristics of systems, components, and their contextual deployment to calculate a quantification of individual digital components for CyTRICS testing. The initial version of the CyTRICS Prioritization Process was premised largely upon the impact which could result to an industrial control system if the digital component under testing was compromised, either through malicious means, faulty engineering, or other modes. The worldwide compromise of the SolarWinds Orion platform, first reported in December 2020, through malicious interference with the digital patching cycle was a watershed event in cyber supply chain security. The SolarWinds compromised demonstrated the strategic importance of certain types of ubiquitous software, and the ability to generate widespread cybersecurity effects. To address this challenge and as a part of the Department of Energy’s response to the SolarWinds compromise, DOE’s Office of Cybersecurity, Energy Security, and Emergency Response (CESER) directed the National Laboratories to evolve the CyTRICS Prioritization Process methodology to encompass additional factors related to the strategic importance of digital components. CESER directed CyTRICS researchers to identify, characterize, and append strategic factors to the CyTRICS Prioritization Process to provide additional weight to these characteristics. National Laboratory expert researchers identified functionality, distribution, and platform characteristics for digital components in ICS and OT that they assessed would be likely targeted in strategic initial-access cyber attack. CyTRICS has termed these factors “ICS Beachhead Systems,” leveraging a definition first advanced by Schneider Electric, which is intended as a blanket term to encompass digital components, products, and systems in OT. This paper describes the ICS Beachhead Systems identified and the rationale for inclusion. As a next step in the research and refinement process, the National Laboratories will validate this initial set of characteristics against digital components evaluated by the CyTRICS program and current implementation of the CyTRICS Prioritization Process. After validation, CyTRICS researchers will then develop a scoring methodology to generate a quantitative score to assess the degree to which a digital component is characterized as an ICS Beachhead System. Finally, the National Laboratories will append this scoring to the existing CyTRICS Prioritization Process algorithm.

97 MATHEMATICS AND COMPUTING↗

Sandia Toolkit Manual Version 5.15.6

This report provides documentation for the Sandia Toolkit (STK) modules. STK modules are intended to provide infrastructure that assists the development of computational engineering software such as finite-element analysis applications. STK includes modules for unstructured-mesh data structures, reading/writing mesh files, geometric proximity search, and various utilities. This document contains a chapter for each module, and each chapter contains overview descriptions and usage examples. Usage examples are primarily code listings which are generated from working test programs that are included in the STK code-base. A goal of this approach is to ensure that the usage examples will not fall out of date.

97 MATHEMATICS AND COMPUTING↗

Prototype Modeling for a Light-Trapping Planar-Cavity Enclosed Particle Solar Receiver

Concentrating solar thermal (CST) systems present a promising avenue for affordable and reliable energy production. Solar receivers are key components that determine the efficiency and longevity of these systems. Particle-based solar receivers have emerged as a compelling alternative to traditional technologies, offering several advantages that address limitations in current CST systems. This is especially true as next-generation CST technologies target applications including electricity generation, thermochemical processes, and industrial process heat, many of which necessitate higher operating temperatures than current commercial molten salt systems. Molten-salt thermal energy storage (TES) systems, commonly used in CSP, face challenges related to freezing and corrosion. Particle-based TES systems, in contrast, do not experience these issues, as particles are stable at high temperatures, exceeding 1000 degrees Celsius. This capability allows for a wider range of applications, including those requiring higher temperatures for industrial processes and efficient electricity generation. A novel innovation in particle-based solar receiver technology is the light-trapping planar cavity receiver (LTPCR) configuration developed by NREL. The LTPCR design consists of small cavity-like structures using opaque planar surfaces, enabling efficient capture and absorption of solar energy. A high incident flux concentration at the cavity aperture is absorbed on the receiver walls, and subsequently transferred to particles on the inside of cavities. The particles flow through the system, forming a fluidized bed inside of the receiver panels, effectively capturing the absorbed solar heat. Air is used as a fluidizing medium in this process to enhance particle heat transfer and mixing. The effectiveness of this design lies in its ability to manage solar flux conditions and ensure high solar-to-thermal receiver efficiency. A 100-kW prototype is currently being tested at the King Saud University in Saudi Arabia to assess the receiver performance. A range of modeling analyses for the optical, thermal, and mechanical effects were conducted to assess the performance of the receiver under on-sun conditions. The solar flux resulting from the KSU heliostat field was modeled using NREL SolTrace software and produced up to 600 kW/m2 at the receiver aperture. The solar flux absorbed on the receiver walls was then used within a computational fluid dynamics (CFD) model to predict wall temperature distributions along with radiation and convection loss. A two-phase CFD model was developed for the fluidized bed of silica sand inside the receiver panels to predict local wall-to-particle heat transfer coefficients, particle temperature distributions, and outlet temperature of the particles. We have also conducted analyses to understand the thermomechanical behavior of these innovative enclosed light-trapping solar receivers optimized for particle heating. We used finite element analysis (FEA) to predict the receiver's performance using temperature distributions obtained from CFD and based on the resulting stress profiles, evaluated creep-fatigue damage with a goal of achieving a 30-year service life. Analysis showed a significant impact of the particle-to-wall heat transfer coefficients (HTCs) on receiver performance, with higher HTCs resulting in reduced stress and increased lifespan. For instance, when using Inconel 740H, increasing the HTC from 800 W/m2 K to 1400 W/m2 K increased the creep life from 4,000 hours to over 100,000 hours. This highlights the importance of understanding and optimizing heat transfer in the design of high-efficiency receivers.

14 SOLAR ENERGY↗

A reusable neural network pipeline for unidirectional fiber segmentation

Abstract Fiber-reinforced ceramic-matrix composites are advanced, temperature resistant materials with applications in aerospace engineering. Their analysis involves the detection and separation of fibers, embedded in a fiber bed, from an imaged sample. Currently, this is mostly done using semi-supervised techniques. Here, we present an open, automated computational pipeline to detect fibers from a tomographically reconstructed X-ray volume. We apply our pipeline to a non-trivial dataset by Larson et al . To separate the fibers in these samples, we tested four different architectures of convolutional neural networks. When comparing our neural network approach to a semi-supervised one, we obtained Dice and Matthews coefficients reaching up to 98%, showing that these automated approaches can match human-supervised methods, in some cases separating fibers that human-curated algorithms could not find. The software written for this project is open source, released under a permissive license, and can be freely adapted and re-used in other domains.

79 ASTRONOMY AND ASTROPHYSICS↗

Streaming Readout of the CLAS12 Forward Tagger Using TriDAS and JANA2

An effort is underway to develop streaming readout data acquisition system for the CLAS12 detector in Jefferson Lab’s experimental Hall-B. Successful beam tests were performed in the spring and summer of 2020 using a 10GeV electron beam from Jefferson Lab’s CEBAF accelerator. The prototype system combined elements of the TriDAS and CODA data acquisition systems with the JANA2 analysis/reconstruction framework. This successfully merged components that included an FPGA stream source, a distributed hit processing system, and software plugins that allowed offline analysis written in C++ to be used for online event filtering. Details of the system design and performance are presented.

Ameli, Fabrizio↗

Variation in forest root image annotation by experts, novices, and AI

Abstract Background The manual study of root dynamics using images requires huge investments of time and resources and is prone to previously poorly quantified annotator bias. Artificial intelligence (AI) image-processing tools have been successful in overcoming limitations of manual annotation in homogeneous soils, but their efficiency and accuracy is yet to be widely tested on less homogenous, non-agricultural soil profiles, e.g., that of forests, from which data on root dynamics are key to understanding the carbon cycle. Here, we quantify variance in root length measured by human annotators with varying experience levels. We evaluate the application of a convolutional neural network (CNN) model, trained on a software accessible to researchers without a machine learning background, on a heterogeneous minirhizotron image dataset taken in a multispecies, mature, deciduous temperate forest. Results Less experienced annotators consistently identified more root length than experienced annotators. Root length annotation also varied between experienced annotators. The CNN root length results were neither precise nor accurate, taking ~ 10% of the time but significantly overestimating root length compared to expert manual annotation ( p = 0.01). The CNN net root length change results were closer to manual ( p = 0.08) but there remained substantial variation. Conclusions Manual root length annotation is contingent on the individual annotator. The only accessible CNN model cannot yet produce root data of sufficient accuracy and precision for ecological applications when applied to a complex, heterogeneous forest image dataset. A continuing evaluation and development of accessible CNNs for natural ecosystems is required.

Handy, Grace↗