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DOE OSTI2020

Hindsight logging for model training

In modern Machine Learning, model training is an iterative, experimental process that can consume enormous computation resources and developer time. To aid in that process, experienced model developers log and visualize program variables during training runs. Exhaustive logging of all variables is infeasible, so developers are left to choose between slowing down training via extensive conservative logging, or letting training run fast via minimalist optimistic logging that may omit key information. As a compromise, optimistic logging can be accompanied by program checkpoints; this allows developers to add log statements post-hoc, and "replay" desired log statements from checkpoint---a process we refer to as hindsight logging. Unfortunately, hindsight logging raises tricky problems in data management and software engineering. Done poorly, hindsight logging can waste resources and generate technical debt embodied in multiple variants of training code. In this paper, we present methodologies for efficient and effective logging practices for model training, with a focus on techniques for hindsight logging. Our goal is for experienced model developers to learn and adopt these practices. To make this easier, we provide an open-source suite of tools for Fast Low-Overhead Recovery (flor) that embodies our design across three tasks: (i) efficient background logging in Python, (ii) adaptive periodic checkpointing, and (iii) an instrumentation library that codifies hindsight logging for efficient and automatic record-replay of model-training. Model developers can use each flor tool separately as they see fit, or they can use flor in hands-free mode, entrusting it to instrument their code end-to-end for efficient record-replay. Our solutions leverage techniques from physiological transaction logs and recovery in database systems. Evaluations on modern ML benchmarks demonstrate that flor can produce fast checkpointing with small user-specifiable overheads (e.g. 7%), and still provide hindsight log replay times orders of magnitude faster than restarting training from scratch.

Computer Science↗

DOE OSTI2024

Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins

This repository of global hydrogeologic datasets contains aquifer properties on 0.5° scale, including depth to groundwater (Fan et al., 2013), aquifer thickness (de Graaf et al., 2015), WHYMap aquifer classes (Richts et al., 2011), porosity and permeability (Gleeson et al., 2014), digitized and geo-processed from their respective sources. Globally gridded aquifer properties could be used independently to estimate global groundwater availability or used as critical inputs to the superwell model to simulate groundwater extraction and provide estimates of pumped volumes and unit costs under user-specific scenarios. Key resources related to this data are: Niazi, H., Ferencz, S., Graham, N., Yoon, J., Wild, T., Hejazi, M., Watson, D., & Vernon, C. (2024; In-prep). Long-term Hydro-economic Assessment Tool for Evaluating Global Groundwater Cost and Supply: Superwell v1. Geoscientific Model Development. superwell model repository which uses this data to simulate groundwater extraction and provides estimates of the global extractable volumes and unit-costs ($/km3) of accessible groundwater production under user-specified extraction scenarios. Repository Overview Main output: aquifer_properties.csv contains all processed outputs, including aquifer properties like porosity, permeability, aquifer thickness, and depth to groundwater. shapefiles.zip: contains all digitized GIS databases and shapefile for all aquifer properties prep_inputs.R: R script that processes the shapefiles to produce the aquifer_properties file plot_inputs.R: R script for plotting the maps and conducting preliminary analysis on the available groundwater volume basin_to_country_mapping.csv, basin_country_region_mapping.csv and continent_county_mapping.csv provide the mapping between continents, 32 energy-economic macro regions, countries, and water basins for post-processing aquifer_properties.csv Maps: Each map visualizes the spatial distribution of one of the aquifer properties across the globe map_in_Porosity.png map_in_Permeability.png map_in_Aquifer_thickness.png map_in_Depth_to_water.png map_in_Grid_area_km.png map_in_WHYClass.png Sample inputs sample_inputs.py: this script samples inputs from the aquifer_properties dataset, ensuring the sampled and original inputs maintain the same distributions sampled_data_100.csv contains 100 sampled data points and sampled_data_100.png compares their distributions Dataset Overview The main outputs are consolidated in a comprehensive aquifer_properties.csv file and include the following fields: GridCellID: Unique identifier for each (roughly 0.5°) grid cell Continent: Continent name Country: Country name GCAM_basin_ID: Identifier for GCAM hydrologic basin Basin_long_name: Full name of the basin WHYClass: Hydrogeologic classification based on WHYMap aquifer classes (Richts et al., 2011) Porosity: Soil porosity (%) (Gleeson et al., 2014) Permeability: Soil permeability (in square meters; Gleeson et al., 2014) Aquifer_thickness: Thickness of the aquifer (in meters; de Graaf et al., 2015) Depth_to_water: Depth to groundwater (in meters; Fan et al., 2013) Grid_area: Area of the grid cell (in square meters) Key References The datasets are digitized versions of global hydrogeologic properties from the following key literature sources: Depth to Groundwater: Fan, Y., Li, H., & Miguez-Macho, G. (2013). Global Patterns of Groundwater Table Depth. Science, 339(6122), 940-943. https://doi.org/10.1126/science.1229881 Aquifer Thickness: de Graaf, I. E. M., Sutanudjaja, E. H., van Beek, L. P. H., & Bierkens, M. F. P. (2015). A high-resolution global-scale groundwater model. Hydrol. Earth Syst. Sci., 19(2), 823-837. https://doi.org/10.5194/hess-19-823-2015 Porosity and Permeability: Gleeson, T., Moosdorf, N., Hartmann, J., & van Beek, L. P. H. (2014). A glimpse beneath earth's surface: GLobal HYdrogeology MaPS (GLHYMPS) of permeability and porosity. Geophysical Research Letters, 41(11), 3891-3898. https://doi.org/10.1002/2014GL059856 Aquifer classes: Richts, A., Struckmeier, W. F., & Zaepke, M. (2011). WHYMAP and the Groundwater Resources Map of the World 1:25,000,000. In J. A. A. Jones (Ed.), Sustaining Groundwater Resources: A Critical Element in the Global Water Crisis (pp. 159-173). Springer Netherlands. https://doi.org/10.1007/978-90-481-3426-7_10 Cite as Niazi, H., Watson, D., Hejazi, M., Yonkofski, C., Ferencz, S., Vernon, C., Graham, N., Wild, T., & Yoon, J. (2024). Global Geo-processed Data of Aquifer Properties by 0.5° Grid, Country and Water Basins. MSD-LIVE Data Repository. https://doi.org/10.57931/2307831 Contact Reach out to Hassan Niazi or open an issue in superwell repository for questions or suggestions.

aquifer thickness↗

DOE OSTI2021

IGRINS RV: A Precision Radial Velocity Pipeline for IGRINS Using Modified Forward Modeling in the Near-infrared

Application of the radial velocity (RV) technique in the near-infrared is valuable because of the diminished impact of stellar activity at longer wavelengths, making it particularly advantageous for the study of late-type stars but also for solar-type objects. In this paper, we present the IGRINS RV open-source python pipeline for computing infrared RV measurements from reduced spectra taken with IGRINS, an R ≡ λ/Δλ ∼ 45,000 spectrograph with simultaneous coverage of the H band (1.49–1.80 μm) and K band (1.96–2.46 μm). Using a modified forward-modeling technique, we construct high-resolution telluric templates from A0 standard observations on a nightly basis to provide a source of common-path wavelength calibration while mitigating the need to mask or correct for telluric absorption. Telluric standard observations are also used to model the variations in instrumental resolution across the detector, including a yearlong period when the K band was defocused. Without any additional instrument hardware, such as a gas cell or laser frequency comb, we are able to achieve precisions of 26.8 m s{sup −1} in the K band and 31.1 m s{sup −1} in the H band for narrow-line hosts. These precisions are empirically determined by a monitoring campaign of two RV standard stars, as well as the successful retrieval of planet-induced RV signals for both HD 189733 and τ Boo A; furthermore, our results affirm the presence of the Rossiter–McLaughlin effect for HD 189733. The IGRINS RV pipeline extends another important science capability to IGRINS, with publicly available software designed for widespread use.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Development of an Enhanced Radiation Physics Toolset for Modeling Spectral and Imaging Signatures in the Warm Dense Matter Experiments

Radiative and atomic processes in plasmas play a critical role in a wide variety of high energy density laboratory plasma (HEDLP) experiments. The emission, absorption, and transport of radiation can strongly affect the overall energetics and evolution of such plasmas. In addition, radiation-based diagnostics – including imaging, spectroscopy, and absolute flux measurements – are widely used to determine key features of HEDLPs. To advance our understanding of HEDLP science, it is vital to have high-fidelity computational physics tools that have well-tested radiation physics modeling, and that are readily accessible to researchers in the HEDLP community. Simulations play an extremely important role for planning and designing the experiments, as well as for post-experiment data analysis. Prism Computational Sciences develops software that is used by National Laboratories and universities (including five members of LaserNetUS network). Prominent examples of such research efforts include z-pinch and short-pulse laser experiments designed to study the basic physics of photoionized plasmas and photoionization fronts, as well as their application to astrophysical plasmas. The main effort was dedicated to the development of non-equilibrium equation-of-state (EOS) models within the HELIOS-CR code, a hydrodynamics code with inline collisional-radiative atomic kinetics. Gas cell experiments on Z and Omega demonstrated the importance of non-equilibrium effects on atomic kinetics in photoionized plasmas. Recent proof-of-principle experiments on Omega EP confirmed the advantages of using a short-pulse laser to create an intense radiation drive, leading to additional experiments being proposed. Photoionization front experiments at LLE also emphasizes the importance of radiation and atomic physics. In both studies, HELIOS-CR simulations played a crucial role in computing non-equilibrium opacities and ionization distributions. A newly developed non-LTE EOS model will help addressing possible non-equilibrium effects, on for example specific heat, and their influence in plasma evolution. Prism also implemented support for open-source atomic data generated by the Flexible Atomic Code. This allows researchers to generate custom atomic tables and use them within the complex framework of simulation tools developed by Prism. The ability to use open-source atomic data would be extremely valuable for hydrodynamics and spectroscopic simulations that include high-Z materials, e.g., picosecond x-ray pulse generation experiments. Support for new atomic structures was fully implemented, and the data can be used by all simulation tools developed at Prism: radiation-hydrodynamics, imaging and spectroscopy, EOS and opacity. The development resulted in a significant fidelity enhancement to the simulations tools developed by Prism that are currently used in other cutting-edge experiments including: opacity measurement experiments performed to both understand the basic radiative and atomic properties of plasmas as well as provide data for more accurately modeling the internal structure of the Sun and other stars, high-intensity short-pulse laser experiments performed to develop short-wavelength light sources for use as backlighters and to investigate fast ignition concepts for inertial fusion energy; capsule implosion experiments designed to develop inertial fusion as an energy source, etc.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2019

Examination of Nutrient Sources and Transport in a Catchment with an Audubon Certified Golf Course

Water bodies in the East Bay Regional Park District (EBRPD), California, United States, provide aesthetic value and critical ecosystem services, but are often adversely affected by the activities and infrastructure of the intensely urban environment that surrounds the parks. EBRPD leases a golf course (Tilden Golf Course (TGC)) in Tilden Regional Park, one of its most popular parks located in the Berkeley Hills, which was certified as an Audubon Cooperative Sanctuary in 2013. Nonetheless, application of nutrients and pesticides (fungicides, plant growth regulators and herbicides) are commonly used to maintain turf systems and may be transported via surface runoff or through subsurface drainage to surface waters, leading to the concern that golf courses are a major contributor to water pollution. We studied the possible contribution of nutrients (NO3-N and PO4-P) and pesticides transported via storm-generated surface runoff and via groundwater from TGC to the primary drainage in the watershed, Wildcat Creek. Lake Anza, a popular open water swimming lake, is located downstream from TGC and experiences occasional nutrient-driven algal blooms that have caused swim beach closures. Measured NO 3 -N and PO 4 -P in the stream, at times, exceeded concentration limits of 1 mg/L (as N) and 0.05 mg/L (as P), respectively, considered protective of aquatic ecosystems by the United States Environmental Protection Agency (1986). We found that phosphorous likely has a dominant natural source, but nitrogen is primarily derived from a golf course fertilizer source and its concentration increases in the stream during runoff events, while other soluble species decrease. Analyses of pesticides in water reveal the presence of Azoxystrobin in stream water at the golf course, but with concentrations well below the regulatory limit. These results indicate that all other pesticides applied on TGC are not likely transported to the stream, suggesting future reactive transport research must treat contaminant species independently based on their specific transport behaviors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling

Mechanistic models of how single cells respond to different perturbations can help integrate disparate big data sets or predict response to varied drug combinations. However, the construction and simulation of such models have proved challenging. Here, we developed a python-based model creation and simulation pipeline that converts a few structured text files into an SBML standard and is high-performance- and cloud-computing ready. We applied this pipeline to our large-scale, mechanistic pan-cancer signaling model (named SPARCED) and demonstrate it by adding an IFNγ pathway submodel. We then investigated whether a putative crosstalk mechanism could be consistent with experimental observations from the LINCS MCF10A Data Cube that IFNγ acts as an anti-proliferative factor. The analyses suggested this observation can be explained by IFNγ-induced SOCS1 sequestering activated EGF receptors. This work forms a foundational recipe for increased mechanistic model-based data integration on a single-cell level, an important building block for clinically-predictive mechanistic models.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2020

HTR solver: An open-source exascale-oriented task-based multi-GPU high-order code for hypersonic aerothermodynamics

In this study, the open-source Hypersonics Task-based Research (HTR) solver for hypersonic aerothermodynamics is described. The physical formulation of the code includes thermochemical effects induced by high temperatures (vibrational excitation and chemical dissociation). The HTR solver uses high-order TENO-based spatial discretization on structured grids and efficient time integrators for stiff systems, is highly scalable in GPU-based supercomputers as a result of its implementation in the Regent/Legion stack, and is designed for direct numerical simulations of canonical hypersonic flows at high Reynolds numbers. Additionally, the performance of the HTR solver is tested with benchmark cases including inviscid vortex advection, low- and high-speed laminar boundary layers, inviscid one-dimensional compressible flows in shock tubes, supersonic turbulent channel flows, and hypersonic transitional boundary layers of both calorically perfect gases and dissociating air.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Abstract Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we develop a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screen multi-billion compound libraries against two unrelated targets, a ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel Na V 1.7. For both targets, we discover hit compounds, including seven hits (14% hit rate) to KLHDC2 and four hits (44% hit rate) to Na V 1.7, all with single digit micromolar binding affinities. Screening in both cases is completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

Science & Technology - Other Topics↗

DOE OSTI2020

LA17-V-InverseRadTransportProblem-PD2Kb. Final Project Report

In the inverse radiation transport problem, a radiation signal emanating from an unknown object is used to reconstruct geometric and material parameters of the object , e.g., the mass of special nuclear material (SNM), the isotopic composition of the SNM (e.g., the enrichment of 235U), the thickness of shielding, etc. The inverse radiation transport problem is one of the most fundamental and important in the emergency response mission, and has been addressed in previous NA-22 and NA-42/84 investments by using derivative-free optimization methods. Our project was aimed at (i) consolidating previous work by applying polynomial chaos expansion (PCE) for reducing significantly the number of forward model simulations required by derivative-free optimization methods; (ii) developing a general-purpose framework and stand-alone software for solving the inverse radiation transport problem by applying a new “predictive modeling” methodology (predictive modeling of coupled multi-physics systems, PM_CMPS) which enables the fusing of experimental and computational information; and (iii) developing several benchmarks (for unscattered gamma rays) for demonstrating the quantification of non-Gaussian features (e.g., skewness and kurtosis, which characterize asymmetries and long tails) of response distributions by deterministically and efficiently propagating parameter uncertainties (covariances and higher-order moments, where available) using high-order sensitivities computed by the recently developed comprehensive adjoint sensitivity analysis methodology (C-ASAM). With regard to (i), application of PCE, the most significant accomplishment of this project was an implementation of PCE into INVERSE that significantly reduced computation time for the DiffeRential Evolution Adaptive Metropolis (DREAM) and Differential Evolution (DE) methods. For inverse transport problems with measurements of neutron leakage, neutron multiplication, and neutron-induced gamma-rays, the solution times for the DREAM and DE methods were reduced by factors of 30-300, reducing run times from hours to minutes while maintaining the same accuracy as the standard (non-PCE) DREAM and DE. Speedups were further improved by exploring sparse grid quadrature sets using the Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN (Tasmanian) toolset. An initial exploration of sparse grids indicated that further speedups factors of 5-10 are obtainable. The implementation of PCE in INVERSE is not in a form that users can easily access. With regard to (ii), solving the inverse problem using a predictive modeling paradigm, the most significant accomplishment of this project were the derivation and implementation of adjoint-based second derivatives in neutron and photon transport theory. There are two codes that compute these derivatives. SENSPG computes them for uncollided gamma rays and SENSMG computes them for neutron leakage. SENSMG is open-source code available on github. Other significant accomplishments included a stand-alone code, MULTI-PRED, that implements the predictive modeling paradigm, along with a detailed manual. The code was implemented in the existing INVERSE code for inverse problems, but a head-to-head comparison of inverse methods was not achieved. We also derived and implemented the capability to compute sensitivities for multiplicity measurements into the SENSMG code, and this capability was used in a data assimilation application, but it was not used for solving inverse problems. With regard to (iii), developing benchmarks to demonstrate the importance of high-order sensitivity and uncertainty analysis, the most significant accomplishment of this project were two test problems that showed how important second-order sensitivities are.

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2022

Tree hydrodynamic modelling of the soil–plant–atmosphere continuum using FETCH3

Modelling the water transport along the soil–plant–atmosphere continuum is fundamental to estimating and predicting transpiration fluxes. A Finite-difference Ecosystem-scale Tree Crown Hydrodynamics model (FETCH3) for the water fluxes across the soil–plant–atmosphere continuum is presented here. The model combines the water transport pathways into one vertical dimension, and assumes that the water flow through the soil, roots, and above-ground xylem can be approximated as flow in porous media. This results in a system of three partial differential equations, resembling the Richardson–Richards equation, describing the transport of water through the plant system and with additional terms representing sinks and sources for the transfer of water from the soil to the roots and from the leaves to the atmosphere. The numerical scheme, developed in Python 3, was tested against exact analytical solutions for steady state and transient conditions using simplified but realistic model parameterizations. The model was also used to simulate a previously published case study, where observed transpiration rates were available, to evaluate model performance. With the same model setup as the published case study, FETCH3 results were in agreement with observations. Through a rigorous coupling of soil, root xylem, and stem xylem, FETCH3 can account for variable water capacitance, while conserving mass and the continuity of the water potential between these three layers. FETCH3 provides a ready-to-use open access numerical model for the simulation of water fluxes across the soil–plant–atmosphere continuum.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Discovery of a Stripe Phase in an Elemental Solid

Translational symmetry breaking is foundational to condensed matter physics because it is associated with crystal formation. At much lower energy scales, the breaking of crystalline translational symmetry can be driven by electronic, rather than ionic, degrees of freedom and may give rise to stripe order, a unidirectional ordered state. Such symmetry breaking has been seen in two-dimensional and strongly correlated systems. Here, for the first time, we report the observation of stripe order in an elemental solid, tellurium. Through topographic and spectroscopic imaging, we discover a commensurate 4 × 1 stripe phase. Surprisingly, this exotic order is so robust that it survives close to room temperature. Notably, our diffraction experiments confirm the bulk nature of the stripe order, showing the minuteness of potential lattice distortion associated with the order. In conclusion, our discovery of the stripe order in tellurium opens new windows to understanding the spontaneous symmetry breaking in elemental solids.

charge order↗

DOE OSTI2026

EC-Bench: A Benchmark for Enzyme Commission Number Prediction

Enzymes are proteins that catalyze specific biochemical reactions in cells. Enzyme Commission (EC) numbers are used to annotate enzymes in a four-level hierarchy that classifies enzymes based on the specific chemical reactions they catalyze. Accurate EC number prediction is essential for understanding enzyme functions. Despite the availability of numerous methods for predicting EC numbers from protein sequences, there is no unified framework for evaluating and studying such methods systematically. This gap limits the ability of the community to identify the most effective approaches for enzyme annotation. We introduce EC-Bench, a benchmark for EC number prediction, consisting of 1) an initial representative set of existing methods (including homology-based, deep learning, contrastive learning, and language model methods), 2) existing and novel accuracy and efficiency performance metrics, and 3) selected datasets to allow for comprehensive comparative study. EC-Bench is open-source and provides a framework for researchers to not only compare among existing methods objectively under uniform conditions, but also to introduce and effectively evaluate performance of new methods in a comparative framework. To demonstrate the utility of EC-Bench, we perform extensive experimentation to compare the existing EC number prediction methods and establish their advantages and disadvantages in a variety of prediction tasks, namely “exact EC number prediction”, “EC number completion” and (partial or additional) “EC number recommendation”. We find wide variation in the performance of different methods, but also subtle but potentially useful differences in the performance of different methods across tasks and for different parts of the EC hierarchy.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

An Open-Source Framework for Rapid Validation of Scientific ASICs

Spacely is an open-source framework for the post-silicon validation of analog, digital, and mixed-signal ASICs (Application-Specific Integrated Circuits) which maximizes the reuse of hardware and software, reducing the time taken to achieve meaningful test results. Spacely specifically addresses the needs of small, flexible ASIC design teams commonly found in academia or research institutions which benefit most from sharing the overhead of test stand creation between many unique ASIC designs. Spacely is a set of software, firmware, and design practices. It targets two primary hardware platforms (NI-PXI and Caribou) as well as offering extensible support for bench instruments. Spacely provides a high-level Python interface to all test hardware for accessibility, while also giving more sophisticated teams the opportunity to integrate custom test firmware. The design principles of Spacely are presented, along with a demonstrative example of using Spacely to test a pixel detector readout ASIC.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2023

PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions

Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca

We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation. Eight different primer pairs targeting different variable regions of the 16S rRNA gene were employed. DNA sequences were analyzed using open-source platform QIIME2 and the Greengenes database. PICRUSt2 was used to determine the predicted function of bacterial communities. Changes in bacterial relative abundance due to 16S primers were determined by GLMs. The average PCR amplicon size ranged from 315 bp (V3) to 769 bp (V4–V6). Alpha- and beta-diversity, taxonomic composition, and predicted functions were significantly affected by the primer choice. Beta diversity analysis based on Unweighted UniFrac distance matrix showed separation of microbiota with four different clusters of bacterial communities. Based on the alpha- and beta-diversity and taxonomic composition, variable regions V1–V3(1) and (2), and V3–V4 and V3–V5 were in most consensus. Our data strongly suggest that selection of particular sets of the 16S rRNA primers can impact microbiota analysis and interpretation of results in chicken as was shown previously for humans and other animal species.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Local Weather Station Design and Development for Cost-Effective Environmental Monitoring and Real-Time Data Sharing

Current weather monitoring systems often remain out of reach for small-scale users and local communities due to their high costs and complexity. This paper addresses this significant issue by introducing a cost-effective, easy-to-use local weather station. Utilizing low-cost sensors, this weather station is a pivotal tool in making environmental monitoring more accessible and user-friendly, particularly for those with limited resources. It offers efficient in-site measurements of various environmental parameters, such as temperature, relative humidity, atmospheric pressure, carbon dioxide concentration, and particulate matter, including PM 1, PM 2.5, and PM 10. The findings demonstrate the station’s capability to monitor these variables remotely and provide forecasts with a high degree of accuracy, displaying an error margin of just 0.67%. Furthermore, the station’s use of the Autoregressive Integrated Moving Average (ARIMA) model enables short-term, reliable forecasts crucial for applications in agriculture, transportation, and air quality monitoring. Furthermore, the weather station’s open-source nature significantly enhances environmental monitoring accessibility for smaller users and encourages broader public data sharing. With this approach, crucial in addressing climate change challenges, the station empowers communities to make informed decisions based on real-time data. In designing and developing this low-cost, efficient monitoring system, this work provides a valuable blueprint for future advancements in environmental technologies, emphasizing sustainability. The proposed automatic weather station not only offers an economical solution for environmental monitoring but also features a user-friendly interface for seamless data communication between the sensor platform and end users. This system ensures the transmission of data through various web-based platforms, catering to users with diverse technical backgrounds. Furthermore, by leveraging historical data through the ARIMA model, the station enhances its utility in providing short-term forecasts and supporting critical decision-making processes across different sectors.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1994

SolSTUS: Solar Source Thermal Upper Stage

This paper was written by members of the Utah State University (USU) Space Systems Design class, fall quarter 1993. The class is funded by NASA and administered by the University Space Research Association (USRA). The focus of the class is to give students some experience in design of space systems and as a source of original ideas for NASA. This paper is a summary of the work done by members of the Space Systems Design class during the opening phase of the course. The class was divided into groups to work on different areas of the Solar Thermal Rocket (STR) booster in order to produce a design reference mission that would identify the key design issues. The design reference mission focused upon a small satellite mission to Mars. There are several critical components in a Solar Thermal Rocket. STR's produce a very low thrust, but have a high specific impulse, meaning that they take longer to reach the desired orbit, but use a lot less fuel in doing it. The complexity of the rocket is discussed in this paper. Some of the more critical design problems discussed are: (1) the structural and optical complexity of collecting and focusing sunlight onto a specific point, (2) long term storage of fuel (liquid hydrogen), (3) attitude control while thrusting in an elliptical orbit and orienting the mirrors to collect sunlight, and (4) power and communications for the rocket and it's internal systems. The design reference mission discussed here is a very general mission to Mars. A first order trajectory design has been done and a possible basic science payload for Mars has been suggested. This paper summarizes the design reference mission (DRM) formulated by the USU students during fall quarter and identifies major design challenges that will confront the design team during the next two quarters here at USU.

Source record↗

DOE OSTI2021

RhizoVision Explorer: open-source software for root image analysis and measurement standardization

Abstract Roots are central to the function of natural and agricultural ecosystems by driving plant acquisition of soil resources and influencing the carbon cycle. Root characteristics like length, diameter and volume are critical to measure to understand plant and soil functions. RhizoVision Explorer is an open-source software designed to enable researchers interested in roots by providing an easy-to-use interface, fast image processing and reliable measurements. The default broken roots mode is intended for roots sampled from pots and soil cores, washed and typically scanned on a flatbed scanner, and provides measurements like length, diameter and volume. The optional whole root mode for complete root systems or root crowns provides additional measurements such as angles, root depth and convex hull. Both modes support providing measurements grouped by defined diameter ranges, the inclusion of multiple regions of interest and batch analysis. RhizoVision Explorer was successfully validated against ground truth data using a new copper wire image set. In comparison, the current reference software, the commercial WinRhizo™, drastically underestimated volume when wires of different diameters were in the same image. Additionally, measurements were compared with WinRhizo™ and IJ_Rhizo using a simulated root image set, showing general agreement in software measurements, except for root volume. Finally, scanned root image sets acquired in different labs for the crop, herbaceous and tree species were used to compare results from RhizoVision Explorer with WinRhizo™. The two software showed general agreement, except that WinRhizo™ substantially underestimated root volume relative to RhizoVision Explorer. In the current context of rapidly growing interest in root science, RhizoVision Explorer intends to become a reference software, improve the overall accuracy and replicability of root trait measurements and provide a foundation for collaborative improvement and reliable access to all.

59 BASIC BIOLOGICAL SCIENCES↗