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DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

GrayQb TM Single-Faced Version 2 (SF2) Open Environment Test Report (Rev. 1)

This report details the design upgrades incorporated into the new version of the GrayQb TM SF2 device and the characterization testing of this upgraded device. Results from controlled characterization testing in the Savannah River National Laboratory (SRNL) R&D Engineering Imaging and Radiation Lab (IRL) and the Savannah River Site (SRS) Health Physics Instrument Calibration Laboratory (HPICL) is presented, as well as results from the open environment field testing performed in the E-Area Low Level Waste Storage Area. Resultant images presented in this report were generated using the SRNL developed Radiation Analyzer (RAzer TM ) software program which overlays the radiation contour images onto the visual image of the location being surveyed.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2017

Novel Infiltration Diagnostics based on Laser-line Scanning and Infrared Temperature Field Imaging

This project targets the building energy efficiency problems induced by building infiltration/leaks. The current infiltration inspection techniques often require extensive visual inspection and/or whole building pressure test. These current techniques cannot meet more than three of the below five criteria of ideal infiltration diagnostics: 1. location and extent diagnostics, 2. building-level application, 3. least surface preparation, 4. weather-proof, and 5. non-disruption to building occupants. These techniques are either too expensive or time consuming, and often lack accuracy and repeatability. They are hardly applicable to facades/facades section. The goal of the project was to develop a novel infiltration diagnostics technology based on laser line-scanning and simultaneous infrared temperature imaging. A laboratory scale experimental setup was designed to mimic a model house of well-defined pressure difference below or above the outside pressure. Algorithms and Matlab-based programs had been developed for recognition of the hole location in infrared images. Our experiment based on laser wavelengths of 450 and 1550 nm and laser beam diameters of 4-25 mm showed that the location of the holes could be identified using laser heating; the diagnostic approach however could not readily distinguish between infiltration and non-infiltration points. To significantly improve the scanning throughput and recognition accuracy, a second approach was explored, developed, and extensively tested. It incorporates a liquid spray on the surface to induce extra phase change cooling effect. In this spray method, we termed it as PECIT (Phase-change Enhanced Cooling Infrared Thermography), phase-change enhanced cooling was used, which significantly amplifies the effect of air flow (infiltration and exfiltration). This heat transfer method worked extremely well to identify infiltration and exfiltration locations with high accuracy and increased throughput. The PECIT technique was systematically developed and tested for through holes with diameters 1 mm to 2 mm, and diagonal lines of 0.5 mm width at different camera-wall distances of 46 cm to 200 cm, under different pressure differences from 5 Pa to 20 Pa, and under different wind conditions. The PECIT technique had either met or exceeded the goals proposed in the project. For exfiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa (proposed one: 50 Pa with stretch goal of 15 Pa). For infiltration, we achieved >90% accuracy under a much lower pressure difference of 10 Pa (proposed one: 50 Pa with stretch goal of 15Pa). For exfiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa. For infiltration, we achieved 100% accuracy under a much lower pressure difference of 10 Pa. The PECIT technique can reach a throughput of 120 m2/h, which is 4 times the proposed goal for the laser line-scanning and simultaneous infrared temperature imaging approach. For commercialization and market penetration, we had meetings with two companies for feedback collection and further improvement for practical use. Also, we have interacted with Office of Intellectual Property and Technology Transfer of Iowa State University for idea disclosure and patent application.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2015

Phage phenomics: Physiological approaches to characterize novel viral proteins

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Phage phenomics: Physiological approaches to characterize novel viral proteins

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

ARM-Related Unmanned Aerial System (UAS) and Tethered Balloon System (TBS) Operational Requirements and Approval

This procedure addresses the requirements and process for obtaining approval for Unmanned Aerial System (UAS) and Tethered Balloon System (TBS) operations at DOE Office of Science (SC) Atmospheric Radiation Measurement user facility observatories (ARM sites), ARM-supported training flights, atmospheric instrument development flights, and campaigns at non-ARM sites. ARM sites include both ARM observatories and ARM mobile facility deployments. The protection of people, property, and the environment during UAS and TBS operations is the foundation of executing a successful mission using UAS or TBS. This procedure is designed to facilitate safe mission execution. It does not address obtaining approval for ARM-supported research, which is approved through the ARM Field Campaign (AFC) or Engineering Evaluation (EE) processes. Approval of UAS and TBS operations is a prerequisite for final approval of an AFC or EE by the Infrastructure Management Board (IMB) and may be conducted in parallel with preparation and submittal of the AFC or EE proposal to the IMB. This procedure addresses UAS and TBS requirements; mission planning; documentation; maintenance; risk assessment; airworthiness determination; operation approval; training and qualification requirements and responsibilities for UAS remote pilots; TBS operators; visual observers; maintenance technicians; and A&P mechanics. It also addresses the responsibilities of ARM site managers, the Office of Science Aviation Safety Manager, principal investigators, requesting organizations, and Range Safety Officers. This procedure is derived from DOE O 440.2C, Aviation Management and Safety, and Federal Aviation Administration (FAA) Regulations (FARs), 14 CFR 107, and 14 CFR 101. It contains two sections: Section 3.0 addresses UAS operations; Section 4.0 addresses TBS operations.

unmanned aerial systems, tethered balloon systems,↗

DOE OSTI2019

Exploration and Analysis of Legacy Data at the Hanford Site Using PHOENIX - 19044

Radioactive contaminants pose risks to human health and the environment. These risks are influenced by factors such as disposal/release and transport mechanisms, location in the environment, potential exposure receptors, and the presence of comingled contaminants. Understanding the behavior, transport, and distribution of radionuclides in the environment is essential to facilitating risk-informed decision-making related to remedial design, action, and monitoring. These decisions are based on significant amounts of complex data that must be accessed, integrated, and analyzed to effectively evaluate data and formulate appropriate conclusions and recommendations. Often, data volume, complexity, and legacy access issues pose severe challenges for analysts, regulators, and stakeholders interested in evaluating scientific data to support decision-making. To address these challenges at the U.S. Department of Energy Hanford Site, Pacific Northwest National Laboratory (PNNL) has developed PHOENIX (PNNL-Hanford Online Environmental Information exchange) to facilitate risk-informed decision-making by streamlining investigative and analytical processes through the integration and visualization of previously isolated datasets created under distinct regulatory or operational regimes, each serving a specific purpose. With the large volume of data dispersed across many Hanford environmental databases, finding the correct sources of relevant data, accessing them, and relating them in a meaningful way can prove challenging and time consuming. By analyzing Hanford databases, performing substantial optimization using modern data processing methods and developing extensive queries on the refactored data, PHOENIX enables users to access, integrate, display, visualize, and retrieve data that would have been historically unfeasible to examine. The data and information accessible through PHOENIX help inform remediation-related assessments and evaluations, predict and quantify the risks that radioactive and chemical contaminants pose to human health and the environment, and communicate this information to decision makers responsible for risk-based remediation actions. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2014

Evaluation methodology for comparing memory and communication of analytic processes in visual analytics

Provenance tools can help capture and represent the history of analytic processes. In addition to supporting analytic performance, provenance tools can be used to support memory of the process and communication of the steps to others. Objective evaluation methods are needed to evaluate how well provenance tools support analyst s memory and communication of analytic processes. In this paper, we present several methods for the evaluation of process memory, and we discuss the advantages and limitations of each. We discuss methods for determining a baseline process for comparison, and we describe various methods that can be used to elicit process recall, step ordering, and time estimations. Additionally, we discuss methods for conducting quantitative and qualitative analyses of process memory. By organizing possible memory evaluation methods and providing a meta-analysis of the potential benefits and drawbacks of different approaches, this paper can inform study design and encourage objective evaluation of process memory and communication.

Ragan, Eric D↗

DOE OSTI2022

The Circular Economy Life Cycle Assessment and Visualization Framework: A Multistate Case Study of Wind Blade Circularity in United States

A circular economy (CE) aims to decouple human activities from economic activities and resource use, and its overall goal is reducing or avoiding negative environmental externalities. The newly developed Circular Economy Lifecycle Assessment and Visualization (CELAVI) framework simulates changes in supply chain environmental impacts as it transitions toward circularity. This study expands CELAVI by incorporating detailed spatial resolution and real-world road routes connecting all facilities within the system. The case study on end-of-life decision making of wind turbine blades in the states of Iowa and Missouri explores how supply chain circularity and environmental impacts are affected by pathway costs and level of wind turbine installations. It demonstrates how high circularity costs might be beneficial for circularity transitions given revenue generated from circular pathways. Finally, impacts have important contributions to the supply chain design and thus show the importance of including detailed spatial resolution in CELAVI and CE studies in general.

circular economy↗

DOE OSTI2019

Development and diagnosis of an atmospheric pressure plasma torch for investigating magnetohydrodynamic instabilities

The development and diagnosis of an atmospheric pressure, non-transferred, DC arc plasma torch for investigating magnetohydrodynamic experiments is presented. Utilizing a custom AC starter circuit coupled with a high power DC power supply a long, laminar plasma jet was successfully generated by adjusting voltage and current characteristics, gas flow rates, and torch geometry (nozzle diameter and length). A complete and detailed description of the design and operation conditions of our torch is presented such that our results may be reproduced. Utilizing copper, aluminum, and tungsten alloy electrode components in conjunction with an electrically isolated water cooling system allows for continuous torch operation. The 50 kV AC starter circuit is coupled with a 15 kW DC power supply via a series injection transformer as a part of the custom arc starter circuit components. Axial and tangential gas flow, with nitrogen as the working gas, is regulated to generate a stable, laminar, atmospheric plasma torch with a jet length of over 80 cm under ideal operating conditions. Here, to visualize the plasma interface in magnetohydrodynamics experiments, a technique was developed to image the cylindrical plasma jet in both the R-Z plane (axial) and R-θ plane (cross sectional) using planar-laser Mie scattering from particles added to the surrounding gas. Plasma emission wavelengths are filtered out allowing scattered light from the particle laden-flow field illuminated at 532 nm by an Nd:YAG laser, to be isolated. Plasma electron temperature and degree of ionization were estimated using a technique based on the well-known Fowler–Milne spectroscopic method. Electron temperatures of up to 14 000 K and degree of ionization up to 27% at the torch exit were obtained.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2015

WE-EF-BRA-03: Catheter- Free Ablation with External Photon Radiation: Treatment Planning, Delivery Considerations, and Correlation of Effects with Delivered Dose

Purpose: To plan, target, and calculate delivered dose in atrioventricular node (AVN) ablation with volume-modulated arc therapy (VMAT) in an intact porcine model. Methods: Seven pigs underwent AVN irradiation, with prescription doses ranging between 25 and 55Gy in a single fraction. Cardiac CT scans were acquired at expiration. Two physicians contoured AVN targets on 10 phases, providing estimates of target motion and inter-physician variability. Treatment planning was conducted on a static phase-averaged CT. The volume designated to receive prescription dose covered the full extent of AVN cardiac motion, expanded by 4mm for setup uncertainty. Optimization limited doses to risk structures according to single-fraction tumor treatment protocols. Orthogonal kV images were used to align bony anatomy at time of treatment. Localization was further refined with respiratory-gated cone-beam CT, and range of cardiac motion was verified under fluoroscopy. Beam delivery was respiratory-gated for expiration with a mean efficiency of 60%. Deformable registration of the 10 cardiac CT phases was used to calculate actual delivered dose for comparison to electro-anatomical and visually evident lesions. Results: The mean [minimum,maximum] amplitude of AVN cardiac motion was LR 2.9 [1.7,3.9]mm, AP 6.6 [4.4,10.4]mm, and SI 5.6 [2.0,9.9]mm. Incorporating cardiac motion into the dose calculation showed the volume receiving full dose was 40–80% of the volume indicated on the static planning image, although the contoured AVN target received full dose in all animals. Initial results suggest the dimensions of the electro-anatomical lesion are correlated with the 40Gy isodose volume. Conclusion: Image-guidance techniques allow for accurate and precise delivery of VMAT for catheter-free arrhythmia ablation. An arsenal of advanced radiation planning, dose optimization, and image-guided delivery techniques was employed to assess and mitigate effects of cardiac and respiratory motion. Feasibility of delivery to the pulmonary veins and left ventricular myocardium will be investigated in future studies. D. Packer Disclosures: Abiomed, Biosense Webster, Inc., Boston Scientific Corp., CardioFocus, Inc., Johnson and Johnson, Excerpta Medica, Ortho-McNeil-Jannsen, Sanofi Aventis, CardioInsight Technologies, InfoBionic, SIEMENS, Medtronic, Inc., CardioDx, Inc., CardioInsight Technologies, FoxP2 Medica, Mediasphere Medical, Wiley-Blackwell, St. Jude Medical, Endosense, Thermedical, EP Advocate LLC, Hansen Medical, American Heart Association, EpiEP, NIH.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2013

Testbed Environment for Space Situational Awareness: The world’s most accurate simulation of space debris and orbital object tracking

The Testbed Environment for Space Situational Awareness (TESSA) is a modeling and simulation environment designed for efficient exploration of scenarios involving satellites and space debris and their detection by both ground and space-based radars and optical sensors. TESSA is a Parallelized Discrete Event Simulator optimized for deployment on a large cluster of high-performance computers running Linux. TESSA includes capabilities for predicting the future location of a satellite using the satellite’s current location and velocity, determining an object’s orbit from sensor data, finding new orbital objects, predicting close approaches, determining the probability of collisions, modeling radar and optical and dynamic sensors, and modeling the generation of debris. TESSA also includes a scalable visualization environment implemented as a post-processor on workstation-class platforms.

42 ENGINEERING↗

DOE OSTI2016

Echo™ User Manual

Echo™ is a MATLAB-based software package designed for robust and scalable analysis of complex data workflows. An alternative to tedious, error-prone conventional processes, Echo is based on three transformative principles for data analysis: self-describing data, name-based indexing, and dynamic resource allocation. The software takes an object-oriented approach to data analysis, intimately connecting measurement data with associated metadata. Echo operations in an analysis workflow automatically track and merge metadata and computation parameters to provide a complete history of the process used to generate final results, while automated figure and report generation tools eliminate the potential to mislabel those results. History reporting and visualization methods provide straightforward auditability of analysis processes. Furthermore, name-based indexing on metadata greatly improves code readability for analyst collaboration and reduces opportunities for errors to occur. Echo efficiently manages large data sets using a framework that seamlessly allocates resources such that only the necessary computations to produce a given result are executed. Echo provides a versatile and extensible framework, allowing advanced users to add their own tools and data classes tailored to their own specific needs. Applying these transformative principles and powerful features, Echo greatly improves analyst efficiency and quality of results in many application areas.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

Rheo-Structural Spectroscopy: Fingerprinting the In Situ Response of Fluids to Arbitrary Flow Fields

The objectives of this project were to develop new sample environments, measurement methodologies and associated modeling tools for characterizing the structural response to arbitrarily complex processing flows using small angle scattering, and to apply these new tools for understanding the fundamental physics governing the structuring of anisotropic particulate and polymeric materials under flow histories and conditions relevant to industrial processing flows. The research resulted in the development and implementation of a new sample environment, the fluidic four roll mill (FFoRM), for in situ small angle neutron and X-ray scattering (SANS/SAXS) measurements. These measurements are capable of generating large data sets that “fingerprint” how a complex fluid responds to a wide range of flow histories involving time variations in deformation type and rate. New modeling tools were developed to extract detailed microstructural information from such data sets, including orientation distribution functions and interparticle correlation functions, as well as reduced-order parametric descriptors of these high-dimensional functions that can be used to readily map, visualize and interpret a fluid’s structural response to its flow history. These new tools were applied to a range of model materials involving elongated particle suspensions in order to provide new insights into the physics of how flow couples with orientational and structural order in complex flows, particularly under non-dilute conditions for which no accurate theories currently exist. Using these investigations, we elucidated a number of new insights into the fundamental phenomena driving such process-structure-property relationships. These findings provide guidance for the further development of rheological models, and ultimately can inform the rational and model-based design of flow processes to achieve optimized orientational ordering that is key to the properties and function of a wide range of energy-relevant materials.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Adaptive Cognitive Mechanisms to Maintain Calibrated Trust and Reliance in Automation

Trust calibration for a human–machine team is the process by which a human adjusts their expectations of the automation’s reliability and trustworthiness; adaptive support for trust calibration is needed to engender appropriate reliance on automation. Herein, we leverage an instance-based learning ACT-R cognitive model of decisions to obtain and rely on an automated assistant for visual search in a UAV interface. This cognitive model matches well with the human predictive power statistics measuring reliance decisions; we obtain from the model an internal estimate of automation reliability that mirrors human subjective ratings. The model is able to predict the effect of various potential disruptions, such as environmental changes or particular classes of adversarial intrusions on human trust in automation. Finally, we consider the use of model predictions to improve automation transparency that account for human cognitive biases in order to optimize the bidirectional interaction between human and machine through supporting trust calibration. The implications of our findings for the design of reliable and trustworthy automation are discussed.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

The Circular Economy Lifecycle Assessment and Visualization Framework - CELAVI

A circular economy (CE) aims to decouple human activities from economic growth and resource use, and its overall goal is reducing or avoiding negative environmental externalities. The newly developed Circular Economy Lifecycle Assessment and Visualization (CELAVI) framework simulates changes in supply chain environmental impacts as it transitions toward circularity. This study expands CELAVI by incorporating detailed spatial resolution and real-world road routes connecting all facilities within the system. The case study on end-of-life decision making of wind turbine blades in the states of Iowa and Missouri explores how supply chain circularity and environmental impacts are affected by pathway costs and level of wind turbine installations. It demonstrates how high circularity costs might be beneficial for circularity transitions given revenue generated from circular pathways. Finally, impacts have important contributions to the supply chain design and thus show the importance of including detailed spatial resolution in CELAVI and CE studies in general.

circular economy↗

DOE OSTI2022

Solar Decathlon Celebrates 20 Years of Building Impact

The U.S. Department of Energy Solar Decathlon® is a collegiate competition that has inspired students worldwide to enter the clean energy workforce since its inception. Celebrating its 20th anniversary in 2022, the Solar Decathlon has challenged more than 25,000 students to create efficient, affordable buildings powered by renewables, while promoting student innovation, STEM education, and workforce development opportunities in the buildings industry. Compelling graphics, videos, and visuals are being developed to launch a 20th anniversary campaign in January 2022. These graphics include an interactive 20th anniversary infographic, a "Solar Decathlon - By the Numbers" video, and a graphic highlighting the diverse group of more than 25,000 past participants. In presenting these graphics at the ACEEE summer 2022 panel, attendees will be exposed to the latest communications techniques to apply to their own work. The Solar Decathlon invests in compelling visuals to recruit and inspire an imaginative and diverse group of participants each year - something that organizations of all sizes in the energy efficiency sector also need to do as they recruit for new talent. The Virtual Village of the 2020 Build Challenge homes (with more than 11,000 unique views) and the map of past competition houses highlight the competition's emphasis on multimedia that connects with competitors and the general public. Using more than 4,400 publicly available photos, including engaging virtual event snapshots with Department of Energy leaders, the Solar Decathlon captures the innovate ideas of the Build Challenge and Design Challenge teams in a way that everyone can understand.

collegiate competition↗

DOE OSTI2023

In Situ Visualization of the Pinning Effect of Planar Defects on Li Ion Insertion

Longevity of Li ion batteries strongly depends on the interaction of transporting Li ions in electrode crystals with defects. However, detailed interactions between the Li ion flux and structural defects in the host crystal remain obscure due to the transient nature of such interactions. Here, by in situ transmission electron microscopy and density function theory calculations, we reveal how the diffusion pathways and transport kinetics of a Li ion can be affected by planar defects in a tungsten trioxide lattice. We uncover that changes in charge distribution and lattice spacing along the planar defects disrupt the continuity of ion conduction channels and dramatically increase the energy barrier of Li diffusion, thus, arresting Li ions at the defect sites and twisting the lithiation front. In conclusion, the atomic-scale understanding holds critical implications for rational interface design in solid-state batteries and solid oxide fuel cells.

25 ENERGY STORAGE↗