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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

AlgaeOrtho, a bioinformatics tool for processing ortholog inference results in algae

Introduction: Microalgae constitute a prominent feedstock for producing biofuels and biochemicals by virtue of their prolific reproduction, high bioproduct accumulation, and the ability to grow in brackish and saline water. However, naturally occurring wild type algal strains are rarely optimal for industrial use; therefore, bioengineering of algae is necessary to generate superior performing strains that can address production challenges in industrial settings, particularly the bioenergy and bioproduct sectors. One of the crucial steps in this process is deciding on a bioengineering target: namely, which gene/protein to differentially express. These targets are often orthologs which are defined as genes/proteins originating from a common ancestor in divergent species. Although bioinformatics tools for the identification of protein orthologs already exist, processing the output from such tools is nontrivial, especially for a researcher with little or no bioinformatics experience. Methods: The present study introduces AlgaeOrtho, a user-friendly tool that builds upon the SonicParanoid orthology inference tool (based on an algorithm that identifies potential protein orthologs based on amino acid sequences) and the PhycoCosm database from JGI (Joint Genome Institute) to help researchers identify orthologs of their proteins of interest in multiple diverse algal species. Results: The output of this application includes a table of the putative orthologs of their protein of interest, a heatmap showing sequence similarity (%), and an unrooted tree of the putative protein orthologs. Notably, the tool would be instrumental in identifying novel bioengineering targets in different algal strains, including targets in not-fully annotated algal species, since it does not depend on existing protein annotations. We tested AlgaeOrtho using three case studies, for which orthologs of proteins relevant to bioengineering targets, were identified from diverse algal species, demonstrating its ease of use and utility for bioengineering researchers. Discussion: This tool is unique in the protein ortholog identification space as it can visualize putative orthologs, as desired by the user, across several algal species.

09 BIOMASS FUELS↗
DOE OSTI2025

Leveraging public AI tools to explore systems biology resources in mathematical modeling

Predictive mathematical modeling is an essential part of systems biology and is interconnected with information management. Systems biology information is often stored in specialized formats to facilitate data storage and analysis. These formats are not designed for easy human readability and thus require specialized software to visualize and interpret results. Therefore, comprehending modeling and underlying networks and pathways is contingent on mastering systems biology tools, which is particularly challenging for users with no or little background in data science or system biology. To address this challenge, we investigated the usage of public Artificial Intelligence (AI) tools in exploring systems biology resources in mathematical modeling. We tested public AI’s understanding of mathematics in models, related systems biology data, and the complexity of model structures. Our approach can enhance the accessibility of systems biology for non-system biologists and help them understand systems biology without a deep learning curve.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

SARS-CoV-2 wastewater variant surveillance: pandemic response leveraging FDA’s GenomeTrakr network

ABSTRACT Wastewater surveillance has emerged as a crucial public health tool for population-level pathogen surveillance. Supported by funding from the American Rescue Plan Act of 2021, the FDA‘s genomic epidemiology program, GenomeTrakr, was leveraged to sequence SARS-CoV-2 from wastewater sites across the United States. This initiative required the evaluation, optimization, development, and publication of new methods and analytical tools spanning sample collection through variant analyses. Version-controlled protocols for each step of the process were developed and published on protocols.io. A custom data analysis tool and a publicly accessible dashboard were built to facilitate real-time visualization of the collected data, focusing on the relative abundance of SARS-CoV-2 variants and sub-lineages across different samples and sites throughout the project. From September 2021 through June 2023, a total of 3,389 wastewater samples were collected, with 2,517 undergoing sequencing and submission to NCBI under the umbrella BioProject,PRJNA757291. Sequence data were released with explicit quality control (QC) tags on all sequence records, communicating our confidence in the quality of data. Variant analysis revealed wide circulation of Delta in the fall of 2021 and captured the sweep of Omicron and subsequent diversification of this lineage through the end of the sampling period. This project successfully achieved two important goals for the FDA’s GenomeTrakr program: first, contributing timely genomic data for the SARS-CoV-2 pandemic response, and second, establishing both capacity and best practices for culture-independent, population-level environmental surveillance for other pathogens of interest to the FDA. IMPORTANCE This paper serves two primary objectives. First, it summarizes the genomic and contextual data collected during a Covid-19 pandemic response project, which utilized the FDA’s laboratory network, traditionally employed for sequencing foodborne pathogens, for sequencing SARS-CoV-2 from wastewater samples. Second, it outlines best practices for gathering and organizing population-level next generation sequencing (NGS) data collected for culture-free, surveillance of pathogens sourced from environmental samples.

Microbiology↗
DOE OSTI2024

An open-source data storage and visualization platform for collaborative qubit control

Developing collaborative research platforms for quantum bit control is crucial for driving innovation in the field, as they enable the exchange of ideas, data, and implementation to achieve more impactful outcomes. Furthermore, considering the high costs associated with quantum experimental setups, collaborative environments are vital for maximizing resource utilization efficiently. However, the lack of dedicated data management platforms presents a significant obstacle to progress, highlighting the necessity for essential assistive tools tailored for this purpose. Current qubit control systems are unable to handle complicated management of extensive calibration data and do not support effectively visualizing intricate quantum experiment outcomes. In this paper, we introduce Qubit Control Storage and Visualization ( QubiCSV ), a platform specifically designed to meet the demands of quantum computing research, focusing on the storage and analysis of calibration and characterization data in qubit control systems. As an open-source tool, QubiCSV facilitates efficient data management of quantum computing, providing data versioning capabilities for data storage and allowing researchers and programmers to interact with qubits in real time. The insightful visualization are developed to interpret complex quantum experiments and optimize qubit performance. QubiCSV not only streamlines the handling of qubit control system data but also improves the user experience with intuitive visualization features, making it a valuable asset for researchers in the quantum computing domain.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Peregrine Software Development: Report on the Code Conversion From Python to C++

This work package seeks to convert the Peregrine software tool from its original Python implementation to a production version based on the C++ language. Peregrine is a powerful research platform with a multitude of advanced data analytics and data visualization functionalities. Developed by scientists to explore multimodal and multidimensional data related to the production of components using powder bed additive manufacturing processes, the tool implements state-of-the-art algorithms to assist machine users in making build or part quality determinations. Given that Peregrine is data-intensive, the goal of this conversion is to enhance the tool’s flexibility and interactivity and reduce the number of code dependencies to facilitate its deployment as part of the ongoing technology transfer campaign. This brief document provides an overview of Peregrine’s functionalities and capabilities, along with a detailed description of the core functionalities that have been implemented to date in the new C++ version. This document serves as a development update at the end of the first year of the ongoing conversion and will be regularly updated as progress continues.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Visualization for Insight and Data Analysis in Energy Research

This talk explores how advanced visualization technologies are transforming analytical reasoning and knowledge discovery in energy research, drawing on recent work at the National Laboratory of the Rockies' Computational Science Center. Through a series of scientific case studies, we demonstrate how immersive and high-resolution visualization environments enable scientists and engineers to identify previously unseen patterns and features - insights that often remain hidden in traditional desktop-based analysis. By embedding richer information into interactive analytics tools, these approaches support the exploration of complex, multivariate parameter spaces, where interaction itself catalyzes understanding. Beyond capability, we emphasize the critical role of visualization design grounded in perception and cognition, showing how visual encodings directly influence analytical outcomes. Spanning applications from materials science to integrated energy systems, these visualization approaches accelerate innovation and improve decision-making by enabling deeper, more reliable insight into increasingly complex energy data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

elm-diagnostics

elm-diagnostics is a Python package for computing diagnostic analyses and visualizations for the E3SM Land Model (ELM) component and is meant to support new feature development in ELM. The tool reads model history files and performs quantitative analyses including budget-closure checking, variable transformations, temporal aggregations, and statistical summaries to support model evaluation, validation, and scientific interpretation. The framework is designed for extensibility, with modular architecture enabling straightforward addition of new diagnostic methods, derived variables, analysis types, visualization approaches, and model-specific adaptations

Hoffman, Matt [Los Alamos National Laboratory]↗
DOE OSTI2025

Direction of impact for explainable risk assessment modeling

Abstract Several graphical indicators have been recently introduced to help analysts visualize the marginal effects of inputs in complex models. The insights derived from such tools may help decision‐makers and risk analysts in designing interventions. However, we know little about the adequacy and consistency of different indicators. This work investigates popular marginal effect indicators to understand whether they yield indications consistent with the properties of the quantitative model under inspection. Specifically, we examine the notions of monotonicity, Lipschitz, and concavity consistency. Surprisingly, only PD functions satisfy all these notions of consistency. However, when selecting the indicators, in addition to consistency, analysts need to consider the risk of model extrapolation. For situations where such risk is under control, we utilize individual conditional expectations together with PD plots. Two applications, on a NASA space risk assessment model and a susceptible exposed infected recovered (SEIR) model for the COVID‐19 pandemic illustrate the insights obtained from these indicators.

Mathematical Methods In Social Sciences↗
DOE OSTI2024

Cyber100 Compass [SWR 23-64]

Cyber100 Compass ("Compass") is a unique risk assessment framework that will enable grid system planners to understand and mitigate cybersecurity risk for grids transitioning to high levels of renewable generation, including 100%. The idea for Compass was developed by NREL based on past work on high-renewable grids and a series of discussions with DOE. Compass is part of Cyber100, a portfolio of proposed research activities that would greatly expand understanding of cybersecurity for high-renewable grids. Compass is a desktop application designed with a user-friendly interface. The tool gathers information from users, conducts probabilistic backend calculations, and outputs a series of visualizations to help users understand and analyze their cybersecurity risks based on the unique features of their future grid. Compass will take as inputs the values for different conditions and produce a risk score of the resulting grid. By trying different configurations, system planners can compare the resultant risks against their own risk tolerance and decide which system-of-system controls to implement as they transition toward a 100% renewable grid.

Martin, Maurice↗
DOE OSTI2024

Muon Detector Visualization in Unreal Engine

This presentation will describe recent efforts to visualize muon collider detector geometries and col- lision events with modern 3D game development tools, particularly Unreal Engine 5. The workflow from HEP-specific tools to industry standard formats will be described, and an interactive demo will be available.

Lee, Lawrence↗
DOE OSTI2024

Some Tools for Blind Physicst

Being blind, as with any disability, brings with it a whole host of challenges. There are not that many people who are visually impaired working in high energy physics. This talk attempts to look at the intersection of those two worlds. It will explore some of the struggles of doing work in this field while being blind -- looking at both the physical challenges as well as the structural and institutional. It will go through the differences in perspective that something like that can bring. As well as taking a gander through some of the tools, technologies and techniques that exist to mitigate those issues; many of which come from the most unexpected sources. It is a humble attempt to raise awareness of these issues in order to make the pursuit of scientific research more accessible to more people who may wish to engage in it.

Neogi, Orgho Anoronyo↗
DOE OSTI2026

A standardized workflow for kinetic metabolic model curation and dissemination

Kinetic metabolic models provide invaluable insights into cellular metabolism, supporting applications in synthetic biology, metabolic engineering, and systems biology. However, reproducibility and utility of these models hinge on clear and rigorous documentation, standardized annotation, and accessible visualization. This paper presents a workflow for building, annotating, visualizing, and sharing kinetic metabolic models. Our method integrates community standards and open-source tools to ensure reproducibility, interoperability, and user accessibility. This procedure enables researchers to produce reusable and well-documented kinetic models, advancing their role as powerful tools in metabolic research.

Cook, Margaret [Univ. of Washington, Seattle, WA (↗
DOE OSTI2024

Quantitative Description and Correction of Longitudinal Drifts in the Fermilab Linac

The Fermilab Linac accepts the 0.75 MeV H- ions from the front end and accelerates them to 400 MeV for injection into the Booster. Day-to-day drifts of the longitudinal trajectory in the Linac, reconstructed from phase readings of Beam Position Monitors, are at the level of several degrees. They are believed to cause additional losses both in the Linac and Booster, and are addressed by empirically adjusting the phases of Linac cavities. This work explores the option of expressing these drifts in terms of phase shifts in two cavities at the low-energy part of the Linac. Such description allows for a simplified visual representation of the drifts, suggest a clear algorithm for their compensation, and provides a tool for estimating efficiency of such compensation.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Cost and Performance Baseline for Fossil Energy Plants – Volume 1: Bituminous Coal and Natural Gas to Electricity: May 2025

This presentation at EPRI's annual Generation Sector Meeting during the Advanced Generation and Carbon Capture and Storage session provides an overview of the recently published Cost and Performance Baseline for Fossil Energy Plants – Volume 1: Bituminous Coal and Natural Gas to Electricity dated May 2025. It further connects viewers with the recently released tool/dashboard, an interactive tool that allows users to manipulate six key study parameters simultaneously for each case and visualize the impact on three metrics: 1) levelized cost of electricity (LCOE), 2) cost of CO2 captured (CCC), and 3) cost of CO2 avoided (CCA).

baseline study↗
DOE OSTI2025

Floating Wind Array Ontology and Modeling Framework

While there are many tools for designing and modeling a single floating turbine, array level design and modeling has much more to consider. Designing floating wind arrays requires a coupled approach considering many variables, from bathymetry to installation and maintenance to failure and risk analysis. With all of these considerations, an array-level modeling tool is needed to quickly evaluate array designs. The Floating Array Model (FAModel) tool developed at the National Renewable Energy Laboratory was created to fill this gap in low-fidelity array modeling. FAModel is a python framework created to streamline holistic low-fidelity floating wind modeling for array-level analysis. FAModel integrates site data and models with a variety of open-source modeling tools developed by NREL, including FLORIS, RAFT, MoorPy, and anchor capacity models. The integration of these tools allows users to quickly and holistically design an array by considering forces, area analysis, visualization, annual energy production, failure modeling, and component costs.

17 WIND ENERGY↗
DOE OSTI2024

Quantitative description and correction of longitudinal drifts in the Fermilab linac

The Fermi National Accelerator Laboratory (Fermilab) Linac accepts 750 keV H- ions from the front end and accelerates them to 400 MeV for injection into the Booster rapid cycling synchrotron. Day-to-day drifts in the beam longitudinal trajectory during regular operation are of the order of several degrees. They are believed to cause additional losses in both the Linac and the Booster and are addressed by empirically adjusting cavity phases of front end and Linac RF cavities. This work explores a scheme for expressing these drifts in terms of phase shifts in the low-energy part of the Linac. Such a description allows for a simplified visual representation of the drifts, suggests a clear algorithm for their compensation, and provides a tool for estimating efficiency of such compensation.

43 PARTICLE ACCELERATORS↗
DOE OSTI2025

Evaluating FRI3D for Cost Savings in Fire Hazard Analysis at DOE Sites

A fire hazard analysis, required for many U.S. Department of Energy (DOE) facilities, is a complex, cumbersome, and costly process. Fire hazard analyses may be viewed as a checkbox, but ideally and in spirit with the DOE-STD-1066, the fire hazard analysis (FHA) should be a part of the workflow and used to help in modifications, maintenance, and improving operational safety. With current FHA development processes, it is both time and cost prohibitive for true integration. A tool called Fire Risk Investigation in 3D or FRI3D was developed under the DOE Light Water Reactor Sustainability program to simplify and automate many aspects of a fire probabilistic risk analysis for existing nuclear power plants. The FRI3D tool automates fire scenarios by combining approved fire simulation codes, U.S. Nuclear Regulatory Commission fire calculations methods, 3D modeling and visualization, and probabilistic risk analysis models into a single workflow supported with a user interface. FRI3D was initially designed for used in combination with a PRA, this case study, evaluated using FRI3D for a plant modification, determined the benefits that detailed fire modeling can have for U.S. Department of Energy facilities with or without a PRA model. It also looked at what tasks from DOE requirements could be reduced using the tool and what is needed to integrate fire hazard analysis into site workflow.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Approach for energy efficient building design during early phase of design process

Energy consumption in the building sector is about 40% of total energy consumed globally and is trending upwards, along with its contribution to greenhouse gas (GHG) emissions. Given the adverse impacts of GHG emissions, it is crucial to integrate energy efficiency into building designs. The most significant opportunities for enhancing energy performance are present during the initial phases of building design, when there is less impact of other design constraints. Various tools exist for simulating different design options and providing feedback in terms of energy consumption and comfort parameters. These simulation outputs must then be analyzed to derive design solutions. This paper presents an innovative approach that utilizes user input parameters, processes them through cloud computing, and outputs easily understandable strategies for energy-efficient building design. The methodology employs Asynchronous Distributed Task Queues (DTQ) - a more scalable and reliable alternative to conventional speedup techniques-for conducting parametric energy simulations in the cloud. The goal of this approach is to assist design teams in identifying, visualizing, and prioritizing energy-saving design strategies from a range of possible solutions for each project. Furthermore, a tool ‘eDOT’ has been developed utilizing the discussed methodology. Unlike existing tools, eDOT leverages artificial intelligence to dynamically generate and provide design strategies during the early phases of design process. By simplifying the simulation process, eDOT enables design teams to make informed, data-driven decisions without needing to interpret complex simulation outputs. A case study simulated for two locations is provided in this paper to demonstrate the effectiveness of eDOT, further underscoring its practical impact on energy-efficient building design.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗