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At least 955 records · Page 53

All sources NASA NTRS DOE OSTI

DOE OSTI2019

Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Cybersecurity Vulnerability Mitigation Framework through Empirical Paradigm (CyFEr): Prioritized Gap Analysis

Cybersecurity vulnerability assessment tools, frameworks, methodologies, and processes are commonly used to understand the cybersecurity maturity and posture of a system or a facility. Although, those tools are strictly developed based on standards defined by organizations such as the National Institute of Standards and Technology (NIST) and the U.S. Department of Energy, the majority of these tools and frameworks do not provide a platform to prioritize the requirements to reach a desired cybersecurity maturity. To address that challenge, we have been developing a framework and a software application called the cybersecurity vulnerability mitigation framework through empirical paradigm (CyFEr). The efficacy of CyFEr was evaluated by implementing it on the NIST Cybersecurity Framework (CSF). This paper provides a detailed architecture of CyFEr and demonstrates its application to CSF by testing against a real-world cyber-attack that targeted industrial control systems in a critical infrastructure facility.

Gourisetti, Sri Nikhil G.↗

DOE OSTI2017

PLEXOS Input Data Generator

The PLEXOS Input Data Generator (PIDG) is a tool that enables PLEXOS users to better version their data, automate data processing, collaborate in developing inputs, and transfer data between different production cost modeling and other power systems analysis software. PIDG can process data that is in a generalized format from multiple input sources, including CSV files, PostgreSQL databases, and PSS/E .raw files and write it to an Excel file that can be imported into PLEXOS with only limited manual intervention.

Source record↗

DOE OSTI2014

Methodology for Sensitivity and Uncertainty-Based Criticality Safety Validation

Monte Carlo radiation transport software is used extensively for determining the effective multiplication factor k of fissionable systems towards assessing the criticality safety of operations. Understanding the predictive capability of the Monte Carlo software and nuclear data libraries for calculations of specific applications is vital towards making these assessments. Recently, sensitivity and uncertainty (S/U) methods have been developed for this purpose. A computational tool has been developed that uses the S/U methods with MCNP6 to select critical experiment benchmarks that have similar sources of computational bias, and extreme value theory is then used to determine suitable and conservative calculational margins. The S/U techniques are then used to perform nuclear data adjustments, which are then used to determine a suitable margin of subcriticality from cross section uncertainties. This document gives an overview of the theory of S/U methods used for criticality safety validation. First an overview is given for using the sensitivity coefficients and nuclear co variance data towards determining neutronic similarity factors is then discussed. Next, the extreme value theory (EVT) to determine a calculational margin is given along with how the similarity factors are used in the analysis. Then, the Generalized Linear Least Squares (GLLS) method for performing data adjustment and how that method is used to reject benchmarks and compute adjusted nuclear data uncertainties in k are discussed. Last, a discussion of the margin of subcriticality is given along with how to apply of the GLLS data adjustment methods to quantify the effect of nuclear data variability on k.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2017

PLEXOS Input Data Generator

Source record↗

DOE OSTI2019

The Next Generation System Analysis Model: Capabilities for Simulating a Waste Management System - 19131

The U.S. Department of Energy (DOE) Office of Nuclear Energy Office of Spent Fuel and Waste Disposition's Integrated Waste Management System (IWMS) program is applying integrated waste management system architecture analysis, system engineering, and decision analysis principles to inform potential future decisions regarding potential nuclear waste management system architectures. Architecture analyses of the IWMS are being conducted to support the future deployment of a comprehensive system for managing nuclear waste that considers all major aspects of the back end of the nuclear fuel cycle (i.e., transportation, storage, and disposal). The system architecture analyses consider alternative disposition pathways for commercial spent nuclear fuel (SNF) being stored dry in at-reactor Independent Spent Fuel Storage Installations (ISFSIs) or wet in spent-fuel pools. One method for evaluating these alternatives is simulating the movement of SNF throughout the system components. Successfully simulating a system on the scale of a national waste management system requires - accurate baseline information (e.g., historic fuel discharges from reactors and dry storage loadings at reactor sites), - modeling all logistic interactions between components of the proposed system, and - tracking and reporting all relevant details regarding the simulation's execution. The Next Generation System Analysis Model (NGSAM) is an agent-based simulation software tool designed for the express purpose of modeling the IWMS. It is based on the Performance Analysis Tool, a simulation platform that has been used to model logistics for the Department of Defense and the Federal Emergency Management Agency. Using existing, government-owned software allows NGSAM developers to modify the software at the level of source code and to develop flexible usability and modeling solutions for developing and running simulations of the IWMS. NGSAM imports data from the Oak Ridge National Laboratory (ORNL) Unified Database (e.g., historic assembly information, thermal profiles for assembly heat, at-reactor dry storage loadings) to ensure that the simulation initializes with a realistic representation of the state of commercial SNF in the United States. NGSAM is designed with the flexibility to model and track the behavior of virtually any IWMS architecture assumptions or design considerations. For example, NGSAM can model multiple interim storage facilities or repositories or none at all. Similarly, all assumptions regarding shipment schedules, operating schedules, and reactor operation assumptions can be modeled and adjusted in NGSAM with relative ease. The development of NGSAM was targeted to waste management system analysts as the primary users. With that in mind, analysts from ORNL, Sandia National Laboratories (SNL), and Argonne National Laboratory (ANL) were intimately involved in the development process. That involvement extended beyond merely defining requirements. System analysts have been involved with design decisions and software benchmarking and tests, and they have provided subject-matter expertise where necessary. The result is a high degree of interaction between professional software developers and system analysts, with a multitude of benefits to both groups. This paper explores some of the underlying methodology of the agile software development process used in the creation of NGSAM. It illustrates the capabilities of NGSAM. Some example use cases are discussed as well, with relevant results providing context for how NGSAM is used by system analysts to gain a greater understanding of alternative waste management system architectures. This is a technical paper that does not take into account the contractual limitations under the Standard Contract for Disposal of Spent Nuclear Fuel and/or High-Level Radioactive Waste (Standard Contract) (10 CFR Part 961). Under the provisions of the Standard Contract, DOE does not consider spent nuclear fuel in multi-assembly canisters to be an acceptable waste form, absent a mutually agreed-to contract amendment. To the extent discussions or recommendations in this paper conflict with the provisions of the Standard Contract, the Standard Contract provisions prevail. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2018

Extreme Heterogeneity 2018 - Productive Computational Science in the Era of Extreme Heterogeneity: Report for DOE ASCR Workshop on Extreme Heterogeneity

The 2018 Basic Research Needs Workshop on Extreme Heterogeneity identified five Priority Research Directions for realizing the capabilities needed to address the challenges posed in this era of rapid technological change. This report captures the outcomes of that workshop. In the context of extreme heterogeneity, it defines basic research needs and opportunities in computer science research to develop smart and trainable operating and runtime systems, programming environments, and predictive tools that will make future systems easier to adapt to scientists’ computing needs and easier for facilities to deploy securely.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Developing Multiphysics, Integrated, High-Fidelity, Massively Parallel Computational Capabilities for Fusion Applications Using MOOSE

As the need for fusion as a clean, sustainable, and abundant energy source grows internationally, so does the need for multiphysics, computational tools to model, study, and predict the complex interactions between plasma, materials, and engineering processes. These tools have a crucial role to play in solving scientific and engineering challenges and accelerating fusion energy deployment. To address these needs, modeling capabilities should enable massively parallel, multiphysics, fully integrated high-fidelity simulations of fusion systems. Additional attributes, such as being open source and modular while maintaining high software quality assurance standards will maximize impact by ensuring accessibility for all and wide acceptance, rapid expansion and development, as well as reliability, efficiency, and robustness. In this paper, we describe how the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, which has a track record of success in the fission space thanks to the attributes listed above, can be leveraged in the fusion energy field. We highlight key successes of the MOOSE application in the fission space and describe how MOOSE has been and is being applied to fusion applications in the United States---e.g., Tritium Migration Analysis Program, version 8 (TMAP8), MOOSE Fusion Module, Fusion ENergy Integrated multiphys-X (FENIX)---and the United Kingdom---e.g., AURORA, Achlys, Apollo. These efforts aim to establish a suite of tools that can be further extended to accelerate fusion energy deployment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2018

GHOST (Grid Hardware Open Source Testbed) [SWR-18-32]

The software was developed for the purpose of Microgrid Controller Procurement where multiple Microgrid Controller vendors were competing to prove the best performance. Each microgrid controller was connected to Real-Time Simulator (Opal-RT) where the Real-Time model of microgrid was simulated. Microgrid controllers were able to control most of the assets in the model. To be able to fairly compare controller's performance each controller was evaluated using exactly the same model, with the same initial conditions and exactly the same test sequence. The microgrid evaluation test sequence lasted 100 minutes and consist of various grid disturbances to which a microgrid controller must respond. The microgrid and power system will experience multiple types of disturbances while performing dispatch functions. Many functions are tested in grid-connected and islanded modes such as unexpended failures of generators, energy storage trip events, and large load fluctuations. The test sequence focuses on fault scenarios that cause the highest short-circuit fault current contribution; force a swing bus or generator capable of being a swing bus offline; cause the most reconfigurations; and cause conflicting objectives for the microgrid controller. During the test sequence execution multiple datapoints are being recorded and stored. During data postprocessing key performance parameters are extracted allowing quantitative comparison of performance on multiple aspects including: resiliency, fuel utilization, grid interconnection, ancillary services and power quality and eventually after summing all key performance parameters by comparing the overall result. To be able to perform such testing multiple tools had to be developed included in this repository including: - Real time model of microgrid (Urban-Banshee, Remote-smaller model) - Test sequence configuration tools - Test execution real-time scripts - Post processing scripts - Human Machine Interface software

Koralewicz, Przemyslaw↗

DOE OSTI2026

Super-resolution model for overlapping peak detection and improved spatial resolution in high-energy diffraction microscopy

Reconstruction quality in Far-field High-Energy Diffraction Microscopy (FF-HEDM) is limited by the spatial resolution of area detectors and the frequent occurrence of overlapping diffraction spots. To address these challenges, we developed a super-resolution (SR) framework using convolutional neural networks (CNNs) to recreate 2D diffraction peaks at up to ×8 resolution from raw detector data. A specialized simulation tool was created to generate synthetic training datasets with varying degrees of peak overlap. Integrated into the Microstructural Imaging using Diffraction Analysis Software (MIDAS), the SR model improves the spatial accuracy and precision of 3D grain reconstruction by an order of magnitude. This approach provides a robust solution for investigation of complex micromechanical states and material classes where the analysis is limited by the presence of overlapping peaks. Furthermore, the methodology developed here can potentially be extended to other techniques that require sub-pixel accuracy for high-fidelity data analysis.

High-energy diffraction microscopy↗

DOE OSTI2018

SSAGES: Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods, and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this study, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

iMicrobe: Tools and data-driven discovery platform for the microbiome sciences

Background: Scientists have amassed a wealth of microbiome datasets, making it possible to study microbes in biotic and abiotic systems on a population or planetary scale; however, this potential has not been fully realized given that the tools, datasets, and computation are available in diverse repositories and locations. To address this challenge, we developed iMicrobe.us, a community-driven microbiome data marketplace and tool exchange for users to integrate their own data and tools with those from the broader community. Findings: The iMicrobe platform brings together analysis tools and microbiome datasets by leveraging National Science Foundation–supported cyberinfrastructure and computing resources from CyVerse, Agave, and XSEDE. The primary purpose of iMicrobe is to provide users with a freely available, web-based platform to (1) maintain and share project data, metadata, and analysis products, (2) search for related public datasets, and (3) use and publish bioinformatics tools that run on highly scalable computing resources. Analysis tools are implemented in containers that encapsulate complex software dependencies and run on freely available XSEDE resources via the Agave API, which can retrieve datasets from the CyVerse Data Store or any web-accessible location (e.g., FTP, HTTP). Conclusions: iMicrobe promotes data integration, sharing, and community-driven tool development by making open source data and tools accessible to the research community in a web-based platform.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Arion

Arion is a library and tool set that enables researchers to holistically define test system models. To define a complex system for testing an algorithm or control requires expertise across multiple domains. Simulating a complex system requires the integration of multiple simulators and test hardware, each with their own specification languages and concepts. This requires extensive set of knowledge and capabilities. Arion was developed to alleviate this challenge. Arion is a library of Java libraries that abstracts the concepts from supported simulators into a cohesive model language that allows someone to build models to their needed level of fidelity and expertise. Arion is also a software tool that translates the users model back into the specification languages of the simulators and test hardware needed for execution.

Fisher, Andy↗

DOE OSTI2016

Arion

Source record↗

DOE OSTI2016

CisSERS: Customizable In Silico Sequence Evaluation for Restriction Sites

High-throughput sequencing continues to produce an immense volume of information that is processed and assembled into mature sequence data. Here, data analysis tools are urgently needed that leverage the embedded DNA sequence polymorphisms and consequent changes to restriction sites or sequence motifs in a high-throughput manner to enable biological experimentation. Cis SERS was developed as a standalone open source tool to analyze sequence datasets and provide biologists with individual or comparative genome organization information in terms of presence and frequency of patterns or motifs such as restriction enzymes. Predicted agarose gel visualization of the custom analyses results was also integrated to enhance the usefulness of the software. Cis SERS offers several novel functionalities, such as handling of large and multiple datasets in parallel, multiple restriction enzyme site detection and custom motif detection features, which are seamlessly integrated with real time agarose gel visualization. Using a simple fasta-formatted file as input, Cis SERS utilizes the REBASE enzyme database. Results from Cis SERSenable the user to make decisions for designing genotyping by sequencing experiments, reduced representation sequencing, 3’UTR sequencing, and cleaved amplified polymorphic sequence (CAPS) molecular markers for large sample sets. Cis SERS is a java based graphical user interface built around a perl backbone. Several of the applications of Cis SERS including CAPS molecular marker development were successfully validated using wet-lab experimentation. Here, we present the tool Cis SERSand results from in-silico and corresponding wet-lab analyses demonstrating that Cis SERS is a technology platform solution that facilitates efficient data utilization in genomics and genetics studies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Coso Geothermal Spectral Library for Rocks and Minerals

An integrated open mineral spectral library designed to enhance the utility and precision of mineral spectral data for geothermal exploration, developed from a reliable and comprehensive digital dataset for seamless sharing by integrating field data, the USGS spectral library, and pertinent information obtained from Coso geothermal field (Coso) in California. The ASD FieldSpec portable spectrometer was utilized for collecting spectral data, which was subsequently analyzed using the THOR Material Identification tool in ENVI, The Spectral Geologist (TSG) software by CSIRO, and the Fully Constrained Linear Spectral Unmixing algorithm (FCLSU) in MATLAB. Scanning Electron Microscopy (SEM) with a mineralogy-analyzing function was employed to assess the mineral composition of samples, ensuring precise mineralogical analysis. A portable X-ray fluorescence (pXRF) spectrometer was also utilized to gather information on elemental enrichment. A framework for developing spectra data and establishing spectral libraries for various geological cases was proposed within this study. The characteristic spectra of six alteration minerals - alunite, chalcedony, epidote, hematite, kaolinite, and opal - were acquired from Coso samples. The spectral library for the Coso alteration minerals was introduced for further application in academic study or industrial exploration. To browse the Coso Geothermal Spectral data and related figures from spreadsheets: #1 Unzip and store the following items in the same folder. 'Contact Probe Data.zip', 'Sample Photos.zip', and 'Coso spectra of higher-certainity minerals.xlsx'. #2 Open 'Coso spectra of higher-certainity minerals.xlsx'. The hyperlinks in the spreadsheet lead to the folders or figures of: spectra .asd file, spectra ASC II file, spectra plots, and sample photos. The spectra data is raw data without splice correction. Spectra .asd files require particular software to open. (These cannot be opened in GIS software such as ArcGIS.) Spectra ASC II files can be opened in a text editor or spread sheet program.

15 GEOTHERMAL ENERGY↗

DOE OSTI2021

Supporting cost-effective watershed management strategies for Chesapeake Bay using a modeling and optimization framework

Extensive efforts to adaptively manage nutrient pollution rely on Chesapeake Bay Program’s (Phase 6) Watershed Model, called Chesapeake Assessment Scenario Tool (CAST), which helps decision-makers plan and track implementation of Best Management Practices (BMPs). We describe mathematical characteristics of CAST and develop a constrained nonlinear BMP-subset model, software, and visualization framework. This represents the first publicly available optimization framework for exploring least-cost strategies of pollutant load control for the United States’ largest estuary. The optimization identifies implementation options for a BMP subset modeled with load reduction effectiveness factors, and the web interface facilitates interactive exploration of >30,000 solutions organized by objective, nutrient control level, and for ~200 counties. We assess framework performance and demonstrate modeled cost improvements when comparing optimization-suggested proposals with proposals inspired by jurisdiction plans. Stakeholder feedback highlights the framework’s current utility for investigating cost-effective tradeoffs and its usefulness as a foundation for future analysis of restoration strategies.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

BeeSwarm: Enabling Parallel Scaling Performance Measurement in Continuous Integration for HPC Applications

Testing is one of the most important steps in software development–it ensures the quality of software. Continuous Integration (CI) is a widely used testing standard that can report software quality to the developer in a timely manner during development progress. Performance, especially scalability, is another key factor for High Performance Computing (HPC) applications. There are many existing profiling and performance tools for HPC applications, but none of these are integrated into CI tools. In this work, we propose BeeSwarm, an HPC container based parallel scaling performance system that can be easily applied to the current CI test environments. BeeSwarm is mainly designed for HPC application developers who need to monitor how their applications can scale on different compute resources. We demonstrate BeeSwarm using a multi-physics HPC application with Travis CI, GitLab CI and GitHub Actions while using ChameleonCloud and Google Compute Engine as the compute backends. Finally, our results show that BeeSwarm can be used for scalability and performance testing of HPC applications.

97 MATHEMATICS AND COMPUTING↗