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All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Material Protection, Accounting and Control Technologies (MPACT) Implementation Plan: Lab-Scale Demonstration of Advanced Safeguard and Security Systems

The Materials Protection, Accounting, and Control Technologies (MPACT) campaign is working towards the goal of developing and demonstrating the next generation of nuclear materials management for the peaceful use of civilian nuclear energy. A major milestone of the campaign is the “Lab-scale demonstration of an advanced safeguards and security system,” due in 2020. This implementation plan describes how tools developed in the MPACT campaign will be used to meet this milestone. These tools consist of instrumentation and devices as well as computer software for modelling, simulation and integration of data and information for safeguard and security analysis. The plan is focused on demonstrating an advanced safeguard and security systems for electrochemical processing plants, but also identifies activities needed to address advanced reactor, aqueous processing and other advanced fuel cycle facilities. A key component to achieving the 2020 milestone is the development of a virtual distributed test bed that incorporates the instruments, data, analysis tools, and models currently under development and provides a framework to link and normalize the data in a way that simulates a facility, including uncertainty quantification. This virtual distributed test bed will integrate computer simulated facilities that make up a fuel cycle of interest, with distributed test beds located in actual operating facilities and laboratories. The MPACT campaign recently issued roadmaps for both Modelling & Simulation and Advanced Integration which address this component, and activities necessary to achieve the 2020 milestone. Research, development and testing of specific technologies have been supported by the MPACT campaign in coordination with other DOE-NE and DOE-NNSA programs. These technologies provide the essential data needed by the safeguard and security systems, and feed into the data analysis and facility models. This plan will identify these technologies, their current status and activities needed to demonstrate the technologies at the laboratory scale. Wherever possible, test of technologies in field conditions using suitable nuclear materials will be used to define performance. Where necessary, surrogate materials and/or simulation will be used to provide useful information for the demonstration. When completed, the 2020 milestone will provide a demonstration of advanced safeguard and security technologies, including advanced modelling, simulation and analysis approaches, applied to electrochemical processing. It will also identify applications of the technology and approaches in other advanced fuel cycle and reactor concepts.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2023

Risk Analysis of Various Design Architectures for High Safety-significant Safety-related Digital Instrumentation and Control Systems of Nuclear Power Plants during Accident Scenarios

This report documents the plus-up activities performed by Idaho National Laboratory (INL) during Fiscal Year (FY) 2022 for the U.S. Department of Energy (DOE) Light Water Reactor Sustainability (LWRS) Program, Risk Informed Systems Analysis (RISA) Pathway, digital instrumentation and control (DI&C) risk assessment project. In FY 2019, the RISA Pathway initiated a project to develop a risk assessment strategy for delivering a strong technical basis to support effective, licensable, and secure DI&C technologies for digital upgrades/designs. An integrated risk assessment technology for the DI&C systems was proposed for this strategy, which aims to (1) provide a best-estimate, risk-informed capability to quantitatively and accurately estimate the safety margin obtained from plant modernization, especially for the high safety-significant safety-related (HSSSR) DI&C systems, (2) support and supplement existing advanced risk-informed DI&C design guides by providing quantitative risk information and evidence, (3) offer a capability of design architecture evaluation of various DI&C systems to support system design decisions and diversity and redundancy applications, (4) assure the long-term safety and reliability of HSSSR DI&C systems, and (5) reduce uncertainty in costs and support integration of DI&C systems in the plant. To achieve these technical goals and deal with the expensive licensing justifications from regulatory insights, the LWRS-developed framework instructs nuclear vendors and utilities on how to effectively lower the costs associated with digital compliance and speed industry advances by: (1) defining an integrated risk-informed analysis process for DI&C upgrade, including hazard analysis, reliability analysis, and consequence analysis, (2) applying systematic and risk-informed tools to address common cause failures (CCFs) and quantify corresponding failure probabilities for DI&C technologies, particularly software CCFs, (3) evaluating the impact of digital failures at the component level, system level, and plant level, and (4) providing insights and suggestions on designs to manage the risks, thus to support the development, licensing, and deployment of advanced DI&C technologies on nuclear power plant (NPPs). Adding diversity within system or components is the main means to eliminate and mitigate CCFs, but diversity also increases plant complexity and errors and may not address all sources of systematic failures. How to optimize the diversity and redundancy applications for the safety-critical DI&C systems remains a challenge. To deal with the technical issues in addressing potential software CCFs in HSSSR DI&C systems of NPPs and supporting relevant design optimization, the framework provides: ? An integrated best-estimate, risk-informed capability to address new technical digital issues quantitatively, accurately, and efficiently in plan modernization progress, such as software CCFs in HSSSR DI&C systems of NPPs ? A common and a modularized platform for DI&C designers, software developers, cybersecurity analysts, and plant engineers to efficiently predict and prevent risk in the early design stage of DI&C systems ? Technical bases and risk-informed insights to assist U.S. Nuclear Regulatory Commission (NRC) and industry to address and fulfill the risk-informed alternatives for evaluation of CCFs in HSSSR DI&C systems of NPPs ? An integrated risk-informed tool that offers a capability of design architecture evaluation of various DI&C systems to support system design decisions in diversity and redundancy applications. The plus-up research and development efforts of this project in FY 2022 are focused on methodology improvement of software CCF modeling and estimation, prevention analysis, importance analysis and risk analysis of various design architectures of HSSSR DI&C systems. This work greatly enhances the capability of the LWRS-developed framework for the risk assessment and design optimization of safety-critical DI&C systems. It should be noted that all the analyses are performed for the demonstration of the LWRS-developed framework, not for the evaluation of relevant systems. Results are obtained based on very limited design information and testing data.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗
DOE OSTI2022

Facilitating Machine Learning Collaborations Between Labs, Universities, And Industry

It is clear from numerous recent community reports, papers, and proposals that machine learning is of tremendous interest for particle accelerator applications. The quickly evolving landscape continues to grow in both the breadth and depth of applications including physics modeling, anomaly detection, controls, diagnostics, and analysis. Consequently, laboratories, universities, and companies across the globe have established dedicated machine learning (ML) and data science efforts aiming to make use of these new state-of-the-art tools. The current funding environment in the U.S. is structured in a way that supports specific application spaces rather than larger collaboration on community software. Here, we discuss the existing collaboration bottlenecks and how a shift in the funding environment, and how we develop collaborative tools, can help fuel the next wave of ML advancements for particle accelerators.

Edelen, J.P.↗
DOE OSTI2020

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Verification and Validation of Optimization of Replacement Portal Monitoring Replay Tools

The Los Alamos National Laboratory and the Johns Hopkins Applied Physics Laboratory (APL) are both developing optimization software to fulfill the objective of Phase III of the Replacement Portal Monitoring (RPM) Program for the Department of Homeland Security. The objective of the Phase III of the RPM Program is to conduct an evaluation of three RPM systems designed to enhance mission effectiveness, gain operational efficiencies, and to address emerging mission needs against the Countering Weapons of Mass Destruction (CWMD ) nuclear threat basis and special nuclear material (SNM) used in performance testing. As such this task involves the use of global optimization algorithms.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2014

Curation and Computational Design of Bioenergy-Related Metabolic Pathways

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manually curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Modeling Tool Development and Validation for Solar Industry Process Heat Using Particle Thermal Energy Storage

U.S. industry sectors used 26.2 quadrillion Btu and accounted for 33% of total energy consumption in 2021 according to the Energy Information Agency. Industrial process heat accounts for 70% of industrial energy use with application temperatures ranging from 60 degrees -1100 degrees C. Industry processes, heavily relying on fossil fuels of cheap coal or natural gas, differ widely in operating conditions and load requirements which makes them difficult to standardize and imposes great challenges in decarbonization. Industry processes require reliable energy supply and vary widely in temperature ranges. Storing energy from renewable sources is necessary to improve reliability and to mitigate renewable intermittency when replacing carbon fuel-based heat supplies to achieve energy savings and reduce emissions. To this end, we have developed a particle-based thermal energy storage (TES) technology using low-cost and highly stable silica sand as a storage medium. The economic and performance-based analysis is key for renewable energy sources to reliably supply industry process heat and ultimately displace fossil fuels for decarbonization. The diversified industrial processes need case-by-case analysis and design. Therefore, an adaptive modeling tool is key for renewable power with energy storage to meet industry demands. Thus, a modeling tool to simulate a solar industry process heat system using the particle TES has been developed using the object-oriented equation-based language Modelica and the commercial platform of Modelon Impact. The Modelica-based software tool provides a general simulation environment for the design of reliable solar energy sources integrated with TES for various industrial process applications at different temperatures for economic competence with fossil fuels such as coal and natural gases. It uses both customized and standard component modeling modules in Modelon libraries for the flexibility to be adapted to a specific energy demand application. The particle TES system establishes a uniform energy supply platform with an efficient heat exchanger and particle thermal energy reservoir integrated with renewable powers. The particle TES system can provide a wide temperature range and can have a large storage temperature difference that increases storage energy density; therefore, it can be an adaptable energy storage system integrated with renewable power to supply 24/7 heat for industry decarbonization.

concentrated solar thermal↗
DOE OSTI2022

The Science of Scientific Software Development and Use

Increasingly powerful and affordable computing has revolutionized scientific and scholarly discovery across a broad range of fields. Computing relies on software, which has been rapidly growing in scope, diversity, and complexity. At the same time, the methods, processes, and tools used to produce and utilize this essential software are often ad hoc, and the study and improvement of them is often done without the benefit of direct funding or prioritization. Consequently, concerns are growing about the productivity of the developers and users of scientific software, its sustainability, and the trustworthiness of the results that it produces. The US Department of Energy Office of Science (DOE-SC) is at the forefront of modern software-enabled scientific discovery across numerous areas of computational, experimental, and observational science, including major investments in national user facilities that support these activities. In December 2021, the DOE-SC Office of Advanced Scientific Computing Research (ASCR) convened a workshop on basic research needs for the Science of Scientific Software Development and Use (SSSDU). Through keynote presentations, lightning talks, and breakout groups, participants discussed the current practice of software development, maintenance, evolution, and use, and considered how the scientific method could be used to examine these practices and develop more evidence-based approaches to enhance the impact of software and computing on all areas of science. Workshop participants identified three priority research directions (PRDs) and three important crosscutting themes that center on the following overarching insight: software has become an essential part of modern science that impacts new discovery, policy, and technological development. To have full confidence in science delivered via software, we must improve the processes and tools that help us create and use it, and this enhancement requires a deep understanding of the diverse array of teams and individuals doing the work. The full workshop report will be available at https://doi.org/10.2172/1846009.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

CalderaCast User Manual Version 1.0

CalderaCast is a user-friendly web-based tool for electrical-load forecast, providing stakeholders with a fully customizable decision-support framework that estimates the likely power draw from a possible future electric-vehicle (EV) charging station at a given location on a given day along an alternative fuel corridor (AFC). These EV charging profiles are accurately modeled in CalderaCast using the Caldera software framework developed by Idaho National Laboratories (INL), reflecting the realistic charging levels observed in actual charge events. This tool was developed as part of the National Electric Vehicle Infrastructure (NEVI) program, which is quickly generating substantial interest from would-be charging station operators (CSO), large and small electric utilities, and state transportation planners, some of whom had not seriously considered EV charging previously. All these entities—with or without background in EV infrastructure—must estimate the electricity load that a proposed charging station will generate. This load forecast is critically important for a utility to properly assess the capacity of their distribution network to support the proposed station or properly size grid upgrades for potential load growth due to future EV adoption, vehicle technology improvements, or station growth. This document describes each aspect of the CalderaCast tool and provides guidance to users who are interested in utilizing the tool for their work.

24 - POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2022

2022 FORCE Development Status Update

Integrated energy systems (IESs) are essential for decarbonizing electricity and industrial sectors and fully exploiting these systems requires sophisticated planning, scheduling, and dispatching tools to maximize their socio-economic benefits. The Framework for Optimization of Resources and Economics (FORCE) is a tool suite developed at Idaho National Laboratory and is dedicated to making robust analyses of IESs easier for analysts and researchers. The report summarizes the improvements and updates to FORCE during the most recent development cycle. Particularly, we demonstrate improvements to user accessibility, stochastic time-series analysis, and vertical integration with the software tools provided in FORCE.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

A statistical approach for detection of anatomical change - Paper 115

The purpose of this study was to develop a novel statistics-based method for automated detection of anatomical changes using cone-beam CT (CBCT) images of head and neck (H and N) patients. Vendor supplied CBCT software provides the user with the basic tools that allow for the visual assessment of the co-registration of the reference CT data and daily CBCT images. Currently there is no commercially available CBCT software that is capable of detecting anatomical changes and giving the clinician an early alert for the treatment plan adaptation. An algorithm was developed that can detect statistically significant changes at a given confidence level for H and N patients. This tool provides a reliable and automated early warning system that enables a 'just-in-time' adaptation of the treatment plan. A method was developed for automated detection of anatomical changes in H and N patients under radiation therapy treatment. The method utilized imaging CT data along with daily CBCT images to quantitatively compare the patient anatomy against the reference CT imaging data. The comparison algorithm was developed using a statistics-based approach as opposed to threshold-based methods. The algorithm allows for reliable detection of statistically significant changes in the observed patient anatomy at a given level of confidence. The method can be employed as an integral part of the adaptive radiotherapy framework. (authors)

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2025

A Tale from the Trenches: Applying Metamorphic and Differential Testing to Bioinformatics Software

Metamorphic and differential testing have been proposed as best practices for testing software that is difficult to test, such as for programs in scientific domains. An assumption is that these approaches can be easily customized and applied to almost any domain. However, scientific software is often data-driven, and metamorphic relations may require significant domain knowledge to develop. In addition, tools are often written for ad-hoc experimentation by the scientists and often embed many assumptions about the importance and representation of different natural phenomena. In this paper, we present our experience applying both metamorphic and differential testing to a set of four computational biology tools that predict the growth of an organism. While our original goal was to evaluate these techniques to improve our system-level testing, we encountered multiple roadblocks along the way. Although we did find faults (some confirmed by developers), we also uncovered a set of challenges, including the considerable manual effort required for (a) defining domain-specific tests, (b) validating correctness, and (c) distinguishing between issues stemming from poor data and those arising from incorrect software.

Marsh, Alexis L [Iowa State University/Ames Labora↗
DOE OSTI2019

A Comparison of GoldSim, RESRAD-Onsite, and NORMALYSA Modeling Tools at Radioactive Waste Sites - 19480

Radioactive waste disposal and associated decision making is a challenging problem around the world. A strong performance assessment model plays a crucial role in making good management and remediation decisions and in optimizing the performance of a site. The International Atomic Energy Agency (IAEA) MODARIA II Working Group 1 (WG1) is comparing the performance of various modeling platforms used at Naturally Occurring Radioactive Material (NORM) and legacy waste sites to support risk-informed decision making. Neptune and Company, Inc. (Neptune) has developed probabilistic performance assessment models using the GoldSim system modeling software at a variety of radioactive waste sites. This paper presents a comparison between GoldSim and two other tools used to evaluate radiation exposure and their associated risks: the NORM And Legacy Site Assessment (NORMALYSA) tool used to assess risk at the Zapadnoe mill tailings site, and the residual radioactivity (RESRAD-Onsite) computer program used to calculate Authorized Limits at the Los Alamos National Laboratory (LANL). The International Atomic Energy Agency (IAEA) supported development of NORMALYSA based off of Ecolego 6.0, in which the user connects several universal modules, representing various environmental transport and exposure pathways, and enters in site-specific data. Further work with NORMALYSA has continued under the MODARIA II WG 1. A radionuclide transport and dose calculation model of the Zapadnoe uranium mill tailings site at the Pridneprovsky Chemical Plant in the Ukraine has been configured by MODARIA II WG1 to test the capabilities of NORMALYSA. Under this test case, contaminant transport and effective dose calculations were performed for two exposure scenarios. The onsite worker is exposed via external ground irradiation and radon and radioactive dust inhalation. The offsite resident defines a residence established 300 years after institutional control has ended, 800 meters downstream from the site with exposure pathways including: ingestion of garden vegetables irrigated by contaminated ground water, ingestion of fish from the Konoplyanka River and agricultural activities in the contaminated garden. GoldSim modeling software is a dynamic probabilistic modeling platform that evaluates uncertainty in a robust and transparent manner. Although GoldSim provides contaminant and radionuclide transport modules to facilitate integrated modeling of radionuclide migration in the environment, these features are not embedded in an existing modeling framework, except as created by the user. Neptune developed a GoldSim model for the two exposure scenarios of the Zapadnoe test case. Neptune's Generic PA Model was used as a starting point for the Zapadnoe site. Input parameters for the GoldSim model include site-specific parameters from the MODARIA Working Group as well as parameters from the Generic PA Model and other PA models created by Neptune. For the other comparison, Version 7.0 of RESRAD-Onsite, developed by Argonne National Laboratory for the U.S. Department of Energy (DOE), was used to calculate Authorized Limits for LANL. Authorized Limits are concentrations of radionuclides in soil that support the evaluation process to clear land for release under different uses. The RESRAD-Onsite computer code was used to calculate Authorized Limits because this program was specifically designed to derive radionuclide soil guidelines corresponding to a specific dose criterion. The scope of the RESRAD dose or risk evaluation is constrained to the transport and exposure pathways that have been included in the computer code. To assist in illustrating the capability of GoldSim modeling software, a GoldSim model was created to replicate the calculation of LANL's Authorized Limits for soil. The main exposure pathways in this model are inhalation of dust and gas, plant ingestion, soil ingestion, and external ground irradiation. All of the processes and outputs of RESRAD-Onsite and NORMALYSA can be created in a GoldSim model, but the value of GoldSim lies in its flexibility for application to any of a wide variety of environmental modeling problems. GoldSim allows development of site-specific inventory, transport mechanisms and risk assessment scenarios. If all potentially complete release, transport, and exposure pathways are addressed in an existing dose and risk assessment computer code, and if the code's capabilities fulfill the project modeling objectives, then expending resources to create a GoldSim model may not be necessary. Site optimization and good decision making about site management are often best when supported with the flexibility of GoldSim as a modeling tool. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

Reverse image search for scientific data within and beyond the visible spectrum

The explosion in the rate, quality and diversity of image acquisition instruments has propelled the development of expert systems to organize and query image collections more efficiently. Recommendation systems that handle scientific images are rare, particularly if records lack metadata. This paper introduces new strategies to enable fast searches and image ranking from large pictorial datasets with or without labels. The main contribution is the development of pyCBIR, a deep neural network software to search scientific images by content. This tool exploits convolutional layers with locality sensitivity hashing for querying images across domains through a user-friendly interface. Our results report image searches over databases ranging from thousands to millions of samples. We test pyCBIR search capabilities using three convNets against four scientific datasets, including samples from cell microscopy, microtomography, atomic diffraction patterns, and materials photographs to demonstrate 95% accurate recommendations in most cases. Furthermore, all scientific data collections are released.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Bridging the Gap between the X-ray Absorption Spectroscopy and the Computational Catalysis Communities in Heterogeneous Catalysis: A Perspective on the Current and Future Research Directions

X-ray absorption spectroscopy (XAS) [extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES)] is a key technique within the heterogeneous catalysis community to probe the structure and properties of the active site(s) for a diverse range of catalytic materials. Furthermore, the interpretation of the raw experimental data to derive an atomistic picture of the catalyst requires modeling and analysis; the EXAFS data are compared to a model, and a goodness of fit parameter is used to judge the best fit. This EXAFS modeling can often be nontrivial and time-consuming; overcoming or improving these limitations remains a central challenge for the community. Considering these limitations, this Perspective highlights how recent developments in analysis software, increased availability of reliable computational models, and application of data science tools can be used to improve the speed, accuracy, and reliability of EXAFS interpretation. In particular, we emphasize the advantages of combining theory and EXAFS as a unified technique that should be treated as a standard (when applicable) to identify catalytic sites and not two separate complementary methods. Building on the recent trends in the computational catalysis community, we also present a community-driven approach to adopt FAIR Guiding Principles for the collection, analysis, dissemination, and storage of XAS data. Written with both the experimental and theory audience in mind, we provide a unified roadmap to foster collaborations between the two communities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Collecting data in the home laboratory: evolution of X-ray sources, detectors and working practices

Recent developments in X-ray crystallographic hardware related to structural biology research are presented and discussed. While the majority of macromolecular X-ray data are currently collected using highly efficient beamlines at an ever-increasing number of synchrotrons, there is still a need for high-performance reliable systems for in-house experiments. In addition to crystal screening and optimization of data-collection parameters before a synchrotron trip, the home system allows the collection of data as soon as the crystals are produced to obtain the solution of novel structures, especially by the molecular-replacement method, and is invaluable in achieving the quick turnover that is often required for ligand-binding studies in the pharmaceutical industry. There has been a continuous evolution of X-ray sources, detectors and software developed for in-house use in recent years and a diverse range of tools for structural biology laboratories are available. An overview of the main directions of these developments and examples of specific solutions available to the macromolecular crystallography community are presented in this paper, showing that data collection ‘at home’ is still an attractive proposition complementing the use of synchrotron beamlines.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Application Characterization at Scale: Lessons learned from developing a distributed Open Community Runtime system for High Performance Computing

Since 2012, the U.S. Department of Energy’s X-Stack program has been developing solutions including runtime systems, programming models, languages, compilers, and tools for the Exascale system software to address crucial performance and power requirements. Fine grain programming models and runtime systems show a great potential to efficiently utilize the underlying hardware. Thus, they are essential to many X-Stack efforts. An abundant amount of small tasks can better utilize the vast parallelism available on current and future machines. Moreover, finer tasks can recover faster and adapt better, due to a decrease in state and control. Nevertheless, current applications have been written to exploit old paradigms (such as Communicating Sequential Processor and Bulk Synchronous Parallel processing). To fully utilize the advantages of these new systems, applications need to be adapted to these new paradigms. As part of the applications’ porting process, in-depth characterization studies, focused on both application characteristics and runtime features, need to take place to fully understand the application performance bottlenecks and how to resolve them. This paper presents a characterization study for a novel high performance runtime system, called the Open Community Runtime, using key HPC kernels as its vehicle. This study has the following contributions: one of the first high performance, fine grain, distributed memory runtime system implementing the OCR standard (version 0.99a); and a characterization study of key HPC kernels in terms of runtime primitives running on both intra and inter node environments. Running on a general purpose cluster, we have found up to 1635x relative speed-up for a parallel tiled Cholesky Kernels on 128 nodes with 16 cores each and a 1864x relative speed-up for a parallel tiled Smith-Waterman kernel on 128 nodes with 30 cores.

Application characterization↗
DOE OSTI2024

Spatially Resolved Raman Spectroscopic Investigation of Uranyl Fluoride: A Case Study in the Importance of Instrument Optimization

Raman spectroscopy is an emerging technique for rapid and nondestructive analysis of nuclear materials for forensic and nonproliferation applications as it is a powerful tool for distinguishing multiple chemical forms of materials with similar stoichiometries. Recent developments in spectroscopic software have enabled rapid data collection with high-speed Raman spectroscopic mapping capabilities. However, some uranium-rich materials are susceptible to degradation in humid air and/or laser-induced phase transformations. To mitigate environmental or measurement-related sample degradation of potential samples of interest, we have taken a systematic approach to define optimized data collection parameters for high-throughput measurements of uranyl fluoride (UO 2 F 2 ), which is an important intermediate material in the nuclear fuel cycle. First, we systematically describe the influence of optical magnification (5× to 100×), laser power, and exposure time on obtained signal for identical particles of UO 2 F 2 and find that at low laser power and exposure times, comparable signal is obtained regardless of optical magnification. Second, we ensure sample integrity during data collection, and third, collect spectroscopic maps that employ optimized parameters to reduce the time required to obtain spatially resolved spectroscopic information. Reductions of 90% and 99% in measurement times are discussed as they relate to differences in resolving spectroscopic features of particles in identical mapping areas. Finally, during this work, we found that additional data processing options were needed and thus developed a customized Python script for importing, processing, analyzing, and visualizing Raman spectroscopic map data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗