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DOE OSTI2017

Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation

Crystal structure determination of biological macromolecules using the novel technique of serial femtosecond crystallography (SFX) is severely limited by the scarcity of X-ray free-electron laser (XFEL) sources. However, recent and future upgrades render microfocus beamlines at synchrotron-radiation sources suitable for room-temperature serial crystallography data collection also. Owing to the longer exposure times that are needed at synchrotrons, serial data collection is termed serial millisecond crystallography (SMX). As a result, the number of SMX experiments is growing rapidly, with a dozen experiments reported so far. Here, the first high-viscosity injector-based SMX experiments carried out at a US synchrotron source, the Advanced Photon Source (APS), are reported. Microcrystals (5–20 µm) of a wide variety of proteins, including lysozyme, thaumatin, phycocyanin, the human A 2A adenosine receptor (A 2A AR), the soluble fragment of the membrane lipoprotein Flpp3 and proteinase K, were screened. Crystals suspended in lipidic cubic phase (LCP) or a high-molecular-weight poly(ethylene oxide) (PEO; molecular weight 8 000 000) were delivered to the beam using a high-viscosity injector. In-house data-reduction (hit-finding) software developed at APS as well as the SFX data-reduction and analysis software suites Cheetah and CrystFEL enabled efficient on-site SMX data monitoring, reduction and processing. Complete data sets were collected for A 2A AR, phycocyanin, Flpp3, proteinase K and lysozyme, and the structures of A 2A AR, phycocyanin, proteinase K and lysozyme were determined at 3.2, 3.1, 2.65 and 2.05 Å resolution, respectively. The data demonstrate the feasibility of serial millisecond crystallography from 5–20 µm crystals using a high-viscosity injector at APS. The resolution of the crystal structures obtained in this study was dictated by the current flux density and crystal size, but upcoming developments in beamline optics and the planned APS-U upgrade will increase the intensity by two orders of magnitude. Furthermore, these developments will enable structure determination from smaller and/or weakly diffracting microcrystals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Faster than Real-Time Dynamic Simulation for Large-Size Power System with Detailed Dynamic Models using High-Performance Computing Platform

This paper presents a faster-than-real-time dynamic simulation software package that is designed for large-size power system dynamic simulation. It was developed on the GridPACKTM high-performance computing (HPC) framework. The key features of the developed software package include (1) faster-than-real-time dynamic simulation for a WECC system (17,000 buses) with different types of detailed generator, controller, and relay dynamic models, (2) a decoupled parallel dynamic simulation algorithm with optimized computation architecture to better leverage HPC resources and technologies, (3) options for HPC-based linear and iterative solvers, (4) hidden HPC details, such as data communication and distribution, to enable development centered on mathematical models and algorithms rather than on computational details for power system researchers, and (5) easy integration of new dynamic models and related algorithms into the software package.

Huang, Renke↗

DOE OSTI2015

The evaluation of a 2D diode array in “magic phantom” for use in high dose rate brachytherapy pretreatment quality assurance

Purpose: High dose rate (HDR) brachytherapy is a treatment method that is used increasingly worldwide. The development of a sound quality assurance program for the verification of treatment deliveries can be challenging due to the high source activity utilized and the need for precise measurements of dwell positions and times. This paper describes the application of a novel phantom, based on a 2D 11 × 11 diode array detection system, named “magic phantom” (MPh), to accurately measure plan dwell positions and times, compare them directly to the treatment plan, determine errors in treatment delivery, and calculate absorbed dose. Methods: The magic phantom system was CT scanned and a 20 catheter plan was generated to simulate a nonspecific treatment scenario. This plan was delivered to the MPh and, using a custom developed software suite, the dwell positions and times were measured and compared to the plan. The original plan was also modified, with changes not disclosed to the primary authors, and measured again using the device and software to determine the modifications. A new metric, the “position–time gamma index,” was developed to quantify the quality of a treatment delivery when compared to the treatment plan. The MPh was evaluated to determine the minimum measurable dwell time and step size. The incorporation of the TG-43U1 formalism directly into the software allows for dose calculations to be made based on the measured plan. The estimated dose distributions calculated by the software were compared to the treatment plan and to calibrated EBT3 film, using the 2D gamma analysis method. Results: For the original plan, the magic phantom system was capable of measuring all dwell points and dwell times and the majority were found to be within 0.93 mm and 0.25 s, respectively, from the plan. By measuring the altered plan and comparing it to the unmodified treatment plan, the use of the position–time gamma index showed that all modifications made could be readily detected. The MPh was able to measure dwell times down to 0.067 ± 0.001 s and planned dwell positions separated by 1 mm. The dose calculation carried out by the MPh software was found to be in agreement with values calculated by the treatment planning system within 0.75%. Using the 2D gamma index, the dose map of the MPh plane and measured EBT3 were found to have a pass rate of over 95% when compared to the original plan. Conclusions: The application of this magic phantom quality assurance system to HDR brachytherapy has demonstrated promising ability to perform the verification of treatment plans, based upon the measured dwell positions and times. The introduction of the quantitative position–time gamma index allows for direct comparison of measured parameters against the plan and could be used prior to patient treatment to ensure accurate delivery.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Intelligent Partitioning based Fully Parallel AC Security-Constrained Optimal Power Flow

Today’s power grid is becoming more diverse and integrated with high-level distributed energy resources and smart control technologies that is creating a new set of grid management challenges in terms of large-scale, nonlinear, and non-convex problem modeling, complex and time-consuming computation, as well as difficult uncertainty handling. This project focused on solving a challenging multi-period security-constrained generation scheduling problem, which is of great importance for maximizing the social welfare of real-time dispatch, day-ahead market, as well as weekly planning of power systems. Our developed software explored parallel optimization algorithms for complex and realistic power system models, and develop fast, efficient, and robust grid optimization solutions on the high-performance computing platform that will enable increased grid economics, flexibility, resilience, as well as energy security in the United States.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2024

Git and Software Tools for CTS

This presentation will provide an overview of the progress made helping the EDX4CCS, SMART, and NRAP projects virtualize their CO2 Transport and Storage software tools to boost their stakeholder availability through the DisCO2ver platform. This presentation will also cover helpful software development tools with a focus on researchers and developers who have not had formal training or many years of experience in software engineering best practices.

Zaengle, Dakota↗

DOE OSTI2016

Life Extension of Nuclear Plant Facilities through Monitoring and Detailed Analysis - 16175

The UK has accumulated a substantial legacy of radioactive waste from various civil nuclear and defence programmes. Presently, however most of the UK radioactive waste is generated from nine power stations which generate approximately one sixth of the of the country's electricity. Irradiated fuel is removed from these reactors and safe management of the radioactive solid and liquid effluents is required. The safe management of these effluents is essential. Sellafield, in West Cumbria UK, contains two reprocessing plants, one designed to process nuclear fuel from Magnox reactors (CO{sub 2} cooled with Uranium bar fuel) and the other to process nuclear fuel from Advanced Gas cooled Reactors and Pressurized Water Reactors. The reprocessing stage enables extraction of fissile material for recycling. This leaves a volume of dilute but high-level waste. The high-level radioactive liquid waste is concentrated to reduce its volume and then incorporated into borosilicate glass, using a process called vitrification. The glass is then poured into stainless steel containers and placed in long term storage. This required concentration of HLW liquor is achieved using a suite of aging evaporators. All evaporators are of similar design constructed from corrosion resistant stainless steel having dimensions height ∼11 m, internal diameter 3.05 m and capable of holding 13.7 m{sup 3} of liquor. The basic principle of operation is to heat the dilute liquor under partial vacuum, at constant volume, until the target concentration is achieved. Heating of the liquor is achieved using steam heated coils within the evaporator, and steam in the jacket which surrounds the lower half of the evaporator vessel. The evaporator is then brought to atmospheric pressure and the concentrated liquor is ejected whilst hot. The evaporator is then cooled with water cooled coils and a water filled jacket. New dilute liquor is then added for a new batch. The process is then repeated. As the evaporators reach the end of their original design life accurate prediction of the current condition of nuclear plant facilities is essential to safely justify continued plant operation by ensuring structural integrity. This poses a significant challenge as many aging UK nuclear facilities were not inherently built with inspection in mind. The potential life limiting components of the HA evaporators at Sellafield are the surfaces that contact the product liquor at elevated temperatures i.e. the steam heated surfaces of the coils within the evaporator vessel and the vessel base and wall surrounded by the steam jacket. Each heating component is critical to the operational life of the evaporator - the removal from service of a coil heating component significantly reduces the operational flexibility and remnant life of this plant. Over the last decade a variety of cutting-edge expertise and methodologies have been utilised to accurately measure and then predict the current condition of the plant and also to predict its remnant life. This paper provides an overview of the development of several techniques deployed, namely non-destructive testing/inspection, in-house software development and finite element modelling. These methods have been validated by lab-scale or full-scale experiments along with historical plant data. These techniques have been evolved and refined for over a decade, providing vital insights into the physical behaviour of this complex reprocessing system. This enables not only accurate assessment of the current condition of the plant equipment but also allows scientifically underpinned predictions to be made of how it will behave into the future. This is critical for Sellafield as this knowledge feeds into their safety case to the Office of Nuclear Regulation to justify continued operation. It is concluded that this integrated approach provides a robust analysis tool which has driven change and optimisation of plant procedures ensuring continued safe operation whilst extending the life of the facility. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2021

Analysis and Recommendation of Tritium Gas Continuous Air Monitor Alarm Setpoints for the RPL Stack Exhaust

The Radiochemical Processing Laboratory (RPL) tritium continuous air monitor (CAM) is used for near real-time detection of tritium gas (i.e., elemental tritium [HT] and tritiated water vapor [HTO]) in the stack exhaust. The CAM interfaces with software developed by the Pacific Northwest National Laboratory (PNNL)—called the “PNNL OS3700 Tritium Monitoring Software”—that provides near real-time estimates of tritium gas air concentrations and integrated daily activities that are calculated from measured CAM counts. The OS3700 software implements alarm setpoints to alert the facility of larger tritium gas releases that if allowed to persist, could begin to challenge permitted emission and established dose constraints. This report performs a detailed review of historical and current tritium alarm setpoints used at RPL, including discussion of the technical basis used in their development, analysis of alarm frequencies using measured historical data, and performs a detailed dose assessment using more realistic release scenarios and meteorology. Based on the results, the tritium air concentration and integrated daily tritium activity alarm setpoints will remain 2.0 × 10 -5 µCi/ml and 25 Ci/day, respectively. These setpoints achieve the right operational balance in identifying larger releases from planned tritium work at RPL, without being overly conservative so as to cause nuisance alarming. Furthermore, implied doses associated with these setpoints are well below defined and regulatory limits.

325RPL↗

DOE OSTI2014

Region templates: Data representation and management for high-throughput image analysis

Compartment fires exhibit unique features associated with smoke accumulation and restricted air ventilation. The objective of the present study is to evaluate the ability of CFD-based fire models to simulate these features and in particular the effects of flame extinction that results from under-ventilated fire conditions. The study is performed using FireFOAM; FireFOAM is an advanced fire modeling software developed by FM Global and is based on a general-purpose open-source software called OpenFOAM. A new flame extinction model based on the concept of a critical value of the flame Damköhler number is incorporated into FireFOAM. The performance of the extinction model is evaluated via comparisons with a previously developed experimental database corresponding to a reduced-scale, heptane-fueled, compartment fire configuration. The numerical simulations also include a description of fuel evaporation driven by the computed gas-to-liquid heat feedback. Comparisons between experimental data and numerical results provide a suitable test bed to evaluate the ability of CFD-based fire models to describe the transition from over- to under-ventilated fire conditions, as well as the transition from extinction-free conditions to conditions in which the flame experiences partial or total quenching.

Energy & Fuels↗

DOE OSTI2021

Analysis and Recommendation of Alpha-Beta Continuous Air Monitor Alarm Setpoints for the RPL Stack Exhaust

The Radiochemical Processing Laboratory (RPL) alpha-beta continuous air monitor (CAM) is used for real-time detection of “artificial” alpha-beta particulates from the stack exhaust. The CAM interfaces with software developed by the Pacific Northwest National Laboratory—called the “PNNL OS3300 Alpha-Beta Monitoring Software”—that provides real-time estimates of alpha-beta air concentrations and integrated activities that are calculated from measured CAM counts. The OS3300 software has alarm setpoints that can be used to provide an early indication of larger releases, that if allowed to persist, could approach defined dose limits. This report performs a detailed review of historical and current alarm setpoints used at RPL, including discussion of the technical basis used in their development, analysis of alarm frequencies using measured historical data, and performs a detailed dose assessment using more realistic release scenarios, meteorology, and adjustment factors used in estimating released stack activity. Based on the results, the alpha and beta air concentration alarm setpoints will remain 1.77 × 10 -8 µCi/ml and 3.47 × 10 -8 µCi/ml, respectively; and the alpha and beta integrated activity alarm setpoints will remain 70.22 µCi and 137.63 µCi, respectively. These setpoints achieve the right operational balance in identifying larger releases from planned radiological work at RPL, without being overly conservative so as to cause nuisance alarming. Furthermore, implied doses associated with these setpoints are below defined and regulatory limits.

325RPL↗

DOE OSTI2017

LK Scripting Language [SWR-16-07]

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Version 3.0+ toolkit.

Source record↗

DOE OSTI2019

Streaming Analytics Machine (SAM) v. 0.0.1

This is software developed in the course of my dissertation work, which was funded by Sandia. The software includes a library (the Streaming Analytics Machine or SAM) for expressing machine learning and subgraph matching over streaming data sources. It also includes a utility that will convert from a high-level language, the Streaming Analytics Language (SAL) to SAM. SAND2019-4322 M

Goodman, Eric↗

DOE OSTI2016

LK Scripting Language

Source record↗

DOE OSTI2014

RELAP-7 Numerical Stabilization: Entropy Viscosity Method

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The code is based on the INL's modern scientific software development framework, MOOSE (Multi-Physics Object Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5's capability and extends the analysis capability for all reactor system simulation scenarios. RELAP-7 utilizes a single phase and a novel seven-equation two-phase flow models as described in the RELAP-7 Theory Manual (INL/EXT-14-31366). The basic equation systems are hyperbolic, which generally require some type of stabilization (or artificial viscosity) to capture nonlinear discontinuities and to suppress advection-caused oscillations. This report documents one of the available options for this stabilization in RELAP-7 -- a new and novel approach known as the entropy viscosity method. Because the code is an ongoing development effort in which the physical sub models, numerics, and coding are evolving, so too must the specific details of the entropy viscosity stabilization method. Here the fundamentals of the method in their current state are presented.

42 ENGINEERING↗

DOE OSTI2019

Combustion Research I.1 Sprays, Flow, Heat Transfer and Turbulent Mixing

LANL is working with the Partnership for Advance Combustion Engines (PACE) a DOE sponsored consortium of national laboratories for the research and development for creating smarter engine design tools for sustainable transportation. Much of that effort is focused on heat, mass and momentum transfer within and engine. LANL’s focus in 2019, in particular under PACE has been spray modeling and engine mixture formulation, development of conjugate heat transfer analysis (heat transfer to the environment surrounding the combustion chamber). Our efforts relay on the Fast, Easy, Accurate and Robust Continuum Engineering (FEARCE) software developed at LANL as the next generation of engine modeling software for turbulent reactive and multiphase flow, a 2019 R&D 100 winner. This work is relevant to the DOE Vehicle Technologies Office efforts at addressing national energy security as well. Less dependence on petroleum products leads to greater energy security. By Environmental Protection Agency standards, some vehicles are now reaching 42–50 mpg mark. These are conventional gasoline engines. With continued investment and research into new technical innovations, the potential exists to save more than 4 million barrels of oil per day or approximately $200 to $400 million per day. This would be a significant decrease in emissions and use of petroleum and a very large stimulus to the U.S. economy. Better understanding of fuel injection and fuel–air mixing, thermodynamic combustion losses, and combustion/emission formation processes enhances our ability to minimize fuel use and unwanted emissions. Helping to accomplish this understanding, the FEARCE modeling program is working to provide state-of-theart capability for accurately simulating combustion processes: to have a predictive methodology in a software helping industry and researchers not only meet national goals on fuel usage and emissions, but global goals. In addition, a predictive, robust, and accurate capability for simulating the engine combustion process helps to minimize time and labor for development of new engine technology.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2015

SU-D-BRD-05: Online Framework for Plan Tracking and Automatic Checks in Radiation Therapy

Purpose: To develop an online framework that tracks a patient’s plan from initial simulation to treatment and that helps automate elements of the physics plan checks usually performed in the record and verify (RV) system and treatment planning system. Methods: We have developed PlanTracker, an online plan tracking system that automatically imports new patients tasks and follows it through treatment planning, physics checks, therapy check, and chart rounds. A survey was designed to collect information about the amount of time spent by medical physicists in non-physics related tasks. We then assessed these non-physics tasks for automation. Using these surveys, we directed our PlanTracker software development towards the automation of intra-plan physics review. We then conducted a systematic evaluation of PlanTracker’s accuracy by generating test plans in the RV system software designed to mimic real plans, in order to test its efficacy in catching errors both real and theoretical. Results: PlanTracker has proven to be an effective improvement to the clinical workflow in a radiotherapy clinic. We present data indicating that roughly 1/3 of the physics plan check can be automated, and the workflow optimized, and show the functionality of PlanTracker. When the full system is in clinical use we will present data on improvement of time use in comparison to survey data prior to PlanTracker implementation. Conclusion: We have developed a framework for plan tracking and automatic checks in radiation therapy. We anticipate using PlanTracker as a basis for further development in clinical/research software. We hope that by eliminating the most simple and time consuming checks, medical physicists may be able to spend their time on plan quality and other physics tasks rather than in arithmetic and logic checks. We see this development as part of a broader initiative to advance the clinical/research informatics infrastructure surrounding the radiotherapy clinic. This research project has been financially supported by Varian Medical Systems, Palo Alto, CA, through a Varian MRA.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

RELAP-7 Closure Correlations

The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at the Idaho National Laboratory (INL). The code is based on the INL’s modern scientific software development framework, MOOSE (Multi-Physics Object Oriented Simulation Environment). The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical integration methods, and physical models. The end result will be a reactor systems analysis capability that retains and improves upon RELAP5’s and TRACE’s capabilities and extends their analysis capabilities for all reactor system simulation scenarios. The RELAP-7 code utilizes the well-posed 7-equation two-phase flow model for compressible two-phase flow. Closure models used in the TRACE code has been reviewed and selected to reflect the progress made during the past decades and provide a basis for the colure correlations implemented in the RELAP-7 code. This document provides a summary on the closure correlations that are currently implemented in the RELAP-7 code. The closure correlations include sub-grid models that describe interactions between the fluids and the flow channel, and interactions between the two phases.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2018

RELAP-7 User's Guide

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2014

Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes (Final Report)

I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of efficient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the final outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

59 BASIC BIOLOGICAL SCIENCES↗