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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

National User Resource for Biological Accelerator Mass Spectrometry (Final Report)

The National User Resource for Biological Accelerator Mass Spectrometry (User Resource) will provide isotopic analysis (primarily radiocarbon or 14C) by accelerator mass spectrometry (AMS) for NIH- funded researchers across the United States and will be the only User Resource of its type in the United States. The User Resource will provide measurement capability and expertise to a research community that requires highly sensitive, quantitative isotope analyses. Since commissioning a new accelerator mass spectrometer in June 2014, we have measured over 4000 samples a year for collaborators and service users. The User Resource will enable us to continue to meet these research needs, as well as provide for new users whose research programs would benefit from AMS as a measurement tool. The User Resource’s forte will be ultra-high sensitivity quantitation of radiocarbon and selected other radioisotopes for research studies where isotopes are required. Radioisotope labeling studies have been and will continue to be an important tool for addressing many complex biomedical science problems. AMS is a specialized and unique type of mass spectrometry that provides absolute quantitation of radiocarbon and other relevant radioisotopes with extreme sensitivity, having limits of detection in real samples on the order of a few attomol/mg of sample at measurement precisions of ~3%. It is the only instrumental method capable of quantifying radioisotope-labeled agents routinely in real-world samples with such precision and sensitivity. The sensitivity of AMS allows for the quantification of radiolabeled metabolites in extremely complex matrices of cells and organisms at very low concentrations and in small samples. AMS allows studies to be conducted without perturbing metabolism leading to more relevant quantification of metabolic rates and pathways. In addition, it enables quantification of pharmacokinetic and metabolic properties of toxicants at environmentally relevant concentrations in model systems as well as the ability to quantify pharmacokinetics and other molecular endpoints directly in humans. Such quantitative assessments can 1) improve risk assessment for toxicants, 2) address safety and efficacy considerations for therapeutic entities, 3) deepen understanding of xenobiotic and intermediary metabolism, 4) help understand the interactions between critical molecular pathways, and 5) improve efforts to model and predict various metabolic and biological states. These capabilities have been applied in a number of areas including research in carcinogenesis, toxicology, nutrition, pharmacology/drug development and basic biological science. As a NIGMS National Resource the National User Resource for Biological Accelerator Mass Spectrometry will help NIH funded scientists achieve a deeper understanding of the etiology of human health concerns by (1) enabling the quantification of pharmacokinetics and other molecular endpoints directly in humans; (2) offering the ability to conduct quantitative studies using biologics such as proteins or lipids, and thereby reducing the amount of radioisotope usage in biomedical labs; and (3) enabling more relevant studies of metabolic pathways in health and disease through the use of much lower, more biologically-relevant, concentrations of metabolic substrates in cells and intact organisms. Such studies support NIGMS’s basic biomedical research areas that contribute to the understanding of fundamental cellular and physiological principles and enable research supported by the Biophysics, Biomedical Technology, and Computational Biosciences (BBCB); Genetics and Molecular, Cellular, and Developmental Biology (GMCDB); Pharmacology, Physiology, Biological Chemistry (PPBC) and Training, Workforce Development, and Diversity (TWD) Divisions. Over the next five years, our goals are to: 1. Improve the efficiency of operation for AMS measurements through installation of new interfaces to our AMS systems, technical modifications to improve gas accepting ion source efficiency and upgrading our data analysis software for improved ease of use and data reporting. 2. Increase the accessibility and visibility of ultra-sensitive 14C measurements for the biomedical research community by training of new investigators and expanding our national user base. 3. Provide high throughput, ultra-sensitive 14C analysis for the NIGMS and NIH user community.

47 OTHER INSTRUMENTATION↗
DOE OSTI2018

Nebraska Integrated Carbon Capture and Storage Pre-Feasibility Study

In collaboration with the Nebraska Public Power District (NPPD), the Energy & Environmental Research Center (EERC) has conducted a pre-feasibility study for a commercial-scale carbon dioxide (CO 2 ) geologic storage complex in western Nebraska integrated with potential CO 2 capture at Gerald Gentleman Station (GGS). GGS is the largest coal-fired electricity-generating station in Nebraska, emitting 8.5 million metric tons (Mt) of CO 2 annually, and is located near the town of Sutherland. This pre-feasibility (Phase 1) project has been executed as part of the U.S. Department of Energy (DOE) CarbonSAFE program, a multiphase initiative to support the deployment of large-scale carbon capture and storage (CCS) projects. Each CarbonSAFE project is required to demonstrate the potential to capture and store at least 50 million tonnes (Mt) of CO 2 over a 25-year operational period. The EERC and NPPD established a coordination team to identify challenges to a potential Nebraska CCS project, comprising local stakeholder organizations, which met twice in Lincoln and via several Webinars, providing feedback and guidance throughout the pre-feasibility study. The EERC also secured the technical support of Schlumberger Carbon Services and Computer Modelling Group Ltd. (CMG). The project comprised four technical themes, all using published information sources. Regional and stakeholder analysis, including identification of sensitive environmental areas, potential resource conflicts, and strategies for public outreach. A review of geographic and socioeconomic characteristics, in combination with geologic characterization in the subbasinal analysis described below, identified an area to the southwest and within a 75-mile radius of GGS as the most prospective for development of a storage site. This area largely avoided lands with protected status such as wetlands. A public outreach plan has also been developed for implementation in any further phases of CCS assessment in western Nebraska, for example a CarbonSAFE Phase 2 feasibility study. Scenario analysis, addressing economic and regulatory factors. GGS is the only single major source of CO 2 emissions capable of satisfying the CarbonSAFE 50-Mt scale requirement within the study region. Chemical absorption using amines was identified as the most viable technology for postcombustion CO 2 capture at GGS. The total cost of a CCS project at GGS was estimated to be between $67/tonne CO 2 for capture and auxiliary boiler to minimize parasitic load and $70/tonne CO 2 avoided cost, using the Carnegie-Mellon University Integrated Environmental Control Model (IECM). The total avoided cost included the capture facility and parasitic load, a flue gas desulfurization plant required for the use of amine solvent technology, transport via pipeline, and dedicated storage infrastructure. Nebraska has no legislation in place to address typical CCS-specific issues, for example pore space ownership for storage. Long-term liability, therefore, falls under the U.S. Environmental Protection Agency Underground Injection Control (UIC) Class 6 program regulations. Subbasinal analysis, addressing the potential for a dedicated subsurface “container” to store the required 50-Mt quantity of CO 2 . Modeling and simulation studies identified an area to the southwest of GGS with the potential for storage of 50 Mt CO 2 in the Cloverly Formation, comprising sandstones with interbedded and intermingled shales. The area of review (AOR) that would be required for monitoring under a Class VI operating permit was estimated to be as high as 400–700 square miles, due to uncertain pressure effects. The viability of this storage option is subject to significant uncertainty due to the relatively limited amount of existing characterization data available to the pre-feasibility study; for example, dynamic simulation indicated that the proposed storage rate might require as little as two or as many as 14 injection wells. A key uncertainty is the relative proportion and distribution of sandstone and shale within the Cloverly Formation. A preliminary, semiquantitative risk assessment also suggested uncertainty over storage capacity and injectivity constitute the most significant project risks at this pre-feasibility stage. No assessed risks were considered to rule out the possibility of a project moving to deployment. National Risk Assessment Partnership (NRAP) validation, using software tools developed by the National Energy Technology Laboratory (NETL) to assess risks associated with the potential 50-Mt CO 2 storage complex. NRAP tools were used to assess hypothetical leakage scenarios. Results broadly supported the conclusion of the semiquantitative risk analysis – for example, even worst-case analysis of theoretical leakage scenarios found limited migration rates and impacts. In summary, the work undertaken in this Phase 1 pre-feasibility study has shown that western Nebraska has potential to host a commercial-scale CCS project, including a dedicated storage “container” for 50 Mt of CO 2 . However, the following key challenges would need to be overcome: The business case for deploying CCS projects is uncertain; recently announced federal tax credits and sales of CO 2 for enhanced oil recovery may not cover the full costs of a CCS project at GGS, as estimated by this pre-feasibility study. The potential 50-Mt CO 2 dedicated storage container defined in this pre-feasibility study should be regarded as having a relatively low level of readiness to support a CCS project. Public outreach would be a vital element in western Nebraska, where sensitivities around such environmental issues as water resource protection and pipeline construction would need to be carefully addressed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2015

Development of Improved Graphical Displays for an Advanced Outage Control Center, Employing Human Factors Principles for Outage Schedule Management

The long-term viability of existing nuclear power plants in the United States (U.S.) is dependent upon a number of factors, including maintaining high capacity factors, maintaining nuclear safety, and reducing operating costs, particularly those associated with refueling outages. Refueling outages typically take 20-30 days, and for existing light water NPPs in the U.S., the reactor cannot be in operation during the outage. Furthermore, given that many NPPs generate between $1-1.5 million/day in revenue when in operation, there is considerable interest in shortening the length of refueling outages. Yet refueling outages are highly complex operations, involving multiple concurrent and dependent activities that are somewhat challenging to coordinate; therefore, finding ways to improve refueling outage performance, while maintaining nuclear safety has proven to be difficult. The Advanced Outage Control Center (AOCC) project is a research and development (R&D) demonstration activity under the LWRS Program. LWRS is an R&D program that works closely with industry R&D programs to establish technical foundations for the licensing and managing of long-term, safe, and economical operation of current fleet of NPPs. As such, the LWRS Advanced Outage Control Center project has the goal of improving the management of commercial NPP refueling outages. To accomplish this goal, INL is developing an advanced outage control center (OCC) that is specifically designed to maximize the usefulness of communication and collaboration technologies for outage coordination and problem resolution activities. The overall focus is on developing an AOCC with the following capabilities that enables plant and OCC staff to; Collaborate in real-time to address emergent issues; Effectively communicate outage status to all workers involved in the outage; Effectively communicate discovered conditions in the field to the OCC; Provide real-time work status; Provide automatic pending support notifications; Provide real-time requirements monitoring; Maximize their collective situational awareness to improve decision-making; and Leverage macro data to better support resource allocation. INL has partnered with several commercial NPP utilities to develop a number of advanced outage management technologies. These outage management technologies have focused on both collaborative technologies for control centers and developing mobile technologies for NPP field workers. This report describes recent efforts made in developing a suite of outage technologies to support more effective schedule management. Currently, a master outage schedule is created months in advance using the plant’s existing scheduling software (e.g., Primavera P6). Typically, during the outage, the latest version of the schedule is printed at the beginning of each shift. INL and its partners are developing technologies that will have capabilities such as Automatic Schedule Updating, Automatic Pending Support Notifications, and the ability to allocate and schedule outage support task resources on a sub-hour basis (e.g., outage Micro-Scheduling). The remaining sections of this report describe in more detail the scheduling challenges that occur during outages, how the outage scheduling technologies INL is developing helps address those challenges, and the latest developments on this task (e.g., work accomplished to date and the path forward)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Calibrating a finite-strain phase-field model of fracture for bonded granular materials with uncertainty quantification

To study the mechanical behavior of mock high explosives, an experimental and simulation program was developed to calibrate, with quantified uncertainty, a material model of the bonded granular material Idoxuridine and nitroplasticized Estane-5703. This paper reports on the efficacy of such a framework as a generalizable methodology for calibrating material models against experimental data with uncertainty quantification. Additionally, this paper studies the effect of two manufacturing temperatures and three initial granular configurations on the unconfined compressive behavior of the resulting bonded granular materials. In each of these cases, the same calibration framework was used; in that, hundreds of high-fidelity direct numerical simulations using a new, graphics processing unit-enabled, high-performance finite element method software, Ratel, were run to calibrate a finite-strain phase-field fracture model against experimental data. It was found that manufacturing temperature influenced the elastic response of the mock high explosives, with higher temperatures yielding a stiffer response. By contrast, it was found that the initial configuration of the grains had a negligible impact on the overall behavior of the mock high explosives though it remains possible that local damage accumulation within the specimens could be altered by the initial configurations. Overall, the calibration framework was successful at creating well-calibrated models, showing its usefulness as an engineering and scientific tool.

36 MATERIALS SCIENCE↗
DOE OSTI2015

New risk metrics and mathematical tools for risk analysis: Current and future challenges

The current status of the food safety supply world wide, has led Food and Agriculture Organization (FAO) and World Health Organization (WHO) to establishing Risk Analysis as the single framework for building food safety control programs. A series of guidelines and reports that detail out the various steps in Risk Analysis, namely Risk Management, Risk Assessment and Risk Communication is available. The Risk Analysis approach enables integration between operational food management systems, such as Hazard Analysis Critical Control Points, public health and governmental decisions. To do that, a series of new Risk Metrics has been established as follows: i) the Appropriate Level of Protection (ALOP), which indicates the maximum numbers of illnesses in a population per annum, defined by quantitative risk assessments, and used to establish; ii) Food Safety Objective (FSO), which sets the maximum frequency and/or concentration of a hazard in a food at the time of consumption that provides or contributes to the ALOP. Given that ALOP is rather a metric of the public health tolerable burden (it addresses the total ‘failure’ that may be handled at a national level), it is difficult to be interpreted into control measures applied at the manufacturing level. Thus, a series of specific objectives and criteria for performance of individual processes and products have been established, all of them assisting in the achievement of FSO and hence, ALOP. In order to achieve FSO, tools quantifying the effect of processes and intrinsic properties of foods on survival and growth of pathogens are essential. In this context, predictive microbiology and risk assessment have offered an important assistance to Food Safety Management. Predictive modelling is the basis of exposure assessment and the development of stochastic and kinetic models, which are also available in the form of Web-based applications, e.g., COMBASE and Microbial Responses Viewer), or introduced into user-friendly softwares, (e.g., Seafood Spoilage Predictor) have evolved the use of information systems in the food safety management. Such tools are updateable with new food-pathogen specific models containing cardinal parameters and multiple dependent variables, including plate counts, concentration of metabolic products, or even expression levels of certain genes. Then, these tools may further serve as decision-support tools which may assist in product logistics, based on their scientifically-based and “momentary” expressed spoilage and safety level.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2019

Comparison of two software systems for quantification of myocardial blood flow in patients with hypertrophic cardiomyopathy

Backgorund: Quantification of myocardial blood flow (MBF) by positron emission tomography (PET) is important for investigation of angina in hypertrophic cardiomyopathy (HCM). Several software programs exist for MBF quantification, but they have been mostly evaluated in patients (with normal cardiac geometry), referred for evaluation of coronary artery disease (CAD). Software performance has not been evaluated in HCM patients who frequently have hyperdynamic LV function, LV outflow tract (LVOT) obstruction, small LV cavity size, and variation in the degree/location of LV hypertrophy. Aim: We compared results of MBF obtained using PMod, which permits manual segmentation, to those obtained by FDA-approved QPET software which has an automated segmentation algorithm. Methods: {sup 13}N-ammonia PET perfusion data were acquired in list mode at rest and during pharmacologic vasodilation, in 76 HCM patients and 10 non-HCM patients referred for evaluation of CAD (CAD group.) Data were resampled to create static, ECG-gated and 36-frame-dynamic images. Myocardial flow reserve (MFR) and MBF (in ml/min/g) were calculated using QPET and PMod softwares. Results: All HCM patients had asymmetric septal hypertrophy, and 50% had evidence of LVOT obstruction, whereas non-HCM patients (CAD group) had normal wall thickness and ejection fraction. PMod yielded significantly higher values for global and regional stress-MBF and MFR than for QPET in HCM. Reasonably fair correlation was observed for global rest-MBF, stress-MBF, and MFR using these two softwares (rest-MBF: r = 0.78; stress-MBF: r = 0.66.; MFR: r = 0.7) in HCM patients. Agreement between global MBF and MFR values improved when HCM patients with high spillover fractions (> 0.65) were excluded from the analysis (rest-MBF: r = 0.84; stress-MBF: r = 0.72; MFR: r = 0.8.) Regionally, the highest agreement between PMod and QPET was observed in the LAD territory (rest-MBF: r = 0.82, Stress-MBF: r = 0.68) where spillover fraction was the lowest. Unlike HCM patients, the non-HCM patients (CAD group) demonstrated excellent agreement in MBF/MFR values, obtained by the two softwares, when patients with high spillover fractions were excluded (rest-MBF: r = 0.95; stress-MBF: r = 0.92; MFR: r = 0.95). Conclusions: Anatomic characteristics specific to HCM hearts contribute to lower correlations between MBF/MFR values obtained by PMod and QPET, compared with non-HCM patients. These differences indicate that PMod and QPET cannot be used interchangeably for MBF/MFR analyses in HCM patients.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Software Quality Assurance for EBR-II Fuels Irradiation and Physics Database (FIPD)

The Fuels Irradiation and Physics Database (FIPD) is an ongoing DOE project on archival of the EBR-II metal-alloy fuel irradiation experiments. As part of its use in support of license applications, the Quality Assurance Program Plan (QAPP) was drafted and endorsed by NRC in an effort to demonstrate its compliance with regulatory expectations. Software Quality Assurance (SQA) for the physics portion of FIPD is intended to qualify the calculated quantities such as fuel and cladding temperatures, neutron fluence and axially varying burnup estimates for irradiated fuel elements. This report covers the initial evaluation of SQA status of three neutron physics and thermo-fluid codes (REBUS, RCT and SE2RCT) that form the basis of calculated quantities for as-irradiated characteristics of the tested metallic fuel elements. The report also introduces an SQA plan to address the identified deficiencies. The REBUS, RCT, and SE2RCT codes are all part of the Argonne Reactor Code (ARC) code system. There is considerable knowledge and experience on REBUS and RCT but relatively less on SE2RCT. During FY2021, efforts focused on an assessment of how the data in the EBR-II Physics and Analysis DataBase (PADB) is generated with SE2RCT and used in FIPD. Additional tasks included considerations of uncertainties for power estimates in REBUS and RCT calculations and their impact on the combined RCT methodology. The RCT software usage in FIPD was assessed this year and the input/output details studied. A “requirements” document was created that identifies the key features of the RCT software being used in FIPD that need to have SQA documentation. A brief discussion on the history of RCT and its input is included in this report along with the basic SQA roadmap laid out in the requirements document. The SE2RCT software usage in FIPD is still being studied noting that there is no current manual. As part of the work done this year, two bugs were identified in the SE2RCT software which have a minor impact on the accuracy of the results it produces. No requirements document has been created, but one identified feature of SE2RCT being used that needs verification was its fuel pin temperature calculation. The work completed this year confirms that the approximations which will be included in the software verification report for SE2RCT are accurate. In addition to software quality assurance work for RCT and SE2RCT, an automated verification framework is proposed to simplify the software quality assurance process. The purpose of this framework is to streamline code verification and documentation while minimizing repetitive tasks for code developers and reviewers. The reduction of repeated input (between reference solution, software, and documentation input) throughout the SQA process reduces potential for human errors during the preparation of the supporting software quality records. The automation of the verification and documentation process proposed for this project leverages the existing verification structure already in place for the SAS4A/SASSYS-1 code.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2021

Numerical Codes for the DESC-LSST Analysis Pipeline: Core Cosmology Library Standard Modules and Beyond wCDM Modules (Final Technical Report)

The overall objective of the project is to investigate and develop specific software modules and analysis components for the software pipeline of LSST Dark Energy Science Collaboration (DESC). Following the key projects of DESC Science Roadmap (SRM), we will write and test computer codes for the Core Cosmology Library (CCL) in order to complete its modules, functionalities, and interface to work with the analysis pipelines from the five science probes of DESC (parts of SRM deliverables CX4.2TJP, CX6.2CS). We will also code modules for CCL to test models beyond w-Cold-Dark-Matter (wCDM) and modification to gravity (MG). Interfaces for MG models will also be developed for the TJPCOSMO software which is the main pipeline of the Theory and Joint Probe (TJP) working group (deliverable TJP2.3). In order to use the full power of LSST data to constrain MG models, we will also work on constraints from nonlinear regime by running and analyzing MG N-Body simulations using a Parameterized-Post-Friedmann framework into the Gadget-2 simulation package (deliverable TJP2.2). Preliminary results for the simulations were obtained in the past. In collaboration with other DESC groups, we plan to make these simulations feedable to cosmic emulators that are practical for likelihood analyzes (deliverable TJP2.2, parts of CX6.2CS). We will also modify and integrate our current codes for consistency tests between data sets and probes into the pipeline (parts of deliverables CX8.2TJP, TJP2.3). We understand that other groups will contribute to some of these objectives but our team will focus and collaborate with others on the particular part of testing MG and models beyond wCDM and refine the DESC pipeline for this purpose. PI has been coordinating his work with the TJP and CS working groups and the DESC management team. PI is a full member of DESC since June 2013. He and his students have been contributing to LSST-DESC activities and work including TJP telecons, collaboration meetings, hack-weeks, and workshops. PI chaired or co-chaired sessions at collaboration meetings and hack-weeks about testing gravity and models beyond wCDM using LSST. He is coordinating the TJP2 projects for testing models beyond wCDM including the writing of DESC-research-note, development of code for pipeline, and N-Body simulations for MG and beyond wCDM models testable with LSST analyses. As stressed in the DESC white paper, SRM, and P5 report, one of the important questions in understanding cosmic acceleration and dark energy is to be able to distinguish whether the acceleration is due to a dark energy component in the universe or a modification to gravity. Answering these questions will have a significant impact on the question of cosmic acceleration and dark energy. The methods that we will use include analytical work, numerical code, and N-Body simulations. A first approach that that we will use consists of using growth rate parameters that enter the perturbed dynamics equations. These parameters take distinctive values for distinct gravity theories and have potential to distinguish between Dark Energy and Modified Gravity. The second method is to look for inconsistencies in Dark Energy parameter spaces using specific combinations of cosmological data sets. Our investigation addresses the Dark Energy problem that is relevant to the mission of the HEP program to understand how our universe works at its most fundamental level. It will allow us to make progress on the HEP mission to explore the nature of Dark Energy and the basic nature of space and time using future surveys such as LSST. The investigation supports the DOE HEP program Cosmic Frontier as it will contribute to the study and understanding of dark energy and fundamental properties of the universe. The investigation contributes directly to LSST-DESC key projects and their deliverables as described in the Science Road-map document to build analysis pipeline and to test dark energy and beyond wCDM models using LSST.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

A geospatial risk analysis graphical user interface for identifying hazardous chemical emission sources

Background: Performing back trajectory and forward trajectory using the Hybrid Single-Particle Lagrangian Integrated Trajectory Model (HYSPLIT) is a reliable approach for assessing particle transport after release among mid-field atmospheric models. HYSPLIT has an externally facing online interface that allows non-expert users to run the model trajectories without requiring extensive training or programming. However, the existing HYSPLIT interface is limited if simulations have a large amount of meteorological data and timesteps that are not coincident. The objective of this study is to design and develop a more robust tool to rapidly evaluate hazard transport conditions and to perform risk analysis, while still maintaining an intuitive and user-friendly interface. Methods: HYSPLIT calculates forward and backward trajectories of particles based on wind speed, wind direction, and the corresponding location, timestamp, and Pasquill stability classes of the regions of the atmosphere in terms of the wind speed, the amount of solar radiation, and the fractional cloud cover. The computed particle transport trajectories, combined with the online Proton Transfer Reaction-Mass Spectrometry (PTR-MS) data (https://figshare.com/articles/dataset/ARL_Data_from_PROS_station_at_Hanford_site/19993964), can be used to identify and quantify the sources and affected area of the hazardous chemicals’ emission using the potential source distribution function (PSDF). PSDF is an improved statistical function based on the well-known potential source contribution function (PSCF) in establishing the air pollutant source and receptor relationship. Performing this analysis requires a range of meteorological and pollutant concentration measurements to be statistically meaningful. The existing HYSPLIT graphical user interface (GUI) does not easily permit computations of trajectories of a dataset of meteorological data in high temporal frequency. To improve the performance of HYSPLIT computations from a large dataset and enhance risk analysis of the accidental release of material at risk, a geospatial risk analysis tool (GRAT-GUI) is created to allow large data sets to be processed instantaneously and to provide ease of visualization. Results: The GRAT-GUI is a native desktop-based application and can be run in any Windows 10 system without any internet access requirements, thus providing a secure way to process large meteorological datasets even on a standalone computer. GRAT-GUI has features to import, integrate, and convert meteorological data with various formats for hazardous chemical emission source identification and risk analysis as a self-explanatory user interface. The tool is available at https://figshare.com/articles/software/GRAT/19426742.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Development of MCNP Training Modules for Safeguards Practitioners [Abstract]

The Monte-Carlo N-Particle (MCNP) software developed at LANL is the most widely used neutron transport code in the world. It is an essential tool for a variety of applications including detector development and design, nuclear fuel burnup simulation, criticality safety, and nondestructive assay system optimization. For this reason, it is indispensable within the safeguards and materials control & accountability (MC&A) communities. Multiple MCNP training courses have been created and taught over the last several decades by the MCNP development team at LANL, however there are no existing courses that cover specialized topics considered fundamental to NDA and safeguards models. To fill this gap, the MCNP team and Safeguards Science and Technology group at LANL have co-created a set of training modules customized to meet the specialized needs of the safeguards and MC&A communities. The basic modules cover concepts such as NDA system optimization, He-specific and other capture tallies, and tools for improved theoretical understanding. An advanced module was also created to cover topics including variance reduction for active interrogation simulations, use of the LANL MCNPTools post-processor, PTRAC (particle tracking) and list-mode data simulations, and fuel burnup simulations. The training modules teach to the latest and most state-of-the-art MCNP features and tools released by the development team at LANL and are intended to be taught jointly by the developers and safeguards experts. Ultimately, we hope that creation of these modules will serve to capture and convey the safeguards modeling and MCNP expertise at LANL, and that we will be able to share the modules more broadly with the MC&A and safeguards communities.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2013

Quantifying Contaminant Mass for the Feasibility Study of the DuPont Chambers Works FUSRAP Site - 13510

The U.S. Army Corps of Engineers (USACE) - Philadelphia District is conducting an environmental restoration at the DuPont Chambers Works in Deepwater, New Jersey under the Formerly Utilized Sites Remedial Action Program (FUSRAP). Discrete locations are contaminated with natural uranium, thorium-230 and radium-226. The USACE is proposing a preferred remedial alternative consisting of excavation and offsite disposal to address soil contamination followed by monitored natural attenuation to address residual groundwater contamination. Methods were developed to quantify the error associated with contaminant volume estimates and use mass balance calculations of the uranium plume to estimate the removal efficiency of the proposed alternative. During the remedial investigation, the USACE collected approximately 500 soil samples at various depths. As the first step of contaminant mass estimation, soil analytical data was segmented into several depth intervals. Second, using contouring software, analytical data for each depth interval was contoured to determine lateral extent of contamination. Six different contouring algorithms were used to generate alternative interpretations of the lateral extent of the soil contamination. Finally, geographical information system software was used to produce a three dimensional model in order to present both lateral and vertical extent of the soil contamination and to estimate the volume of impacted soil for each depth interval. The average soil volume from all six contouring methods was used to determine the estimated volume of impacted soil. This method also allowed an estimate of a standard deviation of the waste volume estimate. It was determined that the margin of error for the method was plus or minus 17% of the waste volume, which is within the acceptable construction contingency for cost estimation. USACE collected approximately 190 groundwater samples from 40 monitor wells. It is expected that excavation and disposal of contaminated soil will remove the contaminant source zone and significantly reduce contaminant concentrations in groundwater. To test this assumption, a mass balance evaluation was performed to estimate the amount of dissolved uranium that would remain in the groundwater after completion of soil excavation. As part of this evaluation, average groundwater concentrations for the pre-excavation and post-excavation aquifer plume area were calculated to determine the percentage of plume removed during excavation activities. In addition, the volume of the plume removed during excavation dewatering was estimated. The results of the evaluation show that approximately 98% of the aqueous uranium would be removed during the excavation phase. The USACE expects that residual levels of contamination will remain in groundwater after excavation of soil but at levels well suited for the selection of excavation combined with monitored natural attenuation as a preferred alternative. (authors)

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2018

Future of Work with Robotics - 18599

The DOE Environmental Management mission continues with remaining tasks that are high-hazards to human workers and high-consequences to the nation, resulting in potentially high risks to project costs and schedules. This is the mission pull. At the same time, robotic technologies are hitting a turning point with increased productivity and reliability within society, supporting a technology push. Enabling this push are better computer processing following Moore's Law, breakthroughs in biometric and learning algorithms,and riding a wave of venture funding for intended commercialization of mechatronic and Internet of Thing (IOT) projects. There has been overall improvements in material technologies, algorithms, and software standardization with tools/libraries such as the Robot Operating System (ROS). The internet has made knowledge ubiquitous and the cell phone sector has pushed the boundaries of systems-on-chip technology. This current growth is a race between large global technology companies, and between countries that understand that there is a prize with increased commerce based on being a leader in the field of robotics and automation. This technological advances have placed this technology solidly within the next 4. Industrial Revolution being tracked by the World Economic Council. Policies and law can slow this progression down, but technological changes in adjacent fields will put additional pressure on human workers by being more economical and in saving lives. A fundamental issue is will this change be gradual or disruptive such as with the forecasted singularity. There is also a realization with automation that the transition of human workers to other fields may be temporary, but in the long run, workers may run out of viable work and long-term occupations. The obvious future of human jobs are most assured by those who can embrace the change through the design, development, installment, and maintenance of the technology. Younger workers can be re-educated while older humans can be re-trained. The goal of this paper is to explore all the forces that are enabling this revolution, investigating its many impacts, and speculating on the future of human jobs during nuclear remediation. Automation has made an impact to the manufacturing sector, and has since expanded to the retail and services sectors. The question is will this same automation transition, including robotics and artificial intelligence, occur to the environmental management and cleanup sector, and how should we prepare ourselves for this change. (author)

42 ENGINEERING↗
DOE OSTI2024

Updates to the Alliance of Genome Resources central infrastructure

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and application programming interfaces (APIs). Here, we focus on developments over the last 2 years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Automated Glovebox Work-cell Design - 18370

Los Alamos National Laboratory (LANL) is the primary plutonium science and manufacturing facility in the United States supporting multiple national security programs. It is responsible for completing a high variety of small-batch manufacturing tasks requiring the handling and precision machining of Special Nuclear Materials (SNM). Given the myriad of tasks that must be completed in a limited workspace, LANL intends to utilize flexible, multi-use robotic work-cells capable of completing a variety of mission critical tasks in a single glovebox with no re-tooling needed between batch jobs. This approach would allow LANL more flexibility in its production schedule and to meet its future production and research objectives. In this paper, we present a system that integrates multiple sensors and other manufacturing peripherals into existing glovebox infrastructure. Currently, a technician can place an object in the work area where vision sensors and supervisory software identify the object and its pose and automatically determine which manufacturing task to complete. Pose uncertainty is addressed in real-time by the task planner, eliminating the need for fixtures. Grasps are validated using pressure sensors, payload sensors, and grasp quality metrics to ensure that objects are not dropped or damaged during manipulation. The robot, sensors, and peripherals are controlled using open-source software built utilizing ROS (Robot Operating System), which minimizes redevelopment and allows for re-use and extensibility. Established capabilities support vision, collision-free path planning, and more, minimizing development time. For this effort, particular attention was given to the integration of general peripheral devices (drill, chuck, etc.), which is critical to efficiently utilizing ROS in manufacturing environments. This integration is achieved with an in-development framework that allows for quick integration of peripherals, including I/O devices and motors. Contact tasks utilize the Generalized Contact Control Framework (GCCF) previously developed at UT Austin. GCCF allows application developers to easily define multiple contact control tasks for a single robot. This paper summarizes the key software components necessary to develop the multi-use work-cell including existing ROS components. UT-developed software for grasp validation, peripheral integration, and contact control is presented in more depth. Finally the glovebox system is demonstrated completing a set of tasks with no fixturing necessary. Primary tasks include surface preparation/ablation, drilling, press-fitting, and sorting, as well as supporting material transfer and inspection tasks. The glovebox work-cell reduces cost, operator dose, ergonomic issues, and time loss due to material transfer between gloveboxes that only support one task. If multiple glovebox work-cells are in use, they have the potential to eliminate bottlenecks and scale production capabilities beyond current limits. (authors)

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

Epi Archive: Automated Synthesis of Global Notifiable Disease Data

ObjectiveLANL has built software that automatically collects global notifiable disease data, synthesizes the data, and makes it available to humans and computers within the Biosurveillance Ecosystem (BSVE) as a novel data stream. These data have many applications including improving the prediction and early warning of disease events.IntroductionMost countries do not report national notifiable disease data in a machine-readable format. Data are often in the form of a file that contains text, tables and graphs summarizing weekly or monthly disease counts. This presents a problem when information is needed for more data intensive approaches to epidemiology, biosurveillance and public health.While most nations likely store incident data in a machine-readable format, governments are often hesitant to share data openly for a variety of reasons that include technical, political, economic, and motivational issues1.A survey conducted by LANL of notifiable disease data reporting in over fifty countries identified only a few websites that report data in a machine-readable format. The majority (>70%) produce reports as PDF files on a regular basis. The bulk of the PDF reports present data in a structured tabular format, while some report in natural language.The structure and format of PDF reports change often; this adds to the complexity of identifying and parsing the desired data. Not all websites publish in English, and it is common to find typos and clerical errors.LANL has developed a tool, Epi Archive, to collect global notifiable disease data automatically and continuously and make it uniform and readily accessible.MethodsWe conducted a survey of the national notifiable disease reporting systems notating how the data are reported and in what formats. We determined the minimal metadata that is required to contextualize incident counts properly, as well as optional metadata that is commonly found.The development of software to regularly ingest notifiable disease data and make it available involves three or four main steps: scraping, detecting, parsing and persisting.Scraping: we examine website design and determine reporting mechanisms for each country/website, as well as what varies across the reporting mechanisms. We then designed and wrote code to automate the downloading of the data for each country. We store all artifacts presented as files (PDF, XLSX, etc.) in their original form, along with appropriate metadata for parsing and data provenance.Detecting: This step is required when parsing structured non-machine-readable data such as tabular data in PDF files. We combined the Nurminen methodology of PDF table detection with in-house heuristics to find the desired data within PDF reports2.Parsing: We determined what to extract from each dataset and parsed these data into uniform data structures, correctly accommodating the variations in metadata (e.g., time interval definitions) and the various human languages.Persisting: We store the data in the Epi Archive database and make it available on the internet and through the BSVE. The data is persisted into a structured and normalized SQL database.ResultsThe Epi Archive tool currently contains national and/or subnational notifiable disease data from twenty nations. When a user accesses the Epi Archive site, they are prompted with four fields: country, subregion, disease of interest, and date duration. Upon form submission, a time series is generated from the users’ specifications. The generated graph can then be downloaded into a CSV file if a user is interested in performing personal analysis. Additionally, the data from Epi Archive can be reached through a REST API (Representational State Transfer Application Programming Interface).ConclusionsLANL, as part of a currently funded DTRA effort, is automatically and continually collecting global notifiable disease data. While 20 nations are in production, more are being brought online in the near future. These data are already being utilized and will have many applications including improving the prediction and early warning of disease events.References[1] van Panhuis WG, Paul P, Emerson C, et al. A systematic review of barriers to data sharing in public health. BMC Public Health. 2014. 14:1144. doi:10.1186/1471-2458-14-1144[2] Nurminen, Anssi. "Algorithmic extraction of data in tables in PDF documents." (2013).

Khalsa, Hari S.↗
DOE OSTI2016

Impact of compressed breast thickness and dose on lesion detectability in digital mammography: FROC study with simulated lesions in real mammograms

Purpose: The aim of this work was twofold: (1) to examine whether, with standard automatic exposure control (AEC) settings that maintain pixel values in the detector constant, lesion detectability in clinical images decreases as a function of breast thickness and (2) to verify whether a new AEC setup can increase lesion detectability at larger breast thicknesses. Methods: Screening patient images, acquired on two identical digital mammography systems, were collected over a period of 2 yr. Mammograms were acquired under standard AEC conditions (part 1) and subsequently with a new AEC setup (part 2), programmed to use the standard AEC settings for compressed breast thicknesses ≤49 mm, while a relative dose increase was applied above this thickness. The images were divided into four thickness groups: T1 ≤ 29 mm, T2 = 30–49 mm, T3 = 50–69 mm, and T4 ≥ 70 mm, with each thickness group containing 130 randomly selected craniocaudal lesion-free images. Two measures of density were obtained for every image: a BI-RADS score and a map of volumetric breast density created with a software application (VolparaDensity, Matakina, NZ). This information was used to select subsets of four images, containing one image from each thickness group, matched to a (global) BI-RADS score and containing a region with the same (local) VOLPARA volumetric density value. One selected lesion (a microcalcification cluster or a mass) was simulated into each of the four images. This process was repeated so that, for a given thickness group, half the images contained a single lesion and half were lesion-free. The lesion templates created and inserted in groups T3 and T4 for the first part of the study were then inserted into the images of thickness groups T3 and T4 acquired with higher dose settings. Finally, all images were visualized using the ViewDEX software and scored by four radiologists performing a free search study. A statistical jackknife-alternative free-response receiver operating characteristic analysis was applied. Results: For part 1, the alternative free-response receiver operating characteristic curves for the four readers were 0.80, 0.65, 0.55 and 0.56 in going from T1 to T4, indicating a decrease in detectability with increasing breast thickness. P-values and the 95% confidence interval showed no significant difference for the T3-T4 comparison (p = 0.78) while all the other differences were significant (p < 0.05). Separate analysis of microcalcification clusters presented the same results while for mass detection, the only significant difference came when comparing T1 to the other thickness groups. Comparing the scores of part 1 and part 2, results for the T3 group acquired with the new AEC setup and T3 group at standard AEC doses were significantly different (p = 0.0004), indicating improved detection. For this group a subanalysis for microcalcification detection gave the same results while no significant difference was found for mass detection. Conclusions: These data using clinical images confirm results found in simple QA tests for many mammography systems that detectability falls as breast thickness increases. Results obtained with the AEC setup for constant detectability above 49 mm showed an increase in lesion detection with compressed breast thickness, bringing detectability of lesions to the same level.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Automating linear accelerator quality assurance

Purpose: The purpose of this study was 2-fold. One purpose was to develop an automated, streamlined quality assurance (QA) program for use by multiple centers. The second purpose was to evaluate machine performance over time for multiple centers using linear accelerator (Linac) log files and electronic portal images. The authors sought to evaluate variations in Linac performance to establish as a reference for other centers. Methods: The authors developed analytical software tools for a QA program using both log files and electronic portal imaging device (EPID) measurements. The first tool is a general analysis tool which can read and visually represent data in the log file. This tool, which can be used to automatically analyze patient treatment or QA log files, examines the files for Linac deviations which exceed thresholds. The second set of tools consists of a test suite of QA fields, a standard phantom, and software to collect information from the log files on deviations from the expected values. The test suite was designed to focus on the mechanical tests of the Linac to include jaw, MLC, and collimator positions during static, IMRT, and volumetric modulated arc therapy delivery. A consortium of eight institutions delivered the test suite at monthly or weekly intervals on each Linac using a standard phantom. The behavior of various components was analyzed for eight TrueBeam Linacs. Results: For the EPID and trajectory log file analysis, all observed deviations which exceeded established thresholds for Linac behavior resulted in a beam hold off. In the absence of an interlock-triggering event, the maximum observed log file deviations between the expected and actual component positions (such as MLC leaves) varied from less than 1% to 26% of published tolerance thresholds. The maximum and standard deviations of the variations due to gantry sag, collimator angle, jaw position, and MLC positions are presented. Gantry sag among Linacs was 0.336 ± 0.072 mm. The standard deviation in MLC position, as determined by EPID measurements, across the consortium was 0.33 mm for IMRT fields. With respect to the log files, the deviations between expected and actual positions for parameters were small (<0.12 mm) for all Linacs. Considering both log files and EPID measurements, all parameters were well within published tolerance values. Variations in collimator angle, MLC position, and gantry sag were also evaluated for all Linacs. Conclusions: The performance of the TrueBeam Linac model was shown to be consistent based on automated analysis of trajectory log files and EPID images acquired during delivery of a standardized test suite. The results can be compared directly to tolerance thresholds. In addition, sharing of results from standard tests across institutions can facilitate the identification of QA process and Linac changes. These reference values are presented along with the standard deviation for common tests so that the test suite can be used by other centers to evaluate their Linac performance against those in this consortium.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Laboratory Instrument Software Controlled Spread Spectrum Time Domain Reflectometry for Electrical Cable Testing

This research discusses development of a software-controlled laboratory instrument based spread spectrum time domain reflectometry system (SSTDR). This constitutes one task within PNNL’s Light Water Sustainability Program (LWRS) whose mission includes advancing nondestructive examination (NDE) techniques for off-line and on-line in-situ cable condition monitoring. In 2022, PNNL evaluated SSTDR for detection and characterization of a number of cable anomalies (Glass et al. 2022). The review included comparison of SSTDR to Frequency Domain Reflectometry (FDR) techniques which have enjoyed encouraging feedback and are starting to be used in nuclear power plants for periodic cable condition monitoring of cable systems as part of the plant’s overall cable aging management program. The FDR test introduces a broad-band chirp onto the cable at the cable end then listens for any reflection from a change of impedance along the cable caused by a damaged conductor or insulation, splices, contact with moisture, or other cable anomalies. The signal is captured in the frequency domain then transformed back to the time domain using an inverse Fourier transform (IFT). Based on the velocity of propagation, the impedance response signal is plotted against distance along the cable. Peak locations along the X-axis indicate the distance along the cable where a portion of the signal has been reflected back to the instrument as a result of a cable anomaly. The FDR test is considered the gold standard of reflectometry however it does require the cable to be de-energized to perform the test. The LIVEWIRE commercial SSTDR produces a similar plot to the FDR however all processing is in the time domain. A pseudo-random noise code (PN code) is input onto the cable conductor and the instrument listens for any reflected response from cable anomalies. The SSTDR processes the signal as an autocorrelation comparing the input PN code to any reflected signal detected. The autocorrelation analysis for thermal aging, water and water ingress detection, ground fault and phase-to-phase fault detection at various locations along the cable and with the cable attached and detached from a motor load, and on both energized and un-energized conditions were performed. These results were contrasted to Frequency Domain Reflectometry (FDR) measurements of the un-energized cable. Results were encouraging but indicated more work was warranted – particularly with the SSTDR, it seemed that the insulation damage would likely be better evaluated with multiple bandwidth cable tests particularly including larger bandwidths than were possible with the current commercial instrument. The commercial instrument’s bandwidth was set at 6, 12, 24, and 48MHz but note that SSTDR and FDR definitions of bandwidth trend similarly but are not the same. The FDR response could be more broadly adjusted, and the bandwidth of 100 to 500 MHz produced the best responses. FDR responses to anomalies were clearer than SSTDR responses and indications were that a broader bandwidth SSTDR may lead to improved SSTDR detection capability. This project used a laboratory instrument based SSTDR (primarily using an Arbitrary Waveform Generator (AWG) and a digital oscilloscope plus Python in-house software) that allowed software adjustment of the SSTDR bandwidth, window functions applied to the exciting Pseudo-random Noise (PN) code plus and other aspects of the SSTDR signal processing. Hereafter, this will be referred to as the PNNL SSTDR. Evaluating specific performance of the PNNL SSTDR is left to a separate report. This report documents hardware and software development to produce the SSTDR cable test system.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗