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SBbadger: biochemical reaction networks with definable degree distributions

Abstract Motivation An essential step in developing computational tools for the inference, optimization and simulation of biochemical reaction networks is gauging tool performance against earlier efforts using an appropriate set of benchmarks. General strategies for the assembly of benchmark models include collection from the literature, creation via subnetwork extraction and de novo generation. However, with respect to biochemical reaction networks, these approaches and their associated tools are either poorly suited to generate models that reflect the wide range of properties found in natural biochemical networks or to do so in numbers that enable rigorous statistical analysis. Results In this work, we present SBbadger, a python-based software tool for the generation of synthetic biochemical reaction or metabolic networks with user-defined degree distributions, multiple available kinetic formalisms and a host of other definable properties. SBbadger thus enables the creation of benchmark model sets that reflect properties of biological systems and generate the kinetics and model structures typically targeted by computational analysis and inference software. Here, we detail the computational and algorithmic workflow of SBbadger, demonstrate its performance under various settings, provide sample outputs and compare it to currently available biochemical reaction network generation software. Availability and implementation SBbadger is implemented in Python and is freely available at https://github.com/sys-bio/SBbadger and via PyPI at https://pypi.org/project/SBbadger/. Documentation can be found at https://SBbadger.readthedocs.io. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

HD ADOPT: Heavy-Duty Vehicle Choice Model Documentation

HD ADOPT is a logit consumer vehicle choice and stock model that analyzes the Class 8 tractor market. The model projects future technology shares, fuel consumption, and greenhouse gas (GHG) emissions under input assumptions of technology progress, energy prices, and policies. ADOPT is distinguished from other vehicle choice models through inclusion of non-linear and heterogenous consumer preferences and characterization of the full range of market options rather than use of composite vehicles. In addition, ADOPT has integrated vehicle simulation capabilities that enable performance assessment and optimization of endogenous technology evolution. Optionally, the model is able to adjust this evolution to enforce compliance with fuel economy and GHG emissions regulations. Primary results include projection of technology shares and future in-use fleet energy demand, petroleum consumption, and GHG emissions. This enables analysis and comparison of future scenarios of technology improvements, economic conditions, and national policies. Recent new features for the HD modeling also enable examination of different on-board hydrogen fuel storage technologies from the lens of consumer preferences for vehicle cost and range. This report documents current ADOPT capabilities and methodologies.

33 ADVANCED PROPULSION SYSTEMS↗

Remote Handled Hot Cell Facility and Other Research Transuranic Waste (Debris)

This acceptable knowledge (AK) Summary Report has been prepared for the Central Characterization Program (CCP) for remote-handled (RH) transuranic (TRU) waste generated and managed by Sandia National Laboratories/New Mexico (SNL/NM) in Albuquerque, New Mexico. The waste described in this report was predominately generated in the SNL/NM Hot Cell Facility (HCF) during the removal and packaging of experimental material and decontamination operations in Building 6580 at Technical Area (TA)-V. The waste stream also includes a very small amount of waste (estimated at less than 1 gram of fuel similar to that used for research at the HCF) originating from classified research at TA-I. In addition, the waste also includes secondary waste termed by SNL/NM as process generated waste (PGW), created during repackaging operations for this waste at the Auxiliary Hot Cell Facility (AHCF). The waste has been stored at the Sandia Pulsed Reactor (SPR) Dense Pack Storage Facility within TA-V or the Manzano Bunkers located at Manzano Base within Kirtland Air Force Base. All of the waste is being repackaged at the AHCF. This report was prepared in accordance with CCP-TP-005, CCP Acceptable Knowledge Documentation (Reference 1), to implement the AK requirements of DOE/WIPP-02-3214, Remote-Handled TRU Waste Characterization Program Implementation Plan (WCPIP) (Reference 2); Waste Isolation Pilot Plant Hazardous Waste Facility Permit, Waste Analysis Plan (WIPP-WAP) (Reference 3); and DOE/WIPP-02-3122, Transuranic Waste Acceptance Criteria for the Waste Isolation Pilot Plant (WIPP-WAC) (Reference 4).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Model Package Report: Central Plateau Vadose Zone Models

This model package report describes concisely the modeling objectives, conceptualization, implementation, uncertainty and sensitivity, configuration control, limitations, data needs, and recommendations for improvement of the Central Plateau Vadose Zone Models. This collection of models is developed to meet the vadose zone simulation needs of the Hanford Site Composite Analysis (CA), the Hanford Site Cumulative Impact Evaluation (CIE), and are expected to find other applications in Hanford Site remedial cleanup decision-making processes. This model package report describes and documents the development of the models themselves to fulfill technical approaches defined for the CA and the CIE. This report does not document any specific calculation using these models: instead, applications of individual vadose models to perform specific calculations will be documented in environmental calculation files, including inputs and results, as appropriate. Configuration management for the Central Plateau Vadose Zone Models is managed through assignment of unique sequential numerical version numbers and archival of the models in the Environmental Modeling Management Archive.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Software Quality Assurance for the MOOSE-Based Open-Source Multiphysics Code Cardinal - An Expanded CI Testing Suite

Cardinal is a wrapping of the GPU-oriented spectral element Computational Fluid Dynamics (CFD) code NekRS and the Monte Carlo particle transport code OpenMC within the Multiphysics Object-Oriented Simulation Environment (MOOSE). Cardinal provides high-resolution thermal-hydraulics and/or radiation transport feedback to MOOSE multiphysics simulations. Multiphysics feedback is implemented in a geometry-agnostic manner which eliminates the need for rigid one-to-one mappings. A generic data transfer implementation also allows NekRS and OpenMC to couple to any MOOSE application, enabling a broad set of multiphysics capabilities. Cardinal simulations can also leverage combinations of MPI, OpenMP, and GPU resources. Cardinal continuous development and improvement efforts have led to the software being considered as a high-fidelity design and licensing tool for key areas of nuclear reactor relevant physics, including neutron transport, fluid flow, heat transfer, and mechanical processes. The fast development and expansion of the software from a pure R&D framework towards its application in the nuclear industry and regulation require a focus on developing, enhancing and, maintaining Cardinal’s software quality through strict adherence to a Software Quality Assurance (SQA) framework and SQA program. To facilitate compliance with SQA standards, the Cardinal SQA Program has been initiated during Fiscal Year 2023 (FY23). During the development of the Cardinal SQA Program, multiple gaps have been identified. These gaps are primarily related to model verification and code pedigree as they relate to the use of Cardinal as a safety analysis tool. These gaps have been captured in a report published in 2023. A second report highlighted the progress made during Fiscal Year 2024 (FY24) and described Argonne’s effort to document and integrate software verification within Cardinal’s software development process. This report documents a snapshot of the verification test cases currently available for Cardinal and NekRS in their assimilation into a Continuous Integration (CI) platform. Following the CI practice permits the integrating of source code changes frequently and ensuring that the integrated codebase clears the verification testing for the software. It should be noted that the SQA program itself, including the program plans, procedures, configuration management, and testing strategies, need to be developed in a future step of this task.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Screening and Brief Interventions for Alcohol Use During Pregnancy: Practices Among US Primary Care Clinicians, DocStyles 2019

Alcohol use during pregnancy can cause birth defects and developmental disabilities. From 2018 through 2020, 13.5% of pregnant women reported current drinking. The US Preventive Services Task Force recommends evidence-based tools (eg, AUDIT-C and SASQ) for implementing screening and brief interventions to reduce excessive alcohol use among adults, including pregnant people, for whom any alcohol use is considered excessive. We used DocStyles 2019 data to conduct a cross-sectional analysis to examine current screening and brief intervention practices that primary care clinicians conduct among pregnant patients; clinicians’ confidence levels in conducting screening, brief interventions, and referral to treatment; and the documentation of brief interventions in the medical record. A total of 1,500 US adult medicine clinicians completed the entire survey. Among the respondents who conduct screening (N = 1,373) and brief interventions (N = 1,357) in their practice, nearly all reported implementing screening (94.6%) and brief interventions (94.9%) with their pregnant patients for alcohol use, but fewer than half felt confident about conducting their screening practices (46.5%). Two-thirds (64%) reported using a tool that met the criteria recommended by the US Preventive Services Task Force (USPSTF). Over half documented brief interventions in electronic health record notes (51.7%) or designated space (50.7%). Pregnancy presents a unique opportunity for clinicians to incorporate screening into routine obstetric care and encourage behavior change among patients. Most providers reported always screening their pregnant patients for alcohol use, but fewer used evidence-based USPSTF-recommended screening tools. Increased clinician confidence in screening and brief intervention, the use of standardized screening tools tailored to pregnant people, and maximal use of electronic health record technology may enhance the benefits of their application to alcohol use, which ultimately can reduce adverse outcomes associated with alcohol use during pregnancy.

60 APPLIED LIFE SCIENCES↗

Neutron Coincidence Measurements of Uranium-233 Oxide

Renewed international interest in thorium-fueled advanced reactors has challenged the safeguards community to address future proliferation concerns. Thorium-based technology presents many benefits but does not eliminate the proliferation risks associated with producing and processing fissile material. A byproduct of thorium-fueled reactors is uranium-233, which is classified as a direct-use material. As a result, the development of new or improved methods to characterize and measure materials containing 233U must mirror the pace of development of reactors and facilities that produce such material. Research is underway to assess, develop, and test approaches for safeguarding nuclear materials within the thorium fuel cycle. Neutron signatures from the nondestructive assay (NDA) of materials containing 233U are being quantified to inform the potential characterization of these materials. Using a traditional neutron coincidence counter and a series of well-documented 233U oxide samples, initial measurements have been made to assess the feasibility of 233U characterization and discrimination from other uranium isotopes, primarily 235U, using a combination of measurement techniques and analysis methods. Data acquisition is performed in list mode, allowing for a variety of analyses to be performed on the raw data that is not available using traditional shift register technology. Measurements were performed in passive and active configurations to quantify the strength of signal and to validate simulations in support of this work. This paper presents and discusses the results of the initial measurements of 233U oxide performed at Oak Ridge National Laboratory.

Lockhart, Madeline↗

Experimental protocol for phase 1 of the APARC QUOCA (QUasibiennial oscillation and Ozone Chemistry interactions in the Atmosphere) working group

The quasi-biennial oscillation (QBO) is the main mode of variability in the tropical stratosphere, influencing the predictability of other regions in the atmosphere through its teleconnections to the stratospheric polar vortices and coupling to surface tropical and extratropical variability. However, climate and forecasting models consistently underestimate QBO amplitudes in the lower stratosphere, likely contributing to their failure to simulate these teleconnections. One underexplored contributor to model biases is missing representation of ozone-radiative feedbacks, which enhance temperature variability in the lower stratosphere, particularly at periods at and greater than the QBO (>28 months). While previous studies suggest that ozone-radiative feedbacks can impact QBO periods, amplitudes and the associated secondary circulation in the lower stratosphere, the reported impacts differ widely among models and are hard to interpret due to differences in methodology. To this end, here we propose a coordinated experimental protocol – held joint between the Atmospheric Processes and their Role in Climate (APARC) Quasi-Biennial Oscillation Initiative (QBOi) and Chemistry Climate Modeling Initiative (CCMI) activities – which is aimed at assessing the coupling between stratospheric ozone, temperature and the circulation. We use the proposed experiments to define the ozone feedback on the QBO in both present-day and idealized (abrupt quadrupling of carbon dioxide) climates. While primary focus is on the QBO, the proposed protocol also enables analysis of other aspects of ozone-radiative-dynamical coupling in the atmosphere, including impacts on the Brewer-Dobson Circulation and tropospheric eddy-driven jet responses to future climate change. Here we document the scientific rationale and design of the QUOCA Phase 1 experiments, summarize the data request, and give a brief overview of participating models. Preliminary results using the NASA Goddard Institute for Space Studies E2-2 climate model are used to illustrate sensitivities to certain methodological choices.

Environmental sciences↗

Sampling and Analysis Plan for Investigation of Undeclared Nuclear Activities - 20104

The nuclear-centered energy policy in South Korea is moving towards a nuclear-free era. It also facilitates an action or progress on the denuclearization of the Korean peninsula. The Nuclear Safety and Security Commission (NSSC) launched a new R and D project which attempts to verify nuclear activities via analyzing environmental samples. Environmental samples possibly contain significant radiological information relevant to past undeclared activities. In order to precisely verify them, it is essential to provide 1) the concrete information of target facilities, 2) appropriate methodologies and procedures, and 3) well-suited instrumentation and equipment corresponding to sample signatures. It is also important to provide scientific reliability or validity in any process such as sample collection, handling, transportation and laboratory analysis. Therefore, the information of nuclear facilities (fuel fabrication plant, graphite moderated reactor, reprocessing plant) in North Korea are reviewed in order to determine parameters for appropriate sampling methods representing a facility's characteristics. Secondly, a sampling procedure for radioactive elements is being developed based on international and domestic standards such as ASTM (American Society for Testing and Materials), KS (Korean industrial Standards), and International Atomic Energy Agency (IAEA) manuals. The procedure contains some specific information including sampling process, sampling tools, amount of sample, sample identification, and other related information. Developing the qualified national guidelines is most important since sampling and analyzing results can be used as evidences of nuclear activities. The guideline developed through this work will clearly define various methodologies such as document verification, sampling procedures, collection methods, sample storage criteria, chain of custody, and transportation conditions. The final objective of this work is to establish the infrastructure and regulatory framework for assessment of nuclear activities, and provide a national guideline for sampling and analysis. This will bring confidence in the results and play a critical role in complete denuclearization progress in South Korea. (authors)

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

Integrated Methane Monitoring Platform Extension, Volume I: Final Technical Report

The IMMPE project, DE-FE0032284, was to enhance methane monitoring technologies and their applications across various natural gas asset classes. The scope included deploying advanced methane detection and monitoring technologies to identify and mitigate fugitive methane emissions, measuring emission rates, and assessing impacts. The findings included the successful mitigation of identified emissions and quantification of emission rates. A key outcome was the development of a comprehensive template and summary of recommendations for methane emissions monitoring, which is replicable for both upstream and downstream applications. Furthermore, the project emphasized the importance of education by providing training opportunities for technicians and regulators, thereby fostering awareness and promoting the adoption of cost-effective methane emissions monitoring and management techniques.

02 PETROLEUM↗

Science of the Van Allen Probes Science Operations Centers

The Van Allen Probes mission operations materialized through a distributed model in which operational responsibility was divided between the Mission Operations Center (MOC) and separate instrument specific SOCs. The sole MOC handled all aspects of telemetering and receiving tasks as well as certain scientifically relevant ancillary tasks. Each instrument science team developed individual instrument specific SOCs proficient in unique capabilities in support of science data acquisition, data processing, instrument performance, and tools for the instrument team scientists. In parallel activities, project scientists took on the task of providing a significant modeling tool base usable by the instrument science teams and the larger scientific community. With a mission as complex as Van Allen Probes, scientific inquiry occurred due to constant and significant collaboration between the SOCs and in concert with the project science team. Planned cross-instrument coordinated observations resulted in critical discoveries during the seven-year mission. Instrument cross-calibration activities elucidated a more seamless set of data products. Specific topics include post-launch changes and enhancements to the SOCs, discussion of coordination activities between the SOCs, SOC specific analysis software, modeling software provided by the Van Allen Probes project, and a section on lessons learned. One of the most significant lessons learned was the importance of the original decision to implement individual team SOCs providing timely and well-documented instrument data for the NASA Van Allen Probes Mission scientists and the larger magnetospheric and radiation belt scientific community.

47 OTHER INSTRUMENTATION↗

Data preservation in high energy physics

Data preservation is a mandatory specification for any present and future experimental facility and it is a cost-effective way of doing fundamental research by exploiting unique data sets in the light of the continuously increasing theoretical understanding. This document summarizes the status of data preservation in high energy physics. The paradigms and the methodological advances are discussed from a perspective of more than ten years of experience with a structured effort at international level. The status and the scientific return related to the preservation of data accumulated at large collider experiments are presented, together with an account of ongoing efforts to ensure long-term analysis capabilities for ongoing and future experiments. Transverse projects aimed at generic solutions, most of which are specifically inspired by open science and FAIR principles, are presented as well. A prospective and an action plan are also indicated.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Software Requirements for a Consequence Management Sample Data Simulator for Training and Drills

This document describes the requirements for a software tool that will enable FRMAC to simulate large sets of sample result data that is based realistically on simulated radionuclide deposition grids from NARAC. The user of this tool would be scientists involved in exercise and drill planning or part of the simulation cell of an exercise controller team. A key requirement is that this tool must be able to be run with a reasonable amount of training and job aids by any person within the Assessment, Laboratory Analysis, or Monitoring and Sampling divisions of the FRMAC to support any level of exercise from the small IPX to the national level full scale exercise. This tool should be relatively lean and stand-alone so that the user can run it in the field with limited IT resources. This document will describe the desired architecture, design characteristics, order of operations, and algorithms that can be given to a software development team to assist them in project scoping, costing, and eventually, development.

61 RADIATION PROTECTION AND DOSIMETRY↗

Google/Makani Energy Kite Modeling (CRADA CRD-18-00569 Final Report)

In support of Makani’s energy kite development program, Makani engaged with NREL to develop, verify, and document a multiphysics engineering model of a megawatt-scale tethered energy kite (named KiteFAST). After the original development of KiteFAST was completed, Makani further engaged NREL to develop a software enhancement of KiteFAST to enable the dynamics modeling of an energy kite tethered to a floating offshore platform (named KiteFAST-OS). Before this project, the capability to model the aero-hydro-servo-elastic dynamics of an airborne wind energy (AWE) system with electricity generation on the flying device (fly gen) and crosswind flight operation did not exist. Such physics-based modeling capability is needed for loads analysis, structural design, and certification of energy kites. Throughout the project, an exclusive license kept KiteFAST and KiteFAST-OS available only to Makani, NREL, and its counterparts. With the ending of Makani, the KiteFAST and KiteFAST-OS software were merged into a single code base (named KiteFAST), the exclusive license was terminated, and the source code, documentation, and example models were released publicly.

17 WIND ENERGY↗

Search for flavour-changing neutral-current couplings between the top quark and the photon with the ATLAS detector at s = 13 TeV

This letter documents a search for flavour-changing neutral currents (FCNCs), which are strongly suppressed in the Standard Model, in events with a photon and a top quark with the ATLAS detector. The analysis uses data collected in pp collisions at TeV during Run 2 of the LHC, corresponding to an integrated luminosity of 139 fb –1 . Both FCNC top-quark production and decay are considered. The final state consists of a charged lepton, missing transverse momentum, a b-tagged jet, one high-momentum photon and possibly additional jets. A multiclass deep neural network is used to classify events either as signal in one of the two categories, FCNC production or decay, or as background. No significant excess of events over the background prediction is observed and 95% CL upper limits are placed on the strength of left- and right-handed FCNC interactions. The 95% CL bounds on the branching fractions for the FCNC top-quark decays, estimated (expected) from both top-quark production and decay, are B(t → uγ) < 0.85 (0.88$^{+0.37}_{-0.25}$) × 10 –5 and B(t → cγ) < 4.2 (3.40$^{+1.35}_{-0.95}$) × 10 –5 for a left-handed tqγ coupling, and B(t → uγ) < 1.2 (1.20$^{+0.50}_{-1.33}$) ×10 –5 and B(t → cγ) < 4.5 (3.70$^{+1.47}_{-1.03}$) × 10 –5 for a right-handed coupling.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Comparison of Light-Weight Radioisotope Heater Unit (LWRHU) Historical Testing to Special Form Testing Requirements

This paper compares the Light-Weight Radioisotope Heater Unit (LWRHU) historical testing to Department of Transportation (DOT) Special Form criteria per 49 CFR Part 173, Shippers-General Requirements for Shipments and Packages, Section 469, Tests for special form Class 7 (radioactive) materials as specified in DOE-STD-1027, Hazard Categorization of DOE Nuclear Facilities. Compliance with the aforementioned criteria allows for the exclusion of radioactive sources from the facility’s nuclear material inventory. As part of a new program at Los Alamos National Laboratory (LANL), LWRHUs are planned to be moved into TA-55, PF-5 Power Source Assembly Area (PSAA) for assembly and testing activities. The PSAA Facility is categorized as a low hazard, non-nuclear facility per DOE STD-1027 and is described in TA55-PF-5-FHC-11-001, Facility Hazard Categorization of the PSAA at PF-5, TA-55. The Facility Hazard Categorization document states, there must be documentation that radioactive sources are engineered to pass the special form testing specified by DOT in 49 CFR 173.469, Tests for special form Class 7 (radioactive) materials or ANSI N43.6, Sealed Radioactive Sources - Classification. This paper documents the extensive historical environmental safety testing of the LWRHU and demonstrates its ability to survive potential launch safety accident scenarios. The testing results are used herein to demonstrate through a comparative analysis that the robust design of the LWRHU meets or exceeds the special form testing specifications in 49 CFR 173.469, enabling the LWRHU to be transported and handled in PF-5 in support of testing and assembly program.

07 ISOTOPE AND RADIATION SOURCES↗

An Eight-County Appraisal of the San Andres Residual Oil Zone (ROZ) 'Fairway' of the Permian Basin

This document assesses the size and distribution of the oil resource in an eight-county portion of the San Andres residual oil zone (ROZ) fairway in the Permian Basin. Using well log analysis, the study divided the ROZ into partitions, developed a database of geologic properties for each partition and estimated the oil in place in each partition. The study then used the FE/NETL CO 2 Prophet Model to estimate the oil that could be produced and CO 2 stored from applying CO 2 EOR to each partition. With the FE/NETL Onshore CO 2 EOR Cost Model, the commercially viable partitions were identified as those that could produce oil and store CO 2 economically at an oil price of $75/STB. The remaining geologically viable partitions could use CO 2 EOR to store CO 2 with production of oil to offset some of the costs. The database used for this study, and a report describing the database is available on NETL's website under the Collection Name Eight-County San Andres ROZ Appraisal.

02 PETROLEUM↗

A Four-County Appraisal of the San Andres Residual Oil Zone (ROZ) 'Fairway' of the Permian Basin

This document assesses the size and distribution of the oil resource in a four-county portion of the San Andres residual oil zone (ROZ) fairway in the Permian Basin. Using well log analysis, the study divided the ROZ into partitions, developed a database of geologic properties for each partition and estimated the oil in place in each partition. The study then used the FE/NETL CO 2 Prophet Model to estimate the oil that could be produced and CO 2 stored from applying CO 2 EOR to each partition. With the FE/NETL Onshore CO 2 EOR Cost Model, the commercially viable partitions were identified as those that could produce oil and store CO 2 economically at an oil price of $75/STB. The remaining geologically viable partitions could use CO 2 EOR to store CO 2 with production of oil to offset some of the costs. The database used for this study, and a report describing the database is available on NETL's website under the Collection Name: Four-County San Andres ROZ Appraisal.

02 PETROLEUM↗