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NuGraph2 with context-aware inputs: physics-inspired improvements in semantic segmentation

Graph neural networks have recently shown strong promise for event reconstruction tasks in Liquid Argon Time Projection Chambers, yet their performance remains limited for underrepresented classes of particles, such as Michel electrons. In this work, we investigate physics-informed strategies to improve semantic segmentation within the NuGraph2 architecture. We explore three complementary approaches: (i) enriching the input representation with context-aware features derived from detector geometry and track continuity, (ii) introducing auxiliary decoders to capture class-level correlations, and (iii) incorporating energy-based regularization terms motivated by Michel electron energy distributions. Experiments on MicroBooNE public datasets show that physics-inspired feature augmentation yields the largest gains, particularly boosting Michel electron precision and recall by disentangling overlapping latent space regions. In contrast, auxiliary decoders and energy-regularization terms provided limited improvements, partly due to the hit-level nature of NuGraph2, which lacks explicit particle- or event-level representations. Our findings highlight that embedding physics context directly into node-level inputs is more effective than imposing task-specific auxiliary losses, and suggest that future hierarchical architectures such as NuGraph3, with explicit particle- and event-level reasoning, will provide a more natural setting for advanced decoders and physics-based regularization. The code for this work is publicly available on Github at https://github.com/vitorgrizzi/nugraph_phys/tree/main_phys.

Other Experiments↗

Evaluation of PBR Spent Fuel Criticality and Dose Rate Compliance for Storage and Transportation

Spent tri-structural isotropic (TRISO)–based fuels have a strong track record in storage and transportation without documented incidents. This work seeks to reduce uncertainty to aid in more informed spent fuel management of TRISO-based fuels by modeling both fresh and spent pebble bed reactor (PBR) fuel and comparing the results to the regulatory standards from 10 CFR 71. SCALE was used for all modeling due to it having fast and accurate methods for handling PBR fuel modeling, as well as having an efficient method for shielding calculations in monaco with automated variance reduction using importance calculations (MAVRIC), which utilizes the consistent adjoint-driven importance sampling (CADIS) and the forward-weighted consistent adjoint-driven importance sampling (FW-CADIS) methods. KENO-VI was used for all criticality calculations, TSUNAMI was used for uncertainty quantification on k-effective, TRITON and the Oak Ridge isotope generation code (ORIGEN) were both used for depletion of the fuel, and MAVRIC was used for shielding calculations. For criticality assessments, this study focused on the requirement that the value of the neutron multiplication factor, k-effective (k-eff), would not exceed a peak value of 0.95, including uncertainty, with 95% confidence. Criticality was initially examined by modeling fresh fuel from three different designs—HTR-10 fuel, PBMR-400 fuel, and demonstration fuel representative of a TRISO-fueled modern high-temperature gas reactor (HTGR) design, henceforth referred to as Demo HTGR—and placing them into various sized containers with conditions described in 10 CFR 71 to quantify the peak k-eff state. When the peak value of 0.95 k-eff was exceeded, mitigation methods were examined in those scenarios. Burnup credit, pebble displacement in areas of strong neutron multiplication, and random pebble replacement using pebbles of various compositions and replacement fractions were examined. In summary, the criticality of PBR fuels can be well accounted for by restricting container size, taking credit for burnup, or by displacing/replacing pebbles. Uncertainty of the k-eff due to nuclear data uncertainties was recorded at ~0.6644%Δk/k, or roughly 664% mil (pcm). The nuclear data–induced uncertainty was relatively small and should not require significant modification in the design to be accounted for. Revisions to the evaluated nuclear data file values have been shown to have a larger impact than nuclear data–induced uncertainty. For dose rate aspects, U.S. Nuclear Regulatory Commission regulations require a maximum dose rate of 10 millirem per hour (mrem/h) at 2 meters. In examining the dose rate behavior of spent PBR fuel, the representative Demo HTGR fuel was modeled exclusively due to it possessing the highest target burnup of the examined fuels. Equilibrium cycle modeling methods were used to produce a higher-fidelity discharge isotopic composition than simple assumptions, such as reflected pebbles. The discharge composition was used as a source term in the fixed-source transport shielding calculations, and dose rates were calculated at 2 m for the shortest possible cooling time. The low concentration of fuel material led to dose rates that were in line with regulatory limits, despite the high burnup when compared to traditional light water reactor fuels. In conclusion, the methods employed in this study would require more work to further verify and validate and are limited to the criticality and dose rate analyses performed.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Multi-Physics Simulations of Molten Chloride Fast Reactor using Nek5000 and PROTEUS-NODAL

This report documents the FY20 work to demonstrate a specific multi-physics capability within NEAMS tools to model molten chloride fast reactors (MCFR). Specifically, the CFD code Nek5000 and the neutronics code PROTEUS-NODAL were coupled off-line to calculate the delayed neutron precursor distribution within the flowing fuel salts in an MCFR core. An MCFR benchmark problem and a 3D test problem based on a conceptual MSR design were successfully solved through the coupled simulation of Nek5000 and PROTEUS-NODAL. In the coupled simulations for these test problems, Nek5000 provided high-quality flow field information, and PROTEUS-NODAL performed the neutron diffusion calculation along with the precursor drift model. The impact of precursor drift on the core status was also investigated. Additionally, the precursor drift model implemented in PROTEUS-NODAL was verified by making use of the reference precursor distribution generated from Nek5000. Results of these test problems suggest that the multi-physics capability of Nek5000 and PROTEUS-NODAL was properly developed for tracking delayed neutron precursor drift.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Flight Software Dictionary Development for the Mars2020 Rover

The Mars2020 project, developed and operated by the Jet Propulsion Laboratory (JPL), successfully landed the Perseverance rover and its flying companion Ingenuity on the surface of Mars on February 18th 2021. Perseverance combines heritage and cutting-edge flight software and hardware to accomplish crucial mission requirements related to Martian surface sampling. The design, development, and operation of NASA’s large strategic science missions require the ability to communicate spacecraft capabilities to hundreds of engineers across multiple disciplines. The interaction between flight and ground software development, Verification and Validation (V&V), Assembly, Test, and Launch Operations (ATLO), and management each demand quick understanding of unique slices of information for each discipline. This information includes the current capabilities of the flight system as well as future capabilities and their status as they are developed and tested. Despite the fundamental and critical nature of this information, the flight software dictionaries used to track it are a stumbling block for many projects. These dictionaries provide the cornerstone for the interpretation of data sent from the spacecraft, allowing for quick comprehension by engineers on the ground. During both spacecraft development and operations, flight software dictionary management includes significant challenges due to the large number of interfacing systems and the subtle yet distinct needs of each.The engineering of flight software dictionaries for Mars2020 had numerous challenges, most-notably: parallel dictionary development to support simultaneous separate flight software build campaigns for each mission phase (cruise and surface), managing requests for operations-enabling information without perturbing the heritage interface with the rover, and the introduction of new tools by the dictionary stakeholders that forced the dictionary team to innovate and redesign the heritage tool chain. These challenges generated guiding principles for the dictionary development effort: emphasize coding best practices and unit testing in the dictionary code development tool chain, use institutionally provided COTS (commercial-off-the-shelf) tools whenever possible, and maintain the heritage flight-ground interface all while advancing operations-enabling information via a loosely coupled interface.Throughout development and operations, the Mars2020 dictionary toolchain included IBM DOORS Next Generation, GitHub, Microsoft Excel, Docker, Jenkins, and a significant custom-built Python codebase. Significant interfaces included JPL’s command and control software, heritage flight software team tools and processes, and the many cloud-based ground tools developed for the mission.This paper will discuss the requirements for the Mars2020 dictionary development, the development team’s response to those requirements, lessons learned throughout the process, steps taken towards automated deliveries and continuous integration of stakeholder inputs, potential toolchain improvements for Mars2020, and key takeaways that could be applied to future missions.

Pyrzak, Guy↗

Numerical modeling of a proof-of-principle experiment on optical stochastic cooling at an electron storage ring

Cooling of beams circulating in storage rings is critical for many applications including particle colliders and synchrotron light sources. A method enabling unprecedented beam-cooling rates, optical stochastic cooling (OSC), was recently demonstrated in the Integrable Optics Test Accelerator (IOTA) electron storage ring at Fermilab [J. Jarvis , ]. This paper describes the numerical implementation of the OSC process in the particle-tracking program and discusses the validation of the developed model with available experimental data. The model is also employed to highlight some features associated with different modes of operation of OSC. The developed simulation tool should be valuable in guiding future configurations of optical stochastic cooling and, more broadly, modeling self-field-based beam manipulations. Published by the American Physical Society 2024

43 PARTICLE ACCELERATORS↗

Virtual Instrument Simulator for CERES

A benchtop virtual instrument simulator for CERES (Clouds and the Earth's Radiant Energy System) has been built at NASA, Langley Research Center in Hampton, VA. The CERES instruments will fly on several earth orbiting platforms notably NASDA's Tropical Rainfall Measurement Mission (TRMM) and NASA's Earth Observing System (EOS) satellites. CERES measures top of the atmosphere radiative fluxes using microprocessor controlled scanning radiometers. The CERES Virtual Instrument Simulator consists of electronic circuitry identical to the flight unit's twin microprocessors and telemetry interface to the supporting spacecraft electronics and two personal computers (PC) connected to the I/O ports that control azimuth and elevation gimbals. Software consists of the unmodified TRW developed Flight Code and Ground Support Software which serves as the instrument monitor and NASA/TRW developed engineering models of the scanners. The CERES Instrument Simulator will serve as a testbed for testing of custom instrument commands intended to solve in-flight anomalies of the instruments which could arise during the CERES mission. One of the supporting computers supports the telemetry display which monitors the simulator microprocessors during the development and testing of custom instrument commands. The CERES engineering development software models have been modified to provide a virtual instrument running on a second supporting computer linked in real time to the instrument flight microprocessor control ports. The CERES Instrument Simulator will be used to verify memory uploads by the CERES Flight Operations TEAM at NASA. Plots of the virtual scanner models match the actual instrument scan plots. A high speed logic analyzer has been used to track the performance of the flight microprocessor. The concept of using an identical but non-flight qualified microprocessor and electronics ensemble linked to a virtual instrument with identical system software affords a relatively inexpensive simulation system capable of high fidelity.

Chapman, John J.↗

Requirements Description of the REBUS Software for the Versatile Test Reactor

This report presents the modeling and simulation capabilities of Argonne National Laboratory’s fuel cycle analysis code, the REactor BUrnup System (REBUS), that will be relied on for the VTR project. These capabilities will then be used to establish the set of REBUS verification tasks necessary to verify REBUS for usage on the VTR project. A similar path was followed for the DIF3D software where its’ requirements and verification tasks were established. REBUS has been maintained by Argonne since the early 1960s to support its reactor design mission. That software transitioned from the original REBUS to REBUS-2 in the mid 1970s and to REBUS-3 in the mid 1980s. Since then REBUS has gone through many revisions to the current REBUS-11. Note that this version numbering is consistent with the progression of DIF3D, the base flux solver that REBUS is built upon. The name REBUS refers to a pictorial based puzzle as the original developers were inspired by having to track thousands of unique fuel assemblies as they are inserted into the reactor, depleted, shuffled, discharged, and reprocessed.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Tracking the Relative Motion of Four Space Payloads Launched from a Sub-Orbital NASA Rocket

One problem, which is comparatively new in the field of GPS applications, is the determination of the relative trajectories of space vehicles. Applications include the docking of spacecraft, collision avoidance in the area of space stations, and trajectory reconstruction of multiple payloads. The required precision in any of these applications will vary, according to the requirements of the task and abilities of GPS to cope with the environment and the dynamics. This paper describes the post-mission reconstruction of the relative trajectories of four GPS receivers attached to four payloads jettisoned from a Black Brant XII rocket. This vehicle was launched by the National Aeronautics and Space Administration (NASA) in January 1999 from the Poker Flats Research Range near Fairbanks, Alaska. The Black Brant XII is a sub-orbital rocket designed to carry payloads of 100 to 500 kg into the upper atmosphere. Flight time is generally in the order of 10-20 minutes. In this experiment, a GPS receiver and antenna was attached to each of the four payloads. One of the GPS receivers was assigned as the "base station", while the other 3 receivers were designated as remotes. GPS time, code and phase measurements were telemetered to a ground station for real-time processing and storage. The object of the mission was to re-compute the position and velocity of the remote units with respect to the base station during the launch phase and after the payloads separated. During the launch segment the 3 baseling distances between the 4 antennas are known from plans and are constant values until each payload is released. On the fly ambiguity determination was used to establish local coordinates from the base antenna to each of the other 3 GPS units during flight. Distance computations were made from the GPS-derived coordinates and compared to plan distances. Using this methodology an error analysis of the relative GPS accuracies has been presented and in addition a description given of the respective payload behaviour following separation from the vehicle.

Martell, Hugh↗

Nozzle Plume/Shock Interaction Experimental and Computational Sonic Boom Analyses from the NASA Ames 9- by 7-Foot Supersonic Wind Tunnel

A wind tunnel test and a computational study were conducted to investigate the complex interactions between a supersonic nozzle plume and shock waves of differing strengths generated from various aft surfaces typical of supersonic aircraft. These analytically-defined aft surfaces were representative of horizontal tails of various sizes, and an aft deck. CFD simulations of many proposed model configurations allowed for assessments of the detailed flow interactions of components in close proximity to the nozzle, as well as assessments of the nozzle jet flow itself. The evaluation of the computational results for many candidate configurations guided the design of model components. The interactions of the waveforms from these surfaces with the jet exhaust plume can have significant adverse effects on the loudness of the sonic boom if the surfaces are not carefully integrated into an aircraft design. The greatest discrepancy in estimating sonic boom loudness for low-boom flight vehicles is currently in predicting the signatures from the aft part of an aircraft, including the interactions with the plume flow. The objectives of this test were to gain a better understanding of these interactions, and to provide a detailed experimental database from multiple sources for use as validation cases for CFD tool development. The subject test was run in the NASA Ames 9- by 7-Ft Supersonic Wind Tunnel in February 2016 at Mach numbers of 1.6 and 2.0, and was funded by the NASA Commercial Supersonics Technology (CST) Project. The nozzle flow was provided by high-pressure air (HPA) pumped through the model, and pressure signature data were acquired with the NASA 14-inch sonic boom pressure rail. The rail measured the locations of the shocks and expansions at various distances and off-track angles from the model. This enabled the impact of the nozzle plume/shock interactions on the near- and mid-field sonic boom pressure waveforms to be quantified. Schlieren images of the flow field around and behind the model were obtained with an RBOS (Retroreflective Background-Oriented Schlieren) technique to determine the origins of the shock and expansion waves, to identify the shape and boundaries of the plume, and to determine the changes in incoming and exiting waveforms within the plume. A total pressure rake was positioned closely behind the model nozzle in order to measure the total pressure profiles of the flow above, within, and below the nozzle exhaust. Model angles and positions in the tunnel were measured by photogrammetry using two cameras since the lack of a model force balance prevented the measurement of model deflections under load.Navier-Stokes computations using two different CFD codes were compared to the experimental sonic boom pressure signature data, and the rake total pressure data in the plume. A computational schlieren technique was used to compare the computed flow field with the RBOS images. The computational results were also used to complement the test data with flow field quantities that could not be measured, such as Mach number and pressure distributions to distinguish shock waves and expansion waves.

sonic boom↗

Tracking Active Phase Behavior on Boron Nitride during the Oxidative Dehydrogenation of Propane Using Operando X-ray Raman Spectroscopy

Hexagonal boron nitride (hBN) is a highly selective catalyst for the oxidative dehydrogenation of propane (ODHP) to propylene. Using a variety of ex situ characterization techniques, the activity of the catalyst has been attributed to the formation of an amorphous boron oxyhydroxide surface layer. The ODHP reaction mechanism proceeds via a combination of surface mediated and gas phase propagated radical reactions with the relative importance of both depending on the surface-to-void-volume ratio. Here we demonstrate the unique capability of operando X-ray Raman spectroscopy (XRS) to investigate the oxyfunctionalization of the catalyst under reaction conditions (1 mm outer diameter reactor, 500 to 550 °C, P = 30 kPa C 3 H 8 , 15 kPa O 2 , 56 kPa He). We probe the effect of a water cofeed on the surface of the activated catalyst and find that water removes boron oxyhydroxide from the surface, resulting in a lower reaction rate when the surface reaction dominates and an enhanced reaction rate when the gas phase contribution dominates. Computational description of the surface transformations at an atomic-level combined with high precision XRS spectra simulations with the OCEAN code rationalize the experimental observations. Finally, this work establishes XRS as a powerful technique for the investigation of light element-containing catalysts under working conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

ACES: Infrastructure As Code. Model Optimization and Performance Capability

Infrastructure as Code (IaC) refers to managing infrastructure (networks, physical/virtual machines, storage, and connection topology) in a descriptive model/language, rather than configuring it manually or using interactive configuration tools. Just like source code can be compiled to generate the same binary code, IaC enables generating the same environment every time it is applied. IaC is a key DevOps practice and is generally used in conjunction with continuous integration (CI) and continuous delivery (CD). In CI, all code changes are merged into a mainline branch and validated multiple times a day as developers check in their changes to the source code. In CD on the other hand, code changes are automatically packaged for a new release-to-production on a regular basis. This typically enables teams to deliver software changes much more quickly and often. Developing and managing the ACES platform using (IaC) is vital for the robust deployment and continued sustainment of this foundational computing capability. IaC and DevOps practices will help us solve many of the common challenges often encountered in developing and maintaining compute infrastructure. First, it will make the provisioning, deployment, and maintenance of the compute infrastructure across multiple environments much more efficient. Second, these processes help make the overall system much more stable by continuously testing new changes as they are introduced to the system. Third, it allows us to be much more confident of the security controls in place since they can be tested as part of the CI process and all new changes can be audited and tracked. Finally, IaC enables the ACES Platform to be adaptable to the emerging technologies due to its ability to spin up different test beds to evaluate and incorporate these technologies. This document addresses common infrastructure-management challenges, describes what happens if they are not addressed, and highlights the value of utilizing IaC to tackle them. Finally, we will provide a high-level overview of the IaC and DevOps practices being utilized by the ACES Platform team.

97 MATHEMATICS AND COMPUTING↗

On the Formation of Massive Stars

We calculate numerically the collapse of slowly rotating, nonmagnetic, massive molecular clumps of masses 30,60, and 120 Stellar Mass, which conceivably could lead to the formation of massive stars. Because radiative acceleration on dust grains plays a critical role in the clump's dynamical evolution, we have improved the module for continuum radiation transfer in an existing two-dimensional (axial symmetry assumed) radiation hydrodynamic code. In particular, rather than using "gray" dust opacities and "gray" radiation transfer, we calculate the dust's wavelength-dependent absorption and emission simultaneously with the radiation density at each wavelength and the equilibrium temperatures of three grain components: amorphous carbon particles. silicates, and " dirty ice " -coated silicates. Because our simulations cannot spatially resolve the innermost regions of the molecular clump, however, we cannot distinguish between the formation of a dense central cluster or a single massive object. Furthermore, we cannot exclude significant mass loss from the central object(s) that may interact with the inflow into the central grid cell. Thus, with our basic assumption that all material in the innermost grid cell accretes onto a single object. we are able to provide only an upper limit to the mass of stars that could possibly be formed. We introduce a semianalytical scheme for augmenting existing evolutionary tracks of pre-main-sequence protostars by including the effects of accretion. By considering an open outermost boundary, an arbitrary amount of material could, in principal, be accreted onto this central star. However, for the three cases considered (30, 60, and 120 Stellar Mass originally within the computation grid), radiation acceleration limited the final masses to 3 1.6, 33.6, and 42.9 Stellar Mass, respectively, for wavelength-dependent radiation transfer and to 19.1, 20.1, and 22.9 Stellar Mass. for the corresponding simulations with gray radiation transfer. Our calculations demonstrate that massive stars can in principle be formed via accretion through a disk. The accretion rate onto the central source increases rapidly after one initial free-fall time and decreases monotonically afterward. By enhancing the nonisotropic character of the radiation field, the accretion disk reduces the effects of radiative acceleration in the radial direction - a process we call the "flashlight effect." The flashlight effect is further amplified in our case by including the effects of frequency-dependent radiation transfer. We conclude with the warning that a careful treatment of radiation transfer is a mandatory requirement for realistic simulations of the formation of massive stars.

Yorke, Harold W.↗

Viscous Gubser flow with conserved charges to benchmark fluid simulations

We present semi-analytical solutions for the evolution of both the temperature and chemical potentials for viscous Gubser flow with conserved charges. Such a solution can be especially useful in testing numerical codes intended to simulate relativistic fluids with large chemical potentials. The freeze-out hypersurface profiles for constant energy density are calculated, along with the corresponding normal vectors, and presented as a new unit test for numerical codes. We also compare the influence of the equation of state on the semi-analytical solutions. We benchmark the newly developed smoothed particle hydrodynamics code ccake that includes both shear viscosity and three conserved charges. Here, the numerical solutions are in excellent agreement with the semi-analytical solution and are also able to accurately reproduce the hypersurface at freeze-out.

Hydrodynamic models↗

Aspirating Seal Development: Analytical Modeling and Seal Test Rig

This effort is to develop large diameter (22 - 36 inch) Aspirating Seals for application in aircraft engines. Stein Seal Co. will be fabricating the 36-inch seal(s) for testing. GE's task is to establish a thorough understanding of the operation of Aspirating Seals through analytical modeling and full-scale testing. The two primary objectives of this project are to develop the analytical models of the aspirating seal system, to upgrade using GE's funds, GE's 50-inch seal test rig for testing the Aspirating Seal (back-to-back with a corresponding brush seal), test the aspirating seal(s) for seal closure, tracking and maneuver transients (tilt) at operating pressures and temperatures, and validate the analytical model. The objective of the analytical model development is to evaluate the transient and steady-state dynamic performance characteristics of the seal designed by Stein. The transient dynamic model uses a multi-body system approach: the Stator, Seal face and the rotor are treated as individual bodies with relative degrees of freedom. Initially, the thirty-six springs are represented as a single one trying to keep open the aspirating face. Stops (Contact elements) are provided between the stator and the seal (to compensate the preload in the fully-open position) and between the rotor face and Seal face (to detect rub). The secondary seal is considered as part of the stator. The film's load, damping and stiffness characteristics as functions of pressure and clearance are evaluated using a separate (NASA) code GFACE. Initially, a laminar flow theory is used. Special two-dimensional interpolation routines are written to establish exact film load and damping values at each integration time step. Additionally, other user-routines are written to read-in actual pressure, rpm, stator-growth and rotor growth data and, later, to transfer these as appropriate loads/motions in the system-dynamic model. The transient dynamic model evaluates the various motions, clearances and forces as the seals are subjected to different aircraft maneuvers: Windmilling restart; start-ground idle; ground idle-takeoff; takeoff-burst chop, etc. Results of this model show that the seal closes appropriately and does not ram into the rotor for all of the conditions analyzed. The rig upgrade design for testing Aspirating Seals has been completed. Long lead-time items (forgings, etc.) have been ordered.

Bharat Bagepalli↗

Phase Space Reconstruction from Accelerator Beam Measurements Using Neural Networks and Differentiable Simulations

Characterizing the phase space distribution of particle beams in accelerators is a central part of accelerator understanding and performance optimization. However, conventional reconstruction-based techniques either use simplifying assumptions or require specialized diagnostics to infer high-dimensional (> $2D$) beam properties. In this Letter, we introduce a general-purpose algorithm that combines neural networks with differentiable particle tracking to efficiently reconstruct high-dimensional phase space distributions without using specialized beam diagnostics or beam manipulations. Furthermore, we demonstrate that our algorithm accurately reconstructs detailed 4D phase space distributions with corresponding confidence intervals in both simulation and experiment using a single focusing quadrupole and diagnostic screen. This technique allows for the measurement of multiple correlated phase spaces simultaneously, which will enable simplified 6D phase space distribution reconstructions in the future.

47 OTHER INSTRUMENTATION↗

GCR Transport in the Brain: Assessment of Self-Shielding, Columnar Damage, and Nuclear Reactions on Cell Inactivation Rates

Radiation shield design is driven by the need to limit radiation risks while optimizing risk reduction with launch mass/expense penalties. Both limitation and optimization objectives require the development of accurate and complete means for evaluating the effectiveness of various shield materials and body-self shielding. For galactic cosmic rays (GCR), biophysical response models indicate that track structure effects lead to substantially different assessments of shielding effectiveness relative to assessments based on LET-dependent quality factors. Methods for assessing risk to the central nervous system (CNS) from heavy ions are poorly understood at this time. High-energy and charge (HZE) ion can produce tissue events resulting in damage to clusters of cells in a columnar fashion, especially for stopping heavy ions. Grahn (1973) and Todd (1986) have discussed a microlesion concept or model of stochastic tissue events in analyzing damage from HZE's. Some tissues, including the CNS, maybe sensitive to microlesion's or stochastic tissue events in a manner not illuminated by either conventional dosimetry or fluence-based risk factors. HZE ions may also produce important lateral damage to adjacent cells. Fluences of high-energy proton and alpha particles in the GCR are many times higher than HZE ions. Behind spacecraft and body self-shielding the ratio of protons, alpha particles, and neutrons to HZE ions increases several-fold from free-space values. Models of GCR damage behind shielding have placed large concern on the role of target fragments produced from tissue atoms. The self-shielding of the brain reduces the number of heavy ions reaching the interior regions by a large amount and the remaining light particle environment (protons, neutrons, deuterons. and alpha particles) may be the greatest concern. Tracks of high-energy proton produce nuclear reactions in tissue, which can deposit doses of more than 1 Gv within 5 - 10 cell layers. Information on rates of cell killing from GCR, including patterns of cell killing from single particle tracks. can provide useful information on expected differences between proton and HZE tracks and clinical experiences with photon irradiation. To model effects on cells in the brain, it is important that transport models accurately describe changes in the GCR due to interactions in the cranium and proximate tissues. We describe calculations of the attenuated GCR particle fluxes at three dose-points in the brain and associated patterns of cell killing using biophysical models. The effects of the brain self-shielding and bone-tissue interface of the skull in modulating the GCR environment are considered. For each brain dose-point, the mass distribution in the surrounding 4(pi) solid angle is characterized using the CAM model to trace 512 rays. The CAM model describes the self-shielding by converting the tissue distribution to mass-equivalent aluminum, and nominal values of spacecraft shielding is considered. Particle transport is performed with the proton, neutron, and heavy-ion transport code HZETRN with the nuclear fragmentation model QMSFRG. The distribution of cells killed along the path of individual GCR ions is modeled using in vitro cell inactivation data for cells with varying sensitivity. Monte Carlo simulations of arrays of inactivated cells are considered for protons and heavy ions and used to describe the absolute number of cell killing events of various magnitude in the brain from the GCR. Included are simulations of positions of inactivated cells from stopping heavy ions and nuclear stars produced by high-energy ions most importantly, protons and neutrons.

Shavers, M. R.↗

An Open Combinatorial Diffraction Dataset Including Consensus Human and Machine Learning Labels with Quantified Uncertainty for Training New Machine Learning Models

Modern machine learning and autonomous experimentation schemes in materials science rely on accurate analysis of the data ingested by these models. Unfortunately, accurate analysis of the underlying data can be difficult, even for domain experts, complicating the training of the models intended to drive experiments. This is especially true when the goal is to identify the presence of weak signatures in diffraction or spectroscopic datasets. In this work, we examine a set of as-obtained diffraction data that track the phase transition from monoclinic to tetragonal in a Nb-doped VO2 film as a function of temperature and dopant concentration. We then task a set of domain experts and a set of machine learning experts with identifying which phase is present in each diffraction pattern manually and algorithmically, respectively; in both cases, the labels can vary dramatically, especially at the phase boundaries. We use the mode of the labels and the Shannon entropy as a method to capture, preserve and propagate consensus labels and their variance. Further we use the expert labels as a benchmark and demonstrate the use of Shannon entropy weighted scoring to test the performance of machine learning generated labels. Finally, we propose a material data challenge centered around generating improved labeling algorithms. This real-world dataset curated with expert labels can act as test bed for new algorithms. The raw data, annotations and code used in this study are all available online at data.gov and the interested reader is encouraged to replicate and improve the existing models

97 MATHEMATICS AND COMPUTING↗

A novel conjugative transposon carrying an autonomously amplified plasmid

Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.

59 BASIC BIOLOGICAL SCIENCES↗