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At least 811 records · Page 45

PlantCV v4: Image analysis software for high‐throughput plant phenotyping

PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data, and the newest release, PlantCV version 4, continues to lower the barrier to entry for users without substantial coding experience through extensive example use-case tutorials and simplified installation. In addition to usability, we document added functionality since the release of PlantCV v2, including support for more image types such as fluorescence, thermal, and hyperspectral data. Finally, we describe the development of a new subpackage focused on morphological trait measurements like leaf angle, and demonstrate its utility as compared to more manual methods of data collection.

Schuhl, Haley [Donald Danforth Plant Science Cente↗

Effects of external kink and fishbone-like modes on energetic particle transport in tokamak plasmas

Transport and loss of beam injected energetic particles (EPs) due to three-dimensional perturbations, associated with the external kink (XK) instability and fishbone-like mode (FLM), are numerically investigated utilizing the guiding center following code ORBIT for static toroidal plasmas in HL-2A. The perturbation structure for the XK is computed by the MARS-F code and then mapped to the Boozer coordinates as defined in ORBIT. The simulation shows that the EP profile experiences a significant change in the middle of the plasma column, when the XK-induced radial magnetic field perturbation amplitude, normalized by the equilibrium field, exceeds a threshold value of about 10 -2 . The EP transport is found to be dominated by a diffusion process instead of convection. Furthermore, by scanning the perturbation frequency as a free parameter while maintaining the XK mode structure (thus mimicking the FLM as observed in DIII-D and JT-60U tokamaks), redistribution and loss of EPs are found to be substantially enhanced due to strong resonances between the FLM and EPs, when the mode frequency exceeds a threshold value of ~2 kHz for the case considered. For either XK or FLM, the response of passing EPs to the perturbation is dominant due to the assumed tangential neutral beam injection. Most lost EPs due to these instabilities are initially passing particles but are eventually lost through trapped orbits.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The Simons Observatory: Beam Characterization for the Small Aperture Telescopes

Abstract We use time-domain simulations of Jupiter observations to test and develop a beam reconstruction pipeline for the Simons Observatory Small Aperture Telescopes. The method relies on a mapmaker that estimates and subtracts correlated atmospheric noise and a beam fitting code designed to compensate for the bias caused by the mapmaker. We test our reconstruction performance for four different frequency bands against various algorithmic parameters, atmospheric conditions, and input beams. We additionally show the reconstruction quality as a function of the number of available observations and investigate how different calibration strategies affect the beam uncertainty. For all of the cases considered, we find good agreement between the fitted results and the input beam model within an ∼1.5% error for a multipole range ℓ = 30–700 and an ∼0.5% error for a multipole range ℓ = 50–200. We conclude by using a harmonic-domain component separation algorithm to verify that the beam reconstruction errors and biases observed in our analysis do not significantly bias the Simons Observatory r -measurement

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

CFD unified approach under Eulerian–Lagrangian framework for methanol and gasoline direct injection sprays in evaporative and flash boiling conditions

Innovative synthetic fuels for advanced propulsion systems, such as methanol and ammonia, and synthetic blended fuels (E00, E10, and E30), known for their high volatility, are often injected directly into combustion chambers. It follows that Eulerian–Lagrangian spray models need to accurately capture the spray collapse as a consequence of flash boiling onset and be capable of proficiently handling the preferential evaporation of multi-component fuels in evaporative scenarios. So, we performed the assessment of an Eulerian–Lagrangian CFD code for simulating methanol and E00 gasoline blend sprays in both early and late injection conditions involving flash boiling conditions and preferential evaporation. The adoption of an effervescent breakup model and of a non-equilibrium phase transition model for the discrete phase allows the adoption of a setup that is almost completely free from specific constant tuning, especially for what concerns the breakup model. We validated the simulations using experimental PLV maps of methanol and E00 sprays issued from the ECN Spray M injector. The results highlight a significantly different morphology of the methanol spray compared to the E00 one under late injection conditions. Under stratified combustion, low-volatile fuels are likely to be ignited first, and the flame propagates toward the high-volatile fuels. In conclusion, the spray collapse was also correctly reproduced, inducing the presence of a low-pressure zone and modifying the spray morphology.

E00↗

Well-balanced treatment of gravity in astrophysical fluid dynamics simulations at low Mach numbers

We report accurate simulations of flows in stellar interiors are crucial to improving our understanding of stellar structure and evolution. Because the typically slow flows are merely tiny perturbations on top of a close balance between gravity and the pressure gradient, such simulations place heavy demands on numerical hydrodynamics schemes. We demonstrate how discretization errors on grids of reasonable size can lead to spurious flows orders of magnitude faster than the physical flow. Well-balanced numerical schemes can deal with this problem. Three such schemes were applied in the implicit, finite-volume SEVEN-LEAGUE HYDRO code in combination with a low-Mach-number numerical flux function. We compare how the schemes perform in four numerical experiments addressing some of the challenges imposed by typical problems in stellar hydrodynamics. We find that the α-β and deviation well-balancing methods can accurately maintain hydrostatic solutions provided that gravitational potential energy is included in the total energy balance. They accurately conserve minuscule entropy fluctuations advected in an isentropic stratification, which enables the methods to reproduce the expected scaling of convective flow speed with the heating rate. The deviation method also substantially increases accuracy of maintaining stationary orbital motions in a Keplerian disk on long timescales. The Cargo–LeRoux method fares substantially worse in our tests, although its simplicity may still offer some merits in certain situations. Overall, we find the well-balanced treatment of gravity in combination with low Mach number flux functions essential to reproducing correct physical solutions to challenging stellar slow-flow problems on affordable collocated grids.

79 ASTRONOMY AND ASTROPHYSICS↗

Analysis of MHD stability and active mode control on KSTAR for high confinement, disruption-free plasma

Long-pulse plasma operation at high normalized beta, $β_N$, above the $\textit{n}$= 1 ideal MHD no-wall stability limit in KSTAR is presently limited by tearing instabilities rather than resistive wall modes. H-mode plasma operation during the recent KSTAR device campaign produced discharges having strong $\textit{m/n}$= 2/1 tearing instabilities at $β_N$ lower than the ideal MHD no-wall beta limit. The unstable tearing mode consequently reduced plasma confinement and toroidal plasma rotation significantly. We report the experiment confirmed that an extended duration of electron cyclotron heating (ECH) at the initial phase of the discharge plays a critical role in mode destabilization. To study destabilizing mechanisms that affect the mode growth, the stability of the observed tearing modes from plasmas with significantly different $β_N$ is computed by using the resistive DCON code and the M3D-C 1 code. Equilibrium reconstructions that include constraints from internal profile diagnostics, and computed fast particle pressure are used as input for reliable computation of stability. The classical tearing stability index, Δ', from resistive DCON is computed to be unstable when the island is fully saturated with large amplitude, while the unstable mode is not computed by M3D-C 1 . The modified Rutherford equation (MRE) describing the evolution of the island width has been constructed for KSTAR plasmas by using plasma parameters computed by the TRANSP code. The MRE model estimates a saturated island width corresponding to ~10% of the plasma minor radius for equilibrium at high $β_N$ 3 having a stable Δ' from the resistive DCON. In preparation for long-pulse plasma operation at higher beta utilizing increased plasma heating power, a resistive wall mode (RWM) active feedback control algorithm has been completed and enabled on KSTAR. To accurately determine the $\textit{n}$= 1component produced by RWMs, an algorithm has been developed that includes magnetic sensor compensation of the prompt applied field and the field from the induced current on the passive conductors. Use of multiple toroidal sensor arrays is enabled by modifying the sensor toroidal angles assumed in mode decomposition to include the effect of varied mode helicities in the outboard region where the mode measurement is made. This analysis on stability, transport, and control provides the required foundation for disruption prediction and avoidance research on KSTAR.

resistive wall mode (RWM)↗

Effects of radial transport on divertor power and particle flux widths under different operational regimes in EAST

Here, a study of the effects of radial transport on the outer divertor particle and power flux widths (λ js and λ q ) is carried out using plasmas under different operational regimes in the Experimental Advanced Superconducting Tokamak (EAST). In the EAST experiments, the λ js values measured during the grassy intra- and inter-ELM phases are similar, and the averaged value of λ js during grassy ELMy discharges is found to be smaller than that of the intra-ELM phase of type-I ELMy discharges but larger than that of the inter-ELM phase of type-I ELMy discharges. Simulations of scans of the radial particle and heat transport coefficients, D and χ e , performed using the BOUT++ transport code show that both λq and λjs increase with D and χe, especially when D or χ e is larger than a threshold value, indicating that background turbulence starts to matter in the determination of λ q and λ js when D or χ e surpasses the threshold value. A comparison between the simulation of the D scan and the experimental results shows that the different values of λ js obtained under different plasma operational regimes are probably due to the different intensities of background turbulence, which is beyond the scope of Goldston's heuristic drift-based model as reported by Goldston et al (2012 Nucl. Fusion 52 013009), since their model was derived by assuming that turbulent transport does not exceed a certain level. The ratio of λ js to λ q is greatly affected by the radial transport; however, simulations carried out using Scrape-off Layer Plasma Simulation (SOLPS) show that divertor geometry and plasma density have big influences on λ js , and thus could also affect the ratio of λ js to λ q .

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Diagnostics: Chapter 8 of the special issue: on the path to tokamak burning plasma operation

This chapter presents the activity conducted by the ITPA topical group (TG) on Diagnostics over about the last 15 years. Following a general introduction of the ITER Diagnostics led by their measurement roles, the document is organized in several subchapters detailing the design support, research and development activity conducted by each of the specialist working groups (WGs) of the TG. Please note that the magnetic diagnostics were supported at the TG without a specific WG. Their status is included in the general introduction. In the following some highlights of the subchapter’s contents are provided. Recent advances in ITER first wall (FW) diagnostics for the measurements of plasma-metallic wall interaction in support of the ITER research plan are reported. An InfraRed imaging Video Bolometer for ITER has been developed and tested on several tokamaks to measure the radiated power loss. A laser-induced breakdown spectroscopy (LIBS) technique which utilizes a pulsed laser beam to ablate locally by forming a crater, will measure local tritium inventory in the FW material. Real-time Residual Gas Analyzers will measure the neutral gas composition in a divertor port and an equatorial port during plasma operation. Due to the full metallic FW environment, the plasma-wall interaction in ITER will face several challenges such as the compromised radiated power and divertor heat flux measurements by reflection. Ray tracing and analysis codes have been developed to eliminate and correct the effects of reflection in the measurements. The characteristics of the reflecting surfaces depending on the roughness and angle of the incidence have been measured by dedicated experiments, and the results were applied to the reflection elimination. For the measurement of the metallic impurity radiation induced by eroded metallic atoms, a vacuum ultraviolet spectrometer has been developed and tested. An extensive thermonuclear diagnostic suite will be required to support the operation of ITER and the planned experimental program for future burning plasma experiments. Due to the harsh environmental conditions, the implementation of diagnostic systems in ITER is a major challenge. These conditions include high levels of neutron and gamma fluxes, neutron heating, particle bombardment. Therefore, the selection and design of diagnostic systems must take into account a number of phenomena previously unseen in diagnostic design. For this reason, the measurement of neutrons and confined or lost fast ions, with particular emphasis on alpha particles, is critical to ITER. The diagnostics associated with these measurements will be important for future plasma-burning experiments at ITER. The high neutron emission and very large plasma size in ITER make neutron diagnostics the main diagnostic method used to measure plasma parameters such as fusion power, fusion power density, ion temperature, energy of fast ions and their spatial distributions in the plasma core. Active spectroscopy techniques are methods where a neutral particle beam is injected into the plasma and information on plasma parameters is extracted from the measurement of line emission resulting from the beam-plasma interaction, either by plasma ions or by beam atoms. Spatial localization is achieved by crossing the beamline and multiple observation lines. The ITER plasma will be a high temperature, moderately dense, fully ionized collisional plasma. The plasma facing surfaces are principally metallic being fashioned from beryllium or tungsten but many other elements, arising from either structural or from operational needs, may enter this plasma. The energy range of the emitted photons range from meV (infra-red) to multi keV (x-rays) and originate from all areas of the plasma volume. The primary role of passive emission diagnostics is to identify what is in the plasma from spectral signatures. Extracting quantitative information from these measurements such as impurity content, ion temperature, rotation, degree of detachment and radiated power depends on calibrated instruments, a physics model of the atomic and molecular processes and plasma transport and an analysis workflow that takes into account environmental effects such as reflections. The particular needs for ITER have prompted a multi-machine, many-year effort to address all these aspects and this chapter reviews the work on diagnostic design, experiments and new analysis techniques. An overview of the laser diagnostics to be implemented on ITER is also provided in this paper. This includes descriptions of the Thomson scattering in the core, edge and divertor regions, polarimetry and interferometry diagnostics used for measuring plasma density and also measurements of helium density in the divertor using Laser Induced Flourescence. Techniques which can allow improvements on current measurements are also addressed in particular expanding poloidal polarimetry measurements to measure field fluctuations and proposed use of dispersion interferometery which has a number of advantages over existing methods. This paper identifies particular areas where further research and testing on existing tokamaks is useful even at this advanced stage to inform the design of diagnostics for ITER. Outstanding areas of concern for the implementation of laser diagnostics, in particular with a view to reliable operation are identified. An overview of the latest developments of microwave diagnostic systems and techniques is given. The primary focus is the contributions for ITER—the next step burning plasma experiment—which is supplemented by describing recent progress of techniques applicable for fusion experiments beyond ITER. The contributions are intentionally kept concise, and are being supplemented by a rich list of references for further studies. Radiation induced effects are receiving continuous and well-deserved attention of the ITER diagnostic community and they are in many cases one of the primary design drivers of the ITER diagnostic systems. The paper summarizes recent progress in this area focusing primarily on the ITER diagnostics but in some cases provides also outlook for the possible solutions for even more demanding radiation environment of fusion reactors beyond ITER. Despite advancements in the area of modeling and simulation of various radiation induced effects, experimental testing in a nuclear environment as close as possible to the target one is still seen as unavoidable for proper qualification of particular diagnostic functional elements. Recent advancement within three diagnostic areas: optical diagnostics, magnetics and bolometers is covered. Encouraging results on qualification of silica glass vacuum window assemblies are presented. In the area of magnetic sensors, progress of irradiation tests performed on ITER in-vessel LTCC inductive sensors is presented with outlook for novel technological approaches to inductive sensors utilizing thick printing and photolithography technologies being highlighted. Summary of advancements in the area of steady state magnetic field sensors based on Hall effect is given. New results of neutron irradiation test of the ITER borosilicate glass inserts for vacuum electrical feedthroughs are summarized finding negligible swelling at target level of neutron fluence. Off-line irradiation tests of fiber optic current sensors for plasma current measurement demonstrated that both for gamma doses up to 5 MGy and a total neutron fluence up to 10 15 cm −2 , radiation induced changes are still compatible with required measurement accuracy on ITER. The ITER bolometers are given as an example how considering radiation effects may influence the diagnostic design. Finally, outlook for future main R&D directions is outlined. All optical and laser-based diagnostics in ITER will be using mirrors to guide plasma radiation toward detectors, cameras and sensors. In the hostile plasma, radiation and particle environment the optical characteristics of diagnostic mirrors will degrade directly affecting the entire performance of involved diagnostic systems. An assessment of factors affecting mirror performance is provided. Among the prime adverse factors are deposition of plasma impurities, sputtering of mirror surface and steam ingress in the vicinity of mirrors. Within the International Tokamak Physics Activity with active support by ITER central team and domestic agencies, the structured research and development (R&D) program on mitigation of risks for diagnostic mirrors is underway. Within this program the mirror material development, the passive mitigation of mirror degradation by using diagnostic ducts and shutters along with an active mirror recovery program comprising the in-situ mirror cleaning and calibration is underway. Recent developments in diagnostic mirror R&D are described in this Chapter along with an example of their implementation of R&D solutions in ITER Infrared Thermography diagnostic. An assessment of still open engineering and physics questions, considerations on mirror risks during an early phase of ITER operation are given along with an overview of diagnostic mirror evolution in the late ITER operation stage toward the demonstration fusion power plant. Several crucial areas of diagnostic R&D outlined in ITER Research Plan are addressed. The basic control groups in a fusion reactor can be broken-down in five categories: (1) plasma position, magnetic configuration, and plasma current control, (2) profile control and confinement optimization, (3) MHD control and suppression, (4) edge dissipation control, radiation and plasma exhaust control and (5) break-down optimization. These categories are coupled via the physics (a control action in one domain will affect the other domains) and via shared actuators (e.g. ECRH for impurity accumulation avoidance, current density distribution control and MHD suppression). Consequently, a supervisory control system should determine the priority of the various control tasks, their couplings, and the interfaces with the safety and interlock system. For the systematic development of the various controllers taking the complexity of the plasma and the control system into account, a model-based approach is required. A short historical overview is given of the developments in systems and control theory and control engineering with special emphasis on those developments that are most relevant for Nuclear Fusion research and operation. An overview is given of the state of the field of fusion plasma control for the control categories. It will be shown how synthetic diagnostics are being developed in ITER and how they are used in diagnostic design and design validation and how they can be in model-based controller synthesis using relatively simple models. In modern control methods, multiple diagnostics are used to constrain relatively simple models. The constrained models provide an estimate for the state. This opens the route to state controllers, such as model predictive control. A major challenge in nuclear fusion research is the coherent combination of data from heterogeneous diagnostics and modeling codes for machine control and safety as well as physics studies. Measured data from different diagnostics often provide information about the same subset of physical parameters. Additionally, information provided by some diagnostics might be needed for the analysis of other diagnostics. A joint analysis of complementary and redundant data allows, e.g. to improve the reliability of parameter estimation, to increase the spatial and temporal resolution of profiles, to obtain synergistic effects, to consider diagnostics interdependencies and to find and resolve data inconsistencies. Physics-based modeling and parameter relationships provide additional information improving the treatment of ill-posed inversion problems. A coherent combination of all kind of available information within a probabilistic framework allows for improved data analysis results. The concept of integrated data analysis (IDA) in the framework of Bayesian probability theory is outlined and contrasted with conventional data analysis. Components of the probabilistic approach are summarized and specific ingredients beneficial for data analysis at fusion devices are discussed.

ITER↗

Machine Learning in Infectious Disease for Risk Factor Identification and Hypothesis Generation: Proof of Concept Using Invasive Candidiasis

Machine learning (ML) models can handle large data sets without assuming underlying relationships and can be useful for evaluating disease characteristics, yet they are more commonly used for predicting individual disease risk than for identifying factors at the population level. We offer a proof of concept applying random forest (RF) algorithms to Candida-positive hospital encounters in an electronic health record database of patients in the United States. Candida-positive encounters were extracted from the Cerner HealthFacts database; invasive infections were laboratory-positive sterile site Candida infections. Features included demographics, admission source, care setting, physician specialty, diagnostic and procedure codes, and medications received before the first positive Candida culture. We used RF to assess risk factors for 3 outcomes: any invasive candidiasis (IC) vs non-IC, within-species IC vs non-IC (eg, invasive C. glabrata vs noninvasive C. glabrata), and between-species IC (eg, invasive C. glabrata vs all other IC). Fourteen of 169 (8%) variables were consistently identified as important features in the ML models. When evaluating within-species IC, for example, invasive C. glabrata vs non-invasive C. glabrata, we identified known features like central venous catheters, intensive care unit stay, and gastrointestinal operations. In contrast, important variables for invasive C. glabrata vs all other IC included renal disease and medications like diabetes therapeutics, cholesterol medications, and antiarrhythmics. Known and novel risk factors for IC were identified using ML, demonstrating the hypothesis-generating utility of this approach for infectious disease conditions about which less is known, specifically at the species level or for rarer diseases.

60 APPLIED LIFE SCIENCES↗

The Pierre Auger Observatory open data

The Pierre Auger Collaboration has embraced the concept of open access to their research data since its foundation, with the aim of giving access to the widest possible community. A gradual process of release began as early as 2007 when 1% of the cosmic-ray data was made public, along with 100% of the space-weather information. In February 2021, a portal was released containing 10% of cosmic-ray data collected by the Pierre Auger Observatory from 2004 to 2018, during the first phase of operation of the Observatory. The Open Data Portal includes detailed documentation about the detection and reconstruction procedures, analysis codes that can be easily used and modified and, additionally, visualization tools. Since then, the Portal has been updated and extended. In 2023, a catalog of the highest-energy cosmic-ray events examined in depth has been included. A specific section dedicated to educational use has been developed with the expectation that these data will be explored by a wide and diverse community, including professional and citizen scientists, and used for educational and outreach initiatives. This paper describes the context, the spirit, and the technical implementation of the release of data by the largest cosmic-ray detector ever built and anticipates its future developments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

WHONDRS River Corridor Surface Water Metabolites and Geochemistry from Global Sites

This dataset supports a broader study examining the character of organic matter that may be delivered to subsurface sediments via hydrologic exchange. To implement the global survey, free stream sampling kits were provided to interested volunteers throughout the world. Samples were collected with minimal constraints in terms of location, but following strict protocols, and shipped for metabolomic analysis via Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). In addition, basic geochemistry analyses (e.g., dissolved organic matter concentration) were conducted, standardized photos of each field system were taken, and extensive metadata were captured. Sampling began in 2018 and is ongoing as of 2025. This dataset is comprised of one folders of field photos, one folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data, and one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) readme; (5) international generic sample number (IGSN) mapping file; (6) field protocol; and (7) a subfolder with sample data. The sample data subfolder contains (1) surface water dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) methods codes; (3) surface water FTICR methods; and (4) a subfolder of 12 Tesla (12T) FTICR-MS data. This folder contains three subfolders, one containing the.xml files, one containing the CoreMS output files, and the other containing instructions and scripts for processing the files in CoreMS (https://github.com/EMSL-Computing/CoreMS). All files are .csv, .pdf, .R, .xml, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, or .png. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About.

Biogeochemistry↗

UQpy: A general purpose Python package and development environment for uncertainty quantification

In this paper, we present the UQpy software toolbox, an open-source Python package for general uncertainty quantification (UQ) in mathematical and physical systems. The software serves as both a user-ready toolbox that includes many of the latest methods for UQ in computational modeling and a convenient development environment for Python programmers advancing the field of UQ. The paper presents an introduction to the software's architecture and existing capabilities, divided in the code in a set of modules centered around different UQ tasks such as sampling methods, generation of random processes and random fields, probabilistic inverse modeling, reliability analysis, surrogate modeling, and active learning. The paper also highlights the importance of the RunModel module, which is used to drive simulations in the uncertainty analyses performed in UQpy. This module conveniently allows the user to define computational models directly in Python, or to run simulations from a third-party software in serial or in parallel. To illustrate the various capabilities, two examples are tracked throughout the paper and analyzed repeatedly for various UQ tasks. The first is a Python model solving a nonlinear structural dynamics problem, used to illustrate UQpy's capabilities in sampling and forward propagation of high dimensional random vectors (stochastic processes), and probabilistic inference. The second model is a third-party Abaqus finite element model solving the thermomechanical response of a beam structure. This example is used to illustrate UQpy's capabilities in variance reduction sampling techniques, reliability analysis, surrogate modeling and active learning techniques.

97 MATHEMATICS AND COMPUTING↗

Accelerated steady-state electrostatic particle-in-cell simulation of Langmuir probes

First-principles particle-in-cell (PIC) simulation is a powerful tool for understanding plasma behavior, but this power often comes at great computational expense. Artificially reducing the ion/electron mass ratio is a time-honored practice to reduce simulation costs. Usually, this is a severe approximation. However, for steady-state collisionless, electrostatic (Vlasov–Poisson) systems, the solution with reduced mass ratio can be scaled to the solution for the real mass ratio, with no approximation. This “scaled mass” method, which works with already-existing PIC codes, can reduce the computation time for a large class of electrostatic PIC simulations by the square root of the mass ratio. The particle distributions of the resulting steady state must be trivially rescaled to yield the true distributions, but the self-consistent electrostatic field is independent of the mass ratio. This method is equivalent to “numerical timestepping,” an approach that evolves electron and ion populations with different time steps. Numerical timestepping can be viewed as a special case of the speed-limited PIC (SLPIC) method, which is not restricted to steady-state phenomena. Although the scaled-mass approach is simplest, numerical timestepping and SLPIC more easily generalize to include other effects, such as collisions. The equivalence of these new approaches is demonstrated by applying them to simulate a cylindrical Langmuir probe in electron–argon plasma, speeding up simulation by two orders of magnitude. Methods such as SLPIC can therefore play an invaluable role in interpreting probe measurements by including geometric effects, collisions, secondary emission, and non-Maxwellian distributions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Linear gyrokinetic simulations of toroidal Alfvén eigenmodes in the Mega-Amp Spherical Tokamak

Linear gyrokinetic (GK) simulations using the Gyrokinetic Toroidal Code (GTC) have been performed to investigate Toroidicity-driven Alfvén Eigenmodes (TAEs) driven by the neutral beam injection (NBI) induced fast ions in the Mega-Amp Spherical Tokamak (MAST) to identify the non-perturbative and kinetic effects of thermal plasma. A specific TAE in MAST discharge 26887, with an on-axis NBI power of approximately 1.5 MW and plasma current around 800 kA, exhibited frequency chirping, and the tangential soft x-ray camera array resolved the radial mode structure peaked near |q|=1.5. Various excitation methods were used in the GTC linear simulations, illustrating this code's capability to realistically represent the mechanisms and behaviors of fast ion-driven TAEs in spherical tokamaks. The radial structures from these GK simulations closely match measurements and calculations performed using the NOVA ideal MHD code, though with the frequencies approximately 10 kHz lower, likely due to various kinetic and non-perturbative effects. The simulations measured the damping rates due to continuum damping, radiative damping, and ion Landau damping, revealing that ion Landau damping has the most significant contribution to the total damping rate of the TAE. A comparison of growth rates of TAEs excited by fast ion Maxwellian and slowing-down distributions shows that the TAEs excited by a fast ion anisotropic pitch distribution (as part of the slowing-down distributions) are more unstable compared to those excited by a Maxwellian distribution with an equivalent fast ion beta. This shows that the use of fast ion anisotropy alters the number of fast ions to be in shear Alfvén resonance, and hence, it can greatly affect the stability of TAEs. These tests can be performed with the GTC but impossible with ideal MHD simulations, highlighting the necessity of kinetic simulations such as the GTC for a precise prediction of the TAE stability.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Cooling and instabilities in colliding flows

ABSTRACT Collisional self-interactions occurring in protostellar jets give rise to strong shocks, the structure of which can be affected by radiative cooling within the flow. To study such colliding flows, we use the AstroBEAR AMR code to conduct hydrodynamic simulations in both one and three dimensions with a power-law cooling function. The characteristic length and time-scales for cooling are temperature dependent and thus may vary as shocked gas cools. When the cooling length decreases sufficiently and rapidly, the system becomes unstable to the radiative shock instability, which produces oscillations in the position of the shock front; these oscillations can be seen in both the one- and three-dimensional cases. Our simulations show no evidence of the density clumping characteristic of a thermal instability, even when the cooling function meets the expected criteria. In the three-dimensional case, the nonlinear thin shell instability (NTSI) is found to dominate when the cooling length is sufficiently small. When the flows are subjected to the radiative shock instability, oscillations in the size of the cooling region allow NTSI to occur at larger cooling lengths, though larger cooling lengths delay the onset of NTSI by increasing the oscillation period.

79 ASTRONOMY AND ASTROPHYSICS↗

Spatial Study 2021: Sample-Based Surface Water Chemistry and Organic Matter Characterization across Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides geochemistry and organic matter characterization data generated from samples collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Related sensor data are published at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1892054. This data package was originally published September 2022. It was updated May 2023 (modified files) and November 2024 (new and modified files). See the change history section in the readme for more details. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved inorganic carbon (DIC), dissolved organic carbon (DOC; reported as non-purgeable organic carbon; NPOC), total nitrogen (TN), total suspended solids (TSS), ions, and benzene polycarboxylic acid (BPCA) concentration and stable isotope data; (5) averaged values from water chemistry data; (6) surface water sampling protocol; (7) sensor protocol (8) readme; (9) methods codes; (10) international generic-sample number (IGSN) mapping file; and (11) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). This folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formultitude (https://github.com/PNNL-Comp-Mass-Spec/Formultitude) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml. We thank the United States Forest Service, Washington Department of Natural Resources, Washington Department of Fish and Wildlife, Washington State Parks, Confederated Tribes and Bands of the Yakama Nation, and Cowiche Canyon Conservancy for access to field locations where these samples were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

User Guide to the Advanced Dimensional Depletion for Engineering of Reactors (ADDER) Software (V.1.0)

The Advanced Dimensional Depletion for Engineering of Reactors (ADDER) software is being developed in the Research and Test Reactor (RTR) Program at Argonne National Laboratory to meet the reactor design and analysis needs of the Conversion Program. ADDER is a flexible tool that (1) provides a depletion capability through coupling external neutronics codes with a built-in CRAM solver or external depletion code and (2) provides a user-friendly interface to perform fuel management and criticality search operations. The ADDER software is a Python 3 application written using modern software development practices subject to a compliant implementation of NQA-1 and applicable Department of Energy software quality assurance standards. This report is the user guide for the initial software release as ADDER v1.0.0. The motivation for a software to have flexible capabilities that ADDER possesses is the need to support a wide variety of geometries that are commonly required in analysis of research and test reactors. These reactors can have complex fuel, experiment, or control material shuffling patterns that persist over several years with many fuel management and partial refueling intervals. The scale of fuel management analysis can require tracking of an inventory that is multiple times the core loading. Many reactors, both power and non-power reactors of various types, will find the features of ADDER useful to facilitate key tasks that a fuel or core design engineer must perform with the convenience of concise input and validated functionality.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Effects of emitting surfaces and trapped ions on the sheath physics and current flow in multidimensional plasma systems

Recent one-dimensional simulations of planar sheaths with strong electron emission have shown that trapping of charge-exchange ions causes transitions from space-charge limited (SCL) to inverse sheaths. However, multidimensional emitting sheath phenomena with collisions remained unexplored, due in part to high computational cost. As such, we developed a novel continuum kinetic code to study the sheath physics, current flow and potential distributions in two-dimensional unmagnetized configurations with emitting surfaces. For small negatively biased thermionic cathodes in a plasma, the cathode sheath can exist in an equilibrium SCL state. The SCL sheath carries an immense density of trapped ions, neutralized by thermoelectrons, within the potential well of the virtual cathode. For further increases of emitted flux, the trapped ion cloud expands in space. The trapped ion space charge causes an increase of thermionic current far beyond the saturation limit predicted by conventional collisionless SCL sheath models without ion trapping. For sufficiently strong emission, the trapped ion cloud consumes the entire 2D plasma domain, forming a mode with globally confined ions and an inverse sheath at the cathode. In situations where the emitted flux is fixed and the bias is swept (e.g. emissive probe), the trapped ions cause a large thermionic current to escape for all biases below the plasma potential. Strong suppression of the thermionic emission, required for the probe to float, only occurs when the probe is above the plasma potential.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗