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Data and scripts associated with “Non-random processes impacting organic matter chemistry are maximized in mid-order streams”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the publication “Non-random processes impacting organic matter chemistry are maximized in mid-order streams” submitted to Limnology and Oceanography (L&O) by Danczak et al. (in review). This package contains data and scripts used to investigate dissolved organic matter (DOM) molecular chemistry and diversification processes across 47 surface-water sampling sites in the Yakima River Basin, Washington, USA, during an August 2021 sampling campaign. The package contains analyses of ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), geochemical measurements, geospatial attributes, molecular diversity, and meta-metabolome ecological null models needed to reproduce the main manuscript results. The underlying field data were pulled from exising data packages at https://doi.org/10.15485/1892052 (Fulton et al., 2022) and https://doi.org/10.15485/1898914 (Grieger et al., 2022). For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. We thank the following organizations for providing access to field locations for sample collection: the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, the Confederated Tribes and Bands of the Yakama Nation, and the Cowiche Canyon Conservatory. Research was conducted under Washington State Parks and Recreation Commission Scientific Research Permit #210901. We are grateful to the Yakama Nation Tribal Council and Yakama Nation Fisheries for their collaboration in facilitating sample collection and ensuring data usage aligns with their values and worldview. This data package contains an R-Markdown file for analyses and five folders: (1) Data, (2) Geospatial Data, (3) Supplemental_Files, (5) Figures_pdf, (4) and src. The Data folder contains tabular inputs and derived files used in the manuscript analysis. The Geospatial Data folder contains climate and water-balance, hydrologic, land-cover, population/regional water-use, stream, topographic, and stream-order attribute CSV files. The src folder contains scripts used to process data, run analyses, and generate figures. The Figures_pdf folder contains manuscript figure outputs. The Supplemental_Files folder contains supplemental analysis products. All files are .csv, .pdf, .html, .png, .R, .Rmd, .svg, or .tre. This data package is associated with the rcfsa-RC2-SPS_Null_Modeling repository found at https://github.com/river-corridors-sfa/rcfsa-RC2-SPS_Null_Modeling.

54 ENVIRONMENTAL SCIENCES↗

WHONDRS Surface Water Geochemistry and Organic Matter Characterization Data from Streams Distributed across Latin America

This dataset supports a broader study examining global transferability of stream biogeochemistry and was generated in collaboration with the MicroSudAqua (µSudAqua) network (https://microsudaqua.netlify.app/en/). The dataset provides surface water geochemistry (dissolved organic carbon, total dissolved nitrogen, cations) and organic matter characterization (FTICR-MS) from streams in Argentina, Brazil, Chile, and Colombia. Samples were collected across stream orders (1st to 6th order) within five basins. Related data were collected and will be published separately in collaboration with the µSudAqua network. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to this readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) a folder of field photos; (2) a folder of surface water sample data, (3) a folder of raw Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) data; (4) file-level metadata; (5) data dictionary; (6) field metadata; (7) readme; (8) international generic sample number (IGSN) mapping file; and (9) field protocol. The sample data subfolder contains (1) dissolved organic carbon (DOC, measured as non-purgeable organic carbon, NPOC) data and averages; (2) total dissolved nitrogen data and averages; (3) anions and averages; (4) methods codes; (5) FTICR-MS methods; and (15) a subfolder of 9.4 Tesla (9.4T) FTICR-MS data. This folder contains the processed data and three subfolders, one containing the .xml files, one containing the water 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, .d, .html, .Rmd, .py, .cal, .json, .jpg, .jpeg, .png, .mov, or .mp4.

Anions↗

Investigation of two-dimensional radio-frequency sheath properties using a microscale fluid model

Abstract In previous work (Kohno and Myra 2023 Comput. Phys. Commun. 291 108841), we developed a numerical scheme based on a two-dimensional microscale radio-frequency (RF) sheath model with periodically curved wall boundaries. Here, we expand the capability of this scheme through modification of the boundary conditions (BCs) on the conducting walls, which allows the ion flow to turn back to the plasma at locations on the walls where the electromagnetic force on the ions is reversed from its usual direction. Numerical simulations are carried out to investigate the dependences of the surface-integrated admittances on the wall bump height, ion magnetization, ion mobility, and the magnetic field angle, and to visualize the sheath structures in several cases. One of the main results is the ion cyclotron admittance resonance observed under the condition of low ion mobility (high normalized frequency). It is shown that the amplitude of the resonance peak depends on the wall bump height and the ion velocity is reversed on the sides of the bump in an RF cycle for the resonance cases. Furthermore, the differences in the admittances between the one- and two-dimensional microscale models are assessed for the purpose of understanding non-locality of the sheath near the wall surface for the parameters considered in this study. This information will be essential for improving the sheath BC for macroscale calculations in the future.

Kohno, H. (ORCID:0000000332690010)↗

The Role of Kinetic Instabilities and Waves in Collisionless Magnetic Reconnection

Magnetic reconnection converts magnetic field energy into particle energy by breaking and reconnecting magnetic field lines. Magnetic reconnection is a kinetic process that generates a wide variety of kinetic waves via wave-particle interactions. Kinetic waves have been proposed to play an important role in magnetic reconnection in collisionless plasmas by, for example, contributing to anomalous resistivity and diffusion, particle heating, and transfer of energy between different particle populations. These waves range from below the ion cyclotron frequency to above the electron plasma frequency and from ion kinetic scales down to electron Debye length scales. This review aims to describe the progress made in understanding the relationship between magnetic reconnection and kinetic waves. We focus on the waves in different parts of the reconnection region, namely, the diffusion region, separatrices, outflow regions, and jet fronts. Particular emphasis is placed on the recent observations from the Magnetospheric Multiscale (MMS) spacecraft and numerical simulations, which have substantially increased the understanding of the interplay between kinetic waves and reconnection. Some of the ongoing questions related to waves and reconnection are discussed.

79 ASTRONOMY AND ASTROPHYSICS↗

Experimental investigation of PDI bifurcation of lower hybrid waves during electron density ramp-up in EAST

Abstract The effect of parametric decay instability (PDI) on the current drive efficiency of 4.6 GHz lower hybrid (LH) waves in EAST is investigated experimentally, showing the PDI channel bifurcation of LH waves for the first time in EAST. First, experiments with three platforms of LH power were performed, achieving the LH power required for the PDI occurrence. Second, PDI bifurcation experiments were further carried out by ramping up the plasma electron density. The loop voltage increases with an increase in density, implying a decrease in the current driven by the LH wave. PDI bifurcation during electron density ramp-up was studied by analyzing the parallel refractive index ( n ∥ ) and the frequency spectrum broadening, which is measured with a radio frequency magnetic probe array recently installed close to the LH antenna. It is observed for the first time that they both first increase with density, then there is not much variation and a clear sideband in the frequency spectrum is also observed when the density is up to 4 × 10 19 m − 3 , suggesting a change in the PDI channel. Calculation of the mode growth rate driven by PDI shows that when the edge electron density is up to 1.9 × 10 18 m − 3 , the growth rate of the ion cyclotron quasi-mode (ICQM) will exceed that of the ion sound quasi-mode (ISQM), quantitively explaining that with an increase in density, the PDI channel partly transits from the ISQM to the ICQM channel. Studies provide a possible way to reduce the power deposition in the edge region and improve drive capability by means of mitigating PDI behavior.

Physics↗

Progress with applications of three-ion ICRF scenarios for fusion research: A review

The viability of magnetic confinement fusion as an energy source depends on achieving the high ion temperatures required for D-T fusion. Among the available techniques, plasma heating with waves in the ion cyclotron range of frequencies (ICRF) is a prominent method for bulk ion heating in fusion plasmas. Furthermore, a detailed understanding of the non-linear physics of alpha heating and the complex impact of MeV-range fast ions on plasma dynamics becomes progressively more important. This paper provides a comprehensive overview of recent developments with the three-ion ICRF scenarios on Alcator C-Mod, ASDEX Upgrade and JET tokamaks. The results demonstrate the flexibility of these novel scenarios for heating bulk ions in D-T ≈ 50%-50% plasmas and efficient generation of MeV-range fast ions in multi-ion species plasmas. In conclusion, several key results relevant for ITER and future fusion reactors are highlighted.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

On the Ion Precipitation due to Field Line Curvature (FLC) and EMIC Wave Scattering and Their Subsequent Impact on Ionospheric Electrodynamics

Both field line curvature (FLC) and electromagnetic ion cyclotron (EMIC) wave scattering are believed to be associated with energetic ion precipitation, but their relative contributions to ionospheric ion precipitation and subsequent effects are still unclear. Here, in this study, by using a kinetic ring current model, we investigate their impact on the ionosphere from two aspects: the global distribution of ion precipitation and resulting ionospheric conductance. Our results show that the intensity and coverage of ion precipitation due to EMIC waves are larger than that due to FLC scattering, while the latter mostly contributes to ion precipitation in outer regions (L > 4–5). We then estimate the conductance with empirical models using the simulated ion precipitation energy flux. When the EMIC wave associated proton precipitation is included, the conductance is significantly enhanced in the dusk-to-midnight sector and has a wide magnetic latitude (MLAT) range from around 52° to 62°, considerably altering the electric potential in the dusk sector, which further influences particle dynamics in the magnetosphere. On the contrary, the proton precipitation caused by FLC scattering only occurs at higher latitudes above MLAT = 60° and the corresponding conductance is slightly enhanced at midnight, with negligible influence on the convective electric potential. Although electron precipitation-associated conductance is predominant globally, the results show that proton precipitation can also play an important role in ionospheric electrodynamics, especially when EMIC wave-associated precipitating proton energy flux exceeds that of electrons in the dusk sector, a region where many subauroral coupling processes occur.

79 ASTRONOMY AND ASTROPHYSICS↗

Fast ion transport by sawtooth instability in the presence of ICRF-NBI synergy in JET plasmas

JET experiments have shown that the three-ion scenarios using waves in the ion cyclotron range of frequencies (ICRF) is an efficient way to build fast ion population through beam ion acceleration by radio frequency (RF) waves. Here, such a heating scheme is applied to plasmas with at least two thermal ion species. Analysis of mixed discharges with complex heating schemes requires a workflow that allows to model thermal and fast ion transport consistently. This paper is dedicated to modelling of a mixed plasma discharge with significant fraction of fast ions and contributes to development of fast ion transport models. For interpretive analysis with the TRANSP code a JET hydrogen-deuterium (HD) plasma discharge with neutral beam injection (NBI) and ICRF heating has been chosen. The task is complicated by NBI-ICRF synergy and plasma magnetohydrodynamic activity, like sawtooth crashes. D beam ions accelerated by RF waves form a high energy tail in fast ion distribution. Significant difference between the neutron rate computed by TRANSP and measured one is observed if the same diffusivity for electrons and ions is assumed. Sensitivity studies show that uncertainties in input plasma parameters and thermal ion transport models are crucial for modelling mixed plasma discharges and increased D transport is required to reach the plasma composition consistent with diagnostic measurements at the plasma edge. Fast ion redistribution by a sawtooth instability is characterised by non-resonant transport due to reconnection of magnetic field lines and resonant transport caused by resonance interaction between the instability and fast ions. With ORBIT simulations it has been shown that resonant interaction strongly affects fast ions of high energies, like beam ions accelerated by RF waves and fusion products. For the considered case, fast ion profiles simulated by ORBIT remain peaked after the sawtooth crashes.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Gaussian mixture model clustering algorithms for the analysis of high-precision mass measurements

The development of the phase-imaging ion-cyclotron resonance (PI-ICR) technique for use in Penning trap mass spectrometry (PTMS) increased the speed and precision with which PTMS experiments can be carried out. In PI-ICR, data sets of the locations of individual ion hits on a detector are created showing how ions cluster together into spots according to their cyclotron frequency. Ideal data sets would consist of a single, 2D-spherical spot with no other noise, but in practice data sets typically contain multiple spots, non-spherical spots, or significant noise, all of which can make determining the locations of spot centers non-trivial. A method for assigning groups of ions to their respective spots and determining the spot centers is therefore essential for further improving precision and confidence in PI-ICR experiments. Here, we present the class of Gaussian mixture model (GMM) clustering algorithms as an optimal solution. We show that on simulated PI-ICR data, several types of GMM clustering algorithms perform better than other clustering algorithms over a variety of typical scenarios encountered in PI-ICR. The mass spectra of 163Gd, 163 mGd, 162 Tb, and 162 mTb measured using PI-ICR at the Canadian Penning trap mass spectrometer were checked using GMMs, producing results that were in close agreement with the previously published values.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Activation, Dehydrogenation, and Carbon–Carbon Coupling of Methane by Iridium Cations Studied by Infrared Multiple Photon Dissociation Spectroscopy and Density Functional Theory

Products resulting from the sequential activation of one, two, three, and four methane molecules by atomic iridium cations were characterized by gas-phase infrared multiple photon dissociation spectroscopy and density functional theory (DFT) calculations. Iridium cations were generated using a laser ablation source and reacted with methane in a linear radiofrequency ion trap before mass analysis and spectroscopic interrogation in a Fourier transform ion cyclotron resonance mass spectrometer coupled to the free-electron laser for intracavity experiments (FELICE) beamline. Product ions were irradiated using infrared light over the 250–1500 cm –1 range. Comparisons between the experimental and DFT-calculated spectra enabled structural determination of the products formed. The observed products include HIrCH + , Ir(CH 2 ) 2 + , H s Ir(C 3 H 5 ) + , and Ir(CH 3 ) s (C 3 H 5 ) + , where the subscript s denotes a syn orientation of the two ligands. Furthermore, formation of the latter two products provides evidence for efficient C–H bond activation and subsequent C–C coupling on the atomic iridium cation.

Chemical reactions↗

Predicting High‐Resolution Spatial and Spectral Features in Mass Spectrometry Imaging with Machine Learning and Multimodal Data Fusion

Recent advancements in molecular Mass Spectrometry Imaging have sparked interest in integrating high spatial resolution methods with molecular mass-spectrometry-based chemical imaging. Fusion-based algorithms have proven effective in generating high spatial-resolution molecular mass spectra. However, a significant challenge stems from the differing physical mechanisms underlying image generation and data upsampling techniques, potentially leading to discrepancies in integrated information channels. Integrating physical constraints into data processing workflows is essential to tackle this issue. In this study, we propose an innovative approach that merges data from Fourier transform ion cyclotron resonance (FTICR), time-of-flight matrix-assisted laser desorption/ionization, and time-of-flight secondary ion mass spectrometry imaging techniques. By leveraging FT-ICR's unparalleled spectral resolution and ToF-SIMS's exceptional spatial resolution, we achieve submicron spatial resolution, enabling the observation of intact molecular species with remarkable spectral precision. Canonical correlation analysis is employed to incorporate physical constraints. Through sophisticated image processing and machine learning techniques, the results of this fusion hold significant promise for advancing our comprehension of complex systems and unveiling concealed molecular intricacies.

canonical correlation analysis↗

Nonlinear Interactions of Alfven Waves in Multi-ion Plasmas (Final Report)

Alfven waves are of fundamental importance in magnetized plasmas, such as the solar wind and Earth’s magnetosphere. When the wave amplitude is large, nonlinear interactions among waves, such as three wave resonance, dominate the dynamics. The nonlinear process can be used as a diagnosis of the plasma composition because the composition affects the dispersion relation of Alfven waves, especially when the wave frequency is close to ion cyclotron frequencies. Previous experiments on the Large Plasma Device (LAPD) had demonstrated that the relative density of two ion species can be determined by examining nonlinear interaction of two counter-propagating Alfven waves. In this project we extended the study to a plasma with three ion species, where multiple wave bands exist, and more nonlinear interactions are possible. We also investigated the feasibility of launching two co-propagating waves to measure the ion composition. The findings of this study have implication in developing new technology to measure cold ion populations in space plasmas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

ICRF wave propagation and absorption modelling via machine learning

A surrogate model of the wave absorption in the ion cyclotron range of frequencies is presented. The model is trained to capture the physics of 1D electron and ion power absorption profiles for both the high harmonic fast wave scheme in NSTX, and the minority heating scheme in WEST. The surrogate models, based on both the random forest regressor and the multilayer perceptron algorithms, reduce inference time of 1D power absorption profiles from 1-5 minutes required by TORIC to ∼50 µs with high accuracy (i.e. R2 = 0.71−0.96).

Sánchez-Villar↗

Alfvénic modes excited by the kink instability in PHASMA

Magnetic flux ropes have been successfully created with plasma guns in the newly commissioned PHAse Space MApping (PHASMA) experiment. The flux ropes exhibit the expected m = 1 kink instability. The observed threshold current for the onset of this kink instability is half of the Kruskal–Shafranov current limit, consistent with predictions for the non-line tied boundary condition of PHASMA. The helicity, paramagnetism, and growth rate of the observed magnetic fluctuations are also consistent with kink instability predictions. The observed fluctuation frequency appears to be a superposition of a real frequency due to a Doppler shift of the kink mode arising from plasma flow (~2kHz) and a contribution from a wave mode (~5 kHz). The dispersion of the wave mode is consistent with an Alfvén wave. Distinct from most previ-ous laboratory studies of flux ropes, the working gas in PHASMA is argon. Thus, the ion cyclotron frequency in PHASMA is quite low and the frequency of the Alfvénic mode plateaus at ~0.5 of the ion gyro frequency with increasing background magnetic field strength.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Binding energies, charge radii, spins, and moments: Odd-odd Ag isotopes and discovery of a new isomer

We report on the masses and hyperfine structure of ground and isomeric states in 114,116,118,120 Ag isotopes, measured with the phase-imaging ion-cyclotron-resonance technique (PI-ICR) with the JYFLTRAP mass spectrometer and the collinear laser spectroscopy beamline at the Ion Guide Isotope Separator On-Line facility, Jyväskylä, Finland. We measured the masses and excitation energies, electromagnetic moments, and charge radii, and firmly established the nuclear spins of the long-lived states. A new isomer was discovered in 118 Ag and the half-lives of 118 Ag long-lived states were reevaluated. We unambiguously pinned down the level ordering of all long-lived states, placing the inversion of the 𝐼 = 0 − and 𝐼 = 4 + states at 𝐴 = 118 (𝑁 = 71). As a result, we compared the electromagnetic moments of each state to empirical single-particle moments to identify the dominant configuration where possible.

90 ≤ A ≤ 149↗

First Penning trap mass measurement of 36 Ca

Background: Isobaric quintets provide the best test of the isobaric multiplet mass equation (IMME) and can uniquely identify higher order corrections suggestive of isospin symmetry breaking effects in the nuclear Hamilto nian. The Generalized IMME (GIMME) is a novel microscopic interaction theory that predicts an extension to the quadratic form of the IMME. Only the A = 20, 32 T = 2 quintets have the exotic T z = –2 member ground state mass determined to high-precision by Penning trap mass spectrometry. Purpose: To establish A = 36 as the third high-precision T = 2 isobaric quintet with the T z = –2 member ground state mass measured by Penning trap mass spectrometry and provide the first test of the predictive power of the GIMME. Method: Here, a radioactive beam of neutron-deficient 36 Ca was produced by projectile fragmentation at the National Superconducting Cyclotron Laboratory. The beam was thermalized and the mass of 36 Ca + and 36 Ca 2+ measured by the Time of Flight - Ion Cyclotron Resonance method in the LEBIT 9.4 T Penning trap. Results: We measure the mass excess of 36 Ca to be ME= –6483.6(56) keV, an improvement in precision by a factor of 6 over the literature value. The new datum is considered together with evaluated nuclear data on the A = 36, T = 2 quintet. We find agreement with the quadratic form of the IMME given by isospin symmetry, but only coarse qualitative agreement with predictions of the GIMME. Conclusion: A total of three isobaric quintets have their most exotic members measured by Penning trap mass spectrometry. The GIMME predictions in the T = 2 quintet appear to break down for A = 32 and greater.

20 ≤ A ≤ 38↗

Oxygen torus and its coincidence with EMIC wave in the deep inner magnetosphere: Van Allen Probe B and Arase observations

We investigate the longitudinal structure of the oxygen torus in the inner magnetosphere for a specific event found on 12 September 2017, using simultaneous observations from the Van Allen Probe B and Arase satellites. It is found that Probe B observed a clear enhancement in the average plasma mass (M) up to 3–4 amu at L = 3.3–3.6 and magnetic local time (MLT) = 9.0 h. In the afternoon sector at MLT ~ 16.0 h, both Probe B and Arase found no clear enhancements in M. This result suggests that the oxygen torus does not extend over all MLT but is skewed toward the dawn. Since a similar result has been reported for another event of the oxygen torus in a previous study, a crescent-shaped torus or a pinched torus centered around dawn may be a general feature of the O + density enhancement in the inner magnetosphere. We newly find that an electromagnetic ion cyclotron (EMIC) wave in the H + band appeared coincidently with the oxygen torus. From the lower cutoff frequency of the EMIC wave, the ion composition of the oxygen torus is estimated to be 80.6% H + , 3.4% He + , and 16.0% O + . According to the linearized dispersion relation for EMIC waves, both He + and O + ions inhibit EMIC wave growth and the stabilizing effect is stronger for He + than O + . Therefore, when the H + fraction or M is constant, the denser O + ions are naturally accompanied by the more tenuous He + ions, resulting in a weaker stabilizing effect (i.e., larger growth rate). From the Probe B observations, we find that the growth rate becomes larger in the oxygen torus than in the adjacent regions in the plasma trough and the plasmasphere.

79 ASTRONOMY AND ASTROPHYSICS↗

High Field Side Launch of RF Waves: A New Approach to Reactor Actuators

Launching radio frequency (RF) waves from the high field side (HFS) of a tokamak offers significant advantages over low field side (LFS) launch with respect to both wave physics and plasma material interactions (PMI). For lower hybrid (LH) waves, the higher magnetic field opens the window between wave accessibility and the condition for strong electron Landau damping, allowing LH waves from the HFS to penetrate into the core of a burning plasma, while waves launched from the LFS are restricted to the periphery of the plasma. The lower of waves absorbed at higher yields a higher current drive efficiency as well. In the ion cyclotron range of frequencies (ICRF), HFS launch allows for direct access to the mode conversion layer where mode converted waves absorb strongly on thermal electrons and ions, thus avoiding the generation of energetic minority ion tails. The absence of turbulent heat and particle fluxes on the HFS, particularly in double null configuration, makes it the ideal location to minimize PMI damage to the antenna structure. The quiescent SOL also eliminates the need to couple LH waves across a long distance to the separatrix, as the antenna can be located close to plasma without risking damage to the structure. Improved impurity screening on the HFS will help eliminate the long-standing issues of high Z impurity accumulation with ICRF.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗