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At least 307 records · Page 17

Elimination of MHD current sheets by modifications to the plasma wall in a fixed boundary model

Models of magnetohydrodynamic (MHD) equilibia that for computational convenience assume the existence of a system of nested magnetic flux surfaces tend to exhibit singular current sheets. These sheets are located on resonant flux surfaces that are associated with rational values of the rotational transform. We study the possibility of eliminating these singularities by suitable modifications of the plasma boundary, which we prescribe in a fixed boundary setting. We find that relatively straightforward iterative procedures can be used to eliminate weak current sheets that are generated at resonant flux surfaces by the nonlinear interactions of resonating wall harmonics. These types of procedures may prove useful in the design of fusion devices with configurations that enjoy improved stability and transport properties.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Computation of linear MHD instabilities with the multi-region relaxed MHD energy principle

Over the last decade, a variational principle based on a generalisation of Taylor's relaxation, referred to as multi-region relaxed magnetohydrodynamics (MRxMHDs) has been developed. The numerical solutions of the MRxMHD equilibria have been constructed using the Stepped Pressure Equilibrium Code (SPEC) (Hudson et al 2012 Phys. Plasmas 19 112502). In principle, SPEC could also be established to describe the MRxMHD stability of an equilibrium. In this work, a theoretical framework is developed to relate the second variation of the energy functional to the so-called Hessian matrix, enabling the prediction of MHD linear instabilities of cylindrical plasmas, and is implemented in SPEC. The negative and positive eigenvalues of the Hessian matrix predict the stability of an equilibrium. Verification studies of SPEC stability results with the M3D-C 1 code and the tearing mode $\Delta^{^{\prime}}$ criterion have been conducted for ideal and resistive MHD instabilities, respectively, in a pressureless cylindrical tokamak, and have shown good agreement. Overall, our stability analysis is a critical step towards understanding the MHD stability of three-dimensional MHDs where nested flux surfaces, magnetic islands and stochastic regions co-exist.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Pressure-driven stochastization of flux surfaces in stellarator equilibria: a review of the experimental observations and their analysis

Stellarator vacuum fields are designed to have a dense set of nested flux surfaces, with only small islands and stochastic regions in the interior of the confinement region. As the plasma pressure is increased, pressure driven currents appear, and they can significantly modify the vacuum field. The question arises whether pressure driven currents can cause significant flux surface breakage. Both the Wendelstein 7-AS and large helical device stellarators had dedicated experimental campaigns to study the β limit in those devices. In this paper, we review the evidence that the flux surfaces in a significant fraction of the plasma volume were stochastized by the pressure-driven currents in the highest β experiments. That phenomenon appears to have been the dominant source of pressure-driven flux surface loss in these experiments.

stellarator equilibrium↗

Structure of pressure-gradient-driven current singularity in ideal magnetohydrodynamic equilibrium

Abstract Singular currents typically appear on rational surfaces in non-axisymmetric ideal magnetohydrodynamic (MHD) equilibria with a continuum of nested flux surfaces and a continuous rotational transition. These currents have two components: a surface current (Dirac δ -function in flux surface labeling) that prevents the formation of magnetic islands, and an algebraically divergent Pfirsch–Schlüter current density when a pressure gradient is present across the rational surface. On flux surfaces adjacent to the rational surface, the traditional treatment gives the Pfirsch–Schlüter current density scaling as J ∼ 1 / Δ ι , where Δ ι is the difference of the rotational transform relative to the rational surface. If the distance s between flux surfaces is proportional to Δ ι , the scaling relation J ∼ 1 / Δ ι ∼ 1 / s will lead to a paradox that the Pfirsch–Schlüter current is not integrable. In this work, we investigate this issue by considering the pressure-gradient-driven singular current in the Hahm–Kulsrud–Taylor problem, which is a prototype for singular currents arising from resonant magnetic perturbations. We show that not only the Pfirsch–Schlüter current density but also the diamagnetic current density are divergent as ∼ 1 / Δ ι . However, due to the formation of a Dirac δ -function current sheet at the rational surface, the neighboring flux surfaces are strongly packed with s ∼ ( Δ ι ) 2 . Consequently, the singular current density J ∼ 1 / s , making the total current finite, thus resolving the paradox. Furthermore, the strong packing of flux surfaces causes a steepening of the pressure gradient near the rational surface, with ∇ p ∼ d p / d s ∼ 1 / s . In general non-axisymmetric MHD equilibrium, contrary to Grad’s conjecture that the pressure profile is flat around densely distributed rational surfaces, our result suggests a pressure profile that densely steepens around them.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Seebeck effect studies in the charge density wave state of organic conductor α-(BEDT–TTF) 2 KHg(SCN) 4

Angular, magnetic field and temperature dependence of the interlayer Seebeck effect of the multiband organic conductor $\alpha -{(\mathrm{BEDT}-\mathrm{TTF})}_{2}\mathrm{KHg}{(\mathrm{SCN})}_{4}$ is experimentally studied at temperatures down to 0.55 K and fields up to 31 T in a wide range of angles. The background magnetic field and angular component of the Seebeck effect as well as the magnetic quantum oscillations that originate from the closed Fermi surface orbits are analyzed. The background interlayer Seebeck effect components show that above certain tilt angle of the magnetic field and above the kink field there is another CDW state in $\alpha -{(\mathrm{BEDT}-\mathrm{TTF})}_{2}\mathrm{KHg}{(\mathrm{SCN})}_{4}$, between previously known CDW0 and CDWx states, in agreement with magnetoresistance and magnetization studies in this material. Our observations show that this state possesses some of the properties of the CDW0 state. The Fermi surface in the third CDW state is still reconstructed but less imperfectly nested as expected as this state develops above the kink field. The temperature dependence of the interlayer Seebeck effect reveals that this state is developed at temperatures below 3 K and at field orientations around the second AMRO maximum. In addition, for the first time, a detailed T - θ phase diagram of $\alpha -{(\mathrm{BEDT}-\mathrm{TTF})}_{2}\mathrm{KHg}{(\mathrm{SCN})}_{4}$ based purely on Seebeck effect measurements is presented. We find that other states and transitions, beside the CDW states, also exist in a given temperature and angular range that have not been previously reported. These observations change the whole picture about the transport processes in the organic conductor $\alpha -{(\mathrm{BEDT}-\mathrm{TTF})}_{2}\mathrm{KHg}{(\mathrm{SCN})}_{4}$ and allow to better understand the complex nature of the CDW order in this and similar compounds.

Physics↗

Quantization of the band at the surface of charge density wave material 2H-TaSe 2

By using angle-resolved photoemission spectroscopy combined with the first-principles electronics atructure calculations, we report the quantum well states at the surface of a single crystal 2H-TaSe 2 . We observed sub-bands at the three-dimensional Brillouin zone center forming the quantized states due to its highly dispersive nature and light effective mass along k z direction. The quantized sub-bands shift upward towards E F with the decrease of temperature across TCDW. The band shift could not be explained by two-dimensional Fermi-surface nesting-driven charge density waves(CDW), nor by purely strong electron-phonon coupling only. The CDW in 2H-TaSe 2 is likely related to the bands at higher binding energy, and the CDW mechanism could be explained by the excitons, and our observation gives support to this scenario.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Inference of experimental radial impurity transport on Alcator C-Mod: Bayesian parameter estimation and model selection

We present a fully Bayesian approach for the inference of radial profiles of impurity transport coefficients and compare its results to neoclassical, gyrofluid and gyrokinetic modeling. Using nested sampling, the Bayesian Impurity Transport InferencE (BITE) framework can handle complex parameter spaces with multiple possible solutions, offering great advantages in interpretative power and reliability with respect to previously demonstrated methods. BITE employs a forward model based on the pySTRAHL package, built on the success of the well-known STRAHL code [Dux, IPP Report, 2004], to simulate impurity transport in magnetically-confined plasmas. In this paper, we focus on calcium (Ca, Z=20) Laser Blow-Off injections into Alcator C-Mod plasmas. Multiple Ca atomic lines are diagnosed via high-resolution X-ray Imaging Crystal Spectroscopy and Vacuum Ultra-Violet measurements. We analyze a sawtoothing I-mode discharge for which neoclassical and turbulent (quasilinear and nonlinear) predictions are also obtained. Here, we find good agreement in diffusion across the entire radial extent, while turbulent convection and density profile peaking are estimated to be larger in experiment than suggested by theory. Efforts and challenges associated with the inference of experimental pedestal impurity transport are discussed.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Experimental inference of flux tunneling between magnetic island chains in tokamaks

We report confinement bifurcations due to flux tunneling in magnetic islands in toroidal plasmas. This occurs in 2/1 islands, triggered by decoupling of non-overlapping adjacent 5/2 islands. While subject to electron cyclotron current drive (ECCD), the temperature at the 2/1 O-point is flat before but peaks after decoupling. Here, this is shown to be due to a bifurcation from stochastic to nested magnetic structure, caused by the removal of flux tunneling through intersecting manifolds of overlapping heteroclinic tangles. 2/1 island stability correlates with coupling events in an ITER baseline scenario plasma where ECCD can not stabilize the coupled islands, showing the critical impact of flux tunneling on disruption avoidance in tokamaks.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Improving ideal MHD equilibrium accuracy with physics-informed neural networks

We present a novel approach to compute three-dimensional magnetohydrodynamic equilibria with isotropic pressure profiles and nested surfaces by parametrizing Fourier modes with artificial neural networks (NNs). The full nonlinear global force residual of single equilibria across the volume in real space is then minimized with first order optimizers and compared to equilibria computed by conventional solvers. Already, we observe competitive computational cost to arrive at the same minimum residuals computable with existing codes. With increased computational cost, lower minima of the residual are computable with the NNs than with any other tested solver, establishing a new lower bound for the force residual. We use minimally complex NNs, and we expect significant improvements for solving not only single equilibria with NNs, but also for creating NN models valid over continuous distributions of equilibria.

ideal magnetohydrodynamics↗

Nonlinear saturation of ballooning modes in stellarators

Ballooning mode saturation is investigated in realistic stellarator configurations using the flux tube approach of Ham et al (2018 Plasma Phys. Control. Fusion 60 075017), Ham et al (2016 Phys. Rev. Lett. 116 235001). The method is adapted to account for the lack of exact force balance in stellarator equilibrium solvers that assume existence of nested flux surfaces. A variational approach for calculating flux tube energy is developed to overcome this force error problem in stellarator numerical equilibria. Saturated (equilibrium) flux tube states that cross 10%–20% of the plasma minor radius are shown to exist for linearly ballooning unstable profiles. It is shown that several features of the displaced flux tube structure in a full nonlinear MHD simulation of Wendelstein 7X are reproduced by our model. Saturated states are found in a compact stellarator equilibrium close but below the marginal ballooning linear instability, i.e. the unperturbed equilibrium is metastable. This suggests that edge-localized-mode-like explosive MHD behavior may be possible in stellarators.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Evaluating Awkward Arrays, uproot, and coffea as a query platform for High Energy Physics Data

Query languages for High Energy Physics (HEP) are an ever present topic within the field. A query language that can efficiently represent the nested data structures that encode the statistical and physical meaning of HEP data will help analysts by ensuring their code is more clear and pertinent. As the result of a multi-year effort to develop an in-memory columnar representation of high energy physics data, the NumPy, Awkward Array, and uproot Python packages present a mature and efficient interface to HEP data. Atop that base, the coffea package adds functionality to launch queries at scale, manage and apply experiment-specific transformations to data, and present a rich object-oriented columnar data representation to the analyst. Recently, a set of Analysis Description Language (ADL) benchmarks has been established to compare HEP queries in multiple languages and frameworks. In this paper we present these benchmark queries implemented within the coffea framework and discuss their readability and performance characteristics. We find that the columnar queries perform as well or better than the implementations given in previous studies.

Gray, L.↗

Monte Carlo method for constructing confidence intervals with unconstrained and constrained nuisance parameters in the NOvA experiment

Measuring observables to constrain models using maximum-likelihood estimation is fundamental to many physics experiments. Wilks' theorem provides a simple way to construct confidence intervals on model parameters, but it only applies under certain conditions. These conditions, such as nested hypotheses and unbounded parameters, are often violated in neutrino oscillation measurements and other experimental scenarios. Monte Carlo methods can address these issues, albeit at increased computational cost. In the presence of nuisance parameters, however, the best way to implement a Monte Carlo method is ambiguous. Furthermore, this paper documents the method selected by the NOvA experiment, the profile construction. It presents the toy studies that informed the choice of method, details of its implementation, and tests performed to validate it. It also includes some practical considerations which may be of use to others choosing to use the profile construction.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Surface Fermi contours and phonon anomalies at the surface of the random alloy

Abstract The impact of compositional disorder on physical properties is a subject of prime focus in many materials systems. In this paper, we report photoemission measurements of Mo 1− x Re x (110)-(1 × 1)H alloy surfaces to probe the relationship between the surface Fermi contours and giant Kohn anomalies observed in the surface phonon dispersion relations. Our measured nesting vectors precisely predict the composition dependence of the anomalous wave vectors.

Okada, Michio (ORCID:0000000276894288)↗

Global perspectives of the bulk electronic structure of URu 2 Si 2 from angle-resolved photoemission

Previous high-resolution angle-resolved photoemission (ARPES) studies of URu 2 Si 2 have characterized the temperature-dependent behavior of narrow-band states close to the Fermi level ( E F ) at low photon energies near the zone center, with an emphasis on electronic reconstruction due to Brillouin zone folding. A substantial challenge to a proper description is that these states interact with other hole-band states that are generally absent from bulk-sensitive soft x-ray ARPES measurements. Here we provide a more global k -space context for the presence of such states and their relation to the bulk Fermi surface (FS) topology using synchrotron-based wide-angle and photon energy-dependent ARPES mapping of the electronic structure using photon energies intermediate between the low-energy regime and the high-energy soft x-ray regime. Small-spot spatial dependence, f -resonant photoemission, Si 2 p core-levels, x-ray polarization, surface-dosing modification, and theoretical surface slab calculations are employed to assist identification of bulk versus surface state character of the E F -crossing bands and their relation to specific U- or Si-terminations of the cleaved surface. The bulk FS topology is critically compared to density functional theory (DFT) and to dynamical mean field theory calculations. In addition to clarifying some aspects of the previously measured high symmetry Γ, Z and X points, incommensurate 0.6 a * nested Fermi-edge states located along Z – N – Z are found to be distinctly different from the DFT FS prediction. The temperature evolution of these states above T HO , combined with a more detailed theoretical investigation of this region, suggests a key role of the N -point in the hidden order transition.

36 MATERIALS SCIENCE↗

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning

Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrarily complex nested knowledge schemas. Results Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against an LLM to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for matched elements. We present examples of applying SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease relationships. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction methods, but greatly surpasses an LLM’s native capability of grounding entities with unique identifiers. SPIRES has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any new training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. Availability and implementation SPIRES is available as part of the open source OntoGPT package: https://github.com/monarch-initiative/ontogpt.

59 BASIC BIOLOGICAL SCIENCES↗

Community composition and abundance of wild bees at row crop-grassland interfaces in west central Nebraska

Abstract Perennial mixed forb and grassland habitats are crucial to conservation of pollinators and connectivity of habitats in intensely farmed landscapes. This study aims to understand the effects of land use on the pollinator community by describing bee abundance, species richness and community composition in perennial conservation grasslands and adjacent annual row crops located in west central Nebraska. In 2022 and 2023, we collected and identified bees via sticky traps at 4 locations (center and edge of adjacent grasslands and crop fields) at 6 replicated sites. We collected 1,768 specimens from sticky traps, resulting in 70 species within 28 genera. Halictidae accounted for 84% of the specimens collected. Bee abundance was influenced by the simple effects of land use (grassland vs. crops), edge adjacency, and the month and year of collection. Differences in bee abundance within a collection date were found mostly in early 2022 (May and June) and late 2023 (September), when the crop center location was generally the lowest, with some evidence for spillover of bees from the grassland into the crop edge during the early summer months. Bee species richness was affected only by month and was not significantly different by land use and edge adjacency. Bee community composition overlapped across the 4 locations, although there were significant dissimilarities between crop fields and grasslands. Surveys of the plant community revealed very low abundance of blooming stems and plant taxonomic richness at crop locations for all sampling periods, while grassland locations were comparatively high and varied over time. Plant communities showed no overlap between crop field and grassland locations. Overall, we found that conservation grasslands, while not seeded specifically with pollinator-attractive forbs, provide diverse resources to support wild bee communities in west central Nebraska; crop edges may also provide non-plant resources such as nesting sites and irrigation water. Going forward, better understanding pollinator species composition and resource utilization relative to land use characteristics and drought conditions will allow for better tailoring of conservation efforts and management strategies in Nebraska and across the larger region.

Entomology↗

Simultaneous dissection of grain carotenoid levels and kernel color in biparental maize populations with yellow-to-orange grain

Maize enriched in provitamin A carotenoids could be key in combatting vitamin A deficiency in human populations relying on maize as a food staple. Consumer studies indicate that orange maize may be regarded as novel and preferred. This study identifies genes of relevance for grain carotenoid concentrations and kernel color, through simultaneous dissection of these traits in 10 families of the US maize nested association mapping panel that have yellow to orange grain. Quantitative trait loci were identified via joint-linkage analysis, with phenotypic variation explained for individual kernel color quantitative trait loci ranging from 2.4% to 17.5%. These quantitative trait loci were cross-analyzed with significant marker-trait associations in a genome-wide association study that utilized ~27 million variants. Nine genes were identified: four encoding activities upstream of the core carotenoid pathway, one at the pathway branchpoint, three within the α- or β-pathway branches, and one encoding a carotenoid cleavage dioxygenase. Of these, three exhibited significant pleiotropy between kernel color and one or more carotenoid traits. Kernel color exhibited moderate positive correlations with β-branch and total carotenoids and negligible correlations with α-branch carotenoids. These findings can be leveraged to simultaneously achieve desirable kernel color phenotypes and increase concentrations of provitamin A and other priority carotenoids.

59 BASIC BIOLOGICAL SCIENCES↗

Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits

Abstract The recent assembly and annotation of the 26 maize nested association mapping population founder inbreds have enabled large-scale pan-genomic comparative studies. These studies have expanded our understanding of agronomically important traits by integrating pan-transcriptomic data with trait-specific gene candidates from previous association mapping results. In contrast to the availability of pan-transcriptomic data, obtaining reliable protein–protein interaction (PPI) data has remained a challenge due to its high cost and complexity. We generated predicted PPI networks for each of the 26 genomes using the established STRING database. The individual genome-interactomes were then integrated to generate core- and pan-interactomes. We deployed the PPI clustering algorithm ClusterONE to identify numerous PPI clusters that were functionally annotated using gene ontology (GO) functional enrichment, demonstrating a diverse range of enriched GO terms across different clusters. Additional cluster annotations were generated by integrating gene coexpression data and gene description annotations, providing additional useful information. We show that the functionally annotated PPI clusters establish a useful framework for protein function prediction and prioritization of candidate genes of interest. Our study not only provides a comprehensive resource of predicted PPI networks for 26 maize genomes but also offers annotated interactome clusters for predicting protein functions and prioritizing gene candidates. The source code for the Python implementation of the analysis workflow and a standalone web application for accessing the analysis results are available at https://github.com/eporetsky/PanPPI.

Genetics & Heredity↗