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At least 271 records · Page 15

A Multiplexed Quantitative Analysis of Germline Single Amino Acid Variants by Targeted Proteomics in Nondepleted Human Plasma

Single amino acid variants (SAAVs) in protein sequences are often a direct result of single-nucleotide polymorphisms (SNPs). Certain germline SAAVs have shown biological relevance in different disease conditions but lack precise quantification in circulation, which could hinder functional investigations and progress in biomarker development. Here, we have developed a multiplexed liquid chromatography-selected reaction monitoring (LC-SRM) assay that monitors 5 wild-type and variant peptide pairs (Complement Factor B: CFB-R32Q/R32W, Clusterin: CLU-N317H, Fetuin B: FETUB-K360R, and Kininogen: KNG1-L212P) in nondepleted human plasma. The assay was optimized for imprecision, linearity, stability, and calibration assessments with CVs of under 20%. The wild-type and variant peptide pairs were characterized in a set of healthy individual plasma samples. These target identifications were also validated by SNP genotyping with more than 99% accuracy. For all protein targets, we observed significantly lower concentrations of WT species in the presence variant peptides. In CFB, the concentration of R32Q was significantly lower than its counterpart R32W variant and WT species. Furthermore, our results distinguished phenotypes of homozygosity and heterozygosity of the SAAV presence through direct concentration level characterization. These findings provide some insights into how SAAVs affect quantitative assessments of target peptides. The assay demonstrates a platform for proteogenomic analyses with potential applications in both research and clinical settings.

genetics↗

Fluid and kinetic nonlinearities of near-acoustic plasma waves

Large amplitude, near-acoustic plasma waves have a temperature-dependent harmonic content and nonlinear frequency shifts. On cold plasmas, experiments show that fluid nonlinearities dominate, and the observed harmonic content is well predicted by a recent fluid analysis. In contrast, the measured nonlinear frequency shift is smaller than this theory prediction, suggesting the presence of other nonlinear effects neglected in this analysis. When the plasma is heated, kinetic effects become important, and we observe an increase in both the harmonic content and nonlinear frequency shift. Quantitative experiments on the stability of these large amplitude, near-acoustic plasma waves strongly support the idea that trapped particles reduce the amplitude threshold for instability below fluid models. Furthermore, at low temperatures, the broad characteristics of the parametric instability are determined by the frequency detuning of the pump and daughter wave and the wave-wave coupling strength, surprisingly consistent with simple cold fluid, three-wave theories. However, at higher temperatures, the pump wave becomes unstable at half the threshold pump wave amplitude, with similar exponential growth rates as for a cold plasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Direct preemptive stabilization of $m,n$ = 2,1 neoclassical tearing modes by electron cyclotron current drive in the DIII-D low-torque ITER baseline scenario

We report the first preemptive direct stabilization of $m,n$ = 2,1 neoclassical tearing modes (NTMs) in DIII-D low-torque ITER baseline scenario plasmas by electron cyclotron waves. These experiments strongly support that the observed stabilization is achieved by replacing the missing bootstrap current in the island by electron cyclotron current drive (ECCD). These plasmas (with and without ECCD) are stable to 2,1 NTMs when the differential rotation between the q = 1 and q = 2 surfaces (Δf 1,2 ) is sustained above a critical value (Δf CRIT ≈ 1 kHz), but those evolving to low differential rotation (Δf 1,2 < Δf CRIT ) routinely develop a disruptive 2,1 island at the time and frequency of a sawtooth precursor. Preemptive, local and direct stabilization by ECCD is tested by scanning the current drive amplitude and location inside and outside of the q = 2 rational surface shot by shot. Analysis of only low differential rotation time windows, i.e. when stabilization from Δf 1,2 is absent, shows focused ECCD at q = 2 prevents the onset of 2,1 NTMs. These results are important, as they give the first demonstration of disruptive NTM control by ECCD in the plasma scenario planned for ITER.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Prospects for a high-field, compact break-even axisymmetric mirror (BEAM) and applications

This paper explores the feasibility of a break-even-class mirror referred to as BEAM (break-even axisymmetric mirror): a neutral-beam-heated simple mirror capable of thermonuclear-grade parameters and $Q\sim 1$ conditions. Compared with earlier mirror experiments in the 1980s, BEAM would have: higher-energy neutral beams, a larger and denser plasma at higher magnetic field, both an edge and a core and capabilities to address both magnetohydrodynamic and kinetic stability of the simple mirror in higher-temperature plasmas. Axisymmetry and high-field magnets make this possible at a modest scale enabling a short development time and lower capital cost. Such a $Q\sim 1$ configuration will be useful as a fusion technology development platform, in which tritium handling, materials and blankets can be tested in a real fusion environment, and as a base for development of higher- $Q$ mirrors.

Physics↗

Toroidal modeling of energetic passing particle drift kinetic effects on tearing mode stability

Abstract Drift kinetic effects of the neutral beam injection induced passing energetic particles (EPs) on the linear stability of the n = 1 tearing mode (TM) (with the dominant poloidal harmonic of m = 2) are numerically investigated utilizing the MARS-K code (Liu et al 2008 Phys. Plasmas 15 112503), in a tokamak plasma with finite equilibrium pressure and anisotropic thermal transport. In the low plasma pressure regime, it is found that co- (counter-) passing EPs stabilize (destabilize) the TM, agreeing with previous studies. However, as the plasma pressure increases beyond a critical value, it is found that co-passing EPs also destabilize the mode. An in-depth analysis reveals that the net effect of co-passing EPs is a result of competition between the stabilizing contribution from the non-adiabatic drift kinetic terms and the destabilizing contribution associated with adiabatic terms, with the latter becoming more dominant at higher equilibrium pressure. Non-perturbative magnetohydrodynamic-kinetic hybrid modeling also finds that co- and counter-passing EPs modify the TM eigenfunction differently, with the counter-passing EPs enhancing the sideband harmonics. Furthermore, effects of the plasma resistivity and toroidal rotation, as well as that of the equilibrium distribution of EPs in the particle pitch angle space, are also investigated, showing asymmetric results on the TM stability between the co- and counter-passing EPs. The first order finite orbit width correction is found to be stabilizing with co-passing EPs and destabilizing with counter-passing particles. Finally, drift resonances between passing EPs and the TM induce finite frequency to the mode and generate finite net torques inside the plasma, due to the neoclassical toroidal viscosity and the Reynolds stress associated with 3D perturbations.

Physics↗

Effects of equilibrium pressure on plasma response to RMPs in a spherical tokamak

This study presents a comprehensive analysis of the equilibrium pressure on the plasma response to resonant magnetic perturbations (RMPs) in the spherical tokamak (ST) MAST-U, employing both single-fluid and MHD-kinetic hybrid models (implemented via the MARS-F/K codes). As a key finding, the study identifies two different pressure-driven eigenmodes, exhibiting Sturmian property, that affect the Troyon no-wall limits for the onset of the n = 1 and n = 2 ( n is the toroidal mode number) ideal external kink instabilities as well as the corresponding plasma response to the applied RMP. With increasing equilibrium pressure, the plasma response to RMPs is significantly enhanced in the ST plasma, particularly in the high-pressure regime where kinetic effects strongly stabilize the external kink instability. The Troyon no-wall limit divides the plasma response into two regions: well below the limit, the response amplitudes and trends (versus pressure) are similar between the fluid and kinetic models; as the equilibrium pressure approaches the Troyon limit, the kinetic model predicts significant amplification of the RMP field, up to 30 times for cases considered. A relatively weak dependence of the optimal coil phasing on the equilibrium pressure is computed in this ST plasma, similar to the trend obtained for the conventional aspect ratio devices. These findings underscore the importance of incorporating kinetic effects in accurate prediction of the plasma response to RMPs in high-pressure ST tokamak plasmas and provide a theoretical basis for optimizing RMP-based control of the edge-localized modes in future ST devices.

RMP↗

Plasma Facing Components with Capillary Porous System and Liquid Metal Coolant Flow

Liquid metal can create a renewable protective surface on plasma facing components (PFC), with an additional advantage of deuterium pumping and the prospect of tritium extraction if liquid lithium (LL) is used and maintained below 450 C, the temperature above which LL vapor pressure begins to contaminate the plasma. LM can also be utilized as an efficient coolant, driven by the Lorentz force created with the help of the magnetic field in fusion devices. Capillary porous systems can serve as a conduit of LM and simultaneously provide stabilization of the LM flow, protecting against spills into the plasma. Recently a combination of a fast-flowing LM cooling system with a porous plasma facing wall (CPSF) was investigated [Khodak and Maingi (2021)]. The system takes an advantage of a magnetohydrodynamics velocity profile, as well as attractive LM properties to promote efficient heat transfer from the plasma to the LL at low pumping energy cost, relative to the incident heat flux on the PFC. In case of a disruption leading to excessive heat flux from the plasma to the LM PFCs, LL evaporation can stabilize the PFC surface temperature, due to high evaporation heat and apparent vapor shielding. The proposed CPSF was optimized analytically for the conditions of a Fusion Nuclear Science Facility [Kessel et al. (2019)]: 10T toroidal field and 10 MW/m2 peak incident heat flux. Computational fluid dynamics analysis confirmed that a CPSF system with 2.5 mm square channels can pump enough LL so that no additional coolant is needed.

High Heat Flux↗

Plasma facing components with capillary porous system and liquid metal coolant flow

Liquid metal can create a renewable protective surface on plasma facing components (PFC), with an additional advantage of deuterium pumping and the prospect of tritium extraction if liquid lithium (LL) is used and maintained below 450 °C, the temperature above which LL vapor pressure begins to contaminate the plasma. LM can also be utilized as an efficient coolant, driven by the Lorentz force created with the help of the magnetic field in fusion devices. Capillary porous systems can serve as a conduit of LM and simultaneously provide stabilization of the LM flow, protecting against spills into the plasma. Recently, a combination of a fast-flowing LM cooling system with a porous plasma facing wall (CPSF) was investigated [A. Khodak and R. Maingi, Nucl. Mater. Energy 26, 100935 (2021)]. The system takes an advantage of a magnetohydrodynamics velocity profile as well as attractive LM properties to promote efficient heat transfer from the plasma to the LL at low pumping energy cost, relative to the incident heat flux on the PFC. In the case of a disruption leading to excessive heat flux from the plasma to the LM PFCs, LL evaporation can stabilize the PFC surface temperature, due to high evaporation heat and apparent vapor shielding. The proposed CPSF was optimized analytically for the conditions of a fusion nuclear science facility [Kessel et al., Fusion Sci. Technol. 75, 886 (2019)]: 10 T toroidal field and 10 MW/m 2 peak incident heat flux. Finally, computational fluid dynamics analysis confirmed that a CPSF system with 2.5 mm square channels can pump enough LL so that no additional coolant is needed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Neural-Network-Enhanced COTSIM: Advancing Predictive Capabilities for Fast DIII-D Simulations

Sustaining fusion reactions in tokamaks requires heating plasma to thermonuclear temperatures while maintaining confinement and stability. Neutral beam injection (NBI) provides heating, current drive, torque, and fueling, while electron cyclotron (EC) waves are widely used for heating and current drive; together, these actuators shape the plasma current, temperature, and density profiles. The control-oriented tokamak simulator (COTSIM), a predictive, control-oriented code, has been enhanced with neural-network surrogates for transport and sources. Turbulent transport is predicted by MMMnet—a neural-network version of the updated multimode model (MMM 9.0.10)—with significantly reduced computation time relative to MMM; neoclassical transport follows the Chang–Hinton model. NUBEAMnet, a surrogate of the Monte Carlo NUBEAM module, predicts beam-driven heating, current, and torque. EC heating and current drive use a control-oriented, empirically scaled source model; plasma resistivity follows the Spitzer formulation; bootstrap current uses the Sauter model. Equilibrium is computed using both prescribed and fixed-boundary solvers (FBSs), and the pedestal structure is modeled with an empirical pedestal model. For a representative DIII-D discharge, COTSIM predicts electron and ion temperature and safety-factor profiles in close agreement with TRANSP predictive and interpretive simulations while extending predictions through the pedestal region to the plasma edge (versus 80% of the minor radius in TRANSP). Furthermore, the equivalent COTSIM simulation runs in under 3 min compared to about 2 h for TRANSP, enabling rapid scenario planning, optimization of tokamak operation, and between-pulse control design.

Control-oriented tokamak simulator (COTSIM)↗

Pressure-driven tearing and thermal transport in finite-beta reversed field pinch computations

In this work, nonlinear resistive-magnetohydrodynamics (MHD) computation with heating and anisotropic transport is applied to examine the interaction between thermal energy and magnetic fluctuations in inductively driven reversed-field pinches (RFPs). The magnetic fluctuations underlie magnetic field reversal through dynamo-like correlations, and they enhance thermal energy transport through fluctuations of parallel heat flux density. With the unfavorable magnetic curvature that exists across the RFP profile, thermal energy also affects the magnetic fluctuations. Computations with the NIMROD code [Sovinec et al., J. Comput. Phys. 195, 355–386 (2004)] integrate nonlinear MHD dynamics with energy transport and reproduce an RFP state with experimentally relevant values of plasma-β. Equilibria constructed from results of the 3D computations are analyzed to assess the sources of free energy in the saturated nonlinear state. Linear computations for these profiles show unstable modes of tearing parity. Their eigenfunctions are used to evaluate and compare stabilizing and destabilizing contributions to the kinetic energy integral. An assessment of the drives in the integral reveals that the pressure gradient drive is of comparable magnitude to the parallel current drive, and only the sum of the two surpasses the stabilizing contributions. Correlation of magnetic and parallel heat flux density fluctuations in the nonlinear computations shows that fluctuation-induced thermal conduction is the dominant mode of energy loss, as expected from experimental evidence. Decomposition of the fluctuating heat flux density shows that second-order correlations, alone, do not explain the total energy transport. Higher-order correlations are also important.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Modeling active control of resistive wall mode with power saturation and sensor noise on HL-2M

The resistive wall mode (RWM) control on the HL-2M tokamak is simulated with the MARS-F code (Liu et al 2000 Phys. Plasmas 7 3681), aiming at quantifying control current and voltage requirements when more realistic issues are taken into account, i.e. the control power saturation and the sensor signal noise. The fluid model predicts a narrow stability region for the n = 1 RWM without magnetic feedback, in the 2D parameter space of the plasma pressure versus the toroidal flow speed. Magnetic feedback can fully stabilize the RWM on HL-2M. Without considering the voltage limitation and the sensor signal noise, it is found that plasma flow helps active control of the mode, by reducing the required critical feedback gain for both flux-to-current and flux-to-voltage control schemes. In the absence of the sensor signal noise, the lowest control voltage saturation level, below which the RWM control is lost, is found to roughly satisfy a linear relation to the plasma flow frequency, indicating that subsonic plasma flow is effective in relaxing the control power requirement for the RWM feedback stabilization. The presence of the sensor signal noise substantially modifies the feedback results. A statistical study finds that the sensor signal noise, with the standard deviation of 0.1 G on HL-2M, roughly doubles the required control voltage for successful mode control. The synergistic stabilization effect due to plasma flow is somewhat weakened by the presence of the sensor signal noise. At a given rotation, the tolerable voltage limit generally increases with increasing feedback gain due to the sensor signal noise.

Physics↗

Core-Pedestal Plasma Configurations in Advanced Tokamaks

Here, several configurations for the core and pedestal plasma are examined for a predefined tokamak design by implementing multiple heating/current drive (H/CD) sources to achieve an optimum configuration of high fusion power in a noninductive operation while maintaining an ideally magnetohydrodynamic (MHD) stable core plasma using the IPS-FASTRAN framework. IPS-FASTRAN is a component-based lightweight coupled simulation framework that is used to simulate magnetically confined plasma by integrating a set of high-fidelity codes to construct the plasma equilibrium (EFIT, TOQ, and CHEASE), calculate the turbulent heat and particle transport fluxes (TGLF), model various H/CD systems (TORIC, TORAY, GENRAY, and NUBEAM), model the pedestal pressure and width (EPED), and estimate the ideal MHD stability (DCON). The TGLF core transport model and EPED pedestal model are used to self-consistently predict plasma profiles consistent with ideal MHD stability and H/CD (and bootstrap) current sources. In order to evaluate the achievable and sustainable plasma beta, varying configurations are produced ranging from the no-wall stability to with-wall stability regimes, simultaneously subject to the self-consistent TGLF, EPED, and H/CD source profile predictions that optimize configuration performance. The pedestal density, plasma current, and total injected power are scanned to explore their impact on the target plasma configuration, fusion power, and confinement quality. A set of fully noninductive scenarios are achieved by employing ion-cyclotron, neutral beam injection, helicon, and lower-hybrid H/CDs to provide a broad profile for the total current drive in the core region for a predefined tokamak design. These noninductive scenarios are characterized by high fusion gain (Q ~ 4) and power (P fus ~ 600 MW), optimum confinement quality (H 98 ~ 1.1), and high bootstrap current fraction (f BS ~ 0.7) for Greenwald fraction below unity. The broad current profile configurations identified are stable to low-n kink modes either because the normalized pressure β N is below the no-wall limit or a wall is present.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Role of sheared E × B flow in self-organized, improved confinement states in magnetized plasmas

A great scientific success story of magnetic fusion research in the past several decades is the theoretical development and experimental testing of the process of turbulence decorrelation and stabilization by sheared E×B flow which shows that E×B shear effects are ubiquitous in magnetized plasmas. This concept of turbulence decorrelation and stabilization has the universality needed to explain the H-mode edge transport barriers seen in limiter and divertor tokamaks, stellarators, and mirror machines; the broader edge transport barrier seen in VHmode plasmas; and the core transport barriers formed in tokamaks. Similar effects are seen in linear devices. These examples of confinement improvement are of considerable physical interest; it is not often that a system self-organizes to reduce transport when an additional source of free energy is applied to it. The transport decrease associated with E×B velocity shear is also of great practical benefit to fusion research, since it contributed to substantially increased fusion yield in all DT magnetic fusion experiments conducted to date. The fundamental physics involved in transport reduction is the effect of E×B shear on the growth, radial extent, and phase correlation of turbulent eddies in the plasma. The same basic transport reduction process can be operational in various portions of the plasma because there are a number of ways to change the radial electric field Er. An important secondary theme in this area is the synergistic effect of E×B velocity shear and magnetic shear. Although the E×B velocity shear appears to have an effect on broader classes of microturbulence, magnetic shear can mitigate some potentially harmful effects of E×B velocity shear and facilitate turbulence stabilization. Our present understanding in this area is the result of a multi-decade, intertwined effort in theory, modeling and diagnostic development combined with continuing experimental investigations. These experiments have clearly demonstrated that increased E×B shear causes reductions in turbulence and transport. Finally, the experimental findings are generally consistent with the basic theoretical models although considerable work remains to be done before we have a fully predictive theory of transport in magnetized plasmas including E×B shear effects.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Global micro-tearing modes in the wide pedestal of an NSTX plasma

Global linear electromagnetic gyrokinetic simulations of micro-tearing modes (MTMs) growing in the wide pedestal of the ELM-free NSTX discharge #132 588 are reported. Two micro-tearing branches growing near the surfaces of safety factor q = 4 (pedestal top) and q=5–6 (pedestal) are simulated. The frequencies of these MTMs with low toroidal mode number (n ranging from 3 to 6) are in agreement with the ones of quasi-coherent fluctuations present on the magnetic spectrogram. No kinetic ballooning mode (KBM) is observed at experimental values of β; instead, the experimental plasma lies 20% below the critical global KBM threshold. This confirms local simulation results stating that experimental NSTX profiles lie in the KBM stability region. Carbon impurities, which are abundant in this plasma, were found to play a significant role. Neglecting them leads to a ∼50% error in the growth rates.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Combined plasma–coil optimization algorithms

Combined plasma–coil optimization approaches for designing stellarators are discussed and a new method for calculating free-boundary equilibria for multiregion relaxed magnetohydrodynmics (MRxMHD) is proposed. Four distinct categories of stellarator optimization, two of which are novel approaches, are the fixed-boundary optimization, the generalized fixed-boundary optimization, the quasi-free-boundary optimization, and the free-boundary (coil) optimization. These are described using the MRxMHD energy functional, the Biot–Savart integral, the coil-penalty functional and the virtual casing integral and their derivatives. The proposed free-boundary equilibrium calculation differs from existing methods in how the boundary-value problem is posed, and for the new approach it seems that there is not an associated energy minimization principle because a non-symmetric functional arises. We propose to solve the weak formulation of this problem using a spectral-Galerkin method, and this will reduce the free-boundary equilibrium calculation to something comparable to a fixed-boundary calculation. In our discussion of combined plasma–coil optimization algorithms, we emphasize the importance of the stability matrix.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Physics basis for the Wisconsin HTS Axisymmetric Mirror (WHAM)

The Wisconsin high-temperature superconductor axisymmetric mirror experiment (WHAM) will be a high-field platform for prototyping technologies, validating interchange stabilization techniques and benchmarking numerical code performance, enabling the next step up to reactor parameters. A detailed overview of the experimental apparatus and its various subsystems is presented. WHAM will use electron cyclotron heating to ionize and build a dense target plasma for neutral beam injection of fast ions, stabilized by edge-biased sheared flow. At 25 keV injection energies, charge exchange dominates over impact ionization and limits the effectiveness of neutral beam injection fuelling. This paper outlines an iterative technique for self-consistently predicting the neutral beam driven anisotropic ion distribution and its role in the finite beta equilibrium. Beginning with recent work by Egedal et al. ( Nucl. Fusion , vol. 62, no. 12, 2022, p. 126053) on the WHAM geometry, we detail how the FIDASIM code is used to model the charge exchange sources and sinks in the distribution function, and both are combined with an anisotropic magnetohydrodynamic equilibrium solver method to self-consistently reach an equilibrium. We compare this with recent results using the CQL3D code adapted for the mirror geometry, which includes the high-harmonic fast wave heating of fast ions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A review of high order strong stability preserving two-derivative explicit, implicit, and IMEX methods

High order strong stability preserving time discretizations ensure the nonlinear non-inner-product strong stability properties of spatial discretizations suited for the stable simulation of hyperbolic PDEs in a wide variety of application areas including fluid dynamics, magnetohydrodynamics, semiconductor devices, electromagnetics, and astrophysics. Over the past decade multiderivative time-stepping have been increasingly used for the time-evolution hyperbolic PDEs, so that the strong stability properties of these methods have become important. In this work we review sufficient conditions for a two-derivative multistage method to preserve the strong stability properties of spatial discretizations in a forward Euler and different conditions on the second derivative. In particular we present the strong stability preserving theory for explicit and implicit two-derivative Runge–Kutta schemes, including a special condition on the second derivative under which these implicit methods may be unconditionally strong stability preserving. This special condition is natural for the stiff component of wide range of plasma physics problems, and can be useful in the context of strong stability preserving implicit-explicit multi-derivative Runge–Kutta schemes, where the time-step restriction is then independent of the stiff term. Lastly, we present the strong stability preserving theory for implicit-explicit multi-derivative general linear methods, and some novel second and third order methods where the time-step restriction is independent of the stiff term.

97 MATHEMATICS AND COMPUTING↗