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Michael Barnes

Publications and source records attributed to Michael Barnes.

At least 19 recordsLinked to original sources

Universal fluctuation spectrum of Vlasov-Poisson turbulence

The thermal fluctuation spectrum of the electric field arising due to particle noise in a quiescent Vlasov-Poisson plasma was derived in the 1960s. Here, we derive the universal fluctuation spectrum of the electric field, at Debye and sub-Debye scales, for a turbulent Vlasov-Poisson plasma. This spectrum arises from what is likely to be the final cascade - a universal regime to be encountered at the extreme small-scale end of any turbulent cascade in a nearly collisionless plasma. The cascaded invariant is $C_2$, the quadratic Casimir invariant of the particle distribution function. $C_2$ cascades to small scales in position and velocity space via linear and nonlinear phase mixing, in such a way that the time scales of the two processes are critically balanced at every scale. We construct a scaling theory of the fluctuation spectrum of $C_2$ and of the electric field in wavenumber space. The electric-field spectrum is sufficiently steep for the nonlinear mixing to be controlled by the largest-scale electric fields, and so the $C_2$ cascade resembles the Batchelor cascade of a passive scalar. Our theory is supported by simulations of a forced 1D-1V plasma. We predict that the cascade is terminated at the wavenumber where the turbulent electric-field spectrum gives way to the thermal noise spectrum. The time scale for this small-scale cutoff to be reached is the dynamical time of phase-space mixing times a logarithmic factor in the plasma parameter - this is the first concrete demonstration of this property of Vlasov-Poisson turbulence, akin to how fluid turbulence dissipates energy at a rate independent (or nearly independent) of molecular diffusion. In the presence of the sub-Debye phase-space cascade - a scenario that may be ubiquitous - standard collisional plasma theory ceases to be valid. This calls for the development of new collision operators suited to such turbulent environments.

physics.plasm-ph

Probabilistic Modelling of Multiple Long-Term Condition Onset Times

The co-occurrence of multiple long-term conditions (MLTC), or multimorbidity, in an individual can reduce their lifespan and severely impact their quality of life. Exploring the longitudinal patterns, e.g. clusters, of disease accrual can help better understand the genetic and environmental drivers of multimorbidity, and potentially identify individuals who may benefit from early targeted intervention. We introduce $\textit{probabilistic modelling of onset times}$, or $\texttt{ProMOTe}$, for clustering and forecasting MLTC trajectories. $\texttt{ProMOTe}$ seamlessly learns from incomplete and unreliable disease trajectories that is commonplace in Electronic Health Records but often ignored in existing longitudinal clustering methods. We analyse data from 150,000 individuals in the UK Biobank and identify 50 clusters showing patterns of disease accrual that have also been reported by some recent studies. We further discuss the forecasting capabilities of the model given the history of disease accrual.

stat.AP

Saturation of magnetised plasma turbulence by propagating zonal flows

Strongly driven ion-scale turbulence in tokamak plasmas is shown to be regulated by a new propagating zonal flow mode, the toroidal secondary mode, which is nonlinearly supported by the turbulence. The mode grows and propagates due to the combined effects of zonal flow shearing and advection by the magnetic drift. Above a threshold in the turbulence level, small-scale toroidal secondary modes become unstable and shear apart turbulent eddies, forcing the turbulence level to remain near the threshold. This threshold condition is used to derive scaling laws for the turbulent heat flux, fluctuation spectra, and zonal flow amplitude, which are validated in nonlinear gyrokinetic simulations and explain previous experimental observations.

physics.plasm-ph

Measurement of zero-frequency fluctuations generated by coupling between Alfven modes in the JET tokamak

We report the first experimental detection of a zero-frequency fluctuation that is pumped by an Alfv\`en mode in a magnetically confined plasma. Core-localized bidirectional Alfv\`en modes of frequency inside the toroidicity-induced gap (and its harmonics) exhibit three-wave coupling interactions with a zero-frequency fluctuation. The observation of the zero-frequency fluctuation is consistent with theoretical and numerical predictions of zonal modes pumped by Alfv\'en modes, and is correlated with an increase in the deep core ion temperature, temperature gradient, and confinement factor $H_{89,P}$. Despite the energetic particle transport induced by the Alfv\`en eigenmodes, the generation of a zero-frequency fluctuation that can suppress the turbulence leads to an overall improvement of confinement.

physics.plasm-ph

Optimisation of Gyrokinetic Microstability Using Adjoint Methods

Microinstabilities drive turbulent fluctuations in inhomogeneous, magnetized plasmas. In the context of magnetic confinement fusion devices, this leads to an enhanced transport of particles, momentum, and energy, thereby degrading confinement. In this work, we elaborate on the application of the adjoint method to efficiently determine the variation of linear growth rates for plasma microstabilities concerning a general set of external parameters within the local $\delta \! f$-gyrokinetic model. We then offer numerical verification of this approach. When coupled with gradient-based techniques, this methodology can facilitate the optimization process for the microstability of the confined plasmas across a high-dimensional parameter space. We present a numerical demonstration wherein the ion-temperature gradient (ITG) instability growth rate in a tokamak plasma is minimized with respect to flux surface shaping parameters. The adjoint method approach demonstrates a significant computational speed-up compared to a finite-difference gradient calculation.

physics.plasm-ph

Phase-space entropy cascade and irreversibility of stochastic heating in nearly collisionless plasma turbulence

We consider a nearly collisionless plasma consisting of a species of `test particles' in 1D-1V, stirred by an externally imposed stochastic electric field. The mean effect on the particle distribution function is stochastic heating. Accompanying this heating is the generation of fine-scale structure in the distribution function, which we characterize with the collisionless (Casimir) invariant $C_2 \propto \iint dx dv \, \langle f^2 \rangle$. We find that $C_2$ is transferred from large scales to small scales in both position and velocity space via a phase-space cascade enabled by both particle streaming and nonlinear interactions between particles and the stochastic electric field. We compute the steady-state fluxes and spectrum of $C_2$ in Fourier space, with $k$ and $s$ denoting spatial and velocity wavenumbers, respectively. Whereas even the linear phase mixing alone would lead to a constant flux of $C_2$ to high $s$ (towards the collisional dissipation range) at every $k$, the nonlinearity accelerates this cascade by intertwining velocity and position space so that the flux of $C_2$ is to both high $k$ and high $s$ simultaneously. Integrating over velocity (spatial) wavenumbers, the $k$-space ($s$-space) flux of $C_2$ is constant down to a dissipation length (velocity) scale that tends to zero as the collision frequency does, even though the rate of collisional dissipation remains finite. The resulting spectrum in the inertial range is a self-similar function in the $(k,s)$ plane, with power-law asymptotics at large $k$ and $s$. We argue that stochastic heating is made irreversible by this entropy cascade and that, while collisional dissipation accessed via phase mixing occurs only at small spatial scales rather than at every scale as it would in a linear system, the cascade makes phase mixing even more effective overall in the nonlinear regime than in the linear one.

physics.plasm-ph

MUSTANG: Multi-Stain Self-Attention Graph Multiple Instance Learning Pipeline for Histopathology Whole Slide Images

Whole Slide Images (WSIs) present a challenging computer vision task due to their gigapixel size and presence of numerous artefacts. Yet they are a valuable resource for patient diagnosis and stratification, often representing the gold standard for diagnostic tasks. Real-world clinical datasets tend to come as sets of heterogeneous WSIs with labels present at the patient-level, with poor to no annotations. Weakly supervised attention-based multiple instance learning approaches have been developed in recent years to address these challenges, but can fail to resolve both long and short-range dependencies. Here we propose an end-to-end multi-stain self-attention graph (MUSTANG) multiple instance learning pipeline, which is designed to solve a weakly-supervised gigapixel multi-image classification task, where the label is assigned at the patient-level, but no slide-level labels or region annotations are available. The pipeline uses a self-attention based approach by restricting the operations to a highly sparse k-Nearest Neighbour Graph of embedded WSI patches based on the Euclidean distance. We show this approach achieves a state-of-the-art F1-score/AUC of 0.89/0.92, outperforming the widely used CLAM model. Our approach is highly modular and can easily be modified to suit different clinical datasets, as it only requires a patient-level label without annotations and accepts WSI sets of different sizes, as the graphs can be of varying sizes and structures. The source code can be found at https://github.com/AmayaGS/MUSTANG.

cs.CV

Bistable turbulence in strongly magnetised plasmas with a sheared mean flow

The prevailing paradigm for plasma turbulence associates a unique stationary state to given equilibrium parameters. We report the discovery of bistable turbulence in a strongly magnetised plasma. Two distinct states, obtained with identical equilibrium parameters in first-principle gyrokinetic simulations, have turbulent fluxes of particles, momentum and energy that differ by an order of magnitude, with the low-transport state agreeing with experimental observations. Occurrences of the two states are regulated by the competition between an externally imposed mean flow shear and "zonal" flows generated by the plasma. With small turbulent amplitudes, zonal flows have little impact, and the mean shear causes turbulence to saturate in a low-transport state. With larger amplitudes, the zonal shear can (partially) oppose the effect of the mean shear, allowing the system to sustain a high-transport state. This poses a new challenge for research that has so far assumed a uniquely defined turbulent state.

physics.plasm-ph

Toroidal and slab ETG instability dominance in the linear spectrum of JET-ILW pedestals

Local linear gyrokinetic simulations show that electron temperature gradient (ETG) instabilities are the fastest growing modes for $k_y \rho_i \gtrsim 0.1$ in the steep gradient region for a JET pedestal discharge (92174) where the electron temperature gradient is steeper than the ion temperature gradient. Here, $k_y$ is the wavenumber in the direction perpendicular to both the magnetic field and the radial direction, and $\rho_i$ is the ion gyroradius. At $k_y \rho_i \gtrsim 1$, the fastest growing mode is often a novel type of toroidal ETG instability. This toroidal ETG mode is driven at scales as large as $k_y \rho_i \sim (\rho_i/\rho_e) L_{Te} / R_0 \sim 1$ and at a sufficiently large radial wavenumber that electron finite Larmor radius effects become important; that is, $K_x \rho_e \sim 1$, where $K_x$ is the effective radial wavenumber. Here, $\rho_e$ is the electron gyroradius, $R_0$ is the major radius of the last closed flux surface, and $1/L_{Te}$ is an inverse length proportional to the logarithmic gradient of the equilibrium electron temperature. The fastest growing toroidal ETG modes are often driven far away from the outboard midplane. In this equilibrium, ion temperature gradient instability is subdominant at all scales and kinetic ballooning modes are shown to be suppressed by $\mathbf{ E} \times \mathbf{ B} $ shear. ETG modes are very resilient to $\mathbf{ E} \times \mathbf{ B}$ shear. Heuristic quasilinear arguments suggest that the novel toroidal ETG instability is important for transport.

physics.plasm-ph

Thermal disequilibration of ions and electrons by collisionless plasma turbulence

Does overall thermal equilibrium exist between ions and electrons in a weakly collisional, magnetised, turbulent plasma---and, if not, how is thermal energy partitioned between ions and electrons? This is a fundamental question in plasma physics, the answer to which is also crucial for predicting the properties of far-distant astronomical objects such as accretion discs around black holes. In the context of discs, this question was posed nearly two decades ago and has since generated a sizeable literature. Here we provide the answer for the case in which energy is injected into the plasma via Alfvénic turbulence: collisionless turbulent heating typically acts to disequilibrate the ion and electron temperatures. Numerical simulations using a hybrid fluid-gyrokinetic model indicate that the ion-electron heating-rate ratio is an increasing function of the thermal-to-magnetic energy ratio, $β_\mathrm{i}$: it ranges from $\sim0.05$ at $β_\mathrm{i}=0.1$ to at least $30$ for $β_\mathrm{i} \gtrsim 10$. This energy partition is approximately insensitive to the ion-to-electron temperature ratio $T_\mathrm{i}/T_\mathrm{e}$. Thus, in the absence of other equilibrating mechanisms, a collisionless plasma system heated via Alfvénic turbulence will tend towards a nonequilibrium state in which one of the species is significantly hotter than the other, viz., hotter ions at high $β_\mathrm{i}$, hotter electrons at low $β_\mathrm{i}$. Spectra of electromagnetic fields and the ion distribution function in 5D phase space exhibit an interesting new magnetically dominated regime at high $β_i$ and a tendency for the ion heating to be mediated by nonlinear phase mixing ("entropy cascade") when $β_\mathrm{i}\lesssim1$ and by linear phase mixing (Landau damping) when $β_\mathrm{i}\gg1$

physics.plasm-ph

Intrinsic rotation driven by turbulent acceleration

Differential rotation is induced in tokamak plasmas when an underlying symmetry of the governing gyrokinetic-Maxwell system of equations is broken. One such symmetry-breaking mechanism is considered here: the turbulent acceleration of particles along the mean magnetic field. This effect, often referred to as the `parallel nonlinearity', has been implemented in the $δf$ gyrokinetic code $\texttt{stella}$ and used to study the dependence of turbulent momentum transport on the plasma size and on the strength of the turbulence drive. For JET-like parameters with a wide range of driving temperature gradients, the momentum transport induced by the inclusion of turbulent acceleration is similar to or smaller than the ratio of the ion Larmor radius to the plasma minor radius. This low level of momentum transport is explained by demonstrating an additional symmetry that prohibits momentum transport when the turbulence is driven far above marginal stability.

physics.plasm-ph

$\texttt{stella}$: a mixed implicit-explicit, delta-f gyrokinetic code for general magnetic field configurations

Here we present details of a mixed implicit-explicit numerical scheme for the solution of the gyrokinetic-Poisson system of equations in the local limit. This scheme has been implemented in a new code called $\texttt{stella}$, which is capable of evolving electrostatic fluctuations with full kinetic electron effects and an arbitrary number of ion species in general magnetic geometry. We demonstrate the advantages of this mixed approach over a fully explicit treatment and provide linear and nonlinear benchmark comparisons for both axisymmetric and non-axisymmetric magnetic equilibria.

physics.plasm-ph

Optimized up-down asymmetry to drive fast intrinsic rotation in tokamaks

Breaking the up-down symmetry of the tokamak poloidal cross-section can significantly increase the spontaneous rotation due to turbulent momentum transport. In this work, we optimize the shape of flux surfaces with both tilted elongation and tilted triangularity in order to maximize this drive of intrinsic rotation. Nonlinear gyrokinetic simulations demonstrate that adding optimally-tilted triangularity can double the momentum transport of a tilted elliptical shape. This work indicates that tilting the elongation and triangularity in an ITER-like device can reduce the energy transport and drive intrinsic rotation with an Alfvén Mach number on the order of $1\%$. This rotation is four times larger than the rotation expected in ITER and is sufficient to stabilize MHD instabilities. It is shown that this optimal shape can be created using the shaping coils of several experiments.

physics.plasm-ph

Poloidal tilting symmetry of high order tokamak flux surface shaping in gyrokinetics

A poloidal tilting symmetry of the local nonlinear $δf$ gyrokinetic model is demonstrated analytically and verified numerically. This symmetry shows that poloidally rotating all the flux surface shaping effects with large poloidal mode number by a single tilt angle has an exponentially small effect on the transport properties of a tokamak. This is shown using a generalization of the Miller local equilibrium model to specify an arbitrary flux surface geometry. With this geometry specification we find that, when performing an expansion in large flux surface shaping mode number, the governing equations of gyrokinetics are symmetric in the poloidal tilt of the high order shaping effects. This allows us to take the fluxes from a single configuration and calculate the fluxes in any configuration that can be produced by tilting the large mode number shaping effects. This creates a distinction between tokamaks with mirror symmetric flux surfaces and tokamaks without mirror symmetry, which is expected to have important consequences for generating toroidal rotation using up-down asymmetry.

physics.plasm-ph

Turbulent momentum transport due to neoclassical flows

Intrinsic toroidal rotation in a tokamak can be driven by turbulent momentum transport due to neoclassical flow effects breaking a symmetry of turbulence. In this paper we categorize the contributions due to neoclassical effects to the turbulent momentum transport, and evaluate each contribution using gyrokinetic simulations. We find that the relative importance of each contribution changes with collisionality. For low collisionality, the dominant contributions come from neoclassical particle and parallel flows. For moderate collisionality, there are non- negligible contributions due to neoclassical poloidal electric field and poloidal gradients of density and temperature, which are not important for low collisionality.

physics.plasm-ph

Equivalence of two different approaches to global $δf$ gyrokinetic simulations

A set of flux tube gyrokinetic equations that includes the effect of the spatial variation of the density, temperature and rotation gradients on the turbulence is derived. This new set of equations uses periodic boundary conditions. In the limit $l_\bot/L \ll 1$, where $l_\bot$ is the characteristic perpendicular length of turbulent structures and $L$ is the characteristic size of the device, this new set of flux tube gyrokinetic equations is shown to be equivalent to the traditional global $δf$ gyrokinetic equations to an order higher in $l_\bot/L$ than the usual flux tube formulations.

physics.plasm-ph

Intrinsic rotation in tokamaks: theory

Self-consistent equations for intrinsic rotation in tokamaks with small poloidal magnetic field $B_p$ compared to the total magnetic field $B$ are derived. The model gives the momentum redistribution due to turbulence, collisional transport and energy injection. Intrinsic rotation is determined by the balance between the momentum redistribution and the turbulent diffusion and convection. Two different turbulence regimes are considered: turbulence with characteristic perpendicular lengths of the order of the ion gyroradius, $ρ_i$, and turbulence with characteristic lengths of the order of the poloidal gyroradius, $(B/B_p) ρ_i$. Intrinsic rotation driven by gyroradius scale turbulence is mainly due to the effect of neoclassical corrections and of finite orbit widths on turbulent momentum transport, whereas for the intrinsic rotation driven by poloidal gyroradius scale turbulence, the slow variation of turbulence characteristics in the radial and poloidal directions and the turbulent particle acceleration can be become as important as the neoclassical and finite orbit width effects. The magnetic drift is shown to be indispensable for the intrinsic rotation driven by the slow variation of turbulence characteristics and the turbulent particle acceleration. The equations are written in a form conducive to implementation in a flux tube code, and the effect of the radial variation of the turbulence is included in a novel way that does not require a global gyrokinetic formalism.

physics.plasm-ph

Intrinsic momentum transport in up-down asymmetric tokamaks

Recent work demonstrated that breaking the up-down symmetry of tokamak flux surfaces removes a constraint that limits intrinsic momentum transport, and hence toroidal rotation, to be small. We show, through MHD analysis, that ellipticity is most effective at introducing up-down asymmetry throughout the plasma. We detail an extension to GS2, a local $δf$ gyrokinetic code that self-consistently calculates momentum transport, to permit up-down asymmetric configurations. Tokamaks with tilted elliptical poloidal cross-sections were simulated to determine nonlinear momentum transport. The results, which are consistent with experiment in magnitude, suggest that a toroidal velocity gradient, $(\partial u_{ζi} / \partial ρ) / v_{th i}$, of 5% of the temperature gradient, $(\partial T_{i} / \partial ρ) / T_{i}$, is sustainable. Here $v_{th i}$ is the ion thermal speed, $u_{ζi}$ is the ion toroidal mean flow, $ρ$ is the minor radial coordinate normalized to the tokamak minor radius, and $T_{i}$ is the ion temperature. Since other intrinsic momentum transport mechanisms scale poorly to larger machines, these results indicate that up-down asymmetry is the most feasible method to generate the current experimentally-measured rotation levels in reactor-sized devices.

physics.plasm-ph