Streamline integration as a method for structured grid generation in X-point geometry

We investigate structured grids aligned to the contours of a two-dimensional flux-function with an X-point (saddle point). Our theoretical analysis finds that orthogonal grids exist if and only if the Laplacian of the flux-function vanishes at the X-point. In general, this condition is sufficient for the existence of a structured aligned grid with an X-point. With the help of streamline integration we then propose a numerical grid construction algorithm. In a suitably chosen monitor metric the Laplacian of the flux-function vanishes at the X-point such that a grid construction is possible. We study the convergence of the solution to elliptic equations on the proposed grid. The diverging volume element and cell sizes at the X-point reduce the convergence rate. As a consequence, the proposed grid should be used with grid refinement around the X-point in practical applications. We show that grid refinement in the cells neighboring the X-point restores the expected convergence rate

Radial convection of finite ion temperature, high amplitude plasma blobs

We present results from simulations of seeded blob convection in the scrape-off-layer of magnetically confined fusion plasmas. We consistently incorporate high fluctuation amplitude levels and finite Larmor radius (FLR) effects using a fully nonlinear global gyrofluid model. This is in line with conditions found in tokamak scrape-off-layers (SOL) regions. Varying the ion temperature, the initial blob width, and the initial amplitude, we found an FLR dominated regime where the blob behavior is significantly different from what is predicted by cold-ion models. The transition to this regime is very well described by the ratio of the ion gyroradius to the characteristic gradient scale length of the blob. We compare the global gyrofluid model with a partly linearized local model. For low ion temperatures we find that simulations of the global model show more coherent blobs with an increased cross-field transport compared to blobs simulated with the local model. The maximal blob amplitude is significantly higher in the global simulations than in the local ones. When the ion temperature is comparable to the electron temperature, global blob simulations show a reduced blob coherence and a decreased cross-field transport in comparison with local blob simulations

The influence of temperature dynamics and dynamic finite ion Larmor radius effects on seeded high amplitude plasma blobs

Thermal effects on the perpendicular convection of seeded pressure blobs in the scrape-off layer of magnetised fusion plasmas are investigated. Our numerical study is based on a four field full-F gyrofluid model, which entails the consistent description of high fluctuation amplitudes and dynamic finite Larmor radius effects. We find that the maximal radial blob velocity increases with the square root of the initial pressure perturbation and that a finite Larmor radius contributes to highly compact blob structures that propagate in the poloidal direction. An extensive parameter study reveals that a smooth transition to this compact blob regime occurs when the finite Larmor radius effect strength, defined by the ratio of the magnetic field aligned component of the ion diamagnetic to the $\vec{E}\times\vec{B}$ vorticity, exceeds unity. The maximal radial blob velocities agree excellently with the inertial velocity scaling law over more than an order of magnitude. We show that the finite Larmor radius effect strength affects the poloidal and total particle transport and present an empirical scaling law for the poloidal and total blob velocities. Distinctions to the blob behaviour in the isothermal limit with constant finite Larmor radius effects are highlighted

Beyond the Oberbeck-Boussinesq and long wavelength approximation

We present the first simulations of a reduced magnetized plasma model that incorporates both arbitrary wavelength polarization and non-Oberbeck-Boussinesq effects. Significant influence of these two effects on the density, electric potential and E x B vorticity and non-linear dynamics of interchange blobs are reported. Arbitrary wavelength polarization implicates so-called gyro-amplification that compared to a long wavelength approximation leads to highly amplified small-scale E x B vorticity fluctuations. These strongly increase the coherence and lifetime of blobs and alter the motion of the blobs through a slower blob-disintegration. Non-Oberbeck-Boussinesq effects incorporate plasma inertia, which substantially decreases the growth rate and linear acceleration of high amplitude blobs, while the maximum blob velocity is not affected. Finally, we generalize and numerically verify unified scaling laws for blob velocity, acceleration and growth rate that include both ion temperature and arbitrary blob amplitude dependence

Angular momentum and rotational energy of mean flows in toroidal magnetic fields

We derive the balance equation for the Favre averaged angular momentum in toroidal not necessarily axisymmetric magnetic field equilibria. We find that the components of angular momentum are given by the covariant poloidal and toroidal components of E x B and parallel flow velocities and we separately identify all relevant stress tensors, torques and source terms for each of these components. Our results feature the Favre stress generalisations of previously found Reynolds stresses like the diamagnetic or parallel E x B stress, as well as the density gradient drive term. Further, we identify the magnetic shear as a source of poloidal E x B angular momentum and discuss the mirror and the Lorentz force. Here, we find that the geodesic transfer term, the Stringer-Winsor spin-up term and the ion-orbit loss term are all part of the Lorentz force and are in fact one and the same term. Discussing the relation to angular velocity we build the inertia tensor with the help of the first fundamental form of a flux-surface. In turn, the inertia tensor is used to construct a flux-surface averaged rotational energy for E x B surface flows of the plasma. The evolution of this rotational energy features a correction of previous results due to the inertia tensor. In particular, this correction suggests that density sources on the high-field side contribute much more to zonal flow energy generation than on the low field side. Our derivation is based on a full-F, electromagnetic, gyro-kinetic model in a long-wavelength limit. The results can be applied to gyro-kinetic as well as gyro-fluid theories and can also be compared to drift-kinetic and drift-fluid models. Simplified cases for the magnetic field geometry including the axisymmetric purely toroidal and purely poloidal magnetic fields are discussed, as are the angular momentum balance of the electromagnetic fields, the ion-orbit loss mechanism and the parallel acceleration

Non-trace full-F gyro-fluid interchange impurity advection

A full-F isothermal gyro-fluid model and code (which is based on the full distribution function F compared to only small fluctuations) is extended to handle self-consistent coupling of multiple quasi-neutral ion species via the polarisation equation in the long wavelength approximation. The numerical model is used to determine two-dimensional interchange driven ‘blob’ transport in a plasma with intrinsic impurity content for a range of impurity parameters. With the same model, the self-consistent advective interaction of a main plasma species blob with a non-trace impurity cloud is studied. For homogeneous impurity distributions an increased effective mass reduces blob transport, whereas it is found that localised impurity clouds can lead either to acceleration or slowing down of blob propagation depending on the alignment of the impurity density gradient during the acceleration phase of the main ion species blob

A Mutation in the Gene Encoding Mitochondrial Mg2+ Channel MRS2 Results in Demyelination in the Rat

The rat demyelination (dmy) mutation serves as a unique model system to investigate the maintenance of myelin, because it provokes severe myelin breakdown in the central nervous system (CNS) after normal postnatal completion of myelination. Here, we report the molecular characterization of this mutation and discuss the possible pathomechanisms underlying demyelination. By positional cloning, we found that a G-to-A transition, 177 bp downstream of exon 3 of the Mrs2 (MRS2 magnesium homeostasis factor (Saccharomyces cerevisiae)) gene, generated a novel splice acceptor site which resulted in functional inactivation of the mutant allele. Transgenic rescue with wild-type Mrs2-cDNA validated our findings. Mrs2 encodes an essential component of the major Mg2+ influx system in mitochondria of yeast as well as human cells. We showed that the dmy/dmy rats have major mitochondrial deficits with a markedly elevated lactic acid concentration in the cerebrospinal fluid, a 60% reduction in ATP, and increased numbers of mitochondria in the swollen cytoplasm of oligodendrocytes. MRS2-GFP recombinant BAC transgenic rats showed that MRS2 was dominantly expressed in neurons rather than oligodendrocytes and was ultrastructurally observed in the inner membrane of mitochondria. Our observations led to the conclusion that dmy/dmy rats suffer from a mitochondrial disease and that the maintenance of myelin has a different mechanism from its initial production. They also established that Mg2+ homeostasis in CNS mitochondria is essential for the maintenance of myelin