Andreas Skyman

Fluid and gyrokinetic simulations of impurity transport at JET

Impurity transport coefficients due to ion-temperature-gradient (ITG) mode and trapped-electron mode turbulence are calculated using profile data from dedicated impurity injection experiments at JET. Results obtained with a multi-fluid model are compared with quasi-linear and nonlinear gyrokinetic simulation results obtained with the code GENE. The sign of the impurity convective velocity (pinch) and its various contributions are discussed. The dependence of the impurity transport coefficients and impurity peaking factor −∇nZ/nZ on plasma parameters such as impurity charge number Z, ion logarithmic temperature gradient, collisionality, E × B shearing, and charge fraction are investigated. It is found that for the studied ITG dominated JET discharges, both the fluid and gyrokinetic results show an increase in the impurity peaking factor for low Z-values followed by a saturation at moderate values of impurity peaking, much below the neoclassical predictions, for large values of Z. The results are in qualitative agreement with the experimental trends observed for the injected impurities (Ne, Ar, Ni) whereas for the background carbon species the observed flat or weakly hollow C profiles are not well reproduced by the simulations. (Some figures in this article are in colour only in the electronic version)

Scan-o-matic: High-Resolution Microbial Phenomics at a Massive Scale

The capacity to map traits over large cohorts of individuals—phenomics—lags far behind the explosive development in genomics. For microbes, the estimation of growth is the key phenotype because of its link to fitness. We introduce an automated microbial phenomics framework that delivers accurate, precise, and highly resolved growth phenotypes at an unprecedented scale. Advancements were achieved through the introduction of transmissive scanning hardware and software technology, frequent acquisition of exact colony population size measurements, extraction of population growth rates from growth curves, and removal of spatial bias by reference-surface normalization. Our prototype arrangement automatically records and analyzes close to 100,000 growth curves in parallel. We demonstrate the power of the approach by extending and nuancing the known salt-defense biology in baker’s yeast. The introduced framework represents a major advance in microbial phenomics by providing high-quality data for extensive cohorts of individuals and generating well-populated and standardized phenomics databases

Impurity transport in temperature gradient driven turbulence

In the present paper, the transport of impurities driven by trapped electron (TE) mode turbulence is studied. Non-linear (NL) gyrokinetic simulations using the code GENE are compared with results from quasilinear (QL) gyrokinetic simulations and a computationally efficient fluid model. The main focus is on model comparisons for electron temperature gradient driven turbulence regarding the sign of the convective impurity velocity (pinch) and the impurity density gradient R/LnZ (peaking factor) for zero impurity flux. In particular, the scaling of the impurity peaking factors with impurity charge Z and with driving temperature gradient is investigated and compared with results for the more studied ion temperature gradient (ITG) driven turbulence. The question of helium ash removal in TE mode turbulence is also investigated. In addition, the impurity peaking is compared to the main ion peaking obtained by a self-consistent fluid calculation of the density gradients corresponding to zero particle fluxes. For the scaling of the peaking factor with impurity charge Z, a weak dependence is obtained from NL GENE and fluid simulations. The QL GENE results show a stronger dependence for low Z impurities and overestimates the peaking factor by up to a factor of two in this region. As in the case of ITG dominated turbulence, the peaking factors saturate as Z increases, at a level much below neoclassical predictions. The scaling with Z is, however, weak or reversed as compared to the ITG case. The results indicate that TE mode turbulence is as efficient as ITG turbulence at removing He ash, with DHe/χeff>1.0. The scaling of impurity peaking with the background temperature gradients is found to be weak in the NL GENE and fluid simulations. The QL results are also here found to significantly overestimate the peaking factor for low Z values. For the parameters considered, the background density gradient for zero particle flux is found to be slightly larger than the corresponding impurity zero flux gradient.

Effects of the equilibrium model on impurity transport in tokamaks

Gyrokinetic simulations of ion temperature gradient mode and trapped electron mode driven impurity transport in a realistic tokamak geometry are presented and compared with results using simplified geometries. The gyrokinetic results, obtained with the GENE code in both linear and non-linear modes are compared with data and analysis for a dedicated impurity injection discharge at JET. The impact of several factors on heat and particle transport is discussed, lending special focus to tokamak geometry and rotational shear. To this end, results using s-alpha and concentric circular equilibria are compared with results with magnetic geometry from a JET experiment. To further approach experimental conditions, non-linear gyrokinetic simulations are performed with collisions and a carbon background included. The impurity peaking factors, computed by finding local density gradients corresponding to zero particle flux, are discussed. The impurity peaking factors are seen to be reduced by a factor of ~2 in realistic geometry compared with the simplified geometries, due to a reduction of the convective pinch. It is also seen that collisions reduce the peaking factor for low-Z impurities, while increasing it for high charge numbers, which is attributed to a shift in the transport spectra towards higher wavenumbers with the addition of collisions. With the addition of roto-diffusion, an overall reduction of the peaking factors is observed, but this decrease is not sufficient to explain the flat carbon profiles seen at JET.

Particle transport in density gradient driven TE mode turbulence

The turbulent transport of main ion and trace impurities in a tokamak device in the presence of steep electron density gradients has been studied. The parameters are chosen for trapped electron mode turbulence, driven primarily by steep electron density gradients relevant to H-mode physics. Results obtained through nonlinear and quasilinear gyrokinetic simulations using the GENE code are compared with results obtained from a fluid model. Impurity transport is studied by examining the balance of convective and diffusive transport, as quantified by the density gradient corresponding to zero particle flux (impurity peaking factor). Scalings are obtained for the impurity peaking with the background electron density gradient and the impurity charge number. It is shown that the impurity peaking factor is weakly dependent on impurity charge and significantly smaller than the driving electron density gradient.

Gyrokinetic modelling of stationary electron and impurity profiles in tokamaks

Particle transport due to Ion Temperature Gradient (ITG)/Trapped Electron Mode (TEM) turbulence is investigated using the gyrokinetic code GENE. Both a reduced quasilinear treatment and nonlinear simulations are performed for typical tokamak parameters corresponding to ITG dominated turbulence. The gyrokinetic results are compared and contrasted with results from a computationally efficient fluid model. A selfconsistent treatment is used, where the stationary local profiles are calculated corresponding to zero particle flux simultaneously for electrons and trace impurities. The scaling of the stationary profiles with magnetic shear, safety factor, electron-to-ion temperature ratio, collisionality, toroidal sheared rotation, plasma β, triangularity, and elongation is investigated. In addition, the effect of different main ion mass on the zero flux condition is discussed. The electron density gradient can significantly affect the stationary impurity profile scaling. It is therefore expected that a selfconsistent treatment will yield results more comparable to experimental results for parameter scans where the stationary background density profile is sensitive. This is shown to be the case in scans over magnetic shear, collisionality, elongation, and temperature ratio, for which the simultaneous zero flux electron and impurity profiles are calculated. A slight asymmetry between hydrogen, deuterium, and tritium with respect to profile peaking is obtained, in particular, for scans in collisionality and temperature ratio.

High frequency geodesic acoustic modes in electron scale turbulence

In this work the finite β-effects of an electron branch of the geodesic acoustic mode (el-GAM) driven by electron temperature gradient (ETG) modes is presented. The work is based on a fluid description of the ETG mode retaining non-adiabatic ions and the dispersion relation for el-GAMs driven non-linearly by ETG modes is derived. The ETG growth rate from the fluid model is compared with the results found from gyrokinetic simulations with good agreement. A new saturation mechanism for ETG turbulence through the interaction with el-GAMs is found, resulting in a significantly enhanced ETG turbulence saturation level compared with the mixing length estimate. It is shown that the el-GAM may be stabilized by an increase in finite β as well as by increasing non-adiabaticity. The decreased GAM growth rates is due to the inclusion of the Maxwell stress.