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 coefficients due to Ion-Temperature-Gradient (ITG) mode and Trapped-Electron (TE) 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 like impurity charge number Z, ion logarithmic temperature gradient, collisionality, ExB 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 of 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.

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 KEYWORDS

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 gra- dient 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 temper- ature gradient is investigated and compared with the results for Ion Temperature Gradient (ITG) driven turbulence. 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. However, the scaling with Z is weak or reversed as compared to the ITG case. 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.Comment: 23 pages, 13 figures. Submitted to AIP: Physics of Plasma

Gyrokinetic simulations of ion temperature gradient mode and trapped electron mode driven impurity transport in 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 mode, are compared with data and analysis for a dedicated impurity injection discharge at JET. The impact of several factors on heat and particle transport are discussed, lending special focus to tokamak geometry and rotational shear. To this end, results using s − α and concentric circular equilibria are compared to 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 to 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 over-all reduction of the peaking factors is observed, but this decrease is not sufficient to explain the flat carbon profiles seen at JET.