Ion orbit loss is considered important for generating the radially inward electric field Er in a tokamak edge plasma. In particular, this effect is emphasized in diverted tokamaks with a magnetic X point. In neoclassical equilibria, Coulomb collisions can scatter ions onto loss orbits and generate a radially outward current, which in steady state is balanced by the radially inward current from viscosity. To quantitatively measure this loss-orbit current in an edge pedestal, an ion-orbit-flux diagnostic has been implemented in the axisymmetric version of the gyrokinetic particle-in-cell code XGC. As the first application of this diagnostic, a neoclassical DIII-D H-mode plasma is studied using gyrokinetic ions and adiabatic electrons. The validity of the diagnostic is demonstrated by studying the collisional relaxation of Er in the core. After this demonstration, the loss-orbit current is numerically measured in the edge pedestal in quasisteady state. In this plasma, it is found that the radial electric force on ions from Er approximately balances the ion radial pressure gradient in the edge pedestal, with the radial force from the plasma flow term being a minor component. The effect of orbit loss on Er is found to be only mild.

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Self-consistent simulations of neoclassical and electrostatic turbulent transport in a DIII-D H-mode edge plasma under resonant magnetic perturbations (RMPs) have been performed using the global total-f gyrokinetic particle-in-cell code XGC, in order to study density-pump out and electron heat confinement.The RMP field is imported from the extended magneto-hydrodynamics (MHD) code M3D-C1, taking into account the linear two-fluid plasma response.With both neoclassical and turbulence physics considered together, the XGC simulation reproduces two key features of experimentally observed edge transport under RMPs: increased radial particle transport in the pedestal region that is sufficient to account for the experimental pump-out rate, and suppression of the electron heat flux in the steepest part of the edge pedestal.In the simulation, the density fluctuation amplitude of modes moving in the electron diamagnetic direction increases due to interaction with RMPs in the pedestal shoulder and outward, while the electron temperature fluctuation amplitude decreases.

21st year

The National Spherical Torus Experiment (NSTX) has undergone a major upgrade, and the NSTX Upgrade (NSTX-U) Project was completed in the summer of 2015. NSTX-U first plasma was subsequently achieved, diagnostic and control systems have been commissioned, H-Mode accessed, magnetic error fields identified and mitigated, and the first physics research campaign carried out. During 10 run weeks of operation, NSTX-U surpassed NSTX-record pulse-durations and toroidal fields, and high-performance ~1MA H-mode plasmas comparable to the best of NSTX have been sustained near and slightly above the n=1 no-wall stability limit and with H-mode confinement multiplier H98y2 above 1. Transport and turbulence studies in L-mode plasmas have identified the coexistence of at least two ion-gyro-scale turbulent micro-instabilities near the same radial location but propagating in opposite (i.e. ion and electron diamagnetic) directions. These modes have the characteristics of ion-temperature gradient and micro-tearing modes, respectively, and the role of these modes in contributing to thermal transport is under active investigation. The new second more tangential neutral beam injection was observed to significantly modify the stability of two types of Alfven Eigenmodes. Improvements in offline disruption forecasting were made in the areas of identification of rotating MHD modes and other macroscopic instabilities using the Disruption Event Characterization and Forecasting (DECAF) code. Lastly, the Materials Analysis and Particle Probe (MAPP) was utilized on NSTX-U for the first time and enabled assessments of the correlation between boronized wall conditions and plasma performance. These and other highlights from the first run campaign of NSTX-U are described.

The effects of recycled neutral atoms on tokamak ion temperaturegradient (ITG) driven turbulence have been investigated in a steepedge pedestal, magnetic separatrix configuration, with the full-fedge gryokinetic code XGC1. Ion temperature gradient turbulence isthe most fundamental and robust edge plasma instability, having a longradial correlation length and an ability to impact other forms ofpedestal turbulence. The neutral atoms enhance the ITG turbulence,first, by increasing the ion temperature gradient in the pedestal viathe cooling effects of charge exchange and, second, by a relativereduction in the ExB shearing rate.

The May 2011 outbreak of an E. coli infection in Europe resulted in serious concerns about the potential appearance of a new deadly strain of bacteria, Escherichia coli O104:H4 TY-2482. In response to this situation, and immediately after the reports of deaths, the University Medical Centre Hamburg-Eppendorf and BGI-Shenzhen worked together to sequence the bacterium and assess its human health risk.

The bacteriums genome was first sequenced using Life Technologies; Ion Torrent sequencing platform. According to the results of the draft assembly, the estimated genome size of this new E. coli strain is about 5.2 Mb. Sequence analysis indicated this bacterium is an EHEC serotype O104 E. coli strain. Comparative analysis showed that this bacterium has 93% sequence similarity with the EAEC 55989 E. coli strain, which was isolated in the Central African Republic and known to cause serious diarrhea. This strain of E. coli, however, has also acquired specific sequences that appear to be similar to those involved in the pathogenicity of hemorrhagic colitis and hemolytic-uremic syndrome. The acquisition of these genes may have occurred through horizontal gene transfer.

To maximize its utility to the research community and aid those fighting the epidemic, this genomic data was released into the public domain under a CC0 license.

To the extent possible under law, BGI Shenzhen has waived all copyright and related or neighboring rights to genomic data from the 2011 E. coli outbreak. This work is published from China.