Impact of pressure anisotropy on tokamak equilibria and the toroidal magnetic precession

Using a generalized anisotropic tokamak equilibrium and an exact guiding centre drift formulation, the effect of parallel and perpendicular anisotropy on the toroidal precession drift is investigated. Significant differences between parallel and perpendicular pressure anisotropy are observed. While the Shafranov shift is not sensitive to the ratio of the parallel and perpendicular pressures p ⊥ /p∥ , the deepening of the magnetic well is found to be sensitive to p ⊥ /p∥ . Here, the diamagnetic effect identified by Connor et al 1983 Nucl. Fusion 23 1702 is generalized and found to depend crucially on the deposition of the energetic ions on which the equilibrium depends, and leads to test particle precessional drifts that depend sensitively on pitch angl

Sawtooth period pacing and locking by EC power control on TCV

Abstract #TP9.127 submitted for the DPP11 Meeting of The American Physical Society

Discovery and genotyping of structural variation from long-read haploid genome sequence data

In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. By using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that &gt;89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF &gt; 1%). We estimate that this theoretical human diploid differs by as much as ∼16 Mbp with respect to the human reference, with long-read sequencing data providing a fivefold increase in sensitivity for genetic variants ranging in size from 7 bp to 1 kbp compared with short-read sequence data. Although a large fraction of genetic variants were not detected by short-read approaches, once the alternate allele is sequence-resolved, we show that 61% of SVs can be genotyped in short-read sequence data sets with high accuracy. Uncoupling discovery from genotyping thus allows for the majority of this missed common variation to be genotyped in the human population. Interestingly, when we repeat SV detection on a pseudodiploid genome constructed in silico by merging the two haploids, we find that ∼59% of the heterozygous SVs are no longer detected by SMRT-SV. These results indicate that haploid resolution of long-read sequencing data will significantly increase sensitivity of SV detection.</jats:p

Sequence and annotation of the 288-kb ATCV-1 virus that infects an endosymbiotic chlorella strain of the heliozoon \u3ci\u3eAcanthocystis turfacea\u3c/i\u3e

Acanthocystis turfacea chlorella virus (ATCV-1), a prospective member of the family Phycodnaviridae, genus Chlorovirus, infects a unicellular, eukaryotic, chlorella-like green alga, Chlorella SAG 3.83, that is a symbiont in the heliozoon A. turfacea. The 288,047-bp ATCV-1 genome is the first virus to be sequenced that infects Chlorella SAG 3.83. ATCV-1 contains 329 putative protein-encoding and 11 tRNA-encoding genes. The protein-encoding genes are almost evenly distributed on both strands and intergenic space is minimal. Thirty-four percent of the viral gene products resemble entries in the public databases, including some that are unexpected for a virus. For example, these unique gene products include ribonucleoside-triphosphate reductase, dTDP-D-glucose 4,6 dehydratase, potassium ion transporter, aquaglyceroporin, and mucindesulfating sulfatase. Comparison of ATCV-1 protein-encoding genes with the prototype chlorella virus PBCV-1 indicates that about 80% of the ATCV-1 genes are present in PBCV-1