Scalar Decay in Chaotic Mixing

I review the local theory of mixing, which focuses on infinitesimal blobs of scalar being advected and stretched by a random velocity field. An advantage of this theory is that it provides elegant analytical results. A disadvantage is that it is highly idealised. Nevertheless, it provides insight into the mechanism of chaotic mixing and the effect of random fluctuations on the rate of decay of the concentration field of a passive scalar.Comment: 35 pages, 15 figures. Springer-Verlag conference style svmult.cls (included). Published in "Transport in Geophysical Flows: Ten Years After," Proceedings of the Grand Combin Summer School, 14-24 June 2004, Valle d'Aosta, Italy. Fixed some typo

Fractal iso-contours of passive scalar in smooth random flows

We consider a passive scalar field under the action of pumping, diffusion and advection by a smooth flow with a Lagrangian chaos. We present theoretical arguments showing that scalar statistics is not conformal invariant and formulate new effective semi-analytic algorithm to model the scalar turbulence. We then carry massive numerics of passive scalar turbulence with the focus on the statistics of nodal lines. The distribution of contours over sizes and perimeters is shown to depend neither on the flow realization nor on the resolution (diffusion) scale $r_d$ for scales exceeding $r_d$. The scalar isolines are found fractal/smooth at the scales larger/smaller than the pumping scale $L$. We characterize the statistics of bending of a long isoline by the driving function of the L\"owner map, show that it behaves like diffusion with the diffusivity independent of resolution yet, most surprisingly, dependent on the velocity realization and the time of scalar evolution

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation; analyses timings and patterns of tumour evolution; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity; and evaluates a range of more-specialized features of cancer genomes