Evolutionary genomics : statistical and computational methods

This open access book addresses the challenge of analyzing and understanding the evolutionary dynamics of complex biological systems at the genomic level, and elaborates on some promising strategies that would bring us closer to uncovering of the vital relationships between genotype and phenotype. After a few educational primers, the book continues with sections on sequence homology and alignment, phylogenetic methods to study genome evolution, methodologies for evaluating selective pressures on genomic sequences as well as genomic evolution in light of protein domain architecture and transposable elements, population genomics and other omics, and discussions of current bottlenecks in handling and analyzing genomic data. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of detail and expert implementation advice that lead to the best results. Authoritative and comprehensive, Evolutionary Genomics: Statistical and Computational Methods, Second Edition aims to serve both novices in biology with strong statistics and computational skills, and molecular biologists with a good grasp of standard mathematical concepts, in moving this important field of study forward

Multiphase wall-bounded turbulence

In many geophysical situations and in all industrial applications, turbulent flows are wall-bounded. Many of these flows are multi-phase, i.e. flows consisting of one or multiple inclusions. The current understanding of these flows is still limited and this makes it important to study them. In this thesis we study these wall-bounded multi-phase flows in two canonical systems: Taylor-Couette flow (TC) and Rayleigh-Bénard convection (RBC). In this work we used spherical and cylindrical particles to investigate if we have reduced skin friction similar to bubbly drag reduction. The global torque measurements showed that these particles barely alter the drag, even at very large particle volume fractions. Surprisingly, we found a preferential alignment for the cylindrical particles with respect to the inner cylinder wall. Using oil and water we are able to create deformable inclusions. Increasing the oil volume fraction over a critical point results in phase inversion with water droplets in oil. In this regime we found drag reduction due to the large water droplets in the flow. This is confirmed with in-situ microscopic imaging. In the last two chapters of this thesis we study the effect of non-homogeneous boundaries in both TC and RBC. Using bands of sandgrain roughness we were able to control the secondary flows in TC. This means that for example roughness like barnacles on the hull of a ship can induce secondary flows that push air bubbles away and thereby, reducing the drag reducing effect