Nucleosome positions alone can be used to predict domains in yeast chromosomes.

We use molecular dynamics simulations based on publicly available micrococcal nuclease sequencing data for nucleosome positions to predict the 3D structure of chromatin in the yeast genome. Our main aim is to shed light on the mechanism underlying the formation of chromosomal interaction domains, chromosome regions of around 0.5 to 10 kbp which show enriched self-interactions, which were experimentally observed in recent MicroC experiments (importantly these are at a different length scale from the 100- to 1,000-kbp-sized domains observed in higher eukaryotes). We show that the sole input of nucleosome positioning data is already sufficient to determine the patterns of chromatin interactions and domain boundaries seen experimentally to a high degree of accuracy. Since the nucleosome spacing so strongly affects the larger-scale domain structure, we next examine the genome-wide linker-length distribution in more detail, finding that it is highly irregular and varies in different genomic regions such as gene bodies, promoters, and active and inactive genes. Finally we use our simple simulation model to characterize in more detail how irregular nucleosome spacing may affect local chromatin structure.

Microfluidic flow of cholesteric liquid crystals.

We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchoring conditions at the wall. Our focus is particularly on the behaviour of "Cholesteric Fingers of the first kind" and of Blue Phase II. Depending on the applied pressure gradient, we observe a number of dynamic regimes with different rheological properties. Our results provide the first insight into the flow response of cholesteric phases with fully two- or three-dimensional director field patterns and normal and planar degenerate anchoring conditions as commonly realised in experiments. They are also of high relevance for a fundamental understanding of complex liquid crystals in confinement and an important step towards future microfluidic applications that are based on cholesteric liquid crystals.