Phylogenetic Analysis of Cell Types using Histone Modifications

In cell differentiation, a cell of a less specialized type becomes one of a more specialized type, even though all cells have the same genome. Transcription factors and epigenetic marks like histone modifications can play a significant role in the differentiation process. In this paper, we present a simple analysis of cell types and differentiation paths using phylogenetic inference based on ChIP-Seq histone modification data. We propose new data representation techniques and new distance measures for ChIP-Seq data and use these together with standard phylogenetic inference methods to build biologically meaningful trees that indicate how diverse types of cells are related. We demonstrate our approach on H3K4me3 and H3K27me3 data for 37 and 13 types of cells respectively, using the dataset to explore various issues surrounding replicate data, variability between cells of the same type, and robustness. The promising results we obtain point the way to a new approach to the study of cell differentiation.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Influence of the Coriolis force in atom interferometry

In a light-pulse atom interferometer, we use a tip-tilt mirror to remove the influence of the Coriolis force from Earth's rotation and to characterize configuration space wave packets. For interferometers with large momentum transfer and large pulse separation time, we improve the contrast by up to 350% and suppress systematic effects. We also reach what is to our knowledge the largest spacetime area enclosed in any atom interferometer to date. We discuss implications for future high performance instruments.Comment: 4 pages, 5 figures, 1 tabl

Topological magneto-optical effects and their quantization in noncoplanar antiferromagnets

Reflecting the fundamental interactions of polarized light with magnetic matter, magneto-optical effects are well known since more than a century. The emergence of these phenomena is commonly attributed to the interplay between exchange splitting and spin-orbit coupling in the electronic structure of magnets. Using theoretical arguments, we demonstrate that topological magneto-optical effects can arise in noncoplanar antiferromagnets due to the finite scalar spin chirality, without any reference to exchange splitting or spin-orbit coupling. We propose spectral integrals of certain magneto-optical quantities that uncover the unique topological nature of the discovered effect. We also find that the Kerr and Faraday rotation angles can be quantized in insulating topological antiferromagnets in the low-frequency limit, owing to nontrivial global properties that manifest in quantum topological magneto-optical effects. Although the predicted topological and quantum topological magneto-optical effects are fundamentally distinct from conventional light-matter interactions, they can be measured by readily available experimental techniques.Comment: 10 pages, 5 figure

Epitaxial growth and magnetic properties of Sr2CrReO6 thin films

The double perovskite Sr2CrReO6 is an interesting material for spintronics, showing ferrimagnetism up to 635 K with a predicted high spin polarization of about 86%. We fabricated Sr2CrReO6 epitaxial films by pulsed laser deposition on (001)-oriented SrTiO3 substrates. Phase-pure films with optimum crystallographic and magnetic properties were obtained by growing at a substrate temperature of 700 degree C in pure O2 of 6.6x10-4 mbar. The films are c-axis oriented, coherently strained, and show less than 20% anti-site defects. The magnetization curves reveal high saturation magnetization of 0.8 muB per formula unit and high coercivity of 1.1 T, as well as a strong magnetic anisotropy.Comment: accepted for publicatio