Cassis: detection of genomic rearrangement breakpoints

Summary: Genomes undergo large structural changes that alter their organization. The chromosomal regions affected by these rearrangements are called breakpoints, while those which have not been rearranged are called synteny blocks. Lemaitre et al. presented a new method to precisely delimit rearrangement breakpoints in a genome by comparison with the genome of a related species. Receiving as input a list of one2one orthologous genes found in the genomes of two species, the method builds a set of reliable and non-overlapping synteny blocks and refines the regions that are not contained into them. Through the alignment of each breakpoint sequence against its specific orthologous sequences in the other species, we can look for weak similarities inside the breakpoint, thus extending the synteny blocks and narrowing the breakpoints. The identification of the narrowed breakpoints relies on a segmentation algorithm and is statistically assessed. Here, we present the package Cassis that implements this method of precise detection of genomic rearrangement breakpoints

The Tolman Surface Brightness Test for the Reality of the Expansion. I. Calibration of the Necessary Local Parameters

The extensive CCD photometry by Postman & Lauer (1995, ApJ, 440, 28) in the Cape/Cousins R photometric band for first ranked cluster elliptical and S0 galaxies in 118 low redshift clusters is analyzed for the correlations between average surface brightness, linear radius, and absolute magnitude. The purpose is to calibrate the correlations between these three parameters in the limit of zero redshift. These local correlations provide the comparisons to be made in Paper IV with the sample of early-type galaxies at high redshift in search of the Tolman surface brightness signal of (1 + z)^4 if the expansion is real. Surface brightness averages are calculated at various metric radii in each galaxy in the sample. The definition of such radii by Petrosian (1976, ApJ, 209, L1) uses ratios of observed surface photometric data. The observed surface brightnesses are listed for 118 first ranked cluster galaxies at Petrosian eta radii of 1.0, 1.3, 1.5, 1.7, 2.0, and 2.5 mag. The three local diagnostic correlation diagrams are defined and discussed. We review the Tolman test and show that, although recipes from the standard cosmological model that already have the Tolman signal incorporated are required to calculate linear radii and absolute magnitudes from the observed data, the test is nevertheless free from the hermeneutical circularity dilemma occasionally claimed in the literature. The reasons are the observed mean surface brightness (1) is independent of any assumptions of cosmological model, (2) does not depend on the existence of a Tolman signal because it is calculated directly from the data using only angular radii and apparent magnitudes, and (3) can be used to search for the Tolman signal because it carries the bulk of that signal.Comment: 34 pages, 4 figures; accepted for publication in Astronomical Journa

Controlled light-matter coupling for a single quantum dot embedded in a pillar microcavity using far-field optical lithography

Using far field optical lithography, a single quantum dot is positioned within a pillar microcavity with a 50 nm accuracy. The lithography is performed in-situ at 10 K while measuring the quantum dot emission. Deterministic spectral and spatial matching of the cavity-dot system is achieved in a single step process and evidenced by the observation of strong Purcell effect. Deterministic coupling of two quantum dots to the same optical mode is achieved, a milestone for quantum computing.Comment: Modified version: new title, additional experimental data in figure

Irreversible magnetization switching using surface acoustic waves

An analytical and numerical approach is developped to pinpoint the optimal experimental conditions to irreversibly switch magnetization using surface acoustic waves (SAWs). The layers are magnetized perpendicular to the plane and two switching mechanisms are considered. In precessional switching, a small in-plane field initially tilts the magnetization and the passage of the SAW modifies the magnetic anisotropy parameters through inverse magneto-striction, which triggers precession, and eventually reversal. Using the micromagnetic parameters of a fully characterized layer of the magnetic semiconductor (Ga,Mn)(As,P), we then show that there is a large window of accessible experimental conditions (SAW amplitude/wave-vector, field amplitude/orientation) allowing irreversible switching. As this is a resonant process, the influence of the detuning of the SAW frequency to the magnetic system's eigenfrequency is also explored. Finally, another - non-resonant - switching mechanism is briefly contemplated, and found to be applicable to (Ga,Mn)(As,P): SAW-assisted domain nucleation. In this case, a small perpendicular field is applied opposite the initial magnetization and the passage of the SAW lowers the domain nucleation barrier.Comment: 11 pages, 4 figure

Dark Matter Prediction from Canonical Quantum Gravity with Frame Fixing

We show how, in canonical quantum cosmology, the frame fixing induces a new energy density contribution having features compatible with the (actual) cold dark matter component of the Universe. First we quantize the closed Friedmann-Robertson-Walker (FRW) model in a sinchronous reference and determine the spectrum of the super-Hamiltonian in the presence of ultra-relativistic matter and a perfect gas contribution. Then we include in this model small inhomogeneous (spherical) perturbations in the spirit of the Lemaitre-Tolman cosmology. The main issue of our analysis consists in outlining that, in the classical limit, the non-zero eigenvalue of the super-Hamiltonian can make account for the present value of the dark matter critical parameter. Furthermore we obtain a direct correlation between the inhomogeneities in our dark matter candidate and those one appearing in the ultra-relativistic matter.Comment: 5 pages, to appear on Modern Physics Letters

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International audienceThe GANIL facility consists of three successive cyclotrons. The tuning of these cyclotrons and of the transfer beam lines isachieved in about 24 hours. Reducing this setting time would enable to increase the time allocated to physics experiments.New tools are realized for automatic beam tuning. These tools are expected to make the tuning easier, shorter and morereproducible