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

Accurate measurement of a 96% input coupling into a cavity using polarization tomography

Pillar microcavities are excellent light-matter interfaces providing an electromagnetic confinement in small mode volumes with high quality factors. They also allow the efficient injection and extraction of photons, into and from the cavity, with potentially near-unity input and output-coupling efficiencies. Optimizing the input and output coupling is essential, in particular, in the development of solid-state quantum networks where artificial atoms are manipulated with single incoming photons. Here we propose a technique to accurately measure input and output coupling efficiencies using polarization tomography of the light reflected by the cavity. We use the residual birefringence of pillar microcavities to distinguish the light coupled to the cavity from the uncoupled light: the former participates to rotating the polarization of the reflected beam, while the latter decreases the polarization purity. Applying this technique to a micropillar cavity, we measure a $53 \pm2 \%$ output coupling and a $96 \pm 1\%$ input coupling with unprecedented precision.Comment: 6 pages, 3 figure

Comment on ``Strength and genericity of singularities in Tolman-Bondi-de Sitter collapse'' and a note on central singularities

It has been claimed that the Lemaitre-Tolman-Bondi-de Sitter solution always admits future-pointing radial time-like geodesics emerging from the shell-focussing singularity, regardless of the nature of the (regular) initial data. This is despite the fact that some data rule out the emergence of future pointing radial null geodesics. We correct this claim and show that in general in spherical symmetry, the absence of radial null geodesics emerging from a central singularity is sufficient to prove that the singularity is censored.Comment: 3 pages, revtex4, submitted to Phys. Lett.

Enhancement of the Spin Accumulation at the Interface Between a Spin-Polarized Tunnel Junction and a Semiconductor

We report on spin injection experiments at a Co/Al$_2$O$_3$/GaAs interface with electrical detection. The application of a transverse magnetic field induces a large voltage drop $\Delta V$ at the interface as high as 1.2mV for a current density of 0.34 nA.$\mu m^{-2}$. This represents a dramatic increase of the spin accumulation signal, well above the theoretical predictions for spin injection through a ferromagnet/semiconductor interface. Such an enhancement is consistent with a sequential tunneling process via localized states located in the vicinity of the Al$_2$O$_3$/GaAs interface. For spin-polarized carriers these states act as an accumulation layer where the spin lifetime is large. A model taking into account the spin lifetime and the escape tunneling time for carriers travelling back into the ferromagnetic contact reproduces accurately the experimental results

Driven activation versus thermal activation

Activated dynamics in a glassy system undergoing steady shear deformation is studied by numerical simulations. Our results show that the external driving force has a strong influence on the barrier crossing rate, even though the reaction coordinate is only weakly coupled to the nonequilibrium system. This "driven activation" can be quantified by introducing in the Arrhenius expression an effective temperature, which is close to the one determined from the fluctuation-dissipation relation. This conclusion is supported by analytical results for a simplified model system.Comment: 5 pages, 3 figure

On matching LTB and Vaidya spacetimes through a null hypersurface

In this work the matching of a LTB interior solution representing dust matter to the Vaidya exterior solution describing null fluid through a null hypersurface is studied. Different cases in which one is able to smoothly match these two solutions to Einstein equations along a null hypesurface are discussed.Comment: 5 pages, to appear in GR

Self-gravitating spheres of anisotropic fluid in geodesic flow

The fluid models mentioned in the title are classified. All characteristics of the fluid are expressed through a master potential, satisfying an ordinary second order differential equation. Different constraints are imposed on this core of relations, finding new solutions and deriving the classical results for perfect fluids and dust as particular cases. Many uncharged and charged anisotropic solutions, all conformally flat and some uniform density solutions are found. A number of solutions with linear equation among the two pressures are derived, including the case of vanishing tangential pressure.Comment: 21 page

Phase ordering induced by defects in chaotic bistable media

The phase ordering dynamics of coupled chaotic bistable maps on lattices with defects is investigated. The statistical properties of the system are characterized by means of the average normalized size of spatial domains of equivalent spin variables that define the phases. It is found that spatial defects can induce the formation of domains in bistable spatiotemporal systems. The minimum distance between defects acts as parameter for a transition from a homogeneous state to a heterogeneous regime where two phases coexist The critical exponent of this transition also exhibits a transition when the coupling is increased, indicating the presence of a new class of domain where both phases coexist forming a chessboard pattern.Comment: 3 pages, 3 figures, Accepted in European Physics Journa