CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers.

BackgroundThe problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce.ResultsWe introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions.ConclusionsCLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/

High-density Skyrmion matter and Neutron Stars

We examine neutron star properties based on a model of dense matter composed of B=1 skyrmions immersed in a mesonic mean field background. The model realizes spontaneous chiral symmetry breaking non-linearly and incorporates scale-breaking of QCD through a dilaton VEV that also affects the mean fields. Quartic self-interactions among the vector mesons are introduced on grounds of naturalness in the corresponding effective field theory. Within a plausible range of the quartic couplings, the model generates neutron star masses and radii that are consistent with a preponderance of observational constraints, including recent ones that point to the existence of relatively massive neutron stars with mass M 1.7 Msun and radius R (12-14) km. If the existence of neutron stars with such dimensions is confirmed, matter at supra-nuclear density is stiffer than extrapolations of most microscopic models suggest.Comment: 27 pages, 5 figures, AASTeX style; to be published in The Astrophysical Journa

CP violation in Charged Higgs Bosons decays H±→W±(γ,Z)H^\pm \to W^\pm (\gamma, Z) in the Minimal Supersymmetric Standard Model (MSSM)

One loop mediated charged Higgs bosons decays $H^\pm\to W^\pm V$, $V= Z, \gamma$ are studied in the Minimal Supersymmetric Standard Model (MSSM) with and without CP violating phases. We evaluate the MSSM contributions to these processes taking into account $B\to X_s\gamma$ constraint as well as experimental constraints on the MSSM parameters. In the MSSM, we found that in the intermediate range of \tan\beta \la 10 and for large A_t and large $\mu$, where the lightest top squark becomes very light and hence non-decoupled, the branching ratio of $H^\pm \to W^{\pm} Z$ can be of the order 10^{-3} while the branching ratio of $H^\pm \to W^{\pm} \gamma$ is of the order 10^{-5}. We found also that the CP violating phases of soft SUSY parameters can modify the branching ratio by about one order of magnitude. We also show that MSSM with CP violating phases lead to CP-violating asymmetry in the decays $H^+ \to W^+V$ and $H^- \to W^-V$. Such CP asymmetry can be rather large and can reach 80% in some region of parameter space.Comment: Invited talk at CTP Symposium on Supersymmetry at LHC: Theoretical and Experimental Prospectives, Cario, Egypt, 11-14 Mar 200

h\to \gamma \gamma In Inert Higgs Doublet Model

Motivated by the recent result reported from LHC on the di-photon search for a Standard Model (SM) Higgs-like boson. We discuss the implications of this possible signal in the framework of the Inert Higgs Doublet Model (IHDM), taking into account previous limits from Higgs searches at LEP, the Tevatron and the LHC as well as constraints from unitarity, vacuum stability and electroweak precision tests. We show that the charged Higgs contributions can interfere constructively or destructively with the W gauge bosons loops leading to enhancement or suppression of the di-photon rate with respect to SM rate. We show also that the invisible decay of the Higgs, if open, could affect the total width of the SM Higgs boson and therefore suppress the di-photon rate.Comment: 15 pages, added reference

Quark deconfinement in neutron star cores: The effects of spin-down

We study the role of spin-down in driving quark deconfinement in the high density core of isolated neutron stars. Assuming spin-down to be solely due to magnetic braking, we obtain typical timescales to quark deconfinement for neutron stars that are born with Keplerian frequencies. Employing different equations of state (EOS), we determine the minimum and maximum neutron star masses that will allow for deconfinement via spin-down only. We find that the time to reach deconfinement is strongly dependent on the magnetic field and that this time is least for EOS that support the largest minimum mass at zero spin, unless rotational effects on stellar structure are large. For a fiducial critical density of $5\rho_0$ for the transition to the quark phase ($\rho_0=2.5\times10^{14}$g/cm$^3$ is the saturation density of nuclear matter), we find that neutron stars lighter than $1.5M_{\odot}$ cannot reach a deconfined phase. Depending on the EOS, neutron stars of more than $1.5M_{\odot}$ can enter a quark phase only if they are spinning faster than about 3 milliseconds as observed now, whereas larger spin periods imply that they are either already quark stars or will never become one.Comment: 4 pages, 4 figures, submitted to ApJ

Numerical Simulation of the Hydrodynamical Combustion to Strange Quark Matter

We present results from a numerical solution to the burning of neutron matter inside a cold neutron star into stable (u,d,s) quark matter. Our method solves hydrodynamical flow equations in 1D with neutrino emission from weak equilibrating reactions, and strange quark diffusion across the burning front. We also include entropy change due to heat released in forming the stable quark phase. Our numerical results suggest burning front laminar speeds of 0.002-0.04 times the speed of light, much faster than previous estimates derived using only a reactive-diffusive description. Analytic solutions to hydrodynamical jump conditions with a temperature dependent equation of state agree very well with our numerical findings for fluid velocities. The most important effect of neutrino cooling is that the conversion front stalls at lower density (below approximately 2 times saturation density). In a 2-dimensional setting, such rapid speeds and neutrino cooling may allow for a flame wrinkle instability to develop, possibly leading to detonation.Comment: 5 pages, 3 figures (animations online at http://www.capca.ucalgary.ca/~bniebergal/webPHP/research.php