REFINEMENT OF PHYLOGENETIC SIGNAL IN MULTIPLE SEQUENCE ALIGNMENT: RESULTS OF SIMULATION STUDY

SUMMARY Motivation: Disparate substitution rates within the different regions of homologous sequences and mutational saturation are well known to cause misalignment of sequences and to hamper accurate tree reconstruction. Therefore, there is a need in tools detecting and filtering out informational noise from the multiple alignment of sequence data; the tools will help to increase accuracy and resolution of phylogenetic analyses. Results: We propose such a tool and tested its ability to improve the quality phylogenetic trees both on the biological COG data, and on the artificial data, where the ideal tree was known a priory. The key operation of the filtering is a removal of noisy columns. It was shown that the tool permits to reconstruct a tree closer to the "true" tree than is the tree reconstructed with data without removal. Procedure can be applied as a tool to pre-process multiple alignments and enhance phylogenetic inference

Cyclotron motion in graphene

We investigate cyclotron motion in graphene monolayers considering both the full quantum dynamics and its semiclassical limit reached at high carrier energies. Effects of zitterbewegung due to the two dispersion branches of the spectrum dominate the irregular quantum motion at low energies and are obtained as a systematic correction to the semiclassical case. Recent experiments are shown to operate in the semiclassical regime.Comment: 6 pages, 1 figure include

Experimental analysis of wear resistance of compacts of fine-dispersed iron powder and tungsten monocarbide nanopowder produced by impulse pressing

The paper presents the results of studying the structure and wear resistance of compacts produced from fine dispersed reduced iron powder (average particle size 3–5μm) with the addition of tungsten carbide (WC) nanopowder with the average particle size of 25–30 nm. The mass fraction of tungsten carbide (wolfram carbide) in the powder composition was 5% and 10% of the total mass. Impulse pressing was conducted using the modified Kolsky method at compacting temperatures of 20 °C to 300 °C. The produced compacts had relative density of over 90%. Metallographic studies using the scanning electronic microscopy method on a TESCAN VEGA II electronic microscope have shown that the produced compacts have a fairly homogeneous fine-grained structure, with a uniform pattern of pore distribution, the form of the pores being close to spherical. X-ray microanalysis using an INCA Energy 250 energy-dispersion spectrometer with scanning along the surface line and transversal laps testifies to the fact that, in the considered temperature range, dynamic compaction does not lead to any noticeable changes in the distribution of the Fe, W and C elements over the bulk of the specimens. The conducted measurements of micro-hardness of the compacts have shown that it increases considerably with the pressing temperature. The produced compacts were tested for wear resistance in a dry friction regime, using the ‘rotating disk – stationary specimen’ configuration. Mass loss of the compacts as a function of testing time is presented. Wear resistance of compacts depends on pressing temperature and concentration of the WC powder in the matrix of reduced iron. It has been experimentally determined that maximal wear resistance is observed in the compacts with the mass fraction of WC equal to 10%, produced at a pressing temperature of 300 °C

Variational theory of elastic manifolds with correlated disorder and localization of interacting quantum particles

We apply the gaussian variational method (GVM) to study the equilibrium statistical mechanics of the two related systems: (i) classical elastic manifolds, such as flux lattices, in presence of columnar disorder correlated along the $\tau$ direction (ii) interacting quantum particles in a static random potential. We find localization by disorder, the localized phase being described by a replica symmetry broken solution confined to the mode $\omega=0$. For classical systems we compute the correlation function of relative displacements. In $d=2+1$, in the absence of dislocations, the GVM allows to describes the Bose glass phase. Along the columns the displacements saturate at a length $l_{\perp}$ indicating flux-line localization. Perpendicularly to the columns long range order is destroyed. We find divergent tilt modulus $c_{44}=\infty$ and a $x \sim \tau^{1/2}$ scaling. Quantum systems are studied using the analytic continuation from imaginary to real time $\tau \to i t$. We compute the conductivity and find that it behaves at small frequency as $\sigma(\omega) \approx \omega^2$ in all dimensions ($d < 4$) for which disorder is relevant. We compute the quantum localization length $\xi$. In $d=1$, where the model also describes interacting fermions in a static random potential, we find a delocalization transition and obtain analytically both the low and high frequency behavior of the conductivity for any value of the interaction. We show that the marginality condition appears as the condition to obtain the correct physical behavior. Agreement with renormalization group results is found whenever it can be compared.Comment: 34 pages, REVTeX, no figure

B1359+154: A Six Image Lens Produced by a z=1 Compact Group of Galaxies

HST V and I-band observations show that the gravitational lens B1359+154 consists of six images of a single z_s=3.235 radio source and its star-forming host galaxy, produced by a compact group of galaxies at z_l = 1. VLBA observations at 1.7 GHz strongly support this conclusion, showing six compact cores with similar low-frequency radio spectra. B1359+154 is the first example of galaxy-scale gravitational lensing in which more than four images are observed of the same background source. The configuration is due to the unique lensing mass distribution: three primary lens galaxies lying on the vertices of a triangle separated by 0.7 arcsec (4/h kpc), inside the 1.7 arcsec diameter Einstein ring defined by the radio images. The gravitational potential has additional extrema within this triangle, creating a pair of central images that supplement the ``standard'' four-image geometry of the outer components. Simple mass models consisting of three lens galaxies constrained by HST and VLBA astrometry naturally reproduce the observed image positions but must be finely-tuned to fit the flux densities.Comment: 28 pages including 6 figures, ApJ submitte

Elastic theory of flux lattices in presence of weak disorder

The effect of disorder on flux lattices at equilibrium is studied quantitatively in the absence of free dislocations using both the Gaussian variational method and the renormalization group. Our results for the mean square relative displacements clarify the nature of the crossovers with distance. We find three regimes: (i) a short distance regime (``Larkin regime'') where elasticity holds (ii) an intermediate regime (``Random Manifold'') where vortices are pinned independently (iii) a large distance, quasi-ordered regime where the periodicity of the lattice becomes important and there is universal logarithmic growth of displacements for $2<d<4$ and persistence of algebraic quasi-long range translational order. The functional renormalization group to $O(\epsilon=4-d)$ and the variational method, agree within $10\%$ on the value of the exponent. In $d=3$ we compute the crossover function between the three regimes. We discuss the observable signature of this crossover in decoration experiments and in neutron diffraction experiments on flux lattices. Qualitative arguments are given suggesting the existence for weak disorder in $d=3$ of a `` Bragg glass '' phase without free dislocations and with algebraically divergent Bragg peaks. In $d=1+1$ both the variational method and the Cardy-Ostlund renormalization group predict a glassy state below the same transition temperature $T=T_c$, but with different behaviors. Applications to $d=2+0$ systems and experiments on magnetic bubbles are discussed.Comment: 59 pages; RevTeX 3.0; 5 postscript figures uuencode

The Inviscid Limit and Boundary Layers for Navier-Stokes Flows

The validity of the vanishing viscosity limit, that is, whether solutions of the Navier-Stokes equations modeling viscous incompressible flows converge to solutions of the Euler equations modeling inviscid incompressible flows as viscosity approaches zero, is one of the most fundamental issues in mathematical fluid mechanics. The problem is classified into two categories: the case when the physical boundary is absent, and the case when the physical boundary is present and the effect of the boundary layer becomes significant. The aim of this article is to review recent progress on the mathematical analysis of this problem in each category.Comment: To appear in "Handbook of Mathematical Analysis in Mechanics of Viscous Fluids", Y. Giga and A. Novotn\'y Ed., Springer. The final publication is available at http://www.springerlink.co

Gravitational Lensing

Gravitational lensing has developed into one of the most powerful tools for the analysis of the dark universe. This review summarises the theory of gravitational lensing, its main current applications and representative results achieved so far. It has two parts. In the first, starting from the equation of geodesic deviation, the equations of thin and extended gravitational lensing are derived. In the second, gravitational lensing by stars and planets, galaxies, galaxy clusters and large-scale structures is discussed and summarised.Comment: Invited review article to appear in Classical and Quantum Gravity, 85 pages, 15 figure

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages

Search for W~1Z~2\widetilde{W}_1\widetilde{Z}_2 Production via Trilepton Final States in ppˉp\bar{p} collisions at s=1.8\sqrt{s}=1.8 TeV

We have searched for associated production of the lightest chargino, $\widetilde{W}_1$, and next-to-lightest neutralino, $\widetilde{Z}_2$, of the Minimal Supersymmetric Standard Model in $p\bar{p}$ collisions at \mbox{$\sqrt{s}$ = 1.8 TeV} using the \D0 detector at the Fermilab Tevatron collider. Data corresponding to an integrated luminosity of 12.5$\pm 0.7$ \ipb were examined for events containing three isolated leptons. No evidence for $\widetilde{W}_1\widetilde{Z}_2$ pair production was found. Limits on $\sigma(\widetilde{W}_1\widetilde{Z}_2)$Br$(\widetilde{W}_1\to l\nu\widetilde{Z}_1)$Br$(\widetilde{Z}_2\to l\bar{l}\widetilde{Z}_1)$ are presented.Comment: 17 pages (13 + 1 page table + 3 pages figures). 3 PostScript figures will follow in a UUEncoded, gzip'd, tar file. Text in LaTex format. Submitted to Physical Review Letters. Replace comments - Had to resumbmit version with EPSF directive