Highly Scalable Algorithms for Robust String Barcoding

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size on a well-equipped workstation, and can be easily parallelized to further extend the applicability range to thousands of bacterial size genomes. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem

Trans-sonic propeller stage

We follow the approach used by Davies and Pringle (1981) and discuss the trans-sonic substage of the propeller regime. This substage is intermediate between the supersonic and subsonic propeller substages. In the trans-sonic regime an envelope around a magnetosphere of a neutron star passes through a kind of a reorganization process. The envelope in this regime consists of two parts. In the bottom one turbulent motions are subsonic. Then at some distance $r_\mathrm{s}$ the turbulent velocity becomes equal to the sound velocity. During this substage the boundary $r_\mathrm{s}$ propagates outwards till it reaches the outer boundary, and so the subsonic regime starts. We found that the trans-sonic substage is unstable, so the transition between supersonic and subsonic substages proceeds on the dynamical time scale. For realistic parameters this time is in the range from weeks to years.Comment: 8 pages with figures, submitted to Astron. Astroph. Transaction

Disks Surviving the Radiation Pressure of Radio Pulsars

The radiation pressure of a radio pulsar does not necessarily disrupt a surrounding disk. The position of the inner radius of a thin disk around a neutron star can be estimated by comparing the electromagnetic energy density generated by the neutron star with the kinetic energy density of the disk. Inside the light cylinder, the near zone electromagnetic field is essentially the dipole magnetic field, and the inner radius is the conventional Alfven radius. Far outside the light cylinder, in the radiation zone, $E=B$ and the electromagnetic energy density is $/c \propto 1/r^2$ where $S$ is the Poynting vector. Shvartsman (1970) argued that a stable equilibrium can not be found in the radiative zone because the electromagnetic energy density dominates over the kinetic energy density, with the relative strength of the electromagnetic stresses increasing with radius. In order to check whether this is true also near the light cylinder, we employ global electromagnetic field solutions for rotating oblique magnetic dipoles (Deutsch 1955). Near the light cylinder the electromagnetic energy density increases steeply enough with decreasing $r$ to balance the kinetic energy density at a stable equilibrium. The transition from the near zone to the radiation zone is broad. The radiation pressure of the pulsar can not disrupt the disk for values of the inner radius up to about twice the light cylinder radius if the rotation axis and the magnetic axis are orthogonal. This allowed range beyond the light cylinder extends much further for small inclination angles. We discuss implications of this result for accretion driven millisecond pulsars and young neutron stars with fallback disks.Comment: Accepted by Astrophysical Journal, final version with a minor correctio

Maximum Mass-Radius Ratios for Charged Compact General Relativistic Objects

Upper limits for the mass-radius ratio and total charge are derived for stable charged general relativistic matter distributions. For charged compact objects the mass-radius ratio exceeds the value 4/9 corresponding to neutral stars. General restrictions for the redshift and total energy (including the gravitational contribution) are also obtained.Comment: 6 pages, 2 figures, RevTex. To appear in Europhys. Let

Three-dimensional MHD Simulations of Radiatively Inefficient Accretion Flows

We present three-dimensional MHD simulations of rotating radiatively inefficient accretion flows onto black holes. In the simulations, we continuously inject magnetized matter into the computational domain near the outer boundary, and we run the calculations long enough for the resulting accretion flow to reach a quasi-steady state. We have studied two limiting cases for the geometry of the injected magnetic field: pure toroidal field and pure poloidal field. In the case of toroidal field injection, the accreting matter forms a nearly axisymmetric, geometrically-thick, turbulent accretion disk. The disk resembles in many respects the convection-dominated accretion flows found in previous numerical and analytical investigations of viscous hydrodynamic flows. Models with poloidal field injection evolve through two distinct phases. In an initial transient phase, the flow forms a relatively flattened, quasi-Keplerian disk with a hot corona and a bipolar outflow. However, when the flow later achieves steady state, it changes in character completely. The magnetized accreting gas becomes two-phase, with most of the volume being dominated by a strong dipolar magnetic field from which a thermal low-density wind flows out. Accretion occurs mainly via narrow slowly-rotating radial streams which `diffuse' through the magnetic field with the help of magnetic reconnection events.Comment: 35 pages including 3 built-in plots and 14 separate jpg-plots; version accepted by Ap

Magnetic Field Limitations on Advection Dominated Flows

Recent papers discussing advection dominated accretion flows (ADAF) as a solution for astrophysical accretion problems should be treated with some caution because of their uncertain physical basis. The suggestions underlying ADAF involve ignoring the magnetic field reconnection in heating of the plasma flow, assuming electron heating due only to binary Coulomb collisions with ions. Here, we analyze the physical processes in optically thin accretion flows at low accretion rates including the influence of an equipartition turbulent magnetic field. For these conditions there is continuous destruction of magnetic flux by reconnection. The reconnection is expected to significantly heat the electrons which can efficiently emit magnetobremstrahlung radiation. Because of this electron emission, the radiative efficiency of the ADAF is not small. We suggest that the small luminosities of nearby galactic black holes is due to outflows rather than ADAF accretion.Comment: 7 pages, 3 figures, Submitted to Ap

Can Thin Disks Produce Anomalous X-Ray Pulsars?

We investigate whether young neutron stars with fall-back disks can produce Anomalous X-Ray Pulsars (AXPs) within timescales indicated by the ages of associated supernova remnants. The system passes through a propeller stage before emerging as an AXP or a radio pulsar. The evolution of the disk is described by a diffusion equation which has self-similar solutions with either angular momentum or total mass of the disk conserved. We associate these two types of solutions with accretor and propeller regimes, respectively. Our numerical calculations of thin disk models with changing inner radius take into account the super-critical accretion at the early stages, and electron scattering and bound-free opacities with rich metal content. Our results show that, assuming a fraction of the mass inflow is accreted onto the neutron star, the fall-back disk scenario can produce AXPs for acceptable parameters.Comment: 16 pages, 4 Figures, to be published in Astrophysical Journal Vol. 599, Dec. 1

Relativistic Structure, Stability and Gravitational Collapse of Charged Neutron Stars

Charged stars have the potential of becoming charged black holes or even naked singularities. It is presented a set of numerical solutions of the Tolman-Oppenheimer-Volkov equations that represents spherical charged compact stars in hydrostatic equilibrium. The stellar models obtained are evolved forward in time integrating the Einstein-Maxwell field equations. It is assumed an equation of state of a neutron gas at zero temperature. The charge distribution is taken as been proportional to the rest mass density distribution. The set of solutions present an unstable branch, even with charge to mass ratios arbitrarily close to the extremum case. It is performed a direct check of the stability of the solutions under strong perturbations, and for different values of the charge to mass ratio. The stars that are in the stable branch oscillates and do not collapse, while models in the unstable branch collapse directly to form black holes. Stars with a charge greater or equal than the extreme value explode. When a charged star is suddenly discharged, it don't necessarily collapse to form a black hole. A non-linear effect that gives rise to the formation of an external shell of matter (see Ghezzi and Letelier 2005), is negligible in the present simulations. The results are in agreement with the third law of black hole thermodynamics and with the cosmic censorship conjecture.Comment: 27 pages, 14 figures, 4 tables, paper accepte

Spherically Symmetric Accretion Flows: Minimal Model with MHD Turbulence

The first spherical accretion model was developed 55 years ago, but the theory is yet far from being complete. The real accretion flow was found to be time-dependent and turbulent. This paper presents the minimal MHD spherical accretion model that separately deals with turbulence. Treatment of turbulence is based on simulations of several regimes of collisional MHD. The effects of freezing-in amplification, dissipation, dynamo action, isotropization, and constant magnetic helicity are self-consistently included. The assumptions of equipartition and magnetic field isotropy are released. Correct dynamics of magnetized flow is calculated. Diffusion, convection, and radiation are not accounted for. Two different types of Radiatively Inefficient accretion flows are found: a transonic non-rotating flow (I), a flow with effective transport of angular momentum outward (II). Non-rotating flow has an accretion rate several times smaller than Bondi rate, because turbulence inhibits accretion. Flow with angular momentum transport has accretion rate about 10-100 times smaller than Bondi rate. The effects of highly helical turbulence, states of outer magnetization, and different equations of state are discussed. The flows were found to be convectively stable on average, despite gas entropy increases inward. The proposed model has a small number of free parameters and the following attractive property. Inner density in the non-rotating magnetized flow was found to be several times lower than density in a non-magnetized accretion. Still several times lower density is required to explain the observed low IR luminosity and low Faraday rotation measure of accretion onto Sgr A*.Comment: Accepted for publication in ApJS. 52 pages, 7 figure

Stellar-Mass Black Holes in the Solar Neighborhood

We search for nearby, isolated, accreting, ``stellar-mass'' (3 to $100M_\odot$) black holes. Models suggest a synchrotron spectrum in visible wavelengths and some emission in X-ray wavelengths. Of 3.7 million objects in the Sloan Digital Sky Survey Early Data Release, about 150,000 objects have colors and properties consistent with such a spectrum, and 87 of these objects are X-ray sources from the ROSAT All Sky Survey. Thirty-two of these have been confirmed not to be black-holes using optical spectra. We give the positions and colors of these 55 black-hole candidates, and quantitatively rank them on their likelihood to be black holes. We discuss uncertainties the expected number of sources, and the contribution of blackholes to local dark matter.Comment: Replaced with version accepted by ApJ. 40 pages, 8 figure