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

Heating and Cooling of Hot Accretion Flows by Non Local Radiation

We consider non-local effects which arise when radiation emitted at one radius of an accretion disk either heats or cools gas at other radii through Compton scattering. We discuss three situations: 1. Radiation from the inner regions of an advection-dominated flow Compton cooling gas at intermediate radii and Compton heating gas at large radii. 2. Soft radiation from an outer thin accretion disk Compton cooling a hot one- or two-temperature flow on the inside. 3. Soft radiation from an inner thin accretion disk Compton cooling hot gas in a surrounding one-temperature flow. We describe how previous results are modified by these non-local interactions. We find that Compton heating or cooling of the gas by the radiation emitted in the inner regions of a hot flow is not important. Likewise, Compton cooling by the soft photons from an outer thin disk is negligible when the transition from a cold to a hot flow occurs at a radius greater than some minimum $R_{tr,min}$. However, if the hot flow terminates at $R < R_{tr,min}$, non-local cooling is so strong that the hot gas is cooled to a thin disk configuration in a runaway process. In the case of a thin disk surrounded by a hot one-temperature flow, we find that Compton cooling by soft radiation dominates over local cooling in the hot gas for \dot{M} \gsim 10^{-3} \alpha \dot{M}_{Edd}, and R \lsim 10^4 R_{Schw}. As a result, the maximum accretion rate for which an advection-dominated one-temperature solution exists, decreases by a factor of $\sim 10$, compared to the value computed under an assumption of local energy balance.Comment: LaTeX aaspp.sty, 25 pages, and 6 figures; to appear in Ap

Special issue on DISC 2010

This special issue of Distributed Computing is based on papers that originally appeared as extended abstracts in the Proceedings of the 24th International Symposium on Distributed Computing (DISC2010), held in Cambridge, Massachusetts on August 13–15, 2010. The papers for the Special Issue were chosen by the Program Committee from the 32 regular papers presented at the Symposium, based on their quality and representation of the spectrum of topics encompassed by the Symposium. In addition to being reviewed, in preliminary form, by the Program Committee, the full papers submitted for the Special Issue were refereed according to the standard practices of Distributed Computing (due to time constrains, some papers could not appear in this volume). We thank the Members of the Editorial Board for their work in editing this issue, and the referees and the authors of these papers for their respective contributions

The influence of nonstationarity of the solar activity and general solar field on modulation of cosmic rays

A numerical model of the propagation of galactic cosmic rays in interplanetary space was constructed for the case when the modulation depth determined by the level of solar activity changed in time. Also the contribution of particle drift in the regular field was calculated, and the agreement with experimental data concerning the ratio of protons and electrons in two solar activity minima is shown

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

Physical properties of Tolman-Bayin solutions: some cases of static charged fluid spheres in general relativity

In this article, Einstein-Maxwell space-time has been considered in connection to some of the astrophysical solutions as previously obtained by Tolman (1939) and Bayin (1978). The effect of inclusion of charge into these solutions has been investigated thoroughly and also the nature of fluid pressure and mass density throughout the sphere have been discussed. Mass-radius and mass-charge relations have been derived for various cases of the charged matter distribution. Two cases are obtained where perfect fluid with positive pressures give rise to electromagnetic mass models such that gravitational mass is of purely electromagnetic origin.Comment: 15 pages, 12 figure

Ultra-high energy cosmic rays from Quark Novae

We explore acceleration of ions in the Quark Nova (QN) scenario, where a neutron star experiences an explosive phase transition into a quark star (born in the propeller regime). In this picture, two cosmic ray components are isolated: one related to the randomized pulsar wind and the other to the propelled wind, both boosted by the ultra-relativistic Quark Nova shock. The latter component acquires energies $10^{15} {\rm eV}<E<10^{18} {\rm eV}$ while the former, boosted pulsar wind, achieves ultra-high energies $E> 10^{18.6}$ eV. The composition is dominated by ions present in the pulsar wind in the energy range above $10^{18.6}$ eV, while at energies below $10^{18}$ eV the propelled ejecta, consisting of the fall-back neutron star crust material from the explosion, is the dominant one. Added to these two components, the propeller injects relativistic particles with Lorentz factors $\Gamma_{\rm prop.} \sim 1-1000$, later to be accelerated by galactic supernova shocks. The QN model appears to be able to account for the extragalactic cosmic rays above the ankle and to contribute a few percent of the galactic cosmic rays below the ankle. We predict few hundred ultra-high energy cosmic ray events above $10^{19}$ eV for the Pierre Auger detector per distant QN, while some thousands are predicted for the proposed EUSO and OWL detectors.Comment: 20 pages, 1 figure. Major revisions in the text. Accepted for publication in the Astrophysical Journa