Tail emission from a ring-like jet: its application to shallow decays of early afterglows and to GRB 050709

Similar to the pulsar, the magnetic axis and the spin axis of the gamma-ray burst source may not lie on the same line. This may cause a ring-like jet due to collimation of the precessing magnetic axis. We analyze the tail emission from such a jet, and find that it has a shallow decay phase with temporal index equal to -1/2 if the Lorentz factor of the ejecta is not very high. This phase is consistent with the shallow decay phase of some early X-ray afterglow detected by {\it{swift}}. The ring-like jet has a tail cusp with sharp rising and very sharp decay. This effect can provide an explanation for the re-brightening and sharp decay of the X-ray afterglow of GRB 050709.Comment: 6 pages, 2 figures. Accepted by ChJA

mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications

Cataloged from PDF version of article.High throughput sequencing (HTS) platforms generate unprecedented amounts of data that introduce challenges for processing and downstream analysis. While tools that report the 'best' mapping location of each read provide a fast way to process HTS data, they are not suitable for many types of downstream analysis such as structural variation detection, where it is important to report multiple mapping loci for each read. For this purpose we introduce mrsFAST-Ultra, a fast, cache oblivious, SNP-aware aligner that can handle the multi-mapping of HTS reads very efficiently. mrsFAST-Ultra improves mrsFAST, our first cache oblivious read aligner capable of handling multi-mapping reads, through new and compact index structures that reduce not only the overall memory usage but also the number of CPU operations per alignment. In fact the size of the index generated by mrsFAST-Ultra is 10 times smaller than that of mrsFAST. As importantly, mrsFAST-Ultra introduces new features such as being able to (i) obtain the best mapping loci for each read, and (ii) return all reads that have at most n mapping loci (within an error threshold), together with these loci, for any user specified n. Furthermore, mrsFAST-Ultra is SNP-aware, i.e. it can map reads to reference genome while discounting the mismatches that occur at common SNP locations provided by db-SNP; this significantly increases the number of reads that can be mapped to the reference genome. Notice that all of the above features are implemented within the index structure and are not simple post-processing steps and thus are performed highly efficiently. Finally, mrsFAST-Ultra utilizes multiple available cores and processors and can be tuned for various memory settings. Our results show that mrsFAST-Ultra is roughly five times faster than its predecessor mrsFAST. In comparison to newly enhanced popular tools such as Bowtie2, it is more sensitive (it can report 10 times or more mappings per read) and much faster (six times or more) in the multi-mapping mode. Furthermore, mrsFAST-Ultra has an index size of 2GB for the entire human reference genome, which is roughly half of that of Bowtie2. mrsFAST-Ultra is open source and it can be accessed at http://mrsfast.sourceforge.net

Measurement of electron-hole friction in an n-doped GaAs/AlGaAs quantum well using optical transient grating spectroscopy

We use phase-resolved transient grating spectroscopy to measure the drift and diffusion of electron-hole density waves in a semiconductor quantum well. The unique aspects of this optical probe allow us to determine the frictional force between a two-dimensional Fermi liquid of electrons and a dilute gas of holes. Knowledge of electron-hole friction enables prediction of ambipolar dynamics in high-mobility electron systems.Comment: to appear in PR

The Role of Fission in Neutron Star Mergers and Its Impact on the r-Process Peaks

Comparing observational abundance features with nucleosynthesis predictions of stellar evolution or explosion simulations, we can scrutinize two aspects: (a) the conditions in the astrophysical production site and (b) the quality of the nuclear physics input utilized. We test the abundance features of r-process nucleosynthesis calculations for the dynamical ejecta of neutron star merger simulations based on three different nuclear mass models: The Finite Range Droplet Model, the (quenched version of the) Extended Thomas Fermi Model with Strutinsky Integral, and the Hartree-Fock-Bogoliubov mass model. We make use of corresponding fission barrier heights and compare the impact of four different fission fragment distribution models on the final r-process abundance distribution. In particular, we explore the abundance distribution in the second r-process peak and the rare-earth sub-peak as a function of mass models and fission fragment distributions, as well as the origin of a shift in the third r-process peak position. The latter has been noticed in a number of merger nucleosynthesis predictions. We show that the shift occurs during the r-process freeze-out when neutron captures and β-decays compete and an (n,γ)-(γ,n) equilibrium is no longer maintained. During this phase neutrons originate mainly from fission of material above A = 240. We also investigate the role of β-decay half-lives from recent theoretical advances, which lead either to a smaller amount of fissioning nuclei during freeze-out or a faster (and thus earlier) release of fission neutrons, which can (partially) prevent this shift and has an impact on the second and rare-earth peak as well.Peer reviewe

Relativistic calculations of the K-K charge transfer and K-vacancy production probabilities in low-energy ion-atom collisions

The previously developed technique for evaluation of charge-transfer and electron-excitation processes in low-energy heavy-ion collisions [I.I. Tupitsyn et al., Phys. Rev. A 82, 042701(2010)] is extended to collisions of ions with neutral atoms. The method employs the active electron approximation, in which only the active electron participates in the charge transfer and excitation processes while the passive electrons provide the screening DFT potential. The time-dependent Dirac wave function of the active electron is represented as a linear combination of atomic-like Dirac-Fock-Sturm orbitals, localized at the ions (atoms). The screening DFT potential is calculated using the overlapping densities of each ions (atoms), derived from the atomic orbitals of the passive electrons. The atomic orbitals are generated by solving numerically the one-center Dirac-Fock and Dirac-Fock-Sturm equations by means of a finite-difference approach with the potential taken as the sum of the exact reference ion (atom) Dirac-Fock potential and of the Coulomb potential from the other ion within the monopole approximation. The method developed is used to calculate the K-K charge transfer and K-vacancy production probabilties for the Ne$(1s^2 2s^2 2p^6)$ -- F$^{8+}(1s)$ collisions at the F$^{8+}(1s)$ projectile energies 130 keV/u and 230 keV/u. The obtained results are compared with experimental data and other theoretical calculations. The K-K charge transfer and K-vacancy production probabilities are also calculated for the Xe -- Xe$^{53+}(1s)$ collision.Comment: 16 pages, 4 figure

Optical tomography of Fock state superpositions

We consider optical tomography of photon Fock state superpositions in connection with recent experimental achievements. The emphasis is put on the fact that it suffices to represent the measured tomogram as a main result of the experiment. We suggest a test for checking the correctness of experimental data. Explicit expressions for optical tomograms of Fock state superpositions are given in terms of Hermite polynomials. Particular cases of vacuum and low photon-number state superposition are considered as well as influence of thermal noise on state purity is studied.Comment: 5 pages, 2 figure

Performance-based financing as a health system reform : mapping the key dimensions for monitoring and evaluation

Peer reviewedPublisher PD

Superconformal Algebras and Mock Theta Functions

It is known that characters of BPS representations of extended superconformal algebras do not have good modular properties due to extra singular vectors coming from the BPS condition. In order to improve their modular properties we apply the method of Zwegers which has recently been developed to analyze modular properties of mock theta functions. We consider the case of N=4 superconformal algebra at general levels and obtain the decomposition of characters of BPS representations into a sum of simple Jacobi forms and an infinite series of non-BPS representations. We apply our method to study elliptic genera of hyper-Kahler manifolds in higher dimensions. In particular we determine the elliptic genera in the case of complex 4 dimensions of the Hilbert scheme of points on K3 surfaces K^{[2]} and complex tori A^{[[3]]}.Comment: 28 page