Anisotropic convection in rotating proto-neutron stars

We study the conditions for convective instability in rotating, non-magnetic proto--neutron stars. The criteria that determine stability of nascent neutron stars are analogous to the Solberg--Hoiland conditions but including the presence of lepton gradients. Our results show that, for standard angular velocity profiles, convectively unstable modes with wave-vectors parallel to the rotation axis are suppressed by a stable angular momentum profile, while unstable modes with wave-vectors perpendicular to the axis remain unaltered. Since the wave-vector is perpendicular to the velocity perturbation, the directional selection of the unstable modes may result in fluid motions along the direction of the rotation axis. This occurs in rigidly rotating stars as well as in the inner core of differentially rotating stars. Our results provide a natural source of asymmetry for proto--neutron stars with the only requirement that angular velocities be of the order of the convective characteristic frequency.Comment: 5 pages, 4 figures, final version to appear in A&

2D and 3D Core-Collapse Supernovae Simulation Results Obtained with the CHIMERA Code

Much progress in realistic modeling of core-collapse supernovae has occurred recently through the availability of multi-teraflop machines and the increasing sophistication of supernova codes. These improvements are enabling simulations with enough realism that the explosion mechanism, long a mystery, may soon be delineated. We briefly describe the CHIMERA code, a supernova code we have developed to simulate core-collapse supernovae in 1, 2, and 3 spatial dimensions. We then describe the results of an ongoing suite of 2D simulations initiated from a 12, 15, 20, and 25 solar mass progenitor. These have all exhibited explosions and are currently in the expanding phase with the shock at between 5,000 and 20,000 km. We also briefly describe an ongoing simulation in 3 spatial dimensions initiated from the 15 solar mass progenitor.Comment: 5 pages, 3 figure

The evolution of novel fungal genes from non-retroviral RNA viruses

<p>Abstract</p> <p>Background</p> <p>Endogenous derivatives of non-retroviral RNA viruses are thought to be absent or rare in eukaryotic genomes because integration of RNA viruses in host genomes is impossible without reverse transcription. However, such derivatives have been proposed for animals, plants and fungi, often based on surrogate bioinformatic evidence. At present, there is little known of the evolution and function of integrated non-retroviral RNA virus genes. Here, we provide direct evidence of integration by sequencing across host-virus gene boundaries and carry out phylogenetic analyses of fungal hosts and totivirids (dsRNA viruses of fungi and protozoans). Further, we examine functionality by tests of neutral evolution, comparison of residues that are necessary for viral capsid functioning and assays for transcripts, dsRNA and viral particles.</p> <p>Results</p> <p>Sequencing evidence from gene boundaries was consistent with integration. We detected previously unknown integrated <it>Totivirus</it>-like sequences in three fungi (<it>Candida parapsilosis</it>, <it>Penicillium marneffei </it>and <it>Uromyces appendiculatus</it>). The phylogenetic evidence strongly indicated that the direction of transfer was from <it>Totivirus </it>to fungus. However, there was evidence of transfer of <it>Totivirus</it>-like sequences among fungi. Tests of selection indicated that integrated genes are maintained by purifying selection. Transcripts were apparent for some gene copies, but, in most cases, the endogenous sequences lacked the residues necessary for normal viral functioning.</p> <p>Conclusions</p> <p>Our findings reveal that horizontal gene transfer can result in novel gene formation in eukaryotes despite miniaturized genomic targets and a need for co-option of reverse transcriptase.</p

Dimension as a Key to the Neutrino Mechanism of Core-Collapse Supernova Explosions

We explore the dependence on spatial dimension of the viability of the neutrino heating mechanism of core-collapse supernova explosions. We find that the tendency to explode is a monotonically increasing function of dimension, with 3D requiring $\sim$40$-$50\% lower driving neutrino luminosity than 1D and $\sim$15$-$25\% lower driving neutrino luminosity than 2D. Moreover, we find that the delay to explosion for a given neutrino luminosity is always shorter in 3D than 2D, sometimes by many hundreds of milliseconds. The magnitude of this dimensional effect is much larger than the purported magnitude of a variety of other effects, such as nuclear burning, inelastic scattering, or general relativity, which are sometimes invoked to bridge the gap between the current ambiguous and uncertain theoretical situation and the fact of robust supernova explosions. Since real supernovae occur in three dimensions, our finding may be an important step towards unraveling one of the most problematic puzzles in stellar astrophysics. In addition, even though in 3D we do see pre-explosion instabilities and blast asymmetries, unlike the situation in 2D, we do not see an obvious axially-symmetric dipolar shock oscillation. Rather, the free energy available to power instabilites seems to be shared by more and more degrees of freedom as the dimension increases. Hence, the strong dipolar axisymmetry seen in 2D and previously identified as a fundamental characteristic of the shock hydrodynamics may not survive in 3D as a prominent feature.Comment: Accepted to ApJ July 7th, Replaced with accepted versio

Ascertaining the Core Collapse Supernova Mechanism: An Emerging Picture?

Here we present the results from two sets of simulations, in two and three spatial dimensions. In two dimensions, the simulations include multifrequency flux-limited diffusion neutrino transport in the "ray-by-ray-plus" approximation, two-dimensional self gravity in the Newtonian limit, and nuclear burning through a 14-isotope alpha network. The three-dimensional simulations are model simulations constructed to reflect the post stellar core bounce conditions during neutrino shock reheating at the onset of explosion. They are hydrodynamics-only models that focus on critical aspects of the shock stability and dynamics and their impact on the supernova mechanism and explosion. In two dimensions, we obtain explosions (although in one case weak) for two progenitors (11 and 15 Solar mass models). Moreover, in both cases the explosion is initiated when the inner edge of the oxygen layer accretes through the shock. Thus, the shock is not revived while in the iron core, as previously discussed in the literature. The three-dimensional studies of the development of the stationary accretion shock instability (SASI) demonstrate the fundamentally new dynamics allowed when simulations are performed in three spatial dimensions. The predominant l=1 SASI mode gives way to a stable m=1 mode, which in turn has significant ramifications for the distribution of angular momentum in the region between the shock and proto-neutron star and, ultimately, for the spin of the remnant neutron star. Moreover, the three-dimensional simulations make clear, given the increased number of degrees of freedom, that two-dimensional models are severely limited by artificially imposed symmetries.Comment: 9 pages, 3 figure

Gravitational Waves from Core Collapse Supernovae

We present the gravitational wave signatures for a suite of axisymmetric core collapse supernova models with progenitors masses between 12 and 25 solar masses. These models are distinguished by the fact they explode and contain essential physics (in particular, multi-frequency neutrino transport and general relativity) needed for a more realistic description. Thus, we are able to compute complete waveforms (i.e., through explosion) based on non-parameterized, first-principles models. This is essential if the waveform amplitudes and time scales are to be computed more precisely. Fourier decomposition shows that the gravitational wave signals we predict should be observable by AdvLIGO across the range of progenitors considered here. The fundamental limitation of these models is in their imposition of axisymmetry. Further progress will require counterpart three-dimensional models.Comment: 10 pages, 5 figure

Modeling core collapse supernovae in 2 and 3 dimensions with spectral neutrino transport

The overwhelming evidence that the core collapse supernova mechanism is inherently multidimensional, the complexity of the physical processes involved, and the increasing evidence from simulations that the explosion is marginal presents great computational challenges for the realistic modeling of this event, particularly in 3 spatial dimensions. We have developed a code which is scalable to computations in 3 dimensions which couples PPM Lagrangian with remap hydrodynamics [1], multigroup, flux-limited diffusion neutrino transport [2], with many improvements), and a nuclear network [3]. The neutrino transport is performed in a ray-by-ray plus approximation wherein all the lateral effects of neutrinos are included (e.g., pressure, velocity corrections, advection) except the transport. A moving radial grid option permits the evolution to be carried out from initial core collapse with only modest demands on the number of radial zones. The inner part of the core is evolved after collapse along with the rest of the core and mantle by subcycling the lateral evolution near the center as demanded by the small Courant times. We present results of 2-D simulations of a symmetric and an asymmetric collapse of both a 15 and an 11 M progenitor. In each of these simulations we have discovered that once the oxygen rich material reaches the shock there is a synergistic interplay between the reduced ram pressure, the energy released by the burning of the shock heated oxygen rich material, and the neutrino energy deposition which leads to a revival of the shock and an explosion.Comment: 10 pages, 3 figure