The advantages of SMRT sequencing

Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes

Unstable Equilibria and Invariant Manifolds in Quasi-Two-Dimensional Kolmogorov-like Flow

Recent studies suggest that unstable, non-chaotic solutions of the Navier-Stokes equation may provide deep insights into fluid turbulence. In this article, we present a combined experimental and numerical study exploring the dynamical role of unstable equilibrium solutions and their invariant manifolds in a weakly turbulent, electromagnetically driven, shallow fluid layer. Identifying instants when turbulent evolution slows down, we compute 31 unstable equilibria of a realistic two-dimensional model of the flow. We establish the dynamical relevance of these unstable equilibria by showing that they are closely visited by the turbulent flow. We also establish the dynamical relevance of unstable manifolds by verifying that they are shadowed by turbulent trajectories departing from the neighborhoods of unstable equilibria over large distances in state space

Models for Type I X-Ray Bursts with Improved Nuclear Physics

Multi-zone models of Type I X-ray bursts are presented that use an adaptive nuclear reaction network of unprecedented size, up to 1300 isotopes. Sequences of up to 15 bursts are followed for two choices of accretion rate and metallicity. At 0.1 Eddington (and 0.02 Eddington for low metallicity), combined hydrogen-helium flashes occur. The rise times, shapes, and tails of these light curves are sensitive to the efficiency of nuclear burning at various waiting points along the rp-process path and these sensitivities are explored. The bursts show "compositional inertia", in that their properties depend on the fact that accretion occurs onto the ashes of previous bursts which contain left-over hydrogen, helium and CNO nuclei. This acts to reduce the sensitivity of burst properties to metallicity. For the accretion rates studied, only the first anomalous burst in one model produces nuclei as heavy as A=100, other bursts make chiefly nuclei with A~64. The amount of carbon remaining after hydrogen-helium bursts is typically <1% by mass, and decreases further as the ashes are periodically heated by subsequent bursts. At the lower accretion rate of 0.02 Eddington and solar metallicity, the bursts ignite in a hydrogen-free helium layer. At the base of this layer, up to 90% of the helium has already burned to carbon prior to the unstable ignition. These helium-ignited bursts have briefer, brighter light curves with shorter tails, very rapid rise times (<0.1 s), and ashes lighter than the iron group.Comment: Submitted to the Astrophysical Journal (42 pages; 27 figures

Capturing Turbulent Dynamics and Statistics in Experiments with Unstable Periodic Orbits

In laboratory studies and numerical simulations, we observe clear signatures of unstable time-periodic solutions in a moderately turbulent quasi-two-dimensional flow. We validate the dynamical relevance of such solutions by demonstrating that turbulent flows in both experiment and numerics transiently display time-periodic dynamics when they shadow unstable periodic orbits (UPOs). We show that UPOs we computed are also statistically significant, with turbulent flows spending a sizable fraction of the total time near these solutions. As a result, the average rates of energy input and dissipation for the turbulent flow and frequently visited UPOs differ only by a few percent.Comment: Accepted for publication in Phys. Rev. Let

Proton Drip-Line Calculations and the Rp-process

One-proton and two-proton separation energies are calculated for proton-rich nuclei in the region $A=41-75$. The method is based on Skyrme Hartree-Fock calculations of Coulomb displacement energies of mirror nuclei in combination with the experimental masses of the neutron-rich nuclei. The implications for the proton drip line and the astrophysical rp-process are discussed. This is done within the framework of a detailed analysis of the sensitivity of rp process calculations in type I X-ray burst models on nuclear masses. We find that the remaining mass uncertainties, in particular for some nuclei with $N=Z$, still lead to large uncertainties in calculations of X-ray burst light curves. Further experimental or theoretical improvements of nuclear mass data are necessary before observed X-ray burst light curves can be used to obtain quantitative constraints on ignition conditions and neutron star properties. We identify a list of nuclei for which improved mass data would be most important.Comment: 20 pages, 9 figures, 2 table

The rp Process Ashes from Stable Nuclear Burning on an Accreting Neutron Star

We calculate the nucleosynthesis during stable nuclear burning on an accreting neutron star. This is appropriate for weakly magnetic neutron stars accreting at near-Eddington rates in low mass X-ray binaries, and for most accreting X-ray pulsars. We show that the nuclear burning proceeds via the rapid proton capture process (rp process), and makes nuclei far beyond the iron group. The final mixture of nuclei consists of elements with a range of masses between approximately A=60 and A=100. The average nuclear mass of the ashes is set by the extent of helium burning via (alpha,p) reactions, and depends on the local accretion rate. Our results imply that the crust of these accreting neutron stars is made from a complex mixture of heavy nuclei, with important implications for its thermal, electrical and structural properties. A crustal lattice as impure as our results suggest will have a conductivity set mostly by impurity scattering, allowing more rapid Ohmic diffusion of magnetic fields than previously estimated.Comment: To appear in the Astrophysical Journal (33 pages, LaTeX, including 11 postscript figures