No abstract

The turbulent Rayleigh-Taylor instability is investigated in the limit of strong mode-coupling using a variety of high-resolution, multimode, three dimensional numerical simulations ͑NS͒. The perturbations are initialized with only short wavelength modes so that the self-similar evolution ͑i.e., bubble diameter D b ϰamplitude h b) occurs solely by the nonlinear coupling ͑merger͒ of saturated modes. After an initial transient, it is found that h b ϳ␣ b Agt 2 , where AϭAtwood number, gϭacceleration, and tϭtime. The NS yield D b ϳh b /3 in agreement with experiment but the simulation value ␣ b ϳ0.025Ϯ0.003 is smaller than the experimental value ␣ b ϳ0.057Ϯ0.008. By analyzing the dominant bubbles, it is found that the small value of ␣ b can be attributed to a density dilution due to fine-scale mixing in our NS without interface reconstruction ͑IR͒ or an equivalent entrainment in our NS with IR. This may be characteristic of the mode coupling limit studied here and the associated ␣ b may represent a lower bound that is insensitive to the initial amplitude. Larger values of ␣ b can be obtained in the presence of additional long wavelength perturbations and this may be more characteristic of experiments. Here, the simulation data are also analyzed in terms of bubble dynamics, energy balance and the density fluctuation spectra.

The microbial mats of Guerrero Negro (GN), Baja California Sur, Mexico historically were considered a simple environment, dominated by cyanobacteria and sulfate-reducing bacteria. Culture-independent rRNA community profiling instead revealed these microbial mats as among the most phylogenetically diverse environments known. A preliminary molecular survey of the GN mat based on only ∼1500 small subunit rRNA gene sequences discovered several new phylum-level groups in the bacterial phylogenetic domain and many previously undetected lower-level taxa. We determined an additional ∼119 000 nearly full-length sequences and 28 000 >200 nucleotide 454 reads from a 10-layer depth profile of the GN mat. With this unprecedented coverage of long sequences from one environment, we confirm the mat is phylogenetically stratified, presumably corresponding to light and geochemical gradients throughout the depth of the mat. Previous shotgun metagenomic data from the same depth profile show the same stratified pattern and suggest that metagenome properties may be predictable from rRNA gene sequences. We verify previously identified novel lineages and identify new phylogenetic diversity at lower taxonomic levels, for example, thousands of operational taxonomic units at the family-genus levels differ considerably from known sequences. The new sequences populate parts of the bacterial phylogenetic tree that previously were poorly described, but indicate that any comprehensive survey of GN diversity has only begun. Finally, we show that taxonomic conclusions are generally congruent between Sanger and 454 sequencing technologies, with the taxonomic resolution achieved dependent on the abundance of reference sequences in the relevant region of the rRNA tree of life.

We present a case study of validating an astrophysical simulation code. Our study focuses on validating FLASH, a parallel, adaptive-mesh hydrodynamics code for studying the compressible, reactive flows found in many astrophysical environments. We describe the astrophysics problems of interest and the challenges associated with simulating these problems. We describe methodology and discuss solutions to difficulties encountered in verification and validation. We describe verification tests regularly administered to the code, present the results of new verification tests, and outline a method for testing general equations of state. We present the results of two validation tests in which we compared simulations to experimental data. The first is of a laser-driven shock propagating through a multi-layer target, a configuration subject to both Rayleigh-Taylor and Richtmyer-Meshkov instabilities. The second test is a classic Rayleigh-Taylor instability, where a heavy fluid is supported against the force of gravity by a light fluid. Our simulations of the multi-layer target experiments showed good agreement with the experimental results, but our simulations of the Rayleigh-Taylor instability did not agree well with the experimental results. We discuss our findings and present results of additional simulations undertaken to further investigate the Rayleigh-Taylor instability.Comment: 76 pages, 26 figures (3 color), Accepted for publication in the ApJ