Three-dimensional instabilities in compressible flow over open cavities

Direct numerical simulations are performed to investigate the three-dimensional stability of compressible flow over open cavities. A linear stability analysis is conducted to search for three-dimensional global instabilities of the two-dimensional mean flow for cavities that are homogeneous in the spanwise direction. The presence of such instabilities is reported for a range of flow conditions and cavity aspect ratios. For cavities of aspect ratio (length to depth) of 2 and 4, the three-dimensional mode has a spanwise wavelength of approximately one cavity depth and oscillates with a frequency about one order of magnitude lower than two-dimensional Rossiter (flow/acoustics) instabilities. A steady mode of smaller spanwise wavelength is also identified for square cavities. The linear results indicate that the instability is hydrodynamic (rather than acoustic) in nature and arises from a generic centrifugal instability mechanism associated with the mean recirculating vortical flow in the downstream part of the cavity. These three-dimensional instabilities are related to centrifugal instabilities previously reported in flows over backward-facing steps, lid-driven cavity flows and Couette flows. Results from three-dimensional simulations of the nonlinear compressible Navier–Stokes equations are also reported. The formation of oscillating (and, in some cases, steady) spanwise structures is observed inside the cavity. The spanwise wavelength and oscillation frequency of these structures agree with the linear analysis predictions. When present, the shear-layer (Rossiter) oscillations experience a low-frequency modulation that arises from nonlinear interactions with the three-dimensional mode. The results are consistent with observations of low-frequency modulations and spanwise structures in previous experimental and numerical studies on open cavity flows

Systematic identification of gene families for use as markers for phylogenetic and phylogeny- driven ecological studies of bacteria and archaea and their major subgroups

With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families that are particularly well suited for the tasks at hand. Such gene families have generally been referred to as marker genes. We are particularly interested in identifying and using such marker genes for phylogenetic and phylogeny-driven ecological studies of microbes and their communities. We therefore refer to these as PhyEco (for phylogenetic and phylogenetic ecology) markers. The dual use of these PhyEco markers means that we needed to develop and apply a set of somewhat novel criteria for identification of the best candidates for such markers. The criteria we focused on included universality across the taxa of interest, ability to be used to produce robust phylogenetic trees that reflect as much as possible the evolution of the species from which the genes come, and low variation in copy number across taxa. We describe here an automated protocol for identifying potential PhyEco markers from a set of complete genome sequences. The protocol combines rapid searching, clustering and phylogenetic tree building algorithms to generate protein families that meet the criteria listed above. We report here the identification of PhyEco markers for different taxonomic levels including 40 for all bacteria and archaea, 114 for all bacteria, and much more for some of the individual phyla of bacteria. This new list of PhyEco markers should allow much more detailed automated phylogenetic and phylogenetic ecology analyses of these groups than possible previously.Comment: 24 pages, 3 figure

Transmission phase of a quantum dot and statistical fluctuations of partial-width amplitudes

Experimentally, the phase of the amplitude for electron transmission through a quantum dot (transmission phase) shows the same pattern between consecutive resonances. Such universal behavior, found for long sequences of resonances, is caused by correlations of the signs of the partial-width amplitudes of the resonances. We investigate the stability of these correlations in terms of a statistical model. For a classically chaotic dot, the resonance eigenfunctions are assumed to be Gaussian distributed. Under this hypothesis, statistical fluctuations are found to reduce the tendency towards universal phase evolution. Long sequences of resonances with universal behavior only persist in the semiclassical limit of very large electron numbers in the dot and for specific energy intervals. Numerical calculations qualitatively agree with the statistical model but quantitatively are closer to universality.Comment: 8 pages, 4 figure

An apertureless near-field microscope for fluorescence imaging

We describe an apertureless near field microscope for imaging fluorescent samples. Optical contrast is generated by exploiting fluorescent quenching near a metallized atomic force microscope tip. This microscope has been used to image fluorescent latex beads with subdiffraction limit resolution. The use of fluorescence allows us to prove that the contrast mechanism is indeed spectroscopic in origin

A few simple steps to improve the description of group results in neuroscience

No abstract available

Geometric Exponents of Dilute Logarithmic Minimal Models

The fractal dimensions of the hull, the external perimeter and of the red bonds are measured through Monte Carlo simulations for dilute minimal models, and compared with predictions from conformal field theory and SLE methods. The dilute models used are those first introduced by Nienhuis. Their loop fugacity is beta = -2cos(pi/barkappa}) where the parameter barkappa is linked to their description through conformal loop ensembles. It is also linked to conformal field theories through their central charges c = 13 - 6(barkappa + barkappa^{-1}) and, for the minimal models of interest here, barkappa = p/p' where p and p' are two coprime integers. The geometric exponents of the hull and external perimeter are studied for the pairs (p,p') = (1,1), (2,3), (3,4), (4,5), (5,6), (5,7), and that of the red bonds for (p,p') = (3,4). Monte Carlo upgrades are proposed for these models as well as several techniques to improve their speeds. The measured fractal dimensions are obtained by extrapolation on the lattice size H,V -> infinity. The extrapolating curves have large slopes; despite these, the measured dimensions coincide with theoretical predictions up to three or four digits. In some cases, the theoretical values lie slightly outside the confidence intervals; explanations of these small discrepancies are proposed.Comment: 41 pages, 32 figures, added reference

Review of the Synergies Between Computational Modeling and Experimental Characterization of Materials Across Length Scales

With the increasing interplay between experimental and computational approaches at multiple length scales, new research directions are emerging in materials science and computational mechanics. Such cooperative interactions find many applications in the development, characterization and design of complex material systems. This manuscript provides a broad and comprehensive overview of recent trends where predictive modeling capabilities are developed in conjunction with experiments and advanced characterization to gain a greater insight into structure-properties relationships and study various physical phenomena and mechanisms. The focus of this review is on the intersections of multiscale materials experiments and modeling relevant to the materials mechanics community. After a general discussion on the perspective from various communities, the article focuses on the latest experimental and theoretical opportunities. Emphasis is given to the role of experiments in multiscale models, including insights into how computations can be used as discovery tools for materials engineering, rather than to "simply" support experimental work. This is illustrated by examples from several application areas on structural materials. This manuscript ends with a discussion on some problems and open scientific questions that are being explored in order to advance this relatively new field of research.Comment: 25 pages, 11 figures, review article accepted for publication in J. Mater. Sc