Stability of Uniform Shear Flow

The stability of idealized shear flow at long wavelengths is studied in detail. A hydrodynamic analysis at the level of the Navier-Stokes equation for small shear rates is given to identify the origin and universality of an instability at any finite shear rate for sufficiently long wavelength perturbations. The analysis is extended to larger shear rates using a low density model kinetic equation. Direct Monte Carlo Simulation of this equation is computed with a hydrodynamic description including non Newtonian rheological effects. The hydrodynamic description of the instability is in good agreement with the direct Monte Carlo simulation for $t < 50t_0$, where $t_0$ is the mean free time. Longer time simulations up to $2000t_0$ are used to identify the asymptotic state as a spatially non-uniform quasi-stationary state. Finally, preliminary results from molecular dynamics simulation showing the instability are presented and discussed.Comment: 25 pages, 9 figures (Fig.8 is available on request) RevTeX, submitted to Phys. Rev.

Long Wavelength Instability for Uniform Shear Flow

Uniform Shear Flow is a prototype nonequilibrium state admitting detailed study at both the macroscopic and microscopic levels via theory and computer simulation. It is shown that the hydrodynamic equations for this state have a long wavelength instability. This result is obtained first from the Navier-Stokes equations and shown to apply at both low and high densities. Next, higher order rheological effects are included using a model kinetic theory. The results are compared favorably to those from Monte Carlo simulation.Comment: 12 pages, including 2 figure

Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data

The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across the order, and three gene regions. Gene trees generated using 28S rRNA, nad1 and cox1 gene data, under maximum likelihood and Bayesian approaches, are highly congruent and suggest the presence of four clades. Clade A is comprised primarily of species of Haliclona and Callyspongia, and clade B is comprised of H. simulans and H. vansoesti (Family Chalinidae), Amphimedon queenslandica (Family Niphatidae) and Tabulocalyx (Family Phloeodictyidae), Clade C is comprised primarily of members of the Families Petrosiidae and Niphatidae, while Clade D is comprised of Aka species. The polyphletic nature of the suborders, families and genera described in other studies is also found here

A model for the atomic-scale structure of a dense, nonequilibrium fluid: the homogeneous cooling state of granular fluids

It is shown that the equilibrium Generalized Mean Spherical Model of fluid structure may be extended to nonequilibrium states with equation of state information used in equilibrium replaced by an exact condition on the two-body distribution function. The model is applied to the homogeneous cooling state of granular fluids and upon comparison to molecular dynamics simulations is found to provide an accurate picture of the pair distribution function.Comment: 29 pages, 11 figures Revision corrects formatting of the figure

Allergen particle binding by human primary bronchial epithelial cells is modulated by surfactant protein D

<p>Abstract</p> <p>Background</p> <p>Allergen-containing subpollen particles (SPP) are released from whole plant pollen upon contact with water or even high humidity. Because of their size SPP can preferentially reach the lower airways where they come into contact with surfactant protein (SP)-D. Our previous work demonstrated that SP-D increases the uptake of SPP by alveolar macrophages. In the present study, we investigated the uptake of SPP in human primary epithelial cells and the potential modulation by SP-D. The patho-physiological consequence was evaluated by measurement of pro-inflammatory mediators.</p> <p>Methods</p> <p>SPP were isolated from timothy grass and subsequently fluorescently labelled. Human primary bronchial epithelial cells were incubated with SPP or polystyrene particles (PP) in the presence and absence of surfactant protein D. In addition, different sizes and surface charges of the PP were studied. Particle uptake was evaluated by flow cytometry and confocal microscopy. Soluble mediators were measured by enzyme linked immunosorbent assay or bead array.</p> <p>Results</p> <p>SPP were taken up by primary epithelial cells in a dose dependent manner. This uptake was coincided with secretion of Interleukin (IL)-8. SP-D increased the fraction of bronchial epithelial cells that bound SPP but not the fraction of cells that internalized SPP. SPP-induced secretion of IL-8 was further increased by SP-D. PP were bound and internalized by epithelial cells but this was not modulated by SP-D.</p> <p>Conclusions</p> <p>Epithelial cells bind and internalize SPP and PP which leads to increased IL-8 secretion. SP-D promotes attachment of SPP to epithelial cells and may thus be involved in the inflammatory response to inhaled allergen.</p

Speckle-tracking echocardiography in comparison with ejection fraction for prediction of cardiovascular mortality in patients with end-stage renal disease

Background. Cardiovascular disease is the major cause of death in end-stage renal disease (ESRD). To develop better means to assess cardiovascular risk in these patients, we compared conventional echocardiography-derived left ventricular ejection fraction (EF) with the novel method of 2D speckle-tracking echocardiography to determine cardiac strain.Methods. Predictive performances of conventional EF and speckle-tracking echocardiography-derived global longitudinal strain (GLS) were compared using receiver-operator curve (ROC) analyses and calibration by calibration plots. We also took into account other known cardiovascular risk factors through multivariable logistic regression analysis.Results. The study comprised 171 ESRD patients (mean age 64 years, 64% male) on maintenance dialysis therapy (93% haemodialysis, 7% peritoneal dialysis) for an average period of 39 months. During 2.1 years of follow-up, 42 patients (25%) died from cardiovascular disease. ROC analysis of GLS resulted in an area under the curve of 0.700 [95% confidence interval (CI) 0.603-0.797] compared with an area under the curve of EF of 0.615 (95% CI 0.514-0.716) (P = 0.059 for difference). The total absolute deviation between predicted and observed outcome frequencies obtained by calibration plots were 13.8% for EF compared with only 6.4% for GLS. Best results of ROC analysis (area under the curve = 0.759; P = 0.06), calibration and goodness-of-fit (chi(2) = 28.34, P <= 0.0001, R-2 = 0.25) were achieved for GLS added to a baseline model consisting of known cardiovascular risk factors in a multivariate regression analysis.Conclusions. In summary, in chronic dialysis patients, GLS is a more precise predictor of cardiovascular mortality than conventional echocardiography-derived EF.Clinical epidemiolog

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745–749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes

Structure and Dynamics of Liquid Iron under Earth's Core Conditions

First-principles molecular dynamics simulations based on density-functional theory and the projector augmented wave (PAW) technique have been used to study the structural and dynamical properties of liquid iron under Earth's core conditions. As evidence for the accuracy of the techniques, we present PAW results for a range of solid-state properties of low- and high-pressure iron, and compare them with experimental values and the results of other first-principles calculations. In the liquid-state simulations, we address particular effort to the study of finite-size effects, Brillouin-zone sampling and other sources of technical error. Results for the radial distribution function, the diffusion coefficient and the shear viscosity are presented for a wide range of thermodynamic states relevant to the Earth's core. Throughout this range, liquid iron is a close-packed simple liquid with a diffusion coefficient and viscosity similar to those of typical simple liquids under ambient conditions.Comment: 13 pages, 8 figure

Mathematical Properties of a New Levin-Type Sequence Transformation Introduced by \v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la. I. Algebraic Theory

\v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la [J. Math. Phys. \textbf{44}, 962 - 968 (2003)] introduced in connection with the summation of the divergent perturbation expansion of the hydrogen atom in an external magnetic field a new sequence transformation which uses as input data not only the elements of a sequence $\{s_n \}_{n=0}^{\infty}$ of partial sums, but also explicit estimates $\{\omega_n \}_{n=0}^{\infty}$ for the truncation errors. The explicit incorporation of the information contained in the truncation error estimates makes this and related transformations potentially much more powerful than for instance Pad\'{e} approximants. Special cases of the new transformation are sequence transformations introduced by Levin [Int. J. Comput. Math. B \textbf{3}, 371 - 388 (1973)] and Weniger [Comput. Phys. Rep. \textbf{10}, 189 - 371 (1989), Sections 7 -9; Numer. Algor. \textbf{3}, 477 - 486 (1992)] and also a variant of Richardson extrapolation [Phil. Trans. Roy. Soc. London A \textbf{226}, 299 - 349 (1927)]. The algebraic theory of these transformations - explicit expressions, recurrence formulas, explicit expressions in the case of special remainder estimates, and asymptotic order estimates satisfied by rational approximants to power series - is formulated in terms of hitherto unknown mathematical properties of the new transformation introduced by \v{C}\'{\i}\v{z}ek, Zamastil, and Sk\'{a}la. This leads to a considerable formal simplification and unification.Comment: 41 + ii pages, LaTeX2e, 0 figures. Submitted to Journal of Mathematical Physic