Three-dimensional water impact at normal incidence to a blunt structure

The three-dimensional (3D) water impact onto a blunt structure with a spreading rectangular contact region is studied. The structure is mounted on a flat rigid plane with the impermeable curved surface of the structure perpendicular to the plane. Before impact, the water region is a rectangular domain of finite thickness bounded from below by the rigid plane and above by the flat free surface. The front free surface of the water region is vertical, representing the front of an advancing steep wave. The water region is initially advancing towards the structure at a constant uniform speed. We are concerned with the slamming loads acting on the surface of the structure during the initial stage of water impact. Air, gravity and surface tension are neglected. The problem is analysed by using some ideas of pressure-impulse theory, but including the time-dependence of the wetted area of the structure. The flow caused by the impact is 3D and incompressible. The distribution of the pressure-impulse (the time-integral of pressure) over the surface of the structure is analysed and compared with the distributions provided by strip theories. The total impulse exerted on the structure during the impact stage is evaluated and compared with numerical and experimental predictions. An example calculation is presented of water impact onto a vertical rigid cylinder. Three-dimensional effects on the slamming loads are of main concern in this study

Incompressible Fluids of the de Sitter Horizon and Beyond

There are (at least) two surfaces of particular interest in eternal de Sitter space. One is the timelike hypersurface constituting the lab wall of a static patch observer and the other is the future boundary of global de Sitter space. We study both linear and non-linear deformations of four-dimensional de Sitter space which obey the Einstein equation. Our deformations leave the induced conformal metric and trace of the extrinsic curvature unchanged for a fixed hypersurface. This hypersurface is either timelike within the static patch or spacelike in the future diamond. We require the deformations to be regular at the future horizon of the static patch observer. For linearized perturbations in the future diamond, this corresponds to imposing incoming flux solely from the future horizon of a single static patch observer. When the slices are arbitrarily close to the cosmological horizon, the finite deformations are characterized by solutions to the incompressible Navier-Stokes equation for both spacelike and timelike hypersurfaces. We then study, at the level of linearized gravity, the change in the discrete dispersion relation as we push the timelike hypersurface toward the worldline of the static patch. Finally, we study the spectrum of linearized solutions as the spacelike slices are pushed to future infinity and relate our calculations to analogous ones in the context of massless topological black holes in AdS$_4$.Comment: 27 pages, 8 figure

Rudimentary G-Quadruplex-Based Telomere Capping In Saccharomyces Cerevisiae

Telomere capping conceals chromosome ends from exonucleases and checkpoints, but the full range of capping mechanisms is not well defined. Telomeres have the potential to form G-quadruplex (G4) DNA, although evidence for telomere G4 DNA function in vivo is limited. In budding yeast, capping requires the Cdc13 protein and is lost at nonpermissive temperatures in cdc13-1 mutants. Here, we use several independent G4 DNA-stabilizing treatments to suppress cdc13-1 capping defects. These include overexpression of three different G4 DNA binding proteins, loss of the G4 DNA unwinding helicase Sgs1, or treatment with small molecule G4 DNA ligands. In vitro, we show that protein-bound G4 DNA at a 3\u27 overhang inhibits 5\u27-\u3e 3\u27 resection of a paired strand by exonuclease I. These findings demonstrate that, at least in the absence of full natural capping, G4 DNA can play a positive role at telomeres in vivo

Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA – a Bayesian approach

<p>Abstract</p> <p>Background</p> <p>Microarrays are widely used for the study of gene expression; however deciding on whether observed differences in expression are significant remains a challenge.</p> <p>Results</p> <p>A computing tool (ArrayLeaRNA) has been developed for gene expression analysis. It implements a Bayesian approach which is based on the Gumbel distribution and uses printed genomic DNA control features for normalization and for estimation of the parameters of the Bayesian model and prior knowledge from predicted operon structure. The method is compared with two other approaches: the classical LOWESS normalization followed by a two fold cut-off criterion and the OpWise method (Price, et al. 2006. BMC Bioinformatics. 7, 19), a published Bayesian approach also using predicted operon structure. The three methods were compared on experimental datasets with prior knowledge of gene expression. With ArrayLeaRNA, data normalization is carried out according to the genomic features which reflect the results of equally transcribed genes; also the statistical significance of the difference in expression is based on the variability of the equally transcribed genes. The operon information helps the classification of genes with low confidence measurements.</p> <p>ArrayLeaRNA is implemented in Visual Basic and freely available as an Excel add-in at <url>http://www.ifr.ac.uk/safety/ArrayLeaRNA/</url></p> <p>Conclusion</p> <p>We have introduced a novel Bayesian model and demonstrated that it is a robust method for analysing microarray expression profiles. ArrayLeaRNA showed a considerable improvement in data normalization, in the estimation of the experimental variability intrinsic to each hybridization and in the establishment of a clear boundary between non-changing and differentially expressed genes. The method is applicable to data derived from hybridizations of labelled cDNA samples as well as from hybridizations of labelled cDNA with genomic DNA and can be used for the analysis of datasets where differentially regulated genes predominate.</p

Streamwise-travelling viscous waves in channel flows

The unsteady viscous flow induced by streamwise-travelling waves of spanwise wall velocity in an incompressible laminar channel flow is investigated. Wall waves belonging to this category have found important practical applications, such as microfluidic flow manipulation via electro-osmosis and surface acoustic forcing and reduction of wall friction in turbulent wall-bounded flows. An analytical solution composed of the classical streamwise Poiseuille flow and a spanwise velocity profile described by the parabolic cylinder function is found. The solution depends on the bulk Reynolds number R, the scaled streamwise wavelength (Formula presented.), and the scaled wave phase speed U. Numerical solutions are discussed for various combinations of these parameters. The flow is studied by the boundary-layer theory, thereby revealing the dominant physical balances and quantifying the thickness of the near-wall spanwise flow. The Wentzel–Kramers–Brillouin–Jeffreys (WKBJ) theory is also employed to obtain an analytical solution, which is valid across the whole channel. For positive wave speeds which are smaller than or equal to the maximum streamwise velocity, a turning-point behaviour emerges through the WKBJ analysis. Between the wall and the turning point, the wall-normal viscous effects are balanced solely by the convection driven by the wall forcing, while between the turning point and the centreline, the Poiseuille convection balances the wall-normal diffusion. At the turning point, the Poiseuille convection and the convection from the wall forcing cancel each other out, which leads to a constant viscous stress and to the break down of the WKBJ solution. This flow regime is analysed through a WKBJ composite expansion and the Langer method. The Langer solution is simpler and more accurate than the WKBJ composite solution, while the latter quantifies the thickness of the turning-point region. We also discuss how these waves can be generated via surface acoustic forcing and electro-osmosis and propose their use as microfluidic flow mixing devices. For the electro-osmosis case, the Helmholtz–Smoluchowski velocity at the edge of the Debye–Hückel layer, which drives the bulk electrically neutral flow, is obtained by matched asymptotic expansion