CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

CONTRAST is a gene predictor that directly incorporates information from multiple alignments and uses discriminative machine learning techniques to give large improvements in prediction over previous methods

Modulated Crystalline-B Phases in Liquid Crystals

Detailed x-ray scattering studies of the modulated phases of 4-n-heptyloxybenzylidene-4-n-heptylaniline (7O.7) are reported. In addition to the previously identified one-dimensional modulation that appears at the transition from the crystalline-B (CrB) phase with AB AB stacking to the CrB phase with orthorhombic stacking, there are two other modulation structures each of which contains two noncolinear modulations. The modulations are explained in terms of a phenomenological model in which domains are separated by walls for which the intralayer packing is identical to the lower-temperature crystalline-G phase. This model yields the measured values for both the modulation wave vector and the lattice distortion.Engineering and Applied Science

X-Ray and Optical Studies of the Thickness Dependence of the Phase Diagram of Liquid-Crystal Films

A comprehensive study of the thickness dependence of the phase diagram of freely suspended films of the liquid crystal 4-n-heptyloxybenzylidene-4-n-heptylaniline (7O.7) between $50 and 69^{\circ}C$ is reported. In thick films (thicker than about 300 layers and characteristic of bulk samples) there is a low-temperature crystalline-G phase followed by five crystalline-B phases with different stacking arrangements at higher temperatures. In thinner films there are two additional crystalline-B phases and two tilted hexatic phases, smectic-F and smectic-I, which do not appear in bulk samples. The in-plane and interlayer correlations in the tilted hexatic phases are anisotropic with a clear dependence on the molecular tilt direction; the in-plane correlations are more developed (longer range) perpendicular to the molecular tilt direction and the interlayer correlations are more developed parallel to the tilt direction.Engineering and Applied Science

X-Ray Studies of Tilted Hexatic Phases in Thin Liquid-Crystal Films

X-ray-diffraction studies of the structures and phase transitions of the tilted hexatic phases (smectic F and smectic I) in thin liquid-crystal films of 4-n-heptyloxybenzylidene-4-n-heptylaniline (70.7) are reported. The measured correlation lengths were strongly anisotropic in both phases. The smectic-I to smectic-F transition is first order as expected from the symmetry change. The smectic-F to smectic-G transition is first order with strong pretransition effects and becomes nearly second order as the film thickness is decreased.Engineering and Applied Science

Synchrotron X-Ray Study of the Thickness Dependence of the Phase Diagram of Thin Liquid-Crystal Films

The phase diagram of freely suspended thin films of heptyloxybenzylidene-heptylaniline shows dramatic changes for thicknesses below 22 layers. The most surprising feature of the phase diagram is the inclusion of two phases lacking long-range crystalline order (smectic-F and hexatic-B phases) between two crystalline phases (crystalline smectic B and smectic G). Neither the smectic F nor the hexatic B occurs in bulk samples. Between sixteen and ten layers the width, in temperature, of the hexatic-B phase increases.Engineering and Applied Science

Synchrotron X-Ray Observation of Surface Smectic-I Hexatic Layers on Smectic-C Liquid-Crystal Films

Synchrotron x-ray diffraction methods employing a position-sensitive detector were used to study smectic-C (SmC) and smectic-I (SmI) phases in thin (2–6 molecular layers) liquid-crystal films of 4-(n-heptyloxy)benzylidene-4-(n-heptyl)aniline (7O.7). Above $\sim 78^{\circ}C$, the entire film is SmC and below $\sim 69^{\circ}C$, the entire film is SmI, a stacked tilted hexatic. Between $69^{\circ}C and 78^{\circ}C$, the surface layers of the films are hexatic SmI and the interior layers are SmC. There is a pretransitional broadening of the surface hexatic peaks as the surface layers melt into the SmC phase.Engineering and Applied Science

Dislocation Model for Restacking Phase Transitions in Crystalline-B Liquid Crystals

A dislocation-mediated model is presented for restacking phase transitions that have been observed in a variety of lamellar (liquid crystalline) systems. The model explains the existence of nonhexagonal crystalline (smectic)-B phases in terms of dislocation-induced tilting of hexagonally packed layers. Ordered dislocation arrays explain both the symmetry and the amplitude of observed modulations. It is likely that the model will also be applicable to modulated lipid-water phases.Engineering and Applied Science

Generation of small-scale structures in the developed turbulence

The Navier-Stokes equation for incompressible liquid is considered in the limit of infinitely large Reynolds number. It is assumed that the flow instability leads to generation of steady-state large-scale pulsations. The excitation and evolution of the small-scale turbulence is investigated. It is shown that the developed small-scale pulsations are intermittent. The maximal amplitude of the vorticity fluctuations is reached along the vortex filaments. Basing on the obtained solution, the pair correlation function in the limit $r\to 0$ is calculated. It is shown that the function obeys the Kolmogorov law $r^{2/3}$.Comment: 18 page

A Classifier-based approach to identify genetic similarities between diseases

Motivation: Genome-wide association studies are commonly used to identify possible associations between genetic variations and diseases. These studies mainly focus on identifying individual single nucleotide polymorphisms (SNPs) potentially linked with one disease of interest. In this work, we introduce a novel methodology that identifies similarities between diseases using information from a large number of SNPs. We separate the diseases for which we have individual genotype data into one reference disease and several query diseases. We train a classifier that distinguishes between individuals that have the reference disease and a set of control individuals. This classifier is then used to classify the individuals that have the query diseases. We can then rank query diseases according to the average classification of the individuals in each disease set, and identify which of the query diseases are more similar to the reference disease. We repeat these classification and comparison steps so that each disease is used once as reference disease

Bifurcations in annular electroconvection with an imposed shear

We report an experimental study of the primary bifurcation in electrically-driven convection in a freely suspended film. A weakly conducting, submicron thick smectic liquid crystal film was supported by concentric circular electrodes. It electroconvected when a sufficiently large voltage $V$ was applied between its inner and outer edges. The film could sustain rapid flows and yet remain strictly two-dimensional. By rotation of the inner electrode, a circular Couette shear could be independently imposed. The control parameters were a dimensionless number ${\cal R}$, analogous to the Rayleigh number, which is $\propto V^2$ and the Reynolds number ${\cal R}e$ of the azimuthal shear flow. The geometrical and material properties of the film were characterized by the radius ratio $\alpha$, and a Prandtl-like number ${\cal P}$. Using measurements of current-voltage characteristics of a large number of films, we examined the onset of electroconvection over a broad range of $\alpha$, ${\cal P}$ and ${\cal R}e$. We compared this data quantitatively to the results of linear stability theory. This could be done with essentially no adjustable parameters. The current-voltage data above onset were then used to infer the amplitude of electroconvection in the weakly nonlinear regime by fitting them to a steady-state amplitude equation of the Landau form. We show how the primary bifurcation can be tuned between supercritical and subcritical by changing $\alpha$ and ${\cal R}e$.Comment: 17 pages, 12 figures. Submitted to Phys. Rev. E. Minor changes after refereeing. See also http://mobydick.physics.utoronto.c