Three-Wave Modulational Stability and Dark Solitons in a Quadratic Nonlinear Waveguide with Grating

We consider continuous-wave (CW) states and dark solitons (DSs) in a system of two fundamental-frequency (FF) and one second-harmonic (SH) waves in a planar waveguide with the quadratic nonlinearity, the FF components being linearly coupled by resonant reflections on the Bragg grating. We demonstrate that, in contrast with the usual situation in quadratic spatial-domain models, CW states with the phase shift between the FF and SH components are modulationally stable in a broad parameter region in this system, provided that the CW wavenumber does not belong to the system's spectral gap. Stationary fundamental DSs are found numerically, and are also constructed by means of a specially devised analytical approximation. Bound states of two and three DSs are found too. The fundamental DSs and two-solitons bound states are stable in all the cases when the CW background is stable, which is shown by dint of calculation of the corresponding eigenvalues, and verified in direct simulations. Tilted DSs are found too. They attain a maximum contrast at a finite value of the tilt, that does not depend on the phase mismatch. At a maximum value of the tilt, which grows with the mismatch, the DS merges into the CW background. Interactions between the tilted solitons are shown to be completely elastic.Comment: 10 pages, 12 figures; Journal of Optics A, in pres

Conservation of a pH-sensitive structure in the C-terminal region of spider silk extends across the entire silk gene family

Spiders produce multiple silks with different physical properties that allow them to occupy a diverse range of ecological niches, including the underwater environment. Despite this functional diversity, past molecular analyses show a high degree of amino acid sequence similarity between C-terminal regions of silk genes that appear to be independent of the physical properties of the resulting silks; instead, this domain is crucial to the formation of silk fibres. Here we present an analysis of the C-terminal domain of all known types of spider silk and include silk sequences from the spider Argyroneta aquatica, which spins the majority of its silk underwater. Our work indicates that spiders have retained a highly conserved mechanism of silk assembly, despite the extraordinary diversification of species, silk types and applications of silk over 350 million years. Sequence analysis of the silk C-terminal domain across the entire gene family shows the conservation of two uncommon amino acids that are implicated in the formation of a salt bridge, a functional bond essential to protein assembly. This conservation extends to the novel sequences isolated from A. aquatica. This finding is relevant to research regarding the artificial synthesis of spider silk, suggesting that synthesis of all silk types will be possible using a single process

Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes

Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies