Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages.

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree.

Imaging performance of finite uniaxial metamaterials with large anisotropy.

Metamaterials with extreme anisotropy overcome the diffraction limit by supporting the propagation of otherwise evanescent waves. Recent experiments in slabs of wire media have shown that images deteriorate away from the longitudinal Fabry-Perot resonances of the slab. Existing theoretical models explain this using nonlocality, surface waves, and additional boundary conditions.

Two stationary nonhomogeneous Markov models of nucleotide sequence evolution.

The general Markov model (GMM) of nucleotide substitution does not assume the evolutionary process to be stationary, reversible, or homogeneous. The GMM can be simplified by assuming the evolutionary process to be stationary. A stationary GMM is appropriate for analyses of phylogenetic data sets that are compositionally homogeneous; a data set is considered to be compositionally homogeneous if a statistical test does not detect significant differences in the marginal distributions of the sequences.

Circular and elliptical birefringence in spun microstructured optical fibres.

We investigate circular birefringence induced by spinning microstructured optical fibres during their fabrication to produce helical-shaped holes. Designs with an offset core which results in a helical path for the light and exhibit only circular birefringence and designs with a linearly birefringent core that result in elliptical birefringence are both investigated.

Iridescence from photonic crystals and its suppression in butterfly scales.

Regular three-dimensional periodic structures have been observed in the scales of over half a dozen butterfly species. We compare several of these structures: we calculate their photonic bandgap properties; measure the angular variation of the reflection spectra; and relate the observed iridescence (or its suppression) to the structures. We compare the mechanisms for iridescence suppression in different species and conclude with some speculations about form, function, development and evolution.

Color, iridescence, and thermoregulation in Lepidoptera.

This paper examines evidence for the hypothesized connection between solar thermal properties of butterfly and moth (Lepidoptera) wings, iridescence/structural color, and thermoregulation. Specimens of 64 species of Lepidoptera were measured spectrophotometrically, their solar absorptances calculated, and their habitat temperatures determined. No correlation was found between habitat temperature and the solar absorptance of the wings.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours.

Many butterfly species possess 'structural' colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species.

Multi-objective and constrained design of fibre Bragg gratings using Evolutionary Algorithms.

We apply a multi-objective evolutionary algorithm to a grating problem where only very specific features of the transmission spectrum are specified during the optimisation process. The design problem analysed here relates to the passive extraction of 10 GHz clock signals from a 10 Gbps OTDM RZ encoded data stream. Four spectral features of interest such as bandwidth and passband quality are explicitly defined.

Small-core single-mode microstructured polymer optical fiber with large external diameter.

A preform sleeving technique is demonstrated that allows the fabrication of single-mode polymer microstructured fiber with the smallest core and hole dimensions yet reported to our knowledge. For a fixed triangular hole pattern a range of fibers is produced by adjustment to the operating conditions of the draw tower. Numerical modeling is carried out for one of the fibers produced with a 570-microm external diameter, a core diameter of 2.

Antisymmetric grating coupler: experimental results.

The principle of an antisymmetric grating coupler was recently proposed theoretically as a planar waveguide add-drop multiplexer. It has the potential to enhance significantly the functionality of an add-drop multiplexer based on grating-assisted coupling. Here we realize the concept experimentally in an all-fiber geometry.

Novel characterization technique with 0.5 ppm spatial accuracy of fringe period in Bragg gratings.

We demonstrate a novel method that can detect period fluctuations of periodic structures such as fiber Bragg gratings at an accuracy of approximately 0.5 ppm. These fluctuations can consist of chirp rates, phase shifts etc.

Fourier decomposition algorithm for leaky modes of fibres with arbitrary geometry.

A new algorithm for calculating the confinement loss of leaky modes in arbitrary fibre structures is presented within the scalar wave approximation. The algorithm uses a polar-coordinate Fourier decomposition method with adjustable boundary conditions (ABC-FDM) to model the outward radiating .elds.