Self-consistent simulation of high-brightness diode lasers with external optical feedback

This paper presents a model for simulating the impact of external optical feedback on large-optical cavity high-brightness diode lasers. The simulations are performed with our 2.5D simulation tool for high-brightness laser diodes. The external cavity is modelled using commercial coherent ray tracing software. We consider the impact of the optical feedback on the excitation of amplified spontaneous emission in the parasitic vertical modes

Design and simulation of high-speed nanophotonic electro-optic modulators

In this work, an ultracompact electro-optic modulator based on refractive index modulation by plasma dispersion effect in PhC all-optical gate (AOG) is proposed. The index modulation is achieved by applying a time-varying bias voltage across the electrical contacts of the AOG. The proposed modulator has potential for high-speed operation, with bandwidths in excess of 30GHz achievable

Factors influencing brightness and beam quality of conventional and distributed Bragg reflector tapered laser diodes in absence of self-heating

In this study, the authors examine some of the factors affecting the brightness and the beam quality of high-power tapered lasers. The large volume resonators required to achieve a high-power, high-brightness operation make the beam quality sensitive to carrier lensing and a multimode operation. These cause bleaching of the regions outside the ridge waveguide. The beam quality in the conventional and the distributed Bragg reflector tapered lasers is examined in the absence of the self-heating effects to investigate the effect of the carrier lensing effects. The influence of the front facet reflectivity and the taper angle on the beam quality is investigated. The beam quality was found to degrade with an increase in the front facet reflectivity and for the larger taper angles in the conventional tapered lasers, especially at low ridge waveguide currents. Finally, the performance of the conventional tapered lasers employing a beamspoiler was assessed. The beam quality was found to be comparable with that achieved in the DBR tapered lasers

Mating ecology explains patterns of genome elimination

This research has been supported by a Royal Society University Research Fellowship (AG), a Royal Society Newton International Fellowship (LR) and two NERC Independent Research Fellowships (AG & LR).Genome elimination – whereby an individual discards chromosomes inherited from one parent, and transmits only those inherited from the other parent – is found across thousands of animal species. It is more common in association with inbreeding, under male heterogamety, in males, and in the form of paternal genome elimination. However, the reasons for this broad pattern remain unclear. We develop a mathematical model to determine how degree of inbreeding, sex determination, genomic location, pattern of gene expression and parental origin of the eliminated genome interact to determine the fate of genome-elimination alleles. We find that: inbreeding promotes paternal genome elimination in the heterogametic sex; this may incur population extinction under female heterogamety, owing to eradication of males; and extinction is averted under male heterogamety, owing to countervailing sex-ratio selection. Thus, we explain the observed pattern of genome elimination. Our results highlight the interaction between mating system, sex-ratio selection and intragenomic conflict.Publisher PDFPeer reviewe

Phylogeny of snakes (Serpentes): combining morphological and molecular data in likelihood Bayesian and parsimony analyses

Copyright © 2007 The Natural history MuseumThe phylogeny of living and fossil snakes is assessed using likelihood and parsimony approaches and a dataset combining 263 morphological characters with mitochondrial (2693 bp) and nuclear (1092 bp) gene sequences. The ‘no common mechanism’ (NCMr) and ‘Markovian’ (Mkv) models were employed for the morphological partition in likelihood analyses; likelihood scores in the NCMr model were more closely correlated with parsimony tree lengths. Both models accorded relatively less weight to the molecular data than did parsimony, with the effect being milder in the NCMr model. Partitioned branch and likelihood support values indicate that the mtDNA and nuclear gene partitions agree more closely with each other than with morphology. Despite differences between data partitions in phylogenetic signal, analytic models, and relative weighting, the parsimony and likelihood analyses all retrieved the following widely accepted groups: scolecophidians, alethinophidians, cylindrophiines, macrostomatans (sensu lato) and caenophidians. Anilius alone emerged as the most basal alethinophidian; the combined analyses resulted in a novel and stable position of uropeltines and cylindrophiines as the second-most basal clade of alethinophidians. The limbed marine pachyophiids, along with Dinilysia and Wonambi, were always basal to all living snakes. Other results stable in all combined analyses include: Xenopeltis and Loxocemus were sister taxa (fide morphology) but clustered with pythonines (fide molecules), and Ungaliophis clustered with a boine-erycine clade (fide molecules). Tropidophis remains enigmatic; it emerges as a basal alethinophidian in the parsimony analyses (fide molecules) but a derived form in the likelihood analyses (fide morphology), largely due to the different relative weighting accorded to data partitions.Michael S. Y. Lee, Andrew F. Hugall, Robin Lawson & John D. Scanlo

Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology

notes: As the primary author, O’Malley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy of biology’s standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology – including biofilm formation, chemotaxis, quorum sensing and gene transfer – that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations