A simple formula for the L-gap width of a face-centered-cubic photonic crystal

The width $\triangle_L$ of the first Bragg's scattering peak in the (111) direction of a face-centered-cubic lattice of air spheres can be well approximated by a simple formula which only involves the volume averaged $\epsilon$ and $\epsilon^2$ over the lattice unit cell, $\epsilon$ being the (position dependent) dielectric constant of the medium, and the effective dielectric constant $\epsilon_{eff}$ in the long-wavelength limit approximated by Maxwell-Garnett's formula. Apparently, our formula describes the asymptotic behaviour of the absolute gap width $\triangle_L$ for high dielectric contrast $\delta$ exactly. The standard deviation $\sigma$ steadily decreases well below 1% as $\delta$ increases. For example $\sigma< 0.1$ for the sphere filling fraction $f=0.2$ and $\delta\geq 20$. On the interval $\delta\in(1,100)$, our formula still approximates the absolute gap width $\triangle_L$ (the relative gap width $\triangle_L^r$) with a reasonable precision, namely with a standard deviation 3% (4.2%) for low filling fractions up to 6.5% (8%) for the close-packed case. Differences between the case of air spheres in a dielectric and dielectric spheres in air are briefly discussed.Comment: 13 pages, 4 figs., RevTex, two references added. For more info see http://www.amolf.nl/external/wwwlab/atoms/theory/index.htm

Emission Spectrum of a Dipole in a Semi-infinite Periodic Dielectric Structure: Effect of the Boundary

The emission spectrum of a dipole embedded in a semi-infinite photonic crystal is calculated. For simplicity we study the case in which the dielectric function is sinusoidally modulated only along the direction perpendicular to the boundary surface plane. In addition to oscillations of the emission rate with the distance of the dipole from the interface we also observed that the shape of the emission spectrum srongly depends on the \em initial \em phase of the dielectric modulation. When the direction of light propagation inside the periodic structure is not normal to the boundary surface plane we observed aditional singularities in the emission spectrum, which arise due to different angle-dependence of the Bragg stop-band for $TE$ and $TM$ polarizations.Comment: 14 pages, 6 figures, to appear in Phys Rev

Angular redistribution of near-infrared emission from quantum dots in 3D photonic crystals

We study the angle-resolved spontaneous emission of near-infrared light sources in 3D photonic crystals over a wavelength range from 1200 to 1550 nm. To this end PbSe quantum dots are used as light sources inside titania inverse opal photonic crystals. Strong deviations from the Lambertian emission profile are observed. An attenuation of 60 % is observed in the angle dependent radiant flux emitted from the samples due to photonic stop bands. At angles that correspond to the edges of the stop band the emitted flux is increased by up to 34 %. This increase is explained by the redistribution of Bragg-diffracted light over the available escape angles. The results are quantitatively explained by an expanded escape-function model. This model is based on diffusion theory and adapted to photonic crystals using band structure calculations. Our results are the first angular redistributions and escape functions measured at near-infrared, including telecom, wavelengths. In addition, this is the first time for this model to be applied to describe emission from samples that are optically thick for the excitation light and relatively thin for the photoluminesence light.Comment: 24 pages, 8 figures (current format = single column, double spaced

Free energy of colloidal particles at the surface of sessile drops

The influence of finite system size on the free energy of a spherical particle floating at the surface of a sessile droplet is studied both analytically and numerically. In the special case that the contact angle at the substrate equals $\pi/2$ a capillary analogue of the method of images is applied in order to calculate small deformations of the droplet shape if an external force is applied to the particle. The type of boundary conditions for the droplet shape at the substrate determines the sign of the capillary monopole associated with the image particle. Therefore, the free energy of the particle, which is proportional to the interaction energy of the original particle with its image, can be of either sign, too. The analytic solutions, given by the Green's function of the capillary equation, are constructed such that the condition of the forces acting on the droplet being balanced and of the volume constraint are fulfilled. Besides the known phenomena of attraction of a particle to a free contact line and repulsion from a pinned one, we observe a local free energy minimum for the particle being located at the drop apex or at an intermediate angle, respectively. This peculiarity can be traced back to a non-monotonic behavior of the Green's function, which reflects the interplay between the deformations of the droplet shape and the volume constraint.Comment: 24 pages, 19 figure

Genomic diversity and differentiation of a managed island wild boar population

The evolution of island populations in natural systems is driven by local adaptation and genetic drift. However, evolutionary pathways may be altered by humans in several ways. The wild boar (WB) (Sus scrofa) is an iconic game species occurring in several islands, where it has been strongly managed since prehistoric times. We examined genomic diversity at 49 803 single-nucleotide polymorphisms in 99 Sardinian WBs and compared them with 196 wild specimens from mainland Europe and 105 domestic pigs (DP; 11 breeds). High levels of genetic variation were observed in Sardinia (80.9% of the total number of polymorphisms), which can be only in part associated to recent genetic introgression. Both Principal Component Analysis and Bayesian clustering approach revealed that the Sardinian WB population is highly differentiated from the other European populations (F ST =0.126-0.138), and from DP (F ST =0.169). Such evidences were mostly unaffected by an uneven sample size, although clustering results in reference populations changed when the number of individuals was standardized. Runs of homozygosity (ROHs) pattern and distribution in Sardinian WB are consistent with a past expansion following a bottleneck (small ROHs) and recent population substructuring (highly homozygous individuals). The observed effect of a non-random selection of Sardinian individuals on diversity, F ST and ROH estimates, stressed the importance of sampling design in the study of structured or introgressed populations. Our results support the heterogeneity and distinctiveness of the Sardinian population and prompt further investigations on its origins and conservation status.</p

Porcine colonization of the Americas: a 60k SNP story.

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Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations

Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates

Background - The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. Methodology/Principal Findings - We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO) term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologuous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. Conclusions - The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems to be selection pressure on economy in genes with a wide tissue distribution, i.e. these genes are more compact. A comparative analysis showed that the expression patterns of orthologous genes are conserved in the terrestrial vertebrates during evolutio

Strong signatures of selection in the domestic pig genome

Domestication of wild boar (Sus scrofa) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig—the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1, and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white, Patch, or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection