Abstract Light-harvesting complexes in natural photosynthetic systems, such as those in purple bacteria, consist of photo-reactive chromophores embedded in densely packed “antenna” systems organized in well-defined nanostructures. In the case of purple bacteria, the chromophore antennas are composed of natural J-aggregates such as bacteriochlorophylls and carotenoids. Inspired by the molecular composition of such biological systems, we create a library of organic materials composed of densely packed J-aggregates in a polymeric matrix, in which the matrix mimics the optical role of a protein scaffold. This library of organic materials shows polaritonic properties which can be tuned from the visible to the infrared by choice of the model molecule. Inspired by the molecular architecture of the light-harvesting complexes of Rhodospirillum molischianum bacteria, we study the light–matter interactions of J-aggregate-based nanorings with similar dimensions to the analogous natural nanoscale architectures. Electromagnetic simulations show that these nanorings of J-aggregates can act as resonators, with subwavelength confinement of light while concentrating the electric field in specific regions. These results open the door to bio-inspired building blocks for metamaterials from visible to infrared in an all-organic platform, while offering a new perspective on light–matter interactions at the nanoscale in densely packed organic matter in biological organisms including photosynthetic organelles.
The evolution of homologous sequences affected by recombination or gene conversion cannot be adequately explained by a single phylogenetic tree. Many tree-based methods for sequence analysis, for example, those used for detecting sites evolving nonneutrally, have been shown to fail if such phylogenetic incongruity is ignored. However, it may be possible to propose several phylogenies that can correctly model the evolution of nonrecombinant fragments. We propose a model-based framework that uses a genetic algorithm to search a multiple-sequence alignment for putative recombination break points, quantifies the level of support for their locations, and identifies sequences or clades involved in putative recombination events. The software implementation can be run quickly and efficiently in a distributed computing environment, and various components of the methods can be chosen for computational expediency or statistical rigor. We evaluate the performance of the new method on simulated alignments and on an array of published benchmark data sets. Finally, we demonstrate that prescreening alignments with our method allows one to analyze recombinant sequences for positive selection.
The<italic>in vitro</italic>prebiotic effects of resistant starch (RS), prepared by different treatments from purple yam, on<italic>Bifidobacterium adolescentis</italic>were investigated.
It has frequently been assumed that the persistence of a deleterious mutation (the average number of generations before its loss) and its pervasiveness (the average number of individuals carrying the gene before its loss) are equal. This is true for a particular simple, widely used infinite model, but this agreement is not general. If hs ≫ 1/(4Ne), where hs is the selective disadvantage of mutant heterozygotes and Ne is the effective population number, the contribution of homozygous mutants can be neglected and the simple approximate formula 1/hs gives the mean pervasiveness. But the expected persistence is usually much smaller, 2(loge(1/2hs) 1 − γ) where γ = 0.5772. For neutral mutations, the total number of heterozygotes until fixation or loss is often the quantity of interest, and its expected value is 2Ne, with remarkable generality for various population structures. In contrast, the number of generations until fixation or loss, 2(Ne/N)(1 loge2N), is much smaller than the total number of heterozygotes. In general the number of generations is less than the number of individuals.
