Green's functions technique for calculating the emission spectrum in a quantum dot-cavity system

We introduce the Green's functions technique as an alternative theory to the quantum regression theorem formalism for calculating the two-time correlation functions in open quantum systems. In particular, we investigate the potential of this theoretical approach by its application to compute the emission spectrum of a dissipative system composed by a single quantum dot inside of a semiconductor cavity. We also describe a simple algorithm based on the Green's functions technique for calculating the emission spectrum of the quantum dot as well as of the cavity which can easily be implemented in any numerical linear algebra package. We find that the Green's functions technique demonstrates a better accuracy and efficiency in the calculation of the emission spectrum and it allows to overcome the inherent theoretical difficulties associated to the direct application of the quantum regression theorem approach

Nonlinear interfaces: intrinsically nonparaxial regimes and effects

The behaviour of optical solitons at planar nonlinear boundaries is a problem rich in intrinsically nonparaxial regimes that cannot be fully addressed by theories based on the nonlinear Schrödinger equation. For instance, large propagation angles are typically involved in external refraction at interfaces. Using a recently proposed generalized Snell's law for Helmholtz solitons, we analyse two such effects: nonlinear external refraction and total internal reflection at interfaces where internal and external refraction, respectively, would be found in the absence of nonlinearity. The solutions obtained from the full numerical integration of the nonlinear Helmholtz equation show excellent agreement with the theoretical predictions

Proving universal common ancestry with similar sequences

Douglas Theobald recently developed an interesting test putatively capable of quantifying the evidence for a Universal Common Ancestry uniting the three domains of life (Eukarya, Archaea and Bacteria) against hypotheses of Independent Origins for some of these domains. We review here his model, in particular in relation to the treatment of Horizontal Gene Transfer and to the quality of sequence alignment

Helmholtz solitons in optical materials with a dual power-law refractive index

A nonlinear Helmholtz equation is proposed for modelling scalar optical beams in uniform planar waveguides whose refractive index exhibits a purely-focusing dual powerlaw dependence on the electric field amplitude. Two families of exact analytical solitons, describing forward- and backward-propagating beams, are derived. These solutions are physically and mathematically distinct from those recently discovered for related nonlinearities. The geometry of the new solitons is examined, conservation laws are reported, and classic paraxial predictions are recovered in a simultaneous multiple limit. Conventional semi-analytical techniques assist in studying the stability of these nonparaxial solitons, whose propagation properties are investigated through extensive simulations

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

We present a fast and flexible software package--SimPhy--for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer--all three potentially leading to species tree/gene tree discordance--and gene conversion. SimPhy implements a hierarchical phylogenetic model in which the evolution of species, locus, and gene trees is governed by global and local parameters (e.g., genome-wide, species-specific, locus-specific), that can be fixed or be sampled from a priori statistical distributions. SimPhy also incorporates comprehensive models of substitution rate variation among lineages (uncorrelated relaxed clocks) and the capability of simulating partitioned nucleotide, codon, and protein multilocus sequence alignments under a plethora of substitution models using the program INDELible. We validate SimPhy's output using theoretical expectations and other programs, and show that it scales extremely well with complex models and/or large trees, being an order of magnitude faster than the most similar program (DLCoal-Sim). In addition, we demonstrate how SimPhy can be useful to understand interactions among different evolutionary processes, conducting a simulation study to characterize the systematic overestimation of the duplication time when using standard reconciliation methods. SimPhy is available at https://github.com/adamallo/SimPhy, where users can find the source code, precompiled executables, a detailed manual and example cases