From one- to two-dimensional solitons in the Ginzburg-Landau model of lasers with frequency selective feedback

We use the cubic complex Ginzburg-Landau equation coupled to a dissipative linear equation as a model of lasers with an external frequency-selective feedback. It is known that the feedback can stabilize the one-dimensional (1D) self-localized mode. We aim to extend the analysis to 2D stripe-shaped and vortex solitons. The radius of the vortices increases linearly with their topological charge, $m$, therefore the flat-stripe soliton may be interpreted as the vortex with $m=\infty$, while vortex solitons can be realized as stripes bent into rings. The results for the vortex solitons are applicable to a broad class of physical systems. There is a qualitative agreement between our results and those recently reported for models with saturable nonlinearity.Comment: Submitted to PR

Drifting instabilities of cavity solitons in vertical cavity surface-emitting lasers with frequency selective feedback

In this paper we study the formation and dynamics of self-propelled cavity solitons (CSs) in a model for vertical cavity surface-emitting lasers (VCSELs) subjected to external frequency selective feedback (FSF), and build their bifurcation diagram for the case where carrier dynamics is eliminated. For low pump currents, we find that they emerge from the modulational instability point of the trivial solution, where traveling waves with a critical wavenumber are formed. For large currents, the branch of self-propelled solitons merges with the branch of resting solitons via a pitchfork bifurcation. We also show that a feedback phase variation of 2\pi can transform a CS (whether resting or moving) into a different one associated to an adjacent longitudinal external cavity mode. Finally, we investigate the influence of the carrier dynamics, relevant for VCSELs. We find and analyze qualitative changes in the stability properties of resting CSs when increasing the carrier relaxation time. In addition to a drifting instability of resting CSs, a new kind of instability appears for certain ranges of carrier lifetime, leading to a swinging motion of the CS center position. Furthermore, for carrier relaxation times typical of VCSELs the system can display multistability of CSs.Comment: 11 pages, 12 figure

Coupled-mode theory for photonic band-gap inhibition of spatial instabilities

We study the inhibition of pattern formation in nonlinear optical systems using intracavity photonic crystals. We consider mean-field models for singly and doubly degenerate optical parametric oscillators. Analytical expressions for the new (higher) modulational thresholds and the size of the "band gap" as a function of the system and photonic crystal parameters are obtained via a coupled-mode theory. Then, by means of a nonlinear analysis, we derive amplitude equations for the unstable modes and find the stationary solutions above threshold. The form of the unstable mode is different in the lower and upper parts of the band gap. In each part there is bistability between two spatially shifted patterns. In large systems stable wall defects between the two solutions are formed and we provide analytical expressions for their shape. The analytical results are favorably compared with results obtained from the full system equations. Inhibition of pattern formation can be used to spatially control signal generation in the transverse plane

Frequency selection by soliton excitation in nondegenerate intracavity downconversion

We show that soliton excitation in intracavity downconversion naturally selects a strictly defined frequency difference between the signal and idler fields. In particular, this phenomenon implies that if the signal has smaller losses than the idler then its frequency is pulled away from the cavity resonance and the idler frequency is pulled towards the resonance and {\em vice versa}. The frequency selection is shown to be closely linked with the relative energy balance between the idler and signal fields.Comment: 5 pages, 3 figures. To appear in Phys Rev Let

Spatial correlations in hexagons generated via a Kerr nonlinearity

We consider the hexagonal pattern forming in the cross-section of an optical beam produced by a Kerr cavity, and we study the quantum correlations characterizing this structure. By using arguments related to the symmetry broken by the pattern formation, we identify a complete scenario of six-mode entanglement. Five independent phase quadratures combinations, connecting the hexagonal modes, are shown to exhibit sub-shot-noise fluctuations. By means of a non-linear quantum calculation technique, quantum correlations among the mode photon numbers are demonstrated and calculated.Comment: ReVTeX file, 20 pages, 7 eps figure

Bilateral symmetry breaking in a nonlinear Fabry-Perot cavity exhibiting optical tristability

We show the existence of a region in the parameter space that defines the field dynamics in a Fabry-Perot cylindrical cavity, where three output stable stationary states of the light are possible for a given localized incident field. Two of these states do not preserve the bilateral (i.e. left-right) symmetry of the entire system. These broken-symmetry states are the high-transmission nonlinear modes of the system. We also discuss how to excite these states.Comment: 5 pages, 5 figure

The influence of nonrandom extra-pair paternity on heritability estimates derived from wild pedigrees

Quantitative genetic analysis is often fundamental for understanding evolutionary processes in wild populations. Avian populations provide a model system due to the relative ease of inferring relatedness among individuals through observation. However, extra-pair paternity (EPP) creates erroneous links within the social pedigree. Previous work has suggested this causes minor underestimation of heritability if paternal misassignment is random and hence not influenced by the trait being studied. Nevertheless, much literature suggests numerous traits are associated with EPP and the accuracy of heritability estimates for such traits remains unexplored. We show analytically how nonrandom pedigree errors can influence heritability estimates. Then, combining empirical data from a large great tit (Parus major) pedigree with simulations, we assess how heritability estimates derived from social pedigrees change depending on the mode of the relationship between EPP and the focal trait. We show that the magnitude of the underestimation is typically small (<15%). Hence, our analyses suggest that quantitative genetic inference from pedigrees derived from observations of social relationships is relatively robust; our approach also provides a widely applicable method for assessing the consequences of nonrandom EPP

Stability of vortex solitons in a photorefractive optical lattice

Stability of off-site vortex solitons in a photorefractive optical lattice is analyzed. It is shown that such solitons are linearly unstable in both the high and low intensity limits. In the high-intensity limit, the vortex looks like a familiar ring vortex, and it suffers oscillatory instabilities. In the low-intensity limit, the vortex suffers both oscillatory and Vakhitov-Kolokolov instabilities. However, in the moderate-intensity regime, the vortex becomes stable if the lattice intensity or the applied voltage is above a certain threshold value. Stability regions of vortices are also determined at typical experimental parameters.Comment: 3 pages, 5 figure

Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

The genus Okavirus (order Nidovirales) includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein

High-Resolution Analysis of Coronavirus Gene Expression by RNA Sequencing and Ribosome Profiling.

Members of the family Coronaviridae have the largest genomes of all RNA viruses, typically in the region of 30 kilobases. Several coronaviruses, such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and Middle East respiratory syndrome-related coronavirus (MERS-CoV), are of medical importance, with high mortality rates and, in the case of SARS-CoV, significant pandemic potential. Other coronaviruses, such as Porcine epidemic diarrhea virus and Avian coronavirus, are important livestock pathogens. Ribosome profiling is a technique which exploits the capacity of the translating ribosome to protect around 30 nucleotides of mRNA from ribonuclease digestion. Ribosome-protected mRNA fragments are purified, subjected to deep sequencing and mapped back to the transcriptome to give a global "snap-shot" of translation. Parallel RNA sequencing allows normalization by transcript abundance. Here we apply ribosome profiling to cells infected with Murine coronavirus, mouse hepatitis virus, strain A59 (MHV-A59), a model coronavirus in the same genus as SARS-CoV and MERS-CoV. The data obtained allowed us to study the kinetics of virus transcription and translation with exquisite precision. We studied the timecourse of positive and negative-sense genomic and subgenomic viral RNA production and the relative translation efficiencies of the different virus ORFs. Virus mRNAs were not found to be translated more efficiently than host mRNAs; rather, virus translation dominates host translation at later time points due to high levels of virus transcripts. Triplet phasing of the profiling data allowed precise determination of translated reading frames and revealed several translated short open reading frames upstream of, or embedded within, known virus protein-coding regions. Ribosome pause sites were identified in the virus replicase polyprotein pp1a ORF and investigated experimentally. Contrary to expectations, ribosomes were not found to pause at the ribosomal frameshift site. To our knowledge this is the first application of ribosome profiling to an RNA virus.NI was supported by a Sir Henry Wellcome Postdoctoral Fellowship (Wellcome Trust, 092334/Z/10/Z). Work in the AEF lab was funded by grants from the Wellcome Trust (088789 and 106207), the U.K. Biotechnology and Biological Research Council (BBSRC) (BB/J007072/1 and BB/J015652/1), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No [646891]). Work in the IB laboratory was supported by the Medical Research Council (MRC) (MR/M011747/1) and the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/L000334/1).This is the final version of the article. It first appeared from PLOS via http://dx.doi.org/10.1371/journal.ppat.100547