Orbital Magnetization of Quantum Spin Hall Insulator Nanoparticles

Both spin and orbital degrees of freedom contribute to the magnetic moment of isolated atoms. However, when inserted in crystals, atomic orbital moments are quenched because of the lack of rotational symmetry that protects them when isolated. Thus, the dominant contribution to the magnetization of magnetic materials comes from electronic spin. Here we show that nanoislands of quantum spin Hall insulators can host robust orbital edge magnetism whenever their highest occupied Kramers doublet is singly occupied, upgrading the spin edge current into a charge current. The resulting orbital magnetization scales linearly with size, outweighing the spin contribution for islands of a few nm in size. This linear scaling is specific of the Dirac edge states and very different from Schrodinger electrons in quantum rings. Modelling Bi(111) flakes, whose edge states have been recently observed, we show that orbital magnetization is robust with respect to disorder, thermal agitation, shape of the island and crystallographic direction of the edges, reflecting its topological protection.Comment: 7 pages, 5 figures, + Supporting Informatio

Long-range spin-qubit interaction mediated by microcavity polaritons

We study the optically-induced coupling between spins mediated by polaritons in a planar micro-cavity. In the strong coupling regime, the vacuum Rabi splitting introduces anisotropies in the spin coupling. Moreover, due to their photon-like mass, polaritons provide an extremely long spin coupling range. This suggests the realization of two-qubit all-optical quantum operations within tens of picoseconds with spins localized as far as hundreds of nanometers apart.Comment: 5 pages, 3 figure

Matreex: Compact and Interactive Visualization for Scalable Studies of Large Gene Families.

Studying gene family evolution strongly benefits from insightful visualizations. However, the ever-growing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualizations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children's information. Here, we introduce Matreex, a new dynamic tool to scale up the visualization of gene families. Matreex's key idea is to use "phylogenetic" profiles, which are dense representations of gene repertoires, to minimize the information loss when collapsing subtrees. We illustrate Matreex's usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multicopy gene families. Second, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5,500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoan Thelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex's potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install Matreex) with the source code and documentation available at https://github.com/DessimozLab/matreex

Spin degree of freedom in two dimensional exciton condensates

We present a theoretical analysis of a spin-dependent multicomponent condensate in two dimensions. The case of a condensate of resonantly photoexcited excitons having two different spin orientations is studied in detail. The energy and the chemical potentials of this system depend strongly on the spin polarization . When electrons and holes are located in two different planes, the condensate can be either totally spin polarized or spin unpolarized, a property that is measurable. The phase diagram in terms of the total density and electron-hole separation is discussed.Comment: 4 pages, 3 figures, Accepted for publication in Physical Review Letter

Hybrid plasmon-magnon polaritons in graphene-antiferromagnet heterostructures

We consider a hybrid structure formed by graphene and an insulating antiferromagnet, separated by a dielectric of thickness up to $d\simeq 500 \,nm$. When uncoupled, both graphene and the antiferromagnetic surface host their own polariton modes coupling the electromagnetic field with plasmons in the case of graphene, and with magnons in the case of the antiferromagnet. We show that the hybrid structure can host two new types of hybrid polariton modes. First, a surface magnon-plasmon polariton whose dispersion is radically changed by the carrier density of the graphene layer, including a change of sign in the group velocity. Second, a surface plasmon-magnon polariton formed as a linear superposition of graphene surface plasmon and the antiferromagnetic bare magnon. This polariton has a dispersion with two branches, formed by the anticrossing between the dispersive surface plasmon and the magnon. We discuss the potential these new modes have for combining photons, magnons, and plasmons to reach new functionalities.YB, MV and NMRP acknowledge support from the European Commission through the project 'Graphene-Driven Revolutions in ICT and Beyond' (Ref. No. 785219), and the Portuguese Foundation for Science and Technology (FCT) in the framework of the Strategic Financing UID/FIS/04650/2013. Additionally, NMRP acknowledges COMPETE2020, PORTUGAL2020, FEDER and the Portuguese Foundation for Science and Technology (FCT) through project PTDC/FIS-NAN/3668/2013 and FEDER and the portuguese Foundation for Science and Technology (FCT) through project POCI-01-0145-FEDER-028114. G A Farias acknowledge support from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) of Brazil. JF-R acknowledges financial support from FCT for the P2020-PTDC/FIS-NAN/4662/2014, the P2020-PTDC/FIS-NAN/3668/2014 and the UTAPEXPL/NTec/0046/2017 projects, as well as Generalitat Valenciana funding Prometeo2017/139 and MINECO Spain (Grant No. MAT2016-78625-C2)

Insights into the Genomics of Clownfish Adaptive Radiation: Genetic Basis of the Mutualism with Sea Anemones.

Clownfishes are an iconic group of coral reef fishes, especially known for their mutualism with sea anemones. This mutualism is particularly interesting as it likely acted as the key innovation that triggered clownfish adaptive radiation. Indeed, after the acquisition of the mutualism, clownfishes diversified into multiple ecological niches linked with host and habitat use. However, despite the importance of this mutualism, the genetic mechanisms allowing clownfishes to interact with sea anemones are still unclear. Here, we used a comparative genomics and molecular evolutionary analyses to investigate the genetic basis of clownfish mutualism with sea anemones. We assembled and annotated the genome of nine clownfish species and one closely related outgroup. Orthologous genes inferred between these species and additional publicly available teleost genomes resulted in almost 16,000 genes that were tested for positively selected substitutions potentially involved in the adaptation of clownfishes to live in sea anemones. We identified 17 genes with a signal of positive selection at the origin of clownfish radiation. Two of them (Versican core protein and Protein O-GlcNAse) show particularly interesting functions associated with N-acetylated sugars, which are known to be involved in sea anemone discharge of toxins. This study provides the first insights into the genetic mechanisms of clownfish mutualism with sea anemones. Indeed, we identified the first candidate genes likely to be associated with clownfish protection form sea anemones, and thus the evolution of their mutualism. Additionally, the genomic resources acquired represent a valuable resource for further investigation of the genomic basis of clownfish adaptive radiation

Microscopic theory for quantum mirages in quantum corrals

Scanning tunneling microscopy permits to image the Kondo resonance of a single magnetic atom adsorbed on a metallic surface. When the magnetic impurity is placed at the focus of an elliptical quantum corral, a Kondo resonance has been recently observed both on top of the impurity and on top of the focus where no magnetic impurity is present. This projection of the Kondo resonance to a remote point on the surface is referred to as quantum mirage. We present a quantum mechanical theory for the quantum mirage inside an ideal quantum corral and predict that the mirage will occur in corrals with shapes other than elliptical

Electronic transport in gadolinium atomic-size contacts

We report on the fabrication, transport measurements, and density functional theory (DFT) calculations of atomic-size contacts made of gadolinium (Gd). Gd is known to have local moments mainly associated with f electrons. These coexist with itinerant s and d bands that account for its metallic character. Here we explore whether and how the local moments influence electronic transport properties at the atomic scale. Using both scanning tunneling microscope and lithographic mechanically controllable break junction techniques under cryogenic conditions, we study the conductance of Gd when only few atoms form the junction between bulk electrodes made of the very same material. Thousands of measurements show that Gd has an average lowest conductance, attributed to single-atom contact, below 2e2h. Our DFT calculations for monostrand chains anticipate that the f bands are fully spin polarized and insulating and that the conduction may be dominated by s, p, and d bands. We also analyze the electronic transport for model nanocontacts using the nonequilibrium Green's function formalism in combination with DFT. We obtain an overall good agreement with the experimental results for zero bias and show that the contribution to the electronic transport from the f channels is negligible and that from the d channels is marginal.B.O., C.S., J.F.R., J.J.P., and C.U. acknowledge financial support by MEC-Spain (Grant No. FIS2013-47328-C2 and MAT2016-78625-C2) and the Generalitat Valenciana under Grant No. PROMETEO/2012/011. C.S. and J.J.P. acknowledge the EU structural funds and the Comunidad de Madrid under NANOFRONTMAG-CM program Grant No. S2013/MIT-2850. J.L.L. and J.F.R. acknowledge Marie Curie ITN SPINOGRAPH FP7 under REA Grant Agreement No. 607904-13. B.O. acknowledges financial support by MEC Spain (Grant No. FIS2010-21883-C02-01) under brief stays abroad scholarship

First draft genome of an iconic clownfish species (Amphiprion frenatus).

Clownfishes (or anemonefishes) form an iconic group of coral reef fishes, principally known for their mutualistic interaction with sea anemones. They are characterized by particular life history traits, such as a complex social structure and mating system involving sequential hermaphroditism, coupled with an exceptionally long lifespan. Additionally, clownfishes are considered to be one of the rare groups to have experienced an adaptive radiation in the marine environment. Here, we assembled and annotated the first genome of a clownfish species, the tomato clownfish (Amphiprion frenatus). We obtained 17,801 assembled scaffolds, containing a total of 26,917 genes. The completeness of the assembly and annotation was satisfying, with 96.5% of the Actinopterygii Benchmarking Universal Single-Copy Orthologs (BUSCOs) being retrieved in A. frenatus assembly. The quality of the resulting assembly is comparable to other bony fish assemblies. This resource is valuable for advancing studies of the particular life history traits of clownfishes, as well as being useful for population genetic studies and the development of new phylogenetic markers. It will also open the way to comparative genomics. Indeed, future genomic comparison among closely related fishes may provide means to identify genes related to the unique adaptations to different sea anemone hosts, as well as better characterize the genomic signatures of an adaptive radiation

Structure of HrcQ(B)-C, a conserved component of the bacterial type III secretion systems

Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQ(B) protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQ(B)-C). Here, we report the crystal structure of HrcQ(B)-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein–protein interactions. Based on the analogies between HrcQ(B) and its flagellum homologues, we propose that HrcQ(B)-C participates in the formation of a C-ring-like assembly