Chiral Surface Waves for Enhanced Circular Dichroism

We present a novel chiral sensing platform that combines a one-dimensional photonic crystal design with a birefringent surface defect. The platform sustains simultaneous transverse electric and transverse magnetic surface modes, which are exploited to generate chiral surface waves. The present design provides homogeneous and superchiral fields of both handednesses over arbitrarily large areas in a wide spectral range, resulting in the enhancement of the circular dichroism signal by two orders of magnitude, thus paving the road toward the successful combination of surface-enhanced spectroscopies and electromagnetic superchirality.Comment: Added references. Corrected typos. Included new design for broadband chiral surface wave

Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex

BACKGROUND: Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC). PAC belongs to the Helotiales, which is one of the most diverse groups of ascomycetes including more than 2,000 species. The gene order was compared to deduce the mt genome evolution in the Pezizomycotina. Genetic variation in coding and intergenic regions of the mtDNA was studied for PAC to assess the usefulness of mt DNA for species diagnosis. RESULTS: The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) and a putative N-acetyl-transferase were recognized. A complete set of tRNA genes as well as the large and small rRNA genes but no introns were found. All protein-coding genes were confirmed by EST sequences. The gene order in P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, the only other helotialean species with a fully sequenced and annotated mt genome. Gene order analysis within Pezizomycotina suggests that the evolution of gene orders is mostly driven by transpositions. Furthermore, sequence diversity in coding and non-coding mtDNA regions in seven additional PAC species was pronounced and allowed for unequivocal species diagnosis in PAC. CONCLUSIONS: The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, which can be used as a reference for the annotation of other mt genomes in the Helotiales. In addition, our analyses show that mtDNA loci will be the marker of choice for future analysis of PAC communities

Statistical Characterization of Heterogeneous Dissolution Rates of Calcite from In situ and Real-Time AFM Imaging

Abstract The evolution of the surface topography of a calcite crystal subject to dissolution is documented through in situ real-time imaging obtained via atomic force microscopy (AFM). The dissolution process takes place by exposing the crystal surface to deionized water. AFM data allow detection of nucleation and expansion of mono- and multilayer rhombic etch pits and are employed to estimate the spreading rate of these structures. Spatially heterogeneous distributions of local dissolution rate are evaluated from the difference between topographic measurements taken at prescribed time intervals. We rest on a stochastic framework of analysis viewing the dissolution rate as a generalized sub-Gaussian (GSG) spatially correlated random process. Our analysis yields: (i) a quantitative assessment of the temporal evolution of the statistics of the dissolution rates as well as their spatial increments; (ii) a characterization of the degree of spatial correlation of dissolution rates and of the way this is linked to the various mechanisms involved in the dissolution process and highlighted through the experimental evidences. Our results indicate that the parameters driving the statistics of the GSG distribution and the spreading rate of the multilayer pits display a similar trend in time, thus suggesting that the evolution of these structures imprints the statistical features of local dissolution rates. Article Highlights We investigate dynamics of dissolution patterns on a calcite crystal in contact with deionized water via AFM imaging Temporal behavior of parameters of our statistical model is consistent with surface pattern evolution A nested model for the spatial correlation of rates embeds multiple mechanisms driving dissolution rate

Evidence for cascaded third harmonic generation in non-centrosymmetric gold nanoantennas

The optimization of nonlinear optical processes at the nanoscale is a crucial step for the development of nanoscale photon sources for quantum-optical networks. The development of innovative plasmonic nanoantenna designs and hybrid nanostructures to enhance optical nonlinearities in very small volumes represents one of the most promising routes. In such systems, the upconversion of photons can be achieved with high efficiencies via third-order processes, such as third harmonic generation (THG), thanks to the resonantly-enhanced volume currents. Conversely, second-order processes, such as second harmonic generation (SHG), are often inhibited by the symmetry of metal lattices and of common nanoantenna geometries. SHG and THG processes in plasmonic nanostructures are generally treated independently, since they both represent a small perturbation in the light-matter interaction mechanisms. In this work, we demonstrate that this paradigm does not hold in general, by providing evidence of a cascaded process in THG, which is fueled by SHG and sizably contributes to the overall yield. We address this mechanism by unveiling an anomalous fingerprint in the polarization state of the nonlinear emission from non-centrosymmetric gold nanoantennas and point out that such cascaded processes may also appear for structures that exhibit only moderate SHG yields - signifying its general relevance in plasmon-enhanced nonlinear optics. The presence of this peculiar mechanism in THG from plasmonic nanoantennas at telecommunication wavelengths allows gaining further insight on the physics of plasmon-enhanced nonlinear optical processes. This could be crucial in the realization of nanoscale elements for photon conversion and manipulation operating at room-temperature.Comment: 25 pages, 4 figure

A systematic performance evaluation of clustering methods for single-cell RNA-seq data [version 2; referees: 2 approved]

Subpopulation identification, usually via some form of unsupervised clustering, is a fundamental step in the analysis of many single-cell RNA-seq data sets. This has motivated the development and application of a broad range of clustering methods, based on various underlying algorithms. Here, we provide a systematic and extensible performance evaluation of 14 clustering algorithms implemented in R, including both methods developed explicitly for scRNA-seq data and more general-purpose methods. The methods were evaluated using nine publicly available scRNA-seq data sets as well as three simulations with varying degree of cluster separability. The same feature selection approaches were used for all methods, allowing us to focus on the investigation of the performance of the clustering algorithms themselves. We evaluated the ability of recovering known subpopulations, the stability and the run time and scalability of the methods. Additionally, we investigated whether the performance could be improved by generating consensus partitions from multiple individual clustering methods. We found substantial differences in the performance, run time and stability between the methods, with SC3 and Seurat showing the most favorable results. Additionally, we found that consensus clustering typically did not improve the performance compared to the best of the combined methods, but that several of the top-performing methods already perform some type of consensus clustering. All the code used for the evaluation is available on GitHub (https://github.com/markrobinsonuzh/scRNAseq_clustering_comparison). In addition, an R package providing access to data and clustering results, thereby facilitating inclusion of new methods and data sets, is available from Bioconductor (https://bioconductor.org/packages/DuoClustering2018)

Ordered assembling of Co tetra phenyl porphyrin on oxygen-passivated Fe(001): from single to multilayer films

Tetra-phenyl prophyrins (TPP) are an interesting class of organic molecules characterized by a ring structure with a metal ion in their centre. An ordered growth of such molecules can be obtained even on metallic substrates by means of a proper modification of the reactive interface, as we demonstrated for ZnTPP molecules coupled to oxygen-passivated Fe(001) [G. Bussetti et al. Appl. Surf. Sci. 390, 856 (2016)]. More recently, we focused on CoTPP molecules, characterized by a not nil magnetic moment and therefore of potential interest for magnetic applications. As in the ZnTPP case, our results for one monolayer coverage report the formation of an ordered assembly of flat-lying molecules. However, some differences between the two molecular species are observed in the packing scheme and in the degree of electronic interaction with the substrate. With the aim of reaching, also for CoTPP, a comprehensive view of molecular organization on Fe, we complement here our previous investigations by following the growth of the CoTPP film for increasing coverage, showing that an ordered stacking of such molecules is indeed realized at least up to four molecular layers

New twist field couplings from the partition function for multiply wrapped D-branes

We consider toroidal compactifications of bosonic string theory with particular regard to the phases (cocycles) necessary for a consistent definition of the vertex operators, the boundary states and the T-duality rules. We use these ingredients to compute the planar multi-loop partition function describing the interaction among magnetized or intersecting D-branes, also in presence of open string moduli. It turns out that unitarity in the open string channel crucially depends on the presence of the cocycles. We then focus on the 2-loop case and study the degeneration limit where this partition function is directly related to the tree-level 3-point correlators between twist fields. These correlators represent the main ingredient in the computation of Yukawa couplings and other terms in the effective action for D-brane phenomenological models. By factorizing the 2-loop partition function we are able to compute the 3-point couplings for abelian twist fields on generic non-factorized tori, thus generalizing previous expressions valid for the 2-torus.Comment: 36 pages, 1 figure; v2: typos corrected, proof in the Appendix improve

Dynamics of four-photon photoluminescence in gold nanoantennas

Two-pulse correlation is employed to investigate the temporal dynamics of both two-photon photoluminescence (2PPL) and four-photon photoluminescence (4PPL) in resonant and nonresonant nanoantennas excited at a wavelength of 800 nm. Our data are consistent with the same two-step model being the cause of both 4PPL and 2PPL, implying that the first excitation step in 4PPL is a three-photon sp->sp direct interband transition. Considering energy and parity conservation, we also explain why 4PPL behavior is favored over three-and five-photon photoluminescence in the power range below the damage threshold of our antennas. Since sizeable 4PPL requires larger peak intensities of the local field, we are able to select either 2PPL or 4PPL in the same gold nanoantennas by choosing a suitable laser pulse duration. We thus provide a first consistent model for the understanding of multiphoton photoluminescence generation in gold nanoantennas, opening new perspectives for applications ranging from the characterization of plasmonic resonances to biomedical imaging

Surfactant-like Effect and Dissolution of Ultrathin Fe Films on Ag(001)

The phase immiscibility and the excellent matching between Ag(001) and Fe(001) unit cells (mismatch 0.8 %) make Fe/Ag growth attractive in the field of low dimensionality magnetic systems. Intermixing could be drastically limited at deposition temperatures as low as 140-150 K. The film structural evolution induced by post-growth annealing presents many interesting aspects involving activated atomic exchange processes and affecting magnetic properties. Previous experiments, of He and low energy ion scattering on films deposited at 150 K, indicated the formation of a segregated Ag layer upon annealing at 550 K. Higher temperatures led to the embedding of Fe into the Ag matrix. In those experiments, information on sub-surface layers was attained by techniques mainly sensitive to the topmost layer. Here, systematic PED measurements, providing chemical selectivity and structural information for a depth of several layers, have been accompanied with a few XRD rod scans, yielding a better sensitivity to the buried interface and to the film long range order. The results of this paper allow a comparison with recent models enlightening the dissolution paths of an ultra thin metal film into a different metal, when both subsurface migration of the deposit and phase separation between substrate and deposit are favoured. The occurrence of a surfactant-like stage, in which a single layer of Ag covers the Fe film is demonstrated for films of 4-6 ML heated at 500-550 K. Evidence of a stage characterized by the formation of two Ag capping layers is also reported. As the annealing temperature was increased beyond 700 K, the surface layers closely resembled the structure of bare Ag(001) with the residual presence of subsurface Fe aggregates.Comment: 4 pages, 3 figure