Perfect imaging: they don't do it with mirrors

Imaging with a spherical mirror in empty space is compared with the case when the mirror is filled with the medium of Maxwell's fish eye. Exact time-dependent solutions of Maxwell's equations show that perfect imaging is not achievable with an electrical ideal mirror on its own, but with Maxwell's fish eye in the regime when it implements a curved geometry for full electromagnetic waves

Superresolution observed from evanescent waves transmitted through nano-corrugated metallic films

Plane EM waves transmitted through nano-corrugated metallic thin films produce evanescent waves which include the information on the nano-structures. The production of the evanescent waves at the metallic surface are analyzed. A microsphere located above the metallic surface collects the evanescent waves which are converted into propagating waves. The equations for the refraction at the boundary of the microsphere and the use of Snell's law for evanescent waves are developed. The magnification of the nano-structure images is explained by a geometric optics description, but the high resolution is related to the evanescent waves properties.Comment: 12 page

Coriolis Effect in Optics: Unified Geometric Phase and Spin-Hall Effect

We examine the spin-orbit coupling effects that appear when a wave carrying intrinsic angular momentum interacts with a medium. The Berry phase is shown to be a manifestation of the Coriolis effect in a non-inertial reference frame attached to the wave. In the most general case, when both the direction of propagation and the state of the wave are varied, the phase is given by a simple expression that unifies the spin redirection Berry phase and the Pancharatnam--Berry phase. The theory is supported by the experiment demonstrating the spin-orbit coupling of electromagnetic waves via a surface plasmon nano-structure. The measurements verify the unified geometric phase, demonstrated by the observed polarization-dependent shift (spin-Hall effect) of the waves.Comment: 4 pages, 3 figure

Dendritic Spine Shape Analysis: A Clustering Perspective

Functional properties of neurons are strongly coupled with their morphology. Changes in neuronal activity alter morphological characteristics of dendritic spines. First step towards understanding the structure-function relationship is to group spines into main spine classes reported in the literature. Shape analysis of dendritic spines can help neuroscientists understand the underlying relationships. Due to unavailability of reliable automated tools, this analysis is currently performed manually which is a time-intensive and subjective task. Several studies on spine shape classification have been reported in the literature, however, there is an on-going debate on whether distinct spine shape classes exist or whether spines should be modeled through a continuum of shape variations. Another challenge is the subjectivity and bias that is introduced due to the supervised nature of classification approaches. In this paper, we aim to address these issues by presenting a clustering perspective. In this context, clustering may serve both confirmation of known patterns and discovery of new ones. We perform cluster analysis on two-photon microscopic images of spines using morphological, shape, and appearance based features and gain insights into the spine shape analysis problem. We use histogram of oriented gradients (HOG), disjunctive normal shape models (DNSM), morphological features, and intensity profile based features for cluster analysis. We use x-means to perform cluster analysis that selects the number of clusters automatically using the Bayesian information criterion (BIC). For all features, this analysis produces 4 clusters and we observe the formation of at least one cluster consisting of spines which are difficult to be assigned to a known class. This observation supports the argument of intermediate shape types.Comment: Accepted for BioImageComputing workshop at ECCV 201

STM observation of electronic wave interference effect in finite-sized graphite with dislocation-network structures

Superperiodic patterns near a step edge were observed by STM on several-layer-thick graphite sheets on a highly oriented pyrolitic graphite substrate, where a dislocation network is generated at the interface between the graphite overlayer and the substrate. Triangular- and rhombic-shaped periodic patterns whose periodicities are around 100 nm were observed on the upper terrace near the step edge. In contrast, only outlines of the patterns similar to those on the upper terrace were observed on the lower terrace. On the upper terrace, their geometrical patterns gradually disappeared and became similar to those on the lower terrace without any changes of their periodicity in increasing a bias voltage. By assuming a periodic scattering potential at the interface due to dislocations, the varying corrugation amplitudes of the patterns can be understood as changes in LDOS as a result of the beat of perturbed and unperturbed waves, i.e. the interference in an overlayer. The observed changes in the image depending on an overlayer height and a bias voltage can be explained by the electronic wave interference in the ultra-thin overlayer distorted under the influence of dislocation-network structures.Comment: 8 pages; 6 figures; Paper which a part of cond-mat/0311068 is disscussed in detai

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

Femtosecond exciton dynamics in WSe2 optical waveguides

Van-der Waals (vdW) atomically layered crystals can act as optical waveguides over a broad range of the electromagnetic spectrum ranging from Terahertz to visible. Unlike common Si-based waveguides, vdW semiconductors host strong excitonic resonances that may be controlled using non-thermal stimuli including electrostatic gating and photoexcitation. Here, we utilize waveguide modes to examine photo-induced changes of excitons in the prototypical vdW semiconductor, WSe2, prompted by femtosecond light pulses. Using time-resolved scanning near-field optical microscopy we visualize the electric field profiles of waveguide modes in real space and time and extract the temporal evolution of the optical constants following femtosecond photoexcitation. By monitoring the phase velocity of the waveguide modes, we detect incoherent A-exciton bleaching along with a coherent optical Stark shift in WSe2

Graphene photodetectors for high-speed optical communications

While silicon has dominated solid-state electronics for more than four decades, a variety of new materials have been introduced into photonics to expand the accessible wavelength range and to improve the performance of photonic devices. For example, gallium-nitride based materials enable the light emission at blue and ultraviolet wavelengths, and high index contrast silicon-on-insulator facilitates the realization of ultra dense and CMOS compatible photonic devices. Here, we report the first deployment of graphene, a two-dimensional carbon material, as the photo-detection element in a 10 Gbits/s optical data link. In this interdigitated metal-graphene-metal photodetector, an asymmetric metallization scheme is adopted to break the mirror symmetry of the built-in electric-field profile in conventional graphene field-effect-transistor channels, allowing for efficient photo-detection within the entire area of light illumination. A maximum external photo-responsivity of 6.1 mA/W is achieved at 1.55 {\mu}m wavelength, a very impressive value given that the material is below one nanometer in thickness. Moreover, owing to the unique band structure and exceptional electronic properties of graphene, high speed photodetectors with an ultra-wide operational wavelength range at least from 300 nm to 6 {\mu}m can be realized using this fascinating material.Comment: 20 pages, 3 figure

Resolving the ancestry of Austronesian-speaking populations

There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The “out-of-Taiwan” model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion