The effect of avian eggshell membrane structure on microbial penetration: A simulation study.

Avian eggshells exhibit excellent antimicrobial properties. In this study, we conducted simulation experiments to explore the defense mechanisms of eggshell membranes with regards to their physical features. We developed a mathematical model for the movement of microorganisms and estimated their penetration ratio into eggshell membranes based on several factors, including membrane thickness, microbial size, directional drift, and attachment probability to membrane fibers. These results not only suggest that an eggshell membrane with multiple layers and low porosity indicates high antimicrobial performance, but also imply that the fibrous network structure of the membrane might contribute to effective defense. Our simulation results aligned with experimental findings, specifically in measuring the penetration time of Escherichia coli through the eggshell membrane. We briefly discuss the significance and limitations of this pilot study, as well as the potential for these results, to serve as a foundation for the development of antimicrobial materials.

Effect of nanostructural irregularities on structural color in the tail feathers of the Oriental magpie Pica serica.

The tail feathers of magpies are iridescent, with hues ranging from navy to violet and green. It has been previously shown that the hexagonal arrangement of melanosomes in the distal barbules is responsible for these colors, but previous simulation models have relied on average values for the parameters associated with this arrangement (e.g., periodicity), and it remains to be studied whether the actual (rather than averaged) structural arrangement and its inherent irregularities reliably predict structural color. Previous studies using unmodified images for the analysis have not focused on the effect of such irregularities on the color production. In this study, we conducted finite-difference time-domain (FDTD) simulations using actual transmission electron microscopy (TEM) images obtained from the distal barbules of a magpie tail feather, compared the reflectance spectra predicted using the FDTD simulation with those measured with a spectrometer, and found a substantial discrepancy between the two. Fourier analysis suggests that the non-uniform arrangement of the melanosomes within the barbule is responsible for this discrepancy by creating variation in the periodicity. Our results suggest that a simple model in which the parameters for internal structures are averaged cannot fully explain the variation in the structural colors observed in biological samples such as the feathers of birds.

Single-Port Coherent Perfect Loss in a Photonic Crystal Nanobeam Resonator.

We numerically demonstrated single-port coherent perfect loss (CPL) with a Fabry-Perot resonator in a photonic crystal (PC) nanobeam by using a perfect magnetic conductor (PMC)-like boundary. The CPL mode with even symmetry can be reduced to a single-port CPL when a PMC boundary is applied. The boundary which acts like a PMC boundary, here known as a PMC-like boundary, and can be realized by adjusting the phase shift of the reflection from the PC when the wavelength of the light is within the photonic bandgap wavelength range. We designed and optimized simple Fabry-Perot resonator and coupler in nanobeam to get the PMC-like boundary. To satisfy the loss condition in CPL, we controlled the coupling loss in the resonator by modifying the lattice constant of the PC used for coupling. By optimizing the coupling loss, we achieved zero reflection (CPL) in a single port with a PMC-like boundary.

Mass Fabrication of 3D Silicon Nano-/Microstructures by Fab-Free Process Using Tip-Based Lithography.

Methods for the mass fabrication of 3D silicon (Si) microstructures with a 100 nm resolution are developed using scanning probe lithography (SPL) combined with metal-assisted chemical etching (MACE). Protruding Si structures, including Si nanowires of over 10 µm in length and atypical shaped Si nano- and micropillars, are obtained via the MACE of a patterned gold film (negative tone) on Si substrates by dip-pen nanolithography (DPN) with polymer or by nanoshaving alkanethiol self-assembled monolayers (SAMs). Furthermore, recessed Si structures with arbitrary patterning and channels less than 160 nm wide and hundreds of nanometers in depth are obtained via the MACE of a patterned gold film (positive tone) on Si substrates by alkanethiol DPN. As an example of applications using protruded Si structures, nanoimprinting in an area of up to a centimeter is demonstrated through 1D and 2D SPL combined with MACE. Similarly, submicrometer polydimethylsiloxane (PDMS) stamps are employed over millimeter-scale areas for applications using recessed Si structures. In particular, the mass production of arbitrarily shaped Si microparticles at submicrometer resolution is developed using silicon-on-insulator substrates, as demonstrated using optical microresonators, surface-enhanced Raman scattering templates, and smart microparticles for fluorescence signal coding.

Bio-Photonic Waveguide of a DNA-Hybrid Semiconductor Prismatic Hexagon.

A successful identification of DNA-DNA recognition, based on the waveguide effect of a 1D hybrid prismatic hexagon crystal interfacing of DNA with an organic semiconductor is achieved. This bio-hybrid 1D crystal simultaneously discerns the complementary case at its one end against a 1-mer mismatch in 27-mer nucleic acid sequence at the other end. The loss coefficient value of this waveguide is estimated to be 0.159 µm-1 for the perfect match, which is a stark discrepancy compared to 0.244 µm-1 for the 1-mer mismatch, implying waveguide performance with a higher efficiency. These results demonstrate successfully that multiple biological interactions can be realized by the optical waveguide of the single 1D bio-hybrid-crystal and will push this class of materials into bio-related applications.

Fabrication of diffraction gratings by top-down and bottom-up approaches based on scanning probe lithography.

Generation of diffraction gratings by top-down and bottom-up approaches based on scanning probe lithography is demonstrated. With regard to top-down fabrication, silicon nanostructured diffraction gratings are fabricated through one-dimensional (1D) dip-pen-nanolithography (DPN). Nanodot arrays (two-dimensional simple cubic lattice) of alkanethiol self-assembled monolayers (SAMs) are printed by 1D DPN on an Au-film-coated silicon substrate with lattice distances of 700, 1000, and 1200 nm. Silicon nanocircular pillars of length hundreds of nanometers are generated by sequential Au etching and reactive ion etching (RIE) of the 1D DPN printed sample. The performance of the silicon diffraction gratings as a microspectrometer is demonstrated through red, green, and blue color diffraction with white light incident at 45°. Moreover, arrays of zirconia nanoparticles (NPs) with an average diameter of visible wavelength (φ ≈ 470 nm) on an Au substrate are generated via bottom-up fabrication of the diffraction gratings. Microarrays of hydrophilic alkanethiol SAMs are obtained by polymer pen lithography (PPL). Self-assembly of zirconia NPs occurs after the passivation of hydrophobic alkanethiol SAMs of the PPL-printed sample. Fraunhofer diffraction with a square aperture is observed for the zirconia NP diffraction grating fabricated by the bottom-up approach.

Enhanced absorption by coherent control in a photonic crystal resonator coupled with a microfiber.

We demonstrate enhanced absorption in a photonic crystal resonator (PCR) coupled with an optical microfiber. Enhanced absorption is based on coherent perfect absorption (CPA) that is time-reversed lasing. The PCR is fabricated on a silicon membrane with optimized parameters obtained from a numerical simulation. In an experiment, we observed 72% of absorption for the PCR with the optimized parameters. We also verified numerically that the absorption required for CPA can be tuned by changing the distance between the PCR and the optical microfiber.

Cryptic iridescence in a fossil weevil generated by single diamond photonic crystals.

Nature's most spectacular colours originate in integumentary tissue architectures that scatter light via nanoscale modulations of the refractive index. The most intricate biophotonic nanostructures are three-dimensional crystals with opal, single diamond or single gyroid lattices. Despite intense interest in their optical and structural properties, the evolution of such nanostructures is poorly understood, due in part to a lack of data from the fossil record. Here, we report preservation of single diamond (Fd-3m) three-dimensional photonic crystals in scales of a 735,000 year old specimen of the brown Nearctic weevil Hypera diversipunctata from Gold Run, Canada, and in extant conspecifics. The preserved red to green structural colours exhibit near-field brilliancy yet are inconspicuous from afar; they most likely had cryptic functions in substrate matching. The discovery of pristine fossil examples indicates that the fossil record is likely to yield further data on the evolution of three-dimensional photonic nanostructures and their biological functions.

Artificial selection for structural color on butterfly wings and comparison with natural evolution.

Brilliant animal colors often are produced from light interacting with intricate nano-morphologies present in biological materials such as butterfly wing scales. Surveys across widely divergent butterfly species have identified multiple mechanisms of structural color production; however, little is known about how these colors evolved. Here, we examine how closely related species and populations of Bicyclus butterflies have evolved violet structural color from brown-pigmented ancestors with UV structural color. We used artificial selection on a laboratory model butterfly, B. anynana, to evolve violet scales from UV brown scales and compared the mechanism of violet color production with that of two other Bicyclus species, Bicyclus sambulos and Bicyclus medontias, which have evolved violet/blue scales independently via natural selection. The UV reflectance peak of B. anynana brown scales shifted to violet over six generations of artificial selection (i.e., in less than 1 y) as the result of an increase in the thickness of the lower lamina in ground scales. Similar scale structures and the same mechanism for producing violet/blue structural colors were found in the other Bicyclus species. This work shows that populations harbor large amounts of standing genetic variation that can lead to rapid evolution of scales' structural color via slight modifications to the scales' physical dimensions.

Position-dependent diffusion of light in disordered waveguides.

We present direct experimental evidence for position-dependent diffusion in open random media. The interference of light in time-reversed paths results in renormalization of the diffusion coefficient, which varies spatially. To probe the wave transport inside the system, we fabricate two-dimensional disordered waveguides and monitor the light intensity from the third dimension. Change the geometry of the system or dissipation limits the size of the loop trajectories, allowing us to control the renormalization of the diffusion coefficient. This work shows the possibility of manipulating wave diffusion via the interplay of localization and dissipation.

Frequency-domain acquisition of fourth-order correlation by spectral intensity interferometry.

We report on the spectral intensity interferometer (SII) which is a frequency-domain variant of the fourth-order interferometry. In the SII, the power spectrum of the intensity is acquired for light fields of an interferometer. It produces a fringed spectral interferogram which can be acquired by means of an electric spectrum analyzer in keeping the relative time delay constant during the acquisition. Through both theoretical and experimental investigations, we have found that the SII interferogram provides the intensity correlation information without concern of field-sensitive disturbances which are vulnerable to minute variations of the optical paths. As an application example, a precision time-of-flight measurement was demonstrated by using a fiber-optic SII with an amplified spontaneous emission (ASE) light source. A large delay of 4.1-km long fiber was successfully analyzed from the fringe period. Its wavelength-dependent group delay or the group velocity dispersion (GVD) was also measured from the phase shift of the cosine fringe with a sub-picosecond delay precision.

Broadband subwavelength focusing of light using a passive sink.

Optical absorption is usually considered deleterious, something to avoid if at all possible. We propose a broadband nanoabsorber that completely eliminates the diffracting wave, resulting in a subwavelength enhancement of the field. Broadband operation is made possible by engineering the dispersion of the complex dielectric function. The local enhancement can be significantly improved compared to the standard plane wave illumination of a metallic nanoparticle. Our numerical simulation shows that an optical pulse as short as 6 fs can be focused to a 11 nm region. Not only the local field, but also its gradient are greatly enhanced, pointing to applications in ultrafast nonlinear spectroscopy, sensing and communication with deep-subwavelength resolution.

Bis(4,4''-difluoro-1,1':3',1''-terphenyl-2'-carboxyl-ato-κO)tetra-kis-(methanol-κO)calcium methanol tetra-solvate.

In the title compound, [Ca(C(19)H(11)F(2)O(2))(2)(CH(3)OH)(4)]·4CH(3)OH, the Ca(2+) ion is located on an inversion centre and is hexa-coordinated by two O atoms of two 4,4''-difluoro-1,1':3',1''-terphenyl-2'-carboxyl-ate ligands and four O atoms of four methanol ligands, forming a CaO(6) polyhedron with a slightly distorted octa-hedral coordination geometry. The Ca-O-C angle between the carboxyl-ate group and the calcium ion is 171.8 (2)°. Two types of inter-molecular hydrogen-bond inter-actions (C=O⋯H and O-H⋯O) between the carboxyl-ate ligand, the methanol solvent mol-ecules and the coordinating methanol ligands generate a two-dimensional network parallel to (001).

Perfect coupling of light to surface plasmons by coherent absorption.

We show theoretically that coherent light can be completely absorbed and transferred to surface plasmons in a two- or three-dimensional metallic nanostructure by exciting it with the time-reversed mode of the corresponding surface plasmon laser ("spaser"). The narrow-band perfect absorption is a generalization and application of the concept of critical coupling to a nanocavity with surface plasmon resonances. Perfect coupling of light to nanostructures has potential applications to nanoscale probing as well as background-free spectroscopy and ultrasensitive detection or sensing.

Structure and optical function of amorphous photonic nanostructures from avian feather barbs: a comparative small angle X-ray scattering (SAXS) analysis of 230 bird species.

Non-iridescent structural colours of feathers are a diverse and an important part of the phenotype of many birds. These colours are generally produced by three-dimensional, amorphous (or quasi-ordered) spongy ß-keratin and air nanostructures found in the medullary cells of feather barbs. Two main classes of three-dimensional barb nanostructures are known, characterized by a tortuous network of air channels or a close packing of spheroidal air cavities. Using synchrotron small angle X-ray scattering (SAXS) and optical spectrophotometry, we characterized the nanostructure and optical function of 297 distinctly coloured feathers from 230 species belonging to 163 genera in 51 avian families. The SAXS data provided quantitative diagnoses of the channel- and sphere-type nanostructures, and confirmed the presence of a predominant, isotropic length scale of variation in refractive index that produces strong reinforcement of a narrow band of scattered wavelengths. The SAXS structural data identified a new class of rudimentary or weakly nanostructured feathers responsible for slate-grey, and blue-grey structural colours. SAXS structural data provided good predictions of the single-scattering peak of the optical reflectance of the feathers. The SAXS structural measurements of channel- and sphere-type nanostructures are also similar to experimental scattering data from synthetic soft matter systems that self-assemble by phase separation. These results further support the hypothesis that colour-producing protein and air nanostructures in feather barbs are probably self-assembled by arrested phase separation of polymerizing ß-keratin from the cytoplasm of medullary cells. Such avian amorphous photonic nanostructures with isotropic optical properties may provide biomimetic inspiration for photonic technology.

Geometrical structure, multifractal spectra and localized optical modes of aperiodic Vogel spirals.

We present a numerical study of the structural properties, photonic density of states and bandedge modes of Vogel spiral arrays of dielectric cylinders in air. Specifically, we systematically investigate different types of Vogel spirals obtained by the modulation of the divergence angle parameter above and below the golden angle value (≈137.507°). We found that these arrays exhibit large fluctuations in the distribution of neighboring particles characterized by multifractal singularity spectra and pair correlation functions that can be tuned between amorphous and random structures. We also show that the rich structural complexity of Vogel spirals results in a multifractal photonic mode density and isotropic bandedge modes with distinctive spatial localization character. Vogel spiral structures offer the opportunity to create novel photonic devices that leverage radially localized and isotropic bandedge modes to enhance light-matter coupling, such as optical sensors, light sources, concentrators, and broadband optical couplers.

The original colours of fossil beetles.

Structural colours, the most intense, reflective and pure colours in nature, are generated when light is scattered by complex nanostructures. Metallic structural colours are widespread among modern insects and can be preserved in their fossil counterparts, but it is unclear whether the colours have been altered during fossilization, and whether the absence of colours is always real. To resolve these issues, we investigated fossil beetles from five Cenozoic biotas. Metallic colours in these specimens are generated by an epicuticular multi-layer reflector; the fidelity of its preservation correlates with that of other key cuticular ultrastructures. Where these other ultrastructures are well preserved in non-metallic fossil specimens, we can infer that the original cuticle lacked a multi-layer reflector; its absence in the fossil is not a preservational artefact. Reconstructions of the original colours of the fossils based on the structure of the multi-layer reflector show that the preserved colours are offset systematically to longer wavelengths; this probably reflects alteration of the refractive index of the epicuticle during fossilization. These findings will allow the former presence, and original hue, of metallic structural colours to be identified in diverse fossil insects, thus providing critical evidence of the evolution of structural colour in this group.

Localized photonic band edge modes and orbital angular momenta of light in a golden-angle spiral.

We present a numerical study on photonic bandgap and band edge modes in the golden-angle spiral array of air cylinders in dielectric media. Despite the lack of long-range translational and rotational order, there is a large PBG for the TE polarized light. Due to spatial inhomogeneity in the air hole spacing, the band edge modes are spatially localized by Bragg scattering from the parastichies in the spiral structure. They have discrete angular momenta that originate from different families of the parastichies whose numbers correspond to the Fibonacci numbers. The unique structural characteristics of the golden-angle spiral lead to distinctive features of the band edge modes that are absent in both photonic crystals and quasicrystals.

Fossilized biophotonic nanostructures reveal the original colors of 47-million-year-old moths.

Structural colors are generated by scattering of light by variations in tissue nanostructure. They are widespread among animals and have been studied most extensively in butterflies and moths (Lepidoptera), which exhibit the widest diversity of photonic nanostructures, resultant colors, and visual effects of any extant organism. The evolution of structural coloration in lepidopterans, however, is poorly understood. Existing hypotheses based on phylogenetic and/or structural data are controversial and do not incorporate data from fossils. Here we report the first example of structurally colored scales in fossil lepidopterans; specimens are from the 47-million-year-old Messel oil shale (Germany). The preserved colors are generated by a multilayer reflector comprised of a stack of perforated laminae in the scale lumen; differently colored scales differ in their ultrastructure. The original colors were altered during fossilization but are reconstructed based upon preserved ultrastructural detail. The dorsal surface of the forewings was a yellow-green color that probably served as a dual-purpose defensive signal, i.e. aposematic during feeding and cryptic at rest. This visual signal was enhanced by suppression of iridescence (change in hue with viewing angle) achieved via two separate optical mechanisms: extensive perforation, and concave distortion, of the multilayer reflector. The fossils provide the first evidence, to our knowledge, for the function of structural color in fossils and demonstrate the feasibility of reconstructing color in non-metallic lepidopteran fossils. Plastic scale developmental processes and complex optical mechanisms for interspecific signaling had clearly evolved in lepidopterans by the mid-Eocene.

Photonic network laser.

We demonstrated lasing in two-dimensional trivalent network structures with short-range order. Despite the lack of translational and rotational symmetries, such structures possess a large isotropic photonic bandgap. Different from those of a photonic crystal, the band-edge modes are spatially localized and have high quality factor.