Protein sensing using deep subwavelength-engineered photonic crystals.

We demonstrate a higher sensitivity detection of proteins in a photonic crystal platform by including a deep subwavelength feature in the unit cell that locally increases the energy density of light. Through both simulations and experiments, the sensing capability of a deep subwavelength-engineered silicon antislot photonic crystal nanobeam (PhCNB) cavity is compared to that of a traditional PhCNB cavity. The redistribution and local enhancement of the energy density by the 50 nm antislot enable stronger light-molecule interaction at the surface of the antislot and lead to a larger resonance shift upon protein binding. This surface-based energy enhancement is confirmed by experiments demonstrating a nearly 50% larger resonance shift upon attachment of streptavidin molecules to biotin-functionalized antislot PhCNB cavities.

Reconstitution of ß-adrenergic regulation of CaV1.2: Rad-dependent and Rad-independent protein kinase A mechanisms.

L-type voltage-gated CaV1.2 channels crucially regulate cardiac muscle contraction. Activation of ß-adrenergic receptors (ß-AR) augments contraction via protein kinase A (PKA)-induced increase of calcium influx through CaV1.2 channels. To date, the full ß-AR cascade has never been heterologously reconstituted. A recent study identified Rad, a CaV1.2 inhibitory protein, as essential for PKA regulation of CaV1.2. We corroborated this finding and reconstituted the complete pathway with agonist activation of ß1-AR or ß2-AR in Xenopus oocytes. We found, and distinguished between, two distinct pathways of PKA modulation of CaV1.2: Rad dependent (∼80% of total) and Rad independent. The reconstituted system reproduces the known features of ß-AR regulation in cardiomyocytes and reveals several aspects: the differential regulation of posttranslationally modified CaV1.2 variants and the distinct features of ß1-AR versus ß2-AR activity. This system allows for the addressing of central unresolved issues in the ß-AR-CaV1.2 cascade and will facilitate the development of therapies for catecholamine-induced cardiac pathologies.

Multiplexed Long-Range Electrohydrodynamic Transport and Nano-Optical Trapping with Cascaded Bowtie Photonic Crystal Nanobeams.

Photonic crystal cavities with bowtie defects that combine ultrahigh Q and ultralow mode volume are theoretically studied for low-power nanoscale optical trapping. By harnessing the localized heating of the water layer near the bowtie region, combined with an applied alternating current electric field, this system provides long-range electrohydrodynamic transport of particles with average radial velocities of 30 µm/s towards the bowtie region on demand by switching the input wavelength. Once transported to a given bowtie region, synergistic interaction of optical gradient and attractive negative thermophoretic forces stably trap a 10 nm quantum dot in a potential well with a depth of 10 k_{B}T using a mW input power.

Photonic crystals with split ring unit cells for subwavelength light confinement.

Here we report a photonic crystal with a split ring unit cell shape that demonstrates an order of magnitude larger peak electric field energy density compared with that of a traditional photonic crystal. Split ring photonic crystals possess several subwavelength tuning parameters, including split ring rotation angle and split width, which can be leveraged to modify light confinement for specific applications. Modifying the split ring's parameters allows for tuning of the peak electric field energy density in the split by over one order of magnitude and tuning of the air band edge wavelength by nearly 10 nm in the near infrared region. Designed to have highly focused optical energy in an accessible subwavelength gap, the split ring photonic crystal is well suited for applications including optical biosensing, optical trapping, and enhanced emission from a quantum dot or other nanoscale emitter that could be incorporated in the split.

High contrast cleavage detection for enhancing porous silicon sensor sensitivity.

Using porous silicon (PSi) interferometer sensors, we show the first experimental implementation of the high contrast cleavage detection (HCCD) mechanism. HCCD makes use of dramatic optical signal amplification caused by cleavage of high-contrast nanoparticle labeled reporters instead of the capture of low-index biological molecules. An approximately 2 nm reflectance peak shift was detected after cleavage of DNA-quantum dot reporters from the PSi surface via exposure to a 12.5 nM DNase enzyme solution. This signal change is 20 times greater than the resolution of the spectrometer used for the interferometric measurements, and the interferometric measurements agree with the response predicted by simulations and fluorescence measurements. These proof of principle experiments show a clear path to achieving a real-time, highly sensitive readout for a broad range of biological diagnostic assays that generate a signal via nucleic acid cleavage triggered by specific molecular binding events.

Peptide-Based Capture of Chikungunya Virus E2 Protein Using Porous Silicon Biosensor.

The detection of pathogens presents specific challenges in ensuring that biosensors remain operable despite exposure to elevated temperatures or other extreme conditions. The most vulnerable component of a biosensor is typically the bioreceptor. Accordingly, the robustness of peptides as bioreceptors offers improved stability and reliability toward harsh environments compared to monoclonal antibodies that may lose their ability to bind target molecules after such exposures. Here, we demonstrate peptide-based capture of the Chikungunya virus E2 protein in a porous silicon microcavity biosensor at room temperature and after exposure of the peptide-functionalized biosensor to high temperature. Contact angle measurements, attenuated total reflectance-Fourier transform infrared spectra, and optical reflectance measurements confirm peptide functionalization and selective E2 protein capture. This work opens the door for other pathogenic biomarker detection using peptide-based capture agents on porous silicon and other surface-based sensor platforms.

Histiocyte-rich rhabdomyoblastic tumor: rhabdomyosarcoma, rhabdomyoma, or rhabdomyoblastic tumor of uncertain malignant potential? A histologically distinctive rhabdomyoblastic tumor in search of a place in the classification of skeletal muscle neoplasms.

Skeletal muscle tumors are traditionally classified as rhabdomyoma or rhabdomyosarcoma. We have identified an unusual adult rhabdomyoblastic tumor not clearly corresponding to a previously described variant of rhabdomyoma or rhabdomyosarcoma, characterized by a very striking proliferation of non-neoplastic histiocytes, obscuring the underlying tumor. Ten cases were identified in nine males and one female with a median age of 43 years (range 23-69 years). Tumors involved the deep soft tissues of the trunk (N = 4), lower limbs (N = 4), and neck (N = 2). Tumors were well-circumscribed, nodular masses, frequently surrounded by a fibrous capsule containing lymphoid aggregates and sometimes calcifications. Numerous foamy macrophages, multinucleated Touton-type giant cells, and sheets/fascicles of smaller, often spindled macrophages largely obscured the underlying desmin, MyoD1, and myogenin-positive rhabdomyoblastic tumor. Cases were wild type for MYOD1 and no other mutations or rearrangements characteristic of a known subtype of rhabdomyoma or rhabdomyosarcoma were identified. Two of four cases successfully analyzed using a next-generation sequencing panel of 170 common cancer-related genes harbored inactivating NF1 mutations. Next-generation sequencing showed no gene fusions. Clinical follow (nine patients; median 9 months; mean 23 months; range 3-124 months) showed all patients received wide excision; four patients also received adjuvant radiotherapy and none received chemotherapy. At the time of last follow-up, all patients were alive and without disease; no local recurrences or distant metastases occurred. We hypothesize that these unusual tumors represent rhabdomyoblastic tumors of uncertain malignant potential. Possibly over time they should be relegated to a new category of skeletal muscle tumors of intermediate (borderline) malignancy.

Camera detection and modal fingerprinting of photonic crystal nanobeam resonances.

We demonstrate in simulation and experiment that the out-of-plane, far-field scattering profile of resonance modes in photonic crystal nanobeam (PCN) cavities can be used to identify resonance mode order. Through detection of resonantly scattered light with an infrared camera, the overlap between optical resonance modes and the leaky region of k-space can be measured experimentally. Mode order dependent overlap with the leaky region enables usage of resonance scattering as a "fingerprint" by which resonant modes in nanophotonic structures can be identified via detection in the far-field. By selectively observing emission near the PCN cavity region, the resonant scattering profile of the device can be spatially isolated and the signal noise introduced by other elements in the transmission line can be significantly reduced, consequently improving the signal to noise ratio (SNR) of resonance detection. This work demonstrates an increase in SNR of ∼ 19 dB in out-of-plane scattering measurements over in-plane transmission measurements. The capabilities demonstrated here may be applied to improve characterization across nanophotonic devices with mode-dependent spatial field profiles and enhance the utility of these devices across a variety of applications.

Photonic crystal nanobeam biosensors based on porous silicon.

Photonic crystal (PhC) nanobeams (NB) patterned on porous silicon (PSi) waveguide substrates are demonstrated for the specific, label-free detection of oligonucleotides. These photonic structures combine the large active sensing area intrinsic to PSi sensors with the high-quality (Q) factor and low-mode volume characteristic of compact resonant silicon-on-insulator (SOI) PhC NB devices. The PSi PhC NB can achieve a Q-factor near 9,000 and has an approximately 40-fold increased active sensing area for molecular attachment, compared to traditional SOI PhC NB sensors. The PSi PhC NB exhibits a resonance shift that is more than one order of magnitude larger than that of a similarly designed SOI PhC NB for the detection of small chemical molecules and 16-base peptide nucleic acids. The design and fabrication of PSi PhC NB sensors are compatible with CMOS processing, sensor arrays, and integration with lab-on-chip systems.

A smartphone biosensor based on analysing structural colour of porous silicon.

We report a smartphone compatible, low-cost porous silicon biosensor, which correlates the structural colour of a porous silicon microcavity (PSiM) to spectral peak position. Molecules captured in the PSiM cause a colour change that can be quantified through image analysis. Minimal external accessories are employed. Spectrometer measurements of the PSiM reflectance spectrum shifts are carried out concurrently with the smartphone measurements to benchmark the accuracy of the smartphone biosensor. We estimate that the smartphone biosensor supports an equivalent accuracy of 0.33 nm for the detection of colour changes corresponding to spectral shifts of the PSiM. Biosensing functionality is demonstrated using a biotin-streptavidin assay with an estimated detection limit of 500 nM. The PSiM-smartphone biosensor is a promising platform for label-free point of care diagnostics.

Realizing high transmission intensity in photonic crystal nanobeams using a side-coupling waveguide.

Side-coupled photonic crystal (PhC) nanobeam cavities were investigated to overcome challenges in measuring low-order resonances in traditional in-line PhC nanobeams that arise due to the trade-off between achieving high quality (Q)-factor and high transmission intensity resonances. On the same PhC nanobeam, we demonstrate that the side-coupling approach leads to measurable resonances even in cases in which high mirror strength unit cells severely limit the intensity of transmitted light through the in-line configuration. In addition, by coupling light directly into the cavity center, the design of side-coupled PhC nanobeams can be simplified such that high Q-factor PhC nanobeams can be achieved using only two different hole radii and uniform hole spacing.

Bloch mode selection in silicon photonic crystal microring resonators.

A novel method of selecting a subset of Bloch modes in silicon-based photonic crystal microring resonators (PhCR)s is demonstrated. Bloch modes in the PhCR are calculated, and their intensity beating patterns are analyzed. Based on the different spatial intensity distribution for each resonance, a subset of resonances is out-coupled using an output coupler waveguide (CWG) which is positioned at an angle θ=90° with respect to the input CWG. As shown in theory and experiment, resonances with an even mode number are selected, while resonances with an odd mode number are rejected. The highest contrast between mode selection and mode rejection is ∼9 dB in the experiments. This approach opens another design freedom for ring resonator-based devices and could potentially reduce the footprint of microring resonator-based multiplexers and add-drop filters.

Fibrous hamartoma of infancy: a clinicopathologic study of 145 cases, including 2 with sarcomatous features.

Fibrous hamartoma of infancy is a rare soft tissue lesion of infants and young children with characteristic triphasic morphology, which typically occurs in the axilla and less commonly in other locations. We reviewed 145 cases of fibrous hamartoma of infancy from our consultation archives. Cases occurred in 106 males and 39 females (mean age-15 months; range-birth to 14 years), and involved both typical sites (eg, axilla/back/upper arm) (n=69) and unusual locations (n=76). Six were congenital. The tumors presented as subcutaneous masses and ranged from 0.4 to 17 cm (mean 3 cm). All displayed triphasic morphology, but varied widely in the relative percentages of fat, fibroblastic fascicles, and primitive mesenchyme. Hyalinized zones with cracking artifact, mimicking giant cell fibroblastoma, were present in a 44 (30%) of cases; however FISH for PDGFB gene rearrangement was negative in five tested cases. In addition to classical fibrous hamartoma of infancy, two lesions contained large sarcomatous-appearing foci with high cellularity, high nuclear grade, and brisk mitotic activity. One occurred in a 10-month-old female as a new mass in a congenital fibrous hamartoma of infancy; the other occurred as a leg mass in a 6-year-old male. ETV6 gene rearrangement was negative in the tumor from the 10-month-old female. Genomic microarray (OncoScan) showed normal molecular karyotype in eight tested cases, whereas the two tumors with sarcomatous features showed a hyperdiploid/near tetraploid molecular karyotype with copy neutral loss of heterozygosity of chromosomes 1p and 11p, and loss of 10p, chromosome 14, and a large portion of chromosome 22q (22q11.23q13.33), respectively. Follow-up (52 patients; range: 1-208 months, median: 8 months) showed only two local recurrences and no metastases. Extensive local disease in the 10-month-old female with sarcomatous-appearing fibrous hamartoma of infancy necessitated forequarter amputation. In summary, our study confirms the classic clinicopathologic features, including the triphasic morphologic appearance of most cases. In contrast to earlier studies, our series illustrates a broader histologic spectrum than previously appreciated, including its close resemblance to giant cell fibroblastoma in one quarter of cases and the rare presence of 'sarcomatous' areas, the latter providing evidence that these are complex neoplasms rather than hamartomas.

Silicon waveguide optical switch with embedded phase change material.

Phase-change materials (PCMs) have emerged as promising active elements in silicon (Si) photonic systems. In this work, we design, fabricate, and characterize a hybrid Si-PCM optical switch. By integrating vanadium dioxide (a PCM) within a Si photonic waveguide, in a non-resonant geometry, we achieve ~10 dB broadband optical contrast with a PCM length of 500 nm using thermal actuation.

Photonic crystal microring resonator for label-free biosensing.

A label-free optical biosensor based on a one-dimensional photonic crystal microring resonator with enhanced light-matter interaction is demonstrated. More than a 2-fold improvement in volumetric and surface sensing sensitivity is achieved compared to conventional microring sensors. The experimental bulk detection sensitivity is ~248nm/RIU and label-free detection of DNA and proteins is reported at the nanomolar scale. With a minimum feature size greater than 100nm, the photonic crystal microring resonator biosensor can be fabricated with the same standard lithographic techniques used to mass fabricate conventional microring resonators.

Flow-Through Porous Silicon Membranes for Real-Time Label-Free Biosensing.

A flow-through sensing platform based on open-ended porous silicon (PSi) microcavity membranes that are compatible with integration in on-chip sensor arrays is demonstrated. Because of the high aspect ratio of PSi nanopores, the performance of closed-ended PSi sensors is limited by infiltration challenges and slow sensor responses when detecting large molecules such as proteins and nucleic acids. In order to improve molecule transport efficiency and reduce sensor response time, open-ended PSi nanopore membranes were used in a flow-through sensing scheme, allowing analyte solutions to pass through the nanopores. The molecular binding kinetics in these PSi membranes were compared through experiments and simulation with those from closed-ended PSi films of comparable thickness in a conventional flow-over sensing scheme. The flow-through PSi membrane resulted in a 6-fold improvement in sensor response time when detecting a high molecular weight analyte (streptavidin) versus in the flow-over PSi approach. This work demonstrates the possibility of integrating multiple flow-through PSi sensor membranes within parallel microarrays for rapid and multiplexed label-free biosensing.

Slow light Mach-Zehnder interferometer as label-free biosensor with scalable sensitivity.

The design, fabrication, and characterization of a label-free Mach-Zehnder interferometer (MZI) optical biosensor that incorporates a highly dispersive one-dimensional (1D) photonic crystal in one arm are presented. The sensitivity of this slow light MZI-based sensor scales with the length of the slow light photonic crystal region. The numerically simulated sensitivity of a MZI sensor with a 16 µm long slow light region is 115,000 rad/RIU-cm, which is sevenfold higher than traditional MZI biosensors with millimeter-length sensing regions. An experimental bulk refractive index detection sensitivity of 84,000 rad/RIU-cm is realized and nucleic acid detection is also demonstrated.

Hybrid Si-VO(2)-Au optical modulator based on near-field plasmonic coupling.

We present a computational design for an integrated electro-optic modulator based on near-field plasmonic coupling between gold nanodisks and a thin film of vanadium dioxide on a silicon substrate. Active modulation is achieved by applying a time-varying electric field to initiate large changes in the refractive index of vanadium dioxide. Significant decrease in device footprint (200 nm x 560 nm) and increase in extinction ratio per unit length (9 dB/µm) compared to state-of-the-art photonic and plasmonic modulators are predicted.

Porous silicon ring resonator for compact, high sensitivity biosensing applications.

A ring resonator is patterned on a porous silicon slab waveguide to produce a compact, high quality factor biosensor with a large internal surface area available for enhanced recognition of biological and chemical molecules. The porous nature of the ring resonator allows molecules to directly interact with the guided mode. Quality factors near 10,000 were measured for porous silicon ring resonators with a radius of 25 µm. A bulk detection sensitivity of 380 nm/RIU was measured upon exposure to salt water solutions. Specific detection of nucleic acid molecules was demonstrated with a surface detection sensitivity of 4 pm/nM.

Regulation of cardiac L-type Ca²âº channel CaV1.2 via the ß-adrenergic-cAMP-protein kinase A pathway: old dogmas, advances, and new uncertainties.

In the heart, adrenergic stimulation activates the ß-adrenergic receptors coupled to the heterotrimeric stimulatory Gs protein, followed by subsequent activation of adenylyl cyclase, elevation of cyclic AMP levels, and protein kinase A (PKA) activation. One of the main targets for PKA modulation is the cardiac L-type Ca²âº channel (CaV1.2) located in the plasma membrane and along the T-tubules, which mediates Ca²âº entry into cardiomyocytes. ß-Adrenergic receptor activation increases the Ca²âº current via CaV1.2 channels and is responsible for the positive ionotropic effect of adrenergic stimulation. Despite decades of research, the molecular mechanism underlying this modulation has not been fully resolved. On the contrary, initial reports of identification of key components in this modulation were later refuted using advanced model systems, especially transgenic animals. Some of the cardinal debated issues include details of specific subunits and residues in CaV1.2 phosphorylated by PKA, the nature, extent, and role of post-translational processing of CaV1.2, and the role of auxiliary proteins (such as A kinase anchoring proteins) involved in PKA regulation. In addition, the previously proposed crucial role of PKA in modulation of unstimulated Ca²âº current in the absence of ß-adrenergic receptor stimulation and in voltage-dependent facilitation of CaV1.2 remains uncertain. Full reconstitution of the ß-adrenergic receptor signaling pathway in heterologous expression systems remains an unmet challenge. This review summarizes the past and new findings, the mechanisms proposed and later proven, rejected or disputed, and emphasizes the essential issues that remain unresolved.