Fluorophore Interactions with the Surface Modes and Internal Modes of a Photonic Crystal.

The metal-ligand complex tris(2,2'-bipyridine)ruthenium(II) chloride (Ru probe) displays a broad emission spectrum ranging from 540 to 730 nm. The emission spectra of Ru probe were measured when placed on top of a one-dimensional photonic crystal (1DPC), which supports both Bloch surface wave (BSW) and internal modes for wavelengths below 640 nm and only internal modes above 640 nm. The S-polarized emission spectra, with the electric vector parallel to the 1DPC surface, were found to be strongly dependent on the observation angle through the coupling prism. Also, the usual single broad-emission spectrum of Ru probe on glass was converted into two or more narrow-band-spectrum on the 1DPC, with emission band maxima dependent on the observation angle. The two S-polarized emission band peaks for Ru probe were found to be consistent with coupling to the BSW and first internal mode (IM1) of the 1DPC. The same spectral shifts and changes in emission maxima were observed by using Kretschmann and reverse Kretschmann illuminations. As the coupling requires the emitter to be in proximity with the photonic structure, we calculated near- and far-field distributions of a dipole directly located on the 1DPC surface. Finite-Difference Time-Domain (FDTD) simulations were performed to confirm fluorophore coupling to the BSW and internal modes (IMs). Both the measured and simulated results showed that IM coupled emission is significant. Coupling to the IM mode occurred at longer wavelengths where the 1DPC did not support a BSW. These results demonstrate that a simple Bragg grating, without a BSW mode, can be used for detection of surface-bound fluorophores.

Overcoming the field-of-view to diameter trade-off in microendoscopy via computational optrode-array microscopy.

High-resolution microscopy of deep tissue with large field-of-view (FOV) is critical for elucidating organization of cellular structures in plant biology. Microscopy with an implanted probe offers an effective solution. However, there exists a fundamental trade-off between the FOV and probe diameter arising from aberrations inherent in conventional imaging optics (typically, FOV < 30% of diameter). Here, we demonstrate the use of microfabricated non-imaging probes (optrodes) that when combined with a trained machine-learning algorithm is able to achieve FOV of 1x to 5x the probe diameter. Further increase in FOV is achieved by using multiple optrodes in parallel. With a 1 × 2 optrode array, we demonstrate imaging of fluorescent beads (including 30 FPS video), stained plant stem sections and stained living stems. Our demonstration lays the foundation for fast, high-resolution microscopy with large FOV in deep tissue via microfabricated non-imaging probes and advanced machine learning.

Chiroptical Response of Aluminum Nanocrescents at Ultraviolet Wavelengths.

Manipulation of plasmon modes at ultraviolet wavelengths using engineered nanophotonic devices allows for the development of high-sensitivity chiroptical spectroscopy systems. We present here an experimental framework based on aluminum-based crescent-shaped nanostructures that exhibit a strong chiroptical response at ultraviolet wavelengths. Through utilization of higher-order plasmon modes in wavelength-scale nanostructures, we address the inherent fabrication challenges in scaling the response to higher frequencies. Additionally, the distinct far-field spectral response types are analyzed within a coupled-oscillator model framework. We find two competing chiroptical response types that contribute toward potential ambiguity in the interpretation of the circular dichroism spectra. The first, optical activity, originates from the interaction between hybridized eigenmodes, whereas the second manifests as a response superficially similar to optical activity but originating instead from differential near-field absorption modes. The study of the chiroptical response from nanoplasmonic devices presented here is expected to aid the development of next-generation chiroptical spectroscopy systems.

Approaches for deep-ultraviolet surface plasmon resonance sensors.

Aluminum (Al) is a preferred metal for designing deep-ultraviolet (DUV) surface plasmon resonance (SPR)-based sensors. The native oxide layer (alumina), which grows when the Al film is exposed to air, adds an extra layer to the multilayer stack and consequently affects the DUV-SPR sensing performance. To mitigate the performance loss in DUV-SPR-based sensing, new, to the best of our knowledge, approaches are considered here. We first consider chromium, indium (In), nickel, and platinum as alternative plasmonic materials to Al. In-film-based DUV-SPR sensors exhibit the best performance parameters compared to these alternative materials. We next consider the approach of replacing the native oxide layer by an ultrathin gold (Au) layer on top of bare Al or In. With an optimal Au thickness, higher sensitivity as compared to oxidized metals is observed. The next approach adds one or more graphene layers on top of the bare metal film. In this case, the performance depends on the number of graphene layers, but improvement in sensor characteristics in the DUV is also obtained. The use of Au or graphene overlayers increases the refractive index sensing dynamic range, which can be significant for In with these overlayers under certain operating conditions.

Maskless wafer-level microfabrication of optical penetrating neural arrays out of soda-lime glass: Utah Optrode Array.

Borrowing from the wafer-level fabrication techniques of the Utah Electrode Array, an optical array capable of delivering light for neural optogenetic studies is presented in this paper: the Utah Optrode Array. Utah Optrode Arrays are micromachined out of sheet soda-lime-silica glass using standard backend processes of the semiconductor and microelectronics packaging industries such as precision diamond grinding and wet etching. 9 × 9 arrays with 1100µ m × 100µ m optrodes and a 500µ m back-plane are repeatably reproduced on 2i n wafers 169 arrays at a time. This paper describes the steps and some of the common errors of optrode fabrication.

In vivo optogenetics using a Utah Optrode Array with enhanced light output and spatial selectivity.

Optogenetics allows manipulation of neural circuits in vivo with high spatial and temporal precision. However, combining this precision with control over a significant portion of the brain is technologically challenging (especially in larger animal models). Here, we have developed, optimised, and tested in vivo, the Utah Optrode Array (UOA), an electrically addressable array of optical needles and interstitial sites illuminated by 181 µLEDs and used to optogenetically stimulate the brain. The device is specifically designed for non-human primate studies. Thinning the combined µLED and needle backplane of the device from 300 µm to 230 µm improved the efficiency of light delivery to tissue by 80%, allowing lower µLED drive currents, which improved power management and thermal performance. The spatial selectivity of each site was also improved by integrating an optical interposer to reduce stray light emission. These improvements were achieved using an innovative fabrication method to create an anodically bonded glass/silicon substrate with through-silicon vias etched, forming an optical interposer. Optical modelling was used to demonstrate that the tip structure of the device had a major influence on the illumination pattern. The thermal performance was evaluated through a combination of modelling and experiment, in order to ensure that cortical tissue temperatures did not rise by more than 1°C. The device was tested in vivo in the visual cortex of macaque expressing ChR2-tdTomato in cortical neurons. It was shown that the strongest optogenetic response occurred in the region surrounding the needle tips, and that the extent of the optogenetic response matched the predicted illumination profile based on optical modelling - demonstrating the improved spatial selectivity resulting from the optical interposer approach. Furthermore, different needle illumination sites generated different patterns of low-frequency potential (LFP) activity.

An optrode array for spatiotemporally-precise large-scale optogenetic stimulation of deep cortical layers in non-human primates.

Optogenetics has transformed studies of neural circuit function, but remains challenging to apply to non-human primates (NHPs). A major challenge is delivering intense, spatiotemporally-precise, patterned photostimulation across large volumes in deep tissue. Such stimulation is critical, for example, to modulate selectively deep-layer corticocortical feedback circuits. To address this need, we have developed the Utah Optrode Array (UOA), a 10×10 glass needle waveguide array fabricated atop a novel opaque optical interposer, and bonded to an electrically addressable µLED array. In vivo experiments with the UOA demonstrated large-scale, spatiotemporally precise, activation of deep circuits in NHP cortex. Specifically, the UOA permitted both focal (confined to single layers/columns), and widespread (multiple layers/columns) optogenetic activation of deep layer neurons, as assessed with multi-channel laminar electrode arrays, simply by varying the number of activated µLEDs and/or the irradiance. Thus, the UOA represents a powerful optoelectronic device for targeted manipulation of deep-layer circuits in NHP models.

An Optrode Array for Spatiotemporally Precise Large-Scale Optogenetic Stimulation of Deep Cortical Layers in Non-human Primates.

Optogenetics has transformed studies of neural circuit function, but remains challenging to apply in non-human primates (NHPs). A major challenge is delivering intense and spatially precise patterned photostimulation across large volumes in deep tissue. Here, we have developed and validated the Utah Optrode Array (UOA) to meet this critical need. The UOA is a 10×10 glass waveguide array bonded to an electrically-addressable µLED array. In vivo electrophysiology and immediate early gene (c-fos) immunohistochemistry demonstrated the UOA allows for large-scale spatiotemporally precise neuromodulation of deep tissue in macaque primary visual cortex. Specifically, the UOA permits both focal (single layers or columns), and large-scale (across multiple layers or columns) photostimulation of deep cortical layers, simply by varying the number of simultaneously activated µLEDs and/or the light irradiance. These results establish the UOA as a powerful tool for studying targeted neural populations within single or across multiple deep layers in complex NHP circuits.

Optical antenna design for fluorescence enhancement in the ultraviolet.

Through rational design, we compare the performance of three plasmonic antenna structures for UV fluorescence enhancement. Among the antenna performance metrics considered are the local increase in excitation intensity and the increase in quantum efficiency, the product of which represents the net fluorescence enhancement. With realistic structures in aluminum, we predict that greater than 100× net enhancement can be obtained.

Maximizing transmittance in two-photon 3D printed materials for micro-optics in the visible.

We characterize three commercial resins suitable for three-dimensional two-photon printing of mm3 volume micro-optical components for visible light - IP-S, IP-n162, and IP-Visio - under different print modes and post-processing conditions. Due to the combination of cured resin absorption and bulk scattering, we find a maximum total printed thickness of 4 mm (or greater) for at least 50% transmittance of red light, up to 2 mm for green light, and large maximum thickness variation for blue light (0.1 to 1 mm).

Exact field solution to guided wave propagation in lossy thin films.

Wave guidance is an important aspect of light trapping in thin film photovoltaics making it important to properly model the effects of loss on the field profiles. This paper derives the full-field solution for electromagnetic wave propagation in a symmetric dielectric slab with finite absorption. The functional form of the eigenvalue equation is identical to the lossless case except the propagation constants take on complex values. Additional loss-guidance and anti-guidance modes appear in the lossy model which do not normally exist in the analogous lossless case. An approximate solution for the longitudinal attenuation coefficient αz is derived from geometric optics and shows excellent agreement with the exact value. Lossy mode propagation is then explored in the context of photovoltaics by modeling a thin film solar cell made of amorphous silicon.

The paradox of multiplex DNA melting on a surface.

Under equilibrium conditions, there are two regimes of target capture on a surface--target limited and probe limited. In the probe limited regime, the melting curve from multiplex target dissociation from the surface exhibits a single transition due to a reverse displacement mechanism of the low affinity species. The melting curve cannot be used in analytical methods to resolve heteroduplexes; only with the simplex system can proper thermodynamics be obtained.

Direct DNA methylation profiling using methyl binding domain proteins.

Methylation of DNA is responsible for gene silencing by establishing heterochromatin structure that represses transcription, and studies have shown that cytosine methylation of CpG islands in promoter regions acts as a precursor to early cancer development. The naturally occurring methyl binding domain (MBD) proteins from mammals are known to bind to the methylated CpG dinucleotide (mCpG) and subsequently recruit other chromatin-modifying proteins to suppress transcription. Conventional methods of detection for methylated DNA involve bisulfite treatment or immunoprecipitation prior to performing an assay. We focus on proof-of-concept studies for a direct microarray-based assay using surface-bound methylated probes. The recombinant protein 1xMBD-GFP recognizes hemimethylation and symmetric methylation of the CpG sequence of hybridized dsDNA, while displaying greater affinity for the symmetric methylation motif, as evaluated by SPR. From these studies, for symmetric mCpG, the K(D) for 1xMBD-GFP ranged from 106 to 870 nM, depending upon the proximity of the methylation site to the sensor surface. The K(D) values for nonsymmetrical methylation motifs were consistently greater (>2 muM), but the binding selectivity between symmetric and hemimethylation motifs ranged from 4 to 30, with reduced selectivity for sites close to the surface or multiple sites in proximity, which we attribute to steric effects. Fitting skew normal probability density functions to our data, we estimate an accuracy of 97.5% for our method in identifying methylated CpG loci, which can be improved through optimization of probe design and surface density.

Optical characterization of coupled resonator slow-light rib waveguides.

We report on the design, fabrication and optical characterization of a slow light waveguide created using a linear array of coupled resonators in a large cross-section rib waveguide. Structures with as many as 25 high aspect ratio resonators are experimentally investigated. The measured propagation loss, group velocity, and delay-bandwidth product (DBP) are presented. The metric DBP/unit loss is also introduced, with a value 38/dB. Finally we discuss a method for further reducing loss in the slow-light rib waveguide.

Psychosocial mediators of a faith-based physical activity intervention: implications and lessons learned from null findings.

Mediation analyses in faith-based physical activity (PA) interventions targeting African-American adults are lacking. The purpose of this study was to examine the psychosocial mediators of a faith-based PA intervention with African-American adults. Churches were randomly assigned to receive immediate or delayed (1-year later) training in PA program implementation. A subsample of participants from randomly selected churches took part in telephone surveys at baseline and at 1 year. The primary outcome was percentage of participants meeting PA recommendations. MacKinnon's product of coefficients was used to test for mediation. Participants (n = 418) from 20 churches completed the baseline and 1-year follow-up surveys. There were no statistically significant changes in PA behavior at 1 year. The intervention had a marginally significant effect on increasing the amount of instrumental church support received by church members. However, none of the psychosocial variables tested were found to be significant mediators of the intervention. Mediation analyses provided insight into potential reasons as to why the Health-e-AME intervention did not change PA. The intervention did not successfully change the targeted mediators hypothesized to change PA. Potential reasons for these shortcomings as well as issues to address in future faith-based studies are discussed.

Quantifying Exciton Heterogeneities in Mixed-Phase Organometal Halide Multiple Quantum Wells via Stark Spectroscopy Studies.

Solution-processable two-dimensional (2D) organic-inorganic hybrid perovskite (OIHP) quantum wells naturally self-assemble through weak van der Waals forces. In this study, we investigate the structural and optoelectronic properties of 2D-layered butylammonium (C4H9NH3+, BA+) methylammonium (CH3NH3+, MA) lead iodide, (BA)2(MA)n-1PbnI3n+1 quantum wells with varying n from 1 to 4. Through conventional structural characterization, (BA)2(MA)n-1PbnI3n+1 thin films showcase high-quality phase (n) purity. However, while investigating the optoelectronic properties, it is clear that these van der Waals heterostructures consist of multiple quantum well thicknesses coexisting within a single thin film. We utilized electroabsorption spectroscopy and Liptay theory to develop an analytical tool capable of deconvoluting the excitonic features that arise from different quantum well thicknesses (n) in (BA)2(MA)n-1PbnI3n+1 thin films. To obtain a quantitative assessment of exciton heterogeneities within a thin film comprising multiple quantum well structures, exciton resonances quantified by absorption spectroscopy were modeled as Gaussian features to yield various theory-generated electroabsorption spectra, which were then fit to our experimental electroabsorption features. In addition to identifying the quantum well heterostructures present within a thin film, this novel analytical tool provides powerful insights into the exact exciton composition and can be utilized to analyze the optoelectronic properties of many other mixed-phase quantum well heterostructures beyond those formed by OIHPs. Our findings may help in designing more efficient and reproducible light-emitting diodes based on 2D mixed-phase metal-organic multiple quantum wells.

Circular photogalvanic spectroscopy of Rashba splitting in 2D hybrid organic-inorganic perovskite multiple quantum wells.

The two-dimensional (2D) Ruddlesden-Popper organic-inorganic halide perovskites such as (2D)-phenethylammonium lead iodide (2D-PEPI) have layered structure that resembles multiple quantum wells (MQW). The heavy atoms in 2D-PEPI contribute a large spin-orbit coupling that influences the electronic band structure. Upon breaking the inversion symmetry, a spin splitting ('Rashba splitting') occurs in the electronic bands. We have studied the spin splitting in 2D-PEPI single crystals using the circular photogalvanic effect (CPGE). We confirm the existence of Rashba splitting at the electronic band extrema of 35±10 meV, and identify the main inversion symmetry breaking direction perpendicular to the MQW planes. The CPGE action spectrum above the bandgap reveals spin-polarized photocurrent generated by ultrafast relaxation of excited photocarriers separated in momentum space. Whereas the helicity dependent photocurrent with below-gap excitation is due to spin-galvanic effect of the ionized spin-polarized excitons, where spin polarization occurs in the spin-split bands due to asymmetric spin-flip.

Directing polyallylamine adsorption on microlens array patterned silicon for microarray fabrication.

The selective adsorption of reagents is often essential for bioarray and lab-on-a-chip type devices. As the starting point for a bioarray, alkyl monolayer terminated silicon shards were photopatterned in a few nanoseconds with thousands of wells (spots) using an optical element, a microlens array. Polyallylamine (PAAm), a primary amine containing polymer, adsorbed with little selectivity to the spots, i.e., silicon oxide, over the hydrophobic background. However, at appropriate concentrations, addition of a cationic surfactant to the PAAm deposition solution, cetyltrimethylammonium chloride, prevented the nonspecific adsorption of PAAm onto the hydrophobic monolayer, while directing it effectively to the active spots on the device. A nonionic surfactant was less effective in preventing the nonspecific adsorption of PAAm onto the hydrophobic monolayer. The localized reactions/interactions of adsorbed PAAm with four species that are useful for bioconjugate chemistry: glutaric anhydride, phenylenediisothiocyanate, biotin NHS ester, and an oligonucleotide (DNA) were shown in the spots of an array. The reactivity of PAAm was further demonstrated with an isocyanate. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) played an important role in confirming selective surface reactivity and adsorption. X-ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry, and wetting confirmed PAAm reactivity on planar substrates.

Real-time DNA microarrays: reality check.

DNA microarrays are plagued with inconsistent quantifications and false-positive results. Using established mechanisms of surface reactions, we argue that these problems are inherent to the current technology. In particular, the problem of multiplex non-equilibrium reactions cannot be resolved within the framework of the existing paradigm. We discuss the advantages and limitations of changing the paradigm to real-time data acquisition similar to real-time PCR methodology. Our analysis suggests that the fundamental problem of multiplex reactions is not resolved by the real-time approach itself. However, by introducing new detection chemistries and analysis approaches, it is possible to extract target-specific quantitative information from real-time microarray data. The possible scope of applications for real-time microarrays is discussed.

Third-harmonic generation from arrays of sub-wavelength metal apertures.

We measure third-harmonic generation (THG) from arrays of sub-wavelength metal apertures in transmission using fundamental input at 800 nm. Samples with different aperture spacings, sizes, and shapes are used. Strong angular dependence of THG is observed, with maxima located at incidence angles corresponding to extraordinary optical transmission (EOT) for the fundamental. We demonstrate an anomalous scaling of TH intensity with aperture size, where at different EOT peaks, the TH may either increase or decrease with aperture size. The aperture shape is also shown to have a strong effect on TH output.