Photonic crystal surfaces represent a class of resonant optical structures that are capable of supporting high intensity electromagnetic standing waves with near-field and far-field properties that can be exploited for high sensitivity detection of biomolecules and cells. While modulation of the resonant wavelength of a photonic crystal by the dielectric permittivity of adsorbed biomaterials enables label-free detection, the resonance can also be tuned to coincide with the excitation wavelength of common fluorescent tags - including organic molecules and semiconductor quantum dots. Photonic crystals are also capable of efficiently channeling fluorescent emission into a preferred direction for enhanced extraction efficiency. Photonic crystals can be designed to support multiple resonant modes that can perform label free detection, enhanced fluorescence excitation, and enhanced fluorescence extraction simultaneously on the same device. Because photonic crystal surfaces may be inexpensively produced over large surface areas by nanoreplica molding processes, they can be incorporated into disposable labware for applications such as pharmaceutical high throughput screening. In this talk, the optical properties of surface photonic crystals will be reviewed and several applications will be described, including results from screening a 200,000-member chemical compound library for inhibitors of protein-DNA interactions, gene expression microarrays, and high sensitivity of protein biomarkers.

Chemical functionalization of bio-molecules, including hemin (an iron porphyrin) and bovine albumin onto Si (100) and GaAs (100) surfaces is reported. Spectroscopic ellipsometry analysis on the optical response of functionalized surfaces provides information on molecular coverage and effective thickness as well as the kinetics of surface attachment. Topographic features of the chemically functionalized surfaces are investigated by atomic force microscopy

Quantum dots play a promising role in the development of novel optical and biosensing devices. In this study, we investigated steady state and time-dependent luminescence properties of InGaP/ZnS core/shell colloidal quantum dots in a solution phase at room temperature. The steady state experiments exhibited an emission maximum at 650 nm with full width at half maximum of ~ 85 nm, and strong first-excitonic absorption peak at 600 nm. The time-resolved luminescence measurements depicted a bi-exponential decay profile with lifetimes of τ1 ~ 47 ns and τ2 ~ 142 ns at the emission maximum. Additionally, luminescence quenching and lifetime reduction due to resonance energy transfer between the quantum dot and an absorber are demonstrated. Our results support the plausibility of using these InGaP quantum dots as an effective alternative to highly toxic conventional Cd or Pb based colloidal quantum dots for biological applications.

In this work, we have theoretically investigated a model for the poly(2-methoxy-5(2'- ethylhexyloxy)-p-phenylenevinylene) (MEH-PPV) photodegradation based on structural models for MEH-PPV oligomers in vacuum and in solvent (chloroform). We investigated how the incorporation of oxygen and breaking of vinyl double bonds affect the absorption spectra. The theoretical results are in excellent agreement with the experimental data if we assume that the incorporation of carbonyl group is the main mechanism associated with the photodegradation processes.

Detection of important biological molecules using surface-enhanced Raman scattering (SERS) has become widely used because of the highly sensitive and label free approach offered by SERS as well as the low cytotoxic response from some SERS substrates. Gold nanoparticles are commonly used in SERS studies; however, the inherent instability of these metal nanostructures in solution adversely influences the reproducibility and quantitative nature of these measurements. Furthermore, the metal surface often denatures biomolecules upon their direct interaction. To combat this incompatibility and improve optical stability, gold nanoparticles have been encapsulated in silica shells. These Au@SiO2 nanostructures have been used extensively in cellular studies, but their SERS capabilities are generally limited to uses that include silica-entrapped SERS reporter molecules rather than direct SERS detection. This work focuses on combating these limitations via the fabrication of Au@SiO2 nanoparticles with porous silica membranes for the direct detection of target molecules in solution. Gold nanoparticles have been designed and coated with a variety of silica morphologies and subsequently interrogated using extinction spectroscopy and SERS. It will be revealed that these gold nanoparticles entrapped in silica membranes serve as optically stable substrates for the quantitative and direct detection of target molecules. These advances in nanomaterial fabrication are envisioned to impact both fundamental and applied studies in a variety of research areas including catalysis, separations, and spectroscopy.

The optical properties of hexagonal nanohole arrays in gold films are investigated. Nanosphere lithography combined with reactive ion etching has been applied as a low cost method to fabricate nanohole arrays with hexagonal symmetry where the size and spacing of the holes can be independently controlled. In this study, the spacing between the nanoholes is 600 nm with the hole diameter varied between 450 and 250 nm. The transmission spectra of the surface patterns with different film thickness are collected with normally incident light. The color of the reflected light from the nanohole array was found to change from green to red as the diameter of the holes was reduced. One application of these films is to study cell adhesion to small areas with controlled size. We explore the possibility of making isolated cell adhesion dots by chemically modifying the nanohole area. Swiss 3T3 cells were adhered onto the patterned surface and imaged using environmental SEM and fluorescent microscopy.

We have used coherent imaging fiber arrays as a platform for preparing chemical sensors and biosensors. Sensors can be made with spatially-discrete sensing sites for multi-analyte determinations. Micrometer sized sensors have been fabricated by etching the cores of an optical imaging fiber to create microwells and loading them with microspheres. These arrays possess both high sensitivity and reproducibility and can be used for making thousands of measurements simultaneously such as for genetic analysis or for the analysis of complex biological fluids. Both optical and optoelectrochemical arrays have been used for multiplexed sensing. In another scheme, the arrays can be used for single molecule detection. In this format, individual molecules, such as enzymes, can be trapped in the microwells by sealing each microwell with a silicone gasket. The enzyme molecules catalyze the formation of a fluorescent product that can be detected readily. The kinetic properties of hundreds to thousands of single enzyme molecules can be monitored simultaneously using this format. By observing the stochastic nature of the single molecule responses, new mechanistic insights into the fundamental nature of the enzymes can be obtained.

The BioCD is a spinning biochip that uses quadrature laser interferometry to detect captured protein on the disc surface. We describe the detection limits of protein binding on this optical biosensor. The fundamental metrology limit is 1 picometer for a single 100-micron diameter spot. Under assay conditions for prostate specific antigen, we can detect 25 pg/ml at 10 assays per disc.

Molecular interferometric imaging (MI2) is a label-free optical biosensor that combines common-path interferometry with shot-noise limited characteristics of a CCD array detector to detect protein binding to surfaces. In the metrology limit, it has achieved roughness-limited surface height resolution of 15 pm per 0.4 micron pixel, corresponding to a scaling mass sensitivity of 7 fg/mm, and a molecular resolution of about 15 IgG molecules per pixel. We have applied MI2 to detect cytokine interleukin-5 at a concentration detection limit of 50 pg/mL with a sandwich immunoassay. Real-time binding assays with MI2 enable the study of reaction kinetics, with a scaling mass sensitivity of 2 pg/mm under 7x magnification. Real-time MI2 measurements of anti-rabbit IgG against rabbit IgG were compared with results from surface plasmon resonance, with identical association rate constants at 5x103 M-1sec-1.

Pt-, Pd-, Ni-, and Ti-silicide films on silicon were evaluated as conducting hosts for surface plasmon polaritons (SPP) in proposed long-wave IR (LWIR) attenuated total reflection biosensors. Original LWIR complex permittivity data was collected, from which SPP properties were determined and compared with those for noble metals. LWIR SPPs on silicide films were found to offer enhanced sensitivity to thinner biological entities than when usual metal films are used.

This work proves that a 1-D porous silicon (PSi) sensor is capable of monitoring the optical changes in a polyacrylamide (PAAm) hydrogel that correlate with swelling capacity. The PSi device was impregnated with PAAm hydrogel with varying crosslinking density and total solids. The optical response of the PSi sensor was utilized to distinguish the changes in refractive index of hydrogels with varying cross-linking densities. Refractive index values calculated by the composite hydrogel-PSi sensor response agree well (≤1% difference) with values measured using a bench-top refractometer. This work serves to build a foundation for creating a composite biochemical-responsive hydrogel-PSi sensor in which competitive binding of a target analyte would cause a reduction in hydrogel cross-linking density. Long-term goals of this work are to exploit the volume sensitivity of a PSi sensor and leverage the added optical response of the responsive hydrogel to increase target detection sensitivity in an affinity based biosensor.

Combining optics and microfluidics to create a portable optofluidic photonic crystal (PhC) biosensor is an approach with promising applications in the fields of counter-terrorism, agricultural sciences, and health sciences. Presented here are fabrication processes of a gallium nitride (GaN)-based PhC biosensor with a resonance-enhanced fluorescence detection mechanism that shows potential for meeting the single molecule detection requirements of these application areas. GaN is being targeted as the photonic crystal slab material for two main reasons: its transparency in the visible spectral range, within which the excitation and emission wavelengths of the commercial fluorescent-labeling dyes fall, and its intrinsic thermal stability which provides an increased flexibility of operating in different environments. Optical modeling efforts indicate a 25-fold enhancement of the fluorescent emission in this portable fluorescentbased PhC biosensor.

Metallo-dielectric screens are periodic structures, which are at resonance with the infrared (IR) wavelength of interest: a standing wave of surface charges is formed at resonance conditions, which enables transmission or, reflection of certain IR bands. Graphene is a monolayer thick crystal of carbon. It is chemically inert and exhibits very large electronic mobility. Recently, we succeeded in fabricating mono and a few-layered suspended graphene on top of these screens. We combined these two unique components in fabricating novel platforms, which enhance IR signals of soft bio-species. Specifically, we used these platforms to examine IR spectra of a model protein, cytochrome c from a bovine heart tissue. Clear Raman signal variation as a function of platform orientation has been demonstrated. Accentuation of the IR absorption spectra was shown as well.

We develop rapid chemical vapor sensors and micro gas chromatography (μGC) analyzers based on the optofluidic ring resonator (OFRR). An OFRR is a micro-sized thin-walled glass capillary; the circular cross-section of the capillary acts as an optical ring resonator while the whispering gallery modes or circulating waveguide modes (WGMs) supported by the ring resonator interact with the vapor samples passing through the capillary. The OFRR interior surface is coated with a vapor-sensitive polymer. The analyte and polymer interaction causes the polymer refractive index (RI) and the thickness to change, which is detected as a WGM spectral shift. Owing to the excellent fluidics, the OFRR vapor sensor exhibits sub-second detection and recovery time with a flow rate of 1 mL/min. On-column separation and detection in the OFRR based μGC system is also demonstrated, showing efficient separation of vapor mixtures and presenting highly reproducible retention time for the individual analyte. Compared to the conventional GC system, the OFRR μGC has the advantage of small size, rapid response, and high selectivity over a short length of column.

Silica-on-silicon label-free biosensor with PMMA (Poly(methyl methacrylate), as the functional layer was designed, fabricated, and tested. The sensor is based on Fabry Perot (FP) interferometry. Specific binding was tested with Human IgG and anti-Human IgG. Non-specific binding was tested with Human IgG and Mouse IgG. The testing results show that the sensor has a nearly six-fold greater response upon specific binding than upon non specific binding. Thermal and long term stability experiments show that the sensor is insensitive to the environment fluctuation. The fabrication process is simple without special surface treatment. In addition, this biosensor is inexpensive and easy to use.