The silicon photonic wire evanescent field (PWEF) sensor platform offers the advantages of small sensor size, high levels of function integration, and low cost manufacturing that comes with the use of established semiconductor fabrication processes. The technology should be fully compatible with existing infrastructure in molecular analysis and research and the manufactured sensor array chip cost should be low enough that the chips can be considered disposable. Furthermore, since many applications require simultaneous monitoring of many different simultaneous binding reactions, the possibility of integrating tens or even hundreds of independent molecular sensors on a single disposable sensor chip is very compelling. We present an overview of our multiplexed photonic wire sensor chip and a reader instrument that allows up to 128 independent binding reactions to be monitored simultaneously [1]. A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is discussed. This microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria based on polyclonal antibody probe molecules. A coherent detection scheme that enables direct read-out of the optical phase and an order of magnitude enhancement of sensitivity compared to conventional detection is also discussed [2]. Finally, we present advances in Fourier-transform interferometer arrays for spectroscopic sensing. A planar waveguide Fourier-transform spectrometer with densely arrayed Mach-Zehnder interferometers is presented. Subwavelength gratings are used to produce an optical path difference without waveguide bends. The fabricated device comprises of an array of 32 Mach-Zehnder interferometers, which produce a spatial interferogram without any moving parts, yielding a spectral resolution of 50 pm and a free-spectral range of 0.78 nm. As a result of similar propagation losses in subwavelength grating waveguides and conventional strip waveguides- loss imbalance is minimized and high interferometric extinction ratio of -25 to -30 dB is obtained. Furthermore, phase and amplitude errors arising from normal fabrication variation are compensated by the spectral retrieval process using calibration measurements [3].

A complete photonic wire molecular biosensor microarray chip architecture and supporting instrumentation is described. Chip layouts with 16 and 128 independent sensors have been fabricated and tested, where each sensor can provide an independent molecular binding curve. Each sensor is 50 μm in diameter, and consists of a millimeter long silicon photonic wire waveguide folded into a spiral ring resonator. An array of 128 sensors occupies a 2 × 2 mm2 area on a 6 × 9 mm2 chip. Microfluidic sample delivery channels are fabricated monolithically on the chip. The size and layout of the sensor array is fully compatible with commercial spotting tools designed to independently functionalize fluorescence based biochips. The sensor chips are interrogated using an instrument that delivers sample fluid to the chip and is capable of acquiring up to 128 optical sensor outputs simultaneously and in real time. Coupling light from the sensor chip is accomplished through arrays of sub-wavelength surface grating couplers, and the signals are collected by a fixed two-dimensional detector array. The chip and instrument are designed so that connection of the fluid delivery system and optical alignment are automated, and can be completed in a few seconds with no active user input. This microarray system is used to demonstrate a multiplexed assay for serotyping E. coli bacteria using serospecific polyclonal antibody probe molecules.

We are developing a photonic wire evanescent field (PWEF) sensor chip using 260 nm x 450 nm cross-section silicon photonic wire waveguides. The waveguide mode is strongly localized near the silicon surface, so that light interacts strongly with molecules bound to the waveguide surface. The millimeter long sensor waveguides can be folded into tight spiral structures less than 200 micrometers in diameter, which can be arrayed at densities up to ten or more independent sensors per square millimeter. The long propagation length in each sensor element gives a response to molecular binding much better than currently available tools for label-free molecular sensing. Cost of instrumentation, cost per measurement, ease-of-use, and the number of sensors that can be simultaneously monitored on a sensor array chip are equally important in determining whether an instrument is practical for the end user and hence commercially viable. The objective of our recent work on PWEF sensor array chips and the associated instrumentation is to address all of these issues. This conference paper reviews our ongoing work on the photonic wire sensor chip design and layout, on-chip integrated fluidics, optical coupling, and chip interrogation using arrays of grating couplers formed using subwavelength patterned structures.

We report on a new waveguide principle using subwavelength gratings. It is known that diffraction effects are suppressed for waves propagating in materials structured at the subwavelength scale. Subwavelength gratings can create artificial media engineered using microscopic inhomogeneities to enact effective macroscopic behaviour. For the high-index-contrast waveguides, a subwavelength grating can be created by the combination of high-refractive-index and low-refractive-index materials, for example single crystal silicon and amorphous silica in silicon-on-insulator platform. These periodic structures frustrate diffraction provided they operate outside the Bragg condition and behave like a homogeneous medium. In a subwavelength grating (SWG) waveguide with a core consisting of a periodic arrangement of segments (Fig. 1), light excites a Bloch mode, which can theoretically propagate through the SWG waveguide with minimal scattering losses. Unlike other periodic waveguides such as line-defects in a 2D photonic crystal lattice, a subwavelength grating waveguide confines the light like a conventional index-guided structure and does not exhibit optically resonant behaviour.

As a result of the evolution semiconductor fabrication tools and methods over several decades, it now possible to routinely design and make optical devices with features comparable to or smaller than the wavelength of the light that propagates through these structures. This paper will review some silicon optical structures with critical features at these extremely short length scales. For example it becomes possible to create segmented waveguide structures with optical properties that can be tuned continuously between those of the cladding and waveguide core, using lithographic patterning rather than varying etch depth. Using thin high index contrast waveguides and the correct polarization, the optical electric field profiles can be shaped to maximize the coupling to molecular monolayers or cladding layers with specific functionality. Examples are given from our recent work on optical biosensors chips which employ grating couplers made by sub-wavelength digital patterning, and use waveguides optimized for coupling to molecular monolayers.

A silicon waveguide evanescent field molecular sensor interrogated by reflection from a surface grating is demonstrated. The sensor is probed by a beam of light incident at theta = 45 degrees through the backside of the silicon-on-insulator (SOI) wafer. The reflected power shows a strong resonant feature near lambda = 1532 rim, arising froth resonant coupling of incident beam, guided mode, and the reflected beam. The resonant wavelength is very sensitive to molecular surface coverage. We have measured a Delta lambda = 1.0 nm resonance shift when a monolayer of streptavidin protein is bound to the sensor surface, or a 60% reflectivity change when measured at a fixed wavelength. (C) 2009 Optical Society of America

We present experimental and theoretical results of label-free molecular sensing with the TM mode of a 0.22 µm thick silicon slab waveguide used in a guided mode resonance configuration. Due to the strong overlap of the evanescent field of the waveguide mode with a molecular layer attached to the surface, these sensors exhibit high sensitivity, while their fabrication and packaging requirements are minimal. Experimentally, we demonstrate a resonance wavelength shift of ~1 nm when a monolayer of streptavidin is attached to the surface, in good agreement with calculations based on rigorous coupled wave analysis.

We present experimental and theoretical results of label-free molecular sensing using the transverse magnetic mode of a 0.22 mum thick silicon slab waveguide with a surface grating implemented in a guided mode resonance configuration. Due to the strong overlap of the evanescent field of the waveguide mode with a molecular layer attached to the surface, these sensors exhibit high sensitivity, while their fabrication and packaging requirements are modest. Experimentally, we demonstrate a resonance wavelength shift of approximately 1 nm when a monolayer of the protein streptavidin is attached to the surface, in good agreement with calculations based on rigorous coupled wave analysis. In our current optical setup this shift corresponds to an estimated limit of detection of 0.2% of a monolayer of streptavidin.

Silicon photonic wire waveguides have a remarkably high response to surface molecular binding. Evanescent field waveguide sensors based on silicon can be interrogated using Mach-Zehnder interferometers, ring resonators, or by probing surface gratings in a reflection geometry. This paper compares these approaches from a theoretical viewpoint and through recent experimental results, with the goal of defining a path from our existing individual sensors to practical biosensor array chips.