Alessandro Massaro

*Italian Institute of Technology IIT Center for Bio-Molecular Nanotecnology, Arnesano, Lecce Italy* 

#### **1. Introduction**

112 Photonic Crystals – Introduction, Applications and Theory

Zandi, K.; Wong, B.; Zou, J.; Kruzelecky, R. V.; Jamroz W. & Peter, Y.-A. (2010). In-Plane

*Electro Mech. Syst.,* pp. 839-842.

Silicon-On-Insulator Optical MEMS Accelerometer Using Waveguide Fabry-Perot Microcavity With Silicon/Air Bragg Mirrors, *in Proc. 23rd IEEE Int. Conf. Micro* 

> Photonic crystals (PCs) are actually implemented as biosensors [Ganesh et al., 2007], optical resonators [Karnutsch et al., 2007] and wavelength filters [D'Orazio et al., 2008; Pierantoni et al., 2006]. Other kinds of photonic crystals can be implemented by considering a periodic structure with defect line and/or central cavities. Several architectures of micro-cavities (see examples in Fig. 1 (a), (b)and (c)) have been studied in the past by using triangular and square lattices layouts [Joannopoulos, 1995] oriented on optoelectronic technology. Optoelectronic technologies are often affected by cost and space problems that prevent them from being used even more widely. The development and implementation of photonic integrated circuits (PICs) could provide a solution to these two major obstacles. Couplers such as tapered waveguides and photonic crystal (PhC) devices can be integrated in the same chip in order to reduce the space, especially concerning complex optical switch systems, and, to provide high transmitted power and high efficiency of the PICs. For example, the use of tapered waveguides is necessary in order couple the light into a W1 PhC waveguide (illustrated in Fig. 1 (a)). This kind of W1 PhC waveguide is object of much interest because of its potential for controlling and manipulating the propagation of light. In particular, sharp bends, junctions, couplers, cavities, add-drop filters, and multiplexers have been experimentally demonstrated or theoretically predicted, thus making these devices very attractive for highly integrated photonic circuits [Mekis et al., 2008; Pottier et al., 2003; Johnson et al., 2002; Sanchis et al., 2002; Chau et al., 2004; Chietera et al., 2004; Xing et al., 2005; Camargo et al., 2004; Talneau et al., 2004; Marki et al., 2005; Camargo et al., 2004; Sanchis et al.,2004; Khoo et al.,2006]. The in-plane coupling of W1 PhC is also an important issue for bio-sensors implemented by micro- and nanofabrication technologies. In fact, the development of micro- and nanofabrication technologies, biomolecular patterning and micro-electromechanical systems (MEMS), has greatly contributed to the realization of miniaturized laboratories applied to genomic and proteomic analysis. The application fields of these biochips are extremely broad, and they have been referred as several different terms (gene-chip, gene-array, DNA microarray, protein chip, and lab-on-chip). Essentially, these chips, developed both in simple stand-alone configurations and integrated devices/architectures, consist of planar structures, realized on several substrates such as glass or plastic materials, where (bio)molecules (such as DNA, proteins or cells, which selectively conjugate with target molecules) can be immobilized on them through chemical surface modification or in situ synthesis [Fan et al., 2006] as happens DNA sensors. These chips require the use of suitable micro-reactors and/or capillary systems, and the

Photonic Crystal Waveguides and Bio-Sensors 115

In the last section we introduce the design criteria for a bio-compatible based polymer

W1 PhC can be obtained by introducing a line defect within the periodic lattice, usually realized through a triangular lattice layout of air holes etched into the substrate. This configuration is compatible with standard planar-semiconductor processing technology. A way to couple efficiently in-plane the light is the use of tapered waveguides. The best geometrical configurations of the tapered profiles are found by performing a good electromagnetic field confinement and low losses. In order to define the frequency response and the electromagnetic coupling of the tapered waveguides, we consider two numerical approach: the finite difference time domain (FDTD) method, and finite element method (FEM). The first one defines accurately the scattered light and the field coupled inside the device, and the second one analyzes the peak frequency resonance and provides the

frequency shift versus different taper lengths. This section is organized as follows:

i. we design and model, according with the technological aspects, the optimum tapered waveguide layout (see Fig. 2 (a) and (b)) which couples the electromagnetic field

ii. by considering the optimum geometrical configuration of the tapered couplers, we

We design integrated tapered waveguides coupled in-plane with an external source (0=1.31 m) and able to focus the energy in a small waveguide region (ridge of the waveguide).

According with the technological limits (technology resolution) we fix the optical and the geometrical parameters indicated in Fig. 2 (a) and (b) as: D=2m, d=1.2m, s=0.3m, *n*(GaAs)=3.408, *n*(AlGaAs)=3.042, w=0.5m, Ls=16.77 m. We analyze the bandpass

the two coupled tapered waveguides. This procedure allows to calculate the best optimum length L of the tapered profile. The inset of Fig. 3 reports a schematic representation of the employed transmission experimental set-up. In this set-up a light probe beam (tungsten broad band lamp) is launched from a tapered fibre and directly injected into the ridge waveguide. The light exiting the waveguide is collected and collimated by a microscope objective with high numerical aperture. The real image of the output facet of the waveguide is then formed on the common focal plane of a telescopic system, where a horizontal slit is placed. This allows us to separate the light coming from the ridge waveguide from the

*<sup>0</sup>*=1.31 m, and evaluate the energy density at the output of

and can be applied to different PhC layouts.

around a working wavelength of 0=1.31 m;

behaviour around the working

simulate the W1 PhC illustrated in Fig. 2 (c) and (d).

**2. In-plane coupling of photonic crystal waveguides** 

PhC suitable as a bio-sensor.

luminescent emitting substance located on the photonic crystal which is characterized by a specific emission band. By starting with the analysis of the periodic passive structures it is possible to define design maps in which are reported the diffraction efficiency versus the incidence angles. The PhC is designed to provide a high diffraction efficiency in the emission band of the luminescent substance. In this way the emission of the luminescent substance is enhanced through the high intensity of the zeroth-order backward diffracted wave. These maps could be used to define an admissible error margin due to the uncertainty of fabrication process. The proposed technique can be utilized in different spectral ranges starting from ultra violet to infrared wavelengths,

detection of complemental reaction between biomolecular is performed in a solution. Biochip technology has revolutionalized the field of molecular biology, finding broad application regarding the study of gene and protein expressions in several fields such as experimental and clinical diagnostics, biomarker detection, and pharmacogenomics. Actually, several chip setups have been used, such as enzyme assays [Hadd et al., 1997], immunochemistry assays [Wang, et al. 2001], polymorphism detection in genetic variations [Dunn et al., 2000], nucleic acids sequencing [Scherer et al., 1999], chips for the realization of ligase reaction [Cheng et al., 1996], and DNA amplification on micro-volumetric scale [Kopp et al., 1998; Daniel et al., 1998]. In particular, due to the high specificity of the hybridization reaction among the oligonucleotides sequences (complementary base-pairing between adenine and thymine, and guanine and cytosine), chips based on biomolecular interactions among DNA filaments have been developed more rapidly than chips based on proteins. In the latter case, despite of keen interest among the scientific community, it slowed down due to the complex bio-recognition mechanism of proteinaceous molecular species [Bodovitz, 2005].

Fig. 1. (a) W1 PhC waveguide. (b) Triangular lattice layout. (c) Circular photonic crystals.

Concerning the discussed topics, we propose to provide examples and design criteria useful to address the reader on the implementation of PhC oriented on bio-applications. The main goal of the chapter is to present an overview about the basic principles of light coupling, light emission and detection approaches of photonic crystals behaving as bio-sensors. In particular, we list below the sections proposed in this chapter.


detection of complemental reaction between biomolecular is performed in a solution. Biochip technology has revolutionalized the field of molecular biology, finding broad application regarding the study of gene and protein expressions in several fields such as experimental and clinical diagnostics, biomarker detection, and pharmacogenomics. Actually, several chip setups have been used, such as enzyme assays [Hadd et al., 1997], immunochemistry assays [Wang, et al. 2001], polymorphism detection in genetic variations [Dunn et al., 2000], nucleic acids sequencing [Scherer et al., 1999], chips for the realization of ligase reaction [Cheng et al., 1996], and DNA amplification on micro-volumetric scale [Kopp et al., 1998; Daniel et al., 1998]. In particular, due to the high specificity of the hybridization reaction among the oligonucleotides sequences (complementary base-pairing between adenine and thymine, and guanine and cytosine), chips based on biomolecular interactions among DNA filaments have been developed more rapidly than chips based on proteins. In the latter case, despite of keen interest among the scientific community, it slowed down due to the complex bio-recognition

Fig. 1. (a) W1 PhC waveguide. (b) Triangular lattice layout. (c) Circular photonic crystals.

Concerning the discussed topics, we propose to provide examples and design criteria useful to address the reader on the implementation of PhC oriented on bio-applications. The main goal of the chapter is to present an overview about the basic principles of light coupling, light emission and detection approaches of photonic crystals behaving as bio-sensors. In

 The first section analyzes the in plane coupling of tapered waveguides with a PhC waveguide around the working wavelength of 1.31 m. We first analyze and characterize the coupling between two tapered waveguides, and, then, we model the coupling between tapered waveguides and PhC with micro-cavity. The analysis and the experimental results show the peak frequency shift obtained by varying the taper length. A maximum efficiency of the coupling is reached by a compromise between electromagnetic field confinement and low reflectivity at the input of the coupled photonic crystal. A good agreement with experimental results validates the 2D and 3D numerical results. The proposed in-plane coupling system can be used for W1 bio PhC. The second section provides technical advantages of a photonic crystal optical read-out in bio-molecular detection systems (deoxyribonucleic acid (DNA) chips, protein chips, micro-array, and lab-on-chip systems) for genomics/proteomics applications. The proposed method is based on arrays of PhC resonators which contribute to improve a detection efficiency of bio-samples marked with luminescent substances. The detection efficiency is characterized in terms of sensitivity of the analysis, the signal/noise ratio,

 The third section introduces an accurate modeling regarding PhC diffraction efficiency in bio-detection systems. The approach optimizes the detection enhancement of a

mechanism of proteinaceous molecular species [Bodovitz, 2005].

particular, we list below the sections proposed in this chapter.

and speed of the optical read-out process.

luminescent emitting substance located on the photonic crystal which is characterized by a specific emission band. By starting with the analysis of the periodic passive structures it is possible to define design maps in which are reported the diffraction efficiency versus the incidence angles. The PhC is designed to provide a high diffraction efficiency in the emission band of the luminescent substance. In this way the emission of the luminescent substance is enhanced through the high intensity of the zeroth-order backward diffracted wave. These maps could be used to define an admissible error margin due to the uncertainty of fabrication process. The proposed technique can be utilized in different spectral ranges starting from ultra violet to infrared wavelengths, and can be applied to different PhC layouts.

 In the last section we introduce the design criteria for a bio-compatible based polymer PhC suitable as a bio-sensor.
