**1. Introduction**

26 Photonic Crystals / Book 2

234 Photonic Crystals – Innovative Systems, Lasers and Waveguides

Neumann, P., Mizuochi, N., Rempp, F., Hemmer, P., Watanabe, H., Yamasaki, S., Jacques, V.,

Politi, A., Cryan, M. J., Rarity, J. G., Yu, S. & O'Brien, J. L. (2008). Silica-on-silicon waveguide

Rabeau, J. R., Chin, Y. L., Prawer, S., Jelezko, F., Gaebel, T., & Wrachtrup, J. (2005). Fabrication

Song, B.-S., Noda, S. & Asano, T. (2007). Photonic devices based on in-plane hetero photonic

Su, C. H., Greentree, A. D. & Hollenberg, L. C. L. (2008). Towards a picosecond

Tamarat, P., Manson, N. B., Harrison, J. P., McMurtrie, R. L., Nizovtsev, A., Santori, C.,

Tomljenovic-Hanic, S., Greentree, A. D., de Sterke, C. M. & Prawer, S. (2009). Flexible design

Tomljenovic-Hanic, S., Steel, M. J., de Sterke, C. M. & Salzman, J. (2006). Diamond based

van Oortt, E., Manson, N. B. & Glasbeekt, M. (1988). Optically detected spin coherence

Wang, C. F., Hanson, R., Awschalom, D. D., Hu, E. L., Feygelson, T., Yang, J. & Butler,

Zhang, Z. & Qiu, M. (2004). Small-volume waveguide-section high q microcavities in 2d

microcavities in nanocrystalline diamond, *Appl.Phys.Lett.* 91: 201112. Young, A., Hu, C. Y., Marseglia, L., Harrison, J. P., O'Brien, J. L. & Rarity, J. G. (2009). Cavity

centre in diamond, *New Journal of Physics* 10: 045004.

photonic crystal microcavities, *Optics Express* 14: 3556.

photonic crystal slabs, *Optics Express* 12: 3988–3995.

spins in diamond, *Science* 320: 1326.

*Phys. Lett.* 86: 131926.

16: 6240.

17: 6465.

21: 4385–4391.

*New Journal of Physics* 11: 013007.

crystals, *Science* 300: 1537.

quantum circuits, *Science* 320: 646–649.

Gaebel, T., Jelezko, F. & Wrachtrup, J. (2008). Multipartite entanglement among single

of single nickel-nitrogen defects in diamond by chemical vapor deposition, *Appl.*

transform-limited nitrogen-vacancy based single photon source, *Optics Express*

Beausoleil, R. G., Neumann, P., Gaebel, T., Jelezko, F., Hemmer, P. & Wrachtrup, J. (2008). Spin-flip and spin-conserving optical transitions of the nitrogen-vacancy

of ultrahigh-q microcavities in diamond-based photonic crystal slabs, *Optics Express*

of the diamond n-v centre in its triplet ground state, *J. Phys. C: Solid State Phys.*

J. E. (2007). Fabrication and charcterization of two-dimensional photonic crystal

enhanced spin measurement of the ground state spin of an nv center in diamond,

The development of fast, efficient, and reliable sensing devices to be used for the detection, identification, and quantification of substances and biological material is one of the main current investigation fields. Among the substances and analytes to be detected we can find gases, liquids, proteins, hormones, bacteria, or DNA. These sensing devices can find applications in many fields, such as medical diagnostics, food safety control, environmental control, or drug detection.

Most of the currently available sensing devices base their detection on labelling the target analytes because of the difficulty to directly detect very small size analytes in a low concentration. By performing a proper treatment of the sample in which the target analyte is contained, it is possible to attach a label to it. The label consists of a material with certain physical properties such as fluorescence, radioactivity, metallic material, etc. so that the analyte detection is indirectly carried out by detecting the physical properties of the label that has been attached to it. However, although analyte labelling is an effective way to detect small size analytes in a small concentration, it requires previous sample preparation which needs to be performed by skilled personnel and is time consuming. Moreover labelling presents the difficulty of finding a proper method to specifically attach the labels only to the target analyte to be detected. It is therefore important to have more sensitive sensing devices or mechanisms at our disposal, which allow performing the detection without the need of labels.

One of the main candidates for the development of these highly sensitive sensing devices able to perform a label-free detection is photonic technology (Fan et al., 2008), and more specifically, integrated planar photonic devices, which have been attracting an increasing interest in the last few years. Although more mature photonic sensing technologies, such as those based on surface plasmon resonances (Homola et al., 1999) or fiber Bragg gratings (Kersey et al., 1997), have even become commercially available some years ago, devices based on integrated planar photonic structures are envisaged as a highly promising alternative for future lab-on-a-chip (LoC) devices.

First demonstrations of the possibility of using these devices for sensing applications were reported by the end of the past century, as for example in (Luff et al., 1996) and (Schubert et al., 1997), but it has not been until 5-6 years ago that many researchers have focused their

Label-Free Biosensing Using Photonic Crystal Waveguides 237

crystals (Huang et al., 2009), photonic crystal waveguides (Skivesen et al., 2007; Buswell et al., 2008; Di Falco et al., 2009; García-Rupérez et al., 2010; Toccafondo et al., 2010; Scullion et al., 2011), and photonic crystal cavities (Loncar et al., 2003; Chow et al., 2004; Lee & Fauchet, 2007; Sünner et al., 2008; Dorfner et al., 2009; Zlatanovic et al., 2009; Xu et al., 2010b). For bulk photonic crystal sensors, the periodic dielectric structure does not present any defects and it is directly used to perform the sensing. For these structures, a variation of the refractive index of the surrounding medium provokes a shift of the position of the photonic bandgap (PBG) edge, which is used to perform the sensing. However, when using bulk photonic crystals, light is not well localized on the in-plane direction of the structure, so that configurations where linear or punctual defects are introduced on the bulk structure are usually preferred in order to enhance the localization of the optical field in an active region

(a) (b) (c)

(d) (e) (f) Fig. 1. SEM (Scanning Electron Microscope) pictures of several integrated planar photonic structures for sensing purposes. (a) SOI ring resonator (De Vos et al., 2007); (b) coupling region of a silicon nitride slot ring resonator (Carlborg et al., 2010); (c) array of SOI MZIs with folded arms (Densmore et al., 2009); (d) SOI photonic crystal waveguide (Buswell et al., 2008); (e) holes-based SOI photonic crystal cavity (Lee & Fauchet, 2007); (f) pillar based

For photonic crystal waveguide (PCW) based sensors, a linear defect is introduced in the propagation direction of the optical wave. In this way, light is localized in the region of the linear defect (and its surroundings), leading to an increased interaction with the target analyte. When the linear defect is created within the bulk photonic crystal, a guided mode appears inside the PBG of the photonic crystal structure. The position of the guided band edge (either lower band edge or upper band edge) is used for sensing, as it is dependent on

silicon photonic crystal cavity (Xu et al., 2010b).

the refractive index variations of the surrounding media.

well below 100 μm2 and thus increase the interaction with the target analyte.

investigations on the application of already developed integrated planar photonic devices for biosensing purposes. The transduction principle of these devices is based on the high dependence of their response to changes in the refractive index (RI) of the surrounding medium. Therefore, when the target analyte is deposited on the top (or generally, the surroundings) of the photonic structure, it induces a RI variation which can be directly detected by means of the change in the device's response.

The two main advantages of integrated planar photonic devices for sensing applications are their high sensitivity due to the high confinement of the electromagnetic field in the photonic structure which enhances the interaction with the target analyte, and their reduced size, which makes it possible both to detect very small analytes and to integrate many of these devices on a single chip to perform a multi-analyte detection. Other advantages of integrated photonic sensing devices are derived from these two, such as a short analysis time, the possibility to perform a label-free detection avoiding a costly previous sample preparation procedure (in terms of time and money), or the requirement of very low volumes of analyte and reagents to perform the analysis. Moreover, if these integrated planar photonic devices are based on CMOS-compatible materials such as Silicon-On-Insulator (SOI), the possibility of using mass manufacturing techniques for the fabrication opens the door to a low cost and high volume production of these devices.

Many different integrated planar photonic structures are widely used for sensing applications, among which resonant structures, Mach-Zehnder Interferometers (MZIs), and photonic crystal structures are the most common. Results reported using these structures range from basic characterization of the sensing device to refractive index variations to more complex bio-sensing experiments where the presence of a specific analyte such as proteins, bacteria or even DNA strands is detected and quantified without the need of any label.

The most popular integrated planar photonic sensing devices are probably those based on resonant structures such as rings or disks, which are coupled to an access waveguide (De Vos et al., 2007, 2009; Barrios et al., 2008; Ramachandran et al., 2008; Carlborg et al., 2010; Iqbal et al., 2010; Xu et al., 2010a). In these structures, variations on the surrounding media provoke a spectral shift of the transmission resonances, which is used to perform the sensing. These kind of sensing structures exhibit high sensitivity and low detection limit values, with a small footprint on the order of a few hundreds of μm2.

Other groups work on the development of photonic biosensors using Mach-Zehnder Interferometers (MZIs) (Schubert et al., 1997; Sepulveda et al., 2006; Densmore et al., 2009), where changes in the refractive index in the proximity of one of the arms provoke an additional phase shift over the propagated wave which is translated into an amplitude variation at the output. Although these sensing structures exhibit performances similar to or even better than resonant structures, their main problem is that very long arm lengths (of some millimetres) are required in order to provide enough interaction to detect the presence of the analyte, thus limiting their integration level. Nevertheless, this issue has been greatly overcome by folding the arms of the MZI, thus significantly reducing the final footprint of the device (Densmore et al., 2009).

The third main alternative for the development of integrated planar photonic biosensors are photonic crystal structures, on which this chapter will focus. Several configurations are typically used when developing photonic crystal based sensing structures: bulk photonic

investigations on the application of already developed integrated planar photonic devices for biosensing purposes. The transduction principle of these devices is based on the high dependence of their response to changes in the refractive index (RI) of the surrounding medium. Therefore, when the target analyte is deposited on the top (or generally, the surroundings) of the photonic structure, it induces a RI variation which can be directly

The two main advantages of integrated planar photonic devices for sensing applications are their high sensitivity due to the high confinement of the electromagnetic field in the photonic structure which enhances the interaction with the target analyte, and their reduced size, which makes it possible both to detect very small analytes and to integrate many of these devices on a single chip to perform a multi-analyte detection. Other advantages of integrated photonic sensing devices are derived from these two, such as a short analysis time, the possibility to perform a label-free detection avoiding a costly previous sample preparation procedure (in terms of time and money), or the requirement of very low volumes of analyte and reagents to perform the analysis. Moreover, if these integrated planar photonic devices are based on CMOS-compatible materials such as Silicon-On-Insulator (SOI), the possibility of using mass manufacturing techniques for the fabrication

Many different integrated planar photonic structures are widely used for sensing applications, among which resonant structures, Mach-Zehnder Interferometers (MZIs), and photonic crystal structures are the most common. Results reported using these structures range from basic characterization of the sensing device to refractive index variations to more complex bio-sensing experiments where the presence of a specific analyte such as proteins, bacteria or even DNA strands is detected and quantified without the need of any label.

The most popular integrated planar photonic sensing devices are probably those based on resonant structures such as rings or disks, which are coupled to an access waveguide (De Vos et al., 2007, 2009; Barrios et al., 2008; Ramachandran et al., 2008; Carlborg et al., 2010; Iqbal et al., 2010; Xu et al., 2010a). In these structures, variations on the surrounding media provoke a spectral shift of the transmission resonances, which is used to perform the sensing. These kind of sensing structures exhibit high sensitivity and low detection limit

Other groups work on the development of photonic biosensors using Mach-Zehnder Interferometers (MZIs) (Schubert et al., 1997; Sepulveda et al., 2006; Densmore et al., 2009), where changes in the refractive index in the proximity of one of the arms provoke an additional phase shift over the propagated wave which is translated into an amplitude variation at the output. Although these sensing structures exhibit performances similar to or even better than resonant structures, their main problem is that very long arm lengths (of some millimetres) are required in order to provide enough interaction to detect the presence of the analyte, thus limiting their integration level. Nevertheless, this issue has been greatly overcome by folding the arms of the MZI, thus significantly reducing the final footprint of

The third main alternative for the development of integrated planar photonic biosensors are photonic crystal structures, on which this chapter will focus. Several configurations are typically used when developing photonic crystal based sensing structures: bulk photonic

opens the door to a low cost and high volume production of these devices.

values, with a small footprint on the order of a few hundreds of μm2.

the device (Densmore et al., 2009).

detected by means of the change in the device's response.

crystals (Huang et al., 2009), photonic crystal waveguides (Skivesen et al., 2007; Buswell et al., 2008; Di Falco et al., 2009; García-Rupérez et al., 2010; Toccafondo et al., 2010; Scullion et al., 2011), and photonic crystal cavities (Loncar et al., 2003; Chow et al., 2004; Lee & Fauchet, 2007; Sünner et al., 2008; Dorfner et al., 2009; Zlatanovic et al., 2009; Xu et al., 2010b). For bulk photonic crystal sensors, the periodic dielectric structure does not present any defects and it is directly used to perform the sensing. For these structures, a variation of the refractive index of the surrounding medium provokes a shift of the position of the photonic bandgap (PBG) edge, which is used to perform the sensing. However, when using bulk photonic crystals, light is not well localized on the in-plane direction of the structure, so that configurations where linear or punctual defects are introduced on the bulk structure are usually preferred in order to enhance the localization of the optical field in an active region well below 100 μm2 and thus increase the interaction with the target analyte.

Fig. 1. SEM (Scanning Electron Microscope) pictures of several integrated planar photonic structures for sensing purposes. (a) SOI ring resonator (De Vos et al., 2007); (b) coupling region of a silicon nitride slot ring resonator (Carlborg et al., 2010); (c) array of SOI MZIs with folded arms (Densmore et al., 2009); (d) SOI photonic crystal waveguide (Buswell et al., 2008); (e) holes-based SOI photonic crystal cavity (Lee & Fauchet, 2007); (f) pillar based silicon photonic crystal cavity (Xu et al., 2010b).

For photonic crystal waveguide (PCW) based sensors, a linear defect is introduced in the propagation direction of the optical wave. In this way, light is localized in the region of the linear defect (and its surroundings), leading to an increased interaction with the target analyte. When the linear defect is created within the bulk photonic crystal, a guided mode appears inside the PBG of the photonic crystal structure. The position of the guided band edge (either lower band edge or upper band edge) is used for sensing, as it is dependent on the refractive index variations of the surrounding media.

Label-Free Biosensing Using Photonic Crystal Waveguides 239

of the PCW as this feature is not sharp enough to provide very low uncertainty. This problem can be overcome by using the sharp Fabry-Perot fringes appearing in the slow-light regime near the edge of the guided band, whose position can be determined very accurately, as will be explained in section 2. Moreover, their use ensures that we are working in the slow-light regime of the PCW, which allows a stronger interaction of the optical field with the target substance. In sections 3, 4 and 5, the application of PCW-based biosensors for the detection of refractive index variations, label-free antibody detection, and label-free DNA detection will be shown. Finally, section 6 will describe an alternative method for the indirect measurement of the shift of the guided band's edge, which will allow having a low-

**2. Photonic crystal waveguide sensor design and sensing principle** 

of this technological platform with CMOS fabrication techniques.

Planar PCWs are one of the preferred photonic structures for the development of biosensing devices because of their reduced size and the high confinement of the optical field in the linear defect region. In this text, we will consider planar SOI PCWs, due to the compatibility

When designing a PCW for biosensing there are several factors to be taken into account. We

 First, we have to select between a pillars-on-air or a holes-on-dielectric photonic crystal structure. For pillars-on-air photonic crystals (Xu et al., 2010b), we can have a higher interaction with the target analyte flowing through the pillars; however, light coupling to these structures is less efficient, and their fabrication process can be more complex. On the other hand, for holes-on-dielectric photonic crystals (Buswell et al., 2008), the fabrication process is easier and the light coupling is more efficient, but a weaker interaction with the target analyte is produced. The photonic crystal configuration will also determine the working polarization, as pillars-on-air photonic crystals present PBGs for TM-polarization and holes-on-dielectric photonic crystals present PBGs for

 We have to select the working wavelength, which is usually determined by the available readout system and light sources, so that typically used wavelengths are those from telecom applications: around 1310 nm and around 1550 nm. A working wavelength around 1310 nm allows having lower water absorption losses, however this is not really a critical point because power is not a major issue for integrated photonic biosensors. On the other hand, working at higher wavelengths, such as 1550 nm, makes

 The thickness of the patterned silicon layer will also affect the sensitivity of the device; the thinner the silicon layer, the higher the sensitivity because of the larger amount of evanescent field traveling through the upper cladding and interacting with the target analytes. This parameter is usually set by the SOI substrates used to fabricate the

 The PCW configuration will also affect the sensitivity of the sensing device. Again, the configuration with a higher amount of evanescent field traveling through the cladding will provide a higher sensitivity due to an enhanced interaction between the optical

the evanescent field wider and thus provides a higher sensitivity.

cost and real-time sensing system.

will focus on five of them:

TE-polarization.

devices.

field and the target analyte.

For photonic crystal cavity based sensors, a punctual or area defect is created in the bulk photonic crystal, leading to the formation of a resonator with a strong localization of the optical field within this region. This can be achieved for instance by changing the dimensions of one or several elements of the periodic structure (see Figs. 1.(e) and 1.(f)), or by eliminating then. The coupling of light to this defect is usually achieved in two different manners:


For both cases, the resonance position depends on the refractive index of the medium surrounding the cavity region, leading to a very high sensitivity to variations produced in a very small active region, which can even be smaller than 1 μm2.

Finally, it is also worth noting that planar 1D periodic waveguides or cavities, such as the ones shown in Fig. 2, which are not usually referred to as photonic crystal structures although they are based in the same principles as them, are also a very promising alternative for the development of integrated planar photonic biosensors (García et al., 2008; Kauppinen et al., 2009; Goddard et al., 2010; Castelló et al., 2011). When using a planar 1D periodic structure, the position of its guided bands or resonant modes is also highly dependant on the refractive index of the surrounding media, so shifts in their position can be used to perform the sensing. Moreover, these structures can be simpler to fabricate and have a smaller footprint than 2D photonic crystal based structures.

(a) (b)

Fig. 2. SEM pictures of two planar 1D periodic structures used for sensing purposes. (a) 1D SOI holes cavity (Goddard et al., 2010); (b) 1D SOI corrugated waveguide (Castelló et al., 2011).

The next sections of this chapter will focus on the use of photonic crystal waveguides for the development of label-free photonic biosensors, as they are very promising thanks to their high sensitivity and small footprint. However, the performance of these sensors may be limited by the difficulty to accurately determine the position of the edge of the guided band

For photonic crystal cavity based sensors, a punctual or area defect is created in the bulk photonic crystal, leading to the formation of a resonator with a strong localization of the optical field within this region. This can be achieved for instance by changing the dimensions of one or several elements of the periodic structure (see Figs. 1.(e) and 1.(f)), or by eliminating then. The coupling of light to this defect is usually achieved in two different

 The defect is created in the bulk photonic crystal, and light is directly coupled to/from it through the access dielectric waveguides. In this configuration, a resonant mode appears inside the PBG of the photonic crystal structure, with a central wavelength

 The defect is created next to the linear defect of a photonic crystal waveguide. In this configuration, light matching the resonance wavelength of the cavity is extracted from the PCW, leading to the appearance of a notch-like response in the transmission

For both cases, the resonance position depends on the refractive index of the medium surrounding the cavity region, leading to a very high sensitivity to variations produced in a

Finally, it is also worth noting that planar 1D periodic waveguides or cavities, such as the ones shown in Fig. 2, which are not usually referred to as photonic crystal structures although they are based in the same principles as them, are also a very promising alternative for the development of integrated planar photonic biosensors (García et al., 2008; Kauppinen et al., 2009; Goddard et al., 2010; Castelló et al., 2011). When using a planar 1D periodic structure, the position of its guided bands or resonant modes is also highly dependant on the refractive index of the surrounding media, so shifts in their position can be used to perform the sensing. Moreover, these structures can be simpler to fabricate and have a

(a) (b) Fig. 2. SEM pictures of two planar 1D periodic structures used for sensing purposes. (a) 1D SOI holes cavity (Goddard et al., 2010); (b) 1D SOI corrugated waveguide (Castelló et al.,

The next sections of this chapter will focus on the use of photonic crystal waveguides for the development of label-free photonic biosensors, as they are very promising thanks to their high sensitivity and small footprint. However, the performance of these sensors may be limited by the difficulty to accurately determine the position of the edge of the guided band

manners:

spectrum.

2011).

determined by the defect profile.

very small active region, which can even be smaller than 1 μm2.

smaller footprint than 2D photonic crystal based structures.

of the PCW as this feature is not sharp enough to provide very low uncertainty. This problem can be overcome by using the sharp Fabry-Perot fringes appearing in the slow-light regime near the edge of the guided band, whose position can be determined very accurately, as will be explained in section 2. Moreover, their use ensures that we are working in the slow-light regime of the PCW, which allows a stronger interaction of the optical field with the target substance. In sections 3, 4 and 5, the application of PCW-based biosensors for the detection of refractive index variations, label-free antibody detection, and label-free DNA detection will be shown. Finally, section 6 will describe an alternative method for the indirect measurement of the shift of the guided band's edge, which will allow having a lowcost and real-time sensing system.
