**3. Photonic crystal resonators array chip for improved optical sensing of (bio) molecules in genomics and proteomics**

One of the main goals of this chapter is to analyze the detection efficiency of an optical signal coming from a bio-sensor chip based on luminescence emission. Our approach is based on the employ of arrays of photonic crystals which resonate with emitted lights from a luminous marker associated to a bio-molecule target at a predetermined wavelength. A proper design of these photonic crystal arrays and a spectral analysis of resonant peak emissions allow us to unambiguously associate each analyte to a peak emission, and pick out a useful signal from source reflection/diffraction noise. The use of properly fabricated PhC patterns in an optical read-out region provides us a freedom to modify local spectral distribution of allowed optical modes [Scully et al., 1997]. This concept has been used to increase both excitation and emission efficiencies of optical markers attached on a PhC pattern in bio-molecule detection devices [Mathias et al., 2007]. In particular, in this section we propose to use PhC resonators for a selective enhancement of a luminescent markeremission only at a specific resonant wavelength. By fabricating several photonic crystal resonators in one bio-chip, each one characterized by a different resonant wavelength and a specific bio-recognition sample attached on each resonator, it is possible to spectrally detect bio-molecule targets in certain positions on a chip. Through the analysis of the total emission spectra collected from the whole read-out area it is thus possible to detect the presence of a certain analyte in a bio-specimen. In comparison with traditional detection systems, based on the spatial scanning of an optical read-out area, this approach permits us to:


One of the main goals of this chapter is to analyze the detection efficiency of an optical signal coming from a bio-sensor chip based on luminescence emission. Our approach is based on the employ of arrays of photonic crystals which resonate with emitted lights from a luminous marker associated to a bio-molecule target at a predetermined wavelength. A proper design of these photonic crystal arrays and a spectral analysis of resonant peak emissions allow us to unambiguously associate each analyte to a peak emission, and pick out a useful signal from source reflection/diffraction noise. The use of properly fabricated PhC patterns in an optical read-out region provides us a freedom to modify local spectral distribution of allowed optical modes [Scully et al., 1997]. This concept has been used to increase both excitation and emission efficiencies of optical markers attached on a PhC pattern in bio-molecule detection devices [Mathias et al., 2007]. In particular, in this section we propose to use PhC resonators for a selective enhancement of a luminescent markeremission only at a specific resonant wavelength. By fabricating several photonic crystal resonators in one bio-chip, each one characterized by a different resonant wavelength and a specific bio-recognition sample attached on each resonator, it is possible to spectrally detect bio-molecule targets in certain positions on a chip. Through the analysis of the total emission spectra collected from the whole read-out area it is thus possible to detect the presence of a certain analyte in a bio-specimen. In comparison with traditional detection systems, based on

**3. Photonic crystal resonators array chip for improved optical sensing of** 

the spatial scanning of an optical read-out area, this approach permits us to:

of analytes in one time;

light source signal;

the PhC.

a. decrease analysis time. Since the detection of analytes is based on detection of resonant peak emissions, simultaneous measurement on the whole read-out area is possible. This feature allows us to detect analytes through a spectral scanning alone. As the bandwidth of a resonant peak becomes narrower, more peaks can be arranged in a spectrum of a luminous marker. Then, it becomes possible to analyze a larger number

b. drastically decrease the reading error caused by diffused, reflected and/or diffracted

c. significantly increase the detection sensitivity through the enhancement of the luminescent marker-signal. This enhancement is generated by the coupling of the luminescent light with a resonant mode of PhC patterns. In the proposed system, the unambiguous assignment of a resonant emission to each analyte does not require spatial scanning and/or the use of different fluorescence markers emitting light at different wavelengths. The unambiguous detection is guaranteed by combining each target (bio) molecule with a properly designed PhC resonator. In this way each PhC resonator can manipulate the light emission of a common luminescent marker. This approach can be further extended by utilizing, in the same chip, more than one fluorescent substances simultaneously, with different resonant emission frequencies. Moreover, the proposed technique can be utilized in different spectral ranges, starting from ultra violet to infrared (by utilizing, for example, organic fluorescent substances and/or colloidal nanocrystals) according to the scalability of target wavelengths and scale order of corresponding photonic crystal design [Yablonovitch, 1987; Joannopoulos et al., 1995]. The optical properties of the structure can be modified with a good accuracy in each desired frequency range, by simply changing the geometrical layout of

**(bio) molecules in genomics and proteomics** 

Our optical signal detecting device featuring high sensitivity and multiplexing detection is composed of an array of PhC resonators with specific probes (e.g. single-stranded DNA (ssDNA) sequences, antibodies, receptors, aptamers, etc…) for analytes (e.g. DNA, proteins, ligands, etc.) attached on them. Analytes are trapped with high spatial precision through chemical, physical, electrostatic techniques, and so on (Fig. 10). The target analytes can be directly (e.g. through syntesis) or indirectly marked by conjugation with one or more fluorophores. The basic schemes for a detection of biomolecules (proteins, ligands, etc.) and nucleic acids are shown in Figs. 11 (a) and (b), respectively. To eliminate background noise caused by scattering of excitation light, excitation light can be selectively provided to readout regions via PhC waveguides. The proposed system is based on a unique optical detection scheme. The detection is performed through the collection of the emission spectrum coming from the whole bio-recognition area of the chip. As previously discussed, by applying a suitable matrix composed by PhC resonators possessing different resonant wavelengths, each bio-recognition element of the device is unambiguously associated to a different resonance peak. By detecting resonant peak emissions at certain wavelengths, it is therefore possible to detect the presence of specific target (bio) molecules contained in the analyzed sample. Thus, it is possible to collect signals from several resonators in a single analysis, increasing the signal collection speed. Moreover, the PhC strongly inhibits the excitation radiation that is diffused or reflected towards the detection direction. Elimination of radiation of excitation light together with the increase in the intensity of the emission signal increases significantly the overall signal-to-noise ratio. This feature helps to reduce reading errors, allowing operators skip the step of complex post-processing to correct readout errors. Photonic crystals can control the light propagation by introducing a 1D, 2D or 3D periodicity in materials having high optical transparency in the frequency range of interest. Light can be trapped, for instance, by introducing a defect in the periodicity. Summarizing, photonic crystals technology could, therefore, be applied to biochip technology in order to provide the following advantages:


Photonic Crystal Waveguides and Bio-Sensors 123

Fig. 11. Schematics of the optical transducer for the analysis of biomolecules in

resonator, in order to perform spectral multiplexing analysis.

genomics/proteomics. (a) General sketch including a selective bio-recognition element for a specific target analyte (oligonucleotides, proteins, ligands, etc.). (b) Example of a devices suitable for DNA analysis: in this case, the probe bound to the resonator surface is a specific ssDNA sequence. Similarly to the above description, the resonators can differ from each other, as far as the (bio) recognition elements (for instance, the DNA probe) bound to each

emitted from the matrix allows a high degree of parallelism on a high number of different analytes, thus also fastening the recognition of the examined samples.

Regarding points (b) and (c), the proper choice of both the materials and the photonic crystal geometry can lead to the realization of a photon energy bandgap. As already mentioned, it is possible to localize specific optical modes to confine them in a small defect region in the photonic crystal. Only the modes which resonate in this small region will be amplified. Photonic crystal cavities are, therefore, designed to separate the useful signal coming from the biological assay from the noise coming from excessive source light. Then, we can obtain very sharp optical signals which are easily recognized thanks to their amplified intensity together with the spectral scanning of the detection system. Figs. 12 (b) and (c) show examples of an intact emission spectrum from a read-out region and signals collected from several read-out regions assisted by the array of photonic crystal resonators, respectively. The presence of each peak in the ensemble spectrum of Fig. 12 (c) reveals the presence of the corresponding target analyte in the analyzed assay. A further spatial separation between the scattered excitation light and a signal can be achieved by providing the excitation light to a read-out region or extracting the excited light from a read- out area through suitable waveguides. In this sense, the PhC can be designed to selectively guide light between resonators and detectors [Aoki et al., 2009].

Fig. 10. Schematic of the optical transducer for biomolecular analysis in genomics/proteomics. The proposed device is essentially characterized by a substrate on which are realized arrays of resonant photonic crystals. On the surface of each resonator specific bio-molecules are fixed (for example, through chemical functionalization), which behave as target probes for the analytes to be detected. In the sketch there have been shown, as an example, arrays of photonic crystal and bio-molecules of the same typology. It is obviously possible to consider, in the same chip array, different photonic crystal structures with different wavelength resonances. Analogously, each bio-recognition element bound on the single resonator can be different from each other, and peculiar for each analyte.

Regarding points (b) and (c), the proper choice of both the materials and the photonic crystal geometry can lead to the realization of a photon energy bandgap. As already mentioned, it is possible to localize specific optical modes to confine them in a small defect region in the photonic crystal. Only the modes which resonate in this small region will be amplified. Photonic crystal cavities are, therefore, designed to separate the useful signal coming from the biological assay from the noise coming from excessive source light. Then, we can obtain very sharp optical signals which are easily recognized thanks to their amplified intensity together with the spectral scanning of the detection system. Figs. 12 (b) and (c) show examples of an intact emission spectrum from a read-out region and signals collected from several read-out regions assisted by the array of photonic crystal resonators, respectively. The presence of each peak in the ensemble spectrum of Fig. 12 (c) reveals the presence of the corresponding target analyte in the analyzed assay. A further spatial separation between the scattered excitation light and a signal can be achieved by providing the excitation light to a read-out region or extracting the excited light from a read- out area through suitable waveguides. In this sense, the PhC can be designed to selectively guide light between

different analytes, thus also fastening the recognition of the examined samples.

resonators and detectors [Aoki et al., 2009].

Fig. 10. Schematic of the optical transducer for biomolecular analysis in

genomics/proteomics. The proposed device is essentially characterized by a substrate on which are realized arrays of resonant photonic crystals. On the surface of each resonator specific bio-molecules are fixed (for example, through chemical functionalization), which behave as target probes for the analytes to be detected. In the sketch there have been shown, as an example, arrays of photonic crystal and bio-molecules of the same typology. It is obviously possible to consider, in the same chip array, different photonic crystal structures with different wavelength resonances. Analogously, each bio-recognition element bound on

the single resonator can be different from each other, and peculiar for each analyte.

emitted from the matrix allows a high degree of parallelism on a high number of

Fig. 11. Schematics of the optical transducer for the analysis of biomolecules in genomics/proteomics. (a) General sketch including a selective bio-recognition element for a specific target analyte (oligonucleotides, proteins, ligands, etc.). (b) Example of a devices suitable for DNA analysis: in this case, the probe bound to the resonator surface is a specific ssDNA sequence. Similarly to the above description, the resonators can differ from each other, as far as the (bio) recognition elements (for instance, the DNA probe) bound to each resonator, in order to perform spectral multiplexing analysis.

Photonic Crystal Waveguides and Bio-Sensors 125

good enhancement of this emitted signal can be obtained by combining a PhC structure with the luminescent substance. The signal enhancement can be optimized by analyzing the diffraction efficiency of the light emitted from the luminescent substance, characterized by the **K** wave-vector (see Fig. 13 (a) and (b)). In general, by exciting a properly designed PhC structure with an optimum incidence angle, it is possible to detect a high-intensity diffracted signal. The presented diffraction modeling takes into account this optimum incidence condition by defining sets of possible incidence angles (working regions) in the emission luminescent band. In this section the diffraction efficiency of a square lattice PhC Si3N4 membrane covered with a luminescent substance is modelled. The structure is excited by a plane wave and the light coming out from the luminescent substance is also modeled as a

angles in the working region (see Fig. 14

angles. In Fig. 14

angle

plane wave with the **K** vector shown in Fig. 13 (a), characterized by *θ* and

for different launch *θ*-angles. By fixing the *θ* and

luminescent substance, is collected in a detection system.

where

of the model.

(a) and (b) we report the diffraction efficiency map versus the wavelength and the

=*θ*=30°), it is possible to analyze the sensitivity of the reflectivity response.

This allows to estimate the error margins due to the limits of the fabrication technology and of the experimental setups. As example, in Fig. 15 (a) is reported the sensitivity of the reflectivity response by varying hole radius in steps of 5 nm. Transverse electric (TE) and transverse magnetic (TM) PhC radiation modes define the diffraction concerning different PhC Brillouin directions. Figure 15 (b) shows the TM PhC radiation modes (diffraction modes) in the luminescent emission band 0.56m0.58m. The PhC Si3N4 membrane structure is excited by a plane wave and the light coming out from the

Fig. 13. (a) Photonic crystal for bio-sensing applications. (b) Source launch coordinate system

Fig. 12. (a) Schematics of a photonic crystal resonators matrix used in the optical DNA micro array chip. Each resonator of the matrix (bounded to a specific bio-recognition element) is designed in order to show a different resonant wavelength. (b) A typical example of the emission collected from a read-out area not assisted by photonic crystal resonators. The lineshape is typical of the original marker, with the presence of a significant noise due to scattered excitation light. (c) Example of the emission signal detected on the whole read-out area, where 1, 2 and i are the spectral peculiar modifications due to the coupling of the fluorophores with the 1st, 2nd and ith resonator in the matrix. The presence of each peak in the ensemble spectrum reveals the presence of the corresponding target analyte in the analyzed assay.

#### **4. Diffraction efficiency modeling of 2D photonic crystals for biosensing applications**

Optical bio-sensing approach usually consists of light intensity detection systems. Typically, the luminescent signal is emitted by a luminescent marker conjugated to the bio-target. A

Fig. 12. (a) Schematics of a photonic crystal resonators matrix used in the optical DNA micro array chip. Each resonator of the matrix (bounded to a specific bio-recognition element) is designed in order to show a different resonant wavelength. (b) A typical example of the emission collected from a read-out area not assisted by photonic crystal resonators. The lineshape is typical of the original marker, with the presence of a significant noise due to scattered excitation light. (c) Example of the emission signal detected on the whole read-out area, where 1, 2 and i are the spectral peculiar modifications due to the coupling of the fluorophores with the 1st, 2nd and ith resonator in the matrix. The presence of each peak in the ensemble spectrum reveals the presence of the corresponding target analyte in the

**4. Diffraction efficiency modeling of 2D photonic crystals for biosensing** 

Optical bio-sensing approach usually consists of light intensity detection systems. Typically, the luminescent signal is emitted by a luminescent marker conjugated to the bio-target. A

analyzed assay.

**applications** 

good enhancement of this emitted signal can be obtained by combining a PhC structure with the luminescent substance. The signal enhancement can be optimized by analyzing the diffraction efficiency of the light emitted from the luminescent substance, characterized by the **K** wave-vector (see Fig. 13 (a) and (b)). In general, by exciting a properly designed PhC structure with an optimum incidence angle, it is possible to detect a high-intensity diffracted signal. The presented diffraction modeling takes into account this optimum incidence condition by defining sets of possible incidence angles (working regions) in the emission luminescent band. In this section the diffraction efficiency of a square lattice PhC Si3N4 membrane covered with a luminescent substance is modelled. The structure is excited by a plane wave and the light coming out from the luminescent substance is also modeled as a plane wave with the **K** vector shown in Fig. 13 (a), characterized by *θ* and angles. In Fig. 14 (a) and (b) we report the diffraction efficiency map versus the wavelength and the angle for different launch *θ*-angles. By fixing the *θ* and angles in the working region (see Fig. 14 where =*θ*=30°), it is possible to analyze the sensitivity of the reflectivity response. This allows to estimate the error margins due to the limits of the fabrication technology and of the experimental setups. As example, in Fig. 15 (a) is reported the sensitivity of the reflectivity response by varying hole radius in steps of 5 nm. Transverse electric (TE) and transverse magnetic (TM) PhC radiation modes define the diffraction concerning different PhC Brillouin directions. Figure 15 (b) shows the TM PhC radiation modes (diffraction modes) in the luminescent emission band 0.56m0.58m. The PhC Si3N4 membrane structure is excited by a plane wave and the light coming out from the luminescent substance, is collected in a detection system.

Fig. 13. (a) Photonic crystal for bio-sensing applications. (b) Source launch coordinate system of the model.

Photonic Crystal Waveguides and Bio-Sensors 127

Fig. 15. Reflectivity of a 2D periodic structure versus the air hole radius R (*a*=300nm, *t*=300nm). Example of TM radiation modes for a square lattice PhC with *a*=300nm.

**discussions** 

**5. Design criteria of a biocompatible polymeric photonic crystal sensor and** 

Concerning bio compatible PhC, we consider in the example of this section, gold pillars growth on Polydimethylsiloxane (PDMS) polymer. In order to improve resonant emitting peaks, we fix as example a square lattice layout with a central micro-cavity defect (see Fig.

Fig. 14. Diffraction efficiency map versus *λ* and angle: *d*=180nm, *a*=300nm, *t*=300nm, *θ*=30 deg. Diffraction efficiency map versus *λ* and angle: *d*=180nm, *a*=300nm, *t*=300nm, *θ*=45 deg.

Fig. 14. Diffraction efficiency map versus *λ* and

deg. Diffraction efficiency map versus *λ* and

deg.

angle: *d*=180nm, *a*=300nm, *t*=300nm, *θ*=30

angle: *d*=180nm, *a*=300nm, *t*=300nm, *θ*=45

Fig. 15. Reflectivity of a 2D periodic structure versus the air hole radius R (*a*=300nm, *t*=300nm). Example of TM radiation modes for a square lattice PhC with *a*=300nm.

### **5. Design criteria of a biocompatible polymeric photonic crystal sensor and discussions**

Concerning bio compatible PhC, we consider in the example of this section, gold pillars growth on Polydimethylsiloxane (PDMS) polymer. In order to improve resonant emitting peaks, we fix as example a square lattice layout with a central micro-cavity defect (see Fig.

Photonic Crystal Waveguides and Bio-Sensors 129

Fig. 17. (a) TE Band diagram of square lattice PhC without (a) and with (b) micro-cavity

central defect, respectively.

16 (a)) [Massaro, 2011]. The input is a laser beam working at a wavelength . The source excites in the PhC waveguides TE and TM modes characterized by the electromagnetic field components reported in Fig. 16 (b). The PDMS material (*nbackground*=1.4) represents the background where will be growth the gold pillars. The design criteria in order to improve efficient emitting cavities are listed by the following points:


By focusing on TE modes we calculate the band gaps illustrated in Fig. 17 (a). Then we introduce the central defect as indicated in Fig. 16 (a) and calculate the new band gaps by observing that one of previous band will be divided into two band gaps. In the analyzed case, the band gap found around *a*/ = 0.3 is divided into two ones as shown in Fig. 17 (b). The cavity modes are defined between the two new band gaps. The cavity modes are confined inside the cavity as proved by Fig. 18 which illustrates the modal profiles of the electric field component *Ey* . It is possible to select the best cavity modes (characterized by the best quality factor) by tuning the source wavelength around the selected mode. In order to improve strong power energy inside the cavity, we excite the PhC slab by a TE polarized source. The light emitting property along the direction orthogonal to the layout plane, could be improved by considering a 3D membrane type configuration or a central defect pillar characterized by a different size or material. The 2D approach allows to mainly fix the geometrical layout and to define the working wavelength. An accurate study of the 3D model will supply information about the best geometrical parameters such as the height of the pillars, the PDMS slab core thickness, and the dimensions of the membrane [Massaro et al., 2008]. Possible measurements of the designed PhC can be performed by Microphotoluminescence setup [Massaro et al., 2008], by Fourier transform infrared (FTIR) and by UV visible analysis.

Fig. 16. (a) Example of square lattice 2D layout of a PhC with central micro-cavity and gold pillars. (b) TE and TM mode classification.

excites in the PhC waveguides TE and TM modes characterized by the electromagnetic field components reported in Fig. 16 (b). The PDMS material (*nbackground*=1.4) represents the background where will be growth the gold pillars. The design criteria in order to improve

2. we calculate the band gaps of the same PhC with central defect obtained by omitting

By focusing on TE modes we calculate the band gaps illustrated in Fig. 17 (a). Then we introduce the central defect as indicated in Fig. 16 (a) and calculate the new band gaps by observing that one of previous band will be divided into two band gaps. In the analyzed case, the band gap found around *a*/ = 0.3 is divided into two ones as shown in Fig. 17 (b). The cavity modes are defined between the two new band gaps. The cavity modes are confined inside the cavity as proved by Fig. 18 which illustrates the modal profiles of the electric field component *Ey* . It is possible to select the best cavity modes (characterized by the best quality factor) by tuning the source wavelength around the selected mode. In order to improve strong power energy inside the cavity, we excite the PhC slab by a TE polarized source. The light emitting property along the direction orthogonal to the layout plane, could be improved by considering a 3D membrane type configuration or a central defect pillar characterized by a different size or material. The 2D approach allows to mainly fix the geometrical layout and to define the working wavelength. An accurate study of the 3D model will supply information about the best geometrical parameters such as the height of the pillars, the PDMS slab core thickness, and the dimensions of the membrane [Massaro et al., 2008]. Possible measurements of the designed PhC can be performed by Microphotoluminescence setup [Massaro et al., 2008], by Fourier transform infrared (FTIR) and by

Fig. 16. (a) Example of square lattice 2D layout of a PhC with central micro-cavity and gold

. The source

16 (a)) [Massaro, 2011]. The input is a laser beam working at a wavelength

efficient emitting cavities are listed by the following points:

3. we define the mode distribution of the cavity modes.

the central pillar;

UV visible analysis.

pillars. (b) TE and TM mode classification.

1. we define the band gaps of the PhC without micro-cavity defect;

Fig. 17. (a) TE Band diagram of square lattice PhC without (a) and with (b) micro-cavity central defect, respectively.

Photonic Crystal Waveguides and Bio-Sensors 131

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