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Cascaded silicon-on-insulator microring resonators for the detection of biomolecules in PDMS microfluidic… Flueckiger, Jonas; Grist, Samantha M.; Bisra, Gurpa; Chrostowski, Lukas; Cheung, Karen C. 2011

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Cascaded silicon-on-insulator microring resonators for the detection of biomolecules in PDMS microfluidic channels Jonas Flueckiger*, Samantha M. Grist, Gurpal Bisra, Lukas Chrostowski, Karen C. Cheung Department of Electrical and Computer Engineering, The University of British Columbia 2332 Main Mall, Vancouver, BC, Canada, V6T1Z4 ABSTRACT Silicon-On-Insulator (SOI) photonic microring resonators have shown promising potential for real time detection of biomolecules because of the sensitivity towards surface binding events. Previous work shows the use of single ring resonators for sensing applications. Each ring requires an input and output coupler and can be addressed only one at a time. We propose a novel use of cascaded ring resonators (width w = 200 nm and bending Radius R = 30 µm) together with a PDMS microfluidic network fabricated by soft lithography to expose each ring individually with different solutions. The SOI substrate with the planar waveguides and the PDMS with the microchannels are reversibly bonded to each other. The use of cascaded ring resonators offers the possibility to measure transmission spectra of multiple rings in different channels simultaneously. We measured Q-factors of >30'000 in air and >10'000 when exposed to water. Using a water/glycerin solution with known refractive indices we determine the sensitivity to be ~40 nm/RIU. Keywords: Nanophotonics, Label-free biosensors, Silicon-on-insulator, Ring Resonator, Microfluidics  1. INTRODUCTION Evanescent field sensors such as Surface Plasmon Resonance (SPR) or planar waveguide based sensors are amongst the most popular optical detection techniques for sensitive and label free biomolecular detection 1. Silicon-On-Insulator (SOI) photonic microcavity resonators have shown promising potential for real time detection of biomolecules because of their sensitivity towards surface binding events. Traditionally, these resonators have been demonstrated in add-drop filter2-3, optical switches4,and laser applications5-6. It has been shown that silicon-on-insulator (SOI) waveguides with dimensions smaller than the wavelength of light have a strong evanescent field at the waveguide surface extending a few hundred nanometers into the surrounding media. Any interaction with molecules in proximity or surface bound molecules will change the effective refractive index of the guided mode and thus alter the resonance behavior. The degree of interaction of the evanescent field and the sample is limited by the number of roundtrips by the light inside the ring and the footprint of the sensing area can be reduced without losing sensitivity. In case of a straight waveguide based sensor, such as a Mach-Zehnder the interaction is limited by the physical length of the sensing waveguide. Optical sensors based on ring and racetrack resonators have been proposed and developed using a variety of materials and for a variety of applications such as chemical sensing7-8 and sensing of biological molecules such as antibodies or antigens 9-12. In particular, the optical, label-free detection of biomolecules is a topic of considerable interest13-14. The sensitivity of a ring resonator is dependent on the overlap of the evanescent field and the sample 15. In a strip waveguide most of the power is contained inside the core and only a small portion propagates outside in the media. To further enhance the sensitivity, slotted waveguides8, 16-20 or resonator disks 21 have been used. Compared to other sensing methods, optical sensors methods have the advantages of high sensitivity, no physical contact, immunity to electromagnetic interference, and multiplexed interrogation. The most basic configuration of a ring or racetrack resonator sensor is to couple the light to individual input and output optical fibers. A vertical-to-horizontal grating coupler design (70 nm trenches) is used for TE-like optical mode injection. It is of interest to integrate multiple resonators on a single chip to perform multiple measurements in parallel or to compensate for temperature drifts 22. By using the basic configuration, the required number of input and output fibers increases proportionally with each added resonator and parallel measurement can only be done with sophisticated measurement and aligment set ups. Ramachandran et al. integrated 5 resonators on a single chip each of those resonators connected individually to input/output optical fibers9. Kwon et al. use two cascaded polymer microring resonators on the *Corresponding author: jonasf@ece.ubc.ca Microfluidics, BioMEMS, and Medical Microsystems IX, edited by Holger Becker, Bonnie L. Gray, Proc. of SPIE Vol. 7929, 79290I · © 2011 SPIE · CCC code: 0277-786X/11/$18 · doi: 10.1117/12.873974  Proc. of SPIE Vol. 7929 79290I-1 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  same straight waveguide fabricated out of Su-823. One resonator was covered by a cladding and the second resonator was exposed to the analytes. The covered resonator was used to compensate for temperature drifts. Dai et al. amongst others investigated the use of cascaded resonators theoretically24-26. Gylfason et al. used a multi-mode interference splitter integrated on the same chip as the resonators to address 8 rings using only one input grating coupler22. The waveguide’s output is focused onto a single pixel photodiode array. The resonators are etched into a silicon nitride film on top of silicon oxide layer. The concept of a lab-on-a-chip combines sample handling and analysis in one single chip, thereby offering the possibility of a portable analysis platform. Picoliter sample volumes can be handled inside micrometer scale fluidic channels using valves and pumps integrated into silicon or polymer chips 27. It is of great interest to include sensor technology into these lab-on-chip devices to automate parallel processing and therefore lower cost and increase throughput. Ksendzov et al. clamped a flow cell down onto the sensor chip28. They achieved sealing by using an o-ring and pressure. However they are not able to expose individual resonators with different analytes. Washburn et al. and Luchansky et al. used a laser cut Mylar gasket aligned over top of the microring arrays to define microfluidic channels1, 11 . They closed the channels off with a Teflon lid and sandwiched the different layers between an aluminum chip holders. These microwells are only useful for steady state measurements. Because mass transport is diffusion limited, they are not suitable to determine dynamics of fast reactions, e.g. binding events of proteins. Moreover, in order to be able to run several experiments with different analytes or different concentrations in parallel individual resonators need to be addressed and exposed. Carlborg et al. used a microfluidic channel network in poly(dimethylsiloxane) (PDMS), with a separate fluid channel to each sensor for sample delivery10. We propose the use of cascaded ring resonators together with a PDMS microfluidic network fabricated by soft lithography to expose each ring individually with different solutions. The SOI substrate with the planar waveguides and the PDMS with the microchannels are reversibly bonded to each other. The use of cascaded ring resonators offers the possibility to measure transmission spectra of multiple rings in different channels simultaneously. The volume refractive index sensitivity of the racetrack resonator is determined by injecting a water – glycerin mixture with different mixing ratios and known refractive indices.  2. MATERIALS AND METHODS  Figure 1. The measurement setup: the optical input fiber is connected to a tunable laser source with wavelength at around 1550 nm and the output optical fiber is connected to an optical power sensor. The measurements are performed on a temperature controlled stage. Fluidic tubing are connected to a syringe pump.  2.1 Fabrication of SOI ring resonators The SOI nanophotonic single-mode waveguides were fabricated with deep UV lithography (193 nm) and standard CMOS etching processes as part of IMEC’s passive photonic ePIXfab cSOI process. It is possible to get features down  Proc. of SPIE Vol. 7929 79290I-2 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  to 120 nm and a minimum pitch of 300 nm. The ring/racetrack resonators are patterned onto a 200 mm SOI wafer. The buried oxide layer is 2000 nm thick and the crystalline top silicon film is 220 nm thick. A vertical-to-horizontal grating coupler design (70 nm trenches) is used for TE-like optical mode injection. The straight waveguides have a width of w = 500 nm. The design includes several configurations with 1-4 cascaded rings or racetracks with different radii and different coupling gaps. DW-2000 mask layout design software from Design Workshop technologies, Quebec, Canada was used to design the resonator mask layout. 2.2 Fabrication of PDMS microfluidic device PDMS is the most widely used polymer in the field of microfluidics. It is a biocompatible, transparent, rubber-like polymer and can be easily patterned using soft lithography, a well established fabrication method. The mold masters were fabricated with standard photolithography techniques on Su-8 2075 (MicroChem, USA). Through replica molding the patterns were transferred onto PDMS. The uncured PDMS (Sylgard 184, Dow Corning USA) was poured onto the mold master to a thickness of about 1 cm, degassed to remove air bubbles, and cured at 80 °C for 2h on a hotplate. The hydrophobic surface properties can be altered in an oxygen plasma by replacing some of the surface methyl groups (CH3) by a hydroxyl groups (-OH). This activated surface can form covalent siloxane bonds (Si-O-Si) when in contact with glass or silicon substrates, forming an irreversible seal. After punching access holes for the fluidic inlet and outlets the PDMS layer and the resonator substrate were aligned and bonded to each other. 2.3 The measurement set up A tunable laser source (Agilent 81681A, Agilent Technologies, Inc., USA) was used with an output wavelength range from 1460 nm to 1580 nm. A single mode optical fiber was aligned with the vertical-to-horizontal grating coupler design to inject light into the SOI waveguides. The output light intensity was collected with a multimode optical fiber and measured with an optical power sensor (Agilent 81635A, Agilent Technologies, Inc., USA). The temperature of the substrate was kept constant with a Peltier element and a temperature controller (Stanford Research System, USA) in a closed feedback loop configuration.  3. FINITE ELEMENT MODELLING The resonators were simulated using Lumerical MODE Solutions and a custom MATLAB script. MODE Solutions was used to simulate the mode profiles, effective refractive indices, and material losses for a straight SOI waveguide, bent waveguides, and coupler regions. This data was then imported into a custom MATLAB script to simulate the resonator response. Due to fabrication process parameter variations, the cross-sections of the waveguides are trapezoidal instead of the desired rectangular shape. The finite element model takes these aberrations into account as presented in 3.1. The simulation procedure and results for the mode profiles are presented in 3.2, while the MATLAB script simulation procedure and results for a single refractive index and simulated shifts in refractive index are presented in 3.3 and 3.4, respectively. 3.1 Corrections for Fabrication Errors In an effort to accurately simulate the waveguide geometry and account for any discrepancies between fabrication and design, Scanning Electron Microscope (SEM) images were taken of the design. In order to image the waveguide crosssection and estimate the sidewall slope of the waveguides, a Focused Ion Beam (FIB) was used to mill trenches over a straight waveguide as well as two coupler regions (one of 200 nm waveguide spacing and the other of 400 nm waveguide spacing). After FIB milling, the waveguides were imaged with a 52° tilt to observe their cross-sections. The pixel lengths of the waveguides were then compared with the pixel length of the scale bar to determine the widths of the top and bottom of the waveguides; the coupler gaps were determined with a similar method. The average of five measurements was used as the waveguide dimensions for simulation. Only one measurement was obtained for each of the coupler gaps. It was determined that the 220 nm (as verified by profilometry) silicon layer was approximately 470 (±17) nm wide at the top edge and 575 (±11) nm wide at the SiO2 interface, indicating a sidewall angle of approximately 14° (±2°). The coupler gaps at the SiO2 interface were determined to be approximately 113 nm for the 200 nm coupler gap design and 327 nm for the 400 nm coupler gap design.  Proc. of SPIE Vol. 7929 79290I-3 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  Figure 2. The SEM imag ges of the FIB-m milled waveguidee cross-sections used u to measure the waveguide dimensions. d Alll a 65 kx magnifiication with a 522° tilt and the scaale bar at the botttom of each imaage represents 5000 three imaages were taken at nm. (a) Single S waveguid de. (b) Directionnal coupler with 200 nm coupler gap. (c) Directiional coupler with 400 nm coupller gap.  3.2 Simulatted Mode Proffiles The waveguiide and coupleer geometries presented p in 3.11 were importeed into Lumeriical MODE Soolutions to simuulate the mode profilees. The waveg guides and SiO O2 substrate weere modeled ussing the defaullt MODE Soluutions material files for silicon and siilicon dioxide. The surroundding media waas simulated byy either using the t default MO ODE Solutions material file for wateer or slightly modifying m it too achieve a coonstant offset in i the real parrt of the refracctive index duue to the addition of glycerin. The offset o used is prresented in table 1. Table 1: Refractive index x of Glycerin-W Water solutions att 20°C.  Glycerin % by b Weight  Reffractive Index n  0  1.33303  5  1.33880  100  1.34481  155  1.35106  200  1.35749  f an incidennt wavelength of o 1500 nm, and a then the mode m was trackked over The mode prrofiles were fiirst simulated for varying waveelengths. A 10 0-point frequenncy sweep was first obtained for a straight waveguide w andd it was determiined that the effective index (neff) vaaried approxim mately linearly over this wavelength range. To conserve resources, eacch of the subsequent measurements m were w only meaasured at 1500 nm and 1600 nm, and the grroup index (ng) was determinned from the slope bettween these daatapoints. Beccause the waveelength dependdence and imagginary part of the refractive index of concentrationss, the same wavvelength the medium was w assumed to t be the same for pure waterr and various water-glycerin w dependence of o the effectivee refractive inddex and the sam me material loss were used for all of the sim mulated media. MODE Soluttions profiles were w obtained for f coupler reggions corresponnding to both of o the resonatorr’s directional couplers and bent wavveguides of the appropriate bend b radii. Eacch of these sim mulations was repeated for various v water - glycerin concentrationns tested, and the detailed mode m data werre exported to text files. Thhe mode crosssover loss betw ween the straight and curved c wavegu uide sections was w also simulaated for each beend radius. The mode profiles p for thee straight waveguide and tw wo directional couplers (2000 nm and 400 nm gap spaccing) are presented in Figure 3.  Proc. of SPIE Vol. 7929 79290I-4 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  Figure 3:: Mode profiles simulated usingg Lumerical MO ODE Solutions. (a) shows the electric field inntensity profile for f a straight waveguide, w (b) shows the energy density proffile for a straighht waveguide, (c) ( and (d) depiict the electric field intensities for the two sup permodes of thee 200 nm gap spacing coupler, and a (e) and (f) deepict the electricc field intensities for he 400 nm gap sppacing coupler the two suupermodes of th  3.3 Simulatted Transmission Spectra After simulaation, the MOD DE Solutions data were impported into a custom c MATL LAB script to simulate the resonator r responses froom analytical models. m This script used thee effective indiices and materrial losses deterrmined from thhe mode profiles to deetermine the phase p differencce (δ) and lossees (α) resultingg from a roundd trip of the reesonator as weell as the field couplinng (κ) and tran nsmission (t) for fo each of thee resonator’s directional d coupplers. The scrript employed analytic functions preeviously presen nted by our grooup 29 to determ mine these valuues. The resonatoor response was then simulateed from these values v using thhe analytical model m for a douuble-bus ring resonator r shown in equuation 130L  E througgh =  t1 − t 2*αe iδ 1 − t1* t 2*αe iδ ,  (1)  where the suubscripts on th he values for field f transmisssion refer to thhe through porrt coupler (t1) and the add/ddrop port coupler (t2). The T simulated transmission spectra s for two cascaded raceetrack resonatorrs with slightlyy different freee spectral ranges (FSR)) are presented d in Figure 4 together with meeasured data.  Proc. of SPIE Vol. 7929 79290I-5 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  Figure 4. Simulated single-resonator responses overlaid upon the measured transmission spectrum for the cascaded tworesonator system. The FSR for the measured Ring 1 response is 2.61±0.03 nm, whereas that for the simulated Ring 1 response is 2.61±0.010 nm. The FSR for the measured Ring 2 response is 3.45±0.014 nm, while that for the simulated response is 3.48±0.015 nm.  The measured and simulated FSRs agree reasonably well for both rings. The small discrepancies are likely due to temperature differences or small inaccuracies in the simulated waveguide geometry (as there were inaccuracies in measuring the waveguide geometry from the SEM cross-sections). 3.4 Simulated Refractive Index Sensitivity As expected, there was a linear relationship between the simulated effective indices for the each of the modes and the expected refractive index change. The plot of simulated effective index (at λ=1500 nm) vs. expected shift in medium refractive index for each of the modes is presented in Figure 5.  Figure 5. Simulated effective index (at λ=1500 nm) vs. bulk refractive index change, for the ring bend regions as well as the two supermodes for each of the two simulated coupler gaps.  Proc. of SPIE Vol. 7929 79290I-6 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  4. RESULTS The volume refractive index sensitivity of the racetrack resonator is determined by injecting a water – glycerin mixture with different mixing ratios and known refractive indices into the corresponding microchannels. The use of the cascaded resonators allows the measurement of individual resonators in different microchannels simultaneously with one frequency sweep. 4.1 Transmission Spectra Figure 6 (a) and (b) show the through port transmission spectra and the center wavelength changes ∆λres for different racetrack resonators as a function of the water – glycerin concentration. Q-factors of >40’000 are measured for certain designs. Figure 6 (a) shows the measured transmission spectrum of two cascaded resonators. Both resonators are exposed individually to different environments. The first resonator (Ring 1) with and FSR of 2.9 ± 0.02 nm is immersed into DI water. The second resonators (Ring 2) with and FSR of 3.45 ± 0.014 nm is exposed to five different water – glycerin concentrations of 0, 5, 10, 15, 20 wt% (see Table 1 for the corresponding refractive indices). The refractive index in channel 1 does not change and therefore there is no resonance peak shift occurring. For Ring 2 the resonance peak shifts linearly with glycerin – water concentration or linearly with increasing refractive index. Similarly Figure 6 (b) shows the measured transmission spectrum of a four resonator system. Again, each resonator can be exposed individually to different environments. Here Ring 1, 2 and 4 are kept constant (exposed to DI water) and Ring 3 is immersed into water and a 10wt% glycerin – water solution respectively.  Figure 6: a) Transmission spectra for a 2 ring system. Ring 1 is exposed to DI water and Ring 2 is exposed to different water – glycerin mixtures. b) Transmission spectra for a 4 ring system. Ring 1,2, and 4 are exposed to DI water. Ring 3 is exposed to two different water-glycerin mixtures.  4.2 Refractive Index Sensitivity For the two resonator system the net shift in resonance peak as a function of refractive index is depicted in Figure 7. The resonance peak for pure DI water for Ring 2 is at λres0 = 1541.35 nm ± 0.008 nm. For a refractive index change of ∆n = 0.02446 which corresponds to a switch from DI water to a 20wt% glycerin – water solution the resonance peak shifts to λres20 = 1542.24 nm ± 0.01 nm. This corresponds to a sensitivity of ~ 36 nm/refractive index unit (RIU). The volume refractive index sensitivity shows a linear relationship. The linear curve fit parameters are a = 36.6385 and b = 1492.5 (for least square fit to y=ax+b). The obtained relationship is compared to the predictions from the finite element model. The diamond shaped data set in Figure 7 represents the modelled values. Despite the fact that the model overestimates the sensitivity, the measured results are sufficiently close to the predicted values, indicating that this model can be used for optimizing the design of the resonator geometries to further enhance Q-factors and sensitivity. The mode simulations (see Figure 3) show that only a small fraction of the field intensity of the optical mode propagates outside the waveguide and can therefore interact with the sample. The use of slotted waveguides would increase the fraction of power propagating outside the waveguide and therefore would increase the sensitivity. The finite element model computed using Lumerical MODE Solutions and a custom MATLAB script can easily be adapted to simulate slotted  Proc. of SPIE Vol. 7929 79290I-7 Downloaded from SPIE Digital Library on 30 May 2011 to Terms of Use: http://spiedl.org/terms  waveguides as a well. Other important paraameters of thee system not quuantified in thiis work are thee sensor resoluution, i.e. the smallest possible specttral shift that can c be accurattely measured,, and the detecction limit, thee minimum am mount of sample analyyte (or RIU chaange) that the sensor s can quaantify. They aree dependent off the systems’ spectral resoluution and noise factorss. In this work resonance peaaks are detecteed by simply trracking the poosition of the minimum m valuees in the transmission spectra thus making m it very sensitive to nooise. The meassurement is done at steady sttate multiple tiimes and the error bars in Figure 7 indicate i the vaariation of the resonance peaak. A better appproach would be to approxim mate the resonant proffiles by a Gausssian distributioon and then compute the meaan value and standard deviatioon.  Figure 7:: Resonance waavelength shift as a a function off the refractive index i of the binnary mixture. Thhe measured daata is comparedd to the predicted d values from thhe finite element model.  5. CO ONCLUSIO ON In summary,, we proposed d and implemented the use of o cascaded rinng resonators together with a PDMS micrrofluidic network fabrricated by soft lithography too expose each ring r individuallly to different solutions. Wee have shown that t each resonator inddividually expo osed to differeent environmennts can be sim multaneously measured m with one single wavvelength sweep. The volume v refracttive index senssitivity of the racetrack r resonnator is determ mined by injectting a water – glycerin mixture withh different mix xing ratios and known refracttive indices. Furthermore wee have shown that we can acccurately predict resonnator properties by implemennting a finite element e modell using Lumerrical MODE Solutions and a custom MATLAB sccript  ACKNOW WLEDGEME ENTS We would likke to thank Drr. Li Yang from m the Simon Fraser Universitty (SFU) nanoo-imaging facillity for kindly assisting with and providing training g for the SEM//FIB used to measure m the wavveguide cross--sections. We would w like to thhanks as well Prof. Niicolas A. F. Jaeeger from the University U of British B Columbbia (UBC) for his insights annd support. Wee are also grateful to Luumerical Soluttions, Inc. for providing p the simulation s softtware and to CMC C Microsysttems for the asssistance in the design of the mask laayout.  REF FERENCES n, L. C. and Baailey, R. C., "L Label-Free Quaantitation of a Cancer C Biomarrker in Compleex Media [1] Washburrn, A. L., Gunn Usinng Silicon Pho otonic Microrinng Resonators,"" Anal. Chem.,, 81, 9499-9506 (2009) [2] Little, B. 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