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Cascaded silicon-on-insulator microring resonators for the detection of biomolecules in PDMS microfluidic.. Flueckiger, Jonas 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 cross- section 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. three ima nm.  (a) S gap.  3.2 Simulat The wavegui mode profile silicon and si file for wate addition of g Table 1:  The mode pr varying wave the effective subsequent m the slope bet the medium w dependence o MODE Solut and bent wav concentration straight and c The mode p presented in  The SEM imag ges were taken a ingle waveguid ed Mode Prof de and couple s.  The waveg licon dioxide. r or slightly m lycerin.  The o Refractive index ofiles were fi lengths.  A 10 index (neff) va easurements w ween these da as assumed t f the effective ions profiles w eguides of th s tested, and urved wavegu rofiles for the Figure 3. es of the FIB-m t 65 kx magnifi e.  (b) Direction iles r geometries p uides and SiO   The surround odifying it to ffset used is pr  of Glycerin-W Glycerin % b 0 5 10 15 20 rst simulated f -point frequen ried approxim ere only mea tapoints.  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All ge represents 50 th 400 nm coupl lutions to simu tions material DE Solutions tive index du ode was track  it was determi resources, eac  was determin the refractive , the same wav ulated media. ’s directional arious water - over loss betw  nm gap spac  0 er late the files for material e to the ed over ned that h of the ed from index of elength couplers glycerin een the ing) are 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: straight w intensitie the two su  3.3 Simulat After simula responses fro profiles to de field couplin functions pre The resonato shown in equ  where the su coupler (t2). T ranges (FSR)  Mode profiles aveguide, (b) s for the two sup permodes of th ed Transmiss tion, the MOD m analytical m termine the p g (κ) and tran viously presen r response wa ation 130L bscripts on th he simulated  are presented simulated using shows the ener ermodes of the e 400 nm gap sp ion Spectra E Solutions odels.  This hase differenc smission (t) fo ted by our gro s then simulate e values for f transmission s  in Figure 4 to  Lumerical MO gy density prof  200 nm gap sp acing coupler data were imp script used the e (δ) and losse r each of the up 29 to determ d from these v Ethroug ield transmiss pectra for two gether with me DE Solutions. ile for a straigh acing coupler, a orted into a c  effective indi s (α) resulting  resonator’s d ine these valu alues using th h = t1 − t2 *αe 1− t1*t2*α ion refer to th  cascaded race asured data.  (a) shows the t waveguide, ( nd (e) and (f) de ustom MATL ces and mater  from a round irectional coup es. e analytical m iδ eiδ ,  e through por track resonator electric field in c) and (d) depi pict the electric AB script to ial losses deter  trip of the re lers.  The scr odel for a dou t coupler (t1) s with slightly tensity profile f ct the electric  field intensitie simulate the r mined from th sonator as we ipt employed ble-bus ring r and the add/d  different free or a field s for esonator e mode ll as the analytic esonator (1)  rop port  spectral 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 two- resonator 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 a the smallest sample analy noise factors transmission the error bar resonant prof Figure 7: compared In summary, network fabr resonator ind sweep. The v mixture with predict reson MATLAB sc We would lik with and pro well Prof. Ni grateful to Lu in the design [1] Washbur Usin [2] Little, B micr [3] Kaalund s well. Other possible spect te (or RIU cha . In this work spectra thus m s in Figure 7 i iles by a Gaus  Resonance wa  to the predicted  we proposed icated by soft ividually expo olume refract  different mix ator propertie ript e to thank Dr viding training colas A. F. Jae merical Solut of the mask la n, A. L., Gunn g Silicon Pho . E., Chu, S. oring resonato , C. J., "Critica important para ral shift that c nge) that the s resonance pea aking it very ndicate the va sian distributio velength shift a  values from th  and impleme lithography to sed to differe ive index sens ing ratios and s by implemen . Li Yang from  for the SEM/ ger from the U ions, Inc. for p yout. , L. C. and Ba tonic Microrin T., Pan, W., R r channel drop lly coupled rin meters of the an be accurat ensor can qua ks are detecte sensitive to no riation of the n and then co s a function of e finite element 5. CO nted the use o  expose each r nt environmen itivity of the r known refract ting a finite e ACKNOW  the Simon F FIB used to m niversity of B roviding the s REF iley, R. C., "L g Resonators," ipin, D., Kan ping filters," I g resonators f  system not qu ely measured, ntify. They are d by simply tr ise. The meas resonance pea mpute the mea the refractive i model. NCLUSIO f cascaded rin ing individual ts can be sim acetrack reson ive indices. F lement model LEDGEME raser Universit easure the wav ritish Columb imulation soft ERENCES abel-Free Qua  Anal. Chem., eko, T., Koku EEE Photo. T or add-drop fil antified in thi  and the detec  dependent of acking the po urement is do k. A better ap n value and st ndex of the bin N g resonators ly to different ultaneously m ator is determ urthermore we  using Lumer NTS y (SFU) nano eguide cross- ia (UBC) for ware and to C ntitation of a C  81, 9499-950 bun, Y. and echnol. Lett., tering," Opt. C s work are the tion limit, the  the systems’ sition of the m ne at steady st proach would andard deviatio ary mixture. Th together with solutions. We easured with ined by inject  have shown ical MODE S -imaging facil sections. 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{[{ mDataHeader[type] }]} {[{ month[type] }]} {[{ tData[type] }]}


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