Applied Science, Faculty of
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Biosensors 12 (10): 840 (2022)
University of British Columbia. Centre for Blood Research
The Stewart Blusson Quantum Matter Institute
Puumala, Lauren S.
Grist, Samantha M.
Wickremasinghe, Kithmin
Al-Qadasi, Mohammed A.
Chowdhury, Sheri Jahan
Liu, Yifei
Mitchell, Matthew
Chrostowski, Lukas
Shekhar, Sudip
Cheung, Karen C.
Silicon photonic (SiP) evanescent-field biosensors aim to combine the information-rich readouts offered by lab-scale diagnostics, at a significantly lower cost, and with the portability and rapid time to result offered by paper-based assays. While SiP biosensors fabricated with conventional strip waveguides can offer good sensitivity for label-free detection in some applications, there is still opportunity for improvement. Efforts have been made to design higher-sensitivity SiP sensors with alternative waveguide geometries, including sub-wavelength gratings (SWGs). However, SWG-based devices are fragile and prone to damage, limiting their suitability for scalable and portable sensing. Here, we investigate SiP microring resonator sensors designed with SWG waveguides that contain a “fishbone” and highlight the improved robustness offered by this design. We present a framework for optimizing fishbone-style SWG waveguide geometries based on numerical simulations, then experimentally measure the performance of ring resonator sensors fabricated with the optimized waveguides, targeting operation in the O-band and C-band. For the O-band and C-band devices, we report bulk sensitivities up to 349 nm/RIU and 438 nm/RIU, respectively, and intrinsic limits of detection as low as 5.1 × 10−⁴ RIU and 7.1 × 10−⁴ RIU, respectively. This performance is comparable to the state of the art in SWG-based sensors, positioning fishbone SWG resonators as an attractive, more robust, alternative to conventional SWG designs.
Citation: Puumala, L.S.; Grist, S.M.;Wickremasinghe, K.; Al-Qadasi, M.A.;Chowdhury, S.J.; Liu, Y.; Mitchell, M.;Chrostowski, L.; Shekhar, S.; Cheung,K.C. An Optimization Framework forSilicon Photonic Evanescent-FieldBiosensors Using Sub-WavelengthGratings. Biosensors 2022, 12, 840.https://doi.org/10.3390/bios12100840Received: 6 September 2022Accepted: 30 September 2022Published: 8 October 2022Publisher’s Note: MDPI stays neutralwith regard to jurisdictional claims inpublished maps and institutional affil-iations.Copyright: © 2022 by the authors.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).biosensorsArticleAn Optimization Framework for Silicon PhotonicEvanescent-Field Biosensors Using Sub-Wavelength GratingsLauren S. Puumala 1,2,*, Samantha M. Grist 1,2,3, Kithmin Wickremasinghe 4 , Mohammed A. Al-Qadasi 4,†,cSheri Jahan Chowdhury 4,†, Yifei Liu 4, Matthew Mitchell 3,5 , Lukas Chrostowski 3,4,5, Sudip Shekhar 3,4cand Karen C. Cheung 1,2,4,*1 School of Biomedical Engineering, University of British Columbia, 251-2222 Health Sciences Mall,Vancouver, BC V6T 1Z3, Canada2 Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall,Vancouver, BC V6T 1Z3, Canada3 Dream Photonics Inc., Vancouver, BC V6T 0A7, Canada4 Department of Electrical and Computer Engineering, University of British Columbia, 5500-2332 Main Mall,Vancouver, BC V6T 1Z4, Canada5 Stewart Blusson Quantum Matter Institute, University of British Columbia, 2355 East Mall,Vancouver, BC V6T 1Z4, Canada* Correspondence: lpuumala@student.ubc.ca (L.S.P.); kcheung@ece.ubc.ca (K.C.C.)† These authors contributed equally to this work.Abstract: Silicon photonic (SiP) evanescent-field biosensors aim to combine the information-richreadouts offered by lab-scale diagnostics, at a significantly lower cost, and with the portability andrapid time to result offered by paper-based assays. While SiP biosensors fabricated with conventionalstrip waveguides can offer good sensitivity for label-free detection in some applications, there is stillopportunity for improvement. Efforts have been made to design higher-sensitivity SiP sensors withalternative waveguide geometries, including sub-wavelength gratings (SWGs). However, SWG-baseddevices are fragile and prone to damage, limiting their suitability for scalable and portable sensing.Here, we investigate SiP microring resonator sensors designed with SWG waveguides that contain a“fishbone” and highlight the improved robustness offered by this design. We present a frameworkfor optimizing fishbone-style SWG waveguide geometries based on numerical simulations, thenexperimentally measure the performance of ring resonator sensors fabricated with the optimizedwaveguides, targeting operation in the O-band and C-band. For the O-band and C-band devices,we report bulk sensitivities up to 349 nm/RIU and 438 nm/RIU, respectively, and intrinsic limits ofdetection as low as 5.1 × 10−4 RIU and 7.1 × 10−4 RIU, respectively. This performance is comparableto the state of the art in SWG-based sensors, positioning fishbone SWG resonators as an attractive,more robust, alternative to conventional SWG designs.Keywords: silicon photonics; evanescent field biosensor; SOI biosensor; ring resonator; fishbonesub-wavelength grating waveguide; sub-wavelength grating waveguide; SWG-assist waveguide;bridged SWG waveguide; microfluidics1. IntroductionThe recent COVID-19 pandemic has highlighted the importance of scalable, rapid,portable, and cost-effective medical diagnostics in public safety and informed decisionmaking [1,2]. Currently, gold-standard medical diagnostics rely on lab-based tests, whichare performed in centralized settings and suffer from high costs, long analysis times, therequirement for highly trained operators, and complex logistics regarding sample transportand information management [3]. Portable, low-cost, and easy-to-use diagnostic tools,such as paper-based assays, allow for rapid and accessible testing in decentralized settings.However, they offer less information-rich readouts and often suffer from poorer sensitivityBiosensors 2022, 12, 840. https://doi.org/10.3390/bios12100840 https://www.mdpi.com/journal/biosensorsBiosensors 2022, 12, 840 2 of 35and accuracy compared with lab-based techniques [4]. Silicon photonic (SiP) biosensorsoffer the potential to bridge the gap between these two classes of diagnostic systems.By leveraging highly scalable complementary metal-oxide semiconductor (CMOS)fabrication processes, SiP chips can be produced in high volumes at low cost [5–8]. Theirscalability, affordability, rapid readout, and millimeter-scale form factor, makes SiP sensorsamenable to testing in point-of-care (POC) settings. In addition to managing infectiousdiseases, rapid POC testing is valuable for the diagnosis of conditions such as stroke andsepsis, where rapid confirmation of clinical findings is critical for timely and effectivetreatment decision-making [9–11]. POC tests can also improve access to diagnostics inremote and resource-limited communities. Dozens of sensors can be fabricated on a singleSiP chip, which, when combined with spatially controlled functionalization, can facilitatehigh-throughput multiplexed diagnostic testing [12]. This opens opportunities for moreselective and information-rich diagnosis of conditions that are challenging to identifybased on a single biomarker alone [9,13]. Extremely sensitive biomarker detection downto the pg/mL scale has been demonstrated on SiP platforms based on well-establishedstrip waveguides (Figure 1c) [14,15]. However, these exceptionally low-limit of detectiondemonstrations have used sandwich assay formats in which the final detected signaloriginated from a detection antibody [16] or subsequent amplification step [14,15], ratherthan from the analyte itself. Label-based strategies such as these offer slower detection andrequire more complex assay operation than label-free formats. While label-free detectionhas been demonstrated with SiP platforms [17,18] and is more suitable for POC applicationsdue to its simplicity, label-free biosensors based on strip waveguides typically have higherdetection limits in the ng/mL range. Many clinical diagnostic assays require lower detectionlimits [19]. This has motivated the design of SiP sensors, such as microring resonators(MRRs), with improved performance criteria, including refractive index sensitivities.Biosensors 2022, 12, x FOR PEER REVIEW 2 of 35 tools, such as paper-based assays, allow for rapid and accessible testing in decentralized settings. However, they offer less information-rich readouts and often suffer from poorer sensitivity and accuracy compared with lab-based techniques [4]. Silicon photonic (SiP) biosensors offer the potential to bridge the gap between these two classes of diagnostic systems. By lev raging highly scalable complementary metal-oxide semicondu tor (CMOS) fabrication processes, SiP chips can be produc d in high volumes at low cost [5–8]. Their scalability, affordability, rapid readout, an millimeter-scale form fact r, makes SiP sen-sors amenable to testing in point-of-care (POC) settings. In addition to anaging infec-tious diseases, rapid POC testing is valuable for the diagnosis of conditions such as stroke and sepsis, where rapid confirmation of clinical findings is critical for timely and effective treatment decision-making [9–11]. POC tests can also improve access to diagnostics in re-mote and resource-limited communities. Dozens of sensors can be fabricated on a single SiP chip, which, when combined with spatially controlled functionalization, can facilitate high-throughput multiplexed diagnostic testing [12]. This opens opportunities for more selective and information-rich diagnosis of conditions that are challenging to identify based on a single biomarker alone [9,13]. Extremely sensitive biomarker detection down to the pg/mL scale has been demonstrated on SiP platforms based on well-established strip waveguides (Figure 1c) [14,15]. However, these exceptionally low-limit of detection demonstrations have used sandwich assay formats in which the final detected signal orig-inated from a detection antibody [16] or subsequent amplification step [14,15], rather than from the analyte itself. Label-based strategies such as these offer slower detection and re-quire more complex assay operation than label-free formats. While label-free detection has been demonstrated with SiP platforms [17,18] and is more suitable for POC applica-tions due to its simplicity, label-free biosensors based on strip waveguides typically have higher detection limits in the ng/mL range. Many clinical diagnostic assays require lower detection limits [19]. This has motivated the design of SiP sensors, such as microring res-onators (MRRs), with improved performance criteria, including refractive index sensitiv-ities. Figure 1. (a) Illustration of microring resonator (MRR) with radius R fabricated with fishbone sub-wavelength grating (SWG) waveguides and (b) expanded view of bus-to-ring coupling region with coupling gap gc. Illustrations of (c) strip, (d) conventional SWG, and (e) fishbone SWG waveguide geometries with width w, thickness t, grating period Λ, duty cycle δ, and fishbone width wfb. (f) Graphical representations of MRR performance criteria, including (clockwise from top left) critically Figure 1. (a) Illustrati f i r ri resonator (M R) with radius R fabricated with fishbone sub-wavelength grating (S ) (b) expanded view of bus-to-ring coupling region withcoupling gap gc. Illustrations of (c) strip, (d) conventional SWG, and (e) fishbone SWG waveg-uide geometries with width w, thickness t, grating period Λ, duty cycle δ, and fishbone width wfb.(f) Graphical representations of MRR performance criteria, including (clockwise from top left) criti-cally coupled quality factor (Qcrit), free spectral range (FSR), intrinsic limit of detection (iLoD), andbulk sensitivity (Sb).MRRs use their sensitivity to surface and cladding refractive index changes to detectanalytes, such as disease biomarkers, captured on the sensor surface. These MRR structuresconsist of a waveguide that is looped back on itself in a ring and a straight bus waveguideBiosensors 2022, 12, 840 3 of 35that couples light into the ring (Figure 1a) [20,21]. The ring and bus waveguides areseparated by a defined coupling gap distance, gc, which controls the amount of lightcoupled into the ring (Figure 1b). Resonance occurs when the optical path length of thering is equal to an integer multiple of the wavelength of light in the waveguide. Thesedevices support resonances at wavelengths, λres, given byλres =ne f f Lm, (1)where neff is the effective refractive index of the waveguide, L is the resonator length(L = 2piR) for a circular MRR with radius, (R), and m is an integer number representingthe order of interference. A portion of the electric field, called the evanescent field, travelsoutside of the waveguide and interacts with the surrounding material, or analyte. Thiscreates a thin refractive index-sensitive region that extends up to a few hundred nanometersoutside of the waveguide [22]. A change in the refractive index surrounding the resonator,for example due to biomolecule binding, changes the neff, leading to a shift in λres. Severalstrategies are available for tracking the resonance shifts. A simplistic setup comprisesa broadband optical source that provides a continuous spectrum of wavelengths and aspectrum analyzer to measure the magnitude of the transmission versus wavelength [23].Another approach uses a combination of a tunable laser and a photodetector to scanthe input wavelength and read the output intensity, respectively [1,24,25]. However,another compact and cost-effective approach recently proposed by Chrostowski et al. [1]replaces off-chip tunable lasers with a chip-integrated fixed wavelength laser. In-resonatorphase shifters [26] are used to tune the resonance, and the transmission is read out usinga photodetector.Three metrics that are particularly valuable for evaluating SiP sensor performance andcomparing different resonator architectures are the bulk sensitivity, Sb, quality factor, Q,and intrinsic limit of detection, iLoD [21,27]. The bulk sensitivity is defined as the changein λres for a one unit change in the bulk refractive index [27]:Sb =∆λres∆nbulk=λresng(∂ne f f∂nbulk), (2)where ng is the group index and ∂neff/∂nbulk is the index susceptibility and relates to theportion of the optical mode that interacts with the analyte [21]. Experimentally, Sb can beobtained by exposing the sensor to several solutions having different known refractiveindices and tracking the corresponding resonance peak shifts. Often, aqueous solutionsprepared with different concentrations of salt [19], isopropanol [3], or glycerol [28,29] areused. Sb is then calculated from the slope of the resonance peak shifts plotted against thebulk refractive index.The quality factor is a dimensionless quantity that represents a photon’s lifetime inthe resonator and is the number of oscillations required for the photon’s energy to decay to1/e [21,22,27]. A high quality factor indicates that light present in the resonator interactswith the analyte for a greater amount of time, and is desirable because it improves theresolution to which the resonance peak shifts can be resolved and reduces the impact of theintensity noise on the resolved shifts [21,22,27,30,31]. The quality factor depends on thetotal distributed optical losses in the resonator, α (dB/m), and can be calculated accordingto Equation (3) [27].Qintrinsic =2ping·10log10(e)λres·α , (3)For MRRs, light must be coupled out of the resonator to observe a resonance change,which degrades the quality factor. In the critically coupled condition, the quality factor isdegraded by half compared with the intrinsic quality factor represented by Equation (3),because the proportion of the power coupled out of the resonator is equal to the round-triploss, effectively doubling the total lost power with each resonator round trip [21]. As such,Biosensors 2022, 12, 840 4 of 35the critically coupled quality factor is a more useful metric for MRR sensors. Experimentally,it can be approximated based on the full width at half maximum (FWHM) at resonance(∆λFWHM) according to Equation (4) [21,22].Qcrit =ping·10log10(e)λres·α =λres∆λFWHM, (4)Finally, the iLoD is a figure of merit introduced to objectively compare sensors, inde-pendent of their experimental setups, functionalization strategies, and assays [21,22,27,32].Unlike the system limit of detection (sLoD (RIU)) [21] or analyte limits of detection (Mor g/mL) [22], it depends only on the intrinsic characteristics of the resonator and repre-sents the minimum refractive index unit change (in RIU) required to shift the resonancewavelength by ∆λFWHM. It is given by Equation (5) [21,22].iLoD =λresQ·Sb , (5)Accordingly, Sb and Q should be maximized for optimal sensor performance. Res-onators designed with conventional strip waveguides (Figure 1c) operating in the quasi-transverse electric mode (hereafter referred to as the TE mode for brevity) can achievevery low optical losses, and therefore, high quality factors [33]. However, the high indexcontrast between the silicon waveguide and cladding material (typically aqueous solutionsfor biosensing applications) results in strong confinement of the electric field in the waveg-uide core. This results in little overlap between the evanescent field and analyte, limitingSb [3]. Different waveguide designs have been investigated to achieve higher sensitivities,including thin strip waveguides [34], strip waveguides operating in the quasi-transversemagnetic (TM) mode (hereafter referred to as the TM mode for brevity) [21,35], and slotwaveguides [36,37].Sub-wavelength grating (SWG) waveguides (Figure 1d) are yet another geometry thathas demonstrated considerable sensitivity enhancements compared to strip waveguidesoperating with both TE and TM polarizations [38]. SWGs are periodic structures that consistof silicon blocks, interspaced with a lower refractive index material, such as the claddingmaterial (e.g., air [39], water [6,19,40], or a polymer such as SU8 [41]). SWG structuressignificantly extend the SiP design space by allowing for the fabrication of metamaterialanisotropic structures using standard single-etch CMOS-compatible techniques [42]. SWGshave been used to create photonic structures with tailored modal confinement, broadbandbehavior, dispersion control, and polarization management [42,43]. For example, the tai-lorability of modal confinement in SWGs has allowed for the design of ultralow loss waveg-uide crossings [41] and efficient couplers to interface on-chip waveguides with off-chipoptical fibers [44]. The tailorable modal confinement and diffraction suppression affordedby SWGs have been employed to design ultracompact and broadband Y-branches [45] andadiabatic couplers [46,47]. Further, the controlled dispersion of SWGs has been leveragedto design broadband 2 × 2 interferometric switching cells [43] and broadband directionalcouplers [48,49]. Finally, SWG structures have been used to design optimized sensingwaveguides [42]. These periodic SWG structures behave as waveguides below the Braggthreshold where the grating period, Λ, is less than half the effective wavelength of lightin the waveguide (Λ << λ2ne f f ) [5,38,41,50]. The optical properties (e.g., neff, ng) of theSWG are highly tunable and depend on the waveguide width (w), thickness (t), and dutycycle (δ, the ratio of the silicon block length to the grating period), in addition to thegrating period (Figure 1d). Compared with strip waveguides, SWGs can offer reducedelectric field confinement in the waveguide core, which increases light interaction withthe analyte [6]. As such, MRRs can be fabricated with SWGs for improved bulk refractiveindex sensitivity Sb. In the literature, many SWG waveguide variants have been used inMRR and racetrack resonator (RTR) sensors, including SWGs that operate in the transverseelectric (TE) [19,21,29,39] and transverse magnetic (TM) [51,52] modes, trapezoidal pillarBiosensors 2022, 12, 840 5 of 35SWGs [53], substrate overetch (SOE) SWGs [6], pedestal SWGs with undercut etching [28],single- and double-slot SWGs [54,55], and multibox SWGs [3].When used for biosensing applications, a major limitation of these SWG waveguides,which are composed of isolated silicon blocks, is that they are fragile and susceptible todamage during and after manufacturing [1]. In contrast to other SWG devices (e.g., waveg-uide crossings, Y-branches, adiabatic couplers, and directional couplers) which are oftenclad with silicon dioxide, an oxide-open etch is typically necessary to expose SWG-basedsensors to the analyte solution [56]. This oxide-open etch can cause delamination of thefragile silicon blocks that make up the SWG waveguides from the sensor substrate [1]. Theexposed SWG waveguides can also be damaged during surface functionalization processesand binding assays [57–59]. This hinders the fabricability and robustness of SWG-basedbiosensors, complicating their translation to scalable POC sensors. One solution is to adda fishbone to the SWG waveguide (Figure 1e), which turns the waveguide into a singlepiece of silicon [1,60–62]. This lowers the risk of delamination and improves fabricability,while maintaining the sensitivity enhancements offered by the SWG design. As an addi-tional advantage, the fishbone eliminates discontinuities in tapers which convert routingwaveguides to the SWG bus region, reducing reflections and optical losses at the taperinterface [1]. To our knowledge, only two other works have reported the design andfabrication of sensors based on fishbone SWG structures [1,62]. Bickford et al. [62] designedMach-Zehnder interferometers based on fishbone SWG waveguides and presented theirtransmission spectra, but did not quantify device performance in terms of Q, Sb, or iLoD.Chrostowski et al. [1] designed a resonator with integrated photoconductive waveguideheater detectors for operation with a fixed-wavelength laser. A fraction of the resonatorconsisted of a fishbone SWG waveguide. This device achieved an experimental qualityfactor of 4.44 × 104 and a simulated bulk sensitivity of 76.0 nm/RIU, yielding an estimatediLoD of 3.77 × 10−4 RIU. No existing works have reported the experimental sensitivity offishbone SWG sensors. Moreover, to the best of our knowledge, no previous works havedemonstrated a comprehensive optimization of the fishbone SWG waveguide geometry forsensing in terms of duty cycle, fishbone width, and grating period.In this work, we present a novel framework for using numerical simulations to opti-mize fishbone SWG waveguides for high sensitivity MRRs, aiming to achieve comparablesensing performance to previously reported MRRs based on non-fishbone SWG waveg-uides, but with improved robustness. For the first time, we demonstrate the experimentalperformance of MRRs entirely fabricated with fishbone SWG waveguides and comparethem to boneless SWG MRRs in terms of the key sensor performance metrics Qcrit (hereafter,simply referred to as Q), Sb, and iLoD. While the full function of a biosensor depends onseveral factors beyond the transducer itself, including the functionalization chemistry andassay design, characterizing the intrinsic resonator performance based on these metrics isessential to drawing fair comparisons to other transducers. In both simulations and experi-ments, we target sensor operation in the O-band (1260–1360 nm) and C-band (1530–1565nm). While most SiP applications use C-band light, the O-band offers lower optical lossesdue to reduced water absorption, which has the potential to enhance sensor performanceby improving Q [21]. To our knowledge, this is the first demonstration of any SWG ringresonators using O-band light for liquid-phase sensing. This is a valuable contribution inthe context of POC biosensing, as compact O-band lasers are less expensive and easier tomanufacture than C-band ones [1,63], making O-band systems more suitable for affordableand scalable SiP biosensing platforms. Lastly, we compare the performance of our fishboneSWG MRRs to other SWG sensors reported in the literature. This thorough optimizationand experimental characterization of fishbone SWG MRRs is an important step towarddesigning sensitive SiP biosensing platforms that are practical for the POC. In the future,we envision that these sensors can be used for robust biosensing in applications suchas the detection of cancer [14–17,64], inflammation [65], cardiac disorders [66,67], viralinfection [68], bacteria [69], and toxins [70,71].Biosensors 2022, 12, 840 6 of 352. Materials and Methods2.1. Numerical Models2.1.1. Index and Bulk Sensitivity SimulationsFinite difference time domain (FDTD) simulations were performed using FDTD Solu-tions from Lumerical (Ansys, Inc., Canonsburg, PA, USA). In these simulations, one unitcell of a SWG waveguide was modeled with Bloch boundary conditions. The periodicity ofSWG waveguides permits the use of band structure simulations for reduced simulationtime compared to discrete time domain calculations. This method has been widely used tosimulate structures such as photonic crystals [19,72]. In this method, light is injected intothe structure over the frequency range of interest and the time-dependent response of thestructure is recorded for a range of swept wavevector values [73]. Spectral analysis is per-formed on this response by searching for local maxima and plotting them in the frequencydomain to provide the band structure. Using linear regression to fit the band structurecurve, the ratio of the angular velocity to the wavevector is obtained as well as higher orderterms. This helps extract the phase and group velocities (vp and vg, respectively) fromwhich the effective and group indices are calculated, according to Equations (6)–(8) [74,75],ω = ω0 + kx∂ω∂kx+ . . . , (6)ne f f =cvp=cω/kx, (7)ng =cvg=c∂ω/∂kx, (8)where ω is the angular frequency, kx is the wavenumber, and c is the speed of light in avacuum. To set up these simulations, the silicon SWG waveguide was drawn on top ofa 2 µm-thick SiO2 buried oxide (BOX) layer with a silicon wafer layer beneath (Figure 2).Water was used as the background (cladding) material. Multi-coefficient material modelsbased on empirical complex refractive index data available from the Lumerical MaterialDatabase were used for the simulations [76,77]. The software’s default material modelfitting parameters were used for silicon and SiO2. As Lumerical’s default fitting parametersyielded an unsatisfying fit for the complex refractive index of water over the O- to C-bandwavelength range (Figure S1a), the fit tolerance for this material was reduced to 1 × 10−6with the maximum coefficients parameter set to 10 [78]. To better capture the absorptionlosses of the water cladding, the imaginary weight was increased to 100. This meant thatthe fitting routine gave 100 times more consideration to the imaginary part of the complexrefractive index than the real part; increasing the imaginary weight is recommended whenthe imaginary refractive index is much smaller than the real refractive index [78]. Thisproduced a model that accurately fit the empirical refractive index data (Figure S1b). Lightwas set to propagate along the x-axis. The FDTD simulation region enclosed one unitcell of the SWG waveguide in the x-direction and extended 0.75 µm above and below thewaveguide in the z-direction and 3 µm on either side of the waveguide in the y-direction.These boundary locations were selected based on convergence testing. Bloch boundaryconditions were used for the x boundaries. Perfectly matched layers (PML) were used forthe z boundaries and one of the y boundaries to absorb waves propagating outwards andavoid reflections, whereas an anti-symmetric condition was used for the other y boundaryto reduce the simulation time. The global mesh accuracy was set to 4 and an override mesh(dx = 0.01 µm, dy = 0.02 µm, dz = 0.02 µm) was included in the FDTD region immediatelyaround the waveguide (dimensions defined by Λ × w × t). A plane wave source was usedto inject light into the structure over a frequency range of 120–270 THz (corresponding toa wavelength range of 1111–2500 nm) to cover the O-C band spectra. A band structureanalysis group was set up in the FDTD region with ten time monitors randomly distributedin the waveguide.Biosensors 2022, 12, 840 7 of 35Biosensors 2022, 12, x FOR PEER REVIEW 7 of 35 around the waveguide (dimensions defined by Λ × w × t). A plane wave source was used to inject light into the structure over a frequency range of 120–270 THz (corresponding to a wavelength range of 1111–2500 nm) to cover the O-C band spectra. A band structure analysis group was set up in the FDTD region with ten time monitors randomly distrib-uted in the waveguide. Figure 2. (a) Illustration of cross-section of finite difference time domain (FDTD) band structure simulation setup. (b) Illustration of top view of FDTD band structure simulation with magnified view of waveguide region. The effective index and group index versus wavelength were then calculated by sweeping kx across ten evenly spaced values within a specified range. For a given SWG waveguide geometry, this range was defined by firstly running a coarse sweep with a kx range of 0.1–0.5 in order to extract the kx values that corresponded to neff at 1310 nm and 1550 nm according to 𝑘௫ = 𝑛௘௙௙Λ/𝜆. These values helped define a narrower simulation range with an added buffer of 0.02, which ran with a finer 10-point sweep. 2.1.2. Propagation Loss Simulations A similar band structure FDTD simulation method to that described in Section 2.1.1 was used to estimate the propagation losses of the SWG waveguides [72]. For these sim-ulations, however, a dipole cloud light source was used to inject light into the structure over a 1-THz frequency range about the operating frequency. For operation in the C-band at 1550 nm, a frequency range of 193.05–194.05 THz (corresponding to a wavelength range of 1546–1554 nm) was used, whereas for operation in the O-band at 1310 nm, a frequency range of 228.51–229.51 THz (corresponding to a wavelength range of 1307–1313 nm) was used. A field decay analysis group was added to the simulation, which included two time monitors placed at different points along the waveguide. The field decay along the wave-guide, captured by the time monitors, and the group velocity, obtained from the FDTD simulations described in Section 2.1.1, were used to calculate the propagation loss, α (dB/m), according to Equation (9): 𝛼 = ఉ∙ଶ଴∙௟௢௚భబ(௘)௩೒ , (9) where β (Np/s) is the slope of the field decay over time obtained from the simulation (1 𝑁𝑝 = 20 ∙ logଵ଴(𝑒) dB) [79]. In these loss simulations, the z-span of the FDTD region and override mesh were extended to 3 µm above and below the waveguide. This reduced the risk of losses to the PML boundaries and extended the simulation region into the Figure 2. (a) Il ustr ti ti n of finite di ference time domain (FDTD) band structuresimulation setup. ( ) Ill strati f t ie of FDTD band structure simulation with magnifiedview of waveguide region.The effective index and group index versus wavelength were then calculated bysweeping kx across ten evenly spaced values within a specified range. For a given SWGwaveguide geo etry, this range as defined by firstly running a coarse sweep with a kxrange of 0.1–0.5 in order to extract the kx values that corresponded to neff at 1310 nm and1550 nm according to kx = ne f fΛ/λ. These values helped define a narrower simulationrange with an added buffer of 0.02, which ran with a finer 10-point sweep.2.1.2. Propagation ss i l ti sA similar ban str ct re F si lation method to that described in Section 2.1.1was used to esti ate the propagation losses of the SWG waveguides [72]. For thesesimulations, however, a dipole cloud light source was used to inject light into the structureover a 1-THz frequency range about the operating frequency. For operation in the C-bandat 1550 nm, a frequency range of 193.05–194.05 THz (corresponding to a wavelength rangeof 1546–1554 nm) was used, whereas for operation in the O-band at 1310 nm, a frequencyrange of 228.51–229.51 THz (corresponding to a wavelength range of 1307–1313 nm) wasused. A field decay analysis group was added to the simulation, which included twotime monitors placed at different points along the waveguide. The field decay along thewaveguide, captured by the time monitors, and the group velocity, obtained from theFDTD simulations described in Section 2.1.1, were used to calculate the propagation loss, α(dB/m), according to Equation (9):α =β·20·log10(e)vg, (9)where β (Np/s) is the slope of the field decay over time obtained from the simulation(1 Np = 20· log10(e) dB) [79]. In these loss simulations, the z-span of the FDTD region andoverride mesh were extended to 3 µm above and below the waveguide. This reduced therisk of losses to the PML boundaries and extended the simulation region into the siliconwafer below the BOX to account for optical losses due to leakage to the substrate. Asthese simulations were less time-consuming than the sweeps described in Section 2.1.1, theglobal mesh accuracy was increased to 6 and the override mesh accuracy was increased(dx, dy, dz = 0.01 µm) to improve the simulation accuracy. For each SWG geometry, the losssimulations were performed using the kx value corresponding to the effective index of thestructure simulated in Section 2.1.1.Biosensors 2022, 12, 840 8 of 352.2. Design and Optimization of Fishbone SWG WaveguidesIn order to optimize fishbone SWG waveguides for sensing applications and comparetheir performance to conventional boneless SWG waveguides, we performed fully vectorial3D-FDTD band structure simulations using Bloch boundary conditions, as described inSection 2.1.1. These simulations were used to predict the effective index, neff, and bulksensitivity, Sb, of SWG waveguides operating with C-band and O-band light in the TE mode.Compared to Sb, surface sensitivity (Ss) is the more important metric for biosensors in thestudy of target molecule quantification, but it must be defined for a specific molecule ofinterest, meaning that Sb is a more suitable criterion for the general comparison of sensorswhen the target is unknown or the sensors are used for different biosensing assays [3,40].As such, Sb was used in this work to compare sensing architectures. For all simulations,a waveguide width of 500 nm, waveguide thickness of 220 nm, and BOX thickness of 2µm, were used. The grating period, Λ, was initially fixed at 250 nm. This grating periodwas selected, as it is below the Bragg threshold (Λ << λ/2neff) for all studied geometries.Further, others [19,39] have studied boneless SWG waveguides with this grating period,providing a valuable benchmark for comparison. The waveguides were optimized byperforming simulation sweeps in which the duty cycle, δ, was varied from 0.2 to 0.8 forSWGs with fishbone widths, wfb, of 0, 60, 100, 140, 180, and 220 nm. Simulations performedwith water cladding were used to extract neff and the group index, ng, for each waveguidegeometry. To extract Sb, band structure simulations were additionally performed usingan index-shifted water cladding material to simulate a dilute salt solution. For this index-shifted material, the real part of the refractive index of water was shifted by 0.01 (∆nbulk)at all wavelengths in the water material model; it was assumed that material absorption,and therefore, the imaginary term of the refractive index, remained constant. By simulatingneff in both materials to extract ∆neff, the susceptibility, ∂neff/∂nbulk, could be estimatedas ∆neff/∆nbulk. Using this susceptibility alongside the group index, Sb was calculatedaccording to Equation (2).Figure 3 presents the results of these simulations. Increasing δ and wfb led to anincrease in neff for the C-band and O-band structures. This reflects an increase in lightconfinement as the volume fraction of silicon in the SWG structure increases. This increasedlight confinement decreases the interaction of light with the bulk material. As seen inFigure 3, this is generally accompanied by a decrease in Sb. However, when neff approachesand falls below ~1.44, which is the refractive index of the BOX, the waveguide no longereffectively guides light, and a considerable decrease in Sb is observed when δ and wfbare decreased further [74]. For the C-band devices, the greatest value of Sb out of all thesimulated structures was roughly 470 nm/RIU, whereas that for the O-band devices wasroughly 400 nm/RIU. The greater sensitivities of the C-band structures can be attributedto lower mode confinement at longer wavelengths at the defined waveguide geometry ofw = 500 nm and t = 220 nm [20].The sensitivity results highlight that fishbone SWG waveguides can achieve compara-ble sensitivities compared with boneless SWG waveguides for appropriate combinationsof δ and wfb. For both fishbone and boneless SWG structures, the electric field is highlyconcentrated in the gaps between the silicon blocks, as shown in Figure 4. This allows forstrong interaction between the evanescent field and the bulk medium.Biosensors 2022, 12, 840 9 of 35Biosensors 2022, 12, x FOR PEER REVIEW 9 of 35 Figure 3. Simulated effective index, neff, versus duty cycle, δ, for SWG waveguides with a grating period Λ = 250 nm, width w = 500 nm, thickness t = 220 nm, and fishbone width wfb = 0–220 nm, operating with (a) 1550 nm and (b) 1310 nm light. The shaded area represents the region where neff is below the substrate leakage loss cutoff of 1.65, as reported by Sarmiento-Merenguel et al. [80]. Dashed regions of curves indicate waveguide geometries with feature sizes smaller than the 60 nm limit of the electron-beam lithography process used for silicon photonic (SiP) chip fabrication in this work. Simulated bulk sensitivity, Sb, versus δ for SWG waveguides with Λ = 250 nm, w = 500 nm, t = 220 nm, and wfb = 0–220 nm, operating with (c) 1550 nm and (d) 1310 nm light. Simulations were performed using a 3D-FDTD approach with water as the cladding. The sensitivity results highlight that fishbone SWG waveguides can achieve compa-rable sensitivities compared with boneless SWG waveguides for appropriate combina-tions of δ and wfb. For both fishbone and boneless SWG structures, the electric field is highly concentrated in the gaps between the silicon blocks, as shown in Figure 4. This allows for strong interaction between the evanescent field and the bulk medium. Figure 4. Cross-sectional electric field profiles for boneless (left) and fishbone (right) SWG wave-guides obtained from 3D-FDTD simulations at 1550 nm, illustrating the electric field intensity in the silicon blocks and gaps between these blocks. The boneless SWG field profiles were simulated for a waveguide with the following geometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.65, and wfb = 0 nm (neff = 1.70). The fishbone SWG field profiles were simulated for a waveguide with the following geometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.60, and wfb = 100 nm (neff = 1.70). The data presented in all subplots have been normalized to the same maximum electric field intensity. Figure 3. Si ulated effective index, neff, versus duty cycle, δ, for S aveguides ith a gratingeriod 250 n , idth 500 , t ickness t 220 , a fi e i t fb = 0– 20 nm,operating ith (a) 1550 a ( ) li t. e s r effis belo the substrate leakage loss cutoff of 1.65, as reported by Sarmiento-Merenguel et al. [80].Dashed regions of curves indicate waveguide geometries with feature sizes smaller than the 60 nmlimit of the electron-beam lithography process used for silicon photonic (SiP) chip fabrication in thiswork. Simulated bulk sensitivity, Sb, versus δ for SWG waveguides with Λ = 250 nm, w = 500 nm,t = 220 nm, and wfb = 0–220 nm, operating with (c) 1550 nm and (d) 1310 nm light. Simulations wereperformed using a 3D-FDTD approach with water as the cladding.Biosensors 2022, 12, x FOR PEER REVIEW 9 of 35 Figure 3. Simulated effective index, neff, versus duty cycle, δ, for SWG waveguides with a grating period Λ = 250 nm, width w = 500 nm, thickness t = 220 nm, and fishbone width wfb = 0–220 nm, operating with (a) 1550 nm and (b) 1310 nm light. The shaded area represents the region where neff is below the substrate leakage loss cutoff of 1.65, as reported by Sarmiento-Merenguel et al. [80]. Dashed regions of curves indicate waveguide geometries with feature sizes smaller than the 60 nm limit of the electron-beam lithography process used for silicon photonic (SiP) chip fabrication in this work. Simulated bulk sens tivity, Sb, versus δ for SWG waveguides with Λ = 250 nm, w = 500 nm, t = 220 nm, and wfb = 0–220 nm, operating with (c) 1550 nm a d (d) 1310 nm light. Simulations were performed using 3D-FDTD approach with water as the cladding. The sensitivity results highlight that fishbone SWG waveguides can achieve compa-rable sensitivities compared with boneless SWG waveguides for appropriate combina-tions of δ and wfb. For both fishbone and boneless SWG structures, the electric field is highly concentrated in the gaps between the silicon blocks, as shown in Figure 4. This allows for strong interaction between the evanescent field and the bulk medium. Figure 4. Cross-sectional electric field profiles for boneless (left) and fishbone (right) SWG wave-guides obtained from 3D-FDTD simulations at 1550 nm, illustrating the electric field intensity in the silicon blocks and gaps between these blocks. The boneless SWG field profiles were simulated for a waveguide with the following geometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.65, and wfb = 0 nm (neff = 1.70). The fishbone SWG field profiles were simulated for a waveguide with the following geometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.60, and wfb = 100 nm (neff = 1.70). The data presented in all subplots have been normalized to the same maximum electric field intensity. Figure 4. ross-sectional electric field profiles for boneless (left) and fishbone (right) SWG waveg-uides obtai i lations at 1 50 nm, illustrating th lectric field intensity in thesilicon blocks and gaps betw en these blocks. The bon less SWG field profiles w re simulated for awaveguide with the following geometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.65, and wfb = 0 nm(neff = 1.70). The fishbone SWG field profiles were simulated for a waveguide with the followinggeometry: Λ = 250 nm, w = 500 nm, t = 220 nm, δ = 0.60, and wfb = 100 nm (neff = 1.70). The datapresented in all subplots have been normalized to the same maximum electric field intensity.Next, to investiga e the effect f Λ on the waveguide performanc , band s ructuresimulations were performed in which the duty cycle was varied fro 0.2 to 0.8 for SWGswith Λ = 200, 250, and 290 nm. These simulations were performed ith wfb = 0 and100 nm to analyze the effect of Λ on both conventional and fishbone SWGs. The resultsof these simulations are presented in Figure 5. Note that O-band simulation results areBiosensors 2022, 12, 840 10 of 35not presented for the fishbone waveguide at δ = 0.7 and 0.8 for Λ = 290, nor are theypresented for the boneless waveguide at δ = 0.8 for Λ = 290, as these structures exceedthe Bragg threshold. For the C-band devices, neff and Sb are nearly constant across allthree values of Λ for a given δ and wfb. Similarly, for the O-band devices, Λ had a smalleffect on neff and Sb, however a small increase in neff is seen with increasing Λ, particularlyfor waveguides approaching the Bragg threshold. Nevertheless, below the Bragg limit,the effect of Λ on the simulated waveguide performance is much less pronounced thanthe effect of δ and wfb. This is consistent with observations regarding the accuracy of theequivalent refractive index method in predicting SWG behavior well below the Braggthreshold [38,50,81]. The equivalent refractive index method approximates the SWG as ahomogeneous strip waveguide with an equivalent refractive index, neq, given by Rytov’sformula, n2eq ≈ δn2Si + (1− δ)n2clad, where nSi and nclad are the refractive indices of thesilicon blocks and the cladding material, respectively [38,50]. Using this method, lesscomputationally taxing 2D simulations can be used to estimate the optical properties ofthe waveguide (e.g., neff, ng, Sb, and α) [19]. It has been reported that this method providessuitable approximations for SWG structures in the deep-SWG regime, which is well belowthe Bragg threshold [37,41]. As neq is independent of Λ for any given δ, in this regime,the waveguide’s optical properties are, therefore, relatively insensitive to Λ. However,the accuracy of this model degrades near the Bragg threshold, and accurate analysis ofthe waveguide requires 3D analysis of the periodic geometry and the propagating Bloch–Floquet modes [19,50]. Therefore, near the Bragg threshold, it can no longer be assumedthat neff and Sb are independent of Λ, which supports the results illustrated in Figure 5.Biosensors 2022, 12, x FOR PEER REVIEW 10 of 35 Next, to investigate the effect of Λ on the waveguide performance, band structure simulations were performed in which the duty cycle was varied from 0.2 to 0.8 for SWGs with Λ = 200, 250, and 290 nm. These simulations were performed with wfb = 0 and 100 nm to analyze the effect of Λ on both conventional and fishbone SWGs. The results of these simulations are presented in Figure 5. Note that O-band simulation results are not pre-sented for the fishbone waveguide at δ = 0.7 and 0.8 for Λ = 290, nor are they presented for the boneless waveguide at δ = 0.8 for Λ = 290, as these structures exceed the Bragg thresh-old. For the C-band devices, neff and Sb are nearly constant across all three values of Λ for a given δ and wfb. Similarly, for the O-band devices, Λ had a small effect on neff and Sb, however a small increase in neff is seen with increasing Λ, particularly for waveguides ap-proaching the Bragg threshold. Nevertheless, below the Bragg limit, the effect of Λ on the simulated waveguide performance is much less pronounced than the effect of δ and wfb. This is consistent with observations regarding the accuracy of the equivalent refractive index method in predicting SWG behavior well below the Bragg threshold [38,50,81]. The equivalent refractive index method approximates the SWG as a homogeneous strip wave-guide with an equivalent refractive index, neq, given by Rytov’s formula, 𝑛௘௤ଶ ൎ 𝛿𝑛ௌ௜ଶ +(1 − 𝛿)𝑛௖௟௔ௗଶ , where nSi and nclad are the refractive indices of the silicon blocks and the clad-ding material, respectively [38,50]. Using this method, less computationally taxing 2D simulations can be used to estimate the optical properties of the waveguide (e.g., neff, ng, Sb, and α) [19]. It has been reported that this method provides suitable approximations for SWG structures in the deep-SWG regime, which is well below the Bragg threshold [37,41]. As neq is independent of Λ for any given δ, in this regime, the waveguide’s optical proper-ties are, therefore, relatively insensitive to Λ. However, the accuracy of this model de-grades near the Bragg threshold, and accurate analysis of the waveguide requires 3D anal-ysis of the periodic geometry and the propagating Bloch–Floquet modes [19,50]. There-fore, near the Bragg threshold, it can no longer be assumed that neff and Sb are independent of Λ, which supports the results illustrated in Figure 5. Figure 5. (a,b) Simulated neff versus δ for SWG waveguides with Λ = 200, 250 and 290 nm, w = 500 nm, t = 220 nm, and wfb = 0 and 100 nm, operating with (a) 1550 nm and (b) 1310 nm light. The shaded area represents the region where neff is below the substrate leakage loss cutoff of 1.65, as reported by Sarmiento-Merenguel et al. [80]. (c,d) Simulated Sb versus δ for SWG waveguides with Λ = 200, 250 and 290 nm, w = 500 nm, t = 220 nm, and wfb = 0 and 100 nm, operating with (c) 1550 nm and (d) 1310 Figure 5. ( , ) i l t ef rs s δ for SWG waveguides withΛ = 200, 250 and 290 nm, w = 500 nm,t = 220 nm, and wfb = 0 and 100 nm, operating with (a) 1550 n an ( ) e shadedarea represents the region where neff is below the substrat le kage loss cut ff of 1.65, as reportedby Sarmiento-Merenguel et al. [80]. (c,d) Simulated Sb versus δ for SWG waveguides with Λ = 200,250 and 290 nm, w = 500 nm, t = 220 nm, and wfb = 0 and 100 nm, operating with (c) 1550 nmand (d) 1310 nm light. Simulations were performed using a 3D-FDTD approach with water as thecladding material.Based on this analysis, we selected two C-band and two O-band fishbone SWGwaveguide designs for fabrication. Given the small effect of Λ on waveguide performance,we chose devices with Λ = 250 nm. Three evaluation criteria were used to select the bestcombinations of δ and wfb for the fabricated structures. First, the minimum feature sizeBiosensors 2022, 12, 840 11 of 35had to exceed 60 nm, which was the minimum fabricable feature size of the ANT electron-beam foundry process used in this work [82]. Next, the reduced modal confinement ofSWG waveguides can lead to considerable optical losses to the substrate [3,80]. Sarmiento-Merenguel et al. reported that these substrate leakage losses are independent of SWGgeometry and established a direct relationship between leakage losses and neff, along withpractical design guidelines [80]. In particular, for a 2 µm BOX layer, for C-band light,substrate leakage losses are negligible when neff > 1.65. Therefore, in this work, onlyfishbone SWG designs with simulated neff values above this cutoff were considered forfabrication. It should be noted that this leakage loss cutoff was only previously validatedfor a wavelength range of 1.5–1.6 µm [80]. The leakage loss cutoff is expected to belower for the O-band than the C-band due to the higher modal confinement at lowerwavelengths [20], making 1.65 a conservative estimate for this wavelength range. Acomprehensive investigation of O-band substrate leakage losses, although beyond thescope of this work, would validate this assumption and establish a more precise substrateleakage loss cutoff for the O-band. As such, in this work, we used the same leakage losscutoff of 1.65 for both the C-band and O-band devices. Lastly, among the fishbone SWGdesigns that satisfied the first two selection criteria, the two C-band and two O-band deviceswith the highest values of Sb were selected. When selecting the optimized C-band devices,an exception was made, as the geometry with the greatest Sb (δ = 0.6 and wfb = 60 nm) onlyexceeded the neff leakage loss cutoff by ~0.02. To mitigate the risk of leakage losses due tosmaller-than-predicted feature sizes, we selected the C-band waveguide geometries withthe second- and third-greatest simulated Sb values. The selected C-band (C1 and C2) andO-band (O1 and O2) designs, along with their simulated neff values, are provided in Table 1.Table 1. Fabricated SWG ring resonator geometries and their expected effective indices obtainedfrom 3D-FDTD band structure simulations with water cladding. All waveguides have a thickness of220 nm.Ring ResonatorDesign Λ (nm) δ w (nm) wfb (nm) neff gc (nm)C1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices an their tra s-mission spectra were collected while sweeping he wavelength of the input laser from 1530–1560 nm for th C-band devices or 1270–1310 nm for the O-band d vices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geom try as design C6 from this work, using a different electron-beam lit ogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricat d with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibit d n experi-mental ng of 3.27 and FSR of 3.936 m, which alig well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experimental factors, such as differences between the designed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Re t r Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 250 0.5 500 180 1.71 450, 500, 550, 600C2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring r sonators with the wave uide eometri s outlined in Table 1 were fabricated on a SOI w fer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors inst ad of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to nsure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable las r was coupl d to t e devices and their trans-mission spec r were coll cte while weeping the w velength of the input laser from 1530–1560 m for the C-band evi es r 1270–1310 nm for th O-band devices. This ch r-acterization was performed with a droplet of ater fully covering th r gions of the chip containing the reson tors. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports th simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicte by simula-tions, ith t boneless SWG devices generally exhibiting a slightly greater iffer nce in ng between the measured and simulated values compared with the fishbone devic s. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m t is work, using a diff re t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reporte here. This indicates that simulation in ccuracies are unlikely to b the source of variation in ng and FSR between the simulated and measure results. Instead, thes variations are likely attributable to experiment l factors, such as ifferenc s between the desi ned and fabricated structures. In particular, we hypothesiz d that the low experimental group in-dices may be due to smaller-than-designed feature sizes on th fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral ange (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 33 83 6 3 83 5 092 .16 .60 . 4.04 .91 .10 C3 ╫ 44 9 5 71 33 74 21 64 4 3 97 4 82 085 12 52 4 09 5 05 10C6 35 7 5 3 81 4 61 81 08 2 57 7 96 5 92 45 3 00 8 64 04O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding th fabricated waveguid morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 250 0.6 500 100 1.70 450, 500, 550, 600C3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring r sonators with the wave uide eometri s outlined in Table 1 were fabricated on a SOI w fer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors inst ad of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to nsure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupl d to t e devices an their tra s-mission spectra wer collecte while sweeping the wav length of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for th O-band devices. This char-acterization was performed with a droplet of ater fully covering th r gions of the chip containing the reson tors. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports th simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicted by simula-tions, ith t boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devic s. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a diff re t electron-beam lithogra-phy abrication process [19]. Previously, 30 µm-ra ius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR f 3.936 nm, which align well with the simulated values reported here. This indicates that simulation in ccuracies are unlikely to b the source of variation in ng and FSR between the simulated and measured results. Instead, thes variations are likely attributable to experiment l factors, such as ifferenc s between the desi ned and fabricated structures. In particular, we hypothesiz d that the low experimental group in-dices may be due to smaller-than-designed feature sizes on th fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) fo SWG rin resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3 33 2 83 ± 0 06 3 83 4 5 ± 0 092 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ .44 .9 . .71 .33 . 7 4 .21 .64 . 4 .97 .82 . 5 .12 . 2 . 4.09 5.05 .10 C6 .3 .7 . 5 3.81 4.61 . 1 ╫ .08 .57 . .96 .5 . 9 2 3 45 3 00 ± 0 08 64 3 04 ± 0O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding th fabricated waveguid morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 290 0.65 500 100 1.77 400, 450, 500, 550290 0.65 500 0 1.71 450, 500, 550, 600C5 250 0.65 500 0 1.70 450, 500, 550, 600C6 250 0.7 500 0 1.77 400, 450, 500, 550O1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the avelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The m asurements were performed on five replicate chips and the m asured spectra were analyzed usi g a custom scr pt, as described in Sectio 2.4. Table 2 reports the simulated and measured group indices and FSR of the fabricat d ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-ental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported ere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simu ated and measured results. Inste d, these variations are like y attrib table to experim ntal factors, such as differences between the designed and fabricated st re . In particular, we hypothesized that th low experimental group in-dices may be due to smaller-than-designed fea ure sizes on th fabricated chips. To testthis hypothesis, SEM imaging was perf rmed on the fabricated structures and feature sizes were measured. Table 2. Gr up index, ng, and free spectral range (FSR) for SWG ring son ors obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices a d 1270–1310 nm for he O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 250 0.4 500 100 1.69 400, 450, 500, 550O2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon icroring r so ators with the wave uide e metri s outlined n Table 1 we e fabricated on a SOI w fer with no oxide cladding using ANT’s electron-beam lithographyprocess [82]. A circular ing geometry was u ed for the sensors inst ad of a racetrack ge-ometry to eliminate mode-mis atch l sses [3]. All microrings we e des gn d with a ra-dius, R, of 30 µm, which w s selected to n low bend losses [3,94]. To characterize he fabricated microring r s nators, a tunable la er was coupl d to t e devices an their transmis ion spectra w r collecte while sw eping the avelength of the input laser from1530–1560 m for the C-ba devices r 1270–1310 nm for th O-band devices. This characterization was performed with a droplet of a er fully covering th r gions of the chip containin the reson tors. The measurements w re perfor ed n five replicate chips and th me sured spectra were analyzed using a c stom script, as d scribed in Section 2.4. Table 2 repo ts th simul te and measured gr up indic and FSRs of th fabricated ring resonators. All measured group indices were lower th n those pre icte by simulatio s, ith t bo eless SWG devices gener lly exhibiting a slightly greater iffer nce in ng between the m asured and simulated values compared wi h the fishbone devic s. Ac-cordingly, the me sured FSRs wer greater than the sim lated values for all geometries. Our r up has previously f bri ated b nele s SWG microring res ator using theidentical geometry as design C6 f m t is work, using a diff re t lect on-beam lithography fabrication proce s [19]. Previously, 30 µm-radius ring resonators f bricated with his waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an expe i-mental ng of 3.27 an FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation in ccuracies are unlikely to b the source of variation in ng and FSR between the simulated and measure results. Instead, thes variations are like y attri t ble to experim nt l f ctors, such as ifferences betwe n the desi ne and fabricated st re . In particular, we hypothesiz d that th low experimental group in-dices may be due to smaller-than-designed fea ure sizes on th fabricated chips. To testthis hypothesis, SEM imaging was perf rmed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 33 83 6 3 83 5 092 .16 .60 . 4.04 .91 .10 C3 ╫ 44 9 5 71 33 74 21 64 4 3 97 4 82 085 12 52 4 09 5 05 10C6 35 7 5 3 81 4 61 81 08 2 57 7 96 5 92 45 3 00 8 64 04O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding th fabricated waveguid morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 250 0.4 500 140 1.77 350, 400, 450, 500O3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silic icroring so tors with th wave uide e metri s outlin d n Table 1 we efabricated on a SOI w fer with no oxid cladding using ANT’s electron-beam lithographyprocess [82]. A circular ing geom try was u ed for the sensors inst ad of a racetrack ge-ometry to eliminate mode-mis atch l sse [3]. All micror ng we e des gn d with ra-dius, R, of 30 µm, which w s selected to n low bend losses [3,94]. To haracter ze he fabricated microri g r nators, a tunable la er was coupl d to t e devices an th ir transmis ion spectra w r collecte while sw eping the avelength of the input laser from1530–1560 m for the C-ba devices r 1270–1310 nm for th O-band devices. This characterization was performed with a droplet of a er fully covering th r gions of the chipcontainin the reson tor . The measurements w re perfor d n five eplicate chips and th me sured spectra were analyzed using a c stom cript, a described in Section 2.4. Table 2 r po ts th simulated and measured gr up indices a d FSRs of th fabricated ring resonators. All measured group i es were lower n those pr ict by simulatio s, th t bo eless SWG devices gener lly exhibiting a slightly greater i ference ing between the m asured and simulated value compared wi h he fis bone devic s. Ac-cordingly, the m sured FSRs wer greater than the sim lat d valu s for all geom tries. Our r p has previously fabri ated b n le s SWG microring r s ator using theidentical geometry as design C6 f m t is work, using a diff re t lect on-beam lith graphy fabrication proce s [19]. Previously, 30 µm-radius ring esonators f bricated with hiswaveguide g ometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an expe i-mental ng of 3.27 an FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation in ccuracies are unlikely to b the source of variation in ng and FSR b tween the simulated and measured results. Instead, th s variat ons are like y attrib table to experim nt l factors, such s ifferences between the esi ned and fabricated st re . In particular, we hypothesiz d that th low experimental group in-dices may be due to smaller-than-designed feature sizes on th fabricated chips. To test th s hypothesis, SEM imaging was performed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3 33 2 83 ± 0 06 3 83 4 5 ± 0 092 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ .44 .9 . .71 .33 . 7 4 .21 .64 . 4 .97 .82 . 5 .12 . 2 . 4.09 5.05 .10 C6 .3 .7 . 5 3.81 4.61 . 1 ╫ .08 .57 . .96 .5 . 9 2 3 45 3 00 ± 0 08 64 3 04 ± 0O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding th fabricated waveguid morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 200 0.5 500 100 1.82 350, 400, 450, 500O 200 0.5 500 0 1.72 400, 450, 500, 550Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulati Overesti tes In-Water Group In ces of SWG Waveguides Silicon mic oring resonators with the w veguid geomet ies outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geomet y w s used for the sensors instead of a racetrack g -ometry to elimin te mode-mis atch losses [3]. All mic orings ere desig ed with a ra-dius, R, of 30 µm, which was selected to ensure low b nd losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coup ed to the devices and their trans-mission spectra ere collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was perfor ed with a drop et of water fully covering the regio s of the chip containing the resonat rs. The mea urements were performed on five replicat hips and the measured spectra were analyzed using a c tom script, as escribed i Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabr cat ring resonators. All measured group indices were lower than those predicted by si u a-tions, with the boneless SWG devices generally exhibiting slightly greater difference in ng between the measured and simulated valu s compared with the fi hbon devic . Ac-cordingly, th measured FSRs were greater than the simulated values for all g ometries. Our group has previo sly fabricated bonel ss SWG microring resonators us ng the identical geometry as design C6 from this ork, using a different lectron-beam lithogra-phy fabrication process [19]. Prev ously, 30 µm-radius ring resonators fabricated with this waveguide g omet y (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experimental factors, such as differences between the designed and fabricated structures. In particular, we hypothesized that the low experi ental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured.Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on al resonances measured over a wavelength ra ge of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than Fishbone SWG designs.In addition to these optimized fishbone SWG designs, an d itional six fishbone andboneless WG wave u des (C3–C6 and O3–O4) with similar neff values to the optimizeddesigns were ncluded on the fabricated hotonic chips. Their geometries and simulatedneff al es are provided in Table 1. These additi al geom tries were included to experi-mentally investigate variations between ring resonators fabricated with fishbone SWGsand conventional SWGs, and to experimentally investigate the effect of grating period ondevice performance.2.3. Sensor Chip Design and FabricationThe SWG MRR photonic circuits were designed using KLayout ask editing software,the open-source SiEPIC tools library, SiEPIC EBeam process design kit, and AppliedNanotools process design kit [82–84]. One half of the chip layout was dedicated to theC-band resonators, whereas the other half was dedicated to the O-band resonators. AllBiosensors 2022, 12, 840 12 of 35fabricated resonator designs are included in Table 1. The layout included input and outputgrating couplers to couple light between the chip and benchtop tunable lasers and detectors.500 nm-wide strip routing waveguides were used to transmit C-band light between theI/Os and resonators, whereas 350 nm-wide strip waveguides were used for the O-bandrouting. Waveguide bends were designed with a bend radius of 5.0 µm and a Bezier bendparameter of 0.2 [85]. 15 µm-long tapers were used to create smooth transitions betweenthe routing waveguides and the SWG bus regions of the resonators.The photonic chips were fabricated on silicon-on-insulator (SOI) wafers by AppliedNanotools Inc. (Edmonton, AB, Canada) using 100 keV electron beam lithography andreactive ion etching [82]. All waveguides and photonic structures consisted of silicon.The chips were fabricated with a 220 nm silicon device layer, comprising the patternedphotonic circuit, on top of a 2.0 µm SiO2 buried oxide (BOX) layer, on top of a 725 µm siliconwafer layer. For this work, the chips were fabricated without cladding. No photoresist orhard mask remained on the waveguide surfaces after fabrication. The chips were used asreceived for testing. The water contact angle of the sensor chips was found to be 28–30◦,representing the hydrophilicity of the BOX layer, which comprises most of the chip’s surfacearea. It is possible, however, that the silicon waveguides with native oxide exhibit differentwetting behavior [86].2.4. Sensor CharacterizationThe photonic sensors’ transmission spectra were measured to characterize their perfor-mance in terms of ng, free spectral range (FSR), extinction ratio, and Q. These measurementswere made using a custom optical testing setup (Maple Leaf Photonics, Seattle, WA, USA)mounted on a pneumatic vibration isolation table (Newport Corporation, Irvine, CA, USA).The photonic chip was placed on a motorized XY stage (Corvus Eco, Micos GmbH, Es-chbach, Germany), maintained at 22 ◦C with a thermoelectric cooler controlled by a laserdiode controller (Stanford Research Systems LDC500, Sunnyvale, CA, USA) and illumi-nated by a cold light illumination source (Hund, Wetzlar, Germany). A 12-channel lidlessfiber array (VGA-12-127-8-A-14.4-5.0-1.03-P-1550-8/125-3A-1-1-0.5-GL-NoLid-Horizontal,OZ Optics, Ottawa, ON, Canada) mounted to a motorized Z stage was aligned to theon-chip grating coupler inputs and outputs. Alignment was performed using open-sourcePyOptomip software (Python 2.7, 32-bit) [87], which controlled the position of the XY andZ stages and communicated with the tunable lasers and detectors. The relative positionsof the photonic chip and fiber array were monitored using top- and side-view microscopecameras (Pixelink, Ottawa, ON, Canada) mounted to 12× zoom lenses (Navitar, Ottawa,ON, Canada). To test the C-band devices, the fiber array was connected to an Agilent 8164Amainframe (Agilent Technologies, Inc. Santa Clara, CA, USA) with a C-band swept tunablelaser (Agilent 81682A); to test the O-band devices, the fiber array was connected to anotherAgilent 8164A mainframe with an O-band swept tunable laser (Agilent 81672B). Eightfiber array channels were connected to Agilent 81635A and Keysight N7744C (KeysightTechnologies, Santa Rosa, CA, USA) optical detectors; therefore, up to eight resonatorscould be probed simultaneously. PyOptomip software was used to control and interfacewith the tunable lasers and optical detectors.Prior to the measurements, the resonators were pipette-spotted with ~20 µL of ultra-pure water from a NANOpure water purification system (Thermo Fisher Scientific Inc.,Waltham, MA, USA). Measurements were then performed by sweeping the tunable laserinput and recording the transmission spectra of the resonators. All of the SWG MRR sensorswere characterized on five replicate chips.To extract the sensor performance criteria from the optical spectra, a custom semi-automated script was written in MATLAB (MathWorks, Natick, MA, USA). First, the userwas presented with a plot of the overlaid optical spectra of the simultaneously measured8 resonators and prompted to select the wavelength range to be analyzed. On each opticalspectrum, the script then performed (1) peak-finding (findpeaks() function) to identifyresonance peak positions and approximate peak widths, (2) fitting of the baseline (non-peak)Biosensors 2022, 12, 840 13 of 35regions of the spectra to a third-degree polynomial function (polyfit()) and subtractionof that baseline from the optical spectra, (3) linearization of the decibel-scale baseline-subtracted data, (4) nonlinear least-squares fitting of each resonance peak to a Lorentzianfunction (lorentzfit() 1.7.0.0 by Jered Wells on the MATLAB File Exchange). During step(1), peaks of interest were automatically distinguished from noise by setting the argumentspassed to findpeaks() based on the expected form of the data. Specifically, the minimumpeak prominence (height of the peak, or extinction ratio) was set to 2 dBm, and the minimumdistance between neighboring peaks (FSR) was set to 2 nm. The script also plotted and savedfigures highlighting the found peaks on the optical spectra so that the user could checkfor anomalous results during or after analysis. The fit was performed on the linearized,baseline-subtracted data, and the peak was inverted and normalized prior to Lorentzianfitting (the fitted peak was positive and extended from 0 to 1). If the goodness-of-fit wassufficiently high (R2 > 0.85), the center wavelength of the Lorentzian function was usedas the resonance peak position in subsequent computations, and the peak’s FWHM wascalculated from the Lorentzian fit. If the goodness-of-fit was insufficient, the raw peaklocation was used as the resonance peak position and the FWHM was not computed (thepeak was not counted in subsequent quality factor analysis). The peak prominence from thepeak-finding function was taken as each peak’s extinction ratio, the FSR was calculated asthe average distance between the resonance peaks in the spectrum (and ng was computedfrom the FSR as ng = λ2L·FSR [52]), and the quality factor was calculated from Equation (4)using the FWHM extracted from the Lorentzian fit.2.5. Microfluidic Design and FabricationMicrofluidic gaskets to deliver aqueous solutions for sensor performance character-ization were fabricated using Sylgard™ 184 poly(dimethylsiloxane) (PDMS) (EllsworthAdhesives, Hamilton, ON, Canada) molded against 3D printed molds using soft lithog-raphy. 2D layouts of the microfluidic channel and mold geometry were designed usingKLayout mask editing software (aligned with the photonic design in the same layout),and the microfluidic layers of the layout (separate layers for the outside of the mold, theinterior mold cavity, the channel features, and the input/output through holes) were ex-ported as a .dxf file which was subsequently imported into SolidWorks (Dassault Systèmes,Vélizy-Villacoublay, France) and extruded into the final 3D geometry of the mold. Themold created gaskets with two parallel microfluidic channels, each designed to be 200 µmin width and 200 µm in height over the region of the photonic chip containing the sensors,expanding into 500 µm diameter circular input/output regions. The inset region of themold into which PDMS was cast was designed to be 4 mm in thickness, and the mold alsocontained 500 µm diameter circular through-hole features to serve as input/output ports.All through-hole features were extruded to a 0.1 mm taller height than the walls of the moldto ensure that thin PDMS membranes did not remain atop through-hole features (the resultsof experimental testing suggested that 0.1 mm additional height was sufficient to createeffective through-holes, whereas 0 mm height differential was insufficient). The gasketmold also contained 3 mm diameter through hole features to self-align the gaskets to thephotonic chip, with the chip positioned in a precision-machined recess in a custom-madealuminum mounting plate with matched 4–40 tapped bolt holes. The cast gasket wasdesigned to have ~3.3 mm of extra PDMS on the long edge closest to the channels to reduceany demolding-related feature distortion. This extra PDMS was manually cut off of thefabricated gasket using a single-edge razor blade after demolding.The molds were printed on a ProFluidics 285D digital light processing (DLP) 3Dprinter (CADworks3D, Toronto, ON, Canada) at 50 µm using Master Mold resin (CAD-works3D). Standard post-processing (isopropanol wash, compressed air dry, and 40 minultraviolet cure in a Creative CADworks CureZone UV curing chamber (CADworks3D))was performed on the molds to prepare for soft lithography. The root-mean-squared rough-ness of the fabricated molds had an upper bound of approximately 65 nm [88]. No moldrelease agent was used. Sylgard™ 184 silicone elastomer prepolymer base and curing agentBiosensors 2022, 12, 840 14 of 35(Ellsworth Adhesives, Hamilton, ON, Canada) were mixed at a 10:1 ratio by hand-stirringand a planetary centrifugal mixer (THINKY ARE-310, THINKY USA, Laguna Hills, CA,USA), cast in the 3D printed molds (slightly overfilling the mold so that the PDMS liquidsurface was convex and approximately 1 mm above the top of the mold), and degassedin a vacuum desiccator for 30–60 minutes. A sheet of overhead projector transparencymaterial (Apollo, ACCO Brands Corporation, Lake Zurich, IL, USA) was cut to ~4 × 7 cmin size and slowly and carefully laid upon the mold, starting from one corner, to reduce theincidence of bubbles between the PDMS and transparency film [88]. A piece of 1/8”-thickacrylic was then placed atop the transparency and a weight (~500–1000 g) was placed onthe acrylic to press the stack together and remove residual PDMS prepolymer between thethrough-hole features and the transparency film. The use of the transparency and weightsystem during fabrication produces flat gaskets with complete through holes. The gasketswere cured overnight at 65 ◦C in an oven (Fisher Isotemp® Incubator 255D, Thermo FisherScientific, Hampton, NH, USA), the transparency film was carefully peeled off, and thegasket was then demolded and cut to size. After inspection with optical microscopy (AvenMicroVue Digital Microscope, Aven Tools, Ann Arbor, MI, USA), the gasket was ready forassembly with the photonic chip and mounting plate.To assemble the setup for fluidic testing (Figure 6), the photonic chip was first placedin the machined recess of the mounting plate. A rectangular washer of the same dimensionsas the fluidic gasket and with 4.5 × 2.5 mm rectangular holes aligned with the fluidic I/Oswas custom laser-cut fromBiosensors 2022, 12, x FOR PEER REVIEW 14 of 35 cast gasket was designed to have ~3.3 mm of extra PDMS on the long edge closest to the channels to reduce any demolding-related feature distortion. This extra PDMS was man-ually cut off of the fabricated gasket using a single-edge razor blade after demolding. The molds were printed on a ProFluidics 285D digital light processing (DLP) 3D printer (CADworks3D, Toronto, ON, Canada) at 50 µm using Master Mold resin (CAD-works3D). Standard post-processing (isopropanol wash, compressed air dry, and 40 min ultraviolet cure in a Creative CADworks CureZone UV curing chamber (CADworks3D)) was performed on the molds to prepare for soft lithography. The root-mean-squared roughness of the fabricated molds had an upper bound of approximately 65 nm [88]. No mold release agent was used. Sylgard™ 184 silicone elastomer prepolymer base and cur-ing agent (Ellsworth Adhesives, Hamilton, ON, Canada) were mixed at a 10:1 ratio by hand-stirring and a planetary centrifugal mixer (THINKY ARE-310, THINKY USA, La-guna Hills, CA, USA), cast in the 3D printed molds (slightly overfilling the mold so that the PDMS liquid surface was convex and approximately 1 mm above the top of the mold), and degassed in a vacuum desiccator for 30–60 minutes. A sheet of overhead projector transparency material (Apollo, ACCO Brands Corporation, Lake Zurich, IL, USA) was cut to ~4 × 7 cm in size and slowly and carefully laid upon the mold, starting from one corner, to reduce the incidence of bubbles between the PDMS and transparency film [88]. A piece of 1/8”-thick acrylic was then placed atop the transparency and a weight (~500–1000 g) was placed on the acrylic to press the stack together and remove residual PDMS prepoly-mer between the through-hole features and the transparency film. The use of the trans-parency and weight system during fabrication produces flat gaskets with complete through holes. The gaskets were cured overnight at 65 °C in an oven (Fisher Isotemp® Incubator 255D, Thermo Fisher Scientific, Hampton, NH, USA), the transparency film was carefully peeled off, an the gasket was then demolded and cut to size. After inspection with optical microscopy (Aven MicroVue Digital Microscope, Aven Tools, Ann Arbor, MI, USA), the gasket was ready for assembly with the hotonic chip and mounting plate. To assemble the setup for fluidic testing (Figure 6), th photonic chip was first placed in the machined rec ss of the mounting plate. A rectangular washer of the same dimen-sions as the fluidic gasket and with 4.5 × 2.5 m rectangular holes aligned with the fluidic I/Os was custom laser-cut fro ⅛” acrylic (McMaster-Carr, Elmhurst, IL, USA) using a Universal Laser Systems VersaLaser VLS2.30 laser cutter (Universal Laser Systems, Inc., Scottsdale, AZ, USA). 4–40 brass bolts (McMaster-Carr, Elmhurst, IL, USA) were threaded through the bolt holes in the acrylic washer (first, so that the washer sat against the bolt head) and the PDMS fluidic gasket to align the two pieces together. The bolts were then aligned with the threaded holes in the mounting plate and screwed into place to align and seal the fluidics against the photonic chip. The washer serves to provide even pressure to the flat PDMS gasket to maintain a good seal without a permanent plasma bond between the PDMS and the photonic chip. cr lic (McMaster-Car , Elmhurst, IL, USA) using a UniversalL ser Systems VersaLaser VLS2.30 laser cutter (Universal L ser Systems, Inc., S ottsdale,AZ USA). 4–40 brass bolts (McMaster-Carr, Elmhurst, IL, USA) were threaded through thebolt holes in the acrylic washer (first, so that the was r s t against the bolt ad) and thePDMS fluidic gasket to lign the two pieces t geth r. Th bolts were then aligned with thethreaded hol s in the mou ing plate a d screwed into place to align and seal the fluidicsagainst the photonic c ip. The washer serves to provide even pressure to the flat PDMSgasket to maintain good seal without a permanent pl sma bond between the PDMS andthe photonic chip.Biosensors 2022, 12, x FOR PEER REVIEW 15 of 35 Figure 6. (a) Schematic and (b–e) photos of microfluidic and photonic chip assembly for fluidic test-ing. (b) The chip is placed on the mounting plate, (c) the chip is positioned into the machined recess of the mounting plate, (d) bolts are threaded through the bolt holes of the acrylic washer and poly(dimethylsiloxane) (PDMS) gasket and aligned to the threaded holes in the mounting plate, and (e) bolts are screwed into place to align and seal the fluidics against the photonic chip. 2.6. Bulk Sensitivity Testing Bulk sensitivity measurements were performed by measuring the resonance wave-length shifts of the SWG MRRs during exposure to NaCl (Fisher Scientific S271-3, Thermo Fisher Scientific, Hampton, NH, USA) solutions with five different salt concentrations (0 M, 0.0625 M, 0.125 M, 0.250 M, and 0.375 M) and known refractive indices. The solutions were prepared using ultra-pure water. The refractive indices of the solutions were meas-ured with an Abbe refractometer (Spectronic Instruments, Inc., Rochester, NY, USA). From lowest to highest concentration, the measured refractive indices of the solutions were 1.3335, 1.3341, 1.3346, 1.3360, and 1.3373. It should be noted, however, that these are visible wavelength refractive indices and do not account for chromatic dispersion. The photonic chip was assembled with the microfluidic gasket and mounting plate, as described in Section 2.5. To perform the bulk refractive index sensing measurements, the photonic chip assembly was secured on the stage of the custom optical testing setup (Maple Leaf Photonics, Seattle, WA, USA) using thermally conductive tape. A Fluigent LineUp™ series fluid control system (Fluigent, Le Kremlin_Bicêtre, France) was used to supply fluid to the photonic chip assembly. Further details about this setup are provided in Section S2 of the Supplementary Materials. Prior to the experiment, all tubing in the Fluigent system was primed with fluid by flowing the NaCl solutions at 500 mbar from each of the five reservoirs of both channels in sequence for two minutes each. The primed PEEK tubing (Idex 1531B, Cole-Parmer Canada, Quebec, QC, Canada) connected to the bubble trap outlets (Diba Omnifit® #006BT-HF, Cole-Parmer Canada, Quebec, QC, Canada) was then inserted into the micro-fluidic inlets of the PDMS gasket. Water was flowed continuously through the microflu-idic channels at 10 µL/min until the beginning of the bulk refractive index sensing exper-iment. The fiber array, connected to the tunable laser and optical detectors, was aligned to the photonic chip, as described in Section 2.4. During the experiment, the salt solutions were flowed over the MRR sensor via the two microfluidic channels in sequence at 30 µL/min for 20 minutes each. In the first repli-cate of the experiment, the salt solutions were flowed over the MRR sensor in order of ascending concentration, starting with water (0 M NaCl), followed by 0.0625 M, 0.125 M, 0.250 M, and lastly 0.375 M NaCl solutions. In the second replicate, the salt solutions were flowed over the MRR sensor in order of descending concentration. This was repeated four more times to reach a total of ten replicates. It is important to note that a known limitation of PDMS is that it can leach uncured oligomers into microchannels, with the oligomer Figure 6. (a) Schematic and (b–e) photos of microfluidic and photonic chip assembly for fluidictesting. (b) T e chi is placed on the mounting plate, (c) the chip s positioned into the machinedrecess of the mounting plate, (d) bolts are thr aded throug the bolt holes of the acrylic asheroly( i ethylsiloxane) ( S) gasket an aligne to the threa e holes in the o nting late, an(e) bolts are screwed into place to align and seal the fluidics against the photonic chip.. . l iti it til s siti it s r ts r rf r s ri t r s ce e-le t s ifts f t e S s ri ex s re t a l ( is er Scie tific S271-3, erFisher Scientific, a pton, NH, USA) solutions with five different salt concentrations (0 M,0.0625 M, 0.125 M, 0.250 M, and 0.375 M) and known refractive indices. The solutions wereBiosensors 2022, 12, 840 15 of 35prepared using ultra-pure water. The refractive indices of the solutions were measured withan Abbe refractometer (Spectronic Instruments, Inc., Rochester, NY, USA). From lowest tohighest concentration, the measured refractive indices of the solutions were 1.3335, 1.3341,1.3346, 1.3360, and 1.3373. It should be noted, however, that these are visible wavelengthrefractive indices and do not account for chromatic dispersion.The photonic chip was assembled with the microfluidic gasket and mounting plate,as described in Section 2.5. To perform the bulk refractive index sensing measurements,the photonic chip assembly was secured on the stage of the custom optical testing setup(Maple Leaf Photonics, Seattle, WA, USA) using thermally conductive tape. A FluigentLineUp™ series fluid control system (Fluigent, Le Kremlin_Bicêtre, France) was used tosupply fluid to the photonic chip assembly. Further details about this setup are provided inSection S2 of the Supplementary Materials.Prior to the experiment, all tubing in the Fluigent system was primed with fluid byflowing the NaCl solutions at 500 mbar from each of the five reservoirs of both channels insequence for two minutes each. The primed PEEK tubing (Idex 1531B, Cole-Parmer Canada,Quebec, QC, Canada) connected to the bubble trap outlets (Diba Omnifit® #006BT-HF, Cole-Parmer Canada, Quebec, QC, Canada) was then inserted into the microfluidic inlets ofthe PDMS gasket. Water was flowed continuously through the microfluidic channels at10 µL/min until the beginning of the bulk refractive index sensing experiment. The fiberarray, connected to the tunable laser and optical detectors, was aligned to the photonic chip,as described in Section 2.4.During the experiment, the salt solutions were flowed over the MRR sensor via the twomicrofluidic channels in sequence at 30 µL/min for 20 minutes each. In the first replicate ofthe experiment, the salt solutions were flowed over the MRR sensor in order of ascendingconcentration, starting with water (0 M NaCl), followed by 0.0625 M, 0.125 M, 0.250 M, andlastly 0.375 M NaCl solutions. In the second replicate, the salt solutions were flowed overthe MRR sensor in order of descending concentration. This was repeated four more times toreach a total of ten replicates. It is important to note that a known limitation of PDMS is thatit can leach uncured oligomers into microchannels, with the oligomer concentration beinginversely proportional to the flow rate [89]. Given the relatively high flow rate of 30 µL/minused in this study (corresponding to a residence time of ~2 s in the microchannels), inaddition to the considerable precedent for use of PDMS-based microfluidics in SiP assays [3,28,71,90], oligomer leaching was expected to have a negligible effect on the bulk refractiveindex sensing experiments performed in this work. PDMS is also known to absorb smallhydrophobic molecules, with absorption increasing with increasing residence time [91,92].While not a concern in this study, which only used aqueous salt solutions and shortresidence times, this would be a relevant consideration in sensing assays using longerresidence times and precious, low-concentration, and hydrophobic samples.During the experiment, a custom Python acquisition script was used to sweep thetunable laser source over a 20 nm wavelength range (1540–1560 nm for the C-band devicesand 1290–1310 nm for the O-band devices) and record the output transmission spectra fromthe photonic chip every 20–30 s. The fiber array alignment was monitored and adjustedevery 30 sweeps using a fine align function to ensure good coupling to the on-chip gratingcouplers throughout the experiment.Acquired optical spectra were analyzed using a custom Python script to Lorentzian-fiteach resonance peak and track the cumulative peak shifts, generating plots and datasetsof average resonance peak shift vs. time for each measured microring resonator sensor.Briefly, the custom Python script identified resonance peaks in the optical spectra and fiteach resonance peak to a 4-parameter Lorentzian function (x-position of the peak center,height of the peak baseline, height of the peak, and peak width at vertical midpoint). It thusparameterized each resonance peak into a 4-element vector and each optical spectrum withn resonance peaks as an n × 4 matrix. It then matched resonance peaks in consecutivelyacquired spectra by computing the cosine similarity of the vectors [93], and computed thedifferential displacement in the x-position of the peak centers of the matched peaks. Finally,Biosensors 2022, 12, 840 16 of 35it averaged the computed differential displacement of all of the matched resonance peaksin the spectra to calculate the overall differential displacement for that sweep iteration (δλ).The overall resonance peak shift at time point i (∆λ(ti)) was calculated as the sum of allpreceding displacements: ∆λ(ti) = ∑i1 δλ.All resonances demonstrated a gradual blue drift throughout these experiments.Therefore, prior to further analysis, the peak shift data were drift-corrected by performinga linear fit to the baseline of each peak shift plot and subtracting this linear fit from thedata. From the resonance peak shift vs. time data, the bulk refractive index sensitivityvalues were computed using a custom MATLAB script. The MATLAB script plotted theresonance peak shift vs. time data and prompted the user to click on the regions of the plotcorresponding resonator response to each bulk refractive index standard saline solution.For each refractive index standard region, the script averaged the resonance peak shift datain a 20-timepoint region (corresponding to approximately 400s of acquisition) centeredat the user’s click location. The bulk refractive index difference was computed as thedifference between the measured refractive index of each refractive index standard salinesolution and that of water. It then performed a linear regression on the peak shift vs.measured bulk refractive index difference (forcing zero intercept), and the slope of thelinear regression was taken to be the bulk refractive index sensitivity.2.7. SEM ImagingA Zeiss Sigma scanning electron microscope (SEM, Carl Zeiss AG, Jena, Germany)was used to image the fabricated photonic chips. Imaging was carried out to compare thedesigned dimensions to the fabricated structures and identify any fabrication limitationsor unexpected effects. In-lens and secondary electron detectors were used to take top-view and angled-view (45◦ tilt) images of the photonic devices. ImageJ was used tomeasure the dimensions of the fabricated SWG waveguides on top-view SEM imagestaken at 50,000× magnification. For each geometrical parameter (w, Λ, δ, and wfb), fivemeasurements were taken and then averaged to give a more representative estimation.3. Results3.1. Simulation Overestimates In-Water Group Indices of SWG WaveguidesSilicon microring resonators with the waveguide geometries outlined in Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithographyprocess [82]. A circular ring geometry was used for the sensors instead of a racetrackgeometry to eliminate mode-mismatch losses [3]. All microrings were designed with aradius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterizethe fabricated microring resonators, a tunable laser was coupled to the devices and theirtransmission spectra were collected while sweeping the wavelength of the input laserfrom 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. Thischaracterization was performed with a droplet of water fully covering the regions of thechip containing the resonators. The measurements were performed on five replicate chipsand the measured spectra were analyzed using a custom script, as described in Section 2.4.Table 2 reports the simulated and measured group indices and FSRs of the fabricatedring resonators. All measured group indices were lower than those predicted by simu-lations, with the boneless SWG devices generally exhibiting a slightly greater differencein ng between the measured and simulated values compared with the fishbone devices.Accordingly, the measured FSRs were greater than the simulated values for all geometries.Our group has previously fabricated boneless SWG microring resonators using theidentical geometry as design C6 from this work, using a different electron-beam lithographyfabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with thiswaveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experimentalng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here.This indicates that simulation inaccuracies are unlikely to be the source of variation inng and FSR between the simulated and measured results. Instead, these variations areBiosensors 2022, 12, 840 17 of 35likely attributable to experimental factors, such as differences between the designed andfabricated structures. In particular, we hypothesized that the low experimental groupindices may be due to smaller-than-designed feature sizes on the fabricated chips. To testthis hypothesis, SEM imaging was performed on the fabricated structures and feature sizeswere measured.Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ngand FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nmfor the C-band devices and 1270–1310 nm for the O-band devices. The reported values are themean ± one standard deviation for these measurements from five replicate chips.Ring Resonator Designng FSR (nm)Simulation Experiment Simulation ExperimentC1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experimental factors, such as differences between the designed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09C2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicte by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measure results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Tabl 2. Group index, ng, and f e spectral range (FSR) for SWG ring resonat rs obtained from 3D-FDTD ban structure simulations with as-designed structures and exp riments. For each resonator, ng and FSR were calculated based on all resonances easured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10C3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicted by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align w ll with the simulated values reported here. This indicates th t simulation inaccurac es are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Inste d, these varia ions are likely attributable to experiment l factors, such as iff rences between the desi n d and fabricat structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure s mulations with as-d sig ed structures and exper ments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chi s. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.44 2.94 ± 0.05 3.71 4.33 ± 0.073.21 2.64 ± 0.04 3.97 4.82 ± 0.083.12 2.52 ± 0.05 4.09 5.05 ± 0.10C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08O1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators w th the waveguide geom tries utlined in Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch loss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was se ected to ensure low bend losses [3,94]. To characterize the fabricated microring r sonators, a tunabl laser was coupled to the evices and thei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 nm for the C-band or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip ntaining the resonators. The measu m n s were perform on five replicat chips and the measured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 reports the simulated and measu ed group indices and FSRs of the fabricated ring reson ors. All measured group indices were lower than those predicted by simula-tions, w th th boneless SWG devices generally exhibiting a slightly greater iffer nc in ng between the easured and si ulated values compared with the fishbone devices. Ac-co dingly, the measured FSRs were greate than the simulated values f r all geometries. Our group has previously f bric te boneless SWG microring resonators usi g thidentical geometry as design C6 from hi work, using a diff rent el ctron-beam lithogra-phy fabrica ion process [19]. Previously, 30 µm-radius ring r s nators fabrica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured esults. I stead, these variations are likely attrib table to experim ntal factors, such as iffer nc s betwe n th designed and fa ricated structures. In particul r, we hypothesized that the low experimental group indices may be due to smaller-than-designed fea ur sizes on th fabricated chips. To test this hypothesis, SEM imagi g was performed on th fabricat d tructures and featuresizes were measured. Table 2. Gr up index, ng, and free spectral range (FSR) for SWG ring son tors obta ned from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.08 2.57 ± 0.07 2.96 3.54 ± 0.092Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon icroring reso ators w th the wave uide e m tries utlined in Table 1 we efabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ing geometry was u ed fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings we e design d with a ra-dius, R, of 30 µm, which w s se ected to n low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl la er was coupled to t e evices an thei tr ns-mis ion spectra w r collecte while sw ping the avele gth of th input laser from 1530–1560 m for the C-ba r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntainin the resonators. The measu m n s w re perfor n five replicat chips and th me sured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 repo ts the simulated and measu ed gr up indices and FSRs of th fabricated ring reson ors. All measured group indices were lower th n those predict by simula-tio s, th t bo eless SWG devices gener lly exhibiting a slightly greater iffer nc in ng between the asured and si ulated values compared with the fishbone devices. Ac-co dingly, the me sured FSRs wer greate than the sim lated values f r all geometries. Our r up has previously f bri te b nele s SWG microring res ator usi g thidentical geometry as design C6 f m i work, using a diff re t l ct on-beam lithogra-phy fabrica ion proce s [19]. Previously, 30 µm-radius ring r s nators f brica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an expe i-mental ng of 3.27 an FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source f variation in g and FSR between the simulated and measure results. Instead, these variations are likely attrib table to experim nt l factors, such as ifferences between the desi ed and fa ricated structures. In particular, we ypothesized that the low experiment l group indices m y be due to smaller-than-designed fea ure sizes on th fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Wat r G oup Indices of SWG WaveguidesSilicon icroring reso ators w th the wave uide e m tries utlined in Table 1 we efabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ing geometry was u ed fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings we e design d with a ra-dius, R, of 30 µm, which w s se ected to n low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl la er was coupled to t e evices and thei tr ns-mis ion spectra w r collecte while sw ping the avele gth of th input laser from 1530–1560 m for the C-ba r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntaining the resonators. The measu m n s w re perfor n five replicat chips and th me sured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 repo ts the simulated and measu ed gr up indices and FSRs of th fabricated ring reson ors. All measured group indices were lower th n those predict by simula-tio s, th t bo eless SWG devices gener lly exhibiting a slightly greater iffer nc in ng between the m asured and simulated values compared with the fishbone devices. Ac-co ingly, the me sured FSRs wer greate than the sim lated valu s f r all geometries. Our r up has pr viously f bri te b n le s SWG microring res ator usi g thidentical geometry as design C6 i work, using a diff re t l ct on-beam lithogra-phy fabrica ion proce s [19]. Previously, 30 µm-radius ring r s nators f brica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an expe i-mental ng of 3.27 an FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attrib table to experim nt l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypo hesis, SEM imaging was performed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08O 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Wat r G oup Indices of SWG Wavegu des Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FS of 3.936 nm, which align well with the simulated values reported here. This indicates that simulatio inaccuracies are unlikely t be the sourc of variation in ng and FSR betwee the simulate and measured result . Instead, these variations are likely attributabl to experimental factors, such as differ nces between the designed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures nd feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated b sed on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than Fishbone SWG designs.The SEM imag ng h ghlighted two unexpected observations regarding the fabric tedwaveguid morphologies. First, re ardin fabrication tolera ces, m st waveguide feat reswere slightly smaller an designed. Typically, w was 18–25 nm smaller than desi n ,wfb was 0–11 nm smaller than designed, and δ was approximately equal to the designs.Corners were slightly rou ded, though this effect was small. Second, boneless SWG designO4, which had the smallest silicon pillars out of the fabricated devices, showed manycollapsed pillars, as seen in F ure 7c. S iction is known to cause dama e to fea ures onmicro- nd nanoscale devices when expose to liquid, hen dried [58]. Capillary forcespull the feature toward the substrate or adjacent features during this process, leading todeformation, and inhibiting reuse of the device [57–59]. The SEM-imaged chip shown inFigure 7 had been exposed to water for characterization prior to imaging, meaning stictionis a likely cause of the visualized damage. Subsequent SEM imaging of an unused chipsuggested that this damage was not present before exposure to liquid. This type of damagewas not observed for any other waveguides, including design O3, which had the samegeometry as O4, but with the addition of a 100 nm fishbone, highlighting the additionalstructural stability conferred by the fishbone. Drying SiP chips in a low-surface tensionsolvent (e.g., pentane) is one strategy employed by foundries to prevent stiction during thefabrication process [59,95]. In many applications, however, this may not be feasible due toincompatibilities between these solvents and microfluidic materials [58]. Additionally, thechemical processes used to functionalize SiP sensors for biosensing often involve aqueoussolutions and expose the chip to multiple cycles of wetting and drying [96]. In theseapplications, fishbone SWGs can reduce the risk of damage prior to biosensing assays.To assess the effect of fabrication tolerance on device performance and determine if thelow experimental group indices could be attributed to the smaller-than-designed featuresizes observed in the SEM images, we re-ran band structure simulations for designs C1 andC4, this time using their measured geometries. The smoothing of corners was not includedin these simulations due to the small magnitude of this effect, as observed in SEM images.However, this corner smoothing should be accounted for in simulation models of waveg-Biosensors 2022, 12, 840 18 of 35uides fabricated with photolithography techniques (e.g., Deep UV lithography), which areknown to cause prominent corner smoothing [83]. The group indices obtained from thesesimulations were 3.108 and 3.110, respectively, which represent a ~3–7% reduction in ngcompared with the original simulations, but not a sufficiently large reduction to completelyaccount for the experimental results.Biosensors 2022, 12, x FOR PEER REVIEW 18 of 35 designed, wfb was 0–11 nm smaller than designed, and δ was approximately equal to the designs. Corners were slightly rounded, though this effect was small. Second, boneless SWG design O4, which had the smallest silicon pillars out of the fabricated devices, showed many collapsed pillars, as seen in Figure 7c. Stiction is known to cause damage to features on micro- and nanoscale devices when exposed to liquid, then dried [58]. Capil-lary forces pull the feature toward the substrate or adjacent features during this process, leading to deformation, and inhibiting reuse of the device [57–59]. The SEM-imaged chip shown in Figure 7 had been exposed to water for characterization prior to imaging, mean-ing stiction is a likely cause of the visualized damage. Subsequent SEM imaging of an unused chip suggested that this damage was not present before exposure to liquid. This type of damage was not observed for any other waveguides, including design O3, which had the same geometry as O4, but with the addition of a 100 nm fishbone, highlighting the additional structural stability conferred by the fishbone. Drying SiP chips in a low-surface tension solvent (e.g., pentane) is one strategy employed by foundries to prevent stiction during the fabrication process [59,95]. In many applications, however, this may not be feasible due to incompatibilities between these solvents and microfluidic materials [58]. Additionally, the chemical processes used to functionalize SiP sensors for biosensing often involve aqueous solutions and expose the chip to multiple cycles of wetting and drying [96]. In these applications, fishbone SWGs can reduce the risk of damage prior to biosensing assays. Figure 7. Scanning electron microscope images of fabricated SWG MRRs. (a) 45° angled view of coupling region for a boneless SWG MRR, (b) top-view of boneless SWG waveguide O4, (c) 45° angled view of boneless SWG waveguide O4, showing collapsed silicon pillars after testing, high-lighting robustness issues with this boneless design (we did not observe any collapsed pillars in images acquired after fabrication but prior to testing with water), (d) 45° angled view of coupling region for a fishbone SWG MRR, (e) top-view of fishbone SWG waveguide C1, and (f) 45° angled view of fishbone SWG waveguide C2. To assess the effect of fabrication tolerance on device performance and determine if the low experimental group indices could be attributed to the smaller-than-designed fea-ture sizes observed in the SEM images, we re-ran band structure simulations for designs C1 and C4, this time using their measured geometries. The smoothing of corners was not included in these simulations due to the small magnitude of this effect, as observed in SEM images. However, this corner smoothing should be accounted for in simulation mod-els of waveguides fabricated with photolithography techniques (e.g., Deep UV lithogra-phy), which are known to cause prominent corner smoothing [83]. The group indices ob-tained from these simulations were 3.108 and 3.110, respectively, which represent a ~3–. ◦region for a bonel ss SWG MRR, (b) top-view of boneless SWG waveguid O4, (c) 45◦ angledview of boneless SWG waveguide O4, showing collapsed silicon pillars after testing, highlightingrobustness issues with this boneless design (we did not observe any collapsed pillars in imagesacquired after fabrication but prior to testing with water), (d) 45◦ angled view of coupling regionfor a fishbone SWG MRR, (e) top-view of fishbone SWG waveguide C1, and (f) 45◦ angled view offishbone SWG waveguide C2.Another possible explanation for the low experimental group indices is incompletewetting of the SWG structures. Nanostructured surfaces can be susceptible to this phe-nomenon, which leads to the entrapment of air between narrow features during wetting [97].As such, air may have been trapped between the silicon pillars when the photonic chipswere coated with water for measurements. Because air has a lower refractive index than wa-ter, this is expected to decrease neff [50]. The group index can be related to neff according tong(λ) = ne f f (λ)− λ·(dne f f /dλ)[74], where dne f f /dλ < 0 for the designed waveguides.While the first term of this equation should decrease in the case of incomplete wetting,the magnitude of the second term should also decrease when air is added to the SWGmetamaterial, as air is less dispersive than water [77]. Depending on the relative effectof trapped air on these two terms, incomplete wetting may cause a decrease in ng. Totheoretically test this hypothesis, simulations were performed with fishbone SWG designC1 in which the gaps between the silicon pillars were filled with air up to a height tair(Figure S2). The fabricated waveguide geometry, as measured from SEM images, was used.Further details regarding these simulations are provided in the Supplementary Materials(Section S3). These simulations showed that the combination of reduced feature sizes andair entrapment considerably reduced ng and an increase in tair led to a decrease in ng (FigureS3). An air pocket height of tair = 120 nm yielded ng = 2.825, which is very close to theexperimentally measured value of ng = 2.83. It should be noted that this model does notaccount for the curvature of the air–water interfaces enclosing the air pocket. Regardless,these simulation results suggest that the low experimental ng values may, indeed, be theresult of incomplete wetting. Similarly to stiction during drying, incomplete wetting cancause deformations and damage to structures adjacent to the trapped air due to capillarypressure [97]. This may have contributed to the feature collapse seen in Figure 7c. AnotherBiosensors 2022, 12, 840 19 of 35similar phenomenon that may have contributed to the low group indices is nanobubbleformation on the waveguide surfaces due to etch roughness [98]. The presence of a thinnative oxide layer on the waveguide surface is yet another factor that may have contributedto these results [99].3.2. Empirical Characterization of Extinction Ratio vs. Coupling Gap Reveals Insights for FurtherOptimization and Highlights Performance Degradation Due to Peak SplittingCritical coupling is achieved when the coupling gap, gc, between the bus waveguideand ring resonator is such that the power coupled into a ring resonator is equal to theround-trip losses in the ring [20]. At critical coupling, the extinction ratios (ERs) of theresonance peaks are maximized, thus enhancing the signal-to-noise ratio; this is a desirablecondition for robust peak tracking and sensitive analyte detection [98]. When gc is relativelysmall, the resonator is over-coupled, giving rise to increased power losses. This decreasesboth ER and Q. When gc is relatively large, the resonator is under-coupled, which increasesQ, but decreases ER. Indeed, under-coupling can be used to enhance iLoD, althougha tradeoff with ER exists for noisy systems that necessitate higher ERs for robust peaktracking [100]. In this work, we aimed to optimize ER to facilitate straightforward extractionof the sensor intrinsic quality factor for comparison with propagation loss simulations, aswell as facilitate meaningful comparison to previously reported sensors operating nearcritical coupling [3,21,28]. Subsequent system design (building upon the optimizationframework presented here) should consider the tradeoff between Q and ER in choosing thebest coupling condition for the application, and may choose to under-couple the resonators.To achieve critical coupling, gc can be selected based on numerical simulations. Forexample, the critical coupling condition can be estimated based on simulated couplingcoefficients extracted from FDTD simulations of the entire coupling region, along withsimulated propagation losses [20,101]. However, one drawback of this approach is thatFDTD simulations of the coupling region are very computationally intensive for SWGresonators. Additionally, while these FDTD coupling coefficient and loss simulationsaccount for loss contributions due to material absorption and substrate leakage, theyoften do not accurately recapitulate the effects of optical scattering, which depend onthe surface roughness of the fabricated waveguides and can increase losses and affect thecoupling condition [20]. Scattering has an increased effect on SWG waveguides compared toconventional strip waveguides owing to the increased surface area of SWG structures [3,39].Considering these limitations, we decided to take an empirical approach to optimize gc forclose-to-critical coupling.Each resonator was fabricated with four different coupling gaps. The fabricatedcoupling gaps for the C-band devices were based on our group’s previous empiricalfindings for conventional SWG ring resonators with similar expected effective indices.As outlined in Table 1, coupling gaps of gc = 450, 500, 550, and 600 nm were fabricatedfor devices C1, C2, C4, and C5, which had simulated effective indices between 1.70–1.71.Smaller coupling gaps of gc = 400, 450, 500, and 550 nm were selected for C3 and C6 due totheir greater predicted effective indices and, therefore, increased optical confinement. It hasbeen reported that coupling increases with increasing wavelengths due to reduced opticalconfinement at the defined waveguide geometry of w = 500 nm and t = 220 nm [20]. Assuch, smaller coupling gaps were selected for the O-band devices, relative to their predictedeffective indices. Coupling gaps of gc = 400, 450, 500, and 550 nm were fabricated for O1and O4, whereas coupling gaps of gc = 350, 400, 450, and 500 nm were fabricated for O2and O3 due to their higher simulated effective indices.The extinction ratios for all resonator designs were measured, as described in Sec-tion 2.4, and the results are presented in Figure 8 and Table 3. This characterization wasperformed for five replicate chips and mean values are reported. Details regarding thenumber of resonance peaks included from each chip in each mean calculation are providedin Section S4, Table S1. As shown in Figure 8b, all C-band devices, excluding C3, exhib-ited maximum extinction ratios at their largest coupling gaps. Consequently, it cannot beBiosensors 2022, 12, 840 20 of 35concluded that critical coupling was achieved for these devices, and future work shouldinclude the fabrication of these resonators with larger coupling gaps to avoid over coupling.In SEM images, the measured coupling gaps were 20–40 nm smaller than designed, whichmay be related to proximity effect correction in the lithography process [102]. This mayhave contributed to this requirement for larger coupling gaps. As illustrated in Figure 8c,devices O1, O2 and O3 exhibited maximum extinction ratios at intermediate values of gcwithin their fabricated ranges. However, the variations in extinction ratio between differentvalues of gc are similar in magnitude to the standard deviations of the measurements, sothese results may not confirm critical coupling. Resonator O4 achieved an extinction ratioat its largest fabricated coupling gap, further highlighting that future work should extendthe coupling gap ranges investigated here.Biosensors 2022, 12, x FOR PEER REVIEW 20 of 35 resonators. Additionally, while these FDTD coupling coefficient and loss simulations ac-count for loss contributions due to material absorption and substrate leakage, they often do not accurately recapitulate the effects of optical scattering, which depend on the surface roughness of the fabricated waveguides and can increase losses and affect the coupling condition [20]. Scattering has an increased effect on SWG waveguides compared to con-ventional strip waveguides owing to the increased surface area of SWG structures [3,39]. Considering these limitations, we decided to take an empirical approach to optimize gc for close-to-critical coupling. Each resonator was fabricated with four different coupling gaps. The fabricated cou-pling gaps for the C-band devices were based on our group’s previous empirical findings for conventional SWG ring resonators with similar expected effective indices. As outlined in Table 1, coupling gaps of gc = 450, 500, 550, and 600 nm were fabricated for devices C1, C2, C4, and C5, which had simulated effective indices between 1.70–1.71. Smaller coupling gaps of gc = 400, 450, 500, and 550 nm were selected for C3 and C6 due to their greater predicted effective indices and, therefore, increased optical confinement. It has been re-ported that coupling increases with increasing wavelengths due to reduced optical con-finement at the defined waveguide geometry of w = 500 nm and t = 220 nm [20]. As such, smaller coupling gaps were selected for the O-band devices, relative to their predicted effective indices. Coupling gaps of gc = 400, 450, 500, and 550 nm were fabricated for O1 and O4, whereas coupling gaps of gc = 350, 400, 450, and 500 nm were fabricated for O2 and O3 due to their higher simulated effective indices. The extinction ratios for all resonator designs were measured, as described in Section 2.4, and the results are presented in Figure 8 and Table 3. This characterization was per-formed for five replicate chips and mean values are reported. Details regarding the num-ber of resonance peaks included from each chip in each mean calculation are provided in Section S4, Table S1. As shown in Figure 8b, all C-band devices, excluding C3, exhibited maximum extinction ratios at their largest coupling gaps. Consequently, it cannot be con-clude that critical oupling was achieved for these devices, and future work should in-clude the fabrication of these resonators with larger coupling aps to avoid over coupling. In SEM images, the eas re co li aps ere 20–40 nm smaller than designed, which may be related to proxi ity effect correction in the lithography process [102]. This may have contributed to this require ent for larger coupling gaps. As illustrated in Figure 8c, devices O1, O2 and O3 exhibited axi u extinction ratios at intermediate values of gc within their fabricated ranges. However, the variations in extinction ratio between differ-ent values of gc are similar in magnitude to the standard deviations of the measurements, so these results may not confirm critical coupling. Resonator O4 achieved an extinction ratio at its largest fabricated coupling gap, further highlighting that future work should extend the coupling gap ranges investigated here. Figure 8. (a) Example spectra of four microring resonators with the same ring radii and waveguide geometries but different coupling gaps, leading to variations in resonance peak extinction ratios. Measured extinction ratios for (b) C-band and (c) O-band microring resonators as a function of Figure 8. (a) Exa ple s t icr ring resonators with the same ring radii and waveguidegeometries but dif ere s, leading to variations in resonance peak extinction ratios.Measured extinction ratios for (b) C-band and (c) O-band microring resonators as a function ofcoupling gap distance (gc). Star-shaped markers indicate designs which achieved the greatestextinction ratios for each waveguide geometry. All measurements were performed with watercladding. Extinction ratios for each sensor geometry were calculated from 0–13 resonance peaksper resonator (those peaks passing the R2 > 0.85 threshold) analyzed over a wavelength range of1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices, with 1–2 replicateresonators on each of five replicate chips. Extinction ratios are reported as the mean ± one standarddeviation. Further details regarding the number of included resonance peaks per resonator on eachchip are provided in Table S1.Variations in maximum extinction ratios between the devices, in particular betweenthe C-band and O-band devices, may be attributable to peak splitting. Peak splitting wasvisible in the resonator spectra and was particularly prominent for the O-band devices.This peak splitting, which is discussed further in the next section, leads to deleteriouseffects on the resonator performance, including a reduction in peak height, potentiallyexplaining why the maximum extinction ratios measured for the O-band resonators werelower than those measured for the C-band resonators [103,104]. Peak splitting largely arisesdue to stochastic scattering effects, which vary with wavelength [20]. This can lead tounpredictability in peak splitting severity between resonances, which may account forthe large standard deviations of the measured extinction ratios [20]. This peak splittingmay also be responsible for the absence of prominent maxima for devices O1, O2 andO3 in Figure 8c. As the measurements were made over wavelength ranges of 30–40 nm,it is likely that the wavelength-dependence of coupling within these wavelength rangesalso contributed to the large standard deviations [20]. Finally, the detectors used in theexperimental characterization of the sensors had a minimum detectable power of −80 dBm,which meant that some high-extinction ratio peaks were clipped at their minima. This mayhave added to the large standard deviations and may have caused an underestimation ofsome extinction ratios for designs close to critical coupling.Biosensors 2022, 12, 840 21 of 35Table 3. Optimal coupling gaps for each ring resonator geometry and their measured extinction ratios.Extinction ratios for each sensor geometry were calculated from 0–13 resonance peaks per resonator(those peaks passing the R2 > 0.85 threshold) analyzed over a wavelength range of 1530–1560 nm forthe C-band devices and 1270–1310 nm for the O-band devices, with 1–2 replicate resonators on eachof five replicate chips. Extinction ratios are reported as the mean ± one standard deviation. Furtherdetails regarding the number of included resonance peaks per resonator on each chip are provided inTable S1.Ring Resonator Design Optimal gc (nm) Extinction Ratio (dB)C1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experimental factors, such as differences between the designed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 600 * 26 ± 12C2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicte by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measure results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 600 * 27 ± 11C3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicted by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices ay be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypoth sis, SEM imaging as performed n the fabricated structures a d feature size were measured. Table 2. Group index, ng, and free sp ctral range (FSR) for SWG ring resonators btained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mea ± ne standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 500 19 ± 5600 * 21 ± 4600 * 20 ± 7C6 550 * 21 ± 4O1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators w th the waveguide geom tries utlined in Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch loss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was se ected to ensure low bend losses [3,94]. To characterize the fabricated microring r sonators, a tunabl laser was coupled to the evices and thei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 nm for the C-band or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip ntaining the resonators. The measu m n s were perform on five replicat chips and the measured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 reports the simulated and measu ed group indices and FSRs of the fabricated ring reson ors. All measured group indices were lower than those predicted by simula-tions, w th th boneless SWG devices generally exhibiting a slightly greater iffer nc in ng between the easured and si ulated values compared with the fishbone devices. Ac-co dingly, the measured FSRs were greate than the simulated values f r all geometries. Our group has previously f bric te boneless SWG microring resonators usi g thidentical geometry as design C6 from hi work, using a diff rent el ctron-beam lithogra-phy fabrica ion process [19]. Previously, 30 µm-radius ring r s nators fabrica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attrib table to experim ntal factors, such as differences between the designed and fa ricated structures. In particular, we hypothesized that the low experimental group indices may be due to smaller-than-designed fea ure sizes on th fabricated chips. To test this hypothesis, SEM imagi g was performed on th fabricat d structures and featuresizes were measured. Tabl 2. Gr up index, ng, and free s ectr l range (FSR) for SWG ring s tors btained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 500 15 ± 52Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon icroring reso ators w th the wave uide e m tries utlined in Table 1 we efabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ing geometry was u ed fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings we e design d with a ra-dius, R, of 30 µm, which w s se ected to n low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl la er was coupled to t e evices an thei tr ns-mis ion spectra w r collecte while sw ping the avele gth of th input laser from 1530–1560 m for the C-ba r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntainin the resonators. The measu m n s w re perfor n five replicat chips and th me sured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 repo ts the simulated and measu ed gr up indices and FSRs of th fabricated ring reson ors. All measured group indices were lower th n those predict by simula-tio s, th t bo eless SWG devices gener lly exhibiting a slightly greater iffer nc in ng between the asured and si ulated values compared with the fishbone devices. Ac-co dingly, the me sured FSRs wer greate than the sim lated values f r all geometries. Our r up has previously f bri te b nele s SWG microring res ator usi g thidentical geometry as design C6 f m i work, using a diff re t l ct on-beam lithogra-phy fabrica ion proce s [19]. Previously, 30 µm-radius ring r s nators f brica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an expe i-mental ng f 3.27 an FSR of 3.936 nm, which align well with th imulated values reportedhere. This indicat s that si ulation in ccuracies are unlikely to be the source of variation in ng and FSR between the simulated an m asure r sults. I stead, these variations are likely attrib table to experim nt l factors, such as ifferences betwee the desi ned and fa ricated structures. In particular, we hypothesized that the low experimental group indices may be due to smaller-than-design d fea ure sizes th fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 400 15 ± 4Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Wat r G oup Indices of SWG WaveguidesSilicon icroring reso ators w th the wave uide e m tries utlined in Table 1 we efabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ing geometry was u ed fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings we e design d with a ra-dius, R, of 30 µm, which w s se ected to n low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl la er was coupled to t e evices and thei tr ns-mis ion spectra w r collecte while sw ping the avele gth of th input laser from 1530–1560 m for the C-ba r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntaining the resonators. The measu m n s w re perfor n five replicat chips and th me sured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 repo ts the simulated and measu ed gr up indices and FSRs of th fabricated ring reson ors. All measured group indices were lower th n those predict by simula-tio s, th t bo eless SWG devices gener lly exhibiting a slightly greater iffer nc in ng between the m asured and simulated values compared with the fishbone devices. Ac-co dingly, the me sured FSRs wer greate than the sim lated values f r all geometries. Our r up has previously f bri te b nele s SWG microring res ator usi g thidentical geometry as design C6 f m i work, using a diff re t l ct on-beam lithogra-phy fabrica ion proce s [19]. Previously, 30 µm-radius ring r s nators f brica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 m, t = 220 nm) xhib ted an expe i-mental ng f 3.27 an FSR f 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated measured results. Ins ad, these variations are likely attrib table to experim nt l factors, such as iffer nces betw en the desi ned and fabricated str ctures. I particular, we hypoth sized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes w re measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 400 16 ± 9O 550 * 19 ± 9Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group In ices of SWG Waveg ides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the si ulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these ariations are likely attributable to xperimental factors, such as diff rences between the d signed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performe on the fabricated str ctures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than Fishbone SWG designs. * The best-performing coupling gap was the largest out of the fabricated range for agiven geometry, indicating potential over coupling.3.3. Fishbone SWG MRRs Achieve Comparable Performance to Previously ReportedSWG-Based SensorsQuality factors were estimated for all fabricated resonator designs by simulating thewaveguide propagation losses, as described in Section 2.1.2, then calculating the criticallycoupled quality factor, according to Equation (4). The simulated losses and correspondingquality factors for all waveguide designs are presented in Ta le 4. Indeed, these simulatedlosses and quality factors do not account for the effects of fabrication-related optical losses,but they do provide the fundamental limit for the device performance [3]. This offers avaluable benchmark against which to compare experimental results, which can help toidentify the contribution of fabrication-related losses to the real device performance andinform future approaches to mitigate these effects.Optical absorption in water is the dominant loss mechanism for waveguides operatingin the C-band. Since the predicted effective indices were similar for all of the fabricatedC-band designs, indicating similar modal confinement, similar losses were expected amongthese devices [3]. The simulated losses aligned well with this, as all simulated losses werebetween 39.9–40.7 dB/cm, suggesting that wfb and δ have little effect on the material lossesof SWG waveguides with similar effective indices.It has been reported that the optical absorption of water is roughly ten times lower inthe O-band than the C-band, allowing for significantly lower material losses [3,21]. Thisis reflected in the simulated propagation losses for the O-band structures, which rangedfrom 6.1–7.5 dB/cm. These losses are roughly six times lower than the C-band propagationlosses, which is a smaller reduction in losses compared to what would be predicted ifthe losses were solely due to material absorption. This discrepancy may be due to smalllosses to the substrate and PML boundaries. Corresponding to their lower losses, thesimulated quality factors for the O-band resonators were considerably greater than thosefor the C-band resonators, highlighting the potential benefit of using the O-band light forsensing applications.Biosensors 2022, 12, 840 22 of 35Table 4. Comparison of SWG ring resonator propagation losses and critically coupled quality factorspredicted by 3D-FDTD simulations with experimentally measured quality factors. Simulations andexperimental characterization were performed with water cladding. Experimental quality factors arereported for the ring resonator designs with the best-performing coupling gaps, as listed in Table 3.Experimental quality factors for each sensor geometry were calculated from 0–13 resonance peaksper resonator (those peaks passing the R2 > 0.85 threshold) analyzed over a wavelength range of1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices, with 1–2 replicateresonators on each of five replicate chips. Experimental quality factors are reported as the mean ± onestandard deviation. Further details regarding the number of included resonance peaks per resonatoron each chip are provided in Table S1.Ring Resonator Design Simulated PropagationLosses (dB/cm)QSimulation * ExperimentC1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experime tal factors, such a differences between the designed and fabricated structures. In particular, we hypothesized that the low exper en al group in-dic s may be due o smaller-than-designed f ature sizes on the fabricated chips. To test this hypothesis, SEM imaging as p rform d on the fabr cated tructures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtain d from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 40.2 7.29 × 103 (5.5 ± 1.0) × 1 3C2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicte by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measure results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, nd free spectral ra ge (FSR) for SWG ing resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 40.7 6.82 × 103 (4.7 ± 0.8) × 1 3C3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicted by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices nd 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 40.5 7.46 × 10 (4.7 ± 0.5) × 1 34 40.4 7.00 × 103 (4.9 ± 0.4) × 1 340.1 6.85 × 103 (4.6 ± 0.3) × 1 3C6 39.9 7.37 × 103 (5.2 ± 0.5) × 1031Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators w th th waveguide geom tries utlin d i Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack geometry o eliminate mod -mis atch loss s [3]. All icrorings were designed with a ra-dius, R, of 30 µm, which was se ected to ensure low b nd losses [3,94]. To ch racterize the fabricated microring r sonators, a tunabl laser was coupled to the evices and hei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 nm for the C-band or 1270–1310 nm for the O-band devices. This characterization was performed with a droplet of water fully covering the regions of the ch p ntaining t resonators. The measu m n s were perform on five replicat chips and the measured sp ctra were analyz d using a custo script, as describ d in Section 2.4. Table 2 re ort the sim lated and measu ed group indices and FSRs of the fabrica ed ring reson ors. All mea ured group indices were lower than those predict d by simultions, w th h boneless SWG device generally exhibit a ligh ly greater iffer nc in ng between the asured and si ulated values compared with the fishbone evic s. Acco dingly, the measured FSRs were greate than the simula ed val es f r all g ometries. Our group has prev ous y f bric te boneless SWG microring re nators usi g thdentical geometry as design C6 from hi w rk, using a diff rent el c ron-be m l thogra-phy fabrica ion process [19]. Previously, 30 µm-r di s ring r nat fabric ted with this wavegui e geometry (Λ = 250 n , δ = 0.7, w = 500 nm, t = 220 nm) exhibited an ex erimental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values rep rtedher . This ind cates that simulation inaccuracies are unlik ly t be the so rce of vari ion in ng and FSR between the simulated and easured results. Instead, th se variations are likely attributable to experimental factors, such as differences between the designed and f icated structures. In particular, we hypothesized that the low xperimental gr up indices m y be d e to sm lle -than-desig ed f ature siz s on th fabricated chips. To test this hypothesis, SEM imagi g was performed on th fabricat d structures and featuresizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ri g resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 7.3 4.40 × 104 (6.7 ± 1.5) × 1 3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimat s In-Water Group Indices of SWG Waveguides Silicon icroring resonators w th th wave uide eom tries utlin d i Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack geometry o eliminate mod -mis atch l ss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s se ected to ensure low b nd losses [3,94]. To ch racterize the fabricated microring r s nators, a tunabl laser was coupled to t e evices and hei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 m for the C-band r 1270–1310 nm for the O-band devices. This characterization was performed with a droplet of ater fully covering the regions of the ch p ntaining t resonators. The measu m n s were perfor on five replicat chips and the measured sp ctra were analyz d using a custom script, as describ d in Section 2.4. Table 2 re ort the sim lated and measu ed gr up indices and FSRs of the fabrica ed ring reson ors. All mea ured group indices were lower th n those predict d by simultions, th boneless SWG device generally exhibit a ligh ly greater iffer nc in ng between the asured and si ulated values compared with the fishbone evic s. Acco dingly, the me sured FSRs were greate than the simula ed val es f r all g ometries. Our r up has prev ous y f bric te boneless SWG microring re ators usi g thdentical geometry as design C6 fr m hi work, using a diff re t el c ron-be m l thogra-phy fabrica ion process [19]. Previously, 30 µm-r dius ring r nators fabrica ed with this wavegui e geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an ex erimental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values rep rtedhere. This ind cates that simulation inaccuracies are unlikely to be the so rce of vari ion in ng and FSR between the simulated and measure results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fa ricated structures. In particular, we hypothesized that the low experimental group indices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were mea ured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 7.5 4.79 × 104 (7.6 ± 1.7) × 1 3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimat s In-Wat r G oup Indices of SWG Waveguides Silicon icroring resonators w th the wave uide eom tries utlined in Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s se ected to ensure low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl laser was coupled to t e evices and thei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 m for the C-band r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntaining the resonators. The measu m n s were perfor on five replicat chips and the measured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 reports the simulated and measu ed gr up indices and FSRs of the fabricated ring reson ors. All measured group indices were lower th n those predicted by simula-tions, th t boneless SWG devices generally exhibiting a slightly greater iffer nc in ng between the measured and simulated values compared with the fishbone devices. Ac-co dingly, the me sured FSRs were greate than the simulated values f r all geometries. Our r up has previously f bric te b neless SWG microring res ators usi g thidentical geometry as design C6 fr m hi work, using a diff re t el ctron-beam lithogra-phy fabrica ion process [19]. Previously, 30 µm-radius ring r s nators fabrica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 . 3 . 3 . 6 3.8 4.5 . 9 2 .16 .60 . 4. 4 4.91 . C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 7.1 4.93 × 104 (6.9 ± 1.6) × 1 34 6.1 5.11 × 104 (7.8 ± 2.0) × 103Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group I dices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the sim lated values reported here. This indicates that simulation inaccuracies are unlikely to b the source of variation in ng and FSR between the simulated and measured results. Inst ad, these variations are likely attributable to experime t l factors, such as differences between the d signed and fabricated structur s. In particular, w hyp thesiz d that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the f bricated st uctures and feature sizes were measured.Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resona ces measured ov r a wavelength r nge of 1530–1560 nm for the C-band devices and 1270–1 10 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than Fishbone SWG designs. * Calculated based on critical coupling assumption.Quality factors for the fabricated ring resonators were calculated from the measuredspectra, as described in Section 2.4, an he results are pr vided in Tabl 4. For the C-banddevices, the simulated quality factors w re 1.3–1.6 times as large as the experimental values.This difference between si u ated and experimental values is likely due to scattering andcoupling l sses, which were not accounted for in the simulations. Scattering losses arisedue to roughness introduced on the waveguide surfaces during fabrication, which makesthem challenging to model. These losses are typically non-n gligible for SWG wav guidesowing to their large surface area [3,94]. Next, overcoupl ng leads to greater optical lossescompared to critical coupling [100]. As d scussed in the previous section, any of theC-band resonators were likely overcoupled, giving rise to this loss mechanis . Since thesimulated quality factors were calculated based on the critical coupling assumption, theselosses are another likely source of variation between the simulated and experimental results.It should be noted that the propagation loss simulations described in this work also didnot include bending losses. Based on previously reported results, we expected negligiblebending losses at the large ring radius of 30 µm considered here [3].The simulated quality factors for the O-band resonators ranged from 4.40 × 104 to5.11 × 104, whereas the experimentally measured values were 6.3–7.2 times lower (Table 4).While scattering and coupling losses, combined with the smaller-than-designed featuresizes of the fabricated structures, likely contributed to this discrepancy, peak splittingappeared to be the dominant source of this variation. In an ideal ring resonator, there existtwo counterpropagating circulating modes, clockwise and counterclockwise, which areuncoupled, and degenerate, meaning they resonate at the same frequency [104,105]. In thiscase, the resonator exhibits single peaks. A small mode perturbation, however, can couplethese modes and break their degeneracy leading to a resonance shift that manifests as splitresonance peaks [20,103,104]. In silicon waveguides, this perturbation typically occurs dueto stochastic backscattering arising from sidewall roughness [20,103,104]. In the spectrameasured for all O-band resonators, peak splitting was prevalent, comprising 18–51% of allresonances. Conversely, split peaks were far less common in the C-band resonator spectra,Biosensors 2022, 12, 840 23 of 35comprising roughly 2–12% of all resonances. While all resonators studied in this workwere fabricated using the same foundry process and, therefore, were subject to similarsidewall corrugations, the exaggerated peak splitting observed among the O-band devicessuggests that sidewall scattering is exacerbated at lower wavelengths. This is consistentwith analytical models for scattering losses in which the losses are proportional to the squareof the ratio of surface roughness to the wavelength of light in the material [106]. Thus, theeffects of scattering, and therefore, peak splitting, increase with decreasing wavelength.Additionally, the higher water absorption at 1550 nm may be hiding peak splitting, whereasa 10× lower water absorption at 1310 nm would reveal scattering induced peak splitting.The analysis script used to extract the quality factors from the measured spectraperformed Lorentzian fitting on the resonance peaks to measure the FWHM, from whichthe quality factors were calculated. In the case of split peaks, the Lorentzian was typicallyfit to the doublet, leading to an underestimation of Q (Figure 9). In this analysis, a R2 cutoffof 0.85 dictated which peaks were used in the calculation of Q. The split peaks typicallyexhibited poor R2 values compared with single peaks (Figure 9b); however, there wasconsiderable overlap, with some apparent split peaks exhibiting higher R2 values thansome single peaks (Figure 9c). However, it should be noted that some peaks, such as theone shown in Figure 9c, exhibited apparent peak splitting that had a similar magnitude tothe spectral noise, making it challenging to confidently confirm the identity of these peaksas split or non-split.Biosensors 2022, 12, x FOR PEER REVIEW 24 of 35 given spectrum, it may also be challenging to confirm the identity of split peaks with high confidence. Overall, the prevalence of these split peaks is likely to cause deleterious effects in the analysis of binding assays. Therefore, a more robust solution for improving sensor performance is to design resonators that are less sensitive to backscattering. Figure 9. (a) Example of a non-split resonance peak from a spectrum measured for resonator C6, showing the Lorentzian fit and full width at half maximum (FWHM) calculated by the analysis script. (b) Example of a split resonance peak with a low R2 (0.794) from a spectrum measured for resonator O3, showing the Lorentzian fit calculated by the analysis script (FWHM not calculated, as this peak exhibited a R2 value below the cutoff of 0.85). (c) Example of an apparent split resonance peak with a high R2 (0.951) from a spectrum measured for resonator O3, showing the Lorentzian fit and FWHM calculated by the analysis script. The back reflections that cause peak splitting have been reported to increase with ng [20]. This is consistent with our experimental results. Resonator design O4, which had the lowest ng out of the O-band devices, demonstrated the least peak splitting, with split peaks comprising approximately 18% of all resonances measured across five chips. Resonator designs O2 and O3, which had the two highest values of ng, demonstrated the most peak splitting, at roughly 50% and 51% of all resonances, respectively. In these estimates, it should be noted that split peaks with very low extinction ratios (e.g., due to overcoupling) were nearly indistinguishable from noise. This meant that some split peaks may have been overlooked, resulting in an underestimation of their true occurrence. Among the resona-tors that had sufficiently high extinction ratios to confirm the identity of split peaks, O1, O2, O3, and O4 exhibited peak splitting on approximately 42%, 54%, 70%, and 27% of their resonances, respectively. Overall, these data suggest that reducing ng by reducing δ and/or wfb may improve the resonator performance. This should be accompanied by a de-tailed analysis of O-band substrate leakage losses to ensure that any feature size reduc-tions do not introduce additional deleterious effects. Finally, electron-beam fabrication processes have been found to yield semi-periodic surface roughness [20]. If the surface roughness of the fabrication process is well-characterized, simulation models can be es-tablished to better predict the extent of backscattering at different wavelengths, which may help predict peak splitting and inform ring resonator design [20]. If possible, a re-duction in etch roughness could further reduce these scattering effects. Fishbone SWG structures fabricated by Deep UV lithography are likely to have reduced sidewall rough-ness. In electron beam lithography processes similar to that used in this work, the shot pitch and machine grid are very small (e.g., 5–6 nm) and the electron beam size is roughly 10–20 nm [83]. The quantization of shots, which are not very well smoothed out by the small beam size, to the machine grid results in high-resolution roughness. In contrast, Deep UV lithography processes use masks made by electron beam lithography, but they are smoothed out by the 193 nm wavelength of light used for the exposure and pattern transfer [83]. Hence, peak splitting is expected to be reduced for devices fabricated by 300 mm wafer 193 nm immersion Deep UV lithography foundries. Moreover, Deep UV li-thography processes now enable high-volume manufacturing of SiP chips with sub-100 Figure 9. (a) Exa ple of a non-split resonance peak from a spectrum measured for resonator C6,showing the Lorentzian fit and full width at half maximu (FWHM) calculated by the analysis script.(b) Example of a split resonanc peak with low R2 (0.794) from a spectrum measured for r sonatorO3, showing the Lorentzian fit calculated by the analysis script (FWHM not calculated, as this peakexhibited a R2 value below the cutoff of 0.85). (c) Example of an apparent split resonance peak with ahigh R2 (0.951) from a spectrum measured for resonator O3, showing the Lorentzian fit and FWHMcalculated by the analysis script.To test whether increasing the selection stringency effectively eliminated split peaksfrom the quality factor calculation, the analysis was repeated on the O-band data withthe R2 threshold increased to 0.95. This analysis did not produce a noticeable differencein the results and incompletely filtered out the split peaks, while eliminating numeroussingle peaks and underestimating the quality factors. While it may be possible to performimproved fitting to the doublets to extract more accurate quality factors in post processing,their extinction ratios will still be degraded. Further improvements could be made tothe analysis algorithm to filter out split peaks and only analyze apparent non-split peaks,but such an approach is confounded by the variable severity of the split peaks. Forexample, split peaks may be visually imperceptible in cases where the splitting is less thana linewidth, yet these peaks will still exhibit degraded extinction ratios and quality factors.As illustrated in Figure 9c, when the magnitude of peak splitting is similar to the noise in agiven spectrum, it may also be challenging to confirm the identity of split peaks with highconfidence. Overall, the prevalence of these split peaks is likely to cause deleterious effectsin the analysis of bi ding assays. Therefore, a more robust solution for improving sensorperformance is to design resonators that are less sensitive to backscattering.Biosensors 2022, 12, 840 24 of 35The back reflections that cause peak splitting have been reported to increase withng [20]. This is consistent with our experimental results. Resonator design O4, whichhad the lowest ng out of the O-band devices, demonstrated the least peak splitting, withsplit peaks comprising approximately 18% of all resonances measured across five chips.Resonator designs O2 and O3, which had the two highest values of ng, demonstratedthe most peak splitting, at roughly 50% and 51% of all resonances, respectively. In theseestimates, it should be noted that split peaks with very low extinction ratios (e.g., dueto overcoupling) were nearly indistinguishable from noise. This meant that some splitpeaks may have been overlooked, resulting in an underestimation of their true occurrence.Among the resonators that had sufficiently high extinction ratios to confirm the identityof split peaks, O1, O2, O3, and O4 exhibited peak splitting on approximately 42%, 54%,70%, and 27% of their resonances, respectively. Overall, these data suggest that reducingng by reducing δ and/or wfb may improve the resonator performance. This should beaccompanied by a detailed analysis of O-band substrate leakage losses to ensure that anyfeature size reductions do not introduce additional deleterious effects. Finally, electron-beam fabrication processes have been found to yield semi-periodic surface roughness [20].If the surface roughness of the fabrication process is well-characterized, simulation modelscan be established to better predict the extent of backscattering at different wavelengths,which may help predict peak splitting and inform ring resonator design [20]. If possible,a reduction in etch roughness could further reduce these scattering effects. FishboneSWG structures fabricated by Deep UV lithography are likely to have reduced sidewallroughness. In electron beam lithography processes similar to that used in this work, theshot pitch and machine grid are very small (e.g., 5–6 nm) and the electron beam size isroughly 10–20 nm [83]. The quantization of shots, which are not very well smoothedout by the small beam size, to the machine grid results in high-resolution roughness. Incontrast, Deep UV lithography processes use masks made by electron beam lithography,but they are smoothed out by the 193 nm wavelength of light used for the exposure andpattern transfer [83]. Hence, peak splitting is expected to be reduced for devices fabricatedby 300 mm wafer 193 nm immersion Deep UV lithography foundries. Moreover, DeepUV lithography processes now enable high-volume manufacturing of SiP chips with sub-100 nm feature sizes, making Deep UV lithography an attractive option for mass productionof SWG-based sensor chips [42,83,107].Next, ring resonator performance was assessed in terms of Sb. The simulated Sb valuesfor all fabricated devices are reported in Table 5. To experimentally measure the bulksensitivities of the fabricated devices, the sensor chips were interfaced with a two-channelPDMS microfluidic gasket and five NaCl solutions with different concentrations (0–0.375 M)were flowed over the sensors in alternating ascending and descending sequences for a totalof ten replicate exposures to each solution. Throughout the experiment, the transmissionspectra were measured using a tunable laser and optical detectors. The measurement setupused for these experiments is shown in Figure 10a. For each resonator design (C1–C6 andO1–O4), two replicate resonators were monitored, one of which was located in microfluidicchannel 1 and the other in channel 2. The same fluid sequence was delivered to bothmicrofluidic channels. On the chip layout, the C-band and O-band devices were accessiblefrom grating couplers on opposite edges of the 9 mm × 9 mm photonic chip. This meantthat the microfluidic gasket had to be rotated 180◦ to access the C-band devices comparedto the O-band. When the gasket was aligned to the C-band devices, the O-band resonatorswere in direct contact with PDMS, and vice versa. As the chips were fabricated withoutan oxide cladding, this made the resonators in direct contact with the PDMS prone todamage during gasket alignment and removal. Therefore, the C-band and O-band deviceswere tested with microfluidics on separate chips to prevent damage to the resonators priorto use. The resonators’ saved spectra were analyzed by a custom retrospective analysisscript to track the resonance wavelength shifts of the sensors, as described in Section 2.6.An example of a spectrogram collected during one of these experiments and an overlaidpeak shift plot generated by the retrospective analysis script are shown in Figure 10b.Biosensors 2022, 12, 840 25 of 35An example of the spectral peak shifts corresponding to each salt solution is shown inFigure 10c.Table 5. SWG ring resonator Sb and iLoD values predicted by 3D-FDTD simulations and mea-sured experimentally. Experimental Sb values are reported as averages ± one standard deviationfrom 8–10 replicate experiments in which the ring resonators were exposed to five NaCl solutionsof different concentrations. Experimental iLoDs were calculated for each resonator using the experi-mentally measured Q values (Table 4) and the mean of the experimentally measured Sb values fromchannels 1 and 2, with errors propagated from the standard deviations reported in Table 4 and for Sbin channels 1 and 2.Ring Resonator DesignSb (nm/RIU) iLoD (RIU)Simulation Experiment,Ch. 1Experiment,Ch. 2 Simulation ExperimentC1Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experimental factors, such as differences between the designed and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed f ature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR ( m) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 381 414 ± 8 389 ± 10 5.58 × 10−4 (7.1 ± 0.9) × 10−4C2Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicte by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measure results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-desig ed featur sizes on the fabricat d chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtaine from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 395 438 ± 8 416 ± 11 5.75 × 10−4 (7.7 ± 0.9) × 10−4C3Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the wave uide eometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch l sses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s selected to ensure low bend losses [3,94]. To characterize the fabricated microring res nators, a tunable laser was coupled to t e devices and their trans-mission spectra were collecte while sweeping the wavelength of the input laser from 1530–1560 m for the C-band devices r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured gr up indices and FSRs of the fabricated ring resonators. All measured group indices were lower th n those predicted by simula-tions, ith t e boneless SWG devices generally exhibiting a slightly greater ifference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the me sured FSRs were greater than the simulated values for all geometries. Our r up has previously fabricated b neless SWG microring res ators using the identical geometry as design C6 fr m this work, using a differe t electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveguide geometry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, whic align well with the simulat d values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the esi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances easured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 ╫ 3.33 2.83 ± 0.06 3.83 4.5 ± 0.09 2 3.16 2.60 ± 0.0 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 357 349 ± 6 323 ± 6 5.82 × 10−4 (9.8 ± 0.7) × 10−44 382 354 ± 5 343 ± 7 5.80 × 10−4 (9.1 ± 0.6) × 10−4392 427 ± 8 392 ± 10 5.77 × 10−4 (8.3 ± 0.4) × 10−4C6 369 413 ± 8 389 ± 10 5.69 × 10−4 (7.5 ± 0.6) × 10−41Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. Results 3.1. Simulation Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators w th th waveguide geom tries utlin d i Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack geometry o eliminate mod -mis atch loss s [3]. All icrorings were designed with a ra-dius, R, of 30 µm, which was se ected to ensure low b nd losses [3,94]. To ch racterize the fabricated microring r sonators, a tunabl laser was coupled to the evices and hei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 nm for the C-band or 1270–1310 nm for the O-band devices. This characterization was performed with a droplet of water fully covering the regions of the ch p ntaining t resonators. The measu m n s were perform on five replicat chips and the measured sp ctra were analyz d using a custo script, as describ d in Section 2.4. Table 2 re ort the sim lated and measu ed group indices and FSRs of the fabrica ed ring reson ors. All mea ured group indices were lower than those predict d by simulti ns, w th h boneless SWG device generally exhibit a ligh ly greater iffer nc in ng between the asured and si ulated values compared with the fishbone evic s. Acco dingly, the measured FSRs were greate than the simula ed val es f r all g ometries. Our group has prev ous y f bric te boneless SWG microring re nators usi g thdentical geometry as design C6 from hi work, using a diff rent el c ron-be m l thogra-phy fabrica ion process [19]. Previously, 30 µm-r dius ring r nators fabrica ed with this wavegui e geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an ex erimental ng of 3.27 and FSR of 3.936 nm, which align well with the simul t d values rep rtedhere. This ind cates that simulation inaccuracies are unl kely to be the so rce of vari ion in ng and FSR between the simulated and easured r sults. Instead, these vari tions are likely attributable to experimental factors, such as differ nces between the d signed and fa ricated structures. In particular, we hypoth sized that th low exp rimental group indices may be due to smalle -tha -designed feature sizes on th fabricated chips. To test this hypothesis, SEM imagi g was performed on th fabricat d structures and featuresizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ 3.33 2.83 ± 0.06 3.83 4.51 ± 0.09 C2 ╫ 3.16 2.60 ± 0.05 4.04 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 354 349 ± 11 349 ± 8 8.42 × 10−5 (5.6 ± 0.9) × 10−4Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimat s In-Water Group Indices of SWG Waveguides Silicon icroring resonators w th th wave uide eom tries utlin d i Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack geometry o eliminate mod -mis atch l ss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s se ected to ensure low b nd losses [3,94]. To ch racterize the fabricated microring r s nators, a tunabl laser was coupled to t e evices and hei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 m for the C-band r 1270–1310 nm for the O-band devices. This characterization was performed with a droplet of ater fully covering the regions of the ch p ntaining t resonators. The measu m n s were perfor on five replicat chips and the measured sp ctra were analyz d using a custom script, as describ d in Section 2.4. Table 2 re ort the sim lated and measu ed gr up indices and FSRs of the fabrica ed ring reson ors. All mea ured group indices were lower th n those predict d by simultions, th boneless SWG device generally exhibit a ligh ly greater iffer nc in ng between the asured and si ulated values compared with the fishbone evic s. Acco dingly, the me sured FSRs were greate than the simula ed val es f r all g ometries. Our r up has prev ous y f bric te b neless SWG microring re ators usi g thdentical geometry as design C6 fr m hi work, using a diff re t el c ron-be m l thogra-phy fabrica ion process [19]. Previously, 30 µm-r dius ring r nators fabrica ed with this wavegui e geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, = 220 nm) exhibited an ex erimental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values rep rt dhere. This ind cates that simulatio inac uracies are unlikely to be the so rce of vari ion in ng and FSR between the simulated and measur results. Ins ead, these variations are likely attributable to experime t l f ctors, such as ifferenc s between he desi ned a d fa ricated structures. In particular, we hypothesized that the low experimental group indices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 .33 .83 . 6 3.83 .5 .09 2 .16 .60 . 4.04 .91 .10 C3 ╫ .44 .9 . 5 .71 .33 . 7 4 .21 .64 . 4 3.97 4.82 .08 5 .12 .52 . 4.09 5.05 .10 C6 .35 .7 . 5 3.81 4.61 . 8 1 .08 2.57 . 7 .96 .5 . 9 2 .45 3.00 . 8 .64 .04 . O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two u expected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 325 33 ± 15 344 ± 7 8.41 × 10−5 (5.1 ± 0.8) × 10−4Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 . Results 3.1. Simulation Overestimat s In-Wat r G oup Indices of SWG Waveguides Silicon icroring resonators w th the wave uide eom tries utlined in Table 1 werefabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circula ring geometry was used fo the sensors instead of a racetrack ge-ometry to eliminate mode-mis atch l ss s [3]. All microrings were designed with a ra-dius, R, of 30 µm, which w s se ected to ensure low bend losses [3,94]. To characterize the fabricated microring r s nators, a tunabl laser was coupled to t e evices and thei tr ns-mission spectra were collected while swe ping the avele gth of th input laser from 1530–1560 m for the C-band r 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of ater fully covering the regions of the chip ntaining the resonators. The measu m n s were perfor on five replicat chips and the measured spectra were analyzed using a custom script, as describ d in Section 2.4. Table 2 reports the simulated and measu ed gr up indices and FSRs of the fabricated ring reson ors. All measured group indices were lower th n those predicted by simula-tions, th t boneless SWG devices generally exhibiting a slightly greater iffer nc in ng between the measured and simulated values compared with the fishbone devices. Ac-co dingly, the me sured FSRs were greate than the simulated values f r all geometries. Our r up has previously f bric te b neless SWG microring res ators usi g thidentical geometry as design C6 fr m hi work, using a diff re t el ctron-beam lithogra-phy fabrica ion process [19]. Previously, 30 µm-radius ring r s nators fabrica ed with this waveguide geome ry (Λ = 250 nm, δ = 0.7, w = 500 nm, t = 220 nm) exhibited an experi-mental ng of 3.27 and FSR of 3.936 nm, which align well with the simulated values reportedhere. This indicates that si ulation inaccuracies are unlikely to be the source of variation in ng and FSR between the simulated and measured results. Instead, these variations are likely attributable to experiment l factors, such as ifferences between the desi ned and fabricated structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on the fabricated structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 nm for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Reso ator Design ng FSR (nm) Simulation Experiment Simulation Experiment 1 . 3 . 3 . 6 3.8 4.5 . 9 2 .16 .60 . 4. 4 4.91 . C3 ╫ 3.44 2.9 ± 0.05 .71 .33 ± 0. 7 4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 5 3.12 2.52 ± 0.0 4.09 5.05 ± 0.10 C6 3.35 .7 ± 0.05 3.81 4.61 ± 0.08 1 ╫ 3.08 2.57 ± 0.07 2.96 3.5 ± 0.09 2 3.45 3.00 ± 0.08 .64 3.04 ± 0. O3 ╫ .34 .8 . 2.73 .15 .08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regardi g fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than 357 331 ± 6 333 ± 8 8.31 × 10−5 (5.8 ± 0.9) × 10−44 382 364 ± 7 383 ± 7 7.69 × 10−5 (4.5 ± 0.8) × 10−4Biosensors 2022, 12, x FOR PEER REVIEW 17 of 35 3. R sults 3.1. Simulat on Overestimates In-Water Group Indices of SWG Waveguides Silicon microring resonators with the waveguide geometries outlined in Table 1 were fabricated on a SOI wafer with no oxide cladding using ANT’s electron-beam lithography process [82]. A circular ring geometry was used for the sensors instead of a racetrack ge-ometry to eliminate mode-mismatch losses [3]. All microrings were designed with a ra-dius, R, of 30 µm, which was selected to ensure low bend losses [3,94]. To characterize the fabricated microring resonators, a tunable laser was coupled to the devices and their trans-mission spectra were collected while sweeping the wavelength of the input laser from 1530–1560 nm for the C-band devices or 1270–1310 nm for the O-band devices. This char-acterization was performed with a droplet of water fully covering the regions of the chip containing the resonators. The measurements were performed on five replicate chips and the measured spectra were analyzed using a custom script, as described in Section 2.4. Table 2 reports the simulated and measured group indices and FSRs of the fabricated ring resonators. All measured group indices were lower than those predicted by simula-tions, with the boneless SWG devices generally exhibiting a slightly greater difference in ng between the measured and simulated values compared with the fishbone devices. Ac-cordingly, the measured FSRs were greater than the simulated values for all geometries. Our group has previously fabricated boneless SWG microring resonators using the identical geometry as design C6 from this work, using a different electron-beam lithogra-phy fabrication process [19]. Previously, 30 µm-radius ring resonators fabricated with this waveg ide geometry (Λ = 250 nm, δ = 0.7, w = 500 m, t = 220 nm) exhibited an experi-ment l ng of 3.27 and FSR of 3.936 nm, which align w l wit the simulated values reported here. This indicates that simulation inaccuracies are unlikely to be the source of variation i g and FSR between the simulat d and m asured r sults. Instead, th se variations are likely attr butable o experi ental fact rs, such as differences between the designed and fabricat d structures. In particular, we hypothesized that the low experimental group in-dices may be due to smaller-than-designed feature sizes on the fabricated chips. To test this hypothesis, SEM imaging was performed on th fabricat d structures and feature sizes were measured. Table 2. Group index, ng, and free spectral range (FSR) for SWG ring resonators obtained from 3D-FDTD band structure simulations with as-designed structures and experiments. For each resonator, ng and FSR were calculated based on all resonances measured over a wavelength range of 1530–1560 n for the C-band devices and 1270–1310 nm for the O-band devices. The reported values are the mean ± one standard deviation for these measurements from five replicate chips. Ring Resonator Design ng FSR (nm) Simulation Experiment Simulation Experiment C1 ╫ .33 2.83 ± .06 3.83 4.51 ± 0.09 C2 ╫ .16 2.60 ± .05 4. 4 4.91 ± 0.10 C3 ╫ 3.44 2.94 ± 0.05 3.71 4.33 ± 0.07 C4 3.21 2.64 ± 0.04 3.97 4.82 ± 0.08 C5 3.12 2.52 ± 0.05 4.09 5.05 ± 0.10 C6 3.35 2.77 ± 0.05 3.81 4.61 ± 0.08 O1 ╫ 3.08 2.57 ± 0.07 2.96 3.54 ± 0.09 O2 ╫ 3.45 3.00 ± 0.08 2.64 3.04 ± 0.08 O3 ╫ 3.34 2.89 ± 0.07 2.73 3.15 ± 0.08 O4 3.01 2.39 ± 0.07 3.02 3.80 ± 0.10 ╫ Fishbone SWG designs. The SEM imaging highlighted two unexpected observations regarding the fabricated waveguide morphologies. First, regarding fabrication tolerances, most waveguide fea-tures were slightly smaller than designed. Typically, w was 18–25 nm smaller than Fishbone SWG designs.Biosensors 2022, 12, x FOR PEER REVIEW 25 of 35 fe ture sizes, making De p UV lithography an attrac ive option for mass production of SWG-based sensor chips [42,83,107]. Next, ring resonator performance w s assessed in terms of Sb. The simulated Sb values for all fabricated devices are reported in Table 5. To experimentally measure the bulk sen-sitivities of the fabricated devices, the sensor chips were interfaced with a two-channel PDMS microfluidic gasket and five NaCl solutions with different concentrations (0–0.375 M) were flowed over the sensors in alter ting asce ding and descen ing sequences for a total of ten replicate exposures to each solution. Throughout the experiment, the trans-missi spectra were using a tunable laser and optical detecto s. The measure-me t s tup used for thes experiment i shown in Figure 10a. Fo each resonator design (C1–C6 and O1–O4), two replicate resonators were monitored, one of which was located in microfluidic chan el 1 nd the other in channel 2. The same fluid sequence was deliv-ered t both microfl idic channels. On the c ip layout, the C-ba d and O-band devices were accessible from grating couplers on opposite edges of the 9 mm × 9 mm photonic chip. This meant that the microfluidic gasket had to be rotated 180° to access the C-band devices compar d to the O-band. When the gasket was alig ed to the C-band devices, the O-band resonators were in direct contact with PDMS, and vice versa. As the chips were fabricated without an oxide cladding, this made the resonators in direct contact with the PDMS prone to damage during asket alignment and r moval. Ther fore, the C-band and O-band devices wer tested with microfluidics on s parate chips to pr vent damage to th resonators prior to use. The resonat rs’ saved sp ctra wer analyzed by a custom ret-rospective analysis script to track the resonance wavelength shifts of the sensors, as de-scribed in Section 2.6. An example of a spectrogram collected during one of these experi-ments and an overlaid peak shift plot generated by the retrospective analysis script are shown in Figure 10b. An example of the spectral peak shifts corresponding to each salt solution is shown in Figure 10c. Figure 10. (a) Measurement setup for bulk sensitivity experiments, showing a SiP sensor chip inter-faced with microfluidics and coupled to a fiber array to connect to benchtop optical inputs and out-puts. (b) Spectrogram with ove la d peak track ng pl t (black line) f r device C3 measured during a bulk sensitivity experiment in which the sensor was exposed to five different NaCl solutions, each with different concentrations, a total of ten times. (c) Overlaid spectra for device C3 illustrating the red shift in resonance peak wavelength with increasing NaCl concentration. The vertical gray lines in (b) indicate the times at which the spectra displayed in (c) were obtained during the bulk sensi-tivity experiment. Figure 10. (a) Measurement setup for bulk sensitivity experiments, showing a SiP sensor chipinterfaced with microfluidics and coupled to a fiber array to connect to benchtop optical inputs andoutputs. (b) Spectrogram with overlaid peak tracking plot (black line) for device C3 measured duringa bulk sensitivity experiment in which the sensor was exposed to five different NaCl solutions, eachwith different concentrations, a total of ten times. (c) Overlaid spectra for device C3 illustrating thered shift in resonance peak avelength with increasing NaCl conc ntration. The ver ical gray li es in(b) indicat the times at which the spectra displayed in (c) were obtained during the bulk sensitivityexperiment.The peak shift plots all demonstrated a gradual baseline blue drift over time(10–72 pm/hr). While the source of this drift is unclear, one contributor may be thegradual etching of silicon by NaCl solution [108]. Prior to further analysis, the peak shiftdata were, therefore, drift-corrected by performing a linear fit to the baseline of each peakshift plot and subtracting this linear fit from the data. Sb was then calculated by performinga linear regression on the resonance peak shifts versus the bulk refractive index of the saltsolutions data, and extracting the slope, as illustrated in Figure 11. For each resonator,Sb was calculated as the average slope from 8–10 linear regressions (on the data fromBiosensors 2022, 12, 840 26 of 358–10 replicate exposures to all five salt solutions), and the average values and their stan-dard deviations are presented in Table 5. It should be noted that only eight replicates wereused when peak shift abnormalities, such as abrupt jumps and drops (likely due to bubblespassing through the fluidic system), were observed during the first replicate. In these cases,the first two replicates were excluded from the calculated averages to maintain an equalnumber of ascending- and descending-concentration replicates.Biosensors 2022, 12, x FOR PEER REVIEW 27 of 35 Figure 11. Measured resonance wavelength shifts as a function of NaCl concentration for (a) C-band and (b) O-band ring resonators. Measurements from the fifth (ascending) and sixth (descending) replicate exposures to five different NaCl concentrations are displayed. Measured resonance wave-length shifts versus bulk refractive index with linear fits for (c) C-band and (d) O-band ring resona-tors. The linear fit slopes were used to calculate Sb for each resonator. Note that the results presented in (c,d) correspond to the fifth replicate of the bulk sensitivity experiments, whereas the Sb values reported in Table 5 represent averages measured across all ten replicates. Solid lines correspond to ring resonators located in microfluidic channel 1, whereas dotted lines correspond to ring resonators located in microfluidic channel 2. Additionally, note that the traces for device C1 are hidden under the traces for device C6 in (a,c). On average, the experimental results aligned well with the simulated ones, but the experimental results showed variations in bulk sensitivity between the two microfluidic channels. For the C-band designs, resonators in channel 1 always demonstrated higher values of Sb, whereas for the O-band designs, excluding O1, resonators in channel 2 always demonstrated higher values of Sb. For O1, Sb was virtually identical between the two chan-nels. This spatial variation in Sb is illustrated in Figure 12a. These variations similarly af-fected the fishbone and boneless structures. To determine if this variation was the result of variability among the fabricated resonator structures, the spatial variation of ng was similarly analyzed based on the results obtained in Section 3.1 (Figure 12b), which showed that ng did not vary as a function of location on the chip for replicate resonator designs, though the boneless devices typically exhibited larger differences between the experi-mental and simulated group indices compared to the fishbone structures. This suggests that experimental factors related to fluidics were the most likely source of variation in Sb. In these experiments, the NaCl solutions used in both channels were aliquots of the same stock solution, eliminating the solutions as a source of error. Further, the fluid con-trol system was programmed to deliver identical flow rates through both channels. These flow rates were monitored by flow sensors throughout the experiments to ensure that the expected flow rates were delivered, making this another unlikely source of error. The re-fractive indices of the NaCl solutions used in the Sb calculations were measured with an Figure 11. easured resonance avelength shifts as a function of aCl concentration for (a) C-bandand (b) O-band ring resonat rs. ts fr t e fift (ascending) and sixth (descending)replicate exposures to fi e iff t l t ti r isplayed. Measured resonance wave-length shifts versus bulk refractive index with linear fits for (c) C-band and (d) O-band ring resonators.The linear fit slopes were used to calculate Sb for each resonator. Note that the results presentedin (c,d) correspond to the fifth replicate of the bulk sensitivity experiments, whereas the Sb valuesreported in Table 5 represent averages measured across all ten replicates. Solid lines correspond toring resonators located in microfluidic channel 1, whereas dotted lines correspond to ring resonatorslocated in microfluidic channel 2. Additionally, note that the traces for device C1 are hidden underthe traces for device C6 in (a,c).On average, the experimental results aligned well with the simulated ones, but theexperimental results showed variations in bulk sensitivity between the two microfluidicchannels. For the C-band designs, resonators in channel 1 always demonstrated highervalues of Sb, whereas for the O-band designs, excluding O1, resonators in channel 2 alwaysdemonstrated higher values of Sb. For O1, Sb was virtually identical between the twochannels. This spatial variation in Sb is illustrated in Figure 12a. These variations similarlyaffected the fishbone and boneless structures. To determine if this variation was the resultof variability among the fabricated resonator structures, the spatial variation of ng wassimilarly analyzed based on the results obtained in Section 3.1 (Figure 12b), which showedthat ng did not vary as a function of location on the chip for replicate resonator designs,though the boneless devices typically exhibited larger differences between the experimentaland simulated group indices compared to the fishbone structures. This suggests thatexperimental factors related to fluidics were the most likely source of variation in Sb.Biosensors 2022, 12, 840 27 of 35Biosensors 2022, 12, x FOR PEER REVIEW 28 of 35 Abbe refractometer at visible wavelengths and chromatic dispersion was not accounted for, which could constitute one source of experimental error. Figure 12. (a) Bright-field micrograph of the sensor chip (converted to grayscale) with markers in-dicating the locations of each ring resonator used for the bulk sensing measurements. The marker colors are mapped to the percent difference between the measured and simulated Sb for each reso-nator. The positions of the two microfluidic channels for each set of testing (O-band and C-band) is denoted by darker gray rectangular overlays. (b) Bright-field micrograph of the sensor chip with markers indicating the locations of each ring resonator characterized in Section 3.1. The marker col-ors are mapped to the percent difference between the measured and simulated ng for each resonator. The presence of trapped air between the silicon pillars of the SWG waveguides due to incomplete wetting may be responsible for the variations in Sb. Firstly, as discussed in Section 3.1, this phenomenon may have contributed to the lower-than-predicted values of ng. Sb is inversely proportional to ng, so a decrease in ng may lead to an increase in Sb. However, this cannot be decoupled from variations in the susceptibility, which may also arise as a result of trapped air. Trapped air in the gaps between the silicon pillars could reduce the interaction between the evanescent field and bulk fluid in these regions of high electric field intensity, reducing susceptibility. Conversely, the decrease in modal confine-ment associated with the decrease in neff may increase modal overlap with the bulk, po-tentially increasing susceptibility. Thus, the effects of this phenomenon on ng, susceptibil-ity, and therefore Sb, are challenging to predict and may account for some of the variability observed here. Supplementary Materials Section S3 presents simulation results for a model of incomplete wetting for waveguide design C1. As shown in Figure S3, an increase in the height of the trapped air pockets between the SWG pillars decreased Sb. It is possible that differences in the speed at which fluid was introduced to the microfluidic channels affected the extent of wetting and the average sizes of these air pockets. This could have contributed to the differences in Sb between the channels. However, based on the simula-tion results, these differences in Sb should correlate to differences in ng between the chan-nels. This was not observed experimentally (Figure S5). Nevertheless, the simulation model does not account for the shape of the air pocket, which may also influence Sb, po-tentially explaining these differences. Lastly, it should also be noted that the simulation results provided in Section S3 generally predict lower values of Sb compared with the ex-perimental results. These simulated values were obtained at a single wavelength (1550 nm), whereas the experimental measurements were obtained from multiple resonances analyzed over a wavelength range of 1530–1560nm, which likely contributed to these dis-crepancies between the experiments and simulations. Overall, the fishbone SWG resonators achieved comparable, and sometimes better, sensitivities than the boneless SWG designs. For the C-band resonators, fishbone device C2 achieved, on average, the greatest bulk sensitivity at 438 and 416 nm/RIU in channels Figure 12. (a) Bright-field micrograph of the sensor chip (converted to grayscale) with markersindicating the locations of each ring resonator used for the bulk sensing measurements. The markercolors are map ed to the percent differ nce between the measured and simulated Sb for each resonator.The positions of the two microfluidic channels for each set of testing (O-band and C-band) is denotedby darker gray rectangular overlays. (b) Bright-field micrograph of the sensor chip with markersindicating the locations of each ring resonator characterized in Section 3.1. The marker colors aremapped to the percent difference between the measured and simulated ng for each resonator.In these experiments, the NaCl solutions used in both channels were aliquots of thesame stock solution, eliminating the solutions as a source of error. Further, the fluid controlsystem was programmed to deliver identical flow rates through both channels. Theseflow rates were monitored by flow sensors throughout the experiments to ensure thatthe expected flow rates were delivered, making this another unlikely source of error. Therefractive indices of the NaCl solutions used in the Sb calculations were measured with anAbbe refractometer at visible wavelengths and chromatic dispersion was not accounted for,which could constitute one source of experimental error.The presence of trapped air between the silicon pillars of the SWG waveguides dueto incomplete wetting may be responsible for the variations in Sb. Firstly, as discussed inSection 3.1, this phenomenon may have contributed to the lower-than-predicted values of ng.Sb is inversely proportional to ng, so a decrease in ng may lead to an increase in Sb. However,this cannot be decoupled from variations in the susceptibility, which may also arise as aresult of trapped air. Trapped air in the gaps between the silicon pillars could reduce theinteraction between the evanescent field and bulk fluid in these regions of high electric fieldinte sity, re ucing susceptibility. Conversely, the decrease in modal confinement associatedwith the decrease in neff may increase modal overlap with the bulk, potentially incre singsusceptibility. Thus, the effects of this phenomenon on ng, susceptibility, and thereforeSb, are challe ging t predic and may account f r some of the variability observed here.Supplementary Materials Section S3 presents simulation results for a model of incompletew tting for waveguide design C1. As shown in Figure S3, an increase in the heig t of thetrapped air pocke betw en the SWG pillars d creased Sb. It is possible that differences inthe speed at which fluid was introduced to the micr fluidic channels affected the extentof wetting and the avera e sizes of these air pockets. T is could have contributed to thediffere in Sb between the channels. However, based on the simulation results, thesedifferenc s in Sb should correlat t differences in ng between the channels. This wasnot observ d experimentally (Figure S5). Nevertheless, the simulation model oes notaccount for the sh pe of the air pocket, which may also influe ce Sb, potentially explainingthese differences. Lastly, it should also be noted that the simulation results provided inSection S3 generally predict lower values of Sb compared with the experimental results.These simulated values were obtained at a single wavelength (1550 nm), whereas theexperimental measurements were obtained from multiple resonances analyzed over aBiosensors 2022, 12, 840 28 of 35wavelength range of 1530–1560nm, which likely contributed to these discrepancies betweenthe experiments and simulations.Overall, the fishbone SWG resonators achieved comparable, and sometimes better,sensitivities than the boneless SWG designs. For the C-band resonators, fishbone deviceC2 achieved, on average, the greatest bulk sensitivity at 438 and 416 nm/RIU in channels1 and 2, respectively. For the O-band resonators, boneless SWG design O4 achieved thegreatest bulk sensitivity at 364 and 383 nm/RIU in channels 1 and 2, respectively. However,these values only surpassed the best-performing O-band fishbone resonator (O1) by 15 and34 nm/RIU in channels 1 and 2, respectively.Figure 13 compares the reported performance of SWG resonators based on qualityfactor, Sb, and iLoD. TE and TM strip waveguide resonators are also included as perfor-mance benchmarks. Lines of constant iLoD are plotted, showing that iLoD decreases andresonator performance improves toward the top right corner of the plot. The C-bandand O-band boneless SWG (C6 and O4) and fishbone SWG (C1 and O2) resonators thatdemonstrated the smallest experimental values of iLoD in this work (listed in Table 5) arealso included on the plot. The plotted bulk sensitivities for these devices are averagesfrom the two microfluidic channels. It should be highlighted that several of the resonatorswith the highest iLoDs on this plot have been characterized based on simulations withgaseous cladding material (legend entries marked with a section sign, §) [54,55]. Thesereported levels of performance are likely considerably greater than what can be achievedwith the same sensor architectures applied to real-world aqueous-phase sensing due to theadditional material and scattering losses. All other sensor performance data are based onexperimental results measured with water cladding.Indeed, this plot highlights that a tradeoff exists between quality factor and Sb, withTE and TM strip waveguide sensors achieving high quality factors, but low sensitivitiesdue to limited light interaction with the analyte. Meanwhile, most SWG designs offer highsensitivities and low quality factors due to increased light interaction with the analyte [1].This plot illustrates that the fishbone SWG resonators presented in this work have compara-ble performance to other SWG sensors that have been experimentally demonstrated to date.Given the improved fabricability and structural robustness of fishbone SWGs compared toall other SWG designs, which involve free-standing silicon blocks, these results positionfishbone SWG resonators as an attractive architecture for scalable and portable sensing.Moreover, the scattering effects that degraded O-band sensor performance in this work canlikely be reduced by fabricating waveguide geometries with slightly lower group indices,designing models to better predict the effects of etch roughness, and using Deep UV lithog-raphy fabrication. These improvements could increase the O-band sensor quality factorsand push their performance toward simulated values, with the potential for extremely lowlimits of detection.Biosensors 2022, 12, 840 29 of 35Biosensors 2022, 12, x FOR PEER REVIEW 29 of 35 1 and 2, respectively. For the O-band resonators, boneless SWG design O4 achieved the greatest bulk sensitivity at 364 and 383 nm/RIU in channels 1 and 2, respectively. How-ever, these values only surpassed the best-performing O-band fishbone resonator (O1) by 15 and 34 nm/RIU in channels 1 and 2, respectively. Figure 13 compares the reported performance of SWG resonators based on quality factor, Sb, and iLoD. TE and TM strip waveguide resonators are also included as perfor-mance benchmarks. Lines of constant iLoD are plotted, showing that iLoD decreases and resonator performance improves toward the top right corner of the plot. The C-band and O-band boneless SWG (C6 and O4) and fishbone SWG (C1 and O2) resonators that demonstrated the smallest experimental values of iLoD in this work (listed in Table 5) are also included on the plot. The plotted bulk sensitivities for these devices are averages from the two microfluidic channels. It should be highlighted that several of the resonators with the highest iLoDs on this plot have been characterized based on simulations with gaseous cladding material (legend entries marked with a section sign, §) [54,55]. These reported levels of performance are likely considerably greater than what can be achieved with the same sensor architectures applied to real-world aqueous-phase sensing due to the addi-tional material and scattering losses. All other sensor performance data are based on ex-perimental results measured with water cladding. Figure 13. Reported silicon photonic resonator sensors performance comparison in terms of quality factor, Sb, and iLoD. All sensors operate in the C-band unless marked otherwise. For works that reported sensor performance data for multiple sensor geometries, the best-performing design has been included in this plot. The sensors include quasi-transverse electric (TE) strip MRR [21], quasi-transverse magnetic (TM) strip MRR [21], TE strip MRR (O-band) [21], TM strip MRR (O-band) [21], SWG MRR [19,21,29,39], fishbone SWG resonator [1], TM SWG racetrack resonator (RTR) [51,52], trapezoidal pillar SWG MRR [53], substrate overetch (SOE) SWG MRR [6], single-slot SWG RTR [54], single-slot SWG MRR [55], double-slot SWG RTR [54], double-slot SWG MRR [55], multibox SWG MRR [3], and the best-performing C-band and O-band boneless (C6 and O4) and fishbone (C1 and O2) SWG MRRs reported in this work (C6 achieved Sb,ave = 401 nm/RIU, Q = 5.2 × 103, and iLoD = 7.5 × 10−4 RIU; O4 achieved Sb,ave = 374 nm/RIU, Q = 7.8 × 103, and iLoD = 4.5 × 10−4 RIU; C1 achieved Sb,ave = 402 nm/RIU, Q = 5.5 × 103, and iLoD = 7.1 × 10−4 RIU; O2 achieved Sb,ave = 337 nm/RIU, Q = 7.6 × 103, and iLoD = 5.1 × 10−4 RIU). Curves of constant iLoD are included on the plot for sensors with resonance wavelengths of 1310 and 1550 nm. Legend entries marked with a section sign (§) indicate sensors for which the reported Q and Sb were obtained from simulations performed with gaseous Figure 13. Reported silicon photonic resonator sensors performance comparison in terms of qualityfactor, Sb, and iLoD. All sensors operate in the C-band unless marked otherwise. For works thatreporte se s r erf r a ce ata f r lti le se sor geo etries, the best-performing design hasbeen i cl s rs include quasi-transverse electric (TE) strip M R [21], quasi-transverse a etic ( ) stri [ ], strip RR (O-band) [21], TM strip M R (O-band) [21],S G MRR [19,21,29,39], fishbone S G resonator [1], TM SWG racetrack resonator (RTR) [51,52],trapezoidal pillar SWG MRR [53], substrate overetch (SOE) SWG MRR [6], single-slot SWG RTR [54],single-slot SWG MRR [55], double-slot SWG RTR [54], double-slot SWG MRR [55], multibox SWGMRR [3], and the best-performing C-band and O-band boneless (C6 and O4) and fishbone (C1and O2) SWG MRRs reported in this work (C6 achieved Sb, ve = 401 nm/RIU, Q = 5.2 × 103, andiLoD 7.5 × 10−4 RIU; O4 achieve Sb,ave = 374 nm/RIU, Q = 7.8 × 103, and iLoD = 4.5 × 10−4RIU; C1 achieved Sb,ave = 402 nm/RIU, Q = 5.5 × 103, and iLoD = 7.1 × 10−4 RIU; O2 achievedSb,ave = 337 nm/RIU, Q = 7.6 × 103, and iLoD = 5.1× 10−4 RIU). Curves of constant iLoD are includedon the plot for sensors with resonance wavelengths of 1310 and 1550 nm. Legend entries marked witha section sign (§) indicate sensors for which the reported Q and Sb were obtained from simulationsperformed with gaseous cladding material (these markers are depicted in grayscale). Values reportedfor all other sensors are based on experimental measurements in water cladding.4. ConclusionsIn this work, we demonstrated the optimization and experimental characterizationof SiP MRR sensors designed with fishbone SWG waveguides for both O-band and C-band operation. Waveguide designs were optimized based on 3D-FDTD simulations tofind combinations of Λ, δ, and wfb that optimize sensitivity while meeting the substrateleakage loss criterion. MRRs were fabricated with the optimized waveguide designsand experimentally tested to evaluate their optical properties, spectral characteristics,and performance compared to boneless SWG MRRs in terms of ng, FSR, extinction ratio,Q, Sb, and iLoD. The O-band fishbone SWG MRRs achieved quality factors as high as7.8 × 103, bulk sensitivities as high as 349 nm/RIU, and intrinsic limits of detection aslow as 5.1 × 10−4 RIU. The C-band fishbone SWG MRRs achieved quality factors as highas 5.5 × 103, bulk sensitivities as high as 438 nm/RIU, and intrinsic limits of detectionas low as 7.1 × 10−4 RIU. In general, the fishbone SWG resonators presented in thiswork have comparable performance to other SWG sensors that have been experimentallydemonstrated to date, while offering improved fabricability and a lower risk of damagecompared with the boneless designs. The performance of the O-band resonators was,however, hindered by peak splitting. This peak splitting was likely the result of scatteringBiosensors 2022, 12, 840 30 of 35effects, which were exaggerated at lower wavelengths and likely exacerbated by fabricationissues. These scattering effects could be reduced by designing waveguides with lower groupindices and designing models to better predict the effects of etch roughness. This highlightsthe potential to realize O-band fishbone SWG MRRs with higher quality factors and lowerlimits of detection than current state-of-the art SWG sensors. One of the challenges withSWG structures is the small feature size required in fabrication. O-band, as opposed to C-band, involves slightly smaller features, which in this paper were a minimum size of 100 nm,and a minimum gap of 100 nm. These sizes are compatible with deep immersion 193 nmCMOS foundry fabrication, hence can be fabricated in high volume. Overall, the resultsof this work indicate that fishbone SWG waveguides allow for improved robustness andfabricability without compromising performance. While we have developed a frameworkfor optimizing fishbone SWG MRRs and have experimentally demonstrated their sensingcapabilities, the POC use of these transducers relies on system-level integration with otherbiosensor components. Sensor biofunctionalization, sample delivery, and signal readoutstrategies must all be optimized for the POC setting in order to successfully translate theseSiP devices into fully portable diagnostic tools.Supplementary Materials: The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/bios12100840/s1, Figure S1: Material model fitting for FDTDsimulations; Figure S2: Illustration of FDTD simulation setup to investigate the effect of incompletewetting on neff and Sb for fishbone SWG design C1; Figure S3: Results of FDTD simulations investi-gating the effect of incomplete wetting on neff and Sb for fishbone SWG design C1; Figure S4: Electricfield intensity profiles for fishbone SWG C1 in complete wetting vs. incomplete wetting conditions;Figure S5: Spatial variation of ng measured during bulk refractive index sensing experiments; TableS1: Resonance peaks included in extinction ratio and quality factor calculations.Author Contributions: Conceptualization, L.S.P., S.M.G., L.C., S.S. and K.C.C.; Methodology, L.S.P.,S.M.G., K.W., M.A.A.-Q., S.J.C. and M.M.; Software, S.M.G., K.W. and Y.L.; Validation, L.S.P. andS.M.G.; Formal Analysis, L.S.P., S.M.G., K.W. and Y.L.; Investigation, L.S.P., S.M.G., K.W., S.J.C.,M.A.A.-Q. and M.M.; Resources, L.C., S.S. and K.C.C.; Data Curation, L.S.P., S.M.G., K.W. and Y.L.;Writing—Original Draft Preparation, L.S.P., S.M.G. and S.J.C.; Writing—Review and Editing, L.S.P.,S.M.G., K.W., M.A.A.-Q., L.C., S.S. and K.C.C.; Visualization, L.S.P. and S.M.G.; Supervision, L.C., S.S.and K.C.C.; Project Administration, L.S.P., S.M.G., L.C., S.S. and K.C.C.; Funding Acquisition, L.C.,S.S. and K.C.C. All authors have read and agreed to the published version of the manuscript.Funding: This project was supported by Canada’s Digital Technology Supercluster and a DigitalTechnology Supercluster Expansion project.Institutional Review Board Statement: Not applicable.Informed Consent Statement: Not applicable.Data Availability Statement: The data presented in this study are available on request from thecorresponding author.Acknowledgments: The authors are grateful to work and live on land that is the traditional, ances-tral, and unceded territory of the Coast Salish Peoples, including the territories of the Musqueam,Squamish, and Tsleil-Waututh First Nations. The authors would also like to acknowledge projectand fellowship support from the Natural Sciences and Engineering Research Council of Canada(NSERC), The Silicon Electronics-Photonics Integrated Circuits Fabrication (SiEPICfab) consortium,Mitacs Elevate and Accelerate programs (postdoctoral fellowships supported by both Mitacs andDream Photonics, Inc.), CMC Microsystems, and Canada’s National Design Network. The authorssincerely appreciate contributions and feedback from Mustafa Hammood, Enxiao Luan, AvineetRandhawa, Yas Oloumi Yazdi, So Jung Kim, the Stewart Blusson Quantum Matter Institute machineshop, and the Materials Engineering Electron Microscope Facility at the Advanced Materials andProcess Engineering Laboratory and Faculty of Applied Science at the University of British Columbia.Conflicts of Interest: The authors declare no conflict of interest.Biosensors 2022, 12, 840 31 of 35References1. 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Article
eng
Reviewed
Vancouver : University of British Columbia Library
Multidisciplinary Digital Publishing Institute
CC BY 4.0
Faculty
silicon photonics
evanescent field biosensor
SOI biosensor
ring resonator
fishbone sub-wavelength grating waveguide
sub-wavelength grating waveguide
SWG-assist waveguide
bridged SWG waveguide
microfluidics
An Optimization Framework for Silicon Photonic Evanescent-Field Biosensors Using Sub-Wavelength Gratings
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