# Sensitive Label-Free Biomolecular Detection Using  Thin  Silicon Waveguides

Authors: A. Densmore; D.-X. Xu; S. Janz; P. Waldron; J. Lapointe; T. Mischki; G. Lopinski; A. Delâge; J. H. Schmid; P. Cheben
Journal: Advances in Optical Technologies
 (2008)

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## Abstract

We review our work developing optical waveguide-based evanescent field sensors for the label-free, specific detection of biological molecules. Using high-index-contrast silicon photonic wire waveguides of submicrometer dimension, we demonstrate ultracompact and highly sensitive molecular sensors compatible with commercial spotting apparatus and microfluidic-based analyte delivery systems. We show that silicon photonic wire waveguides support optical modes with strong evanescent field at the waveguide surface, leading to strong interaction with surface bound molecules for sensitive response. Furthermore, we present new sensor geometries benefiting from the very small bend radii achievable with these high-index-contrast waveguides to extend the sensing path length, while maintaining compact size. We experimentally demonstrate the sensor performance by monitoring the adsorption of protein molecules on the waveguide surface and by tracking small refractive index changes of bulk solutions.


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## Body

## 1. Introduction

Sensing techniques  employing fluorescent labeling of molecules are commonly used for
simple binding event detection to determine the presence or absence of
molecular targets in solution. However, there are few tools available that are
capable of providing quantitative, label-free, and real-time monitoring of
molecular interactions. There has been extensive activity in both the academic
and commercial sectors to develop new sensing technologies that offer these
capabilities, allowing important information such as molecular concentrations,
binding affinities, and rate constants to be obtained. There have been numerous
proposed solutions using planar waveguide optics such as surface plasmon
resonance (SPR) [1], ridge waveguide evanescent field sensors [2–6],
waveguide-based microcantilevers [7, 8], porous silicon resonant structures [9],
optofluidic waveguides [10] as well as many others. The two methods that have
been the most widely studied are the SPR sensors and the ridge waveguide
evanescent field sensors. These methods employ a waveguide structure as the
transducer and surface functionalization chemistry to immobilize receptor
molecules on the sensor surface. The receptors capture target molecules thereby
accumulating material on the waveguide surface, which serves to induce a phase
shift of the propagating optical field. In the case of SPR sensors, the optical
field is the surface plasmon mode which propagates along the metal-analyte
interface, whereas for the planar waveguide evanescent field sensor it is the
evanescent tail of the optical waveguide mode. The induced phase shift of these
devices can be monitored in real time to determine the density of molecules
attached to the waveguide surface.Although only SPR sensors have become widely commercially available, there is significant
interest in developing planar waveguide evanescent field sensors due to the
potential advantages offered by this technology. For example, these sensors are
expected to provide increased sensitivity over SPR due to the much lower
optical transmission losses [1]. It is possible for light to propagate through
planar optical waveguides for distances of several centimeters with little
loss, whereas for the surface plasmon devices the field is effectively
extinguished after propagating a few tens of micrometers. This allows a much
larger interaction length of the light with the biomolecules to be achieved,
thereby allowing a larger phase shift to be observed in the sensor output. In
addition, the planar waveguide evanescent field sensor is well suited for
arraying permitting the development of high density, waveguide-based microarray
biochips for multianalyte monitoring.Ridge waveguide evanescent field sensors have been demonstrated in many planar
material systems such as silica [2], polymer [3], and silicon nitride [4, 5] as
well as nonplanar systems including optical fibers [11]. The planar devices
offer many well-known advantages over the nonplanar approaches including the
possibility of creating arrays of sensors on a compact chip, the ability to integrate additional optical and
electrical components on chip thereby increasing functionality, the capability
for mass production using high volume semiconductor manufacturing techniques,
and the possibility to integrate microfluidic systems on chip permitting
convenient analyte delivery and reduced consumed sample volumes. Waveguide
evanescent field sensors have been demonstrated using various waveguide circuit
configurations including grating couplers [12], Mach-Zehnder interferometers [2, 3, 5], ring resonators [4, 6], and microdisks [13, 14]. It has been shown that the
sensitivity achievable with these devices improves with increasing refractive
index contrast between the waveguide core and the surrounding cladding materials
[15, 16]. Motivated by these predictions, as well as other important advantages
that will be discussed, we have developed evanescent field sensors using the
silicon-on-insulator (SOI) material platform. The SOI material system consists
of a top silicon waveguide core layer positioned on a silicon dioxide lower
cladding layer grown on a silicon substrate [17] and has the highest refractive
index contrast of all commonly available planar waveguide systems.In this manuscript, we review our work developing evanescent field sensors in SOI. We
show that silicon nanophotonic waveguides with dimensions smaller than the
wavelength of light they guide have a strong evanescent field at the waveguide
surface for the transverse magnetic (TM) polarized waveguide mode. This results
in increased interaction with surface bound molecules, which leads to larger response
compared to waveguide sensors fabricated on traditional low-index-contrast
material platforms [16, 18]. Furthermore, we show that using submicrometer dimension
silicon waveguides with rectangular cross section, known as silicon photonic
wires, allows extremely compact devices to be realized using well-established
silicon fabrication technology. The compact footprint of these sensors allows two-dimensional
sensor arrays to be fabricated allowing both spotter-based functionalization and
microfluidic delivery systems to be used. We present experimental results
demonstrating the performance of these devices using two different waveguide
configurations: the Mach-Zehnder interferometer (MZI) and the ring resonator. We
illustrate the performance of these sensors to track homogeneous refractive
index change of bulk solutions and to monitor the formation of thin molecular
layers on the waveguide surface.


## 2. Theory: High-Index-Contrast Waveguides for Evanescent Field Sensing

A schematic of a planar waveguide evanescent field sensor is shown in Figure1, where specific
target molecules are captured by receptor molecules on the waveguide surface.
This induces an effective index change of the propagating optical mode, causing
a phase shift to be observed at the device output. A primary goal in the design
of these devices is to maximize their sensitivity for the application of
interest. These applications can be divided into two categories including
homogeneous sensing, which involves a uniformly distributed analyte extending
over a distance well exceeding the evanescent field penetration depth, and
surface sensing in which the analyte is bound to the waveguide surface in a
layer that is usually much thinner than the evanescent field penetration. The intrinsic
sensitivity of the devices is determined by the overlap of the squared waveguide
mode field with the analyte. For
homogeneous sensing, the intrinsic sensitivity is defined as the change of
effective index ∂Neff of the waveguide mode relative to homogeneous
refractive index change of the bulk solution ∂nc: ∂Neff/∂nc.
For the case of surface sensing, it is defined as the effective index change relative
to the variation of thickness d of an adsorbed molecular layer with a given refractive
index: ∂Neff/∂d  [12]. These sensitivity constants are independent
of waveguide length and are used to compare waveguides of different
cross-sectional geometries and refractive index profiles.Figure 1
Illustration of a waveguide evanescent field sensor. Molecular targets are captured by receptor molecules at the waveguide surface thereby changing the waveguide mode effective index. This creates a phase shift of the propagating optical mode.From the variational theorem of waveguides [19], ∂Neff caused by a local
change of dielectric constant Δε(x,y) can be expressed as(1)∂Neff=c∫ΔεE⋅E*dxdy, where E(x,y) is the normalized modal electric
field vector. The sensitivity of the device thus scales with the squared
amplitude of the electric field within the perturbation, and therefore with the
fraction of the modal power contained in the surface volume where the dielectric
constant is modified by the analyte. This fraction can be increased by reducing
the waveguide core layer thickness to a point where the mode becomes less
confined and expands from the core, raising the field magnitude at the
interface. Furthermore, given the boundary condition that the normal component
of the electric displacement vector D=εE must be
continuous across the interface, the field amplitude above the surface is
increased by using a high-index-contrast waveguide and the TM mode, for which
the dominant field component is polarized normal to the sensing surface. This
results in a discontinuity of the normal component of E at the surface, which serves to enhance the field at the analyte side
of the interface relative to that on the core side by a factor of the ratio of the
respective dielectric constants. This enhancement factor thereby increases with
index contrast.For surface
sensing, it is important that the evanescent tail of the waveguide mode is
localized near the waveguide surface where the biomolecules are located and not
extend too far into the analyte solution. The penetration depth of the
waveguide mode into the cladding material of refractive indexnc is
given by [20](2)γ=λ2πNeff2−nc2. From (2), it follows
that as the index contrast increases (which raises Neff) the evanescent field becomes more
localized near the waveguide surface.Finally, it is important to maximize the proportion of the evanescent field on the analyte
side of the waveguide core relative to that on the substrate (lower cladding)
side. In most practical sensing applications where the lower cladding
refractive index is greater than the analyte medium index, the sensitivity can
be shown to be an increasing function of the waveguide symmetry [15]. The use
of high refractive index core materials on low refractive index cladding
materials increases the effective waveguide index symmetry, and the fraction of
the optical power traveling through the lower cladding can be minimized.


## 3. Waveguide Optimization and Sensing Configurations

### 3.1. Waveguide Design

The above arguments suggest that a high refractive index, thin waveguide core layer on a low
refractive index lower cladding is an ideal choice for evanescent field sensors.
Submicron dimension waveguides fabricated on the SOI material platform strongly
meet these requirements. To optimize the SOI waveguide parameters and to
examine how the thickness of the silicon waveguide core layer influences the
evanescent field interaction with molecules located at the waveguide surface,
we performed transfer-matrix-based waveguide simulations using a simple
step-index, one-dimensional slab waveguide model. This model was used to
calculate the effective index change induced by the adsorption of a thin
biomolecular layer on the silicon waveguide core layer. An aqueous upper waveguide
cladding and a silica lower cladding were assumed, and the signal wavelength was
taken as 1550 nm. Working at this optical wavelength allows low cost and widely
available optical test equipment developed for the telecommunications industry to
be used. The calculations were performed for varying silicon waveguide
thickness for both the transverse electric (TE) and TM polarization modes and
are shown in Figure2(a). As seen, the sensitivity has a clear maximum at a specific
silicon waveguide thickness, which is 0.06 μm for TE polarization and 0.22 μm for TM polarization. Advantageously,
the optimum silicon thickness value of ∼0.2 μm for the more sensitive TM
polarization is a commonly used SOI wafer structure and is readily available from
commercial suppliers.(a) Calculated sensitivity constants for a SOI slab waveguide as a function of waveguide core thickness.  (b) Calculated maximum∂Neff/∂d obtained for slab waveguides with varying refractive index contrast.
(a)(b)Similar calculations were performed for waveguide systems with varying refractive index
contrast (Δn) to confirm the sensitivity
arguments discussed in Section 2. For consistency, all calculations were
performed for a signal wavelength of 1550 nm, and an aqueous upper cladding and
a silica lower cladding were assumed. The maximum achievable sensitivity is
plotted in Figure 2(b). For the lower-index contrast systems (Δn≤0.16), a
minor increase in sensitivity is obtained for the TE polarized mode compared
with the TM mode. For larger index contrast platforms, the sensitivity is higher
for the TM mode as expected from the electric field boundary conditions
discussed above. From Figure 2(b), the sensitivity advantage of using high-index-contrast waveguides such as SOI is clearly seen.For a practical sensor, the waveguide should provide confinement in two dimensions
and support only a single optical mode. The latter is required to obtain a well-defined
spectral transmission function that can be easily analyzed. For single mode
operation near the optimum silicon core thickness, silicon photonic wire
waveguides, with the silicon etched fully down to the buried oxide, are a
natural choice. The calculated TM mode field is shown in Figure3 for the 0.26 μm ×
0.45 μm photonic
wire waveguide used in our experiments. A large surface field magnitude is
obtained along the top of the waveguide, which is localized within ∼120 nm of
the waveguide surface for strong interaction with surface bound molecules.Figure 3
The electric field distribution for the TM polarization of a 0.26μm × 0.45 μm silicon photonic wire waveguide covered with an aqueous cladding. As seen, large electric field magnitude is obtained at the waveguide surface.


### 3.2. Fiber-to-Waveguide Optical Coupling

A major challenge with the use of photonic wire
waveguides is the difficulty of coupling light from an optical fiber with a
mode size diameter of severalμm to
these waveguides with a submicron mode size. Due to the large mismatch, coupling
losses exceeding 15 dB are common with such structures. To overcome this
problem, we have developed optical mode transformers using inversely tapered
waveguides covered with a 2-μm-thick
SU-8 photoresist upper cladding layer. The sensor waveguide (nominal width of
0.45 μm) is
adiabatically tapered to a 0.15 μm wide
coupling section at the device facet, as shown in Figure 4. At this narrow
width, the mode becomes weakly confined in the core layer, thereby increasing
its size in both the horizontal and vertical directions for greater overlap
with the light emerging from the optical fiber. The mode transformers utilize a
similar principle to the design reported in [21] and were developed for use
with a lensed single-mode fiber. Using such a design, we have achieved less than 3 dB fiber-to-waveguide
coupling loss, thus significantly improving the signal-to-noise ratio of our
measurements compared to devices without mode transformers. Furthermore, since
a large fraction of the optical field is traveling through the cladding
materials in the tapered section near the device facet, the mode effective
index is reduced. This minimizes reflection loss and Fabry-Pérot cavity effects,
which cause instability of the fiber coupling due to mechanical vibration.Figure 4
Schematic of the inversely tapered mode transformer used for improved fiber-to-waveguide coupling. The nominal 0.45μm wide photonic wire sensor waveguide is laterally tapered down to 0.15 μm for adiabatic expansion of the waveguide mode near the device facet.


### 3.3. The Mach-Zehnder Interferometer Sensor

An evanescent field sensor relies on the perturbation
of waveguide mode effective index that induces a phase shift of the propagating
optical signal. This phase shift is not easily monitored directly and various interferometeric
waveguide circuits can be used to transform it to a more easily detectable
intensity change. A simple and effective waveguide device for this purpose is
the Mach-Zehnder interferometer (MZI), which is illustrated in Figure5(a). In a
typical configuration, light of wavelength λ (in
vacuum) and intensity Io is
split into two paths: a sensing path that is exposed to the analyte and an
isolated reference path. These waveguide paths are then recombined causing the
signals from the two arms to interfere producing a phase dependent intensity I, to be observed at the MZI output. The
transfer function of the MZI is(3)I=Io2[1+cos(2πλ(Neff,sLs−Neff,rLr))], where Neff,s
and Ls are the effective
refractive index and length of the sensing waveguide, and Neff,r and Lr are the effective refractive index and length of the reference waveguide. The
phase difference between the two arms is given by the argument of the cosine
function in (3). By differentiating this quantity, the sensitivity of the phase ϕ to
homogeneous and surface sensing can be expressed as
(4)∂φ∂nc=2πLsλ∂Neff,s∂nc(homogeneoussensing),∂φ∂d=2πLsλ∂Neff,s∂d(surfacesensing).
It is seen that the phase sensitivity scales with sensing waveguide length Ls and with the waveguide sensitivity
constants: ∂Neff/∂nc
or ∂Neff/∂d. MZI devices provide important practical
advantages over other waveguide circuit designs. Since the intensity change is
monitored, they can be used with a low cost, fixed wavelength laser source and by
tracking the sinusoidal output variations they can function over a large
dynamic range of surface loading conditions. Furthermore, by balancing the
optical path lengths of the sensor and reference arms the MZI can be designed
to function independently of temperature and signal wavelength. This reduces
the requirements for temperature stability of the chip and wavelength stability
of the laser source, thereby reducing potential instrumentation costs
associated with this technology.(a) Schematic of an MZI evanescent field sensor. The input waveguide is split into two paths where one is exposed to the analyte and the other is isolated from the analyte. The paths are recombined and the signals interfere causing a sinusoidal phase dependent intensity signal to be transmitted through the output waveguide. (b) A conventional ring resonator design employing a directional coupler between the straight bus waveguide and the ring cavity. The dashed lines indicate the positions of the sensor windows where the upper SU-8 isolation layer is removed.
(a)(b)


### 3.4. The Ring Resonator Sensor

The high lateral index contrast provided by silicon photonic wire waveguides allows waveguide bends to
be fabricated with a radius of curvature of only a few micrometers with little
excess loss. This has led to the development of ultracompact ring resonator
structures, which have been used for many applications, including optical
add/drop filtering [22], sensing [18], optical logic [23], nonlinear optics [24],
and optical modulation [25].In the simplest form, a ring resonator contains a
straight bus waveguide evanescently coupled to a ring cavity using a
directional coupler, as illustrated in Figure5(b). Light of specific
wavelengths couples from the bus waveguide to the ring waveguide and circulates,
making many round trips and building up intensity within the ring cavity. At
these resonant wavelengths, a sharp dip is observed in the transmission
spectrum of the bus waveguide. The sharpness of the resonance dip is described
by the quality factor Q of the ring [26]:(5)Q≡λΔλFWHM≅πngLλαt1−αt, where ΔλFWHM is the full width at half
maximum of the resonance, L is the
ring cavity length, ng is the ring waveguide group index, t is
the through coupling coefficient between the bus and ring waveguides, and α is the total resonator
loss including the coupler loss and the round trip propagation loss in the
ring.An undesirable characteristic of conventional ring
resonators with a directional coupler is the inherent wavelength dependence of the
coupling between the bus and ring waveguides. This causes a slowly varying
modulation of the resonance depths in the output spectrum, limiting the useable
wavelength range over which a uniform transmission spectrum is obtained. To
overcome this limitation, we have designed a new ring resonator structure in
SOI that utilizes a multimode-interference coupler (MMI) between the bus and
ring waveguides [26]. The MMI significantly reduces the wavelength dependence
of the coupling, producing a more uniform resonance spectrum over a broad range
of wavelengths. In addition, the MMI structure improves the fabrication
tolerance by eliminating the narrow gap of the directional coupler.As molecules bind to the ring surface (or if the bulk
refractive index of the analyte solution changes) a phase shift of the optical
mode is induced, resulting in a wavelength shift of the resonances. This
wavelength shift scales with the number of adsorbed molecules to the ring waveguide
(or with the refractive index change of a bulk solution) and is typically the
parameter being measured in this type of sensor. Alternatively, it is also
possible to track the intensity change at a fixed wavelength over a single
resonance peak. In this case, the dynamic range is limited and the sensor can
only be used to track comparatively low analyte concentrations or low
refractive index changes of bulk solutions since the peak position may shift
away from the input wavelength. However, active tuning of the resonance through
temperature or other means may provide a solution to this tradeoff at the price
of increased complexity.Ring resonators have very sharp resonances and may provide
higher sensitivity compared to other waveguide circuit configurations such as
the MZI. Since light at the resonance wavelengths circulates around the ring
cavity, it has numerous interactions with the same molecules amplifying the
measured response. They also offer a more compact geometry desirable for the
fabrication of high-density sensor arrays. However, when the resonance
wavelengths are monitored, ring resonators require either a tunable laser
source or a broadband optical source and a means to monitor the output
wavelengths. In either case, this increases the potential instrumentation costs
for this technology. Ring resonators also do not provide for internal referencing
for temperature or wavelength drifts and therefore require either precise
temperature control of the sensor and optical source, or they require a second reference
device.Due to the different
characteristics of the ring resonator and the MZI, we are currently developing
both types of sensors where we believe that the optimal circuit choice will depend
on the sensitivity and cost requirements of the particular application.


## 3.1. Waveguide Design

The above arguments suggest that a high refractive index, thin waveguide core layer on a low
refractive index lower cladding is an ideal choice for evanescent field sensors.
Submicron dimension waveguides fabricated on the SOI material platform strongly
meet these requirements. To optimize the SOI waveguide parameters and to
examine how the thickness of the silicon waveguide core layer influences the
evanescent field interaction with molecules located at the waveguide surface,
we performed transfer-matrix-based waveguide simulations using a simple
step-index, one-dimensional slab waveguide model. This model was used to
calculate the effective index change induced by the adsorption of a thin
biomolecular layer on the silicon waveguide core layer. An aqueous upper waveguide
cladding and a silica lower cladding were assumed, and the signal wavelength was
taken as 1550 nm. Working at this optical wavelength allows low cost and widely
available optical test equipment developed for the telecommunications industry to
be used. The calculations were performed for varying silicon waveguide
thickness for both the transverse electric (TE) and TM polarization modes and
are shown in Figure2(a). As seen, the sensitivity has a clear maximum at a specific
silicon waveguide thickness, which is 0.06 μm for TE polarization and 0.22 μm for TM polarization. Advantageously,
the optimum silicon thickness value of ∼0.2 μm for the more sensitive TM
polarization is a commonly used SOI wafer structure and is readily available from
commercial suppliers.(a) Calculated sensitivity constants for a SOI slab waveguide as a function of waveguide core thickness.  (b) Calculated maximum∂Neff/∂d obtained for slab waveguides with varying refractive index contrast.
(a)(b)Similar calculations were performed for waveguide systems with varying refractive index
contrast (Δn) to confirm the sensitivity
arguments discussed in Section 2. For consistency, all calculations were
performed for a signal wavelength of 1550 nm, and an aqueous upper cladding and
a silica lower cladding were assumed. The maximum achievable sensitivity is
plotted in Figure 2(b). For the lower-index contrast systems (Δn≤0.16), a
minor increase in sensitivity is obtained for the TE polarized mode compared
with the TM mode. For larger index contrast platforms, the sensitivity is higher
for the TM mode as expected from the electric field boundary conditions
discussed above. From Figure 2(b), the sensitivity advantage of using high-index-contrast waveguides such as SOI is clearly seen.For a practical sensor, the waveguide should provide confinement in two dimensions
and support only a single optical mode. The latter is required to obtain a well-defined
spectral transmission function that can be easily analyzed. For single mode
operation near the optimum silicon core thickness, silicon photonic wire
waveguides, with the silicon etched fully down to the buried oxide, are a
natural choice. The calculated TM mode field is shown in Figure3 for the 0.26 μm ×
0.45 μm photonic
wire waveguide used in our experiments. A large surface field magnitude is
obtained along the top of the waveguide, which is localized within ∼120 nm of
the waveguide surface for strong interaction with surface bound molecules.Figure 3
The electric field distribution for the TM polarization of a 0.26μm × 0.45 μm silicon photonic wire waveguide covered with an aqueous cladding. As seen, large electric field magnitude is obtained at the waveguide surface.


## 3.2. Fiber-to-Waveguide Optical Coupling

A major challenge with the use of photonic wire
waveguides is the difficulty of coupling light from an optical fiber with a
mode size diameter of severalμm to
these waveguides with a submicron mode size. Due to the large mismatch, coupling
losses exceeding 15 dB are common with such structures. To overcome this
problem, we have developed optical mode transformers using inversely tapered
waveguides covered with a 2-μm-thick
SU-8 photoresist upper cladding layer. The sensor waveguide (nominal width of
0.45 μm) is
adiabatically tapered to a 0.15 μm wide
coupling section at the device facet, as shown in Figure 4. At this narrow
width, the mode becomes weakly confined in the core layer, thereby increasing
its size in both the horizontal and vertical directions for greater overlap
with the light emerging from the optical fiber. The mode transformers utilize a
similar principle to the design reported in [21] and were developed for use
with a lensed single-mode fiber. Using such a design, we have achieved less than 3 dB fiber-to-waveguide
coupling loss, thus significantly improving the signal-to-noise ratio of our
measurements compared to devices without mode transformers. Furthermore, since
a large fraction of the optical field is traveling through the cladding
materials in the tapered section near the device facet, the mode effective
index is reduced. This minimizes reflection loss and Fabry-Pérot cavity effects,
which cause instability of the fiber coupling due to mechanical vibration.Figure 4
Schematic of the inversely tapered mode transformer used for improved fiber-to-waveguide coupling. The nominal 0.45μm wide photonic wire sensor waveguide is laterally tapered down to 0.15 μm for adiabatic expansion of the waveguide mode near the device facet.


## 3.3. The Mach-Zehnder Interferometer Sensor

An evanescent field sensor relies on the perturbation
of waveguide mode effective index that induces a phase shift of the propagating
optical signal. This phase shift is not easily monitored directly and various interferometeric
waveguide circuits can be used to transform it to a more easily detectable
intensity change. A simple and effective waveguide device for this purpose is
the Mach-Zehnder interferometer (MZI), which is illustrated in Figure5(a). In a
typical configuration, light of wavelength λ (in
vacuum) and intensity Io is
split into two paths: a sensing path that is exposed to the analyte and an
isolated reference path. These waveguide paths are then recombined causing the
signals from the two arms to interfere producing a phase dependent intensity I, to be observed at the MZI output. The
transfer function of the MZI is(3)I=Io2[1+cos(2πλ(Neff,sLs−Neff,rLr))], where Neff,s
and Ls are the effective
refractive index and length of the sensing waveguide, and Neff,r and Lr are the effective refractive index and length of the reference waveguide. The
phase difference between the two arms is given by the argument of the cosine
function in (3). By differentiating this quantity, the sensitivity of the phase ϕ to
homogeneous and surface sensing can be expressed as
(4)∂φ∂nc=2πLsλ∂Neff,s∂nc(homogeneoussensing),∂φ∂d=2πLsλ∂Neff,s∂d(surfacesensing).
It is seen that the phase sensitivity scales with sensing waveguide length Ls and with the waveguide sensitivity
constants: ∂Neff/∂nc
or ∂Neff/∂d. MZI devices provide important practical
advantages over other waveguide circuit designs. Since the intensity change is
monitored, they can be used with a low cost, fixed wavelength laser source and by
tracking the sinusoidal output variations they can function over a large
dynamic range of surface loading conditions. Furthermore, by balancing the
optical path lengths of the sensor and reference arms the MZI can be designed
to function independently of temperature and signal wavelength. This reduces
the requirements for temperature stability of the chip and wavelength stability
of the laser source, thereby reducing potential instrumentation costs
associated with this technology.(a) Schematic of an MZI evanescent field sensor. The input waveguide is split into two paths where one is exposed to the analyte and the other is isolated from the analyte. The paths are recombined and the signals interfere causing a sinusoidal phase dependent intensity signal to be transmitted through the output waveguide. (b) A conventional ring resonator design employing a directional coupler between the straight bus waveguide and the ring cavity. The dashed lines indicate the positions of the sensor windows where the upper SU-8 isolation layer is removed.
(a)(b)


## 3.4. The Ring Resonator Sensor

The high lateral index contrast provided by silicon photonic wire waveguides allows waveguide bends to
be fabricated with a radius of curvature of only a few micrometers with little
excess loss. This has led to the development of ultracompact ring resonator
structures, which have been used for many applications, including optical
add/drop filtering [22], sensing [18], optical logic [23], nonlinear optics [24],
and optical modulation [25].In the simplest form, a ring resonator contains a
straight bus waveguide evanescently coupled to a ring cavity using a
directional coupler, as illustrated in Figure5(b). Light of specific
wavelengths couples from the bus waveguide to the ring waveguide and circulates,
making many round trips and building up intensity within the ring cavity. At
these resonant wavelengths, a sharp dip is observed in the transmission
spectrum of the bus waveguide. The sharpness of the resonance dip is described
by the quality factor Q of the ring [26]:(5)Q≡λΔλFWHM≅πngLλαt1−αt, where ΔλFWHM is the full width at half
maximum of the resonance, L is the
ring cavity length, ng is the ring waveguide group index, t is
the through coupling coefficient between the bus and ring waveguides, and α is the total resonator
loss including the coupler loss and the round trip propagation loss in the
ring.An undesirable characteristic of conventional ring
resonators with a directional coupler is the inherent wavelength dependence of the
coupling between the bus and ring waveguides. This causes a slowly varying
modulation of the resonance depths in the output spectrum, limiting the useable
wavelength range over which a uniform transmission spectrum is obtained. To
overcome this limitation, we have designed a new ring resonator structure in
SOI that utilizes a multimode-interference coupler (MMI) between the bus and
ring waveguides [26]. The MMI significantly reduces the wavelength dependence
of the coupling, producing a more uniform resonance spectrum over a broad range
of wavelengths. In addition, the MMI structure improves the fabrication
tolerance by eliminating the narrow gap of the directional coupler.As molecules bind to the ring surface (or if the bulk
refractive index of the analyte solution changes) a phase shift of the optical
mode is induced, resulting in a wavelength shift of the resonances. This
wavelength shift scales with the number of adsorbed molecules to the ring waveguide
(or with the refractive index change of a bulk solution) and is typically the
parameter being measured in this type of sensor. Alternatively, it is also
possible to track the intensity change at a fixed wavelength over a single
resonance peak. In this case, the dynamic range is limited and the sensor can
only be used to track comparatively low analyte concentrations or low
refractive index changes of bulk solutions since the peak position may shift
away from the input wavelength. However, active tuning of the resonance through
temperature or other means may provide a solution to this tradeoff at the price
of increased complexity.Ring resonators have very sharp resonances and may provide
higher sensitivity compared to other waveguide circuit configurations such as
the MZI. Since light at the resonance wavelengths circulates around the ring
cavity, it has numerous interactions with the same molecules amplifying the
measured response. They also offer a more compact geometry desirable for the
fabrication of high-density sensor arrays. However, when the resonance
wavelengths are monitored, ring resonators require either a tunable laser
source or a broadband optical source and a means to monitor the output
wavelengths. In either case, this increases the potential instrumentation costs
for this technology. Ring resonators also do not provide for internal referencing
for temperature or wavelength drifts and therefore require either precise
temperature control of the sensor and optical source, or they require a second reference
device.Due to the different
characteristics of the ring resonator and the MZI, we are currently developing
both types of sensors where we believe that the optimal circuit choice will depend
on the sensitivity and cost requirements of the particular application.


## 4. Design and Fabrication

MZI sensors and ring resonators were designed having 0.26μm × 0.45 μm photonic wire sensing waveguides.
The waveguide height was chosen to be near the optimum sensitivity point of Figure 2(a) for TM polarization. The waveguide width was designed to be narrow enough
to provide single mode operation, while being wide enough to permit sharp bends
of the waveguide with a radius of curvature of a few microns. Optical mode
transformers having a 0.26 μm × 0.15 μm cross section were integrated at
both waveguide facets for improved input and output coupling. Our early designs
used conventional waveguide layout geometries for the ring and MZI sensors and
are shown in Figure 6.  We have
demonstrated sensitive evanescent field sensors using these devices, capable of
detecting less than 1% of a monolayer of streptavidin molecules adsorbed to the
biotinylated waveguide surface [18].Scanning electron microscope images of our early sensor designs employing silicon photonic wire waveguides arranged in: (a) a conventional MZI structure and (b) a ring cavity containing a MMI coupler.
(a)(b)Here, we will
focus on our more recent sensor designs that further exploit the high lateral
index contrast of the silicon photonic wire waveguide, which allows very sharp
waveguide bends to be achieved. As mentioned above, the phase sensitivity of
evanescent field sensors is determined by both the intrinsic waveguide
sensitivity constants (∂Neff/∂nc or ∂Neff/∂d) and the
waveguide length. By increasing the waveguide length, a larger number of molecules
will be captured on the waveguide surface for a given analyte concentration and
interaction time, thereby inducing a larger phase shift (see (4)). However,
long straight waveguides are not desirable for two-dimensional arraying
purposes and are not suited for common functionalization techniques using
commercial spotting apparatus. To address these issues, we have designed coiled
waveguide sensing structures as shown in Figure 7. For the MZI devices, several
mm of sensing path length have been designed in a circular area of 150 μm diameter, comparable to the drop
size employed by modern spotting tools. Spiral ring cavities with 1.3 mm length
have also been designed with similar dimensions. The additional length over
conventional circular/oval cavities leads to improvement of the quality factor
of the resonance allowing increased measurement accuracy of the resonance
wavelengths. Both the spiral MZI and ring designs offer the high sensitivity of
a long waveguide without sacrificing size, and their increased surface areas
provide more efficient molecular capture.Sensor designs with double spiral waveguide geometries providing increased sensing path length while maintaining a compact sensor footprint. (a) MZI sensor with 2 mm sensing path length contained within a circular 150μm diameter area. (b) Spiral cavity ring resonator design with 1.3 mm sensor length contained within a circular 110 μm diameter area.
(a)(b)The devices
in Figure7 were fabricated on SOI wafers having a 0.26-μm-thick silicon layer on a 2-μm-thick buried oxide layer.
Waveguides were patterned by electron beam lithography and etched in an
inductively coupled plasma reactive ion etching system. To isolate the optical
mode of the nonsensing portions of the device from the environment, a 2-μm-thick layer of SU-8 photoresist was
spun on the wafer and windows were opened over the active sensing area using
optical contact lithography. The devices were then baked to cure the SU-8 film.
Finally, samples were exposed to an O2 plasma to remove any residual
photoresist in the sensor windows as well as to increase the thickness of the native
oxide layer (used later for functionalization). The sensors were then diced
into individual chips and some were then used for homogeneous solution sensing
experiments as described in Section 5.For surface sensing experiments, the sensors were functionalized by
immobilizing biotin on the chip surface in order to monitor the affinity
reaction between the vitamin biotin and the protein streptavidin. The oxide on
the silicon waveguide surface, measured to be2.7±0.2 nm thick by ellipsometry, was left
intact so that standard glass-based functionalization procedures to attach biotin to
the surface could be used. The functionalization procedure began with a
cleaning step where the sample was rinsed with ethanol and then cleaned and
activated with nitric acid for 5 minutes. The samples were then rinsed with
deionized water and ethanol and dried under nitrogen. Surfaces were then
silanized with 3-aminopropyltriethoxysilane (APTES) vapor. The surfaces were
rinsed with ethanol, dried and biotinylated by coating the surface in a
solution of 1 mg/mL of N-hydroxysuccinimide (NHS) activated biotin in dimethylformamide
(DMF) for 1 hour, followed by rinsing with DMF and ethanol. The incremental
thickness change induced by adsorption of streptavidin to the sensor surface
was assessed using a functionalized silicon wafer, which was immersed in a
streptavidin solution for 1 hour followed by rinsing with phosphate buffered
saline (PBS). Based on ellipsometry measurements, we estimate a surface mass
coverage of 2.2 ng/mm2 of streptavidin, following Elwing [27]. The
above process was performed on the entire sensing chip. Future experiments will
attempt to functionalize individual sensor elements using a microarray spotter for
multianalyte detection.Analyte was delivered to the sensor through a microfluidic component fabricated in
polydimethylsiloxane (PDMS). Channels with a width of 200μm were
defined in the PDMS by using a surface relief mold fabricated using 50 μm thick
SU-8 resist tracks defined on a silicon wafer. The PDMS component was
subsequently aligned and fixed to the sensor chip, and a syringe pump was used
to drive solutions through the microfluidic channels.


## 5. Experimental Demonstration

Using a tapered optical input fiber, a tunable laser source, and an InGaAs photodetector, the
propagation loss of the fabricated waveguides was assessed by the Fabry-Pérot
technique. Several waveguides were measured with loss values varying between
0.3-0.4 dB/mm. The optical coupling loss from a tapered optical fiber was
found to be less than 3 dB per facet using the inversely tapered mode converters.The response of an MZI sensor
with a 2-mm-long spiral sensing arm, to homogeneous refractive index change of
the analyte solution, was then evaluated by passing sucrose solutions of
varying concentration through the microfluidic channel. The solutions were
drawn over the exposed sensor arm at a rate of 2 mL/hour, and the transmission
of the sensor was measured for each solution. The corresponding phase shift
values are shown in Figure8 as a function of sucrose solution refractive index
change (with respect to water). At a
signal wavelength of 1550 nm, these phase shift values correspond to a large intrinsic
sensitivity constant of ∂Neff/∂nc=0.35, which is only
approximately three times less than that achievable using a free-space beam
passing through a bulk solution cell. These results agree to within 5% of the
calculated phase shift values from the effective indices obtained in mode
expansion-based waveguide simulations.Figure 8
MZI sensor response to homogeneous solution refractive index change. The calculated phase shift values are shown by the dotted line.Using the biotin-streptavidin binding system, the response of an
MZI with a 2-mm-long spiral sensing arm and a ring resonator sensor with a 1.3-mm-spiral
cavity length to the adsorption of a thin protein monolayer was then examined. The
intensity change at the MZI output was monitored at a constant signal
wavelength of∼1550 nm, whereas the wavelength shift of the ring resonator
resonance was monitored during the experiment by sweeping a tunable laser and recording
the transmission spectrum. The results of the measurements are shown in Figure 9(a)
for the ring resonator sensor and Figure 9(b) for the MZI sensor.Surface adsorption measurements using the sensors to monitor the affinity reaction between streptavidin and the biotinylated waveguide surface. (a) Measured shift in the resonance wavelength for a∼1.3-mm-long double spiral ring resonator sensor. (b) Measured intensity change (grey) and phase shift (black) of an MZI sensor with a 2-mm-long double spiral sensing arm.
(a)(b)For the ring resonator, the first analyte solution consisted of 0.1μg/mL of streptavidin in PBS. It was
passed through the microfluidic channel over the ring cavity, and the
transmission spectrum of the ring was recorded every 5 seconds over a 3-nm-wavelength
range. Molecular binding is observed by the wavelength shift in the ring
resonator response as shown in Figure 9(a). The streptavidin concentration was
then increased to 1 μg/mL and then to 10 μg/mL, where successively increased
binding rates are observed. For the MZI device, a constant wavelength laser
source was used, and the transmitted power was recorded as solutions were drawn
over the sensing arm. The results of the experiment are shown in Figure 9(b)
for both the raw transmitted intensity signal and the corresponding phase
change. The experiment began by flowing PBS solution through the microfluidic
channel for 60 seconds. The solution was then switched to a 10 μg/mL streptavidin solution, followed by
a PBS solution to rinse nonspecifically bound molecules from the waveguide
surface. A typical high-affinity binding curve is obtained. Taking the RMS
noise levels in Figure 9 as the minimum detectable phase change or wavelength
shift, we estimate that the MZI sensor is capable of detecting ∼0.3% of a
protein monolayer, while the ring resonator demonstrates a resolution of ∼0.2% of a monolayer. These values correspond
to a minimum detectable surface coverage of ∼6 pg/mm2 for the MZI sensor and ∼4 pg/mm2 for the ring resonator,
which are comparable to the sensitivities reported for state-of-the-art SPR
sensors. We have established that the sensor performance is currently limited
by intensity noise resulting from Fabry-Pérot cavity effects between the fiber
tip and the device facet. These effects are lessened with the inverse tapered
mode transformers and can be further reduced by depositing an antireflection
coating on the input waveguide facet. Furthermore, for applications where a
larger sensor area is permitted the waveguide length can be increased for
improved performance. With further optimization of the sensor design and with
improvement of the experimental setup to reduce the measurement noise, we expect
that minimum detectable surface coverage values well below 1 pg/mm2 are
attainable.


## 6. Summary

We have reviewed our work developing biological sensors based on silicon
photonic wire waveguides arranged in an MZI and ring resonator configuration. We
have shown that high-index-contrast SOI waveguides provide a large and
localized evanescent field for the TM polarized waveguide mode, resulting in high
surface sensitivity. We have also used the high lateral index contrast of
silicon photonic wires to make densely coiled sensor waveguide structures that
provide the advantages of long sensing path length without compromising the
sensor footprint. Due to their compact size, these sensors are compatible with
spotter functionalization, microfluidic sample delivery, and the fabrication of
two-dimensional arrays. Our future work will focus on the development of an
evanescent field-based microarray biochip for multianalyte monitoring that
exploits the benefits offered by this technology.



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*Source: 725967-2008-06-16.xml*