Investigation of bulk material sensing using

TEL AVIV UNIVERSITY THE IBY AND ALADAR FLEISCHMAN FACULTY OF ENGINEERING Department of Electrical Engineering – Physical Electronics

On the subject of

Investigation of bulk material sensing using Periodically Segmented Waveguide MachZehnder Interferometer for chemical / biosensing Submitted for the degree “Doctor of Philosophy”

by Noam Kinrot

May 2005

This work was carried out under the supervision of Prof. Menachem Nathan.

I would like to thank Prof. Shlomo Ruschin for the smart advice and encouragement. I would like to thank Prof. Yoram Shapira for his encouragements, concern and practical help. Warm thanks to Mr. Vadim Dubrosin, and Mr. Stanislav Stepanov for the friendship, help, advice, and cooperation throughout my thesis. Also, warm thanks to Mr. Noel Elman, for the friendship and practical advice. I would like to thank Mr. Mark Oksman, Dr. Boris Yofis and Mrs. Natasha Kalinchenko for their cooperation in the clean room, encouragement and help. In addition, I would like to thank Dr. Emma Rabinovich and Dr. Alexander Gurevtich for their concern and help in fabrication processes. Last, but not least, I would like to thank my parents, sister and two brothers for their support and encouragement throughout the thesis. Without you none of this work would have happened.

Abstract In this work, bulk material sensing using an unbalanced Periodically Segmented Waveguide Mach-Zehnder Interferometer (PSW-MZI) for chemical / bio- sensing is investigated. The device is designed to switch between two behavior regimes. Its common behavior regime is of a periodically segmented waveguide Fabry-Perot interferometer (PSW-FPI), which is intended to switch to that of a PSW-MZI behavior regime and back again. A sensitivity limit criterion predicts the device sensitivity from a theoretical analysis. Design arguments, applicable to integrated optical devices, and fabrication process are explained in detail. The measurement method and noise sources (optical, electronic and mechanical) are addressed and described. The investigation, using Glucose and Sucrose based solutions, of various concentrations demonstrates the sensitivity of the unbalanced PSW-MZI, and good agreement of the measured values with the PSW-FPI theory. A minimal sensitivity value of δn = 4·10-5 was measured and is of similar value as previously reported sensitivities of optical biosensors (2·10-5 – 5·10-5). The main advantage of the unbalanced PSW-MZI was found to be its significantly shorter sensing length, compared with other devices, enabling future production of smaller devices. The use of SU8 photoepoxy, as the device material, simplifies and lowers the costs of device fabrication. The multimode waveguide cross section provides easier light coupling (reducing insertion losses), easier alignment and polarization insensitivity (reducing polarization dependent loss).

TABLE OF CONTENTS 1

INTRODUCTION............................................................. 1

1.1

Basic concepts in planar waveguide analysis ........................4

1.1.1 Waveguide mode calculations .........................................................................4 1.1.2 Material choice for the implemented optical devices and investigated samples ..........................................................................................................................9 1.2

Analysis of planar waveguide geometric elements .............. 10

1.2.1 ‘L-bend’, ‘S-bend’, and ‘Y- branch’ calculations .........................................12 1.2.2 Periodically Segmented Waveguide ..............................................................19 1.3

Unbalanced Periodically segmented Waveguide Mach-Zehnder Interferometer (unbalanced PSW-MZI)..................................... 25

1.3.1 Classical Mach-Zehnder Interferometer .......................................................26 1.3.2 Unbalanced PSW-MZI...................................................................................29 1.4

Sensitivity limit criterion ......................................................... 33

1.5

Measurement approach........................................................... 35

1.6

Goals and methodology of this dissertation ......................... 35

2

Light source – waveguide coupling Methods........... 37

2.1

End-Butt coupling .................................................................... 38

2.2

End-fire coupling...................................................................... 39

2.3

Prism coupling ......................................................................... 41

i

2.4

Grating coupling ...................................................................... 42

2.5

Taper coupling ......................................................................... 46

3

DEVICE FABRICATION................................................ 48

3.1

Chip fabrication process overview......................................... 49

3.2

Mask design.............................................................................. 50

3.3

Photolithography ..................................................................... 51

3.4

Photolithography characterization......................................... 54

3.5

Dicing ........................................................................................ 55

3.6

Flow-cell design & fabrication ................................................ 57

4

MEASURING APPARATUS.......................................... 60

4.1

Low frequency noise ............................................................... 62

4.1.1 Optical noise ..................................................................................................62 4.1.2 Electronics noise............................................................................................63 4.2

Baseline drift ............................................................................ 65

4.2.1 Optical sub-system drift .................................................................................65 4.2.2 Electronic sub-system drift ............................................................................66 4.3

Mechanical Isolation of the sub-systems .............................. 67

ii

4.4

The Apparatus Fabrication...................................................... 68

4.4.1 Fabrication issues explained in detail...........................................................68 4.4.2 Measurement apparatus characterization.....................................................70

5

EXPERIMENTAL RESULTS ......................................... 74

5.1

Unbalanced PSW-MZI general functionality investigation ... 74

5.2

Glucose solution series measurements ................................ 78

5.3

Sucrose solution series experiments .................................... 85

6

DISCUSSION ................................................................ 88

6.1

PSW-FPI theory and the measured solutions........................ 88

6.2

PSW-FPI to PSW-MZI transition.............................................. 91

6.3

Unbalanced PSW-MZI sensitivity and sensing length .......... 95

7

SUMMARY AND CONCLUSIONS................................ 97

7.1

Summary................................................................................... 97

7.2

Future trends ............................................................................ 98

List of abbreviations ..........................................................100 Acronyms................................................................................. 100 Chemicals ................................................................................ 101 Physical quantities.................................................................. 102

REFERENCES ..........................................................................105

iii

1 INTRODUCTION

Miniature biosensors are fast becoming a major tool for rapid inexpensive bioanalysis. Bioanalysis serves to identify pathogens, DNA sequences or monitor Glucose levels in the blood. Due to biological material (biomaterial) vulnerability to electrical fields [1], sensing is done by other means (as opposed to electrophoresis, which is based on applied field). Some of the field-related sensing methods include indirect measurement of adsorbed layers on an enzyme-functionalized field effect transistor gate (ENFET) [2], and magnetic sensing [3]. By far, the most popular methods are based on optical sensing. Most optical analysis procedures are based on post-process detection of luminescent, tagged, biomaterial [4-6]. Tagging is a process in which luminescent chemical groups are attached to biomaterials. Luminescence occurs as a result of the biomaterial interaction. Detection of the resulting luminescence is performed only after the reaction takes place, and not while the reaction takes place. Tag-free optical methods simplify the sample preparation, and reduce costs and measurement time. Two major classes are common. One is based on surface plasmon resonance (SPR) [79], while the other is based on interferometry, of which the MachZehnder interferometer is by far the most common [10-16]. Interferometry is a very sensitive method for optical biomaterial process analysis. Detection of refractive index changes (RIC) in the sample, through light output intensity modulation, eliminates the need for tagging and enables “real-time” monitoring of processes. Mach-Zehnder Interferometers (MZIs) are common for this 1

type of biosensing. Two main approaches have been reported so far. The first is evanescent wave sensing [Fig. 1-1 a, b]. Surface adsorbed biomaterial/ evanescentwave interactions (i.e., the samples constitute a cover layer of the waveguide), in the MZI “sensing” arm [Fig. 1-1 a], relative to its reference arm, create phase-difference shifts, which modulate the output intensity [10,11,12,13,14-15]. The second approach, for evanescent- wave sensing, is using a periodically modulated waveguide (PMW) sensing arm [Fig. 1-1 b], in which the refractive index of the sensing arm is periodically modulated [15, 16], or a shallow grating structure is embossed on the sensing arm top surface, to promote the existence of evanescent waves and ensuing interaction with the sample [17]. Both approaches require relatively long (e.g., commonly on the order of 10–20 mm) evanescent-wave/ biomaterial interaction paths (sensing lengths). The sensing length does not comprise the total length of the devices, which is not reported in any paper as far as we know. This is due to the required length for a cumulative effect from a single pass of the light through the sensing arm, while interaction takes place in the beam fringes (e.g., the interface between the waveguide and cover layer sample). A way of overcoming the ‘single pass’ requirement is by using a periodically segmented waveguide (PSW) structure, allowing the light passage through the biomaterial (denoted as bulk sensing). Multiple reflections inside the PSW structure compensate for the short geometrical sensing length (~ 720 microns for 48 PSW cycles of 15 microns cycle length). The use of a single cavity extrinsic Fabry-Perot interferometer (EFPI) as a bulk biomaterial biosensor was reported [18]. Analysis of a periodically segmented waveguide Mach-Zehnder interferometer (forty-eight cycles 2

PSW-MZI) was reported recently [19], and indicates the advantages and limitations when used as a biosensing method. The PSW section in its sensing arm creates Stop bands, in which the device is insensitive to RIC. Overcoming the insensitivity of the device in its stop band regions leads to a hybrid approach, in which a large cross section, multimode, unbalanced PSW-MZI structure is used, behaving alternatively as a periodically segmented waveguide Fabry-Perot interferometer (PSW-FPI) and as a PSW-MZI. Outside the stop band regions the device is expected to behave as a PSWFPI, while inside the stop bands it is expected to switch to a PSW-MZI behavior.

Fig. 1-1: Schematic of unbalanced homodyne MachZehnder interferometers: (a) a ‘classical’ evanescentwave structure, where the sensing arm interacts with the top mounted sample. (b) A periodically modulated evanescent-wave structure, where the refractive index of the sensing arm is periodically modulated, promoting existence of evanescent waves, and hence interaction with the top mounted sample. (c) The unbalanced PSW-MZI structure, in which the sample is introduced in-between the waveguide segments and the guided light, traveling through the sample, interacts with it.

3

1.1 Basic concepts in planar waveguide analysis 1.1.1 Waveguide mode calculations

Fig. 1-2: Schemes of a slab and rectangular waveguide: (a) A slab waveguide, side view, and a guided mode propagating in it. Snell’s law governs Total Internal Reflection (TIR) conditions. (b) A rectangular cross section ridge waveguide, font view, and corresponding indices.

The following analysis addresses a ridge waveguide with a rectangular cross section of 60 by 60 microns. The assumed light wavelength is 632.8 nm, and the refractive indices are assumed to be: n1 = 1.598, n2 = n3 = n5 = 1.333 and n4 = 1.46 (see Fig. 1-1 b). Guided waves propagate by reflecting between the waveguide walls without exiting the waveguide [Fig. 1-2 a]. This state is called total internal reflection (TIR). The critical angle (θC) for TIR conditions is determined using Snell’s law:

n1 sin θ C = n x

(1)

These reflections were described by Fresnel for TE and TM modes. In the general case, where the incident light propagates, with an incident angle (θ 1) and is reflected

4

upon crossing a media boundary at an angle (θ 2), the Fresnel reflections can be described by: ⎧ n cos(θ1 ) − n 2x ⎪ RTE ≡ n1 cos(θ1 ) − n x cos(θ 2 ) = 1 n1 cos(θ1 ) + n x cos(θ 2 ) n1 cos(θ1 ) + n 2 ⎪ x ⎪ ⎨ 2 ⎪ n x cos(θ1 ) − n1 cos(θ 2 ) n x cos(θ1 ) − n1 = ⎪ RTM ≡ nx cos(θ1 ) + n1 cos(θ 2 ) n 2 cos(θ1 ) + n1 ⎪⎩ x

− n12 sin 2 (φ1 ) − n12 sin 2 (φ1 ) n 2x − n12 sin 2 (φ )

(2)

n 2x − n12 sin 2 (φ )

Here, θ 1 and θ 2 are the incident and reflected refraction angles. The index ‘x’ refers to the reflection from the top or bottom waveguide surfaces, depending on the computed refraction. Under TIR conditions the refraction is purely imaginary: R = e j 2φ

(3)

The reflected mode acquires a phase shift φ, which for a full cycle is 2φ. Using Euler’s formulation and some trigonometric calculations, the phase shift expressions are given by: ⎧ ⎛ n 2 sin 2 θ − n 2 ⎞ 1 x ⎟ ⎪φTE = tan −1 ⎜ 1 ⎜ ⎟ n1 cos θ1 ⎪⎪ ⎝ ⎠ ⎨ ⎛ 2 n 2 sin 2 θ − n 2 ⎪ x 1 −1 ⎜ n1 φ tan = ⋅ 1 ⎪ TM 2 ⎜ n1 cos θ1 n ⎪⎩ ⎝ x

⎞ ⎟ ⎟ ⎠

(4)

For a slab waveguide (a →∞, b = b), a description of the conditions for valid solutions to the wave equations can be deduced geometrically, when describing the acquired phases and the modal spacing, for a propagation cycle of a mode[Fig. 1-2 a and b]. The mathematical expression for such a cycle is called the transverse resonant condition [20]: 2kn1b cosθ = 2νπ + 2φ2 + φ4

5

(5)

Here, the subscripts 2 and 4 represent the Fresnel reflection phase shifts from the top and bottom surfaces of the slab waveguide (see Fig. 1-1 b). The mode number and spacing index is ν, and k is the wavenumber in free space. Substitution of the expressions for the Fresnel phase shifts into the transverse resonance conditions yields max ) in a slab waveguide: the number of guided modes (ν slab

max ν slab

⎧ 2b 2 1 n2 n1 − n42 − tan −1 42 ⎪ π n1 ⎪λ =⎨ ⎛ 2 1 ⎪ 2b 2 2 −1 ⎜ n1 ⎪ λ n1 − n4 − π tan ⎜ n 2 ⎝ 2 ⎩

− n22 2b 2 n1 − n42 , TE ≈ 2 λ − n4 n42 − n22 ⎞⎟ 2b 2 n1 − n42 , TM ≈ 2 2 ⎟ n1 − n4 ⎠ λ

(6)

The number of guided modes, under the assumed conditions, is ~ 123 modes. The influence of the Fresnel phase shifts is found to be negligible under the assumed conditions. A similar procedure is employed to extract the number of modes for a wall waveguide (i.e., a vertical slab waveguide with a = a and b → ∞). Substituting n4 with n2 for the boundary condition, and addressing the wall thickness (a), yields the number of guided modes ~ 167. Calculation of the guided modes, in a rectangular cross section ridge waveguide [Fig. 1-2 b], requires multiplication of the results for slab and wall waveguides and yields the total number of guided modes (νxy):

ν xy ≈

2b

λ

n12 − n42 ⋅

2a

λ

n12 − n22

(7)

For the assumed conditions, the estimated number of guided modes is of ~ 2.0541·104 modes. The high estimated number of modes follows basic logics, which appears in other physical areas as well. If there is an infinite number of solutions to the wave equation in free space, and there is a discrete number of solutions for guided modes in

6

a slab waveguide, for the finite dimension, but infinite number in the infinite dimension, further confinement (e.g., boxing the waveguide cross section into finite dimensions) will reduce the number of stable solutions even more. For a more accurate calculation of the number of guided modes, both TE and TM polarizations should be considered for each of the calculations. The effective index method [20-22] is a more accurate way for calculating the number of guided modes, as well as extracting parameters such as the field decay outside the waveguide (necessary for proper optical insulation of the device from the substrate). This approach takes into account that, for a rectangular cross section ridge waveguide, mode polarization is not purely transverse electric (TE) or transverse magnetic (TM), but hybrid. Thus, the modal propagation constants of TE guided modes in a slab waveguide are calculated, and substituted into the calculation of the propagating constants for TM guided modes in a wall waveguide (upright slab waveguide). The results produce the discrete propagation constants of the hybrid guided modes, for the slab waveguide. A similar procedure is applied for TE modes in a wall waveguide, substituted into the TM mode calculations for a slab waveguide, to obtain the number hybrid modes in a wall waveguide. Subsequent multiplication of the results for slab (~ 121 hybrid modes) and wall (~165 hybrid modes) guided mode calculations, yield a total number (ν xy ) of ~ 1.9965⋅104 guided modes. Proper optical isolation of the device from the substrate via an isolating layer is essential to ensure device functionality. Calculations of the minimal thickness, required for isolation, can be done by computing the field distribution of the guided modes in a slab waveguide. The criterion for optical isolation is taken to be a decay of 7

90% of the guided modes amplitude into the isolating layer. Using a formalism established by Anemogiannis et al. [23-25], calculations of the guided mode field distribution and penetration depth into the optical isolation layer were performed. Fig. 1-3 shows the schematic representation of the guided modes and the penetration depth into the optical isolation layer. Isolation is achieved by using a 5 microns thick isolating layer (n4).

Fig. 1-3: A schematic representation, using the Anemogiannis based formalism. The intensity is normalized, but should be treated as qualitative only. The guided modes penetration depth into the isolation layer is 5 microns.

Although the mode amplitude is denoted as a normalized light intensity, it should be taken only qualitatively. Modal power analysis requires convolution with the beam profile, or knowledge of the modal power distribution. 8

1.1.2 Material choice for the implemented optical devices and investigated samples The

choice

of

plausible

materials

for

optical

PSW –based

device

implementation involves birefringence considerations (as means for device operation or as an unwanted phenomenon), appropriate light-source/wavelength selection, phase dispersion and material attenuation. A suitable waveguide material for the case of the device is SU8, which is transparent to visible light (98% transparency at 300nm-1000nm) and has a refractive SU 8 index of n632 .8 nm = 1.598 (measured using a M-2000 Woolam ellipsometer, USA, which

corresponds well to the literature values -[26]). As it is a negative photosensitive epoxy, it is amorphous (i.e., non-birefringent). Due to its >90% transparency to all visible and near visible light wavelengths, a suitable light source can be readily selected from a variety of lasers (in our case a 2mW, 632.8nm, CW, HeNe laser). Possible biomaterials can be DNA segments in saline solution (0.9% NaCl in saline +DNA H2O), with an initial refractive index of ~ n632 = 1.4 [27], or Avidin, with an initial .8 nm Avidin refractive index of - n632 .8 nm = 1.46 [12]. DNA segments are typically used for genetic

sequence recognition through template-target hybridization, or polymerase chain reaction (PCR) [28,29]. Avidin is habitually used as a standard, to assess biosensor capabilities, through the Avidin-Biotine reaction [12]. A feasibility proof of concept can be done by using aqueous solutions of Glucose [14,30] and Sucrose [11] with varied concentrations. In the present work, the samples are introduced into the PSW voids (separated along the entire waveguide cross-section). Light attenuation effects, due to light absorption in the sample (liquid solutions) and polarity rotation (the 9

optically active Sucrose), are assumed negligible with respect to the PSW Fresnel induced attenuations. The multimode conditions render the device insensitive to polarization rotation, whereas all the sample solutions are water based and exhibit no appreciable absorption of the laser light. The use of a large cross section enhances the light-sample interaction per PSW cycle. Efficient optical isolation of the light from the silicon substrate ( nSi = 3.505 ), was achieved by a buffer silicon dioxide layer (between the waveguide and substrate) of ~ 5.0 microns. The fabricated waveguide cross-section was 62 by 87 microns, which covers the core diameter of commercially available multimode fibers. This provides easier light coupling into the device, as well as higher throughput and signal. The rectangular cross section provides also inherent mode matching of the light source and waveguide, reduced insertion losses (IL) and minimized polarization induced loss (PDL) [31]. Computation of the different coupling approaches, their relations to mode matching, and their efficiency in the present case, are presented in chapter 2. Insertion losses are addressed there as well as polarization dependent losses.

1.2 Analysis of planar waveguide geometric elements

Most integrated optical devices make use of basic geometries (optical elements). Proper consideration in designing these elements determines their functionality and serves to tailor them seamlessly together to function as a single device. Analysis and considerations of these elements is considered in the following subsections. Fig. 1-4 shows the unbalanced PSW-MZI qualitative structure, which 10

comprises several geometric elements, requiring understanding of their physics for proper design of the device.

Fig. 1-4: A schematic description of the unbalanced PSW-MZI structure. The geometric elements from right to left are: an L-bend, a Y-branch (comprised of two mirrored and superimposed Sbends), a PSW section and corresponding straight section, and another Y-branch. Inset: a close up view of the PSW section in the sensing arm and corresponding linear waveguide section in the reference arm.

Light is introduced into the device through an L-bend element which prevents stray light from the source to be detected as part of the device output. The light is split in two via a Y-branch. The sensing arm, in which the light travels through next, is discernable from the reference arm (into which ~ 50% of the light is introduced via the Y-branch) by its PSW section. The beams are converged by another Y-branch, upon which they interfere. Next, the different geometric elements, and their physical nature are addressed.

11

1.2.1 ‘L-bend’, ‘S-bend’, and ‘Y- branch’ calculations. Reliable detection of the light emanating from a waveguide structure, eliminating stray light, can be obtained by introduction of a 900 lateral bend (referred to as: Lbend), preceding/following the device inlet/outlet, respectively. The device inlet-outlet reciprocity prevents stray light from being measured as part of the output signal [Fig. 1-5].

Fig. 1-5: Schematic description of a L-bend, with reference to the waveguide straight-bent offset, as proposed by Neumann [34]. The offset δ is suggested as means of reducing the bend loss.

Calculations for an optimal L-bend radius were done by several groups [32-35]. The basic arguments governing L-bend loss were presented by Marcatili [33]: (a) A choice of materials, i.e., higher refractive index difference between the waveguide and cover, reduces the loss; (b) The waveguide minimal width, for which the conducted light becomes insensitive to the waveguide sidewalls uniformity or lack of, is governed by the material choice as well as the bend radius (measured from the centerline of the waveguide). (c) A minimal bend radius, which is determinable using

12

refractive index differences, the choice of wavelength, and the waveguide width, using Marcatili’s formulation [33] is: Rmin ≥

24π 2 ξ 3

3

λ2

(8)

Here, ξ3 represents the decay of the field outside the waveguide [33] in the lateral direction, and is computed in our case to be ~ 0.1 micron. The downscaling of optical integrated circuits leads to dimensional constraints which often do not allow the use of quasi-adiabatic curvatures. Thus, an effort to optimize bend induced losses, using rules for waveguide offset (δ), in the interface between the straight and bent waveguide elements, were done by Neumann et al. [34]. These calculations are effective for weakly guided modes [Fig. 1-5]. However, for strong guidance ( Δn =

n12 − n42 2 ⋅ n1

≈ 0.276 , for the parameters mentioned above), the offset

value becomes negligible. An effort to improve and generalize Neumann’s work was done by Van der Tol et al. [36]. The conclusions of this effort, using Gaussian mode and conformal mapping, predict an offset which is negligible for large radii (an order of magnitude larger than the wavelength of choice). A more recent work was done by Veldhuis et al. [35], and addresses explicit calculations under strong guidance conditions. Since the calculations for minimal loss are done for strong guidance and are angle dependent, it is useful as a comparison tool to previous calculations. It also provides a measure for the expected bend induced attenuation. Assuming a constant bend radius, the right angle (900) semiempirical attenuation expression [dB] can be derived (AT):

13

1 ⋅ 10 AT = n1 − n2 5π n2

n R ⎛ n −n ⎞ 2.29− 2.17⋅ 2 ⋅⎜⎜ 1 2 ⎟⎟ λ ⎝ n2 ⎠

3/ 2

⋅1.137

n1 − n2 − 0.01 n2

n1 − n2 3/ 2 ⎛ − 0.01 ⎞ ⎟ ⎜ n R ⎛ n −n ⎞ −0.58 ⎜ 2 ⋅⎜⎜ 1 2 ⎟⎟ ⋅1.137 n2 ⎟ ⎟ ⎜ λ ⎝ n2 ⎠ ⎠ ⎝

2

(9)

A graphical description of the attenuation in a right angle L-bend is shown in Fig. 1-6.

Attenuation [dB]

10 8 6 4 2 0

1

2

3

4

5

6

7

8

9

10

R/λ Fig. 1-6: The attenuation curve as a function of bend radius to wavelength ratio. A simple graphical derivation, for the present conditions, is taking a radius of over 7·λ. After Veldhuis et al. [35].

A comparison between the minimal bend radii, calculated by using Marcatili’s definitions (rmin ~ 149 microns), and the minimal radius for negligible attenuation (under the assumed conditions ~ 7⋅λ), chosen using Veldhuis formulation, leads to a minimal radius of ~ 4.43 microns. Thus, Marcatili’s formulation, as the criterion for minimal radius, ensures minimal bend induced loss. Verification of the bend induced loss can be done through substitution of the minimal radius, determined by Marcatili’s formulation, into the attenuation equation (Eq. 9), and comparison with the attenuation 14

for 7⋅λ, determined graphically from Veldhuis’s formulation. Doing so, under the conditions chosen for Veldhuis’s minimal radius, the attenuation is -0.021 dB. The minimal radius obtained using Marcatili’s formulation, yields zero predicted attenuation. A choice of a larger radius, such as- Rbend = 505 ⋅ 10 −6 [m], selected for the actual device, ensures negligible attenuation by any standard. When constructing integrated optical devices, it is often useful to use a doublebended shape, for parallel displacement of light, aligned in its original direction. Such shapes are called ‘S-bends’ (Fig. 1-7). A comparison of S-bends to a linear tilted waveguide segment, connecting two displaced parallel waveguides, was published by Hutcheson et al. [37]. Significant reduction of the S-bend induced loss is achieved by substituting the linear tilted waveguide with two 450 circular bends, which together construct the S-bend.

Fig. 1-7: ‘S-bend’ scheme, where L is the S-bend length, R is the 450 circular bend radius, and h is the displacement. The straight-bent interface offset (δ) is suggested as an optimization for weak guidance (Neumann [34]).

15

An effort to improve S-bend design, through the use of a waveguide element offset, was carried out by Van der Tol et al. [36]. Under strong guidance (Δn > 0.2), the offset becomes negligible. An effort to optimize the S-bend shape, by replacing the two 450 circular bends by a Fourier series construction, was carried out by Pant et al. [38]. The effort yields a parametric description of the S-bend curve (Fig. 1-8), in which the main curvature is controlled by the first non-zero element of the Fourier series (a2), while the fine structure is controlled by the second non-zero element of the series (a4): y( z) =

h⋅ z ⎛ 2π ⎞ ⎛ 4π ⎞ + a2 ⋅ sin ⎜ z ⎟ + a 4 ⋅ sin ⎜ z⎟ L ⎝ L ⎠ ⎝ L ⎠

(10)

Here, h is the S-bend displacement, L is the length of the S-bend, z is the parametric index along the waveguide axis, and a2 and a4 are the parameters that govern the Sbend shape. A calculation for strong guidance leads to: a2 = −

h , 10

a4 = −

π a2

⋅ 2 10

(11)

Alternatively, an effort by Munowitz et al. [39], suggests a formulation, which is intended for a mirror-like double S-bend structure, called ‘Y-branch’ or ‘Y-junction’ (Fig. 1-9). The parametric formulation for a single S-bend is: y( z) =

h⎡ ⎛ π ⎞⎤ 1 − cos⎜ z ⎟⎥ ⎢ 2⎣ ⎝ L ⎠⎦

(12)

Here, h is the S-bend displacement, L is the S-bend curvature length, and z is the parametric index. There is a definite similarity between the approaches, however, while Munowitz’s method does not take into account fine structure corrections, Pant’s formulation does (a4). On the other hand, none take into account any of the waveguide 16

material parameters, nor the choice of wavelength. Both methods assume that there are negligible bend induced losses as well as negligible waveguide offsets, due to their quasi-adiabatic way of construction, which is suggested to confine adequately all the

Waveguide displacement [μm]

guided modes [Fig. 1-8].

60 50 40 30 20 10 0

0

20

40

60

Length [μm]

80

100

Fig. 1-8: S-bend, according to Pant et al. [38] (denoted by ‘___’), and Munowitz [39] (denoted by ‘- - -’). The fine structure constant in Pant’s calculation, serves as a correction parameter. The bend displacement from each other was introduced for clarity.

A design based on Pant’s formulation, which is aimed at quasi-adiabatic displacement of the waveguide path, leads to a displacement of 260 microns over a distance of 20.8⋅103 microns. A Y-branch is a geometric element which splits a single beam into two beams, often requiring a power ratio of 50% for each of its outlets (Fig. 1-9). Weissman et al. [40], presented a way to optimize the Y-branch design, using the beam propagation 17

method (BPM). However, the effort was directed at linear Y-branch structures, and not S-bend based. A more recent effort to optimize losses in Y-branch structures was done by Yabu et al. [41]. This effort, like Weissman’s, concentrates on optimizing a Ybranch with linear waveguide arms. However, since there is widespread use of S-bend type Y-branches, the use of the calculations made by Munowitz et al., mentioned earlier are considered more appropriate.

Fig. 1-9: Scheme of an S-bend based ‘Y-branch’. This type of Y-branch allows better separation between the branch arms. After Pant et al. [38].

Radiative mode excitation by bends and beat formation inside bends are avoided by using quasi-adiabatic bends and a wide cross-section waveguide as design rules [42], which lead to a Y-branch arm eventual separation of 520 microns over a length of 20.8⋅103 microns. A waveguide amorphous dielectric material (SU8) and strong guidance conditions (e.g., Δn ~ 0.276 ) reduce the polarization dependent loss (PDL). The multimode rectangular cross-section renders it polarization insensitive, and makes insertion loss (IL) effects negligible [31,43]. 18

1.2.2 Periodically Segmented Waveguide

Fig. 1-10: A periodically segmented waveguide (PSW) waveguide scheme. The cycle length, consisting of a waveguide segment of length ls and void of length lv, is denoted by Λ.

A key element in this dissertation is the periodically segmented waveguide (PSW) structure (Fig. 1-10). In the particular case of bulk biosensing, the waveguide structure is segmented periodically, rather than the refractive index periodical modulation of a continuous waveguide [15]. Each period consists of a waveguide segment (its length denoted by ls), and a void (its length denoted by lv), intended to accommodate the sample material, while their sum comprises the cycle length (Λ), and the ratio of the void to the cycle lengths determines the duty cycle (Γ). The PSW cycle length is given by: Λ ≡ l s + lv =

lv Γ

(13)

A cumulative influence of the number of segment cycles on light traveling through such an optical element is inherent to this type of structures. It is manifested through a 19

cumulative phase change ( φ ) via its power transmittance function (T). The periodic nature of the PSW creates a one-dimensional photonic-bandgap (1D-PBG) structure, alternatively treated as a Fabry-Perot etalon, or a multilayer Bragg reflector. This means that there are PSW regimes in which light passes (referred to as bands), and regimes in which no light will pass (referred to as stop bands). Correct parameter choices (duty cycle, cycle length) leads to enhancement of the throughput, by choosing off-resonant conditions of the PSW cavities (voids). The voids are assumed to be filled with sample material. The duty cycle of the PSW throughout the calculations was chosen to be (lv/Λ = 0.8), using the considerations, presented by Ortega et al. [44]. As a result, the phase shift contribution of each segmented cycle is reduced, but light throughput of the PSW is increased. The following analysis of the light propagation through the PSW is based on the formulations by Oron et al. [45] and Yeh et al. [46]. A common approach of treating the periodically modulated index is by using a weighting function called the ‘effective index’ ( neff ): neff =

nWG ⋅ l s + nsa ⋅ lv Λ

(14)

Here, nWG is the refractive index of the waveguide (equivalent to n1 in Fig. 1-2), and

nsa is the refractive index of the biomaterial in the voids (equivalent to n2 in Fig. 1-2). The PSW induced phase changes, per cycle, and for a round trip in the step and void parts are expressed by (φs and φv, respectively): ⎧φs = k ⋅ nWG ⋅ l s ⎨ ⎩φv = k ⋅ nsa ⋅ lv

20

(15)

The Fresnel field reflection coefficient, for a reciprocal incident angle, from a single boundary is defined as: r≡±

nWG − nsa nWG + nsa

(16)

Taking into account multiple reflections between two adjacent PSW walls, one can express the field reflection per cycle as:

r1 =

(

)

r ⋅ 1 − e i⋅2(φs +φv ) 1 − r 2 ⋅ e i⋅2 (φs +φv )

(17)

2

The calculated power reflectivity factor, per cycle ( c ), can be defined as: r1

2

c ≡

2

1 − r1

2

(18)

Due to its periodical nature, the PSW section can be considered as a 1D lattice. Thus, the Bloch periodic translation condition applies. According to the Bloch condition, in conjunction with the Floquet theorem [47], a periodical phase shift coefficient (κ), which is equivalent to the k-space representation of the first Brilluoin zone, appears [46]. According to Yeh et al. and Oron et al., the resulting dispersion relation, for guided modes is: κ=

⎧⎪ ⎫⎪ ⎡ 1⎛ n n ⎞⎤ 1 ⋅ cos −1 ⎨cos(kneff Λ ) + ⎢1 − ⎜⎜ 1 + sa ⎟⎟⎥ sin(φ s ) sin(φv )⎬ Λ ⎪⎩ ⎪⎭ ⎣ 2 ⎝ nsa n1 ⎠⎦

(19)

The expression holds in the bands (for real values of κ). In the stop bands κ takes a complex form, which can be expressed by the parabolic approximation of π Λ

+ i ⋅ c − (π − k ⋅ neff ⋅ Λ ) . 2

2

21

The cumulative power reflection, for the case of N cycles, respectively, is: RN =

c

2

⎡ sin (κΛ ) ⎤ c +⎢ ⎥ ⎣ sin (NκΛ ) ⎦

(20)

2

2

Substitution of the complex k values inside the stop band yields: RN =

c

2

⎡ sinh (κΛ ) ⎤ c +⎢ ⎥ ⎣ sinh (NκΛ )⎦

(20a)

2

2

Calculation of a ‘worst case’ Fresnel loss of the output intensity (ψ) can be obtained by using twice the Fresnel power loss for N cycles of the PSW section:

(

Ψ = 1− 2 ⋅ r 2

)

N

(21)

The output intensity transmittance is defined now as: Tsens ≡ (1 − RN ) ⋅ Ψ

(22)

Hence, substituting equations 20 and 21 into 22 will result in the explicit PSW transmittance function: ⎡ sin (κΛ ) ⎤ ⎢ sin (NκΛ ) ⎥ ⎦ ⋅ 1− 2 ⋅ r 2 = ⎣ 2 ⎡ sin (κΛ ) ⎤ 2 c +⎢ ⎥ ⎣ sin (NκΛ ) ⎦ 2

Tsens

(

)

N

(23)

From equation 23, the cumulative effect of the number of segmented cycles is strongly dependent on the sine ratio of phase shift per cell to the cumulative phase shift of the PSW. A typical throughput curve (Tsens) of the PSW structure is calculated as a function of the sample refractive index (Fig. 1-11). The periodical conditions create stop bands, some full, some with mini-bands in them. 22

80

Tsens [%]

60

40

20

0 1.34 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45

nSample

Fig. 1-11: The throughput response curve of a PSW structure, for a wavelength of 632.8nm, at 25C. Visible are four stop bands, in which two have mini-bands.

This type of behavior is typical to Fabry-Perot based devices. In the present case, it is referred to as periodically segmented waveguide Fabry-Perot interferometry (PSW-FPI). The ‘worst case’ calculation, assumes that all reflected and dispersed light dissipates, and yields a loss of ~ − 0.0721 dB per cycle (waveguide segment + void + Deionized water sample). So, a cumulative loss, for a PSW structure of 48 cycles, yields an attenuation of -3.46 dB.

23

The PSW theory is based on single mode analysis, which is treated as a plane wave. In the case of multimode conditions (section 1.1.1), the output is the sum over the weighted contributions (Tsens) of each mode of the PSW throughput. This is possible under the present conditions since there is no interaction between the PSW section throughput modes. Calculation of the weighted power of each guided mode was necessary for this type of calculation. To this end, beam profiling measurements of the source (see section 6.2, pp. 92-93) were made, and a Gaussian fit was calculated. Normalized values of the different guided modes were assigned, in accordance with their respective order. Then the calculation of the PSW throughput was done by summing the weighted contribution of all the modes emerging from the PSW. Fig. 1-12 shows the modal power distribution curves of the PSW throughput, as a function of sample RI. Inside the stop bands, the number of emerging modes and their respective energies is severely reduced. Its effect on the PSW-MZI (section 1.3) expected behavior is addressed later. In the bands, the number of emerging modes, carrying at least 1% of the total input power (the power that was coupled into the device before reaching the PSW structure), average at ~ 25 modes. ‘Worst case’ calculations, based on Fresnel reflections and are expected to be by far the most dominant loss mechanism of the guided modes power. Although simplistic, under strong guidance (e.g., Δn ~ 0.276 ) and for minimal material dispersion (SU8 > 90% flat transmission curve in the 300-1000 nm region), these calculations hold (see section 5.1). An attempt to measure the surface roughness and thickness variations of the device using a profilometer (alpha-step 500, KLA Tencor) at several locations,

24

reveals that it is negligible compared to the wavelength (< 2nm). Thus, the greatest roughness is present in toe device inlet and outlet facets, due to the dicing procedure (section 3.5). As for the PSW structure, due to the multimode cross section, the guided modes travel well inside the waveguide cross section, and thus are insensitive to corner effects.

Normalized Thourghput [%]

5 nSample_____ 1.332086 1.335185 1.339386 1.340994 1.346831 1.366831 1.396831 1.416831 1.450224

4

3

2

1

0

0

10

20

30

40

50

60

70

80

Mode number Fig.1-12: Modal power distribution of the PSW throughput under samples with various RI. The dashed curves signify two of the sample refractive indices which fall inside the 1st and 2nd stop bands.

Calculations for L-bend, S-bend and Y-branch elements in this chapter assume ideal fabrication conditions (no defects, surface roughness or deformation). For fabrication, the selected dimensions, mentioned in the section (SU8 on Silica, surrounded by water based solutions, see section 1.1.1), were chosen to be at least an order of magnitude greater than their critical dimension values. 24a

1.3 Unbalanced periodically segmented waveguide MachZehnder Interferometer (unbalanced PSW-MZI)

The unbalanced PSW-MZI comprises several of the elements analyzed in section 1.2: a right-angle L-bend is used to butt-couple the light into the interferometer, preventing any stray light from the coupling source to reach detection. A Y-branch is used to split the light into the reference and sensing arms, while another Y-branch is used to recombine the light from the arms serves as the MZI outlet. In this section the fundamentals of Mach-Zehnder interferometry (Fig. 1-13 a) will be addressed. Then, based on that analysis, the analysis of the unbalanced PSW-MZI will be given. Analysis of a balanced PSW-MZI (Fig. 1-13 b) was recently reported by Kinrot [19]. This analysis was based on introduction of similar sample material to both arms, and chemical/biological “activation” of the material in the sensing arm alone, and is valid only for single mode conditions. Although basically differential (measuring the RIC between interacted and non-interacted materials), this type of PSW-MZI presents a problem of introducing the material to both arms while activating the material only in the sensing arm. As soon as miniaturization is considered, independent delivery problems pop up. The easier solution for this problem necessitates fabrication and analysis of a geometrically unbalanced PSW-MZI. The reference arm section, corresponding to the PSW section in the sensing arm, is substituted by a continuous section of SU8 (Fig. 1-14). Thus, the sample material can be introduced only into the PSW section of the 25

sensing arm, while covering both arms (e.g., n2 = n3 = n5 in Fig. 1-2). As a result, the interaction with the sample, as well as the main light attenuation, occur only in the sensing arm (specifically, in the PSW section of the arm) and not in both arms.

1.3.1 Classical Mach-Zehnder Interferometer

Fig. 1-13: Symmetrical Mach-Zehnder Interferometer schemes: The classical MZI (a) and the symmetrical periodically segmented MZI (b). The light inlet in both is bent in a right-angle using a large radius L-bend, so as to prevent any stray light detection. The right Y-branch splits the light into the reference and sensing arms. Then the light emerging from the arms is collected by the left Y-branch, and the two light beams interfere inside the Y-branch outlet.

An ideal balanced homodyne Mach-Zehnder waveguide interferometer (Fig. 1-13 a) has no losses/ dispersion sources. This type of interferometer compares the optical path of two light beams, traveling through the same geometrical length. The difference in the optical paths, due to refractive index difference (RID) between the two arms, is subsequently measured. Light is introduced into a waveguide and is split in two via a Y-branch. One beam is used as reference (reference arm) to the other, which interacts with an investigated sample/ externally applied electric field (sensing arm), changing its optical path length. The change in optical path length is caused by 26

refractive index change (RIC) in the sensing arm, relative to the reference arm, and is manifested by a phase difference between the beams. The two beams then converge into another Y-branch and interfere. The output intensity is typically measured by a photodetector. In the ideal case, the output intensity will vary between zero (completely destructive interference/ logical ‘0’) and the equivalent of the incident light intensity (completely constructive interference/ logical ‘1’), due to the varying phase difference. The expression for an ideal homodyne symmetrical Mach-Zehnder interferometer (MZI) output intensity is therefore [48]: I out =

I in ⋅ (1 + cosϑ ) 2

(24)

Here, Iout is the measured light intensity output of the interferometer, Iin is the incident light intensity coupled into the interferometer, and the phase difference is ϑ. The first non-ideal factor is the phase shift between the two arms, which is influenced by two independent factors. The first is a permanent phase shift difference, due to imbalance of the two arms (φ0). The imbalance, in the present case, is due to the continuous geometry of the reference arm and segmented geometry of the sensing arm. The second factor is the variable phase shift (Δφ), due to refractive index change (RIC) in the sensing arm. Depending on the nature of the sensing arm interaction, the variable phase shift may be time dependent or time independent (constant). When using a dynamically changing sample (such as an activated biomaterial or chemical reaction), the variable phase shift will be time-dependent, while use of chemically/ biologically inactive samples (such as sugar-based solutions) with various concentrations, will yield a time-independent variable phase shift.

ϑ = φ0 + Δφ 27

(25)

Since experiments show that there are losses of light intensity due to material and phase dispersions as well as device geometry and configuration (in both arms independently) a visibility factor (Vf) is introduced: Vf ≡

I max − I min I max + I min

(26)

Here, Imax and Imin are the maximum and minimum intensities of the output power. A more detailed analysis of the visibility factor reveals three independent sub-factors ( V f = V pol ⋅Vcoh ⋅VT ). The first is due to polarization dispersion effect (Vpol), which, in the case of a dielectric waveguide device using a non-birefringent (e.g., amorphous) material is expected to be negligible (Vpol=1). Next, coherence problems ( Vcoh ) of the light source are addressed. If the optical path inside the device exceeds the coherence length of the source, the interferometry result will become meaningless as no meaningful interference can occur. An appropriate choice of wavelength and device dimensions eliminates this potential problem (Vcoh=1). The last sub-factor is the power transmittance effect ( VT ), i.e., the power output from the two arms, which is assumed to be the only non-unity visibility factor henceforth denoted simply by (Vf) and is: Vf ≡

(Tref + Tsens ) − (Tref − Tsens ) (Tref + Tsens ) + (Tref − Tsens )

=

Tsens Tref

(27)

Here Tsens and Tref are the sensing and reference arm throughputs before converging and interfering, respectively. Thus, when substituting equations 25 and 27 into equation 24, the expression for the MZI output intensity becomes: I out =

I in 2

⎡ T ⎤ ⋅ ⎢1 + sens ⋅ cos(φ0 + Δφ )⎥ ⎣⎢ Tref ⎦⎥

28

(28)

1.3.2 Unbalanced PSW-MZI

Fig. 1-14: Unbalanced periodically segmented Mach-Zehnder Interferometer (PSW-MZI) scheme. The sensing arm is periodically segmented while the reference arm is continuous. Inlet: a close-up of the sensing area of the sensing and reference arms.

Analysis of the unbalanced periodically segmented waveguide Mach-Zehnder interferometer (PSW-MZI) takes into account the separate throughputs, and relative phase changes between its arms. The throughput of the sensing arm, including its inherent losses was analyzed in section 1.2.2, and equation 23 gives the expression for Tsens. Since the reference arm is linear and continuous, there are no inherent losses

attributed to it (ideally), so that its throughput is considered to be Tref = 1. The phase shift difference between the two arms of the MZI, due to the cumulative effect of the RIC difference, can be expressed by: Δφ = N ⋅ [(φv + φ s ) − k ⋅ n1 ⋅ Λ ]

(29)

For the unbalanced PSW-MZI, the phase difference and visibility factor are valid only for values of κ which reside in the stop bands, under quasi-single mode conditions. In addition, the throughputs of both arms are unequal, and lead to modified expressions 29

for the interference part of the equation as well as the overall output. The resulting unbalanced PSW-MZI behavior is characterized by its output: ⎛ Tref − Tsens I out = ⎜⎜ 2 ⎝

⎞ Tsens ⎟⎟ + 2 ⎠

⎡ T ⎤ ⋅ ⎢1 + sens cos(φ0 + N ⋅ [(φv + φ s ) − k ⋅ n1 ⋅ Λ ])⎥ ⎢⎣ Tref ⎥⎦

(30)

Since in the present case there are multimode conditions inside the bands (~ 1.99·104 guided modes), and quasi-single mode in the stop bands, its output intensity (Iout) is expected to be:

I out

⎧Tref + Tsens , band ⎪ 2 ⎪ =⎨ (31) ⎡ ⎤ ⎪⎛⎜ Tref − Tsens ⎞⎟ + Tsens ⋅ ⎢1 + Tsens cos(φ + N ⋅ [(φ + φ ) − k ⋅ n ⋅ Λ ])⎥, stop − band 0 v s 1 ⎟ ⎪⎜⎝ 2 2 ⎣⎢ Tref ⎠ ⎦⎥ ⎩

This final expression of the unbalanced PSW-MZI output intensity is given here in its simplified form and not explicitly, because of the complex expressions for the sensing arm throughput (Tsens) in equation 23, which also appears in the explicit expression for the visibility factor (Vf). Fig. 1-15 shows the two types of behavior which in the first investigated stop band. The stop band region is bordered and marked. Also, the typical response curves of both behaviors are outlined.

30

85 PSW.MZI PSW.FPI

80

Stop band

75

Iout [%]

70 65 60 55 50 45 40 35

1.334

1.336

1.338

1.340

1.342

1.344

1.346

nSample Fig. 1-15: The output intensity of the unbalanced PSW-MZI: The PSW-FPI and the PSW-MZI regimes. The refractive index spectrum covers the first investigated stop band, which are closest to the RI of deionized water.

Fig. 1-15 shows refractive indices ranging from deionized water to the first adjacent stop band. The output intensity is higher for PSW-FPI than that of the PSWMZI one. Inside the stop band, the PSW-MZI behavior shows continued response to the RIC due to a mini-band which splits the stop band into a double notch shape. If modal conditions are sufficiently close to single mode, the behavior of the device might change from the PSW-FPI to that of the PSW-MZI and back again, which will cover both the bands and stop bands.

31

The refractive index of the sample solutions was evaluated by using known concentrations, and monitored measurement temperatures (Error margin of scale ~ 0.1C). The solution refractive index calculations are based on the semi-empirical formula [49], in conjunction with data from the CRC handbook of chemistry [50]:

⎛ bC ⎞ nsample = asugar ⋅ ⎜ e sugar − 1⎟ + 1.3285-4.28833 ⋅ 10 - 5 ⋅ T-1.4032 ⋅ 10 - 6 ⋅ T 2 + .. ⎜ ⎟ ⎝ ⎠ 2077.64-9.9528 ⋅ 10 - 3 ⋅ T-8.5048 ⋅ 10 - 5 ⋅ T 2 + + .. (32) λ2 6.7691 ⋅ 10 7 -32.634 ⋅ T-3360.915 ⋅ T 2 + λ4 Here, C is the concentration of additives (Wt%) to the deionized water, the temperature is measured in Celsius, and the wavelength in nanometers. For sugar based solutions

(Glucose and Sucrose) the gauge factors are: asugar = 0.189 and

bsugar = 131.93378.

An estimation tool for the device RIC efficiency can be its correlation to previously reported devices. For this purpose a criterion is needed to enable rough translation of the theoretical results into reasonable experimental values. Since experimental apparatii suffer from noise, their signal-to-noise ratio (SNR) is a common bottleneck of performance. Thus, a sensitivity limit criterion is presented here [19].

32

1.4

Sensitivity limit criterion

The theoretical sensitivity limit (δnmin) is commonly defined as the RIC for which the output signal varies by 1 mV from its original value [11,12,14,16 and 18]. This is due to the typical noise level of detection systems, roughly translatable to a SNR of 50 dB. The definition can be generalized to a change of ~ 0.1% of the normalized output intensity, which will serve as the criterion for comparison of theoretical values and experiments. For the unbalanced PSW-MZI, under the assumed 50 dB material and wavelength choices, the calculated value is δnmin = 3 ⋅10 −7 .

Devices with similar or better sensitivities than that of the functional PSW-MZI were reported in the past. Liu et al. [14] reported a sensitivity limit of

δnmin = 1.4 ⋅ 10 −4 , while Kunz et al. [51, 52] with a reported value of δnmin = 5.0 ⋅ 10 −5 , Weissman et al. [15, 16] and Brosinger et al. [12] with similar values of

δnmin = 2.0 ⋅ 10 −5 . Also, Luff et al. [2] reported a value of δnmin = 5.0 ⋅ 10 −6 , while Elster et al. [18] reported a value of δnmin = 1⋅10 −6 , and recently Prieto et al. [30] indicated a value of δnmin = 7 ⋅10 −6 . All of the reported devices require a sensing length ranging from 9 to 20 millimeters, while the PSW-MZI required sensing length, under the assumed conditions (forty-eight cycles with a cycle length of 15 microns and a 0.8 duty cycle), is 720 microns. The total length of devices was not addressed in previously reported papers, while their required sensing length was. Fig. 1-16 shows the device sensitivity, as a function of sensing length, comparing previously reported devices with that of the unbalanced PSW-MZI. The previously reported devices were labeled by their author. The advantage of the 33

unbalanced PSW-MZI, over those reported by Luff et al. [11] and Prieto et al. [30], is its relatively short sensing length, providing theoretically an improved sensitivity limit. The use of logarithmic ordinate serves to differentiate the sensitivity limits.

Sensitivity Limit [δnmin]

-4

10

Kunz et al.

Liu et al.

Brosinger et al. Weissman et al.

-5

10

Prieto et al.

-6

10

unbalanced PSW-MZI -Sensitivity limit criterion

-7

10

0

2

4

6

8

10

12

14

16

18

20

Sensing area length [mm]

Fig. 1-16: Sensitivity as a function of sensing length. Previously reported devices (denoted by- ‘◊’) and labeled by author are compared with the unbalanced PSW-MZI device (denoted by – ‘●’) which requires shorter sensing length and provides theoretically better sensitivity.

Since the device is of large cross section (62 by 87 microns) light coupling is easy. Its near square shape renders it insensitive to polarization dependent losses (PDL). Since the PSW section itself requires only 720 microns, the rest of the device can be easily downscaled, using the arguments for its elements, to produce a much smaller device.

34

1.5 Measurement approach

The implementation of the unbalanced PSW-MZI classically necessitates the use of single mode conditions. A multimode unbalanced PSW-MZI device, exhibiting two interchangeable behaviors, was analyzed and investigated, to asses its benefits as a biosensor. The PSW sensing section forms optical stop bands in which it is relatively insensitive to RIC. Outside the stop bands it is intended to function as a PSW-FPI, while in the stop bands (due to attenuation of most modes, leaving only several power carrying modes with more than 1% of the power) it is intended to switch behavior to PSW-MZI. The use of multimode cross section can simplify light coupling, while providing insensitivity to PDL and other loss types. The higher power input, relative to single mode devices, provides stronger output signal and is more robust where SNR is addressed. DC measurements were done, to obtain as much data as possible from the measurements (i.e., stability, asses ‘worst case’ SNR, etc.).

1.6 Goals and methodology of this dissertation

In section 1.1, the motivation of using optical methods to sense/monitor biological reactions was presented. The use of planar waveguide device technology is inherent to this type of devices. In section 1.2, the theoretical considerations and calculations governing planar waveguide device elements, as well as the influence of material choice, samples, geometry and light source were addressed. The 35

considerations for parameter choice for each device element, serve throughout this dissertation as guidelines for the device design. Section 1.3 covered the different methods for coupling light into optical devices, and presented the method of choice. Section 1.4 presented the measurement approach. The purpose of this dissertation is to present a novel approach to biosensing, both theoretically and in practice (analysis, fabrication and measurements). Comparison to previously reported biosensors, with regards to their sensitivity and geometrical scale serve as a measure of the attractive qualities of PSW based devices. A light source (632.8 nm, CW, fiber-coupled HeNe laser) was used to investigate the unbalanced PSW-MZI. Glucose solutions of various concentrations were used as a tool of assessing the devices sensitivity to RIC and hence their applicability as biosensors. Sucrose solutions of varied concentrations were measured and used to emulate biomaterials, thereby demonstrating the device capabilities as a biosensor. Finally, the two regimes of behavior, of a PSW-FPI and PSW-MZI were analyzed and investigated.

36

2 Light source – waveguide coupling Methods

Integrated optical circuitry downscaling requires integration of light sources, waveguide structures, and detectors. Such integration is expected to enable downscaling of whole systems, passivation and encapsulation, and reduced sensitivity to environmental factors. Also, the coupling efficiencies of light into and out of the waveguide structures are expected to improve [17]. Often, light is detected by placing an external detector in front of the waveguide output (referred to as, ‘out-coupled’ light), and externally measuring its intensity (photodetectors, CCD cameras) or intensity distribution (CCD cameras + CAD, or spectrum analyzers). Thus, the bigger problem remains the ‘in-coupling’ of light (into the waveguide structures). In this section, we present five major methods of incoupling light. In the case of a 62 by 87 microns waveguide cross-section, the rectangular shape provides polarization insensitivity, while insertion loss is reduced by the mode compatibility of the waveguide and light source. Explicit calculations for each incoupling method are presented in the chapter, and the choice of one is explained.

37

2.1 End-Butt coupling

End-Butt coupling [53], is the simplest approach to light in-coupling. The light source is positioned as close as possible (pressed against, if possible) to the waveguide input (referred to as ‘Butt’), and with its maximal output intensity aligned in the waveguide direction, and in the middle of the waveguide thickness, to couple as much light as possible into the waveguide [Fig. 2-1]. The coupling efficiency is determined by the mode overlap integral, tilt angle between the source output and the waveguide butt, and the cross-section correlation of the waveguide and source output.

Fig. 2-1: End-Butt coupling scheme. The light source output is positioned as close as possible (pressed against, if possible) the waveguide butt [Ref. 54].

The in-coupling efficiency is predominantly determined by the mode overlap integral between the light source and waveguide. Light source divergence and waveguide cross section dimensions compatibility, enhances the efficiency. Thus, the expression for coupling efficiency (ηE-B) is: 38

η E−B

⎤ ⎡ 64 ⎛ π ⋅b ⎞ n1n f 1 ⎟⋅ × ..⎥ ⋅ cos 2 ⎜ ⎢ 2 2⋅ 2 2 ⎜ 2 ⋅φ ⎟ ⎡ 2 π3 (n1 + n f ) ⎥ ⎢ ν12 f ⎠ ⎝ ⎛ b ⎞ ⎤ 1 4 2 4 3 Normalizat ion ⎟ ⎜ ⎢ ⎥ ⎥ ⎢ 1 − Re flection m ⎢ ⎢ ⎜⎝ ν ⋅ φ f ⎟⎠ ⎥ ⎥ ⎦ 4 = ∑⎢ 144444 4⎣244444 3⎥ Overlap int egral ν =1 ⎢ ⎥ ⎥ ⎢ b ⎛ νπ ⎞ ⎥ ⎢× ⋅ cos 2 ⎜ ⎟ ⎝ 2 ⎠ ⎥ ⎢ φf 44244 3 ⎥⎦ ⎢⎣ 1area mismatch

(33)

Hereν is the mode number and m the total number of modes. The waveguide crosssection diagonal and the fiber-core diameter are expressed by- b and φf, respectively. SU 8 SU8 ( n632 .8 nm = 1.598 ) is the waveguide material, and doped silica is the fiber-core SiO material ( n632 .8 nm = 1.463 ). The waveguide cross-section is 62 by 87 microns, light 2

source wavelength of 632.8 nm, and multimode fiber-core diameter of ~ 62 microns, so the theoretical efficiency is ~ 100% for a fiber end pressed to the waveguide facet (no free space travel). Typical reported experimental values are 68%, since usually pressed butt coupling cannot be achieved and, as a result, Fresnel reflections decrease the coupling efficiency.

2.2 End-fire coupling

End-fire coupling is a more flexible method than end-butt coupling. The light source is output is focused via a lens/series of optical elements (e.g., Faraday isolators, polarizers, neutral density filters, and focusing lens) into a spot-size which is typically matched to the waveguide cross-section requirements. The beam waste (focal point) is usually positioned at a ‘skin depth’ (Δ) inside the waveguide inlet plane [Fig. 2-2].

39

Fig. 2-2: An end-fire coupling setup often uses microscope lens as the focusing element. The focus itself is adjusted to a skin depth inside the waveguide inlet (Δ).

The coupling efficiency is determined by the modal overlap integral between the light source modes and the waveguide supported modes [53]. Thus:

[∫ A( x) B ( x)dx] *

η E −F =

2

ν

* * ∫ A( x) A ( x)dx ⋅ ∫ Bν ( x) Bν ( x)dx

(34)

Here, ηE-F is the coupling efficiency, A(x) is the amplitude distribution of the source output, and Bν(x) is the waveguide modal amplitude distribution. Again for a 62 by 87 microns cross-section, the total calculated efficiency is ~ 100%. While theoretically possible, the typical reported experimental values are 60% [53] – 84% [55]. The variance in efficiencies is caused by the surface roughness of the waveguide inlet facet. The roughness varies with the fabrication and dicing fabrication processes, and the waveguide material.

40

2.3 Prism coupling

Prism coupling involves positioning a prism with a higher refractive index than TiO the waveguide (e.g., titanium-oxide/‘rutile’ that has a refractive index of- n632 .8 nm = 2.6 ) 2

on the top surface of the waveguide at the inlet area. The coupling prism is usually a right angle prism, with a prism angle of 900, 600, and 300 [Fig. 2-3].

Fig. 2-3: The prism coupling uses a high refractive index, right-angle prism (usually, 300, 600, and 900). Calculation of the incident angle (θm) are carried out backwards, i.e., from the coupled mode matching to the Snell angle of refraction.

The light source output beam is positioned along the waveguide ‘z’ axis in the Y-Z plane, while the coupling angle, determined by Snell’s law, is implemented for its position in the X-Z plane. The overlap integral of the leaky modes between the prism and waveguide surface and the higher order guided modes inside the waveguide determine the coupling efficiency. Since Snell’s law dominates the beam behavior outside the waveguide, the overall expression for the angle of coupling (θm), taking into account only the fundamental mode, for simplicity, is [Deg.]: 41

⎡ ⎛ ⎛ β ⎢ n p ⋅ ⎜ a sin ⎜ m ⎜k n ⎜ ⎢ ⎝ 0 p θ m = a sin ⎢ ⎝ n2 ⎢ ⎢ ⎣

⎞⎤ ⎞ ⎟ − 30 ⎟ ⎥ ⎟ ⎟ ⎥ 180 ⎠ ⎠ ⋅ ⎥ ⎥ π ⎥ ⎦

(35)

Here, θm is the coupling angle, np and n2 are the prism and ambient refractive indices,

βm is the modal propagation constant and k0 is the wavenumber in vacuum. For a SU8 waveguide, on a silica substrate and a rutile coupling prism, the coupling incident angle for the incident angle (θm) is ~ 150. Assuming no appreciable dispersion of the light beam in the prism, its beam waste diameter (w) will be ~ 70 microns. Its coupling coefficient (κprism) is: κ prism =

π ⋅ cosθ m w

(36)

This type of coupling is limited by dispersions due to the air gap in the prismwaveguide interface. Dispersion through the prism spreads the light beam diameter. Thus, collimating the light and focusing it into a small spot size is advantageous. Theoretical calculations for our case result in efficiency of ~ 100%. Typical reported experimental coupling efficiency values are 80% [53] - to 88% [55].

2.4 Grating coupling

Grating coupling involves relocating the in-coupling area to the top surface of the waveguide inlet. A periodically corrugated structure is fabricated on top/ into the top surface of the waveguide inlet [53]. There are two approaches for creating of such a structure. The first is patterning the top surface of the waveguide inlet (shallow etch 42

into the waveguide top surface). The other is fabricating a corrugated layer on top of the waveguide inlet. The corrugation cycle length (Λ), duty cycle (Γ) and depth (tg) are determined by the coupled mode of choice. The cycle length is usually proportional to approximately half the wavelength in vacuum. The duty cycle is defined as the ratio between the cycle length and the waveguide ‘step’ length (e.g. the tooth-like part in the corrugation cycle). Determining the grating depth is more complex. It can be chosen as equal to the cycle length for a deep grating, or calculated from the overlap integral for a shallow grating. The nature of such a structure can be described by Bragg’s law of diffraction. n1 = n2 ⋅ sin(θ m ) +

mλ Λ

(37)

Here, n1 and n2 are the waveguide and cover refractive indices, respectively. The angle

θm is the mode (of order- m) corresponding in-coupling angle, λ is the wavelength in vacuum and Λ is the grating cycle length. Hence, in its linear form, it is useful only for coupling of specific mode orders. The advantage of such a method is in its ability to match the area of the incident beam, thereby increasing the coupling efficiency. Also, for some applications, this type of coupling method serves as a mode filter, which couples only a desired mode, and rejects the rest. In its structure lays also its biggest drawback. If the grating is etched into the waveguide, its effective index is smaller than that of the waveguide itself. Thus, some of the light is expected to couple through the waveguide and into the substrate, without contributing to the in-coupling [56]. A grating can be constructed with constant periodicity, for coupling of a single mode (i.e., Λ and Γ are constant), or chirped periodicity for the coupling of a number of modes (i.e., Λ or Γ vary continuously to create a chirp). Its step structure can be 43

linear [Fig. 2-4a, b and c] or blazed [Fig. 2-4d]. Hence, if the coupling angle is picked correctly, much of a single mode, or a number of modes, can be efficiently coupled to the waveguide, and even directionally focused.

Fig. 2-4: Several grating schemes. A deposited corrugated linear grating is described by (a). A corrugated embedded linear grating is described by (b). A deposited blazed linear grating structure is described by (c). And, an embedded blazed linear grating structure is described by (d).

According to Hunsperger [53], the cycle length can be determined by the resonance condition of the grating periodic structure: Λm =

2πm

βm

(38)

Here, βm is the m-th order guided mode propagation constant. Using the propagation constant for the fundamental mode in a SU8 waveguide, and the SU8 waveguide related parameters (mentioned in section 1.1), the cycle length is Λ = 417 nm, which is around two thirds of the wavelength (632.8 nm). Also, using Snell’s law, we extract the in-coupling angle [Deg.], corresponding to the guided mode: k 0 n1 ⋅sin θ m = β m

44

(39)

The in-coupling angle is therefore, θ = 72.360. Trying to match the grating depth to the overlap integral through the use of the intensity decay distance, into the waveguide, the depth is determined by: tg = ηm

(40)

Here, tg is the grating depth, while ηm is the intensity decay distance, determined using Marcatili’s formulation [33]. In our case, shallow grating calculations, and yield tg = 88 nm. This is consistent with the work done by Tamir and Peng [57]. The efficiency of such grating structures is usually ~ 30%. A grating depth equal to its cycle length (deep grating) was used by Ogawa et al. [58]. The calculated efficiency was approximately 100%, and it required 100 grating periods. A calculation of a shallow grating structure was done by Waldhausl et al. [59]. Here, the effective index of an etched grating structure is taken into account. The resulting calculation, using SU8 as the single-mode waveguide material, and 632.8 nm wavelength, are a cycle length of Λ = 1214 nm, which is almost twice the wavelength (instead of the previous two-thirds of the wavelength), an in-coupling angle of θ = 570, and a grating depth of tg = 88 nm. The calculated efficiency, for the SU8, PSW based device is ~ 93%. Reported experimental efficiencies are ~ 80% [53] for linear grating structures to 84% [55] for blazed grating structures.

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2.5 Taper coupling

Taper coupling is based on a slowly receding thickness of a layer, set on top of a waveguide, which is designed to promote dissipation of its guided modes, when reaching sub-cutoff thickness, into the waveguide [Fig. 2-5].

Fig. 2-5: A tapered layer on top of a waveguide, for which after reaching a thickness below cutoff radiates its modes into the waveguide. The receding angle is typically ~ 1 degree, which requires a long coupling length.

The cutoff thickness is defined as the thickness under which no light can be supported by the taper. The coupling efficiency is determined by the overlap integral between the radiated modes, coupled into the waveguide, and supported modes in the waveguide [53]. Efficiencies are reported to be ~ 70%. The main problem in linear thickness thinning tapers is the determination of the receding thickness angle [60]. Thus, for efficient in-coupling the receding angle should lay in the range of: ⎛ β cutoff ⎞ ⎟⎟ ⎝ βm ⎠

θ r > a sin ⎜⎜

46

(41)

Here, θr is the recline angle, and βcutoff and βm are the propagation constants in the taper, at the point of cutoff thickness, and guided mode, respectively. Mode matching requires focusing of the radiated modes into the waveguide, as suggested by Brenner et al. [ 61 ]. The receding angle in their case is 5.70. The efficiency is reported to be close to ~ 100%. A more recent work was done by Frish et al. [62]. The receding angle was ~ 10, and efficiency of ~ 100%. Their drawback is their length (typically ~ 1 mm). Work on irregular shaped tapers, referred to as spotsize converters, was done by Spuhler et al. [63]. It offers an irregular shape, developed by using a step-by-step calculated evolutionary model, to obtain an efficiency of ~ 80% over a coupling length of ~ 150 microns. However, fabrication of a taper requires the use of grey-scale lithography, currently not available to us. Thus, it is considered impractical for our uses. As a conclusion, the most practical and easy to implement is the butt-coupling method. For the 62 by 87 microns cross-section, the source (fiber-end) with a core diameter of φcore ~ 9 microns, and a clad of φclad ~ 125 microns, notwithstanding the beam divergence upon exiting the fiber end, allows virtually 100% efficiency. This efficiency is hindered by the bare fiber tip (at least 4% losses) which was cleaved, and by the waveguide inlet facet (at least 10%-15%) which was diced using as diamond circular saw but not polished. The distance between the fiber tip and waveguide inlet was ~ 0.1 mm. This restricts the number of coupled modes from 121 in the lateral plane to ~ 40 with significant power, out of possible ~ 2·104 hybrid modes.

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3 DEVICE FABRICATION

Implementation of an efficient sample solution delivery system to a balanced PSW-MZI structure is complex. Separate delivery of sample material to the sensing and reference arms, in small volumes (~ 2.7 nl), while maintaining identical solution volumes in both arms, is the source of the complexity. Also, both arms reside in close geometrical proximity, which make the separate delivery even more complex. The first step to an efficient delivery for proof of concept is to fabricate an unbalanced structure (section 1.3.2), in which the sensing area consists of a PSW section, while in the reference arm it is just a continuous linear waveguide section. The sample separate delivery issue is avoided, by providing similar cover conditions for both arms, with a single difference, which is the presence of the investigated solution in the light path inside the sensing arm. The next step is avoiding dependency of the measured device output on investigated solution volume size variations. This was achieved by using the ‘flowcell’ concept. This chapter presents the steps towards realizing the device geometry, from the design stages of the device itself, through its fabrication process, dicing the wafer into separate dies, and the eventual assembly of the flow-cell to construct the chip.

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3.1 Chip fabrication process overview

The photolithography mask plays a key role in the device eventual geometry. When using a ‘single step’ photolithographic fabrication process, such as the case when using SU8, it has paramount influence on the outcome. This influence is demonstrated by the photolithography process flow chart (Fig. 3-1).

Fig. 3-1: SU8 photolithography flow-chart process: a 4” diameter, 550 micron thick Silicon wafer, with a 5 micron thick polished SiO2 layer on one side is cleaned (a), then spin-coated with SU8 (b), exposed through a negative mask to uniform light (c), and spin-developed to yield the ridge SU8 structure on top of the Silicon oxide layer (d).

Fig. 3-1 shows the SU8 photolithography flow-chart process. A 4” diameter, 550 micron thick Silicon wafer (SQI, USA), with a 5 micron thick polished Silicon

49

Oxide layer on one side is cleaned (Fig. 3-1 a), then spin-coated with SU8 (Fig. 3-1 b), exposed through a negative mask to uniform light (Fig. 3-1 c), and spin-developed to yield the ridge SU8 structure on top of the Silicon oxide layer (Fig. 3-1 d). So, while the chemical processes (photoinduced and otherwise) will determine the quality of the fabrication, the mask design will determine the general shape, and its accuracy, the quality of the process (alignment of the different optical elements in the PSW-MZI geometry).

3.2 Mask design

Fig. 3-2: An L-Edit Pro software, SU8 mask view of the PSW-MZI structure. A right angle bend precedes the device itself.

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Fig. 3-2 shows the photolithography mask design which was done using the LEdit Pro software (Tanner Research, USA), and the device scheme. A right angle Lbend (r = 4.5 mm), acts as the light source coupling area and as a geometrical isolator from stray light eventual detection by preceding the device structure. Two elongated Y-branches (20 mm long) split the incoming light into the two MZI arms (0.5 mm separation distance), followed by linear PSW/ continuous sections (0.72 long) of the sensing/ reference arms, and reunite them using an identical Y-branch element to interfere near the outlet. The mask (Adtek photomask, Canada), was a 5” Chrome plated quartz plate. Since the SU8 is a negative photoepoxy, the waveguide features are clear, while the rest of the mask is covered with Chrome.

3.3 Photolithography

The photolithography process was done in the Tel-Aviv University cleanroom (a.k.a. – TAU Microfab). The said substrate (SiO2/Si) was cleaned by rinsing in Acetone, then by 2-Isopropanol, and drying with nitrogen purge-gas. Manual cleaning was done between two sets of rinsing procedures using a microposit cleaning cloth. The Mask was cleaned by a 20 minutes immersion, upside down, in Piranha solution (75% vol. – H2SO2, and 25% vol. – H2O2). Post Piranha rinsing using deionized water, and drying with nitrogen purge gas was essential for Piranha residue removal. Optical inspection of the wafer and mask cleanness was done by scanning them under a metallurgical microscope (Olympus MX-40, USA). Removal of residual material from the wafer surface was done by pre-baking it on a hot-plate (Karl-Suss RC8, USA) for 51

20 minutes at 170 Celsius. A cool-down time was designated to prevent the wafer from stress cracking. The SU8 (SOTEC SM1070, Switzerland) was spin-coated (Headway Research Inc., PWM 32) on the wafer. SU8 deposition was done by spin-coating on an opened top spinner, rotated at 230 RPM nominal speed, closing the spinner top and ramping to 988 RPM at a rate of 100 RPM/sec and then maintaining at the target speed for 120 seconds. Uniform coverage of the wafer is achieved by using this low speed and long duration with no dendrite-like coverage borders or coverage deficiencies. This was followed up by a slow-down at a rate of 100 RPM/sec. Due to a ‘pullback’ effect, caused by the SU8 viscosity, the spin-coating process was repeated twice, with a 30 minute interval to allow the pullback to occur. Soft-bake was performed on a hot-plate (Karl-Suss RC8, USA), by increasing the temperature from 650C to 950C, holding it for 30 minutes, and cooling it down to room temperature for 5 minutes (cool-down) before proceeding. Uniformity of the desired residual humidity in the SU8 layer (~ 3%) was achieved by leaving it for 12 hours in a black box at room temperature. Patterning of the SU8 was done by exposing it to 405 nm wavelength light in a mask aligner (Karl-Suss MA6). Since the heat conduction of the SU8 is not very high, it was exposed in four intervals of 15 seconds, when the light flux was set to 8.5 [mW/cm2], and a heat dissipation interval between the exposure fits of 30 seconds was set. Vacuum contact between the mask and wafer was used to achieve maximum resolution.

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Enhancement of the contrast between exposed and unexposed areas of the SU8 was done by performing a post-exposure-bake (Karl-Suss RC8, USA). The temperature was elevated from 650C to 950C, maintained at 950C for 15 minutes, and decreased back to 650C. Again, a controlled cool-down procedure was implemented to prevent stress cracking of the SU8 layer due to thermal shock. Finally, residual SU8 was removed by spin-developing the SU8. The wafer was attached inside the spinner which was kept open during the spin-development. The wafer was rotated at a nominal speed of 1425 RPM for 180 seconds, while being sprayed with an SU8 developer (Shipley-EC-Solvent, 2-Methyloxy-1-Methylethyl Acetate) through a nozzle continuously. Afterwards, the spinner was slowed down to 100 RPM and the wafer was spray-rinsed using 2-Isopropanol, which also acts as the developer neutralizer, for 120 seconds. This was followed by, spin-drying the wafer, using Nitrogen purge gas, while keeping it in the spinner at 100 RPM. The test for a successful development was absence of any ‘white spots’ on the dried SU8 structures. The fabricated structures were optically examined under a metallurgical microscope (Olympus MX40), to verify the process quality (no ‘tails’, due to under exposure, nor cracks from over-exposure, etc.). After a satisfactory optical inspection, the glassy transition of the SU8 (turning the epoxy into glass-like material) was done by hard-baking the wafer. The wafer was returned to a hot-plate (Karl-Suss RC8, USA) for which the temperature was elevated from 650C to 2100C. Upon reaching this temperature, the wafer was taken off and put on a 3 hinge rib structure, to facilitate a slow-cool down to room temperature.

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3.4 Photolithography characterization

Fig. 3-3: A scanning electron microscopy (SEM) photo, showing the cross-section of 62 μm by 87μm (JEOL JSM-6300, USA). This was taken from the chip edges while dicing the chip (a). The top view of the fabricated PSW section in a device was captures using an Olympus MX50 metallurgical microscope with CCD mounted camera (b).

Fig. 3-3 shows the typical rectangular cross-section, as portrayed by a scanning electron microscope (JEOL JSM-6300, USA) picture (Fig. 3-3 a), and the typical PSW section of the device, as portrayed by an optical (Olympus MX50, USA) picture (Fig. 3-3 b). The slanted pattern on the SEM surface was created by the diamond saw marks, due to the dicing process. These marks will be characterized in the next section. Analysis of the optical characteristics of the PSW fabricated features reveals a change 54

from the intended design. The PSW features, as defined by the photolithography mask were of 3 micron thick walls (steps), and 12 micron long voids. In reality, the steps were of thickness of ~ 4.3 microns, and the void length was ~ 10.7 microns (duty cycle of ~ 0.713 instead of the intended 0.8). This estimate is based on an accurate (SEM based) measurements of the waveguide width of 62 microns. The reason for the deviation from the mask defined features was the high aspect ratio of the PSW steps (62 μm wide, 87 μm high, and 4.3 μm thick).

3.5 Dicing

The dicing process (separation of the chips from each other, and from the wafer scrap areas), was done by the following procedure. After fabrication of the PSW-MZI structures, the wafer was coated by a thick positive photoresist (AZ 4562, USA), and baked on a hot-plate (Karl-Suss RC8, USA) at 1100C for 2 minutes. This procedure was done in order to protect the wafer, while in the dicing machine, from debris. The wafer was not spin-coated with the photoresist, to preserve as much photoresist thickness as possible. After the baking, the wafer was attached by a sticky nylon sheet from its back side, to a dicing frame. The frame was positioned and lock into the dicing machine (K&S 982-6 Plus, USA), with a diamond dicing wheel. The dicing wheel shears off ~ 58 microns in thickness. Since the dicing is done between the dies, it is useful to know and plan in advance, the die spacing so as to protect them from the dicing induced damage. Coordinates for wafer absolute positioning were fed into the

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machine. Then an orientation (XY plane) procedure was applied for alignment. After choosing the dicing coordinates, the dicing was done automatically by the saw. After dicing, the dicing frame was released from the machine, and the sticky sheet was separated from the frame. The next step was to release the dies from the sticky sheet, clean them from the protective photoresist layer, and check for dicing induced damage in the separate dies. Releasing the dice from the sticky sheet and cleaning them from the protective photoresist was done by rinsing them repeatedly with Acetone, and finally, washing off the Acetone with 2-Isopropanol. The next step was removal of the residual materials by baking the dies on the hot-plate at 1100C for 2 minutes. Then optical inspection using a metallurgical microscope (Olympus MX40) was performed. After the dicing process, the dicing marks were characterized, to assess the necessity of post-dicing polish of the die edges. A Scanning electron microscope (SEM) photo of close-up on a partial cross section for the waveguide, after dicing (JEOL JSM-6300, USA) is shown in Fig. 3-4. The slanted lines are the dicing saw marks. These marks, range from less than 0.1 microns to 0.5 microns. Although scarce, arbitrary defects with an approximate diameter of 2 microns, act as scattering centers. Bearing in mind that the coupled light wavelength is 632.8 nm, both the saw marks (~ 0.1 μm to ~ 0.6 μm in width, and ~ 0.3 μm in depth), and scattering centers (average diameter of ~ 2.3 μm) reduce the coupling efficiency to ~ 50%.

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Fig. 3-4: A Scanning electron microscope (SEM) photo of close-up on a partial cross section for the waveguide, after dicing (JEOL JSM-6300, USA). The slanted lines are the dicing saw marks. These marks, are usually less than 0.5 micron in width, and act as scattering centers for the incoupled light (632.8 nm).

3.6 Flow-cell design & fabrication

Next, the delivery of solutions onto the PSW-MZI had to be addressed. Sealing off the solutions inside the device, while maintaining its integrity, and providing the environment for sample volume insensitive measurements had to be addressed. Thus, the ‘flow-cell’ concept was conceived. The flow-cell consists of the optical chip, a polycarbonate cover, and a thin sealant frame from RTV (Silicon glue). The chip, contains the unbalanced PSW-MZI as well as several test devices (Fig. 3-5 a – denoted 1-4). The polycarbonate cover was constructed like an altar (Fig. 3-5 b). This means that its top (external) face contains 57

solution inlet and outlet nipples and extends to four holes at the cover extremes (corners), to enable locking the chip onto the measuring apparatus. Mechanical stress absorption, of the expected pressure applied by the solution inside the flow-cell, is distributed between a set of metal poles and Teflon bolts, attached on top of the cover corners and the RTV sealant. The bottom face of the cover (internal) is engraved so the only contact between it and the chip is through a thin frame ~ 0.8 mm wide and 1 mm high. This frame is referred to as the sidewall of the flow-cell. Finally, the RTV sidewall sealant, which connects the cover to the chip, to create the full flow-cell (Fig. 632.8 nm 3-5 c) was selected so its fully cured refractive index is nRTV = 1.4 . This means that

there is a refractive index difference (RID) of 0.241, between the waveguide and sealant, ensuring negligible power leaks to the sealant (taking into account that only the first 40 coupled modes carry significant power). Another contributing factor is its tangential contact with the waveguide and guided modes. Since the cover does not come in contact with the SU8 waveguide, and is positioned so it is tangent at all overlapping areas with it, no appreciable light scattering into the polycarbonate was expected or observed. Moreover, no apparent influence of the RTV as a scattering material was observed.

Fig. 3-5 c shows the flow-cell which seals off a large portion on the chip. The closed space accommodates a solution volume of ~ 1.61 ml, while the partial volume that resides in the PSW section of PSW-MZI is ~ 2.7 nl.

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Fig. 3-5:

The flow-cell elements consist of

the optical chip (a) on which there are several test devices (denoted 1-4) in addition to the unbalanced PSW-MZI structures (denoted as such), the polycarbonate cover (and denoted niches) with solution inlet and outlet metal nipples (b), and a thin square frame (denoted by RTV frame base extrude) which extrudes 1mm from the cover and provides, in conjunction with the RTV layer on top of it, the sidewall structure of the full flow-cell (c).

Thus any random variation in the solution volume has negligible effect on the measured device output (the solution is “infinitely” larger than the actual volume in the PSW voids). The geometry of the cover was dictated by three factors. The first was the need to harness (position) the chip in. This is due to the expected upward pressure of the solution, under static conditions (no flow into the chip or out of it), of ~ 914 [N/m2]. The two niches, as inlet and outlet niches in Fig. 3-5 c, provide accessibility of the bare fiber of the coupled light source to the PSW-MZI inlet, and the photodetector positioned at its outlet.

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4 MEASURING APPARATUS

Due to its simplicity, availability, low cost, and relative stability, a HeNe 2mW continuous-wave (CW) laser (JDS Uniphase 1122/P, USA) was chosen as a light source for continuous wave (DC) measurements. An overview of the measuring apparatus is necessary for clearer analysis of its components.

Fig. 4-1: Schematic description of the measurement apparatus. There are three different sub-systems. The top mounted solution reservoir (a) for solution introduction into the chip and evacuation of the used solution to a bottom waste reservoir. The optical system of JDS HeNe 2mW CW laser fitted with a free-space-to-fiber coupler and single-ended fiber (b), delivering the light into the chip. The electronic system which includes two photodiodes, pre-amplified and connected to 2nd stage amplification, low-pass-filter (LPF) and offset trimmers, which are fed into a voltagedivider that is sampled by a Fluke 189 datalogger DMM, recorded by a laptop (c). The heart of the apparatus is the assembly of positioning stages and the chip (d).

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Fig. 4-1 shows the schematics of the measurement apparatus. There are three different sub-systems. The fluid feeding sub-system, which consists of a top mounted solution reservoir (Fig. 4-1 a), for introducing the investigated solutions into the chip, and evacuating used solution to a bottom waste reservoir. The optical sub-system, which consists of the HeNe laser, fitted with a free-space-to-fiber coupler (OZOPTICS HPUC-23AF-633-S-3.9AS-20, USA), and connected to a single-ended fiber (Thorlabs P-4224-FC), which delivers the light into the chip (Fig. 4-1 b). Last is the electro-optic detection sub-system, which is based on light detection by two pre-amplified photodiodes (Burr-Brown OPT101), externally wired to a 10MΩ feedback resistor, where one is butt-coupled to the chip outlet and the other picks up stray light from the chip butt-coupled inlet. These photodiodes feed 2nd stage amplification, low-pass-filter (LPF) and offset trimming circuits (based on a Burr-Brown OPA177). After the amplification, offsets and noise trimming, the output signals are fed into a voltagedivider (based on a Burr-Brown MPY634). The voltage divider output signal is picked up by a Fluke 189 datalogger DMM, which optically transfers the logged data into the laptop (Fig. 4-1 c). Prevention of external power supply fluctuations is achieved by powering the electronic circuits from a stabilized +/-9V, +/-5V and a real (not virtual) ground, using a stabilized dual-battery source. The datalogger is powered by a separate four 1.5V battery pack, while the interface between the datalogger and the laptop is optical, so electronic isolation is maintained.

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DC measurements in optics and electronics are known to suffer from two major drawbacks. These drawbacks are low frequency noise and a ‘drift’ of the measurement baseline. Hence, addressing these issues is essential for an operable measurement apparatus. The different possible noise sources, were briefly mentioned (not analyzed) as well as the ways to avoid or reduce some of them. The measured noise (recorded on the laptop) was taken to be the overall noise in the system.

4.1 Low frequency noise

In electro-optical systems both the electronic noise and optical noise contribute to an overall system noise level.

4.1.1 Optical noise The optical sub-system components include the HeNe 2mW 632.8 nm CW laser module, the OZOPTICS free-space-to-fiber coupler, and a FC/PC single ended bare fiber, around 60 centimeters long. The laser noise sources are associated with its thermal/power/current stabilization feedback circuits, and optical phase noise. The specifications of the laser indicate a maximal laser module noise of ~ 4 μW (for the range of 30Hz – 10MHz). Since DC measurements are performed, this value presents the nominal value for the laser module noise.

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The free-space-to-fiber coupler was attached to the laser’s free-space outlet, to commute the emitted light into a fiber. This part is responsible for focusing of the emitted beam (φ ~ 810 microns) into the fiber (φ ~ 9 microns core, and 125 microns clad). The focusing procedure is done by using a multimode (MM) short FC/APC single-ended fiber, and a remote target. The light is then aimed at the target, first in its free-space configuration, then with the coupler and without the MM fiber, and then with the MM fiber where speckle patterns appear. These patterns serve as indication for the relative axial positioning of the laser-coupler-fiber system. When the flange is well adjusted (axial position), the speckle patterns should disappear almost entirely. Attaching the single mode fiber and checking for speckle patterns, reveals some changes and reappearance of some speckles. This is due to inaccuracies in the alignment and induced noise due to multiple reflections inside the coupler. Measurements show that it brings the overall noise of the optical system to ~ 40 μW. So, the overall noise generated in the optical system, and delivered through the fiber to the in-coupling area (between the fiber end and device inlet) can amount to ~ 40 μW. Assuming a 2 mW output, the maximal signal-to-noise ratio (SNR) is ~ 17 dB.

4.1.2 Electronics noise The electro-optic sub-system comprises of the detection circuits, datalogger and laptop. Since the datalogger and laptop provide no apparent noise source, the detection circuitry needs addressing.

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Fig. 4-2: A schematic presentation of the electronic system consisting of the two pre-amplified photodiodes (BB OPT101), 2nd stage amplification (BB OPA177), low-pass-filter and trimming circuits, a voltage divider (BB MPY634) and DC stabilized power supply with +/- 9V, +/- 5V and a grounded zero point.

Fig. 4-2 shows the schematics of the detection circuits. This is the 4th generation of circuitry, and the most stable. Two on-chip pre-amplified photodiodes (BBOPT101), are externally wired to 10MΩ feedback resistors. Each amplified signal is amplified again by a 2nd stage amplification (based on BB-OPA177) circuit, where frequencies are cut using low-pass filters (LPFs), adjusted to have the identical lowpass range of ~ 127 Hz. Offset trimmers enable selection of the detection work point (saturation prevention), and compensation of leakage (quiescent) currents. The

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amplified signals are then fed to a voltage-divider (BB-MPY634), so as to nullify the optical power temporal fluctuations, due to the optical sub-system noise. The output is measured by the Fluke 189 datalogger DMM, and optically transferred into the laptop for storage. The voltage divider output is function: Vout ≅ 10 v ⋅

Vsens _ PD Vref _ PD

. Here Vsens_PD and

Vref_PD represent the amplified signal from the sensing and reference photodiodes, respectively. The 10v multiplication factor is factory determined and was verified using emulated Vsens_PD and Vref_PD voltages. The reference photodiode picks up the power fluctuations of the laser while the sensing photodiode picks up the signal from the device output. The output signal (Vout) is proportional to the transfer function of the device. The stabilized dual-battery power supply is based on positive and negative power stabilization chips (ST7805 and ST7905, respectively). Any distortion/ fluctuation of power is compensated by capacitors and diodes.

4.2 Baseline drift

4.2.1 Optical sub-system drift Baseline drift, in the present case, is caused by two major factors. The first is the HeNe laser warm-up power drift, which is caused by the lasing chamber thermal expansion during the laser warm-up time (typically ~ 15 minutes). Increased lasing chamber length diminishes the problem through decreased relative expansion to original length ratio. After warm-up these effects usually level off and then two other 65

effects may take place. The first is longitudinal mode-drift. The HeNe laser emits 2-3 longitudinal modes (for a 6” long tube). These modes drift along the 1.5GHz gain curve. When one of them ‘drops off’ to re-appear at the other end of the gain curve, a power fluctuation occurs (for the JDS 1122/P, the specified value is of up to 5% of its output power). This means that the maximum drift is of ~ 0.1 mW, and is continuous throughout the measurements.

4.2.2 Electronic sub-system drift Electronic circuitry drift is usually caused by insufficient charge evacuation through the ground connection, or through slow dissipation of accumulated charge at one or more locations inside the circuits. This is the reason a coaxial cord was used as the ground outlet port. When the photodiodes were substituted by electronic DC signals, corresponding to the expected values from the pre-amplified photodiodes, no measurable drift was logged. External electromagnetic interference (EMI) problems, such as the power grid noise (in Israel ~ 50Hz), were reduced by electrically shielding the electronic circuits. The shielding was obtained by covering the bottom of the measurement table with a grounded metal sheet, while connecting all of the measurement equipment and shielding to a common ground.

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4.3 Mechanical Isolation of the sub-systems

Achieving mechanical isolation from random vibrations was one of the main issues for concern, and several tests were conducted to prove its efficiency. The mechanical isolation was achieved by isolating the sub-systems from each other. The whole apparatus was mounted on a heavy table, with thick foam vibration isolation under each of its legs. The fluid delivery sub-system (Fig. 4-1 a) was isolated from the chip by positioning the top mounted solution reservoir on a heavy base pole, where flexible tubes connect to the solution inlet nipple, from the flow-cell outlet nipple to the waste reservoir, and from the solution reservoir directly to the waste reservoir (not included in the figure for simplicity). The tubes were hinged to the table, and minimal slack was designated so as to prevent vibration transfer between the sub-system and the chip. The optical sub-system (Fig. 4-1 b) was connected to the chip butt-coupling position mechanism via its fiber. The fiber was hinged to the table top, while a small portion of it was suspended in air, between the positioning mechanism and one of the fiber hinging points, to prevent vibration transfer between the sub-system and the chip. The electronic sub-system (Fig. 4-1 c) was situated beside the chip, while the photodiodes were connected through minimal length suspended flexible electronic strips, to prevent the vibration transfer between the sub-system and the chip. The flow-cell and mechanical positioning stages for the fiber and photodiodes (Fig. 4-1 d), were mounted on a heavy metal plate, situated on a partially filled air cushion, suspending them “in air”. 67

4.4 The Apparatus Fabrication

Fig. 4-3: The fabricated measurement apparatus. The solution delivery sub-system from which the desktop reservoir is pointed out. The electronic detection sub-system of which the circuitry boxes, photodiodes and power supply are pointed out. The Fluke DMM and laptop can be seen in the background. The suspended positioning stages and chip assembly is visible but requires a detailed view. Last, the optical sub-system of which the JDS HeNe laser is pointed out.

4.4.1 Fabrication issues explained in detail Fig. 4-3 shows an overview of the measurement apparatus. The fabrication choice for the different elements in the fluid delivery sub-systems merit further explanation, as well as a detailed view and explanation of the suspended chip and positioning stages assembly. 68

The solution delivery sub-system was designed using the “water tower” approach (Fig. 4-3) to avoid several problems. No air bubbles were introduced into the chip as these come out the top of the fluid in the reservoir. A thermal cup was used to maintain a constant solution temperature inside the reservoir. When the flow for solution delivery is turned on, no sudden shifts in pressure are created, and a controlled steady-state flow can be established. The top mounted solution reservoir was a thermal cup with two outlet nipples at its bottom, mounted on a desktop stand. The two outlets were positioned so the chip delivery outlet was slightly higher than the waste outlet. The waste outlet facilitated removal of solution residues when switching between solutions. The chip solution delivery tube was kept always open, and connects to the chip flow-cell via its inlet nipple (see Fig. 3-5 b). The flow and solution delivery rate were controlled through an adjustable valve situated on the chip evacuation tube. The flow rate was monitored by a flow-gauge situated after (under) the flow valve. The maximal measured flow (delivery) rate was ~ 130 ml/min. The suspended chip and positioning stages assembly was shown in (Fig. 4-4). The bare fiber end was placed in a bare-fiber holder (Newport FPH-J) on top of a multi-axis positioning stage (Newport 561D-XYZ), fitted with an additional YZ tilt plane (Newport M-561-TILT series). The sensing photodiode (Vsens_PD) was mounted on a short steel (resembling the FPH-J holder) rod, and placed on a 561D-XYZ supplemented by an YZ tilt plane manipulator. The chip (flow-cell) was harnessed into a custom made base, which was mounted on an YZ stage (Newport D561-YZ). The reference photodiode (Vref_PD) was mounted on a metal pole, with XYZ hinges, and

69

positioned facing the bare fiber end. The degrees of freedom enabled a flexible choice of a common lateral plane connecting the light source, device and sensing photodiode.

Fig. 4-4: A top view of the positioning stages and chip. The sensing photodiode is mounted on a Newport D561-XYZ stage, with a Newport M-561-TILT piece (referred to as ‘sensing photodiode & stage’). The laser fiber, in a Newport FPH-J bare fiber holder, was mounted on a 561D-XYZ stage, with an M-561-TILT piece (referred to as ‘laser coupling stage’). The Flow-cell was pinned to a custom made base, mounted on a Newport 561D-YZ stage (referred to as ‘flow-cell & stage’). The reference photodiode was mounted on an XYZ tilt pole, directed at the laser butcoupling area (referred to as ‘reference photodiode & pole’).

4.4.2 Measurement apparatus characterization Fig. 4-5 shows the chip and flow-cell in operation. The light, visible because of dissipation of modes from the initially overmoded waveguide, goes through a 900 bend. After the bend no modes escape from the device except from its PSW section in

70

the sensing arm, indicated by a faint light dot (Fig. 4-5 indicated by “PSW scattered light”).

Fig. 4-5: The SU8 device in action – TOP VIEW: the light is butt-coupled into the device (as indicated at the bottom left side), travels through a 900 bend (pointed out with an arrow, and referred to as a ’90 bend’) and enters the device. The small dot at the top-center of the figure (referred to as ‘PSW scattered light’), is due to the light that is dissipates from the PSW section of the device. Most of the light exits the device out the top of the figure.

A daylight indication of the light intensity, which emanates from the device and is detected by the appropriate photodiode, is visible in Fig. 4-6. The spot light is reflected (in a Lambertian manner) off a simple paper slip, pinned to the face of the photodiode. The PSW scattered light (indicated in Figs. 4-5 and 4-6), dissipates from the PSW ridge structure and is associated with Fresnel induced losses. The sensing photodiode (indicated by ‘sensing photodiode’ in Fig. 4-6), was positioned far from the device outlet, to enable a clear view of the light spot on the paper slip. This light spot is the light which exits the device and is measured.

71

Fig. 4-6: A daylight view of the chip and flow-cell, accentuating the light that is emitted from the device. The output light spot (indicated as ‘output’) is reflected off a piece of paper, pinned to the face of the sensing photodiode (indicated by ‘sensing photodiode’). The PSW scattered light is visible even under daylight conditions (indicated by ‘PSW scattered light’).

Fig. 4-7 shows a daylight top view of the chip and flow-cell. The devices and neighboring test structures (indicated in Fig. 3-5 a) are visible through the flow-cell cover. The PSW section of the measured device is indicated by ‘PSW scattered light’. The solution delivery tubes are connected to the flow-cell nipples. The four corners of the altar-like flow-cell cover (referred to as ‘altar’ and indicated with sequenced arrows), the matching base extrude screws and locking Teflon bolts, pin the chip down and free the RTV interface from the mechanical force of the fluids (under static conditions, a pressure of ~ 914 [N/m2]). The sensing photodiode is also indicated. The reddish area near the top left corner is the in-coupling area. The red color is caused by the scattered light from the fiber.

72

Fig. 4-7: A daylight top view of the chip and flow-cell. On the top left corner the fiber end is visible. The four corners of the altar-like flow-cell cover (referred to as ‘altar’ and indicated with sequenced arrows), the matching metal base extrude screws and locking Teflon bolts, pin the chip down and free the RTV interface from the mechanical force of the fluids. Indicated by ‘PSW scattered light’, is the investigated device with visible arms, and the slightly pale light spot from scattered from the PSW section. Adjacent test structures are also visible. The sensing photodiode is also indicated.

In short, the measurement apparatus involves multidisciplinary aspects, such as mechanical vibration critical damping (by suspending the sub-system connections), liquid solution flow control (maximal flow rate ~ 130 ml/min), light stability issues (maximal SNR level of ~ 17 dB), electro-optical detection (with a transfer function of: Vout ≅ 10 v ⋅

Vsens _ PD Vref _ PD

), compensating for the laser power fluctuations, and EMI reduction

(by grounding the backside of the apparatus table). Solution temperature was monitored using a single decimal point accuracy thermometer (Manhattan, USA).

73

5 EXPERIMENTAL RESULTS

Preliminary investigation of the relative influence of the PSW section throughput on the device output light intensity was necessary to ascertain its general functionality and its feasibility as a chemical/ biosensor. Then, verification of the theory was performed, and different types of solutions with various concentration levels were used to enable comparison between the unbalanced PSW-MZI and previously reported devices. Finally, its feasibility as a biosensor was investigated through emulation of biomaterials.

5.1 Unbalanced PSW-MZI general functionality investigation

The device general functionality test was based on using a 632.8nm light absorbing solution, which absorbs the light in the PSW section voids in the sensing arm, and has minimal effect on the reference arm. To this end, a water based solution containing blue #1 industrial food color was chosen. A preliminary test showed that no light emission from the PSW section (i.e., ‘PSW scattered light’ and not output light) when using this solution, while the output light intensity was decreased. Since PSW scattered light was observed when using other investigated solutions (e.g., Glucose and Sucrose) it is safe to assume that it absorbs the 632.8nm light completely, when using it at a concentration level of ~ 10 [Wt%] (higher concentrations do not influence the output). The food color was found to behave as a contaminant (attaches well to the 74

solution reservoir plastic sidewalls). For each 150 ml of blue #1 solution, five doses of deionized water (DW), 200 ml each, were fed into the solution reservoir successively. Each dose filled the reservoir to a certain level which dropped continuously because of steady-state flow, and when reaching a predefined low level in the reservoir, the next dose was fed into the reservoir, refilling it again. This procedure was established using complete signal recovery as an indicator. Similar tests using Glucose and Sucrose solutions of various concentrations, showed good signal recovery when using a single

Voltage [V]

dose of 200 ml of DW, after any 150 ml of the investigated solutions.

3.6 3.4 3.2 3.0 2.8 2.6 2.4 2.2 2.0 1.8 1.6 1.4 1.2 1.0 0.8 0.6 0.4 0.2 0.0 0

200

400

600

800

1000

1200

1400

Time [sec] Fig. 5-1: The raw data of the feasibility test. The first and last 30 seconds represent a state where the laser light was shut off. There are two cycles of DW-Blue #1-DW sequential solutions. The gradual signal recovery can be clearly seen.

75

When in the PSW-FPI regime (which is effective outside the stop bands), the predicted theoretical output intensity for DW is ~ 72% (at 25.40C) of the input light intensity, while a value of ~ 50% of the input intensity is predicted for the blue #1, assuming it absorbs the laser light in the PSW section of the sensing arm, effectively leaving only the power from the reference arm to be detected. The corresponding voltage change, measured between the two states, is ΔV ~ 0.8 [V], for a signal of ~ 2.75V. Since the raw data is noisy, the Savitzky-Golay (SG) smoothing method was adopted and applied as a preliminary stage in analyzing the measured data [64,65]. The SG was specially tailored for analysis of noisy measurements (originally for spectroscopic measurements) as a noise filter. Fig. 5-2 shows a higher resolution view at the blue #1 food color experiment measured signal. The gradual signal recovery, due to the food color reservoir contamination is discernable through the signal staircase recovery, using five doses of DW.

76

3.7 3.6 3.5

Voltage [V]

3.4

DW

DW

3.3

DW Blue #1

3.2 3.1 3.0 2.9 2.8 2.7 2.6

0

200

400

600

800

1000

1200

Time [sec] Fig. 5-2: A higher resolution view of the DW→blue #1→DW→blue #1→DW, sequential solution feasibility experiment. The staircase signal recovery is due to five doses of DW, following each blue #1 dose. The voltage change is of 0.8V, for a signal of ~ 2.75V, at a temperature of 25.4C.

Here, the solution sequence was DW → Blue #1 → DW → Blue #1 → DW, using 200 ml dosage impact refill of the solution reservoir. The Blue #1was introduced in two doses of 150ml each. For DW, at 25.40C, the predicted attenuation per PSW cycle was ~ -0.0721 dB and a 48 cycle overall attenuation of ~ -3.46 dB, meaning more than half the light intensity introduced into the PSW section was lost to scattering (calculated as the ‘worst case’ attenuation), yielding a change of 22.5% in the predicted output intensity. Translated into measured intensity, when using deionized water (DW) and blue #1 food color (100% attenuation of the light input into the sensing arm) alternatively, the predicted 22.5% intensity change, measured as a voltage change of 77

0.8V (the ratio of the voltage change to the base signal ~ 2.75V yields the same percentage as predicted). In our case, the blue #1 was used to disable the influence of the sensing arm. If an investigated solution absorbs the laser light significantly, a complex attenuation coefficient should be amended into the theory, to account for it. The next step was to ascertain the device sensitivity to refractive index changes (RIC), and the range for which it behaves as a viable biosensor. The use of Glucose based solution, served in previously reported devices [14,30] to prove biosensor functionalities. Thus, a series of Glucose based solutions, with varied concentrations were used. All the results were first denoised (noise was stripped out) using the Savitzky-Golay smoothing filter.

5.2 Glucose solution series measurements

The Glucose solution concentrations were of: 1.25 Wt%, 2.5 Wt%, 5 Wt%, and 10 Wt% (‘Dextrose’ for IV injection, TEVA medical, Israel). The outlined measurement procedure was applied using Glucose solutions. Each measurement was performed by successive introduction of alternated DW 150 ml doses (acting as buffers between solution measurements), and a single series of four varied concentration solution doses (150 ml each). In short, such a sequence can be described by: DW→Glucose1→DW→Glucose2→DW→ Glucose 3→DW→ Glucose 4→DW.

Here the subscript (y) refers to different solution concentrations in Wt%. To

obtain measurement robustness, each measurement series was repeated for ten times. Statistical variation was found negligible for higher number of measurements. 78

Fig. 5-3 shows a typical raw data measurement of a Glucose solution series. The first and last ~ 30 secs, the laser shutter was off (no light was fed into the apparatus). The elevated average voltage, compared to that of DW values in Fig. 5-2, is due to realignment of the experimental setup.

4.5 4.0

Voltage [V]

3.5 3.0 2.5 2.0 1.5 1.0 0.5 0.0

Glucose

0

100

200

300

400

500

Time [sec] Fig. 5-3: A typical raw data measurement of a Glucose solution series superimposed, for brevity. The first and last ~ 30 seconds the laser shutter was off.

A close-up on the measurement values reveals several phenomena. The first is the slow (~ 6 secs) transients, when switching to and from the solutions and DW. The second is the presence of drift despite our efforts to reduce it (Fig. 5-4).

79

4.30 4.25

Voltage [V]

4.20 4.15 4.10 4.05 4.00 3.95 3.90 Glucose

3.85 100

200

300

400

500

Time [sec]

Fig. 5-4: A close-up on the measured values for the Glucose solution series, reveals slow (~ 6 secs) transients when switching between DW and a solution. Also, a general drift in the measurement values is observed.

Flow-rate experiments show that the most plausible explanation for slow transients is a differential rate of solution interchange in the PSW section itself. This means that upon introduction of different solutions into the flow-cell, the PSW section if initially still filled with the former solution. A double mirror effect is generated, in which a progressing part of the PSW is gradually filled with the new solution. It is safe to assume that the central part of the PSW exchanges the solution, while separating the internal reflections in the PSW into three adjacent flow regions. The PSW start and end regions, where the solution exchange is slower due to the flow local regime, and the middle region of the PSW where the flow and exchange are faster. The progressive exchange leads to eventual total exchange of the solutions in the PSW and stabilization 80

of the DC measured value for the specific solution at a specific temperature. Further studies, using more viscous solutions (Sucrose based solutions of ~ 64 Wt% concentrations –referred to further on), reveal slower transients, which reaffirm this explanation. Analysis and data extraction of the DC measured values, from the already Savitzky-Golay denoised (filtered) data, necessitates computing and subtracting a baseline, relaying on the DW measured values only. This means that the transient boundaries should be defined, and only the ‘DC’ data taken into account. The same applies to the solutions themselves. A 9th order polynomial function is fitted to the DW measured DC values (transient truncated), and subtracted from the whole data. This process was dubbed ‘baselining’.

4.45 4.40 4.35

Voltage [V]

4.30 4.25 4.20 4.15 4.10 4.05 4.00 3.95

Glucose

3.90 100

200

300

400

500

Time [sec]

Fig. 5-5: The ‘Baselined’ measured data for typical Glucose solution series measurements. The baseline is generated by using a 9th order polynomial, fitted to the DW segments only.

81

Fig. 5-5 show the close-up view of the ‘baselined’ data from the typical Glucose solution series experiments. Similar observations (drift and transients) for a similar experimental procedure were reported by Prieto et al. [30]. This type of data manipulation eliminates the measurement drift, while conserving the fluctuations and transients from the raw data. The next step was averaging the value for each measured solution (Fig. 5-6), extracting it from the DC measured values (transient truncated). Each of the averages was based on ~ 60 consecutive measured points, so that the standard deviation of the averaged values was low (typically ~ 2mV – 5mV, which corresponds to the measurement noise level).

4.45 4.40 4.35

Voltage [V]

4.30 4.25 4.20 4.15 4.10 4.05 4.00 3.95

Glucose

3.90 100

200

300

400

500

Time [sec]

Fig. 5-6: The Average value of the measured Glucose solution series. The transients were unaltered after baselining the data. The DW measured values are of identical value in each of the measured instances. Each averaging segment is based on ~ 60 measured points, which usually yields a small standard deviation.

82

Up to now, that data extraction was not treated relative to the refractive index of the different solutions, which leaves it temperature dependent. Using semiempirical equation 32 in chapter 1, an accurate evaluation of the different solutions RI was made and is given in Table 1.

Table 1: Glucose solutions, refractive index of the as a function of concentration [Wt%] at a temperature of 25.5C, and for a wavelength of 632.8nm.

Refractive index as a function of concentration [Wt%] @ 25.5C, 632.8nm No.

Refractive index

Glucose concentration

1

1.333685

1.25

2

1.335185

2.5

3

1.339386

5

4

1.346831

10

Each measured solution was assigned a single averaged value, enabling its reference to a single refractive index value, depending on the measurement temperature (Fig. 5-7). Robustness was achieved by assigning to adjacent points artificially, by taking an error margin of +/- 0.250C, for each measured point, although the temperature scale is of 0.10C accuracy. Most of the measurements were done at exactly the same temperature (25.50C), and exhibited a drift of 0.20C to 0.30C. Fig. 5-7 shows the different concentrations of the Glucose solutions, where the numbers beside each data point correspond to that which is stated in Table 1. The

83

lateral ‘thickness’ of the points is due to the temperature fluctuation RI error margins.

Normalized Output [%]

The vertical error bars correspond to the measurement noise.

75.0 74.8 4 74.6 74.4 74.2 74.0 73.8 73.6 73.4 3 73.2 73.0 72.8 1 2 72.6 72.4 Glucose 72.2 72.0 1.332 1.334 1.336 1.338 1.340 1.342 1.344 1.346 1.348

nSample Fig. 5-7: The averaged values for the measured Glucose solution series. The lateral thickness of the points is due to the temperature dependent RI error margins of +/- 0.25C. The measurement noise was normalized with the data, and appears as the Y error bars.

Normalized values were achieved by using a fitting expression: I % ≡ (10 ⋅

Vsens _ PD Vref _ PD

− b fit ) ⋅ a fit

(42)

Here, Vsens_PD and Vref_PD are the measured photodiodes (Chapter 4), and correspond to the voltage divider output function. The gauge factor afit and offset factor bfit are mandatory for compensating the alignment and butt-coupling efficiency dependencies. 84

The normalized measured intensity is represented by I% and is in percentage of the maximal output light intensity [%]. The resulting gauge coefficients for the Glucose solutions were: afit = 15 and bfit = -1.192. Justification for these coefficients is presented in chapter 6. The next stage was an examination of the PSW-FPI feasibility as a biosensor. It was done by using concentrated Sucrose solutions which emulate the reported refractive index for Avidin-Biotine reactions [12], as well as a range of biological materials such as DNA segments in solution [27].

5.3 Sucrose solution series experiments

Thus, a batch of six Sucrose based solutions, of varied concentrations, was ordered. The solution concentrations were: 63.5 Wt%, 63.6 Wt%, 63.7 Wt%, 63.8 Wt%, 63.9 Wt% and 64 Wt%. These solutions emulate the reported refractive index values (n ~ 1.45) of Avidin-Biotine reactions [12]. Again a series of ten repetitive experiments, each of successive measurement for the six Sucrose solutions, was made.

Table 2 shows the solution refractive index as at a specific temperature and for a specific wavelength. Again, RI error margins were taken to be +/- 0.25C, for a temperature scale accuracy of 0.1C. The temperature in this series of measurements was 19.90C, to maintain the Sucrose solubility in the concentrated solutions.

85

Table 2: Sucrose solutions, refractive index as a function of concentration [Wt%], at a temperature of 19.9C, and for a wavelength of 632.8nm.

Refractive index as a function of concentration [Wt%] @ 19.9C, 632.8nm No.

Refractive index

Sucrose concentration

1

1.449528

63.5

2

1.44976

63.6

3

1.449992

63.7

4

1.450224

63.8

5

1.450457

63.9

6

1.450689

64

Fig. 5-8 Shows the Savitzky-Golay smoothed measured data. The transients are slower (~ 23 secs) here than those observed in for the Glucose solutions. Using the same data extraction procedure, refractive index values were assigned to the specific Sucrose solutions (Fig. 5-8). Error margins were assigned both by assigning temperature fluctuation margins, and by scaling the measurement noise with the measured data. The concentrations in Table 2 correspond to the marked solutions in Fig. 5-8. The higher measured values, for these solutions, indicate higher PSW throughput value, which also correspond to decreased levels of light scattering from the PSW section of the PSW-FPI. Due to realignment of the measurement setup, the resulting gauge coefficients for the Sucrose solutions were afit = 8.5 and bfit = -5.96. Justification for these coefficients is presented in chapter 6.

86

90.2

Normalized Output [%]

6 90.0

3

1

4

89.8

5 2

89.6

89.4 Sucrose

89.2

1.4495

1.4500

1.4505

1.4510

nSample Fig. 5-8: The Sucrose solution series, refractive index assigned, measured values. Higher measured values correspond to higher throughput of the PSW section in the PSW-FPI.

In short, the measurement procedure, and data interpretation were addressed. Robustness was achieved by taking into account error margins, which for the temperature are well beyond the observed fluctuations. The measurement noise was used as the error margin of the measured values. Translation of the measured values to normalized values (%) was presented and is discussed in the next chapter.

87

6 DISCUSSION

So far, the functionality of the unbalanced PSW-MZI was investigated, in terms of its reaction to dilute Glucose solutions and concentrated Sucrose solutions of varied refractive indices. No reference was made to the degree of agreement between the theory of PSW-FPI and the measurements.

6.1 PSW-FPI theory and the measured solutions

76

Normalized Output [%]

74

1

3

2

4

72 70 68 66 64 62 Theory Glucose -measured

60 58

1.334 1.336 1.338 1.340 1.342 1.344 1.346

nSample Fig. 6-1: The PSW-FPI theory superimposed on the normalized measured Glucose solutions. The error margins are smaller than the point marks.

88

Fig. 6-1 shows the PSW-FPI theory superimposed on the normalized values of the measured Glucose solutions, presented in the previous chapter. The error margins are smaller than the point marks, in this scale. The sensitivity of the PSW-FPI is determined by the minimal measurable interval between two adjacent measurements. Fig. 6-2 shows two adjacent points separated by the measurement noise and temperature fluctuation margins. The refractive index difference between two such points determines the sensitivity of the device while acting as a PSW-FPI. Here, the smaller scale enables clear view of the error margins. The resulting minimal measured RIC (PSW-FPI sensitivity) is ~ 4·10-5.

Normalized Output [%]

73.00

Theory Minimal measurable RIC

72.75

72.50

72.25 -5

RIC ~ 4*10

72.00 1.33350 1.33375 1.33400 1.33425 1.33450 1.33475 1.33500

nSample Fig. 6-2: Determination of the sensitivity of the device, acting as a PSW-FPI, using the error margins for the measurement setup noise and the temperature fluctuations. The sensitivity is determined by the minimal RIC value of two separately measurable RI values, and is ~ 4·10-5.

89

A similar fitting session, as was applied to the normalized measurement values of the Sucrose solutions, superimposed on the PSW-FPI theory. Fig. 6-3 shows the superimposed theory and normalized measured Sucrose values.

90.2

Normalized Output [%]

90.1

6

90.0 89.9

3

1

89.8

4 5

89.7 89.6

2

89.5 89.4

Theory Sucrose -measured

89.3 89.2

1.4490

1.4495

1.4500

1.4505

1.4510

1.4515

nSample Fig. 6-3: The PSW-FPI theory, superimposed on the Sucrose measured values. Although the noise level in these measurements is higher, the agreement to theory is apparent.

The measurements of the Sucrose solutions and their agreement with theory, validate the PSW-FPI capabilities as a biosensor.

90

6.2 PSW-FPI to PSW-MZI transition

Fig. 6-4 shows a close-up of the superimposed PSW-FPI and PSW-MZI theories. The hypothesis is that for refractive indices in the stop-band region, most guided modes are attenuated to < 1% of the guided power in the PSW arm. This leads to a quasi-single mode behavior and subsequent PSW-MZI behavior of the device.

85 80

PSW.MZI PSW.FPI

75

Iout [%]

70 65 60 55 50 45 40 35

1.34

1.35

1.36

1.37

nSample Fig. 6-4: A close-up of the superimposed PSW-MZI and PSW-FPI theories. If the modal attenuation of the PSW section does create conditions for quasi-single mode operation, the light attenuation should be clearly visible.

91

To this end, the modal power distribution of the modes, coupled into the device, was measured. Measuring the modal power distribution was done using lateral linescanning of the laser beam profile. Since this was done manually, sampling arguments and aliasing issues had to be addressed. The line-scan was done by lateral displacement of a pinhole (~ 0.1 mm in diameter), across a centerline of the laser beam spot. An optimum number of sampling points had to be computed to gain as much data as possible (Shannon sampling theorem) without obtaining overlapping data (aliasing)

1.5 1.4 1.3 1.2 1.1 1.0 0.9 0.8 0.7 0.6 0.5 0.4 0.3 0.2 0.1 0.0

Volt Gaussian beam profile

6 5 4 3 2 1

-5

-4

-3

-2

-1

0

1

2

3

4

5

Normalized Intensity [%]

Measured Signal [V]

of neighbor sampling points [67,68].

0

Displacement [mm] Fig. 6-5: A lateral displacement line-scanned beam profile, presented both by measured signal and by normalized intensity.

Fig. 6-5 shows the modal power distribution as measured and its Gaussian profile fitting curve. The fundamental mode does not exceed 6% of the normalized 92

power, coupled into the device. The modal power, after transition through the PSW section of the sensing arm, was calculated for multiple points (Fig. 6-6), which indicate that aside from the stop-band regions, the power distribution stays Gaussianlike. Since a multimode Gaussian beam exhibits spherical phase shifts, the device is expected to behave as a PSW-FPI. This leaves the stop band regions, where only a few fundamental modes retain power over 1% of the incident intensity, as regions where a PSW-MZI behavior may be observed.

3.0

Intensity [%]

2.5 Sample RI 1.333 1.335 1.337 1.339 1.341 1.343 1.345 1.347 1.338 1.34

2.0 1.5 1.0 0.5 0.0

0

10

20

30

40

50

60

Mode number Fig. 6-6: A modal power profile calculation for the light emerging from the PSW section of the device sensing arm. The potential transition from PSW-FPI to a PSW-MZI behavior is proposed only in the stop band regions, where most of the modes are attenuated below 1% of the overall power. The two values inside the stop band are marked by dashed line values (‘---’), instead of the solid line (‘―’).

93

The first of the stop band regions leaves ~ 5 fundamental modes out of the initial 1.99·104, which still carry over 1% of the input light intensity. Fig. 6-7 shows a return visit to the Glucose solutions, revealing a single solution, measured in the first stop-band region. The peak output is expected to be ~ 60% for a PSW-MZI behavior, while the peak output for the PSW-FPI behavior, in the stop band region, is expected to be ~ 73%.

75

Normalized Output [%]

70

PSW-MZI PSW-FPI Glucose

65 60 55 50 45 40 35

1.337

1.338

1.339

1.340

1.341

1.342

1.343

nSample Fig. 6-7: A revisit to the Glucose solution which was measured to asses the possibility of a PSW-MZI behavior of the device, in the stop band regions. The device maintains a PSW-FPI behavior.

The normalized measured value of the single Glucose solution, reveal a PSWFPI behavior in the range of the PSW-FPI predicted 73% output, which proves that the device behaves consistently as a PSW-FPI. 94

6.3 Unbalanced PSW-MZI sensitivity and sensing length

A continuous PSW-FPI behavior of the unbalanced PSW-MZI for the different solution concentrations and measurement conditions has been established. Next, the measured and theoretical sensitivity limit values of the unbalanced PSW-MZI are compared to previously reported devices as a function of their required sensing length.

Sensitivity Limit [δnmin]

-4

10

Kunz et al.

unbalanced PSW-MZI -measured

Liu et al.

Brosinger et al. Weissman et al.

-5

10

Prieto et al.

-6

10

unbalanced PSW-MZI -Sensitivity limit criterion

-7

10

0

2

4

6

8

10

12

14

16

18

20

Sensing area length [mm] Fig. 6-8: A revisit to the sensing length vs. sensitivity limit relations. The previously reported devices are marked by author and (‘◊’), while the sensitivity limit criterion and minimal measurable value of the unbalanced PSW-MZI are marked by (‘●’) and (‘♦’), respectively.

Fig. 6-8 shows the sensitivity limits for the unbalanced PSW-MZI (theoretical and measured) and previously reported devices as a function of their required sensing 95

length. Although the measured value indicates poorer sensitivity than the device reported by Prieto et al [30], it is worth noting that in both cases the sensitivity limit reported was estimated by the authors and does not represent the actual measured data. Thus, when addressing the results reported by Kunz et al. [51,52], Brosinger et al. [12], Weissman et al. [15,16] and Liu et al. [14], the measured value of the PSW-FPI falls in the same ballpark, while requiring a much shorter sensing length. As far as the measurement apparatus signal-to-noise ratio (SNR), remembering that the sensitivity limit criterion was established for 50dB, the resulting overall SNR of the measurement apparatus (a noise level of ~ 4.6 mV for a signal level of ~ 3.55V) was ~ 29 dB. In short, the PSW-FPI theory was in good agreement with the measured results. The expected transition in behavior of the device from a ‘PSW-FPI’ to ‘PSW-MZI’ was investigated and is found to be non existent under the investigated stop band conditions (i.e., quasi-single mode conditions). The unbalanced PSW-MZI was shown to be effective as a biosensor (refractive index range of ~ 1.333 – 1.45). The measured minimal sensitivity value (detectible Δn) was 4·10-5. The overall SNR was found to be ~ 29 dB. A compact PSW-FPI can be easily constructed from a 900 L-bend (~ 4mm) and a PSW section (720μm) and waveguide inlet/outlet extensions (~ 140μm each), which lead to an overall length of ~ 5 mm (much smaller than the sensing lengths of any reported devices).

96

7 SUMMARY AND CONCLUSIONS

7.1 Summary

In this work bulk material sensing, using a large cross section unbalanced PSWMZI, for chemical / bio- sensing was investigated. The PSW-FPI predicted behavior regime was observed, while the predicted transition to PSW-MZI behavior regime in the stop band regions was found not to take place. However, a sensitivity limit of the device, acting as a PSW-FPI, was found to be δnmin = 4·10-5. The device is easy to fabricate, the light throughput is large, due to the use of a large waveguide cross section, and is insensitive to light polarization due to its nearly square shaped cross section. The theories of unbalanced PSW-MZI and PSW-FPI were presented, and a sensitivity limit criterion [19] was explained and applied. Design arguments, applicable to integrated optical devices and the fabrication process, were explained in detail. Various aspects concerning the measurement method were addressed, such as the various noise sources (optical, electronic and mechanical), and the DC measurement drift phenomenon. The different sub-systems of the measurement apparatus were addressed, from explaining the motivation for using each one, to the inherent problems and how to circumvent or reduce their influence on the apparatus performance.

97

The investigation was done by using Glucose and Sucrose based solutions of various concentrations. The measurement results show good agreement with the presented theory of the PSW-FPI. The sensitivity limit (δnmin = 4·10-5) of low SNR (29 dB) measurement system was found to be compatible with previously reported biosensing devices. This sensitivity is achieved for a significantly shorter required sensing length, which enables future downscaling of the device. The use of large cross section made light in-coupling easy, and relaxed the fabrication tolerances to surface defects. In addition, it enabled enhanced interaction with the sample per PSW void, retaining a small required sample volume (~ 2.7 nl, for 48 PSW cycles).

7.2 Future trends

Since the device behavior, was found to be continuously of a PSW-FPI nature (including the stop band regions), the use of a Y-branch structure, in which one arm is periodically segmented and the other serves as a reference to the laser source power fluctuations, is most advantageous. It not only simplifies the geometry of the device, but also downscaling. Its only drawback is its stop band regions in which careful design may lead to closing of the stop bands or translation outside the required RI range for chemical/bio- sensing (discussed in chapter 1). Another possibility is improving the range of performance by using large cross section single mode waveguide profile [30,66], or an anti-reflection-resonantwaveguide (ARROW) structure [67,68], for construction of a single mode PSW-MZI biosensor. The later method (ARROW) is easier to implement, as it does not 98

complicate the fabrication process as much as the large cross section single mode profile does. Improved measurement apparatus SNR, and temperature control will yield better results as far as sensitivity limit is concerned, even when using the present unbalanced PSW-MZI device. Improved SNR can be achieved by using a heterodyne measurement approach (modulated light source and frequency band limited detection) in which the source is modulated by a frequency in the KHz region, and the signal detection is done only for the corresponding frequency range. As most noise relates to low frequencies, the SNR is expected to be inherently better. The integration of a thermoelectric chiller, and a heater into the measurement apparatus base will enable the desired temperature control and stabilization. When addressing multimode structures (using large cross section waveguide structures), an entirely different approach can be adopted. Instead of fabricating a very sensitive structure (PSW-MZI/ PSW-FPI), and trying to stabilize its output signal, one can take a 1x2 MMI directional coupler [69,70,71] (1 inlet by 2 outlets multimode interference directional coupler) and try to sensitize it to biomaterials. Based on selfimaging rather than classical interference, it is geometrically simple, and comprises fewer optical elements than the present device. Its basic operation involves light introduction via the single input port, into the MMI chamber, which is constructed so two output ports receive half of the light intensity each. It has two output ports which can be measured separately or differentially.

99

List of abbreviations

Acronyms Acronym

Description

BPM

Beam propagation method

CAD

Computer aided design

CCD

Charge coupled device

CW

Continuous wave

DC

Direct current. Generalized, it refers to any type of detected phenomenon in which the phenomenon and/ or detection regimes are continuous, and fluctuations happen slowly

DMM

Digital multimeter (the common name for the new AVO meters)

EFPI

Extrinsic Fabry-Perot interferometer

EIM

Effective index method

EMI

Electromagnetic interference. The influence of externally induced electromagnetic waves on the investigated system. One of the peskiest sources is the electrical network (~ 50 Hz in Israel). The alternating current in the room walls “echo off” inside the room and influence electronic equipment inside it.

FC/PC

Flat faced connector/ Polished. A type of optical fiber connection, in common use for single mode fibers

IL

Insertion loss

LPF

Low pass filter. A filter which is designed to block signals with a frequency which is higher than its pre-designed “knee” frequency

MM

Multi mode

MMI

Multimode interference

MZI

Mach-Zehnder Interferometer

100

PBG

Photonic band gap

PCR

Polymerase chain reaction

PDL

Polarization dependent loss

PMW

Periodically modulated waveguide

PSW

Periodically segmented waveguide

PSW-FPI

Periodically segmented waveguide Fabry-Perot Interferometer

PSW-MZI

Periodically segmented waveguide Mach-Zehnder Interferometer

RI

Refractive index

RIC

Refractive index change

RID

Refractive index difference

RPM

Rounds per minute

SNR

Signal-to-noise ratio. The common term to asses a device/ apparatus sensitivity to changes and its detectability

TIR

Total internal reflection.

Chemicals Acronym

Description

Blue # 1

The commercial name for a food color (Chemical name: disodium 3,3'-dioxo-2,2'-bi-indolylidene-5,5'-disulphonate).

DW

Deionized water. Water which were strip of their radical ion contaminants (Such as Calcium ions, etc.)

EC

SU8 developer. 2-Methyloxy-1-Methylethyl Acetate.

Glucose

Simple sugar – C6H12O6

(Dextrose) RTV

Room temperature vulcanizing (setting) Silicon sealant

SU8

A commercial name for a negative UV formable photoepoxy

Sucrose

The cane sugar - C12H22O12

101

Physical Quantities

Quantity

Description

a2, a4

Fourier series coefficients

afit, bfit

The fitting coefficients for the adaptation of the functional and dysfunctional theories to measured data

amin

The minimal waveguide width [μm]

AT

The right angle bend attenuation coefficient [dB]

a, b

The ridge waveguide width and height [μm]

asugar, bsugar

The coefficients for the sugar solution refractive index calculation expression.

A(x), Bν(x)

amplitude distribution of the source output, and the waveguide modal amplitude distribution

C c

the solution base material concentration [Wt%] 2

x , E pqy E pq

Power reflection factor per cycle [fractional] Hybrid mode determination according to the nonzero electric field

h

The S-bend displacement [μm]

Imin, Imax

The minimal and maximal intensities, derivable from the MachZehnder interferometer [%]

Iout

The Mach-Zehnder Interferometer (MZI) output intensity [%]

I%

The normalized measured intensity [%]

k0

The wavenumber in air

k

The wave vector

k y , kz , k

Propagation constant, and wave vector components

kq

The modal spacing in a slab waveguide [m-1]

L

The S-bend length [μm]

l s, l v

The ‘step’ and ‘void’ lengths in a PSW cycle [μm]

102

x n1−5 , neff , n x , n632 .8 nm

Refractive indices, where x represents different materials

nf

The fiber core refractive index

np

The refractive index of a prism

N

The number of PSW cycles

r

Fresnel field reflection coefficient [fractional]

r1

Field reflection per PSW cycle [fractional]

RN

The cumulative power reflection expression [fractional]

x Rmin , Rmin , Rbend

The minimal bend radii, where x stands for the different formalisms [μm]

T, Tx

Transmittance function/ expression. The x stands for sensing arm or reference arm relations [fractional]

tg

The grating depth [μm]

V

The normalized frequency of guided modes

Vout

The voltage divider measured output

Vsens_PD, Vref_PD

The sensing photodiode and reference photodiode signals [V], respectively

V pol ,Vcoh ,VT ,V f

The Mach-Zehnder visibility factor and sub-factors

w

The coupled beam waste diameter [μm]

y(z)

The S-bend numerical curve expression

βcutoff

The boundary value for guided modes

β, βm

The propagation constant and modal propagation constant, respectively

Γ

The figure of merit for PSW duty cycle [fractional]

δ

The axial offset between waveguide bent elements, for minimal loss [μm]

x δnmin

The minimal detectible RIC. The x stands for functional/ dysfunctional theory. If there is only subscript, it pertains to the specific reported value from a specific source

Δ

the skin depth penetration distance [μm]

103

Δn

The refractive index difference (RID)

ΔV

The measured voltage swing due to RID between solutions [V]

ηm

The modal intensity decay distance

ηx-y, ηx-y(ν)

Coupling efficiency, and modal coupling coefficients. The x and y stand for the abbreviated coupling methods

Θ

The interference factor for unbalanced PSW-MZI [Rad.]

θC

The Snell’s law critical angle [Rad.]

θμ

The modal angle of reflection [Rad.]

θi

Total internal reflection incident angle [Rad.]

θm

A prism coupling incident angle [Rad.]

θr

The recline angle [Rad.]

κ

The dispersion relation factor

κprism

The coupling coefficient for prism coupling

λ

Wavelength in air [nm]

Λ

The PSW cycle length [μm]

ν

Mode number indicator

νm

The total number of modes for a slab waveguide

νxy

The total number of modes in a rectangular cross section ridge waveguide

ξ3

The electric field “tail”, declining outside the waveguide boundaries [μm]

φcore, φclad

The fiber core and clad diameters [μm]

φf

The fiber core diameter [μm]

φ, φ0, φs, φv

Phase, relative phase, or partial cumulative phase [Rad.]

Δφ

The phase difference between the sensing and reference arms of the MZI [Rad.]

Ψ

The cumulative attenuation Fresnel loss expression [dB]

104

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‫תקציר‬ ‫בעבודה זו נחקרה אפשרות למימוש אינטרפרומטר מאך‪-‬זנדר מבותר מחזורית )אמזמ"מ(‪ ,‬המיועד‬ ‫לשימוש כחישן כימי ‪ /‬ביולוגי‪.‬ההתקן תוכנן לעבור בין שני סוגי התנהגות‪ .‬ההתקן אמור לתפקד‬ ‫כאינטרפרומטר פברי‪-‬פרוט מבותר מחזורית )אפפמ"מ(‪ ,‬ולעבור לתפקוד כאמזמ"מ חליפות‪ .‬קריטריון‬ ‫הרגישות המינימאלית מיושם להערכת רגישות ההתקן מתוך הניתוח התיאורטי‪ .‬כללי תכנון לאלמנטים‬ ‫בהתקנים אופטיים מוכללים ותהליכי ייצור התקנים כאלה מובאים בהרחבה‪ .‬בעבודה התייחסות לשיטת‬ ‫גילוי תוצא ההתקן וטיפול בנושאים כגון מקורות רעש )אופטיים אלקטרוניים ומכאניים(‪ .‬שימוש‬ ‫בתמיסות גלוקוזה וסוכרוז‪ ,‬בריכוזים שונים‪,‬מעיד על רגישות ההתקן ומראה התאמה טובה בין הערכים‬ ‫המדודים ותיאורית אפפמ"מ‪ .‬הרגישות המינימאלית של ההתקן נמדדה כ‪ , δn = 4·10-5 -‬ודומה‬ ‫לרגישויות שנמדדו בהתקני חישה ביולוגית אופטיים בעבר )‪ .(2·10-5 – 5·10-5‬היתרון המרכזי של ההתקן‬ ‫נעוץ בהיותו קצר בהרבה מההתקנים האחרים‪ ,‬המאפשר ייצור עתידי של התקנים ממוזערים‪ .‬שימוש ב‪-‬‬ ‫‪ SU8‬פוטואפוקסי‪ ,‬כחומר ממנו עשוי ההתקן‪,‬מפשט ומוריד את מחיר ייצור ההתקן‪ .‬חתך הרוחב המרובה‬ ‫אופנים‪ ,‬מאפשרת צימוד אור קל )הפחתת איבודי‪-‬צימוד(‪ ,‬מפשטת את יישור וכיוון המערך‪ ,‬וגורמת‬ ‫לחוסר רגישות לקיטוב האור )הפחתת איבודים עקב אי‪-‬תאימות קיטוב(‪.‬‬

‫העבודה בוצעה בהנחיית פרופסור מנחם נתן‪.‬‬

‫אוניברסיטת תל‪-‬אביב‬ ‫הפקולטה להנדסה ע"ש איבי ואלדר פליישמ‬ ‫המחלקה להנדסת אלקטרוניקה – אלקטרוניקה פיסיקלית‬

‫חיבור בנושא‬

‫חקר חישת חומר על‪-‬ידי שימוש באינטרפרומטר מאך‪-‬‬ ‫זנדר מבותר מחזורית לצורכי חישה כימית\ביולוגית‬ ‫החיבור מוגש לשם קבלת תואר "דוקטור לפילוסופיה"‬ ‫ע"י‬ ‫נועם כנרות‬

‫יוני ‪2005‬‬