This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

This thesis describes work carried out on the research, development and implementation of new processes for the fabrication of surface plasmon waveguide biosensors. Fabrication of surface plasmon resonance (SPR) based waveguides embedded in a thick CYTOP cladding with the incorporation of fluidic channels was achieved with improved quality and operability compared to previous attempts. The fabrication flow was modified in key areas including lithography for feature definition, gold evaporation and the upper cladding deposition procedure. The combined result yielded devices with sharper resolution of waveguides, gold surfaces with minimal aberrations, reduced surface roughness and minimization of waveguide deformation due to reduction of solvent diffusion into the lower cladding. The fabricated waveguides consisted of a thin, 35 nm, patterned gold film, embedded in a thick, 18 µm, CYTOP fluoroploymer cladding. The gold devices were exposed by O2 plasma etching through the upper cladding to form fluidic channels for the facilitation of flow of an index matched sensing medium. Optical and physical characterization of devices revealed structures of significantly improved quality over previous attempts, rendering the platform competitive for biosensing applications.

Electrowetting is an electromechanical response that can be used to change the equilibrium shape of droplets on a surface through the application of an electric potential. By applying this potential asymmetrically to a droplet, the droplet can be moved. Typical electrowetting devices use an electrode covered by a dielectric to reduce electrochemical interactions. Successful electrowetting requires electrodes and dielectric layers that can resist damage through many cycles of voltage. Continuous Electrowetting (CEW) is performed on high resistivity silicon wafers. In this process, when an electric potential difference is applied between the substrate ends, the droplet on the substrate moves towards the side with positive voltage. The diode behavior of consecutive metallic spots, placed in the oxide layer, is the root of the droplet movement. This thesis investigates electrode, dielectric, and electrolyte material combinations that can achieve long stable performance with a particular emphasis on continuous electrowetting. Incorporation of diodes can also improve standard EW conditions to achieve lower voltage operation. In passivating systems, a reverse biased electrode becomes electrochemically passive. This way we have performed low voltage and reliable Electrowetting on Dielectric (EWOD) for 5000 test cycles. This is while, in non-passivating systems, EWOD degrades significantly from the first cycles. In CEW devices, SiO2 can also serve as a steady dielectric. It is observed that, with larger electrolytes, contact angle change would remain consistent for 10000 cycles with less than 19% degradation, while would be as high as 47% with small electrolytes. In CEW device, consistent and ideal behavior of electrochemical diodes is expected. Even though diode pairs reduces current flow and the extend of electrochemical reactions, the diode behavior can degrade over test cycles due to electrochemical reactions. To evaluate the diode behavior of different electrodes, a coefficient (referred to as actuation coefficient) is introduced which varies between zero (the least favorable diode behavior) and one (the best diode behavior) It is shown that, with the use of titanium as the electrode, the diodes behave more ideally and they behave consistently over 2000 test cycles. The best diode performance was observed with Na2SO4 electrolyte solution, where actuation coefficient remains at around 0.8 for 10000 test cycles. Aluminum can perform well in the beginning of the test cycles, but its performance degrades significantly over the first cycles.

Electrowetting is the change in apparent surface energy in the presence of an electric field. Recently, this phenomenon has been used to control the shape and location of individual droplets on a surface. However, many microfluidics researchers have acknowledged unexplained behaviors and performance degradation. In this work, electrowetting systems are characterized with different methods. The electrowetting response is measured by measuring contact angle for different applied voltages. A novel technique for direct measurement of Electrowetting Force (EWF) using nano indenter is proposed in this work. The EWF measurements show that, for aqueous solution the EWF is more as compared to DI water. Additionally, the electrowetting system is found to be more susceptible for degradation when aqueous solution is used. The performance degradation due to defective dielectric layer is also investigated by measuring the electrowetting force. Degradation of EWOD systems with environmental exposure over time is further studied experimentally by contact angle and electrochemical impedance spectroscopy (EIS) measurements. The time constant of 'contact angle decay' with environmental exposure is found to be similar to the time constant of electrolyte diffusion in dielectric layer.

This thesis report works on optically characterizing waveguide based biosensors consisting of thin, narrow Au stripes embedded in CYTOP. The devices were examined using an ever evolving and improving interrogation setup, variations of which are described in detail in this document. A number of changes were made to the setup configuration in order to reduce noise levels and increase efficiency and accuracy of acquired measurements. Waveguides of varying configurations (straight waveguides and Mach-Zehnder Interferometers with etched and cladded channels) are described and optically characterized. The characterization results of these devices are presented in this thesis. Bulk index measurements are carried out in order to determine a suitable bio-sensing solution with a refractive index matched to that of CYTOP. Step index measurements clearly distinguishing the introduction of sensing solutions of refractive indices varying from one another, are made available. Preliminary bio-sensing experiments involving detection of change in refractive index of sensing fluid as well as adlayer thickness with the introduction of analytes binding to the waveguide surface that has been functionalized with antibodies, using both straight and cladded waveguides with single mode outputs are studied.

This thesis report works on optically characterizing waveguide based biosensors consisting of thin, narrow Au stripes embedded in CYTOP. The devices were examined using an ever evolving and improving interrogation setup, variations of which are described in detail in this document. A number of changes were made to the setup configuration in order to reduce noise levels and increase efficiency and accuracy of acquired measurements. Waveguides of varying configurations (straight waveguides and Mach-Zehnder Interferometers with etched and cladded channels) are described and optically characterized. The characterization results of these devices are presented in this thesis. Bulk index measurements are carried out in order to determine a suitable bio-sensing solution with a refractive index matched to that of CYTOP. Step index measurements clearly distinguishing the introduction of sensing solutions of refractive indices varying from one another, are made available. Preliminary bio-sensing experiments involving detection of change in refractive index of sensing fluid as well as adlayer thickness with the introduction of analytes binding to the waveguide surface that has been functionalized with antibodies, using both straight and cladded waveguides with single mode outputs are studied.

This thesis details the fabrication of three different plasmon-polariton based devices: a plasmon-polariton Bragg grating (PPBG) biosensor, an intensity modulator incorporating grating couplers, and optically separated electrical contact, and finally an array of nanoholes in an ultrasmooth Au film. The biosensor involves a 35 nm Au stripe, lithographically stepped in width to produce a Bragg reflector. The waveguide is embedded in symmetric, Cytop claddings 8 µm thick. Channels are etched into the top cladding, exposing the waveguides and allowing for the integration of fluidics. The modulator involves a 20 nm Au pad, overlaid with 80 nm Au diffraction gratings, supported by an ultrathin (~3 nm) SiO2 insulator, on a p-doped Silicon wafer backed by an Al Ohmic contact. Electrical contact pads are separated from the waveguide by a thick dielectric (700 nm PMMA), and 2.5 µm vias in-filled with Au allow for electrical connection between the contact pads and waveguides. The nanohole array is machined by focused ion beam into an ultrasmooth Au film revealed by template stripping. The Au film is stacked on a thick film of Cytop between ~5 µm thick.

The biggest challenge with magnesium alloy biodegradable implants is the rapid corrosion at the earlier stages of the healing process after implantation. In this research, the impact of surface roughness generated by different means on the corrosion rate of AZ31 magnesium alloy in a simulated biologic environment is investigated. In order to perform accurate experimentation, an in vitro setup is assembled that simulates the human body environment accurately has been prepared using Schinhammer’s in vitro immersion testing setup and Kokubo’s Simulated Body Fluid (SBF). For the immersion test of Mg in SBF, several surface texture groups of Mg have been prepared and submerged into the in vitro tank. The Mg samples’ comparative analysis has been made in terms of corrosion rate, total weight loss and hydrogen gas evolution within a span of 7 days for the first experiment to narrow down the scope and 14 days for the follow up experiment. After 14 days of in vitro immersion test with varying roughness and hydrophobic modifications such as Cytop coating and stearic acid modification, it has been observed that the roughness group created by etching in aqueous NaCl solution for three minutes, shows better corrosion resistance compared to the polished control group. Hydrophobic modifications on the surfaces did not affect the corrosion behavior significantly.

In this thesis by articles, I propose and demonstrate the full design, fabrication and characterization of optical biosensors based on (Bloch) Long Range Surface Plasmon Polaritons (LRSPPs). Gold waveguides embedded in CYTOP with an etched microfluidic channel supporting LRSPPs and gold waveguides on a one-dimensional photonic crystal (1DPC) supporting Bloch LRSPPs are exploited for biosensing applications. Straight gold waveguides embedded in CYTOP supporting LRSPPs as a biosensor, are initially used to measure the kinetics constants of protein-protein interactions. The kinetics constants are extracted from binding curves using the integrated rate equation. Linear and non-linear least squares analysis are employed to obtain the kinetics constants and the results are compared. The device is also used to demonstrate enhanced assay formats (sandwich and inhibition assays) and protein concentrations as low as 10 pg/ml in solution are detected with a signal-to-noise ratio of 20 using this new optical biosensor technology. CYTOP which has a refractive index close to water is the fluoropolymer of choice in current state of the art waveguide biosensors. CYTOP has a low glass transition temperature which introduces limitations in fabrication processes. A truncated 1D photonic crystal can replace a low-index polymer cladding such as CYTOP, to support Bloch LRSPPs within the bandgap of the 1DPC over a limited ranges of wavenumber and wavelength. Motivated by quality issues with end facets, we seek to use grating couplers in a broadside coupling scheme where a laser beam emerging from an optical fiber excites Bloch LRSPPs on a Au stripe on a truncated 1D photonic crystal. Adiabatic and non-adiabatic flared stripes accommodating wide gratings size-matched to an incident Gaussian beam are designed and compared to maximise the coupling efficiency to LRSPPs. The gratings are optimized, initially, through 2D modelling using the vectorial finite element method (FEM). Different 3D grating designs were then investigated via 3D modelling using the vectorial finite difference time domain (FDTD) method. Given their compatibility with planar technologies, gratings and waveguides can be integrated into arrays of biosensors enabling multi-channel biosensing. A multi-channel platform can provide, e.g., additional measurements to improve the reliability in a disease detection problem. Thus, a novel optical biosensor based on Bloch LRSPPs on waveguide arrays integrated with electrochemical biosensors is presented. The structures were fabricated on truncated 1D photonic crystals comprised of 15 period stack of alternating layers of SiO2/Ta2O5. The optical biosensors consist of Au stripes supporting Bloch LRSPPs and integrate grating couplers as input/output means. The Au stripes also operate as a working electrode in conjunction with a neighboring Pt counter electrode to form an electrochemical sensor. The structures were fabricated using bilayer lift-off photolithography and the gratings were fabricated using overlaid e-beam lithography. The planar waveguides are integrated into arrays capable of multichannel biosensing. The wafer is covered with CYTOP as the upper cladding with etched microfluidic channels, and wafer-bonded to a borofloat silica wafer to seal the fluidic channels and enable side fluidic interfaces. The proposed device is capable in principle of simultaneous optical and electrochemical sensing and could be used to address disease detection problems using a multimodal strategy.