Porous Silicon Photonics at Unity Confinement Factors for Surface Adlayer Biosensing

Guided wave-optics is an emergent platform for label free optical biosensing. However, device sensitivity toward surface-attached biomolecules is directly restricted because of only evanescent interaction and low modal overlap with the active sensing region. In this work, we demonstrate a mesoporous silicon waveguide design created via a novel inverse processing technique that overcomes the limitations imposed by evanescent field sensing by achieving maximal transverse confinement factor in the active sensing region. Our sensor can also maintain this confinement factor and sensitivity across a large dimensional variation while preserving single-mode operation. Our devices are characterized in a Fabry-Perot interferometer configuration and the ultra-high sensitivity to small molecule adlayers is shown. We also discover dispersion to be a promising degree of freedom for exceeding the bulk sensitivity limits predicted by non-dispersive and isotropic effective medium theory

Porous Silicon Photonics for Label-Free Interferometric Biosensing and Flat Optics

This dissertation uses porous silicon as a material platform to explore novel optical effects in three domains: (i) It studies dispersion engineering in integrated waveguides to achieve high performance group index sensing. With proper design parameters, the sensor waveguides can theoretically achieve 6 times larger group index shift compared to the actual bulk effective refractive index shift. We demonstrate the guided mode confinement factor to be a key parameter in design and implementation of these waveguides. (ii) It explores multicolor laser illumination to experimentally demonstrate perceptually enhanced colorimetric sensing, overcoming the limitations faced by many contemporary colorimetric sensors. Our technique allows our sensor to achieve ~ 7 to 30 times higher sensitivities and ~ 30 to 1000 times lower limits of detection compared to current colorimetric sensors. (iii) It develops a novel imprinting technique to laterally pattern arbitrary refractive index on the porous silicon surface to realize nanoscale flat optical components. We demonstrate and characterize imprinted flat lens arrays and show how myriads of possible applications are to be implemented using this nanoimprinting technique. While the material primarily used in this dissertation is porous silicon, many of the demonstrated techniques are generalizable and can be extended towards other materials of interest to achieve high performance patterning and sensing

Properties and Applications of Love Surface Waves in Seismology and Biosensors

Shear horizontal (SH) surface waves of the Love type are elastic surface waves propagating in layered waveguides, in which surface layer is “slower” than the substrate. Love surface waves are of primary importance in geophysics and seismology, since most structural damages in the wake of earthquakes are attributed to the devastating SH motion inherent to the Love surface waves. On the other hand, Love surface waves found benign applications in biosensors used in biology, medicine, and chemistry. In this chapter, we briefly sketch a mathematical model for Love surface waves and present examples of the resulting dispersion curves for phase and group velocities, attenuation as well as the amplitude distribution as a function of the depth. We illustrate damages due to Love surface waves generated by earthquakes on real-life examples. In the following of this chapter, we present a number of representative examples for Love wave biosensors, which have been already used to DNA characterization, bacteria and virus detection, measurements of toxic substances, etc. We hope that the reader, after studying this chapter, will have a clear idea that deadly earthquakes and a beneficiary biosensor technology share the same physical phenomenon, which is the basis of a fascinating interdisciplinary research

Plasmonic Structures for Subwavelength Guiding and Enhanced Light-Matter Interactions

In this dissertation we design and analyze nanostructures for subwavelength guiding and enhanced light-matter interactions. We first investigate three-dimensional plasmonic waveguide-cavity structures, built by side-coupling stub resonators that consist of plasmonic coaxial waveguides of finite length, to a plasmonic coaxial waveguide. These structures are capable of guiding and manipulating light in deep-subwavelength volumes. We show that three-dimensional plasmonic coaxial waveguides offer a platform for practical realization of deep-subwavelength optical waveguides. We then introduce compact wavelength-scale slit-based structures for coupling free space light into the fundamental mode of plasmonic coaxial waveguides. We consider single-, double-, and triple-slit structures optimized at the optical communication wavelength and find that, when the slits are at resonance, the coupling to the plasmonic coaxial waveguide increases. We also investigate slit-based outcoupling structures for light extraction from the waveguide into free space. We also numerically design and experimentally test a SERS-active substrate for enhancing the SERS signal of a single layer of graphene in water. The graphene is placed on top of an array of silver-covered nanoholes in a polymer and is covered with water. We report a large enhancement in the SERS signal of the graphene on the patterned plasmonic nanostructure for a 532 nm excitation wavelength. We find that the enhancement is due to the increase in the confinement of electromagnetic fields on the location of graphene that results in enhanced light absorption in graphene at the excitation wavelength. We also find that water droplets increase the density of optical radiative states at the location of graphene, leading to enhanced spontaneous emission rate of graphene. Finally, we introduce a structure for near total absorption in a graphene monolayer at visible wavelengths. The optical interaction of graphene with local fields is enhanced by means of critical coupling. The graphene monolayer is placed on a grating slab without being covered with other structures, so the quality of graphene remains intact. We investigate the enhanced light-graphene interactions in this structure. We use experimental data for the dielectric permittivity of the materials used in the structure. The structure could find applications in the design of efficient nanoscale photodetectors and modulators

Theoretical and experimental development of a ZnO-based laterally excited thickness shear mode acoustic wave immunosensor for cancer biomarker detection

The object of this thesis research was to develop and characterize a new type of acoustic biosensor - a ZnO-based laterally excited thickness shear mode (TSM) resonator in a solidly mounted configuration. The first specific aim of the research was to develop the theoretical underpinnings of the acoustic wave propagation in ZnO. Theoretical calculations were carried out by solving the piezoelectrically stiffened Christoffel equation to elucidate the acoustic modes that are excited through lateral excitation of a ZnO stack. A finite element model was developed to confirm the calculations and investigate the electric field orientation and density for various electrode configurations. A proof of concept study was also carried out using a Quartz Crystal Microbalance device to investigate the application of thickness shear mode resonators to cancer biomarker detection in complex media. The results helped to provide a firm foundation for the design of new gravimetric sensors with enhanced capabilities. The second specific aim was to design and fabricate arrays of multiple laterally excited TSM devices and fully characterize their electrical properties. The solidly mounted resonator configuration was developed for the ZnO-based devices through theoretical calculations and experimentation. A functional mirror comprised of W and SiO2 was implemented in development of the TSM resonators. The devices were fabricated and tested for values of interest such as Q, and electromechanical coupling (K2) as well as their ability to operate in liquids. The third specific aim was to investigate the optimal surface chemistry scheme for linking the antibody layer to the ZnO device surface. Crosslinking schemes involving organosilane molecules and a phosphonic acid were compared for immobilizing antibodies to the surface of the ZnO. Results indicate that the thiol-terminated organosilane provides high antibody surface coverage and uniformity and is an excellent candidate for planar ZnO functionalization. The fourth and final specific aim was to investigate the sensitivity of the acoustic immunosensors to potential diagnostic biomarkers. Initial tests were performed in buffer spiked with varying concentrations of the purified target antigen to develop a dose-response curve for the detection of mesothelin-rFc. Subsequent tests were carried out in prostate cancer cell line conditioned medium for the detection of PSA. The results of the experiments establish the operation of the devices in complex media, and indicate that the acoustic sensors are sensitive enough for the detection of biomolecular targets at clinically relevant concentrations.Ph.D.Committee Chair: William D Hunt; Committee Member: Bruno Frazier; Committee Member: Dale Edmondson; Committee Member: Marie Csete; Committee Member: Peter Edmonson; Committee Member: Ruth O'Rega

Acoustic Wave Biosensors for Biomechanical and Biological Characterization of Cells

During past decades, interest in development of cell-based biosensors has increased considerably. In this study, two kinds of acoustic wave sensors are adopted as the cell-based biosensors to investigate the biomechanical and biological behaviors of cells, the quartz thickness shear mode (TSM) resonator and Love wave sensor. For the first part, the quartz TSM resonator is applied to detect the structural and mechanical properties of tendon stem/progenitor cells (TSCs), which are one kind of newly discovered adult cells in tendons, and the platelets from blood. Through the TSM resonator, the related viscoelastic properties of cells are extracted, which could indicate the state of cells in different physiological conditions. The TSM resonator sensor is utilized to characterize the aging-related viscoelasticity differences between the aging and young TSCs, and also to monitor the dynamic activation process of platelets. For the second part, a 36˚ YX-LiTaO3 Love wave sensor with a parylene-C wave guiding layer is proposed as a cell-based biosensor. A theoretical model is derived, to describe the Love wave propagation in the wave guiding layer, the adherent cell layer, and penetration into the liquid medium. The Love wave sensor is used to monitor the adhesion process of cells. Compared with TSM resonator, the response of Love wave sensor to the cell adhesion is primarily induced by the formation of bonds between cells and the substrate. The numerical results indicate that the adherent cell layer of various storage or loss shear modulus in certain range can cause evident, characteristic variations in propagation velocity and propagation loss, revealing the potential of Love wave sensors in providing useful quantitative measures on cellular mechanical properties. In addition, a Love wave sensor with a phononic wave guiding layer is introduced for non-operation signal filtering and sensor sensitivity improvement. Both two kinds of acoustic wave sensors present their own advantages as the cell-based biosensors, indicating advisable techniques for investigating cell biology in general and certain physiological processes in particular

Estudio y diseño de dispositivos ópticos biosensores depositados con películas delgadas basados en detección de longitud de onda de resonancias

A lo largo de esta tesis se presenta el estudio y diseño de varias plataformas de guía-ondas ópticas, con el fin de ver su viabilidad a la hora de usarlas como biosensores sobre fibra óptica u otros sustratos fotónicos. En este trabajo se depositan estructuras ópticas como una fibra monomodo desnuda, un estrechamiento en fibra óptica o una fusión de fibras mono – multi – monomodo (SMS) con películas delgadas de materiales usando técnicas nanotecnológicas como el ensamblado capa a capa (LbL-assembly) o el sputtering. Además, se dedica un capítulo al estudio de microresonadores toroidales depositados por rotación (spin-coating). El objetivo es generar o mejorar las prestaciones en resolución y sensibilidad de los fenómenos resonantes que se pueden obtener en estas estructuras ópticas, para luego detectar reacciones biológicas que den lugar a un futuro diagnóstico precoz de enfermedades.Along this thesis, the study and design of several optical waveguide platforms is presented, in order to check their viability when used as biosensors based on either optical fiber or other photonic substrates. In this work, some fiber-optic-based structures such as cladding removed multimode structures, tapered single-mode fibers and single-mode – multimode – single-mode fibers are deposited with thin-films of materials, using nanotechnology-based methods such as layer-by-layer assembly (LbL-assembly) or sputtering. Moreover, a brief chapter is focused on the study of toroidal microring resonators deposited by spin-coating. The final objective is to generate or enhance the parameters of the resonant phenomena obtained in these structures, in terms of resolution and sensitivity. Then, a biological detection is addressed and characterized, to see if they are able to perform a future early diagnosis for illnesses.La realización de este trabajo ha sido posible gracias a las aportaciones económicas recibidas por parte de la Universidad Pública de Navarra (UPNA), así como del patrocinio de la UPNA y del Ministerio de Economía y Competitividad, a través de los proyectos CICYT fondos FEDER TEC2010-17805, TEC2013-43679-R e IPT-2011-1212-920000 (PMEL).Programa Oficial de Doctorado en Ingeniería y Arquitectura (RD 1393/2007)Ingeniaritzako eta Arkitekturako Doktoretza Programa Ofiziala (ED 1393/2007

Selective and sensitive electrochemical DNA biosensor for the detection of Bacillus anthracis

The development of a selective and sensitive electrochemical DNA biosensor for detection of the pathogen Bacillus anthracis is proposed here. The technique is based on the characteristic cyclic voltammetry (CV) redox peaks and the very selective nature of DNA hybridization. The designed system consists of a self-assembled layer of mercaptohexanol (MCH) and thiol linked probe (ssDNAthiol) immobilized on gold-modified screen-printed electrodes. This direct detection technique studies the change in potential and intensity of the surface-modified screen-printed electrodes when a 5mM Fe(CN)6 3- solution in 0.1M KClis presented to the electrodic system in the range between -0.5 to 0.7V. The increase or decrease in the electron transfer along with the varied redox potential during immobilization of the probe and hybridization of the target was observed as CV peak current and potential change. The proposed system showed reliable results with sensitivity up to 10pM and selective enough to distinguish signals from DNA fragments presenting 1bp mismatches. The fabricated system with the thiol probe once produced could be shelved for 2-3 months.Thus the strong selective binding nature of the DNA along with the sensitive CV characters, prove to be an efficient system for reliable detection of pathogens