Yes / Aggregating and forming biofilms on biotic or abiotic surfaces are ubiquitous bacterial behaviors under various conditions. In clinical settings, persistent presence of biofilms increases the risks of healthcare-associated infections and imposes huge healthcare and economic burdens. Bacteria within biofilms are protected from external damage and attacks from the host immune system and can exchange genomic information including antibiotic-resistance genes. Dispersed bacterial cells from attached biofilms on medical devices or host tissues may also serve as the origin of further infections. Understanding how bacteria develop biofilms is pertinent to tackle biofilm-associated infections and transmission. Biofilms have been suggested as a continuum of growth modes for adapting to different environments, initiating from bacterial cells sensing their attachment to a surface and then switching cellular physiological status for mature biofilm development. It is crucial to understand bacterial gene regulatory networks and decision-making processes for biofilm formation upon initial surface attachment. Pseudomonas aeruginosa is one of the model microorganisms for studying bacterial population behaviors. Several hypotheses and studies have suggested that extracellular macromolecules and appendages play important roles in bacterial responses to the surface attachment. Here, I review recent studies on potential molecular mechanisms and signal transduction pathways for P. aeruginosa surface sensing. / This work is supported by University of Bradford

Surface plasmon resonance (SPR) sensors using multiwavelength light coupling are investigated to probe changes in refractive index that occur as a result of chemical or biochemical processes. Traditional SPR sensors have used angle modulation to facilitate detection at the sensor surface; however, the multiwavelength approach is novel and brings new functionality to SPR sensors. The multiwavelength sensors are constructed on both fiber optic and bulk waveguides such as prisms. A thin metal film is deposited on the waveguide surface to support the surface plasmon (SP) mode. The evanescent field produced by light propagating through the waveguide can be coupled into the surface plasmon mode thus attenuating the transmitted light. This coupling is dependent upon phase matching between the light wavevector and the surface plasmon wavevector. The wavevectors are directly related to the wavelength of light, thickness of analyte on the sensor surface and the refractive index of the analyte. As these parameters change, the light output from the sensor will be affected. Other thin films can be subsequently deposited on the metal to functionalize the sensor surface for a particular analyte of interest. A theoretical background and details of the sensor construction is given. The developed sensors are tested in a variety of application systems. Experimental results for refractive index sensing in bulk liquid applications is shown. Observed sensitivity approaches that of conventional SPR techniques. Alkyl-thiol monolayer systems are studied to investigate kinetics of formation and the thickness resolution of the sensor. A biochemical system is investigated to compare the sensors with other immunoassay techniques. Ionic self-assembled monolayer (ISAM) systems are investigated to probe structure and determine their usefulness as an immobilization layer for biochemical species. A mathematical model based on Fresnel reflection equations is developed to predict sensor response. This model can be used to selectively vary sensor parameters to optimize the response for a specific analyte system or to calculate system parameters based on experimental results. Results from the various experiments are compared with the model. Experimental results and interpretations are discussed along with future work and potential improvements. Classical SPR sensors are also discussed along with comparisons with the multiwavelength sensors. Future improvements to SPR sensors design are considered, as is the application of the technology to high-throughput drug screening for pharmaceuticals. / Ph. D.

In this thesis, we have designed and optimized strip waveguide based micro-ring and micro-ring and micro-racetrack resonators for biosensing applications. Silicon-On-Insulator (SOI) platform which offers several advantages over other materials such as Lithium Niobate, Silica on Silicon and Silicon nitride is considered here. High index contrast enables us to miniaturize the biosensor devices and monolithic integration of source and detectors on the same chip. We have considered the dispersive nature of the waveguide and proceeded towards optimization. Finite difference schemes and Finite Difference Time Domain (FDTD) methods are the primary tools used to model the biosensor. Various structures such as channel waveguides and beam structures are analyzed on the basis of their suitability for sensing applications. Strip and Rib waveguides are the two geometries considered in our studies. In an optical guiding structure, effective index of the propagating optical mode can be induced by two different phenomena: i. Homogeneous Sensing In this category, effective index of a propagating optical mode changes with uniformly distributed analytes extending over a distance well exceeding the evanescent field penetration depth. The sample serves as the waveguide cover. ii. Surface Sensing In the case of surface sensing, analytes bound to the surface of the waveguide. The effective index of an optical mode changes with the refractive index as well as the thickness of an adlayer. A thin layer of adsorbed or bound molecules transported from liquid or gaseous medium serving as waveguide cover is referred as an adlayer. Both homogeneous and surface sensing schemes are addresses in this work. By bulk sensing method, the characteristics of bioclad covering the device are studied. Optimization of the resonator structure involves the analysis of following parameters: • Gap between the ring and bus waveguides • Free spectral range • Extinction ratio • Quality factor We have achieved a maximum bulk sensitivity of 115 nm / RIU with ring waveguide width of 450 nm and bus width of 350 nm which is better than an earlier reported value of 70 nm/ RIU. We have proposed a novel detection scheme consisting of a micro-racetrack resonator formed over a cantilever structure. The devoice works on the principle of opto-mechanical coupling to detect conformational changes due to biomolecular adherence. BSA (Bovine Serum Albumin) and IgG ( Immuno Globulin G) are the two proteins considered in the work. Mechanical analysis of the beam for tensile and compressive stresses and corresponding spectral responses of the racetrack resonators are analyzed both by semi-analytical and method and numerical analyzes. We compared various aspects of rib and strip waveguide racetrack resonators. We have proved by numerical simulation, that the device is capable of distinguishing tensile and compressive stress. Two strip waveguides of dimensions : 450 nm X 220 nm and 400 nm X 180 nm, former supporting both Quasi-TE and Quasi-TM modes where as the second configuration allows only Quasi-TE mode alone. Sensitivity of the cantilever sensor is : 0.3196 x 10-3 nm/ µɛ at 1550 nm wavelength.