Semester

Summer

Date of Graduation

2011

Document Type

Thesis

Degree Type

MS

College

Statler College of Engineering and Mineral Resources

Department

Lane Department of Computer Science and Electrical Engineering

Committee Chair

Jeremy M Dawson

Abstract

Detecting biomolecules at very low concentrations is of a significant importance for a wide variety of applications ranging from human health to national security. A diverse class of sensing platforms utilizing the specificity of physical properties of materials and their change in the presence of target analytes has been developed. The main objective of such systems is to deliver cost-effective, ultrasensitive, and reliable sensors that can withstand noisy environments (i.e. dirty samples) with efficient operational characteristics (low power, high throughput, etc.). Optical, electrochemical, and mechanical sensors have demonstrated promising detection capabilities, which further encouraged research aimed at producing even much more sensitive systems that are capable of extending detection limits to single molecules.;The unique optical properties of photonic crystals (PhCs) as well as their nano-meter scale features, which can be comparable to that of single molecules, make them well suited as a basis for sensors capable of fulfilling the ultra-sensitive detection requirements. Semiconductor materials are commonly used to engineer PhCs that can either trap light at high efficiency in high-quality factor resonant cavities to enhance fluorescence emission from labeled molecules, or cause a very precise attenuation of the transmitted or reflected light after the adsorption of unlabeled molecules to the surface of these PhC structures. However, the high cost of sensing platforms utilizing semiconductor materials motivates the development of soft lithographic techniques to fabricate photonic crystals in biocompatible polymer materials and simplify their integration with microfluidic channels and optical waveguides.;The theory, design, fabrication, and optical characterization of PhC lattice structures as biosensing platforms in both semiconductor and polymer materials will be demonstrated throughout this thesis. Electron Beam Lithography as well as soft lithographic techniques are presented to achieve submicrometer scale PhC lattices in silicon, Polydimethylsiloxane (PDMS), and epoxy. The main focus will be on a passive detection modality in which the PhC structures are used to manipulate light emitted from fluorescing molecules to achieve an enhancement of this emission. A 27-fold enhancement factor has been recorded when IR-emitting quantum dots were utilized as the emitting molecules within the PhCs.

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