This thesis presents consolidated research results of a low-cost, high efficiency, high throughput detection system for fluorescence-based bio-assays. Such high throughput screening process is an invaluable tool for the multifaceted field of Systems Biology, where it is widely used in genomics and proteomics for drug and gene discovery applications. The thesis is divided into three parts: addressing the feasibility of using hydrogenated amorphous silicon photodiodes as the sensor, the development of an associated compact model suitable for circuit-level simulations, and integration of the sensors and switches to realize the array. Requirements of fluorescent bio-assays demand low sensor dark current densities in the order of 10¯¹¹A/cm² at room temperature. Fabrication of high quality segmented a–Si:H n–i–p photodiodes with such specification is achieved by tailoring defects at photodiode junction sidewalls, where both the dry etching and passivation conditions play important roles. Measurements of the fabricated photodiodes at different temperatures allowed the extraction of reverse current components, which are necessary in modeling such sensors in Verilog-A. Two prototype array designs are fabricated with pixel dimensions matching ANSI standard microwell plates. The functionalities of the small arrays are demonstrated with green LEDs to simulate fluorescent dyes that are commonly used in the high throughput bio-assay processes.

This thesis presents consolidated research results of a low-cost, high efficiency, high throughput detection system for fluorescence-based bio-assays. Such high throughput screening process is an invaluable tool for the multifaceted field of Systems Biology, where it is widely used in genomics and proteomics for drug and gene discovery applications. The thesis is divided into three parts: addressing the feasibility of using hydrogenated amorphous silicon photodiodes as the sensor, the development of an associated compact model suitable for circuit-level simulations, and integration of the sensors and switches to realize the array. Requirements of fluorescent bio-assays demand low sensor dark current densities in the order of 10¯¹¹A/cm² at room temperature. Fabrication of high quality segmented a–Si:H n–i–p photodiodes with such specification is achieved by tailoring defects at photodiode junction sidewalls, where both the dry etching and passivation conditions play important roles. Measurements of the fabricated photodiodes at different temperatures allowed the extraction of reverse current components, which are necessary in modeling such sensors in Verilog-A. Two prototype array designs are fabricated with pixel dimensions matching ANSI standard microwell plates. The functionalities of the small arrays are demonstrated with green LEDs to simulate fluorescent dyes that are commonly used in the high throughput bio-assay processes.