Identifier

etd-04142009-174010

Degree

Doctor of Philosophy (PhD)

Department

Mechanical Engineering

Document Type

Dissertation

Abstract

A modular high throughput microsystem was developed using microfabrication technology and nucleic acid analysis. The purpose of developing this microsystem is to identify acute infectious disease and prevent contagious outbreak in a matter of time. This microsystem included three major components, a reagent distribution device, a 96 CFPCR array, and a multi-zone thermal system, to efficiently amplify specific DNA fragments to determine the disease status or precisely pinpoint a disease from multiple patients. Polymerase chain reaction (PCR) is the key component in the nucleic acid analysis for disease because it can be used to amplify interested DNA fragments by repeatedly thermal cycles. Temperature distribution is critical to the PCR reaction, and thermal management was studied; the approaches which reached good biochemical results were applied to the design of a 96 CFPCR array and a multi-zone thermal system. Protein adsorption is another issue when PCR is realized in a micro device because of the increased surface-to-volume ratio, which might terminate the biochemical reaction. A series of experiments were carried out to understand the protein adsorption in the microchannels with different geometries. A disposable 96 CFPCR was designed and fabricated on a polycarbonate substrate by double-sided hot embossing and its requirement of multiple temperature zones was fulfilled by building a multi-zone thermal system. Their thermal performance was characterized by numerical simulations and validated by infrared camera experiments. To evenly distribute the analyte with reducing pipetting steps, a reagent distribution device was designed to assemble with the 96 CFPCR array by using passive alignment structures to perform a systematic performance. The passive alignment structures including three pairs of v-groove and hemisphere-tipped post was studied and modified to ensure a smooth passage for mass, momentum, and energy of chemical analyte. Biochemical experiments demonstrated parallel amplifications of both identical and different DNA fragments from the multiple CFPCRs on the multi-zone thermal system, which implied the potential to detect acute infectious disease with acceleration, accuracy, specificity, and high throughput.

Date

2009

Document Availability at the Time of Submission

Release the entire work immediately for access worldwide.

Committee Chair

Michael C. Murphy

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