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Multiplexed Optofluidics for Single-Molecule Analysis Matthew Alan Stott Brigham Young University

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Multiplexed Optofluidics for Single-Molecule Analysis Matthew Alan Stott Brigham Young University Brigham Young University BYU ScholarsArchive All Theses and Dissertations 2018-04-01 Multiplexed Optofluidics for Single-Molecule Analysis Matthew Alan Stott Brigham Young University Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Electrical and Computer Engineering Commons BYU ScholarsArchive Citation Stott, Matthew Alan, "Multiplexed Optofluidics for Single-Molecule Analysis" (2018). All Theses and Dissertations. 6740. https://scholarsarchive.byu.edu/etd/6740 This Dissertation is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in All Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. Multiplexed Optofluidics for Single-Molecule Analysis Matthew Alan Stott A dissertation submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Doctor of Philosophy Aaron Hawkins, Chair Stephen Schultz Brian Mazzeo Adam T. Woolley Brian D. Jensen Department of Electrical and Computer Engineering Brigham Young University Copyright © 2018 Matthew Alan Stott All Rights Reserved ABSTRACT Multiplexed Optofluidics for Single-Molecule Analysis Matthew Alan Stott Department of Electrical and Computer Engineering, BYU Doctor of Philosophy The rapid development of optofluidics, the combination of microfluidics and integrated optics, since its formal conception in the early 2000’s has aided in the advance of single-molecule analysis. The optofluidic platform discussed in this dissertation is called the liquid core anti- resonant reflecting optical waveguide (LC-ARROW). This platform uses ARROW waveguides to orthogonally intersect a liquid core waveguide with solid core rib waveguides for the excitation of specifically labeled molecules and collection of fluorescence signal. Since conception, the LC- ARROW platform has demonstrated its effectiveness as a lab-on-a-chip fluorescence biosensor. However, until the addition of optical multiplexing excitation waveguides, the platform lacked a critical functionality for use in rapid disease diagnostics, namely the ability to simultaneously detect different types of molecules and particles. In disease diagnostics, the ability to multiplex, detect and identify multiple biomarkers simultaneously is paramount for a sensor to be used as a rapid diagnostic system. This work brings optofluidic multiplexing to the sensor through the implementation of three specific designs: (1) the Y-splitter was the first multi-spot excitation design implemented on the platform, although it did not have the ability to multiplex it served as a critical stepping stone and showed that multi- spot excitation could improve the signal-to-noise ratio of the platform by ~50,000 times; (2) a multimode interference (MMI) waveguide which took the multi-spot idea and then demonstrated spectral multiplexing capable of correctly identifying multiple diverse biomarkers simultaneously; and, (3) a Triple-Core design which incorporates excitation and collection along multiple liquid cores, enabling spatial multiplexing which increases the number of individual molecules to be identified concurrently with the MMI waveguide excitation. In addition to describing the development of optical multiplexing, this dissertation includes an investigation of another LC-ARROW based design that enables 2D bioparticle trapping, the Anti-Brownian Electrokinetic (ABEL) trap. This design demonstrates two-dimensional compensation of a particle’s Brownian motion in solution. The capability to maintain a molecule suspended in solution over time enables the ability to gain a deeper understanding of cellular function and therapies based on molecular functions. Keywords: Matthew Alan Stott, Aaron Hawkins, optofluidics, single-molecule analysis, fluorescence, biosensor, lab-on-a-chip, integrated optics, microfluidics, multimode interference waveguides, Y-splitter waveguides, Anti-Brownian Electrokinetic trap, ARROWs, microfabrication, optofluidic multiplexing ACKNOWLEDGEMENTS First and foremost I would like to thank my wife, Megan, for her continued support throughout my studies. She is the love of my life and has sustained me through it all and allowed me to succeed. I would also like to thank Mabel, my daughter, for the joy she brought and the stress she relieved through her laughter and happy nature. I would like to thank my family, immediate and extended. My parents have always supported and helped me throughout my life. I would like to thank them for raising me to be a hard worker and to enjoy a challenge. I would also like to thank my in-laws for raising their daughter and for the advice from their perspective of having gone through the BYU PhD experience. I would like to express my gratitude to the many colleagues I have worked with during my time here. I especially appreciate Dr. Thomas Wall for his friendship and the many white board discussions we had on the project, for his ability to communicate ideas and easily explain to me the complexities of the project; my first mentors Michael Olson and Lynnell Zempoaltecatl who trained me on the project and in the cleanroom, and for all the students, graduate and undergraduate, that have worked with me on this project and generously given me their time and friendship: John Stout, Erik Hamilton, Steven Hammon, Joel Wright, Matthew Hamblin, Roger Chu, Craig Maughn, Maclain Olsen, Marcos Orfila, Johnny McMurray, Gabriel Zacheu and Alan Weinert. I am grateful to Jim Fraser for keeping the cleanroom running, answering my questions and keeping the environment safe. Without his constant frustration and work in keeping machines up and running, I would not have been able to make anything happen. I would also like to thank our collaborators from the University of California Santa Cruz, for their expertise in biological testing and optics. A special thanks goes to Dr. Holger Schmidt for sharing his experience and for his editing skills and perspective. Thanks also to those I worked closely with in California: Dr. Damla Ozcelik, Jennifer Black, Dr. Joshua Parks, Gopikrishnan Meena, Alexandra Stambaugh, Vahid Ganjalizadeh, Anik Duttaroy, Mahmudur Rahman, and Dr. Hong Cai. Finally, and the most influential of all, I would like to deeply express my gratitude for my graduate advisor, Dr. Aaron Hawkins, who first presented the idea of studying at a graduate level to me. He always made himself available to counsel with me through my frustrations and difficulties in research, and his counsel and teachings will continue with me throughout my life and career. I am also grateful for the funding provided by the grants Dr. Hawkins secured from the NSF and NIH. TABLE OF CONTENTS TITLE PAGE ................................................................................................................................... i ABSTRACT .................................................................................................................................... ii ACKNOWLEDGEMENTS ........................................................................................................... iii TABLE OF CONTENTS ................................................................................................................ v LIST OF TABLES .......................................................................................................................... x LIST OF FIGURES ....................................................................................................................... xi 1 Introduction .............................................................................................................................. 1 Project Overview ............................................................................................................ 1 Organization ................................................................................................................... 4 Contributions .................................................................................................................. 6 List of Publications ........................................................................................................ 7 1.4.1 Peer-Reviewed Journal Articles ...................................................................... 7 1.4.2 Conference Papers and Presentations .............................................................. 8 2 Disease Diagnostics ............................................................................................................... 10 Virus Diagnostic Tools ................................................................................................ 11 Bacterial Diagnostics ................................................................................................... 12 Lab-on-a-Chip .............................................................................................................. 14 3 Optofluidics ........................................................................................................................... 17 Multiplexed Optofluidics ............................................................................................. 17 Single-Molecule Analysis ............................................................................................ 22 3.2.1 Optofluidic Single-Molecule Detection ........................................................ 23 Reason for ARROWs ..................................................................................................
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