The Design and Evaluation of Microelectrode Patterns on a Multilayer Biochip Platform for Trapping Single Cells using Dielectrophoresis Siti Noorjannah Ibrahim A thesis presented for the degree of DOCTOR OF PHILOSOPHY (PhD) In Nanostructure Sciences and Technology Department of Electrical and Computer Engineering University of Canterbury, New Zealand July 2012 For my beloved husband, Shamsul Mazalan and my sweet little girl who was born during my Phd journey, Ilham Najihah. Abstract Trapping ability on a biochip device is useful for systematic cell addressing and real-time observation of single cells analysis, however, precise control over the cell movements remains challenging. This thesis addresses the problem of controlling movement of single cells on a biochip platform by a technique called the Dielectrophoretic (DEP) force. Existing researches showed that the DEP force offers precise control of cell movements through various microelectrode designs which generate strong polarization effects i.e., DEP forces, but with the expense of damaging cell’s structure. The thesis contribute three new microelectrode designs for trapping single cells: the dipole, the quadrupole and the adaptive octupole, structured on a metal-insulator-metal (multilayer) biochip platform called the Sandwiched Insulator with Back Contact (SIBC) biochip. Cores of the study lie on the microelectrode designs that are capable of generating strong DEP holding forces, the back contact to enhance trapping of single cells and the fabrication process of creating a metal-insulator-metal structure. This thesis also presents details on the experimental setups of the trapping experiments and the numerical analysis of the microelectrode designs. The SIBC biochip comprises of the back contact on the first metal layer, the microcavity (cell trap) on the insulator layer and the three microelectrodes on the second metal layer. Together, the three microelectrodes and the back contact generate DEP forces that attract particles/single cells toward microcavities and maintain their positioning in the traps. Prior to the fabrication, profiles of the DEP force generated by the microelectrodes are studied using COMSOL3.5a software. Simulation results suggest that the DEP trapping region can be created surrounding the microcavity if the microelectrode and the back contact are connected with AC signals that have different phases. The strongest DEP force can be obtained by setting the back contact and the microelectrodes with AC signals that have 180 phase difference. i Evaluations on the trapping functionality for the three microelectrodes were conducted using polystyrene microbeads and Ishikawa cancer cells line suspended in various medium. Trapping capability of the three microelectrodes was demonstrated through experiments with 22 percent of the Ishikawa cancer cells and 17 percent of the polystyrene microbeads were successfully trapped. With these promising results, the new microelectrode designs together with the SIBC biochip structure have huge potentials for biomedical applications particularly in the field of diagnosis and identification of diseases. ii Acknowledgments This PhD thesis would not have been possible without the tremendous help and support from my supervisors, the research group, my colleagues, my friends and my family. Above all, I would like to thank my husband for his personal support and great patience at all times. Not to forget, my parents, sisters and brothers who have given me their unequivocal supports throughout my PhD journey. I am greatly thankful to my supervisor, Assoc. Prof. Maan Alkaisi for his guidance, encouragement and advise to this project. In fact, the last couple of years have been very challenging for me, but his patience and dedication to this research have encouraged me countless times to work on the SIBC biochip’s thin films adhesion problem and proceed towards the completion of this thesis. I was honoured to have him as my supervisor and mentor. I would like to thank my other supervisor, Assoc. Prof. John Evans for his biological expertise and insights to the study. Without his advices, details on the biological aspects of the research will be left untold. Ultimately the thesis was a result of the strong collaborative efforts between both supervisors. I also would like to thank Mr. Mike Arnold of Industrial Research, for his helps and practical advices that have improved my work tremendously. I would like to express my gratitude to the people who involves in this thesis: Volker Nock for teaching and introducing me to the worlds of microfluidic and SU-8, Fahmi Samsuri, Lynn Murray and Muthanna Majid for the continuous supply of Ishikawa cancer cells, Xianming Liu for advice on SU-8 etching, Suzanne Furkert for her advise on NiCr and Au depositions, Jessica Chai, Khairudin Mohamed and for their advices on fabrication processes. Special thanks to Gary Turner and Helen Devereux for teaching me how to use the machines and tips and tricks in the fabrication processes. Not to forget, room A217 people: Ciaran Moore, Prateek Mehrorta, David Kim, John Foulkes, Mikkel Scholer, and my fellow postgraduate friends: Rezaul Bari, Senthuran and Shazlina Johari for their supports. iii I would also like to acknowledge the financial support of the Ministry of Higher Education of Malaysia and the International Islamic University Malaysia and its staff, particularly in the award of a Postgraduate Scholarship that provided the necessary financial support for my study in New Zealand. Finally, I would like to acknowledge the support from the MacDiarmid Institute for Advanced Materials, New Zealand. iv Table Of Content ABSTRACT .................................................................................................... I ACKNOWLEDGMENTS .......................................................................... III TABLE OF CONTENT ............................................................................... V LIST OF FIGURES .................................................................................. VII LIST OF TABLES ................................................................................... XIII CHAPTER ONE ........................................................................................... 1 INTRODUCTION ...............................................................................................................1 1.1 The Emergence of Bionanotechnology ................................................................ 2 1.2 Research Objectives ............................................................................................. 4 1.3 Thesis Outline and Contributions ........................................................................ 6 CHAPTER TWO ........................................................................................ 13 INTRODUCTION TO SINGLE CELLS MANIPULATION .......................................................13 2.1 Single Cell Structure and Physiology ................................................................ 14 2.2 Microfabrication Technology in Single Cells Study .......................................... 20 2.3 Trends of DEP manipulation on Biochip ........................................................... 29 2.4 Development of the SIBC Biochip...................................................................... 34 2.5 Summary ............................................................................................................ 37 CHAPTER THREE .................................................................................... 45 THEORETICAL BACKGROUND OF THE MICROELECTRODE DESIGN ................................45 3.1 DEP Force and Cell Movements ....................................................................... 39 3.2 DEP Force Trapping Mechanisms .................................................................... 49 3.3 SIBC Microelectrode Design ............................................................................. 54 3.4 Theory of Hydrodynamic Force ......................................................................... 64 3.5 The SIBC Biochip Concept ................................................................................ 67 3.6 Summary ............................................................................................................ 68 CHAPTER FOUR ....................................................................................... 77 NUMERICAL ANALYSIS OF THE MICROELECTRODE .......................................................77 4.1 Microelectrode Design using COMSOL3.5a ..................................................... 71 v 4.2 Simulations of the SIBC biochip Horizontal Plane............................................ 78 4.3 Simulations on Vertical Plane of the Microcavity ........................................... 102 4.4 Summary .......................................................................................................... 109 CHAPTER FIVE ....................................................................................... 111 FABRICATION PROCESS OF THE SIBC BIOCHIP ...........................................................111 5.1 Fabrication Process of the SIBC Biochip ........................................................ 112 5.2 Fabrication of the SIBC Microfluidic Channels .............................................. 140 5.3 Integration of the SIBC Biochip and the Microfluidic Channels ..................... 149 5.4 Summary .........................................................................................................