Dual-Mode Electro-photonic Silicon Biosensors (eBook)

Supervisor’s Foreword 7
Abstract 9
Acknowledgements 10
Contents 11
1 Preamble 14
1.1 The Need for Biosensors 14
1.2 Dual-Mode Silicon Electro-Photonic Biosensors 15
1.3 Goals of This Thesis 17
1.4 Outline of the Thesis 18
References 19
2 Introduction to Label-Free Biosensing 20
2.1 Motivation 20
2.2 State-of-the-Art Label-Free Technologies 22
2.3 Single-Domain Techniques 23
2.3.1 Electronic Biosensing 24
2.3.2 Photonic Waveguide-Based Detection Strategies 26
2.4 Bi-Domain Techniques 37
2.4.1 Electrochemical Surface Plasmon Resonance 37
2.4.2 Electrochemical Quartz Crystal Microbalance with Dissipation Monitoring 38
2.4.3 Electrochemical Optical Waveguide Lightmode Spectroscopy 40
2.4.4 Electro-Photonic Silicon Biosensing 40
2.5 Self-assembled Monolayers 41
2.5.1 Formation of Self-assembled Monolayers 43
2.5.2 Assembly of Silane SAMs on Silicon 43
2.6 Summary 44
References 45
3 Fabrication and Experimental Techniques 49
3.1 Introduction 49
3.2 Nanofabrication Processes 49
3.2.1 Diffusion Doping 50
3.2.2 Thermal Evaporation 53
3.2.3 Electron Beam Lithography 53
3.2.4 Reactive Ion Etching 57
3.2.5 Microfluidics 58
3.3 Electrochemistry 61
3.3.1 Semiconductor-Electrolyte Interfaces 61
3.3.2 Electrochemical Measurements 64
3.3.3 Cyclic Voltammetry 66
3.4 Electro-Optical Characterisation Setup 67
3.5 Summary 67
References 69
4 The Electro-Photonic Silicon Biosensor 70
4.1 Alternatives 70
4.2 Profile Controlled N-Type Doping 73
4.2.1 Bulk Doping Characterisation 75
4.2.2 Doping Profile Characterisation 76
4.3 Ohmic Contacts on Silicon 79
4.4 Combining Optical and Electrochemical Sensing 83
4.4.1 Summary of the Sample Fabrication Process 88
4.5 Doping Impact on the Optical Device Performance 89
4.5.1 Assisted Optical Validation of the Q-Factor of a Lossy Cavity 91
4.5.2 Correlation Between Doping Concentration and Optical Loss 93
4.6 Dual-Mode Photonic/Electrochemical Validation 94
4.7 Limitations 98
4.8 Comparison to Similar Bi-Domain Approaches 100
4.9 Summary 101
References 102
5 Study and Application of Electrografted Layers of Diazonium Ions 105
5.1 Introduction 105
5.2 Application of Diazonium Ions 106
5.3 Structure of Electrografted Layers of Diazonium Ions 108
5.3.1 Electrografting of 4-Ethynylbenzene Diazonium 108
5.3.2 Electrografting of the Diazonium Salt of N-(4-aminophenyl)maleimide 110
5.3.3 Electrografting of 4-Azidoaniline 110
5.3.4 Control Experiments of the Electroreduction of Diazonium Salts 113
5.4 Functionalisation of Electrografted Layers of Diazonium Ions 115
5.4.1 Immobilisation of Thiolated Molecules 116
5.4.2 Functionalisation Through Copper-Catalyzed Azide-Alkyne Huisgen Cycloaddition (CuAAC) 117
5.5 Site-Selective Functionalisation of Optical Biosensors 118
5.5.1 Sensor Microarray Fabrication 119
5.5.2 Selectively Functionalised Photonic DNA Microarray 119
5.5.3 Control Experiments for Selective DNA Hybridization 124
5.6 Summary 126
References 127
6 Tailoring Light-Matter Interaction for Quantification of Biological and Molecular Layers 129
6.1 Introduction 129
6.2 Geometry Control on Silicon Electro-Photonic Biosensors: The Cascaded Ring Resonator Configuration 130
6.2.1 Cascaded Ring Design and Fabrication 131
6.3 Extraction of Thickness and Refractive Index 135
6.4 Cascaded Rings for Characterising Biological and Molecular Monolayers 137
6.4.1 Control Experiment: Adsorption of BSA on a Silicon Surface 138
6.4.2 Characterisation of a MPTS SAM 139
6.4.3 Characterisation of an Affimers Biolayer 141
6.5 Dual-Mode Analysis of Electroactive Hairpin Shaped DNA Strands Conformational Changes 143
6.5.1 Hairpin Shaped DNA Strands 143
6.5.2 Dual-Mode Interrogation 144
6.6 Comparison to Similar Approaches 150
6.7 Conclusions 150
References 151
7 Conclusions and Outlook 153
7.1 Summary and Conclusions 153
7.2 Outlook 155
References 156
Curriculum Vitae 157
Conferences and Publications 158
Awards 159