Biophotonics (eBook)

Lorenzo Pavesi is Professor of experimental physics at the university of Trento (Italy). Born the 21st of november 1961, he received the phd in physics in 1990 at the ecole polytechnique federale of lausanne (switzerland). in 1990 he became assistant professor, an associate professor in 1999 and full professor in 2002 at the university of Trento. He founded the research activity in semiconductor optoelectronics at the university of Trento and started several laboratories of optical spectroscopy, growth and advanced treatment of materials. During the last years, he concentrated on Si-based photonics, of which is one the leading experts worldwide. Recently his interested moved to nanoscience including nanobiotechnology and to the convergence of the nano- with the microtechnologies.Professor Philippe Fauchet is a Distinguished Professor of Electrical and Computer Engineering at the University of Rochester (USA), where he is also Professor of Optics, Biomedical Engineering, and Materials Science. He received his Ph.D. in Applied Physics from Stanford University in 1984 and taught at Stanford and Princeton Universities before joining the University of Rochester in 1990. His research areas are in nanoscience and nanotechnology with silicon, optical and electrical biosensors, electroluminescent materials and devices, and optical diagnostics. In 1998, he founded the Center for Future Health, a multidisciplinary center involving scientists, engineers, physicians, nurses, and social scientist working together to develop devices and systems that can keep people healthy. He is a Fellow of the Optical Society of America, the American Physical Society, and the Institute of Electrical and Electronic Engineering.

Preface 7
List of Contributors 16
1 Light Conversion in Photosynthetic Organisms 22
1.1 Introduction 22
1.2 Chloroplast Structure 23
1.3 Pigments and Light Absorption 24
1.4 Photosynthetic Apparatus 25
1.5 Cyclic Phosphorylation 30
1.6 Photoinhibition 31
2 Exploiting Photosynthesis for Biofuel Production 36
2.1 Biological Production of Vehicle Traction Fuels: Bioethanol and Biodiesel 38
2.2 Hydrogen Biological Production by Fermentative Processes 40
2.3 Hydrogen Production by Photosynthetic Organisms 42
2.4 Challenges in Algal Hydrogen Production 44
3 In Between Photosynthesis and Photoinhibition: The Fundamental Role of Carotenoids and Carotenoid-Binding Proteins in Photoprotection 50
3.1 When Light Becomes Dangerous for a Photosynthetic Organism 50
3.2 Acclimation 52
3.3 State 1–State 2 Transitions 53
3.4 Carotenoids Play a Fundamental Role in Many Photoprotection Mechanisms 54
3.5 Analysis of Xanthophyll Function In Vivo 57
3.6 Nonphotochemical Quenching 59
3.7 Feedback Deexcitation of Singlet-Excited Chlorophylls: qE 60
3.8 .pH - Independent Energy Thermal Dissipation (qI) 61
3.9 Chlorophyll Triplet Quenching 62
3.10 Scavenging of Reactive Oxygen Species 62
3.11 Conclusions 64
4 Non-Linear Microscopy 68
4.1 Introduction 68
4.2 Chronological Notes on MPE 69
4.3 Principles of Confocal and Two-Photon Fluorescence Microscopy 70
4.4 Two-Photon Excitation 76
4.5 Two-Photon Optical Sectioning 80
4.6 Two-Photon Optical Setup 81
4.7 Second Harmonic Generation (SHG) Imaging 84
4.8 Conclusions 86
5 Applications of Optical Resonance to Biological Sensing and Imaging: I. Spectral Self-Interference Microscopy 91
5.1 High-Resolution Fluorescence Imaging 91
5.2 Self-Interference Imaging 91
5.3 Physical Model of SSFM 93
5.4 Acquisition and Data Processing 95
5.5 Experimental Results 97
5.6 SSFM in 4Pi Con.guration 102
5.7 Conclusions 104
6 Applications of Optical Resonance to Biological Sensing and Imaging: II. Resonant Cavity Biosensors 107
6.1 Multianalyte Sensing 107
6.2 Resonant Cavity Imaging Biosensor 108
6.3 Optical Sensing of Biomolecules Using Microring Resonators 114
6.4 Conclusions 118
7 Biodetection Using Silicon Photonic Crystal Microcavities 120
7.1 Photonic Crystals: A Short Introduction 120
7.2 One-Dimensional PhC Biosensors 126
7.3 Selected Biosensing Results 133
7.4 Two-Dimensional PhC Biosensors 137
7.5 Conclusions 143
8 Optical Coherence Tomography with Applications in Cancer Imaging 146
8.1 Introduction 146
8.2 Principles of Operation 147
8.3 Optical Sources for Optical Coherence Tomography 152
8.4 Fourier-Domain Optical Coherence Tomography 152
8.5 Beam Delivery Instruments for Optical Coherence Tomography 154
8.6 Spectroscopic Optical Coherence Tomography 155
8.7 Applications to Cancer Imaging 157
8.8 Optical Coherence Tomography Contrast Agents 160
8.9 Molecular Imaging using Optical Coherence Tomography 164
9 Coherent Laser Measurement Techniques for Medical Diagnostics 170
9.1 Introduction 170
9.2 Electronic Speckle Pattern Interferometry (ESPI) 171
9.3 Endoscopic Electronic Speckle Pattern Interferometry (ESPI) 175
9.4 Microscopic (Speckle) Interferometry 180
9.5 Digital Holographic Microscopy 183
9.6 Discussion and Conclusions 192
10 Biomarkers and Luminescent Probes in Quantitative Biology 195
10.1 Fluorophores and Genetic Dyes 195
10.2 Microspectroscopy in Quantitative Biology: Where and How 201
11 Fluorescence-Based Optical Biosensors 216
11.1 Introduction 216
11.2 Biological Recognition Molecules and Assay Formats 217
11.3 Displacement Immunosensors 220
11.4 Fiber Optic Biosensors 221
11.5 Bead-Based Biosensors 226
11.6 Planar Biosensors 227
11.7 Critical Issues and Future Opportunities 229
12 Optical Biochips 233
12.1 Taxonomy of Optical Biochips 233
12.2 Analyte Classes for Optical Biochips 236
12.3 Optical E.ects for Biochemical Sensors 238
12.4 Preferred Sensing Principles for Optical Biochips 240
12.5 Readout Methods for Evanescent Wave Sensors 245
12.6 Substrates for Optical Biochips 246
12.7 Realization Example of an Optical Biosensor/Biochip: WIOS 247
12.8 Outlook: Lab-on-a-Chip Using Organic Semiconductors 248
12.9 Conclusions and Summary 252
13 CMOS Single-Photon Systems for Bioimaging Applications 254
13.1 Introduction 254
13.2 Spectroscopy 255
13.3 Lifetime Imaging 257
13.4 Time-of-Flight in Bio- and Medical Imaging 259
13.5 System Considerations 260
13.6 Conclusions 262
14 Optical Trapping and Manipulation for Biomedical Applications 264
14.1 Introduction 264
14.2 Theoretical Models for the Calculation of Optical Forces 267
14.3 Experimental Measurements of Optical Forces 270
14.4 Potential Biomedical Applications 280
14.5 Summary and Conclusion 286
15 Laser Tissue Welding in Minimally Invasive Surgery and Microsurgery 289
15.1 Introduction 289
15.2 Laser Welding in Ophthalmology 295
15.3 Applications in Microvascular Surgery 303
15.4 Potentials in Other Surgical Fields 305
15.5 Perspectives of Nanostructured Chromophores for Laser Welding 307
16 Photobiology of the Skin 314
16.1 Basics of Skin Structure: Cell Types, Skin Structures, and Their Function 314
16.2 E.ects of Light Exposure on Skin 317
16.3 Sun Protection and Sunscreens 322
16.4 Phototherapy: Use of Light for Treatment for Skin Disease 324
17 Advanced Photodynamic Therapy 328
17.1 Introduction 328
17.2 Basic Principles and Features of “Standard PDT” 329
17.3 Novel PDT Concepts 332
17.4 PDT Dosimetry Using Photonic Techniques 340
17.5 Biophotonic Techniques for Monitoring Response to PDT 343
17.6 Biophotonic Challenges and Opportunities in Clinical PDT 344
17.7 Conclusions 346
Index 348