David L. Andrews 
Photonics, Volume 4 [EPUB ebook] 
Biomedical Photonics, Spectroscopy, and Microscopy

List of Contributors ix

Preface xiii

1 Fluorescence 1
David J. S. Birch, Yu Chen, and Olaf J. Rolinski

1.1 Introduction 1

1.2 Spectra 2

1.3 Quantum Yield 6

1.4 Lifetime 12

1.5 Quenching 23

1.6 Anisotropy 30

1.7 Microscopy 38

1.8 Conclusions 48

Acknowledgments 48

References 49

2 Single-Molecule Detection and Spectroscopy 59
Michel Orrit

2.1 Introduction 59

2.2 Experimental Setups 62

2.3 Fluorescence Spectroscopy 66

2.4 Fluorescence Correlation Spectroscopy 72

2.5 Fluorescence Excitation Spectroscopy 78

2.6 Other Detection Methods 86

2.7 Conclusion 93

Acknowledgments 94

References 94

3 Resonance Energy Transfer 101
David L. Andrews, David S. Bradshaw, Rayomond Dinshaw, and Gregory D. Scholes

3.1 Introduction 101

3.2 History of RET 102

3.3 The Photophysics of RET 103

3.4 Investigative Applications of RET in Molecular Biology 113

3.5 The Role of RET in Light-Harvesting Complexes 118

Acknowledgments 122

References 122

4 Biophotonics of Photosynthesis 129
Valter Zazubovich and Ryszard Jankowiak

4.1 Introduction 129

4.2 Structure of Pigment–Protein Complexes and Structure–Function Relationships 130

4.3 Key Concepts in Physics of Pigment–Protein Complexes 133

4.4 Experimental Techniques 141

4.5 Examples 145

4.6 Conclusions 156

Acknowledgments 157

References 157

5 Optical Sectioning Microscopy and Biological Imaging 165
John Girkin

5.1 Introduction and Background 165

5.2 Confocal Imaging 168

5.3 Nonlinear Microscopy 172

5.4 Practical Implementation of Nonlinear Microscopy 181

5.5 Recent Advances in Nonlinear Microscopy 184

5.6 Widefield Optical Sectioning by Specialized Illumination Methods 186

5.7 Summary 190

References 191

6 Cell Handling, Sorting, and Viability 197
Darwin Palima, Thomas Aabo, Andrew Bañas, and Jesper Glückstad

6.1 Handling Cells with Light 198

6.2 Optical Sorting 215

6.3 Cell Viability 220

References 230

7 Tissue Polarimetry 239
Alex Vitkin, Nirmalya Ghosh, and Antonello de Martino

7.1 Introduction 239

7.2 Polarized Light Fundamentals 240

7.3 Instrumentation 266

7.4 Forward Modeling and Testing in Phantoms 282

7.5 Applications 297

7.6 Conclusions and Outlook 313

References 314

8 Optical Waveguide Biosensors 323
Daphné Duval and Laura M. Lechuga

8.1 Introduction 323

8.2 Fundamentals of Label-Free Optical Waveguide Biosensing 324

8.3 Surface Biofunctionalization 328

8.4 Evaluation of Optical Biosensors 331

8.5 Integrated Optical Waveguide-Based Biosensors 334

8.6 Optical Fiber-Based Biosensors 349

8.7 Lab-On-A-Chip Integration 354

8.8 Summary 357

References 358

9 Light Propagation in Highly Scattering Turbid Media: Concepts, Techniques, and Biomedical Applications 367
R. R. Alfano, W. B. Wang, L. Wang, and S. K. Gayen

9.1 Introduction 367

9.2 Physics Behind Optical Imaging Through a Highly Scattering Turbid Medium 369

9.3 Study of Ballistic and Diffused Light Components 378

9.4 Photon-Sorting Gates 384

9.5 Transition From Ballistic to Diffuse Imaging in Turbid Media 402

9.6 Conclusion 404

Acknowledgments 404

References 404

10 Photodynamic Therapy 413
Rakkiyappan Chandran, Tyler G. St. Denis, Daniela Vecchio, Pinar Avci, Magesh Sadasivam, and Michael R. Hamblin

10.1 Historical Overview of PDT 413

10.2 Introduction to PDT 415

10.3 Photosensitizer Structure and Photophysical Properties 418

10.4 Light Dosimetry and Photodynamic Therapy Light Sources 422

10.5 Light-Based Strategies to Enhance PDT 423

10.6 PDT Targeting and Nanotechnology 425

10.7 PDT for Dermatology 428

10.8 PDT for Oncology 433

10.9 PDT for Infectious Disease 435

10.10 PDT in Ophthalmology 445

10.11 PDT and The Immune System 446

10.12 Conclusion 449

Acknowledgment 449

References 449

11 Imaging and Probing Cells Beyond the Optical Diffraction Limit 469
Mark Schüttpelz and Thomas Huser

11.1 The Quest for Achieving Optical Resolution Beyond ABBE’S Limit 469

11.2 Stimulated Emission Depletion Microscopy 474

11.3 Photoactivated Localization Microscopy and Stochastic Optical Reconstruction Microscopy 477

11.4 Structured Illumination Microscopy 483

11.5 Super-Resolution Optical Fluctuation Imaging and Other Approaches 491

11.6 Outlook 495

Acknowledgments 496

References 497

12 Technology 503
Ann E. Elsner and Christopher A. Clark

12.1 Basic Ocular Anatomy and Physiology 503

12.2 Measurement Techniques 514

12.3 Anterior Segment Diagnostics, Refractive Measurements, and Treatment 522

12.4 Diagnostic Applications and Treatment of Posterior Segment 529

References 534

Index 543

DAVID L. ANDREWS leads research on fundamental molecular photonics and energy transport, optomechanical forces, and nonlinear optical phenomena. He has over 300 research papers and a dozen of books to his name—including the widely adopted textbook, Lasers in Chemistry. The current focus of his research group is on optical vortices, novel mechanisms for optical nanomanipulation and switching, and light harvesting in nanostructured molecular systems. The group enjoys strong international links, particularly with groups in Canada, Lithuania, New Zealand, and the United States. Andrews is a Fellow of the Royal Society of Chemistry, a Fellow of the Institute of Physics, and a Fellow of SPIE, the international society for optics and photonics.