Photonics -- Contents -- List of Contributors -- Preface -- 1 Fluorescence -- 1.1 Introduction -- 1.2 Spectra -- 1.2.1 Background and Theory -- 1.2.2 Experimental -- 1.2.3 Application Example-Melanin Spectra -- 1.3 Quantum Yield -- 1.3.1 Theory -- 1.3.2 Experimental -- 1.3.3 Application Example-ThT Detection of Sheet Structure -- 1.4 Lifetime -- 1.4.1 Theory -- 1.4.2 Experimental -- 1.4.3 Application Example-In Vivo Glucose Sensing -- 1.5 Quenching -- 1.5.1 Theory -- 1.5.2 Application-Metal Ion Quenching -- 1.6 Anisotropy -- 1.6.1 Theory -- 1.6.2 Experimental -- 1.6.3 Application Example-Nanoparticle Metrology -- 1.7 Microscopy -- 1.7.1 Systems and Techniques -- 1.7.2 Application Example-Gold Nanorods in Cells -- 1.8 Conclusions -- Acknowledgments -- 2 Single-Molecule Detection and Spectroscopy -- 2.1 Introduction -- 2.2 Experimental Setups -- 2.2.1 Principles -- 2.2.2 Correction of Aberrations -- 2.2.3 Polarization Structure at the Focus -- 2.2.4 Various Microscopy Methods -- 2.3 Fluorescence Spectroscopy -- 2.3.1 Introduction, Signal-to-Noise Ratio -- 2.3.2 Sample Preparation -- 2.3.3 Orientation -- 2.3.4 Blinking -- 2.3.5 Bleaching -- 2.3.6 Superresolution -- 2.4 Fluorescence Correlation Spectroscopy -- 2.4.1 Photon Counting Histograms, Burst Analysis -- 2.4.2 Fluorescence Correlation Spectroscopy -- 2.4.3 Multiparameter Analysis -- 2.5 Fluorescence Excitation Spectroscopy -- 2.5.1 Zero-Phonon Line and Phonon Wing -- 2.5.2 Inhomogeneous Broadening -- 2.5.3 Hole-Burning [30] -- 2.5.4 Single-Molecule Spectroscopy -- 2.5.5 Scope of Low-Temperature Single-Molecule Spectroscopy -- 2.6 Other Detection Methods -- 2.6.1 General Considerations on Signal, Background, and Noise -- 2.6.2 Dark-Field Scattering, Total Internal Reflection -- 2.6.3 Absorption, Extinction, Interference-Based Methods -- 2.6.4 Pump-Probe and Photothermal Detections.

2.7 Conclusion -- Acknowledgments -- References -- 3 Resonance Energy Transfer -- 3.1 Introduction -- 3.2 History of RET -- 3.2.1 The First Experiments -- 3.2.2 Early Developments of Theory -- 3.2.3 Förster Theory -- 3.3 The Photophysics of RET -- 3.3.1 Primary Excitation Processes -- 3.3.2 Coupling of Electronic Transitions -- 3.3.3 Dissipation and Line Broadening -- 3.3.4 Förster Equation -- 3.3.5 Orientation Dependence -- 3.3.6 Polarization Features -- 3.3.7 Diffusion Effects -- 3.3.8 Long-Range Transfer -- 3.3.9 Dexter Transfer -- 3.4 Investigative Applications of RET in Molecular Biology -- 3.4.1 Spectroscopic Ruler -- 3.4.2 Conformational Change -- 3.4.3 Intensity-Based Imaging -- 3.4.4 Lifetime-Based Imaging -- 3.4.5 Other Applications -- 3.5 The Role of RET in Light-Harvesting Complexes -- 3.5.1 Introduction -- 3.5.2 Photosynthetic Excitons -- Acknowledgments -- References -- 4 Biophotonics of Photosynthesis -- 4.1 Introduction -- 4.2 Structure of Pigment-Protein Complexes and Structure-Function Relationships -- 4.2.1 Photosystem I (PS I) and Photosystem II (PS II) -- 4.2.2 PCs of Purple Bacteria -- 4.3 Key Concepts in Physics of Pigment-Protein Complexes -- 4.3.1 Excitons -- 4.3.2 Excitation Energy Transfer -- 4.3.3 Homogeneous and Inhomogeneous Broadening, Zero-Phonon Lines (ZPLs), and Phonon Sidebands (PSBs) -- 4.3.4 Proteins at Low Temperatures -- 4.4 Experimental Techniques -- 4.4.1 Spectral Hole-Burning, Fluorescence Line-Narrowing, and DFLN -- 4.4.2 Single Photosynthetic Complex Spectroscopy -- 4.5 Examples -- 4.5.1 LH2 Antenna Complex of Purple Bacteria -- 4.5.2 Cyanobacterial Photosystem I -- 4.5.3 Plant LHC II-Single Complex Spectroscopy and Nonphotochemical Quenching -- 4.5.4 CP43-The Protein Energy Landscape Parameters -- 4.5.5 Probing Electron Transfer (ET) Times and Their Distributions in Photosynthetic RCs by SHB.

4.6 Conclusions -- Acknowledgments -- References -- 5 Optical Sectioning Microscopy and Biological Imaging -- 5.1 Introduction and Background -- 5.1.1 The Biological Context and Limitations -- 5.1.2 Definitions and Terms -- 5.2 Confocal Imaging -- 5.2.1 Introduction to Confocal Imaging -- 5.2.2 Point Scanned Microscopy -- 5.2.3 Summary on Basic Confocal Microscopy -- 5.3 Nonlinear Microscopy -- 5.3.1 Multiphoton Fluorescence Microscopy -- 5.3.2 Harmonic Microscopy (SHG and THG) -- 5.3.3 Coherent Anti-Stokes Raman Scattering Microscopy -- 5.3.4 Stimulated Raman Scattering Microscopy -- 5.4 Practical Implementation of Nonlinear Microscopy -- 5.5 Recent Advances in Nonlinear Microscopy -- 5.5.1 Miniature Instrumentation and Clinical applications -- 5.5.2 Adaptive Optics for In-Depth Imaging -- 5.6 Widefield Optical Sectioning by Specialized Illumination Methods -- 5.6.1 Single Plane Illumination Microscopy (SPIM) -- 5.6.2 Structured Illumination Microscopy -- 5.6.3 Sub-diffraction-Limited Imaging -- 5.7 Summary -- References -- 6 Cell Handling, Sorting, and Viability -- 6.1 Handling Cells with Light -- 6.1.1 Light-Cell Interaction: Momentum Exchange -- 6.1.2 Dielectric Tagging: Using Microspheres as Optical Handles -- 6.1.3 Cell Positioning -- 6.1.4 Cellular Biomechanics: Mechanotransduction and Cell Deformations -- 6.1.5 Cytometry -- 6.2 Optical Sorting -- 6.2.1 Active Sorting -- 6.2.2 Passive Sorting -- 6.3 Cell Viability -- 6.3.1 Choosing the Optimal Wavelength -- 6.3.2 Thermal Effects -- 6.3.3 Power and Energy Dose -- 6.3.4 Growth and Division Time -- 6.3.5 Propidium Iodide -- 6.3.6 Internal pH (pHi) -- 6.3.7 Reactive Oxygen Species -- References -- 7 Tissue Polarimetry -- 7.1 Introduction -- 7.2 Polarized Light Fundamentals -- 7.2.1 Polarization States -- 7.2.2 Interaction with a Sample -- 7.2.3 Decompositions into "Elementary" Component Matrices.

7.2.4 Summary -- 7.3 Instrumentation -- 7.3.1 General Principles -- 7.3.2 Commonly Used PSAs -- 7.3.3 Examples of Tissue Polarimetry Instruments -- 7.3.4 Summary -- 7.4 Forward Modeling and Testing in Phantoms -- 7.4.1 Forward Modeling of Polarized Light Propagation in Tissue -- 7.4.2 Experimental Testing and Validation in Tissue Phantoms -- 7.4.3 Summary -- 7.5 Applications -- 7.5.1 Polarization-Gated Surface and Subsurface Imaging -- 7.5.2 Tissue Assessment with Mueller Polarimetry -- 7.5.3 Summary -- 7.6 Conclusions and Outlook -- References -- 8 Optical Waveguide Biosensors -- 8.1 Introduction -- 8.2 Fundamentals of Label-Free Optical Waveguide Biosensing -- 8.2.1 Principle of Operation -- 8.2.2 Optical Waveguide Technology -- 8.3 Surface Biofunctionalization -- 8.3.1 Bioreceptors -- 8.3.2 Immobilization Techniques -- 8.3.3 Biofunctionalization Strategies for Multiplexing -- 8.4 Evaluation of Optical Biosensors -- 8.5 Integrated Optical Waveguide-Based Biosensors -- 8.5.1 Interferometric Biosensors -- 8.5.2 Integrated Optical Microcavity-Based Biosensors -- 8.5.3 Grating-Based Biosensors -- 8.5.4 Photonic Crystal-Based Biosensors -- 8.5.5 Recent Trends in Label-Free Integrated Optics-Based Waveguide Biosensors -- 8.6 Optical Fiber-Based Biosensors -- 8.6.1 Fiber Bragg Grating-Based Biosensors -- 8.6.2 Long-Period Grating-Based Biosensors -- 8.6.3 Optical Fiber-Based Interferometric Biosensors -- 8.6.4 Evanescence Wave Absorbance-Based Optical Fiber -- 8.7 Lab-On-A-Chip Integration -- 8.8 Summary -- References -- 9 Light Propagation in Highly Scattering Turbid Media: Concepts, Techniques, and Biomedical Applications -- 9.1 Introduction -- 9.2 Physics Behind Optical Imaging Through a Highly Scattering Turbid Medium -- 9.2.1 Components of Transmitted Light -- 9.2.2 Key Optical Parameters for Describing Light Propagation in Highly Scattering Media.

9.2.3 Values of Key Optical Parameters for Human Tissues and Some Model Media -- 9.2.4 Optical Absorption Spectra of Key Chromophores in Tissues -- 9.3 Study of Ballistic and Diffuse Light Components -- 9.4 Photon-Sorting Gates -- 9.4.1 Time Gate -- 9.4.2 Absorption Gate -- 9.4.3 Fourier Space Gate and Microscopic Imaging -- 9.4.4 Polarization Gate -- 9.5 Transition From Ballistic to Diffuse Imaging in Turbid Media -- 9.6 Conclusion -- Acknowledgments -- References -- 10 Photodynamic Therapy -- 10.1 Historical Overview of PDT -- 10.2 Introduction to PDT -- 10.2.1 Photophysics -- 10.2.2 Photochemistry -- 10.3 Photosensitizer Structure and Photophysical Properties -- 10.4 Light Dosimetry and Photodynamic Therapy Light Sources -- 10.4.1 Tissue Optics -- 10.4.2 Fundamental Dosimetry Concepts -- 10.5 Light-Based Strategies to Enhance PDT -- 10.5.1 Two-Photon Excitation-PDT -- 10.5.2 Metronomic PDT -- 10.6 PDT Targeting and Nanotechnology -- 10.7 PDT for Dermatology -- 10.7.1 Actinic Keratosis -- 10.7.2 Bowens Disease Squamous Cell Carcinoma In Situ -- 10.7.3 Basal Cell Carcinoma -- 10.7.4 Melanoma -- 10.7.5 Mycosis Fungoides -- 10.7.6 Acne Vulgaris -- 10.7.7 Photorejuvenation -- 10.8 PDT for Oncology -- 10.9 PDT for Infectious Disease -- 10.9.1 In Vitro Studies of PDT -- 10.9.2 Photoinactivation of Viruses, Fungi, and Parasites -- 10.9.3 Animal Models of Wound Infections -- 10.9.4 Oral and Dental Infections -- 10.9.5 Leishmania -- 10.9.6 Mycobacterium tuberculosis -- 10.9.7 Otitis Media with Effusion (OME) -- 10.9.8 Osteomyelitis -- 10.9.9 Viral Infections -- 10.9.10 Clinical Applications for Peptic Ulcer Disease (PUD) -- 10.10 PDT in Ophthalmology -- 10.11 PDT and The Immune System -- 10.12 Conclusion -- Acknowledgment -- References -- 11 Imaging and Probing Cells Beyond the Optical Diffraction Limit.

11.1 The Quest for Achieving Optical Resolution Beyond ABBE'S Limit.