Note: Intro -- INTRODUCTION TO BIOPHOTONICS -- SUMMARY OF CONTENTS -- CONTENTS -- Preface -- Acknowlegments -- 1. Introduction -- 1.1 Biophotonics-A New Frontier -- 1.2 An Invitation to Multidisciplinary Education, Training, and Research -- 1.3 Opportunities for Both Basic Research and Biotechnology Development -- 1.4 Scope of this Book -- 2. Fundamentals of Light and Matter -- 2.1 Nature of Light -- 2.1.1 Dual Character of Light -- 2.1.2 Propagation of Light as Waves -- 2.1.3 Coherence of Light -- 2.1.4 Light as Photon Particles -- 2.1.5 Optical Activity and Birefringence -- 2.1.6 Different Light Sources -- 2.2 Quantized States of Matter -- 2.2.1 Introductory Concepts -- 2.2.2 Quantized States of Atoms -- 2.2.3 Quantized States of Molecules: Partitioning of Molecular Energies -- 2.2.4 Electronic States of a Molecule -- 2.2.5 Bonding in Organic Molecules -- 2.2.6 Conjugated Organic Molecules -- 2.2.7 Vibrational States of a Molecule -- 2.3 Intermolecular Effects -- 2.4 Three-Dimensional Structures and Stereoisomers -- Highlights of the Chapter -- References -- 3. Basics of Biology -- 3.1 Introductory Concepts -- 3.2 Cellular Structure -- 3.3 Various Types of Cells -- 3.4 Chemical Building Blocks -- 3.5 Interactions Determining Three-Dimensional Structures of Biopolymers -- 3.6 Other Important Cellular Components -- 3.7 Cellular Processes -- 3.8 Protein Classification and Function -- 3.9 Organization of Cells into Tissues -- 3.10 Types of Tissues and Their Functions -- 3.11 Tumors and Cancers -- Highlights of the Chapter -- References -- 4. Fundamentals of Light-Matter Interactions -- 4.1 Interactions Between Light and a Molecule -- 4.1.1. Nature of Interactions -- 4.1.2. Einstein's Model of Absorption and Emission -- 4.2 Interaction of Light with a Bulk Matter -- 4.3 Fate of Excited State -- 4.4 Various Types of Spectroscopy. , 4.5 Electronic Absorption Spectroscopy -- 4.6 Electronic Luminescence Spectroscopy -- 4.7 Vibrational Spectroscopy -- 4.8 Spectroscopy Utilizing Optical Activity of Chiral Media -- 4.9 Fluorescence Correlation Spectroscopy (FCS) -- Highlights of the Chapter -- References -- 5. Principles of Lasers, Current Laser Technology, and Nonlinear Optics -- 5.1 Principles of Lasers -- 5.1.1 Lasers: A New Light Source -- 5.1.2 Principles of Laser Action -- 5.1.3 Classification of Lasers -- 5.1.4 Some Important Lasers for Biophotonics -- 5.2 Current Laser Technologies -- 5.3 Quantitative Description of Light: Radiometry -- 5.4 Nonlinear Optical Processes with Intense Laser Beam -- 5.4.1 Mechanism of Nonlinear Optical Processes -- 5.4.2 Frequency Conversion by a Second-Order Nonlinear Optical Process -- 5.4.3 Symmetry Requirement for a Second-Order Process -- 5.4.4 Frequency Conversion by a Third-Order Nonlinear Optical Process -- 5.4.5 Multiphoton Absorption -- 5.5 Time-Resolved Studies -- 5.6 Laser Safety -- Highlights of the Chapter -- References -- 6. Photobiology -- 6.1 Photobiology-At the Core of Biophotonics -- 6.2 Interaction of Light with Cells -- 6.2.1 Light Absorption in Cells -- 6.2.2 Light-Induced Cellular Processes -- 6.2.3 Photochemistry Induced by Exogenous Photosensitizers -- 6.3 Interaction of Light with Tissues -- 6.4 Photoprocesses in Biopolymers -- 6.4.1 The Human Eye and Vision -- 6.4.2 Photosynthesis -- 6.5 In Vivo Photoexcitation -- 6.5.1 Free-Space Propagation -- 6.5.2 Optical Fiber Delivery System -- 6.5.3 Articulated Arm Delivery -- 6.5.4 Hollow Tube Waveguides -- 6.6 In Vivo Spectroscopy -- 6.7 Optical Biopsy -- 6.8 Single-Molecule Detection -- Highlights of the Chapter -- References -- 7. Bioimaging: Principles and Techniques -- 7.1 Bioimaging: An Important Biomedical Tool -- 7.2 An Overview of Optical Imaging. , 7.3 Transmission Microscopy -- 7.3.1 Simple Microscope -- 7.3.2 Compound Microscope -- 7.3.3 Kohler Illumination -- 7.3.4 Numerical Aperture and Resolution -- 7.3.5 Optical Aberrations and Different Types of Objectives -- 7.3.6 Phase Contrast Microscopy -- 7.3.7 Dark-Field Microscopy -- 7.3.8 Differential Interference Contrast Microscopy (DIC) -- 7.4 Fluorescence Microscopy -- 7.5 Scanning Microscopy -- 7.6 Inverted and Upright Microscopes -- 7.7 Confocal Microscopy -- 7.8 Multiphoton Microscopy -- 7.9 Optical Coherence Tomography -- 7.10 Total Internal Reflection Fluorescence Microscopy -- 7.11 Near-Field Optical Microscopy -- 7.12 Spectral and Time-Resolved Imaging -- 7.12.1 Spectral Imaging -- 7.12.2 Bandpass Filters -- 7.12.3 Excitation Wavelength Selection -- 7.12.4 Acousto-Optic Tunable Filters -- 7.12.5 Localized Spectroscopy -- 7.13 Fluorescence Resonance Energy Transfer (FRET) Imaging -- 7.14 Fluorescence Lifetime Imaging Microscopy (FLIM) -- 7.15 Nonlinear Optical Imaging -- 7.15.1 Second-Harmonic Microscopy -- 7.15.2 Third-Harmonic Microscopy -- 7.15.3 Coherent Anti-Stokes Raman Scattering (CARS) Microscopy -- 7.16 Future Directions of Optical Bioimaging -- 7.16.1 Multifunctional Imaging -- 7.16.2 4Pi Imaging -- 7.16.3 Combination Microscopes -- 7.16.4 Miniaturized Microscopes -- 7.17 Some Commercial Sources of Imaging Instruments -- Highlights of the Chapter -- References -- 8. Bioimaging: Applications -- 8.1 Fluorophores as Bioimaging Probes -- 8.1.1 Endogenous Fluorophores -- 8.1.2 Exogenous Fluorophores -- 8.1.3 Organometallic Complex Fluorophores -- 8.1.4 Near-IR and IR Fluorophore -- 8.1.5 Two-Photon Fluorophores -- 8.1.6 Inorganic Nanoparticles -- 8.2 Green Fluorescent Protein -- 8.3 Imaging of Organelles -- 8.4 Imaging of Microbes -- 8.4.1 Confocal Microscopy -- 8.4.2 Near-Field Imaging -- 8.5 Cellular Imaging. , 8.5.1 Probing Cellular Ionic Environment -- 8.5.2 Intracellular pH Measurements -- 8.5.3 Optical Tracking of Drug-Cell Interactions -- 8.5.4 Imaging of Nucleic Acids -- 8.5.5 Cellular Interactions Probed by FRET/FLIM Imaging -- 8.6 Tissue Imaging -- 8.7 In Vivo Imaging -- 8.8 Future Directions -- 8.9 Commercially Available Optical Imaging Accessories -- Highlights of the Chapter -- References -- 9. Optical Biosensors -- 9.1 Biosensors: An Introduction -- 9.2 Principles of Optical Biosensing -- 9.2.1 Biorecognition -- 9.2.2 Optical Transduction -- 9.2.3 Fluorescence Sensing -- 9.2.4 Fluorescence Energy Transfer Sensors -- 9.2.5 Molecular Beacons -- 9.2.6 Optical Geometries of Biosensing -- 9.3 Support for and Immobilization of Biorecognition Elements -- 9.3.1 Immobilization -- 9.4 Fiber-Optic Biosensors -- 9.5 Planar Waveguide Biosensors -- 9.6 Evanescent Wave Biosensors -- 9.7 Interferometric Biosensors -- 9.8 Surface Plasmon Resonance Biosensors -- 9.9 Some Recent Novel Sensing Methods -- 9.10 Future Directions -- 9.11 Commercially Available Biosensors -- Highlights of the Chapter -- References -- 10. Microarray Technology for Genomics and Proteomics -- 10.1 Microarrays, Tools for Rapid Multiplex Analysis -- 10.2 DNA Microarray Technology -- 10.2.1 Spotted Arrays -- 10.2.2 Oligonucleotide Arrays -- 10.2.3 Other Microarray Technologies -- 10.3 Protein Microarray Technology -- 10.4 Cell Microarray Technology -- 10.5 Tissue Microarray Technology -- 10.6 Some Examples of Application of Microarrays -- 10.7 Future Directions -- 10.8 Companies Producing Microarrays -- Highlights of the Chapter -- References -- 11. Flow Cytometry -- 11.1 A Clinical, Biodetection, and Research Tool -- 11.2 Basics of Flow Cytometry -- 11.2.1 Basic Steps -- 11.2.2 The Components of a Flow Cytometer -- 11.2.3 Optical Response -- 11.3 Fluorochromes for Flow Cytometry. , 11.4 Data Manipulation and Presentation -- 11.5 Selected Examples of Applications -- 11.5.1 Immunophenotyping -- 11.5.2 DNA Analysis -- 11.6 Future Directions -- 11.7 Commercial Flow Cytometry -- Highlights of the Chapter -- References -- 12. Light-Activated Therapy: Photodynamic Therapy -- 12.1 Photodynamic Therapy: Basic Principles -- 12.2 Photosensitizers for Photodynamic Therapy -- 12.2.1 Porphyrin Derivatives -- 12.2.2 Chlorins and Bacteriochlorins -- 12.2.3 Benzoporphyrin Derivatives -- 12.2.4 5-Aminolaevulinic Acid (ALA) -- 12.2.5 Texaphyrins -- 12.2.6 Phthalocyanines and Naphthalocyanines -- 12.2.7 Cationic Photosensitizers -- 12.2.8 Dendritic Photosensitizers -- 12.3 Applications of Photodynamic Therapy -- 12.4 Mechanism of Photodynamic Action -- 12.5 Light Irradiation for Photodynamic Therapy -- 12.5.1 Light Source -- 12.5.2 Laser Dosimetry -- 12.5.3 Light Delivery -- 12.6 Two-Photon Photodynamic Therapy -- 12.7 Current Research and Future Directions -- Highlights of the Chapter -- References -- 13. Tissue Engineering with Light -- 13.1 Tissue Engineering and Light Activation -- 13.2 Laser Tissue Contouring and Restructuring -- 13.3 Laser Tissue Welding -- 13.4 Laser Tissue Regeneration -- 13.5 Femtolaser Surgery -- 13.6 Future Directions -- Highlights of the Chapter -- References -- 14. Laser Tweezers and Laser Scissors -- 14.1 New Biological Tools for Micromanipulation by Light -- 14.2 Principle of Laser Tweezer Action -- 14.3 Design of a Laser Tweezer -- 14.4 Optical Trapping Using Non-Gaussian Beams -- 14.5 Dynamic Holographic Optical Tweezers -- 14.6 Laser Scissors -- 14.6.1 Laser Pressure Catapulting (LPC) -- 14.6.2 Laser Capture Microdissection (LCM) -- 14.7 Selected Examples of Applications -- 14.7.1 Manipulation of Single DNA Molecules -- 14.7.2 Molecular Motors -- 14.7.3 Protein-Protein Interactions. , 14.7.4 Laser Microbeams for Genomics and Proteomics.