Introduction to Biophotonics

Cover Page......Page 1
Title Page......Page 3
ISBN 0471287709......Page 4
SUMMARY OF CONTENTS......Page 5
2. Fundamentals of Light and Matter......Page 6
5. Principles of Lasers, Current Laser Technology, and Nonlinear Optics......Page 7
7. Bioimaging: Principles and Techniques......Page 8
8. Bioimaging: Applications......Page 9
9. Optical Biosensors......Page 10
12. Light-Activated Therapy: Photodynamic Therapy......Page 11
14. Laser Tweezers and Laser Scissors......Page 12
16. Biomaterials for Photonics......Page 13
Preface......Page 14
ACKNOWLEDGMENTS......Page 16
1.1 BIOPHOTONICS—A NEW FRONTIER......Page 17
1.2 AN INVITATION TO MULTIDISCIPLINARY EDUCATION, TRAINING, AND RESEARCH......Page 18
1.3 OPPORTUNITIES FOR BOTH BASIC RESEARCH AND BIOTECHNOLOGY DEVELOPMENT......Page 20
1.4 SCOPE OF THIS BOOK......Page 21
CHAPTER 2 Fundamentals of Light and Matter......Page 27
2.1.1 Dual Character of Light......Page 28
2.1.2 Propagation of Light as Waves......Page 30
2.1.3 Coherence of Light......Page 33
2.1.4 Light as Photon Particles......Page 35
2.1.5 Optical Activity and Birefringence......Page 36
2.2.1 Introductory Concepts......Page 37
2.2.2 Quantized States of Atoms......Page 40
2.2.3 Quantized States of Molecules: Partitioning of Molecular Energies......Page 43
2.2.4 Electronic States of a Molecule......Page 45
2.2.5 Bonding in Organic Molecules......Page 51
2.2.6 Conjugated Organic Molecules......Page 53
2.2.7 Vibrational States of a Molecule......Page 55
2.3 INTERMOLECULAR EFFECTS......Page 57
2.4 THREE-DIMENSIONAL STRUCTURES AND STEREOISOMERS......Page 59
HIGHLIGHTS OF THE CHAPTER......Page 62
REFERENCES......Page 64
CHAPTER 3 Basics of Biology......Page 66
3.1 INTRODUCTORY CONCEPTS......Page 67
3.2 CELLULAR STRUCTURE......Page 68
3.3 VARIOUS TYPES OF CELLS......Page 74
3.4 CHEMICAL BUILDING BLOCKS......Page 76
3.5 INTERACTIONS DETERMINING THREE-DIMENSIONAL STRUCTURES OF BIOPOLYMERS......Page 84
3.6 OTHER IMPORTANT CELLULAR COMPONENTS......Page 88
3.7 CELLULAR PROCESSES......Page 89
3.8 PROTEIN CLASSIFICATION AND FUNCTION......Page 98
3.9 ORGANIZATION OF CELLS INTO TISSUES......Page 101
3.10 TYPES OF TISSUES AND THEIR FUNCTIONS......Page 103
3.11 TUMORS AND CANCERS......Page 104
HIGHLIGHTS OF THE CHAPTER......Page 105
REFERENCES......Page 107
CHAPTER 4 Fundamentals of Light–Matter Interactions......Page 108
4.1.1 Nature of Interactions......Page 109
4.1.2 Einstein’s Model of Absorption and Emission......Page 111
4.2 INTERACTION OF LIGHT WITH A BULK MATTER......Page 113
4.3 FATE OF EXCITED STATE......Page 115
4.4 VARIOUS TYPES OF SPECTROSCOPY......Page 118
4.5 ELECTRONIC ABSORPTION SPECTROSCOPY......Page 121
4.6 ELECTRONIC LUMINESCENCE SPECTROSCOPY......Page 125
4.7 VIBRATIONAL SPECTROSCOPY......Page 129
4.8 SPECTROSCOPY UTILIZING OPTICAL ACTIVITY OF CHIRAL MEDIA......Page 133
4.9 FLUORESCENCE CORRELATION SPECTROSCOPY (FCS)......Page 138
HIGHLIGHTS OF THE CHAPTER......Page 140
REFERENCES......Page 143
CHAPTER 5 Principles of Lasers, Current Laser Technology, and Nonlinear Optics......Page 145
5.1.1 Lasers: A New Light Source......Page 146
5.1.2 Principles of Laser Action......Page 147
5.1.3 Classification of Lasers......Page 151
5.2 CURRENT LASER TECHNOLOGIES......Page 155
5.3 QUANTITATIVE DESCRIPTION OF LIGHT: RADIOMETRY......Page 158
5.4.1 Mechanism of Nonlinear Optical Processes......Page 159
5.4.2 Frequency Conversion by a Second-Order Nonlinear Optical Process......Page 161
5.4.3 Symmetry Requirement for a Second-Order Process......Page 162
5.4.4 Frequency Conversion by a Third-Order Nonlinear Optical Process......Page 164
5.4.5 Multiphoton Absorption......Page 165
5.5 TIME-RESOLVED STUDIES......Page 168
5.6 LASER SAFETY......Page 170
HIGHLIGHTS OF THE CHAPTER......Page 172
REFERENCES......Page 173
CHAPTER 6 Photobiology......Page 175
6.2 INTERACTION OF LIGHT WITH CELLS......Page 176
6.2.1 Light Absorption in Cells......Page 177
6.2.2 Light-Induced Cellular Processes......Page 179
6.2.3 Photochemistry Induced by Exogenous Photosensitizers......Page 183
6.3 INTERACTION OF LIGHT WITH TISSUES......Page 184
6.4 PHOTOPROCESSES IN BIOPOLYMERS......Page 191
6.4.1 The Human Eye and Vision......Page 192
6.4.2 Photosynthesis......Page 197
6.5.1 Free-Space Propagation......Page 202
6.5.2 Optical Fiber Delivery System......Page 203
6.5.3 Articulated Arm Delivery......Page 205
6.6 IN VIVO SPECTROSCOPY......Page 206
6.7 OPTICAL BIOPSY......Page 207
6.8 SINGLE-MOLECULE DETECTION......Page 211
HIGHLIGHTS OF THE CHAPTER......Page 213
REFERENCES......Page 215
CHAPTER 7 Bioimaging: Principles and Techniques......Page 219
7.1 BIOIMAGING: AN IMPORTANT BIOMEDICAL TOOL......Page 221
7.2 AN OVERVIEW OF OPTICAL IMAGING......Page 222
7.3.1 Simple Microscope......Page 225
7.3.2 Compound Microscope......Page 226
7.3.3 Kohler Illumination......Page 228
7.3.4 Numerical Aperture and Resolution......Page 230
7.3.5 Optical Aberrations and Different Types of Objectives......Page 231
7.3.7 Dark-Field Microscopy......Page 232
7.3.8 Differential Interference Contrast Microscopy (DIC)......Page 233
7.4 FLUORESCENCE MICROSCOPY......Page 235
7.5 SCANNING MICROSCOPY......Page 236
7.7 CONFOCAL MICROSCOPY......Page 237
7.8 MULTIPHOTON MICROSCOPY......Page 239
Merits of TPLSM......Page 240
7.9 OPTICAL COHERENCE TOMOGRAPHY......Page 241
Advantages of OCT......Page 243
7.10 TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY......Page 244
7.11 NEAR-FIELD OPTICAL MICROSCOPY......Page 248
7.12 SPECTRAL AND TIME-RESOLVED IMAGING......Page 250
7.12.2 Bandpass Filters......Page 251
7.12.4 Acousto-Optic Tunable Filters......Page 252
7.13 FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) IMAGING......Page 253
7.14 FLUORESCENCE LIFETIME IMAGING MICROSCOPY (FLIM)......Page 254
7.15 NONLINEAR OPTICAL IMAGING......Page 256
7.15.1 Second-Harmonic Microscopy......Page 257
7.15.3 Coherent Anti-Stokes Raman Scattering (CARS) Microscopy......Page 259
7.16.2 4Pi Imaging......Page 261
7.17 SOME COMMERCIAL SOURCES OF IMAGING INSTRUMENTS......Page 262
HIGHLIGHTS OF THE CHAPTER......Page 263
REFERENCES......Page 265
CHAPTER 8 Bioimaging: Applications......Page 271
8.1.1 Endogenous Fluorophores......Page 272
8.1.2 Exogenous Fluorophores......Page 273
8.1.3 Organometallic Complex Fluorophores......Page 280
8.1.5 Two-Photon Fluorophores......Page 281
8.2 GREEN FLUORESCENT PROTEIN......Page 285
8.3 IMAGING OF ORGANELLES......Page 287
8.4.1 Confocal Microscopy......Page 289
8.4.2 Near-Field Imaging......Page 290
8.5.1 Probing Cellular Ionic Environment......Page 292
8.5.2 Intracellular pH Measurements......Page 293
8.5.3 Optical Tracking of Drug–Cell Interactions......Page 295
8.5.4 Imaging of Nucleic acids......Page 297
8.5.5. Cellular Interactions Probed by FRET/FLIM Imaging......Page 303
8.6 TISSUE IMAGING......Page 305
8.7 IN VIVO IMAGING......Page 310
8.8 FUTURE DIRECTIONS......Page 317
HIGHLIGHTS OF THE CHAPTER......Page 319
REFERENCES......Page 322
CHAPTER 9 Optical Biosensors......Page 327
9.1 BIOSENSORS: AN INTRODUCTION......Page 328
9.2.1 Biorecognition......Page 330
9.2.2 Optical Transduction......Page 332
9.2.4 Fluorescence Energy Transfer Sensors......Page 333
9.2.5 Molecular Beacons......Page 336
9.2.6 Optical Geometries of Biosensing......Page 337
9.3.1 Immobilization......Page 339
9.4 FIBER-OPTIC BIOSENSORS......Page 343
9.5 PLANAR WAVEGUIDE BIOSENSORS......Page 347
9.6 EVANESCENT WAVE BIOSENSORS......Page 350
9.7 INTERFEROMETRIC BIOSENSORS......Page 354
9.8 SURFACE PLASMON RESONANCE BIOSENSORS......Page 355
9.9 SOME RECENT NOVEL SENSING METHODS......Page 359
9.10 FUTURE DIRECTIONS......Page 363
HIGHLIGHTS OF THE CHAPTER......Page 365
REFERENCES......Page 368
CHAPTER 10 Microarray Technology for Genomics and Proteomics......Page 373
10.1 MICROARRAYS, TOOLS FOR RAPID MULTIPLEX ANALYSIS......Page 374
10.2.1 Spotted Arrays......Page 379
10.2.2 Oligonucleotide Arrays......Page 382
10.2.3 Other Microarray Technologies......Page 383
10.3 PROTEIN MICROARRAY TECHNOLOGY......Page 384
10.4 CELL MICROARRAY TECHNOLOGY......Page 391
10.6 SOME EXAMPLES OF APPLICATION OF MICROARRAYS......Page 395
10.7 FUTURE DIRECTIONS......Page 398
10.8 COMPANIES PRODUCING MICROARRAYS......Page 399
HIGHLIGHTS OF THE CHAPTER......Page 400
REFERENCES......Page 402
CHAPTER 11 Flow Cytometry......Page 406
11.1 A CLINICAL, BIODETECTION, AND RESEARCH TOOL......Page 407
11.2.1 Basic Steps......Page 410
11.2.2 The Components of a Flow Cytometer......Page 411
11.2.3 Optical Response......Page 419
11.3 FLUOROCHROMES FOR FLOW CYTOMETRY......Page 421
11.4 DATA MANIPULATION AND PRESENTATION......Page 424
11.5.1 Immunophenotyping......Page 431
11.5.2 DNA Analysis......Page 434
11.6 FUTURE DIRECTIONS......Page 439
HIGHLIGHTS OF THE CHAPTER......Page 442
REFERENCES......Page 446
CHAPTER 12 Light-Activated Therapy: Photodynamic Therapy......Page 449
12.1 PHOTODYNAMIC THERAPY: BASIC PRINCIPLES......Page 450
12.2 PHOTOSENSITIZERS FOR PHOTODYNAMIC THERAPY......Page 453
12.2.1 Porphyrin Derivatives......Page 454
12.2.2 Chlorins and Bacteriochlorins......Page 456
12.2.3 Benzoporphyrin Derivatives......Page 457
12.2.4 5-Aminolaevulinic Acid (ALA)......Page 458
12.2.6 Phthalocyanines and Naphthalocyanines......Page 459
12.2.8 Dendritic Photosensitizers......Page 461
12.3 APPLICATIONS OF PHOTODYNAMIC THERAPY......Page 463
12.4 MECHANISM OF PHOTODYNAMIC ACTION......Page 466
12.5.1 Light Source......Page 469
12.5.2 Laser Dosimetry......Page 470
12.6 TWO-PHOTON PHOTODYNAMIC THERAPY......Page 471
12.7 CURRENT RESEARCH AND FUTURE DIRECTIONS......Page 473
HIGHLIGHTS OF THE CHAPTER......Page 476
REFERENCES......Page 477
CHAPTER 13 Tissue Engineering with Light......Page 480
13.1 TISSUE ENGINEERING AND LIGHT ACTIVATION......Page 481
13.2 LASER TISSUE CONTOURING AND RESTRUCTURING......Page 483
13.3 LASER TISSUE WELDING......Page 488
13.4 LASER TISSUE REGENERATION......Page 491
13.5 FEMTOLASER SURGERY......Page 492
13.6 FUTURE DIRECTIONS......Page 494
HIGHLIGHTS OF THE CHAPTER......Page 495
REFERENCES......Page 496
CHAPTER 14 Laser Tweezers and Laser Scissors......Page 498
14.1 NEW BIOLOGICAL TOOLS FOR MICROMANIPULATION BY LIGHT......Page 499
14.2 PRINCIPLE OF LASER TWEEZER ACTION......Page 503
14.3 DESIGN OF A LASER TWEEZER......Page 506
14.4 OPTICAL TRAPPING USING NON-GAUSSIAN BEAMS......Page 511
14.5 DYNAMIC HOLOGRAPHIC OPTICAL TWEEZERS......Page 512
14.6 LASER SCISSORS......Page 515
14.6.1 Laser Pressure Catapulting (LPC)......Page 516
14.7.1 Manipulation of Single DNA Molecules......Page 518
14.7.2 Molecular Motors......Page 522
14.7.3 Protein–Protein Interactions......Page 523
14.7.4 Laser Microbeams for Genomics and Proteomics......Page 525
14.7.5 Laser Manipulation in Plant Biology......Page 526
14.7.6 Laser Micromanipulation for Reproduction Medicine......Page 527
14.8 FUTURE DIRECTIONS......Page 528
14.8.2 Single Molecule Biofunctions......Page 529
HIGHLIGHTS OF THE CHAPTER......Page 530
REFERENCES......Page 532
CHAPTER 15 Nanotechnology for Biophotonics: Bionanophotonics......Page 536
15.1 THE INTERFACE OF BIOSCIENCE, NANOTECHNOLOGY, AND PHOTONICS......Page 537
15.2 NANOCHEMISTRY......Page 539
15.3 SEMICONDUCTOR QUANTUM DOTS FOR BIOIMAGING......Page 544
15.5 UP-CONVERTING NANOPHORES......Page 548
15.6 PEBBLE NANOSENSORS FOR IN VITRO BIOANALYSIS......Page 552
15.7 NANOCLINICS FOR OPTICAL DIAGNOSTICS AND TARGETED THERAPY......Page 553
15.8 FUTURE DIRECTIONS......Page 555
HIGHLIGHTS OF THE CHAPTER......Page 557
REFERENCES......Page 559
16.1 PHOTONICS AND BIOMATERIALS......Page 561
16.2 BIODERIVED MATERIALS......Page 564
16.3 BIOINSPIRED MATERIALS......Page 575
16.4 BIOTEMPLATES......Page 576
16.5 BACTERIA AS BIOSYNTHESIZERS FOR PHOTONIC POLYMERS......Page 580
16.6 FUTURE DIRECTIONS......Page 583
HIGHLIGHTS OF THE CHAPTER......Page 584
REFERENCES......Page 585
A......Page 589
B......Page 590
C......Page 591
D......Page 593
E......Page 594
F......Page 595
G......Page 596
I......Page 597
L......Page 598
M......Page 600
N......Page 601
O......Page 602
P......Page 603
R......Page 605
S......Page 606
T......Page 607
U......Page 608
X,Y,Z......Page 609
Color Plates......Page 610
Back Page......Page 618