World of Nano-Biomechanics (eBook)

Cover 1
Contents 6
Contributors 12
Preface 14
Chapter 1. Force in Biology 18
1.1 What are We Made of? 18
1.2 Human Body and Force 20
1.3 Biomechanics as the Big Brother 23
1.4 Molecular Basis for Structural Design 25
1.5 Soft versus Hard Materials 28
1.6 Biological and Biomimetic Structural Materials 33
1.7 Wear and Tear of Biological Structures 34
1.8 Thermodynamics and Mechanics in Nanometer Scale Biology 36
Bibliography 37
Chapter 2. Introduction to Basic Mechanics 40
2.1 Elastic and Plastic Deformation of Materials 40
2.2 Stress and Strain Relationship 41
2.3 Mechanical Breakdown of Materials 44
2.4 Viscoelasticity 44
2.5 Mechanical Moduli of Biological Materials 46
2.6 Fluid and Viscosity 52
2.7 Adhesion and Friction 53
2.8 Mechanically Controlled Systems 55
Bibliography 58
Chapter 3. Force and Force Measurement Apparatuses 60
3.1 Mechanical, Thermal, and Chemical Forces 60
3.2 Laser Trap 62
3.3 Atomic Force Microscope 65
3.4 Biomembrane Force Probe 71
3.5 Magnetic Beads 73
3.6 Gel Columns 73
3.7 Cantilever Force Sensors 74
3.8 Loading-rate Dependence 75
3.9 Force Clamp Method 80
3.10 Specific versus Nonspecific Forces 81
Bibliography 83
Chapter 4. Polymer Chain Mechanics 86
4.1 Polymers in Biological World 86
4.2 Polymer Chains 88
4.3 End-to-End Distance 91
4.4 Persistence Length 96
4.5 Polymers in Solution 99
4.6 Polymers on the Surface 100
4.7 Polymers as Biomimetic Materials 101
4.8 Polymer Pull-out 102
Bibliography 103
Chapter 5. Interaction Forces 106
5.1 Covalent versus Noncovalent Force 106
5.2 Basics of Electrostatic Interaction Force 107
5.3 Various Types of Noncovalent Forces 109
5.4 Application of External Force 115
5.5 Interaction Force Between Macromolecules 116
5.6 Water at the Interface 118
Bibliography 120
Chapter 6. Single-Molecular Interaction Forces 122
6.1 Ligand–receptor Interactions 123
6.2 Sugar–lectin Interactions 128
6.3 Antigen–antibody Interactions 128
6.4 GroEL and Unfolded-Protein Interactions 129
6.5 Lipid–protein Interactions 131
6.6 Anchoring Force of Proteins to the Membrane 132
6.7 Receptor Mapping 133
6.8 Protein Unanchoring and Identification 136
6.9 Membrane Breaking 137
Bibliography 139
Chapter 7. Single-molecule DNA and RNA Mechanics 144
7.1 Stretching of Double-stranded DNA 144
7.2 Hybridization and Mechanical Force 147
7.3 Chain Dynamics and Transition of DNA and RNA 148
7.4 DNA–protein Interaction 149
7.5 Prospect for Sequence Analysis 151
Bibliography 152
Chapter 8. Single-molecule Protein Mechanics 154
8.1 Protein-stretching Experiments 154
8.2 Intramolecular Cores 158
8.3 Stretching of Modular Proteins 161
8.4 Dynamic Stretching 163
8.5 Catch Bond 164
8.6 Protein-compression Experiments 164
8.7 Internal Mechanics of Protein Molecules 171
8.8 Mechanical Control of Protein Activity 172
8.9 Computer Simulation of Protein Deformation 174
Case Study: Carbonic Anhydrase II 176
Bibliography 184
Chapter 9. Motion in Nano-biology 190
9.1 Cell Movement and Structural Proteins 190
9.2 Muscle and Motor Proteins 193
9.3 Single-motor Measurements 195
9.4 Flagella for Bacterial Locomotion 196
9.5 Mycoplasma Gliding 196
9.6 Mechanics and Efficiency of Motor Proteins 198
Bibliography 198
Chapter 10. Cell Mechanics 202
10.1 Changes in Shape of Red Blood Cell 202
10.2 Membrane and Cytoskeleton 206
10.3 Association of Membrane Proteins with Cytoskeleton 207
10.4 Deformation of 2D Membrane 209
10.5 Helfrich Theory of Membrane Mechanics 212
10.6 Cytoplasm and Subcellular Structures 214
10.7 Indentation Experiment and the Use of Sneddon’s Formulae 216
10.8 Deformation Mechanics of a Thin Plate 219
Bibliography 222
Chapter 11. Manipulation at the Molecular Level 226
11.1 Prospects for Useful Applications of Nanomechanics 226
11.2 Cell Surgery 227
11.3 Chromosomal Surgery and Gene Manipulation 227
11.4 Tissue Surgery 228
11.5 Liposomal Technology 230
11.6 Drug Delivery 230
11.7 DNA and RNA Recovery from the Chromosome and the Cell 231
Bibliography 235
Chapter 12. Finite Element Analysis of Microscopic Biological Structures 238
12.1 Introduction 239
12.2 A Brief History of the Finite Element Method 239
12.3 The Finite Element Method 240
12.4 Application of the Finite Element Method to Microbiological Samples 242
12.5 Conclusion 256
Bibliography 257
Appendix 1. Beam Bending 262
A.1.1 Beam Bending 262
A.1.2 Buckling 273
A.1.3 Basics of Linear Mechanics According to Landau and Lifshitz 276
Bibliography 277
Appendix 2. V-shaped Cantilever 278
A.2.1 V-shaped Cantilever 278
Bibliography 279
Appendix 3. Persistence Length and Kuhn Statistical Segment 280
A.3.1 Persistence Length and Kuhn Statistical Segment 280
Appendix 4. Hertz Model 282
A.4.1 Hertz Model 282
Bibliography 292
Index 294