The World of Nano-Biomechanics: Mechanical Imaging and Measurement by Atomic Force Microscopy
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Table of contents
- Cover
- Contentsv
- Contributorsxi
- Prefacexiii
- Chapter 1. Force in Biology1
- 1.1 What are We Made of?1
- 1.2 Human Body and Force3
- 1.3 Biomechanics as the Big Brother6
- 1.4 Molecular Basis for Structural Design8
- 1.5 Soft versus Hard Materials11
- 1.6 Biological and Biomimetic Structural Materials16
- 1.7 Wear and Tear of Biological Structures17
- 1.8 Thermodynamics and Mechanics in Nanometer Scale Biology19
- Bibliography20
- Chapter 2. Introduction to Basic Mechanics23
- 2.1 Elastic and Plastic Deformation of Materials23
- 2.2 Stress and Strain Relationship24
- 2.3 Mechanical Breakdown of Materials27
- 2.4 Viscoelasticity27
- 2.5 Mechanical Moduli of Biological Materials29
- 2.6 Fluid and Viscosity35
- 2.7 Adhesion and Friction36
- 2.8 Mechanically Controlled Systems38
- Bibliography41
- Chapter 3. Force and Force Measurement Apparatuses43
- 3.1 Mechanical, Thermal, and Chemical Forces43
- 3.2 Laser Trap45
- 3.3 Atomic Force Microscope48
- 3.4 Biomembrane Force Probe54
- 3.5 Magnetic Beads56
- 3.6 Gel Columns56
- 3.7 Cantilever Force Sensors57
- 3.8 Loading-rate Dependence58
- 3.9 Force Clamp Method63
- 3.10 Specific versus Nonspecific Forces64
- Bibliography66
- Chapter 4. Polymer Chain Mechanics69
- 4.1 Polymers in Biological World69
- 4.2 Polymer Chains71
- 4.3 End-to-End Distance74
- 4.4 Persistence Length79
- 4.5 Polymers in Solution82
- 4.6 Polymers on the Surface83
- 4.7 Polymers as Biomimetic Materials84
- 4.8 Polymer Pull-out85
- Bibliography86
- Chapter 5. Interaction Forces89
- 5.1 Covalent versus Noncovalent Force89
- 5.2 Basics of Electrostatic Interaction Force90
- 5.3 Various Types of Noncovalent Forces92
- 5.4 Application of External Force98
- 5.5 Interaction Force Between Macromolecules99
- 5.6 Water at the Interface101
- Bibliography103
- Chapter 6. Single-Molecular Interaction Forces105
- 6.1 Ligand–receptor Interactions106
- 6.2 Sugar–lectin Interactions111
- 6.3 Antigen–antibody Interactions111
- 6.4 GroEL and Unfolded-Protein Interactions112
- 6.5 Lipid–protein Interactions114
- 6.6 Anchoring Force of Proteins to the Membrane115
- 6.7 Receptor Mapping116
- 6.8 Protein Unanchoring and Identification119
- 6.9 Membrane Breaking120
- Bibliography122
- Chapter 7. Single-molecule DNA and RNA Mechanics127
- 7.1 Stretching of Double-stranded DNA127
- 7.2 Hybridization and Mechanical Force130
- 7.3 Chain Dynamics and Transition of DNA and RNA131
- 7.4 DNA–protein Interaction132
- 7.5 Prospect for Sequence Analysis134
- Bibliography135
- Chapter 8. Single-molecule Protein Mechanics137
- 8.1 Protein-stretching Experiments137
- 8.2 Intramolecular Cores141
- 8.3 Stretching of Modular Proteins144
- 8.4 Dynamic Stretching146
- 8.5 Catch Bond147
- 8.6 Protein-compression Experiments147
- 8.7 Internal Mechanics of Protein Molecules154
- 8.8 Mechanical Control of Protein Activity155
- 8.9 Computer Simulation of Protein Deformation157
- Case Study: Carbonic Anhydrase II159
- Bibliography167
- Chapter 9. Motion in Nano-biology173
- 9.1 Cell Movement and Structural Proteins173
- 9.2 Muscle and Motor Proteins176
- 9.3 Single-motor Measurements178
- 9.4 Flagella for Bacterial Locomotion179
- 9.5 Mycoplasma Gliding179
- 9.6 Mechanics and Efficiency of Motor Proteins181
- Bibliography181
- Chapter 10. Cell Mechanics185
- 10.1 Changes in Shape of Red Blood Cell185
- 10.2 Membrane and Cytoskeleton189
- 10.3 Association of Membrane Proteins with Cytoskeleton190
- 10.4 Deformation of 2D Membrane192
- 10.5 Helfrich Theory of Membrane Mechanics195
- 10.6 Cytoplasm and Subcellular Structures197
- 10.7 Indentation Experiment and the Use of Sneddon’s Formulae199
- 10.8 Deformation Mechanics of a Thin Plate202
- Bibliography205
- Chapter 11. Manipulation at the Molecular Level209
- 11.1 Prospects for Useful Applications of Nanomechanics209
- 11.2 Cell Surgery210
- 11.3 Chromosomal Surgery and Gene Manipulation210
- 11.4 Tissue Surgery211
- 11.5 Liposomal Technology213
- 11.6 Drug Delivery213
- 11.7 DNA and RNA Recovery from the Chromosome and the Cell214
- Bibliography218
- Chapter 12. Finite Element Analysis of Microscopic Biological Structures221
- 12.1 Introduction222
- 12.2 A Brief History of the Finite Element Method222
- 12.3 The Finite Element Method223
- 12.4 Application of the Finite Element Method to Microbiological Samples225
- 12.5 Conclusion239
- Bibliography240
- Appendix 1. Beam BendingA1
- A.1.1 Beam BendingA1
- A.1.2 BucklingA12
- A.1.3 Basics of Linear Mechanics According to Landau and LifshitzA15
- BibliographyA16
- Appendix 2. V-shaped CantileverA17
- A.2.1 V-shaped CantileverA17
- BibliographyA18
- Appendix 3. Persistence Length and Kuhn Statistical SegmentA19
- A.3.1 Persistence Length and Kuhn Statistical SegmentA19
- Appendix 4. Hertz ModelA21
- A.4.1 Hertz ModelA21
- BibliographyA31
- Index277
By using nanotechnological methods, we can now poke around protein molecules, genes, membranes, cells and more. Observation of such entities through optical and electron microscopes tempt us to touch and manipulate them. It is now possible to do so, and scientists around the world have started pulling, pushing and cutting small structures at the base of life processes to understand the effect of our hand work.
The book describes the physical properties of such life supporting structures from the molecular level with a special emphasis on their designs based on the mechanical strength and flexibility, membrane and other biological nanostructures.
- Describes the basic mechanical features of proteins, DNA, cell membrane and other biological nanostructures
- Explains the basic concepts and mathematics of elementary mechanics needed to understand and perform experimental work
The book describes the physical properties of such life supporting structures from the molecular level with a special emphasis on their designs based on the mechanical strength and flexibility, membrane and other biological nanostructures.
- Describes the basic mechanical features of proteins, DNA, cell membrane and other biological nanostructures
- Explains the basic concepts and mathematics of elementary mechanics needed to understand and perform experimental work