The world of nano-biomechanics : mechanical imaging and measurement by atomic force microscopy / by Atsushi Ikai.

Format:

Book

Author/Creator:

Ikai, Atsushi.

Contributor:

Louis A. Duhring Fund.

Language:

English

Subjects (All):

Biomechanics.

Nanostructures.

Atomic force microscopy.

Physical Description:

xvi, 283 pages : illustrations (some color) ; 24 cm

Edition:

First edition.

Place of Publication:

Amsterdam ; New York : Elsevier, 2008.

Summary:

Biomechanics in the nanometer-scaled world is an exciting recent development where biology meets physics and engineering. Surrounded by the thermal agitation of solvent molecules, proteins, DNAs, polysaccharides, lipid membranes, and the functional structures based on their interactions mustkeep their integrity as information processing machineries for their biological functions. The requirements for their mechanical rigidity and flexibility for this purpose is now being studied at the single molecular level using state-of-the-art technologies from recent developments. This book introduces elementary mechanics, necessary to understand the biology of the nano-world. Breathtaking experiments such as single molecule stretching of DNA, RNA and proteins are now revealing the internal mechanics of their molecular structure. Just looking into the response of protein molecules against the tensile stretching exposing their interior under the physiological/conditions is phenomenal. Written by an author with both a biochemical and biophysical background, this book is an ideal for, offering guidance to bio-nanomechanics who are unfamiliar with mechanical concepts.

Contents:

1 Force in Biology 1

1.1 What Are We Made Of? 1

1.2 Human Body and Force 3

1.2.1 Gravity and hydrodynamic force 3

1.2.2 Frictional coefficients 5

1.3 Biomechanics as the Big Brother 6

1.4 Molecular Basis for Structural Design 8

1.5 Soft versus Hard Materials 11

1.6 Biological and Biomimetic Structural Materials 16

1.7 Wear and Tear of Biological Structures 17

1.8 Thermodynamics and Mechanics in Nanometer Scale Biology 19

2.1 Elastic and Plastic Deformation of Materials 23

2.2 Stress and Strain Relationship 24

2.3 Mechanical Breakdown of Materials 27

2.4 Viscoelasticity 27

2.5 Mechanical Moduli of Biological Materials 29

2.5.1 Mechanical deformations 29

2.5.2 Shear deformation and rigidity modulus 30

2.5.3 Triaxial deformation and bulk compressibility 30

2.5.4 Y, G, and K are all related through Poisson's ratio 31

2.5.5 What is Poisson's ratio? 34

2.6 Fluid and Viscosity 35

2.7 Adhesion and Friction 36

2.8 Mechanically Controlled Systems 38

3 Force and Force Measurement Apparatuses 43

3.1 Mechanical, Thermal, and Chemical Forces 43

3.2 Laser Trap 45

3.3 Atomic Force Microscope 48

3.3.1 History and principle 48

3.3.2 How to use AFM for force measurement 50

3.4 Biomembrane Force Probe 54

3.4.1 Equation of force transduction 56

3.5 Magnetic Beads 56

3.6 Gel Columns 56

3.7 Cantilever Force Sensors 57

3.8 Loading-rate Dependence 58

3.8.1 Derivation of the loading-rate dependence of the mean rupture force 61

3.9 Force Clamp Method 63

3.10 Specific versus Nonspecific Forces 64

4 Polymer Chain Mechanics 69

4.1 Polymers in Biological World 69

4.2 Polymer Chains 71

4.3 End-to-End Distance 74

4.3.2 Randomly coiled polymer 75

4.3.3 The FJC (Freely Jointed Chain) 76

4.4 Persistence Length 79

4.4.1 Effect of cross-links 82

4.5 Polymers in Solution 82

4.5.1 General cases 82

4.5.2 Denatured proteins and DNA 83

4.6 Polymers on the Surface 83

4.7 Polymer as Biomimetic Materials 84

4.8 Polymer Pull-out 85

5 Interaction Forces 89

5.1 Covalent versus Noncovalent Force 89

5.2 Basics of Electrostatic Interaction Force 90

5.3 Various Types of Noncovalent Forces 92

5.3.1 Charge-charge interaction 92

5.3.2 Charge-dipole interaction 93

5.3.3 Dipole-dipole interaction 93

5.3.4 Dipole-induced dipole interaction 94

5.3.5 Dispersion interaction 95

5.3.6 Hydrogen-bonding interaction 96

5.3.7 Hydrophobic interaction 97

5.4 Application of External Force 98

5.5 Interaction Force Between Macromolecules 99

5.5.1 Exclusion effect 99

5.5.2 Depletion effect 100

5.6 Water at the Interface 101

6 Single-Molecular Interaction Forces 105

6.1 Ligand-receptor Interactions 106

6.1.1 Biotin-avidin interaction 106

6.1.2 Interaction of synaptic-vesicle fusion proteins 109

6.1.3 Interaction between transferrin and its membrane receptor 110

6.2 Sugar-lectin Interactions 111

6.3 Antigen-antibody Interactions 111

6.4 GroEL and Unfolded-protein Interactions 112

6.5 Lipid-protein Interactions 114

6.6 Anchoring Force of Proteins to the Membrane 115

6.7 Receptor Mapping 116

6.8 Protein Unanchoring and Identification 119

6.9 Membrane Breaking 120

7 Single-molecule DNA and RNA Mechanics 127

7.1 Stretching of Double-stranded DNA 127

7.2 Hybridization and Mechanical Force 130

7.3 Chain Dynamics and Transition of DNA and RNA 131

7.4 DNA-protein Interaction 132

7.5 Prospect for Sequence Analysis 134

8 Single-molecule Protein Mechanics 137

8.1 Protein-stretching Experiments 137

8.2 Intramolecular Cores 141

8.3 Stretching of Modular Proteins 144

8.4 Dynamic Stretching 146

8.5 Catch Bond 147

8.6 Protein-compression Experiments 147

8.6.1 Hertz model 148

8.6.2 Tatara model 152

8.7 Internal Mechanics of Protein Molecules 154

8.8 Mechanical Control of Protein Activity 155

8.9 Computer Simulation of Protein Deformation 157

Case Study: Carbonic Anhydrase II / R. Afrin 159

9 Motion in Nano-biology 173

9.1 Cell Movement and Structural Proteins 173

9.2 Muscle and Motor Proteins 176

9.3 Single-motor Measurements 178

9.4 Flagella for Bacterial Locomotion 179

9.5 Mycoplasma Gliding 179

9.6 Mechanics and Efficiency of Motor Proteins 181

10 Cell Mechanics 185

10.1 Changes in Shape of Red Blood Cell 185

10.2 Membrane and Cytoskeleton 189

10.3 Association of Membrane Proteins with Cytoskeleton 190

10.3.1 Detergent treatment 191

10.3.2 Diffusion coefficients 191

10.3.3 Force-curve measurement 192

10.4 Deformation of 2D Membrane 192

10.5 Helfrich Theory of Membrane Mechanics 195

10.6 Cytoplasm and Subcellular Structures 197

10.7 Indentation Experiment and the Use of Sneddon's Formulae 199

10.7.1 Sneddon's formula 199

10.7.2 Correction for thin samples 201

10.8 Deformation Mechanics of a Thin Plate 202

11 Manipulation at the Molecular Level 209

11.1 Prospects for Useful Applications of Nanomechanics 209

11.2 Cell Surgery 210

11.3 Chromosomal Surgery and Gene Manipulation 210

11.4 Tissue Surgery 211

11.5 Liposomal Technology 213

11.6 Drug Delivery 213

11.7 DNA and RNA Recovery From the Chromosome and the Cell 214

12 Finite Element Analysis of Microscopic Biological Structures / S. Kasas, T. Gmur, G. Dietler 221

12.2 A Brief History of the Finite Element Method 222

12.3 The Finite Element Method 223

12.4 Application of the Finite Element Method to Microbiological Samples 225

12.4.1 Proteins 227

12.4.2 Axonemata and cilia 229

12.4.3 Cell nuclei 232

12.4.4 Micro-organisms 232

12.4.5 Single cells 233

12.4.6 Embryology and cell division 236

A.1 Beam Bending 245

A.1.1 Beam Bending 245

A.1.1.1 Supported beam at two ends 245

A.1.1.2 Cantilever bending 251

A.1.1.3 Distributed force 252

A.1.1.4 Radius of curvature 254

A.1.2 Buckling 256

A.1.3 Basics of Linear Mechanics According to Landau and Lifshitz 259

A.2 V-shaped Cantilever 261

A.2.1 V-shaped Cantilever 261

A.3 Persistence Length and Kuhn Statistical Segment 263

A.3.1 Persistence Length and Kuhn Statistical Segment 263

A.4 Hertz Model 265

A.4.1 Hertz Model 265

A.4.1.1 Concentrated load 265

A.4.1.2 Distributed load 265

A.4.1.3 Contact problem of two spheres 271.

Notes:

Includes bibliographical references and index.

Local Notes:

Acquired for the Penn Libraries with assistance from the Louis A. Duhring Fund.

ISBN:

9780444527776

044452777X

OCLC:

155681235