Description
The World of Nano-Biomechanics, Second Edition, focuses on the remarkable progress in the application of force spectroscopy to molecular and cellular biology that has occurred since the book's first edition in 2008. The initial excitement of seeing and touching a single molecule of protein/DNA is now culminating in the development of various ways to manipulate molecules and cells almost at our fingertips, enabling live cell operations.
Topics include the development of molecular biosensors, mechanical diagnosis, cellular-level wound healing, and a look into the advances that have been made in our understanding of the significance of mechanical rigidity/flexibility of protein/DNA structure for the manifestation of biological activities.
The book begins with a summary of the results of basic mechanics to help readers who are unfamiliar with engineering mechanics. Then, representative results obtained on biological macromolecules and structures, such as proteins, DNA, RNA, polysaccharides, lipid membranes, subcellular organelles, and live cells are discussed. New to this second edition are recent developments in three important applications, i.e., advanced AFM-data analysis, high-resolution mechanical biosensing, and the use of cell mechanics for medical diagnosis.
- Explains the basic physical concepts and mathematics of elementary mechanics needed to understand and perform experimental work on small-scale biological samples
- Presents
Chapter
PREFACE TO THE FIRST EDITION
1.2.1 Gravity and Hydrodynamic Force
1.2.2 Frictional Coefficients
1.3 MACROSCOPIC BIOMECHANICS
1.4 MOLECULAR BASIS FOR STRUCTURAL DESIGN
1.5 SOFT VERSUS HARD MATERIALS
1.6 BIOLOGICAL AND BIOMIMETIC STRUCTURAL MATERIALS
1.7 THERMODYNAMICS AND MECHANICS IN NANOMETER-SCALE BIOLOGY
Two - Introduction to Basic Mechanics
2.1 ELASTIC AND PLASTIC DEFORMATION OF MATERIALS
2.2 STRESS AND STRAIN RELATIONSHIP
2.3 MECHANICAL BREAKDOWN OF MATERIALS
2.4.1 Shear Deformation and Rigidity Modulus
2.4.2 Triaxial Deformation and Bulk Compressibility
2.4.4 Y, G, and K Are All Related Through Poisson's Ratio
2.6 ADHESION AND FRICTION
2.7 WEAR AND TEAR OF BIOLOGICAL STRUCTURES
2.8 MECHANICALLY CONTROLLED SYSTEMS
Three - Force Measurement and Mechanical Imaging Apparatuses
3.1 MECHANICAL, THERMAL, AND CHEMICAL FORCES
3.3 ATOMIC FORCE MICROSCOPE
3.3.1 History and Principle
3.3.2 Mechanical Imaging by Atomic Force Microscope (AFM)
3.3.2.1 Contact Mode and Tapping Mode
3.3.2.4 Scanning Ion Conductance Microscope
3.3.2.5 MultiFrequency AFM
3.3.3 How to Use AFM for Force Measurement
3.3.4 Cantilever Force Constant
3.4 SURFACE FORCE APPARATUS
3.5 BIOMEMBRANE FORCE PROBE
3.8 CANTILEVER FORCE SENSORS
3.9 LOADING-RATE DEPENDENCE
3.11 SPECIFIC VERSUS NONSPECIFIC FORCES
Four - Interaction Forces
4.1 COVALENT VERSUS NONCOVALENT BONDS
4.2 BASICS OF ELECTROSTATIC INTERACTION
4.3 VARIOUS TYPES OF NONCOVALENT INTERACTIONS
4.3.1 Charge–Charge Interaction
4.3.2 Charge (Ion)–Dipole Interaction
4.3.3 Dipole–Dipole Interaction
4.3.4 Dipole–Induced Dipole Interaction
4.3.5 Dispersion Interaction
4.3.6 Hydrogen-Bonding Interaction
4.3.7 Hydrophobic Interaction
4.4 APPLICATION OF EXTERNAL FORCE
4.5 INTERACTION FORCE BETWEEN MACROMOLECULES
4.6 WATER AT THE INTERFACE
Five - Polymer Chain Mechanics
5.1 POLYMERS IN THE BIOLOGICAL WORLD
5.3.2 Randomly Coiled Polymer
5.3.3 Freely Jointed Chain (FJC)
5.4.2 Effect of Cross-Links
5.5.2 Denatured Proteins and DNA
5.6 POLYMERS ON THE SURFACE
5.7 POLYMERS AS BIOMIMETIC MATERIALS
Six - Analysis of Data Gleaned by Atomic-Force Microscopy
6.2 GENERAL PROCESSING OF TOPOGRAPHIC AFM IMAGES
6.2.3 Enhancement of Images
6.2.4 Display in Three Dimensions
6.3 SPECIMEN-SPECIFIC ANALYSIS PROCEDURES
6.3.2 Analysis of Protein Filaments (Amyloid Fibrils)
6.3.3 Quantification of Cytoskeletal Morphology
6.3.4 Analysis of Fractal Dimension
6.4 PROCESSING OF FORCE SPECTROSCOPY DATA
6.4.1 Analysis of Mechanical Properties
Seven - Single–Molecular Interaction
7.1 LIGAND–RECEPTOR INTERACTIONS
7.1.1 Biotin–Avidin Interaction
7.1.2 Interaction of Synaptic-Vesicle Fusion Proteins
7.1.3 Interaction Between Transferrin and Its Membrane Receptor
7.2 SUGAR–LECTIN INTERACTIONS
7.3 ANTIGEN–ANTIBODY INTERACTIONS
7.4 GROEL AND UNFOLDED-PROTEIN INTERACTIONS
7.5 LIPID–PROTEIN INTERACTIONS
7.6 ANCHORING FORCE OF PROTEINS TO THE MEMBRANE
7.8 PROTEIN UNANCHORING AND IDENTIFICATION
Eight - Single-Molecule DNA and RNA Mechanics
8.1 STRETCHING OF DOUBLE-STRANDED DNA
8.1.2 DNA With Bound Proteins
8.3 CHAIN DYNAMICS AND TRANSITION OF DNA AND RNA
8.4 DNA–PROTEIN INTERACTION
8.6 PROSPECT FOR SEQUENCE ANALYSIS
Nine - Single-Molecule Protein Mechanics
9.1 INTRODUCTION TO PROTEIN MANIPULATION
9.2 PROTEIN-STRETCHING EXPERIMENTS
9.4 STRETCHING OF MODULAR PROTEINS
9.7 PROTEIN-COMPRESSION EXPERIMENTS
9.7.3 Rigidity of Proteins
9.8 INTERNAL MECHANICS OF PROTEIN MOLECULES
9.9 MECHANICAL CONTROL OF PROTEIN ACTIVITY
9.10 COMPUTER SIMULATION OF PROTEIN DEFORMATION
9.11 CASE STUDIES: PROTEINS AND POLYPEPTIDES OF NOTABLE STRUCTURAL CHARACTERISTICS
9.11.1 Poly-l-alanine: A Typical α-helical Polypeptide
9.11.2 Wheat Germ Agglutinin: A Compact Dimeric Lectin
9.11.3 Bovine Carbonic Anhydrase II (BCA II): Protein With a Knot
Ten - Nanomechanics of Motion-Supporting Molecular Systems
10.1 CELL MOVEMENT AND STRUCTURAL PROTEINS
10.2 MUSCLE AND MOTOR PROTEINS
10.3 SINGLE MOLECULE/FILAMENT MEASUREMENTS
10.4 FLAGELLA FOR BACTERIAL LOCOMOTION
10.6 MECHANICS AND EFFICIENCY OF MOTOR PROTEINS
10.7 VIDEO VIEW OF MOTOR PROTEINS IN ACTION BY HIGH-SPEED AFM
Eleven - Finite-Element Analysis of Microbiological Structures
11.2 A BRIEF HISTORY OF THE FINITE-ELEMENT METHOD
11.3 THE FINITE-ELEMENT METHOD
11.4 APPLICATION OF THE FINITE-ELEMENT METHOD TO MICROBIOLOGICAL STRUCTURES
11.4.2 Axonemata and Cilia
11.4.6 Embryology and Cell Division
Twelve - Nanomechanical Bases of Cell Structure
12.1 RED BLOOD CELL: MODEL CELL IN BIOMECHANICS
12.2 HELFRICH THEORY OF MEMBRANE MECHANICS
12.3 DEFORMATION OF 2D MEMBRANE
12.4 MEMBRANE AND CYTOSKELETON
12.5 ASSOCIATION OF MEMBRANE PROTEINS WITH CYTOSKELETON
12.5.1 Detergent Treatment
12.5.2 Diffusion Coefficients
12.5.3 Force Curve Measurement
12.6 NANO-INDENTATION EXPERIMENTS ON LIVE CELLS
12.6.1 Indentation Experiment
12.6.2 Sneddon's Formulas
12.6.3 Examination of Indentation Experiments
12.6.4 Correction for Thin Samples
12.7 STIFFNESS TOMOGRAPHY AND CELL RESPONSE STUDIES
Thirteen - Nanorheology of Living Cells
13.2 AFM MEASUREMENTS OF CELL MODULUS
13.2.2 Frequency Domain AFM
13.3 HIGH-THROUGHPUT MEASUREMENTS OF CELL RHEOLOGICAL PROPERTIES
13.4 ELASTIC MODULUS OF NORMAL AND CANCER CELLS
13.5 AFM IMAGING MODE FOR MEASURING VISCOELASTIC PROPERTIES OF CELLS
Fourteen - Molecular and Cellular Manipulations for Future Nanomedicine
14.1 PROSPECTS FOR USEFUL APPLICATIONS FOR NANOMEDICINE
14.2 BIOCONJUGATION OF MATERIALS
14.3 NANOMECHANICAL MANIPULATION OF CELLS AIMING AT NANOMEDICAL APPLICATIONS
14.5 CHROMOSOMAL SURGERY AND GENE MANIPULATION
14.7 LIPOSOMAL TECHNOLOGY
14.9 DNA AND RNA RECOVERY FROM THE CHROMOSOME AND THE CELL
A.1.1.1 Supported Beam at Two Ends
A.1.1.2 Cantilever Bending
A.1.1.3 Distributed Force
A.1.1.4 Radius of Curvature
A.1.3 BASICS OF LINEAR MECHANICS ACCORDING TO LANDAU AND LIFSHITZ
Two - V-Shaped Cantilever
A.2.1 V-SHAPED CANTILEVER
Three - Persistence Length Versus Kuhn Length
A.4.1.1 Concentrated Load
A.4.1.2.1 Hertz Pressure (n=1/2)
A.4.1.2.2 Details of Integration of A.4.10
A.4.1.3 Contact Problem of Two Spheres
Five - Derivation of the Loading-Rate Dependence of the Mean Rupture Force
The World of Nano-Biomechanics
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