Advanced Mechanical Models of DNA Elasticity

Dedication

Biography

Preface

Acknowledgments

Chapter 1: DNA Molecules Mechanical Properties and Models

• Abstract
• 1.1. Mechanical properties
• 1.2. Discrete, flexible chains, and atomistic models: WLC, FJC, DPC, WLRC, HW, ZZM
• 1.3. Continuum and approximation models
• 1.4. Dynamics and fluctuation
• 1.5. Persistence length features
• 1.6. A, B, Z DNA forms, S- and P-DNA phases
• 1.7. Polymer materials
• 1.8. DNA technical applications
• 1.9. DNA size and mass conversion
• 1.10. Deflection at equilibrium

Chapter 2: Force Application, Measurement, and Manipulation Accessories

• Abstract
• 2.1. Stretching micropipette, glass microneedles, and hydrodynamics
• 2.2. Optical trap and tweezers
• 2.3. Small-angle X-ray scattering interference (SAXSI)
• 2.4. Magnetic tweezers
• 2.5. Atomic force microscopy
• 2.6. Concave notch hinges

Chapter 3: AFM with Higher Mode Oscillations and Higher Sensitivity

• Abstract
• 3.1. Effects of the resonance modes. Kinetostatic method
• 3.2. Effective spring constants ratio
• 3.3. Cantilever end inclination spring constants
• 3.4. Quality factor influence
• 3.5. End extended mass (V-shaped cantilever)
• 3.6. Shift of resonant frequency
• 3.7. Actuators and detectors
• 3.8. Internal and external damping
• 3.9. Calibration

Chapter 4: Kinematics and Nonlinear Motion Transformation in Elastic Helicoids

• Abstract
• 4.1. Helix parameters
• 4.2. Motion stability
• 4.3. Transmission nonlinearity
• 4.4. Motion transformation in a thin helicoidal strip
• 4.5. Coiled ribbon helicoids
• 4.6. Transmission relations
• 4.7. Fatigue options and statistical fluctuations

Chapter 5: Dynamics of the Elastic Systems with Helicoids

• Abstract
• 5.1. Dynamic functions
• 5.2. Helicoids dynamics
• 5.3. Vibration of a thin helicoid
• 5.4. Internal friction (damping) in a helicoid
• 5.5. Shells and quasi-helicoids
• 5.6. Dynamic rate in helicoidal sensors
• 5.7. Flexural wave propagation
• 5.8. Limits of the transmission entropic fluctuations

Chapter 6: Double-Stranded DNA Elasticity

• Abstract
• 6.1. Helix chain
• 6.2. Properties of explicit helicoidal model (EHM)
• 6.3. Twist-stretch coupling
• 6.4. Statistical fluctuation
• 6.5. Stretch stiffness and Poisson’s ratio
• 6.6. Persistence length relations and Poisson’s ratio
• 6.7. Overwinding options
• 6.8. Nonlinear length fluctuations
• 6.9. Speed factor

Chapter 7: DNA Elasticity with Transition

• Abstract
• 7.1. Discrete persistence chain (DPC)
• 7.2. Reverse WLC modeling
• 7.3. Approximation by sequence of linear springs
• 7.4. Explicit helicoidal model (EHM) transition
• 7.5. Buckling of DNA molecule
• 7.6. Elasticity of ssDNA, ZZM, DPC, and EHMR models
• 7.7. Mechanical stability
• 7.8. Nonlinear dynamics and traveling waves
• 7.9. EHM in chains

Index