Advanced Mechanical Models of DNA Elasticity

Advanced Mechanical Models of DNA Elasticity

1st Edition - March 29, 2016

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  • Author: Yakov Tseytlin
  • Paperback ISBN: 9780128019993
  • eBook ISBN: 9780128020364

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Description

Advanced Mechanical Models of DNA Elasticity includes coverage on 17 different DNA models and the role of elasticity in biological functions with extensive references. The novel advanced helicoidal model described reflects the direct connection between the molecule helix structure and its specific properties, including nonlinear features and transitions. It provides an introduction to the state of the field of DNA mechanics, known and widely used models with their short analysis, as well as coverage on experimental methods and data, the influence of electrical, magnetic, ionic conditions on the persistence length, and dynamics with viscosity influence. It then addresses the need to understand the nature of the non-linear overstretching transition of DNA under force and why DNA has a negative twist-stretch coupling.

Key Features

  • Includes coverage of 17 contemporary models of DNA mechanics with analysis
  • Provides comparison of DNA and RNA mechanical features
  • Covers advances in experimental techniques including AFM, X-ray, and optical tweezers
  • Contains extensive references for further reading

Readership

Researchers and students in molecular biology, physical biology, biomedical sciences, and biophysics

Table of Contents

  • 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

Product details

  • No. of pages: 316
  • Language: English
  • Copyright: © Academic Press 2016
  • Published: March 29, 2016
  • Imprint: Academic Press
  • Paperback ISBN: 9780128019993
  • eBook ISBN: 9780128020364

About the Author

Yakov Tseytlin

YAKOV M. TSEYTLIN is a mechanical engineer, educator, and research scientist. Born in Leningrad, Russia; he arrived in the USA in 1992, becoming naturalized in 1997. His qualifications and professional positions include: MS in Mechanical Engineering, Leningrad Polytechnic Institute, PhD, 1965; Doctor of Technical Sciences, All-Russian Research Institute of Metrology, Russia, 1991; Chief of research laboratory, senior designer, senior and lead researcher, Leningrad Instrumental Plant, All-Russian Research Institute of Metrology, Russia; senior designer, senior researcher Federal Products Co. USA, 1992; project engineer in Automatic Machinery Co. US, 1999; assistant to associate professor in Leningrad Polytechnic Institute; visiting professor in Leningrad Institute of Precise Mechanics and Optics; Manager and Engineer, All-Russian Institute of Advanced Education in Standardization and Metrology;

Adviser and Opponent of Graduate Dissertations in Central Research Institute for Fuel Apparatus, All-Russian Research Institute of Metrology, Leningrad Polytechnic Institute. He has contributed numerous articles to professional journals, and authored 4 monographs. He is also a member of International Society of Automation (recognition awards 1998-2012, ISA). His achievements include development of methods and concepts in micro elasticity, DNA elasticity modeling, atomic force microscopy, and information criterion of measurement uncertainty negligibility.

Affiliations and Expertise

Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia

Ratings and Reviews

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  • AlanWhite Mon Dec 23 2019

    First Rate Scholarship

    Very complete, very comprehensive treatment. I think the next edition should include illustrations of base pair geometry from the texts by Calladine and Drew.