Statistical Physics of DNA

Statistical Physics of DNA

An Introduction to Melting, Unzipping and Flexibility of the Double Helix

Nikos Theodorakopoulos


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The stability of the DNA double helix is contingent on fine-tuning a number of physicochemical control parameters. Varying any one of them leads to separation of the two strands, in what constitutes a rare physical example of a thermodynamic phase transition in a one-dimensional system. The present book aims at providing a self-contained account of the statistical physics of cooperative processes in DNA, e.g. thermal and mechanical dissociation, force-induced melting, equilibria of hairpin-like secondary structures. In addition, the book presents some fundamental aspects of DNA elasticity, as observed in key experiments, old and new. The latter include some recently published scattering data on apparently soft, short DNA chains and their interpretation in terms of local structural defects (permanent bends, 'kinky DNA', after the original Crick–Klug hypothesis).

The development of mathematical models used (Kratky–Porod polymer chain, Poland–Scheraga and Peyrard–Bishop–Dauxois models of DNA melting) emphasizes the use of realistic parameters and the relevance of practical numerical methods for comparing with experimental data. Accordingly, a large number of specially produced figures has been included.

The presentation is at the level of an advanced undergraduate or introductory graduate course. An extra chapter provides the necessary mathematical background on elasticity of model polymer chains.

  • Foreword
  • Statistical Mechanics of Simple Polymer Chain Models
  • Entropic Elasticity: The DNA Force-Extension Relationship
  • DNA Packaging and Wrapping
  • Scattering from DNA in Solution
  • Thermal Unbinding of the Double Helix
  • Mechanical Unbinding of the Double Helix
  • Helix-Coil Theory of DNA Melting
  • Dynamical Theory of DNA Melting I: Fundamentals
  • Dynamical Theory of DNA Melting II: Nonlinear Stacking Interaction
  • Dynamical Theory of DNA Melting III: Long, Heterogeneous Chains
  • Temperature Dependent DNA Flexibility
  • Is DNA Softer at the 100-nm Scale?
  • Thermodynamic Stability of DNA Hairpins
  • Appendices:
    • Monte Carlo Simulations of the Kratky–Porod Chain
    • Landau's Theorem on the Absence of Phase Transitions in One-Dimensional Systems
    • Dynamical Theory of DNA Melting: The Soliton Analogy
    • Numerical Solution of the Transfer Integral Equation
  • Bibliography
  • Index

Readership: Undergraduate students with an elementary background in statistical mechanics; graduate students; researchers.DNA;Statistical Physics;Statistical Mechanics;Unzipping;Overstretching;Flexibility;Hairpins;Melting;Kratky–Porod;Peyrard–Bishop;Poland–Scheraga0Key Features:
  • It provides a self-contained account of the statistical physics of cooperative processes in DNA
  • It focuses on DNA statistical physics — not general mathematical biophysics, nor (more general) biological physics
  • It provides step-by-step approach to mathematical models which is useful as a specializedtextbook
  • The author has made numerous significant contributions to the field of DNA statistical physicsover the last 20 years