Statistical Physics of DNA

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.
Contents: ForewordStatistical Mechanics of Simple Polymer Chain ModelsEntropic Elasticity: The DNA Force-Extension RelationshipDNA Packaging and WrappingScattering from DNA in SolutionThermal Unbinding of the Double HelixMechanical Unbinding of the Double HelixHelix-Coil Theory of DNA MeltingDynamical Theory of DNA Melting I: FundamentalsDynamical Theory of DNA Melting II: Nonlinear Stacking InteractionDynamical Theory of DNA Melting III: Long, Heterogeneous ChainsTemperature Dependent DNA FlexibilityIs DNA Softer at the 100-nm Scale?Thermodynamic Stability of DNA HairpinsAppendices:Monte Carlo Simulations of the Kratky–Porod ChainLandau's Theorem on the Absence of Phase Transitions in One-Dimensional SystemsDynamical Theory of DNA Melting: The Soliton AnalogyNumerical Solution of the Transfer Integral EquationBibliographyIndex
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 DNAIt focuses on DNA statistical physics — not general mathematical biophysics, nor (more general) biological physicsIt provides step-by-step approach to mathematical models which is useful as a specializedtextbookThe author has made numerous significant contributions to the field of DNA statistical physicsover the last 20 years