Nonlinear Physics of DNA / Edition 1

Nonlinear Physics of DNA / Edition 1

by Ludmila V. Yakushevich, L. V. Iakushevich, Yakushevich
     
 

ISBN-10: 0471978248

ISBN-13: 9780471978244

Pub. Date: 04/30/1998

Publisher: Wiley

The study of DNA is one of the most important areas of research in modern biochemistry and biology. It is an extremely complex field, and in recent years researchers have found that the application of nonlinear physics methods has led to significant increases in our understanding of the subject. This, the first book on the subject, examines both the experimental

Overview

The study of DNA is one of the most important areas of research in modern biochemistry and biology. It is an extremely complex field, and in recent years researchers have found that the application of nonlinear physics methods has led to significant increases in our understanding of the subject. This, the first book on the subject, examines both the experimental and theoretical methods which have been used to study the DNA molecule. Beginning with introductory chapters on DNA structure and dynamics, Nonlinear Physics of DNA goes on to discuss the more advanced recent work. This includes a comparison between linear and nonlinear approaches to the DNA molecule, a chapter devoted to the statistics of nonlinear excitations of DNA, and examples of the interpretation of experimental data on the dynamics of DNA in terms of nonlinear theory. Nonlinear Physics of DNA will prove essential reading for graduate students and researchers in biophysics and nonlinear physics as well as allowing biologists, biochemists and physicists to continue to develop nontraditional techniques of investigating the DNA molecule.

Product Details

ISBN-13:
9780471978244
Publisher:
Wiley
Publication date:
04/30/1998
Series:
Wiley Series in Nonlinear Science Series, #20
Pages:
218
Product dimensions:
6.52(w) x 9.45(h) x 0.80(d)

Table of Contents

CHAPTER 1 DNA STRUCTURE
1.1 Chemical composition and primary structure
1.2 Spatial geometry and secondary structure
1.3 Forces stabilizing secondary structure
1.3.1 Hydrogen interactions
1.3.2 Stacking interactions
1.3.3 Long range intra- and inter- backbone forces
1.3.4 Electrostatic field of DNA
1.4 Polymorphism
1.5 Tertiary structure
1.5.1 Superhelicity
1.5.2 Structural organization in cells
1.6 Approximate models of DNA structure
1.6.1 General comments
1.6.2 Hierarchy of structural models
1.7 Experimental methods of studying DNA structure
CHAPTER 2 DNA DYNAMICS
2.1 General picture of the internal mobility
2.2 Twisting and bending motions
2.3 Dynamics of bases
2.3.1 Equilibrium state
2.3.2 Possible motions of bases
2.4 Dynamics of sugar-phosphate backbone
2.4.1 Equilibrium state
2.4.2 Possible motions of sugar-phosphate backbone
2.5 Conformational transitions
2.5.1 B®A transition
2.5.2 B®Z transition
2.6 Motions associated with local strand separation
2.6.1 Base-pair opening due to rotations of bases
2.6.2 Transverse displacements in strands
2.7 Approximate models of DNA dynamics
2.7.1 The main principles of modeling
2.7.2 Hierarchy of dynamical models
2.8 Experimental methods of studying DNA dynamics
2.8.1 Raman scattering
2.8.2 Neutron scattering
2.8.3 Infra-red spectroscopy
2.8.4 Hydrogen-deuterium (-tritium) exchange
2.8.5 Microwave absorption
2.8.6 NMR
2.8.7 Detection of charge transfer
CHAPTER 3 DNA FUNCTIONING
3.1 Physical aspects of DNA functioning
3.2 Intercalation
3.3 DNA-protein recognition
3.4 Gene expression
3.5 Regulation of geneexpression
3.6 Replication
CHAPTER 4 LINEAR THEORY OF DNA
4.1 The main mathematical models
4.1.1 Linear rod-like model
4.1.2 Linear double rod-like model
4.1.3 Linear models of higher levels
4.2 Statistics of linear excitations
4.2.1 Phonons in the rod-like model
4.2.2 Phonons in the double rod-like model
4.2.3 Phonons in the higher-level models
4.3 Scattering problem
4.3.1 Scattering by "frozen" DNA
4.3.2 Elastic scattering
4.3.3 Inelastic scattering
4.4 Linear theory and experiment
4.4.1 Fluorescence depolarization
4.4.2 Low-frequency spectra: neutron scattering, infra-red scattering, Raman scattering, speed of sound
CHAPTER 5 NONLINEAR THEORY OF DNA: IDEAL DYNAMICAL MODELS
5.1 Nonlinear mathematical modeling: general principles and restrictions
5.2 Nonlinear rod-like models
5.2.1 The rod-like model of Muto
5.2.2 The model of Christiansen
5.2.3 The rod-like model of Ichikawa
5.3 Nonlinear double rod-like models
5.3.1 General case: hamiltonian
5.3.2 General case: dynamical equations
5.3.3 The Y-model
5.3.4 The model of Peyrard and Bishop
5.3.5 The double rod-like model of Muto
5.3.6 The model of Barbi
5.3.7 The model of Campa
5.3.8 Assymetrical model of DNA
5.4 Nonlinear models of higher levels
5.4.1 The model of Krumhansl and Alexander
5.4.2 The model of Volkov
CHAPTER 6 NONLINEAR THEORY OF DNA: NON-IDEAL MODELS
6.1 Effects of environment
6.1.1 General approach
6.1.2 Particular examples
6.1.3 DNA in thermal bath
6.2 Effects of inhomogeneity
6.2.1 Boundary
6.2.2 Local region

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