Nonlinear Physics of DNA

Ludmila V. Yakushevich is a Doctor of Science and leading research worker of the Laboratory of Physical and Chemical Mechanisms of Gene Expression, which is part of the Institute of Cell Biophysics of the Russian Academy of Sciences. The main research field is the dynamics of biopolymers, especially the nonlinear dynamics of DNA. The principal methods of investigations include theoretical physics and mathematical modeling.

CHAPTER 1 DNA STRUCTURE 1.1 Chemical composition and primary structure 1.2 Spatial geometry and secondary structure 1.3 Forces stabilizing secondary structure 1.4 Polymorphism 1.5 Tertiary structure 1.6 Approximate models of DNA structure 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 2.4 Dynamics of sugar-phosphate backbone 2.5 Conformational transitions 2.6 Motions associated with local strand separation 2.7 Approximate models of DNA dynamics 2.8 Experimental methods of studying DNA dynamics 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 gene expression 3.6 Replication CHAPTER 4 LINEAR THEORY OF DNA 4.1 The main mathematical models 4.2 Statistics of linear excitations 4.3 Scattering problem 4.4 Linear theory and experiment CHAPTER 5 NONLINEAR THEORY OF DNA: IDEAL DYNAMICAL MODELS 5.1 Nonlinear mathematical modeling: general principles and restrictions 5.2 Nonlinear rod-like models 5.3 Nonlinear double rod-like models 5.4 Nonlinear models of higher levels CHAPTER 6 NONLINEAR THEORY OF DNA: NON-IDEAL MODELS 6.1 Effects of environment 6.2 Effects of inhomogeneity