By Ludmila V. Yakushevich
The 1st version of this booklet used to be the 1st at the physics of DNA to move past the easy (simplified) 'linear' strategy, and it has considering been came across that the inclusion of nonlinear results results in a considerably greater interpretation of experimental facts. This new version evidently keeps this procedure, yet has been thoroughly revised, up to date and improved to hide fresh advancements. starting with introductory chapters on DNA constitution and dynamics, the booklet additionally contains a comparability among linear and nonlinear ways to the DNA molecule, a bankruptcy dedicated to the data of nonlinear excitations of DNA, and examples for the translation of experimental info at the dynamics of DNA when it comes to nonlinear thought. crucial interpreting for researchers in biophysics and nonlinear physics, permitting biologists, chemists and physicists to proceed constructing new and enhanced recommendations of investigating the DNA molecule.
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Extra info for Nonlinear Physics of DNA
Sample text
3 Dynamics of the Bases To describe the dynamics of the bases, it is convenient to begin with a brief description of the equilibrium state of the bases and then to describe possible motions of the bases as deviations from their equilibrium positions. 2. 3 ) and not regular, the base structure can be considered as planar. 2). 6). But in the first approximation, we can assume that for B-DNA the plates are perpendicular to the helix axis. 2 Purine and pyrimidine sketched as two rectangular plates.
Models of the fourth level of the hierarchy. The fourth group of the structural models comprises the so-called lattice models where a finite group of atoms (named nucleotide) forms a unit cell’ quasi-periodically repeating along the DNA molecule [121]. 12. 12 (a) One-dimensional lattice (b) with a unit cell (a pair of nucleotides) containing A-T base-pair. For simplicity, the screw symmetry of the model is not shown here. 5. Models of the fifth level of the hierarchy. 13). 13 The most accurate model of the internal DNA structure.
The BfiA transitions may occur in some fragment of the DNA molecule with changes in the external conditions or with protein attachment. The transitions have a relatively small potential barrier and they are weakly dependent on nucleotide composition [9]. Nevertheless, there are some special examples of synthetic polynucleotides which cannot transform from the B-form to the A-form. For example, polynucleotide poly(dA-dG) . poly(dC-dT), one chain of which consists of purines and the other of pyrimidines, cannot transform from the B-form to the A-form [72].