Kinks and Breathers Associated with Collective Sugar Puckering in DNA

Variety of rotation modes in a small chain of coupled pendulums

This article studies the rotational dynamics of three identical coupled pendulums. There exist two parameter areas where the in-phase rotational motion is unstable and out-of-phase rotations are realized. Asymptotic theory is developed that allows us to analytically identify borders of instability areas of in-phase rotation motion. It is shown that out-of-phase rotations are the result of the parametric instability of in-phase motion. Complex out-of-phase rotations are numerically found and their stability and bifurcations are defined. It is demonstrated that the emergence of chaotic dynamics happens due to the period doubling bifurcation cascade. The detailed scenario of symmetry breaking is presented. The development of chaotic dynamics leads to the origin of two chaotic attractors of different types. The first one is characterized by the different phases of all pendulums. In the second case, the phases of the two pendulums are equal, and the phase of the third one is different. This regime can be interpreted as a drum-head mode in star-networks. It may also indicate the occurrence of chimera states in chains with a greater number of nearest-neighbour interacting elements and in analogical systems with global coupling.

Charge transport in DNA model with vibrational and rotational coupling motions

The dynamics of the Peyrard-Bishop model for vibrational motion of DNA dynamics, which has been extended by taking into account the rotational motion for the nucleotides (Silva et al., J. Biol. Phys. 34, 511-519, 2018) is studied. We report on the presence of the modulational instability (MI) of a plane wave for charge migration in DNA and the generation of soliton-like excitations in DNA nucleotides. We show that the original differential-difference equation for the DNA dynamics can be reduced in the continuum approximation to a set of three coupled nonlinear equations. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Numerical simulations show the validity of the analytical approach with the generation of wave packets provided that the wave numbers fall in the instability domain.

Exceptional discretizations of the sine-Gordon equation

The method of one-dimensional maps was recently introduced as a means of generating exceptional discretizations of the phi(4) theory, i.e., discrete phi(4) models which support kinks centered at a continuous range of positions relative to the lattice. In this paper, we employ this method to obtain exceptional discretizations of the sine-Gordon equation (i.e., exceptional Frenkel-Kontorova chains). We also use one-dimensional maps to construct a discrete sine-Gordon equation supporting kinks which move with arbitrary velocities without emitting radiation.