Interaction of a soliton with an impurity in the sine-Gordon model of a commensurate charge-density-wave system

Ideas and methods of nonlinear mathematics and theoretical physics in DNA science: the McLaughlin-Scott equation and its application to study the DNA open state dynamics

The review is devoted to a new and rapidly developing area related to the application of ideas and methods of nonlinear mathematics and theoretical physics to study the internal dynamics of DNA and, in particular, the behavior of the open states of DNA. There are two main competing approaches to this research. The first approach is based on the molecular dynamics method, which takes into account the motions of all structural elements of the DNA molecule and all interactions between them. The second approach is based on prior selection of the main (dominant) motions and their mathematical description using a small number of model equations. This review describes the results of the study of the open states of DNA performed within the framework of the second approach using the McLaughlin-Scott equation. We present the results obtained both in the case of homogeneous sequences: poly (A), poly (T), poly (G) and poly (C), and in the inhomogeneous case when the McLaughlin-Scott equation has been used for studying the dynamics of open states activated in the promoters A1, A2 and A3 of the bacteriophage T7 genome, in the genes IFNA17, ADRB2, NOS1 and IL-5, in the pBR322 and pTTQ18 plasmids. Particular attention is paid to the results concerning the effect of various external fields on the behavior of open states. In the concluding part of the review, new possibilities and prospects for the development of the considered approach and especially of the McLaughlin-Scott equation are discussed.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12551-021-00801-0.

Leapfrogging of electrical solitons in coupled nonlinear transmission lines: effect of an imperfect varactor

The leapfrogging dynamics of a pair of electrical solitons is investigated, by considering two capacitively coupled nonlinear transmission lines with and without intraline resistances. We discuss two distinct transmission line set-ups: in the first, we assume two RLC ladder lines with intraline varactors and a coupling linear capacitor, and in the second, we consider two capacitively coupled lossless lines with a varactor carrying impurity (imperfect diode) in one of the two interacting transmission lines. In the first context, we find that the soliton-pair leapfrogging mimics the motion of a damped harmonic oscillator, the frequency and damping coefficient of which are obtained analytically. Numerical simulations predict leapfrogging of the soliton pair when the differences in the initial values of the amplitude and phase are reasonably small, and the resistance is not too large. In the second context, leapfrogging occurs when the impurity rate is small enough and the differences in the initial values of the amplitude as well as phase are also small. As the impurity rate increases, the soliton signal in the imperfect line gets accelerated upon approaching the defective diode, causing only this specific soliton signal to move faster than its counterpart, leading to the suppression of leapfrogging.