The stochastic, damped KdV equation

Collective coordinate framework to study solitary waves in stochastically perturbed Korteweg-de Vries equations

Stochastically perturbed Korteweg-de Vries (KdV) equations are widely used to describe the effect of random perturbations on coherent solitary waves. We present a collective coordinate approach to describe the effect on coherent solitary waves in stochastically perturbed KdV equations. The collective coordinate approach allows one to reduce the infinite-dimensional stochastic partial differential equation (SPDE) to a finite-dimensional stochastic differential equation for the amplitude, width and location of the solitary wave. The reduction provides a remarkably good quantitative description of the shape of the solitary waves and its location. Moreover, the collective coordinate framework can be used to estimate the timescale of validity of stochastically perturbed KdV equations for which they can be used to describe coherent solitary waves. We describe loss of coherence by blow-up as well as by radiation into linear waves. We corroborate our analytical results with numerical simulations of the full SPDE.

Bubble solitons in an inhomogeneous, helical DNA molecular chain with flexible strands

Base pair opening in an inhomogeneous, DNA double helical molecular chain with flexible strands is investigated by studying its internal dynamics. For the study, a generalized model which takes into account the energies involved in stacking and hydrogen bonds along with inhomogeneity, helicity, and phonons coupled to the stacking and hydrogen bonds is proposed. The internal dynamics of the proposed DNA model is governed by a perturbed nonlinear Schrödinger equation. The unperturbed, completely integrable nonlinear Schrödinger equation which admits soliton solutions and forming a bubble corresponds to DNA dynamics with homogeneous and rigid strands. The results of the soliton perturbation analysis show that the inhomogeneity in stacking and hydrogen bonds in localized and periodic forms and the helicity do not alter the amplitude under perturbation. However, the flexibility of the strands diminishes the perturbed amplitude. On the other hand, the velocity of the soliton and bubble are unaltered due to all the above effects. However, the position and phase of the soliton and the bubble vary linearly in time. While the position of the soliton depends on the initial velocity, the phase depends on both the initial velocity and the initial amplitude of the soliton. The above effects introduce small fluctuation in the tail of the soliton, without affecting the robust nature of the soliton and the bubble during propagation. The soliton and the bubble obtained as solutions of the internal dynamics of the DNA molecule represent an opening of the base pairs which is essential for the transcription process.

Thermal diffusion of supersonic solitons in an anharmonic chain of atoms

We study the nonequilibrium diffusion dynamics of supersonic lattice solitons in a classical chain of atoms with nearest-neighbor interactions coupled to a heat bath. As a specific example we choose an interaction with cubic anharmonicity. The coupling between the system and a thermal bath with a given temperature is made by adding noise, delta correlated in time and space, and damping to the set of discrete equations of motion. Working in the continuum limit and changing to the sound velocity frame we derive a Korteweg-de Vries equation with noise and damping. We apply a collective coordinate approach which yields two stochastic ODEs which are solved approximately by a perturbation analysis. This finally yields analytical expressions for the variances of the soliton position and velocity. We perform Langevin dynamics simulations for the original discrete system which confirm the predictions of our analytical calculations, namely, noise-induced superdiffusive behavior which scales with the temperature and depends strongly on the initial soliton velocity. A normal diffusion behavior is observed for solitons with very low energy, where the noise-induced phonons also make a significant contribution to the soliton diffusion.