Related papers: Propagation of twist solitons in real DNA chains
In many physical applications solitons propagate on supports whose topological properties may induce new and interesting effects. In this paper, we investigate the propagation of solitons on chains with a topological inhomogeneity generated…
We investigate propagation of a kink soliton along inhomogeneous chains with two different constituents, arranged either periodically, aperiodically, or randomly. For the discrete sine-Gordon equation and the Fibonacci and Thue-Morse chains…
We study the propagation of solitons on complex chains built by inserting finite graphs at two sites of an unbranched chain. We compare numerical findings with the results of an analytical linear approximation scheme describing the…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Some recent results for a three--dimensional, semi--classical, tight--binding model for DNA show that there are two types of polarons, named radial and twist polarons, that can transport charge along the DNA molecule. However, the existence…
In the present paper we investigate the influence of inhomogeneities in the dynamics and stability of DNA open states, modeled as propagating solitons in the spirit of a Generalized Yakushevish Model. It is a direct consecuence of our model…
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
We study the persistent random walk of photons on a one-dimensional lattice of random asymmetric transmittances. Each site is characterized by its intensity transmittance t (t') for photons moving to the right (left) direction.…
Droplet solitons are a strongly nonlinear, inherently dynamic structure in the magnetization of ferromagnets, balancing dispersion (exchange energy) with focusing nonlinearity (strong perpendicular anisotropy). Large droplet solitons have…
We study the tautomeric transitions in base pairs of DNA considering elastic properties of DNA as classical and tunneling of protons as quantum, and show that the dynamics of the transitions admits of soliton like solutions whose shape and…
We have studied the soliton propagation through a segment containing random point-like scatterers. In the limit of small concentration of scatterers when the mean distance between the scatterers is larger than the soliton width, a method…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Exact propagating topological solitons are found in the easy-plane phase of ferromagnetic spin-1 Bose-Einstein condensates, manifesting themselves as kinks in the transverse magnetization. Propagation is only possible when the…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
Diffusion of tracer particles in the cytoplasm of mammalian cells is often anomalous with a marked heterogeneity even within individual particle trajectories. Despite considerable efforts, the mechanisms behind these observations have…
We study families of solitons in a two-dimensional (2D) model of the light transmission through a photorefractive medium equipped with a (quasi-)one-dimensional photonic lattice. The soliton families are bounded from below by finite minimum…