Related papers: Breathers in a system with helicity and dipole int…
We consider a chain of torsionally-coupled, planar pendula shaken horizontally by an external sinusoidal driver. It has been known that in such a system, theoretically modeled by the discrete sine-Gordon equation, intrinsic localized modes,…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
Qualitative information about breather initial profiles in the weak coupling limit of a chain of identical one-dimensional anharmonic oscillators is found by studying the linearized equations of motion at a one-site breather. In particular,…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We consider a long Josephson junction excited by a suitable external ac-signal, in order to generate control and detect breathers. Studying the nonlinear supratransmission phenomenon in a nonlinear sine-Gordon chain sinusoidally driven,…
We study the symmetric collisions of two mobile breathers/solitons in a model for coupled wave guides with a saturable nonlinearity. The saturability allows the existence of breathers with high power. Three main regimes are observed:…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
We numerically study the breathing dynamics induced by collision between bright solitons in the one-dimensional Bose-Einstein condensates with strong dipole-dipole interaction. This breathing phenomenon is closely related to the…
We propose a new mechanism of long-range coupling to excite low-frequency discrete breathers without the on-site potential. This mechanism is universal in long-range systems irrespective of the spatial boundary conditions, of topology of…
We consider a polaron model where molecular \emph{rotations} are important. Here, the usual hopping between neighboring sites is affected directly by the electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This model…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
In the present work we revisit the existence, stability and dynamical properties of moving discrete breathers in $\beta$-FPU lattices. On the existence side, we propose a numerical procedure, based on a continuation along a sequence of…
We review research on the role of nonlinear coherent phenomena (e.g breathers and kinks) in the formation linear decorations in mica crystal. The work is based on a new model for the motion of the mica hexagonal K layer, which allows…
Recent experimental evidence shows that the pi-orbitals along the stacking of base pairs can facilitate the long-range charge transfer in DNA. Proton motion in the base pair hydrogen bonds has also been found to affect the transfer rate. To…
Eukaryotic cilia and flagella are chemo-mechanical oscillators capable of generating long-range coordinated motions known as metachronal waves. Pair synchronization is a fundamental requirement for these collective dynamics, but it is…
We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time $\tau$. We find that the dynamical exponent $\alpha$ of the anomalous scaling…
We calculate the influence of dynamical exchange effects on the response properties and the static properties of a two-dimensional many-polaron gas. These effects are not manifested in the random-phase approximation which is widely used in…
We consider the long-time evolution of weakly perturbed discrete nonlinear Schroedinger breathers. While breather growth can occur through nonlinear interaction with one single initial linear mode, breather decay is found to require…
In the present work, we explore the possibility of excited breather states in a nonlinear Klein--Gordon lattice to become nonlinearly unstable, even if they are found to be spectrally stable. The mechanism for this fundamentally nonlinear…