Related papers: Moving breathers in a bent DNA-related model
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
The role of the rigidity of a peptide chain in its equilibrium dynamics is investigated within a realistic model with stringent microscopically derived coupling interaction potential and effective on-site potential. The coupling interaction…
We study the properties of discrete breathers, also known as intrinsic localized modes, in the one-dimensional Frenkel-Kontorova lattice of oscillators subject to damping and external force. The system is studied in the whole range of…
We predict that oblique breathers can be generated by a flow of two-component Bose-Einstein condensate past a polarized obstacle which attracts one component of the condensate and repels the other one. The breather exists if intra-species…
For the James breathers in the K2-K3-K4 chain and for breathers in the K4-chain, we prove numerically that these dynamical objects are not strictly time-periodic. Indeed, for the both cases, there exist certain deviations in the vibrational…
The dynamics of a system composed of elastic hard particles confined by an isotropic harmonic potential are studied. In the low-density limit, the Boltzmann equation provides an excellent description, and the system does not reach…
A systematic correlation between the initial profile of discrete breathers and their frequency is described. The context is that of a very weakly harmonically coupled chain of softly anharmonic oscillators. The results are structurally…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
A quasi-one-dimensional Bose-Einstein condensate loaded into a quasi-periodic potential created by two sub-lattices of comparable amplitudes and incommensurate periods is considered. Although the conventional tight-binding approximation is…
We study the effects of electron-lattice interaction in the presence of discrete breathers. The lattice is treated classically. We consider two different situations - i) the scattering of an electron by a discrete breather in the…
We show for the first time that highly localized in-plane breathers can propagate in specific directions with minimal lateral spreading in a model 2-D hexagonal non-linear lattice. The lattice is subject to an on-site potential in addition…
We study localized waves in chains of oscillators coupled by Hertzian interactions and trapped in local potentials. This problem is originally motivated by Newton's cradle, a mechanical system consisting of a chain of touching beads subject…
Breathing solitons are nonlinear waves in which the energy concentrates in a localized and oscillatory fashion. Similarly to stationary solitons, breathers in dissipative systems can form stable bound states displaying molecule-like…
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…
We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDE). In both cases, Fourier…
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…
By applying an out-of-phase actuation at the boundaries of a uniform chain of granular particles, we demonstrate experimentally that time-periodic and spatially localized structures with a nonzero background (so-called dark breathers)…
We prove nonexistence of breathers (spatially localized and time-periodic oscillations) for a class of Fermi-Pasta-Ulam lattices representing an uncompressed chain of beads interacting via Hertz's contact forces. We then consider the…
We study the dynamics of discrete breathers -- spatially localized and time-periodic solutions -- inside the bandgap of a nonlinear honeycomb lattice where the dispersion landscape approaches a so-called semi-Dirac point in which the bands…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…