Related papers: Moving breathers in a bent DNA-related model
In this paper, interstitial migration generated by scattering with a mobile breather is investigated numerically in a Frenkel-Kontorova one-dimensional lattice. Consistent with experimental results it is shown that interstitial diffusion is…
We present a theoretical study of inhomogeneous dynamic (resistive) states in a single plaquette consisting of three Josephson junctions. These breather states are found to exist in a large range of control parameters (dc bias, anisotropy…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
We study nonlinear phonon excitations in a one-dimensional quantum nonlinear lattice model using numerical exact diagonalization. We find that multi-phonon bound states exist as eigenstates which are natural counterparts of breather…
We study coupled transport in the nonequilibrium stationary state of a model consisting of independent random walkers, moving along a one-dimensional channel, which carry a conserved energy-like quantity, with density and temperature…
We consider the driven dynamics of a probe particle moving through an assembly of particles with competing long-range repulsive and short-range attractive interactions, which form crystal, stripe, labyrinth, and bubble states as the ratio…
The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
We investigate the existence of spatially localised solutions, in the form of discrete breathers, in general damped and driven nonlinear lattice systems of coupled oscillators. Conditions for the exponential decay of the difference between…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
We present an experimental study of discrete breathers in an underdamped Josephson-junction array. Breathers exist under a range of dc current biases and temperatures, and are detected by measuring dc voltages. We find the maximum allowable…
Nonlinear lattice models can support "discrete breather" excitations that stay localized in space for all time. By contrast, the localized Wannier states of linear lattice models are dynamically unstable. Nevertheless, symmetric and…
We describe an explicitly discrete model of the process of DNA branch migration. The model matches the existing data well, but we find that branch migration along long strands of DNA ($N \simge 40$~bp) is also well modeled by continuum…
We study a locally resonant granular material in the form of a precompressed Hertzian chain with linear internal resonators. Using an asymptotic reduction, we derive an effective nonlinear Schr\"odinger (NLS) modulation equation. This, in…
We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to…
We report analytical and numerical results on breather-like field configurations in a theory which is a deformation of the integrable sine-Gordon model in (1+1) dimensions. The main motivation of our study is to test the ideas behind the…
It is demonstrated that the breather solutions recently discovered in the weakly coupled topological discrete sine-Gordon system are spectrally unstable. This is in contrast with more conventional spatially discrete systems, whose breathers…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…