Related papers: Breathers in a system with helicity and dipole int…
On a two-dimensional planar parity-time-($\mathcal{PT}$-)symmetric nonlinear magnetic metamaterial, consisting of split-ring dimers with balanced gain and loss, discrete breather solutions can be found. We extend these studies and by…
The quantum modes of a nonlinear Klein Gordon lattice have been computed numerically [L. Proville, Phys. Rev. B, vol. 71, 104306 (2005)]. The on-site nonlinearity has been found to lead to a phonon pairing and consequently some phonon bound…
We study metastable behavior in a discrete nonlinear Schr\"odinger equation from the viewpoint of Hamiltonian systems theory. When there are $n < \infty$ sites in this equation, we consider initial conditions in which almost all the energy…
DNA is structurally and mechanically altered by the binding of intercalator molecules. Intercalation strongly affects the force-extension behavior of DNA, in particular the overstretching transition. We present a statistical model that…
Relative lifetimes of inherent double stranded DNA openings with lengths up to ten base pairs are presented for different gene promoters and corresponding mutants that either increase or decrease transcriptional activity, in the framework…
We derive a Hamiltonian version of the ${\cal PT}$-symmetric discrete nonlinear Schr\"{o}dinger equation that describes synchronized dynamics of coupled pendula driven by a periodic movement of their common strings. In the limit of weak…
The nonlinear excitations induced in DNA by external force are considered on the basis of Peyrard-Bishop-Dauxois model. It is shown that such impact can lead to creation of bubbles which can propogate through the molecule. The interaction…
In this paper we consider a 2D hexagonal crystal lattice model first proposed by Marin, Eilbeck and Russell in 1998. We perform a detailed numerical study of nonlinear propagating localized modes, that is, propagating discrete breathers and…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as…
We investigate the properties of discrete breathers in a Bose-Einstein condensate with two- and three-body interactions in optical lattice. In the tight-binding approximation the Gross-Pitaevskii equation with periodic potential for the…
The distribution of bubble lengths in double-stranded DNA is presented for segments of varying guanine-cytosine (GC) content, obtained with Monte Carlo simulations using the Peyrard-Bishop-Dauxois model at 310 K. An analytical description…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
The existence of breather type solutions, i.e., periodic in time, exponentially localized in space solutions, is a very unusual feature for continuum, nonlinear wave type equations. Following an earlier work [Comm. Math. Phys. {\bf 302},…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
We present analytical and numerical studies of phase-coherent dynamics of intrinsically localized excitations (breathers) in a system of two weakly coupled nonlinear oscillator chains. We show that there are two qualitatively different…
We present a systematic study of the existence and stability of discrete breathers that are spatially localized in the bulk of a one-dimensional chain of compressed elastic beads that interact via Hertzian contact. The chain is diatomic,…
The unique geometry of the two-dimensional tripartite Kagome lattice is responsible for shaping diverse families of spatially localized and time-periodic nonlinear modes known as discrete breathers. We state conditions for the existence of…
We consider a previously experimentally realized discrete model that describes a mechanical metamaterial consisting of a chain of pairs of rigid units connected by flexible hinges. Upon analyzing the linear band structure of the model, we…
The mobility of high-frequency discrete breathers in monatomic chains with nonlinear interatomic potentials of the nearest neighbours is considered. It was found that the odd (cubic and fifth) anharmonicity strongly affects the mobility of…