Related papers: Nonlinear dynamics of damped DNA systems with long…
We study the parameter sensitivity of hetero-polymeric DNA within the purview of DNA breathing dynamics. The degree of correlation between the mean bubble size and the model parameters are estimated for this purpose for three different DNA…
Nonlinear classical Hamiltonian lattices exhibit generic solutions in the form of discrete breathers. These solutions are time-periodic and (typically exponentially) localized in space. The lattices exhibit discrete translational symmetry.…
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…
We demonstrate that period-doubled discrete breathers appear from the anti-continuum limit of the driven Peyrard-Bishop-Dauxois model of DNA. These novel breathers result from a stability overlap between sub-harmonic solutions of the driven…
A couple of models are explained. Helicoidal PB model is studied in more details. It is shown that semi-discrete approximation yields to breather-type soliton moving along the chain. The model can explain local opening as a resonance mode.…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
We explore dynamics of discrete breathers and multi-breathers in finite one-dimensional chain. The model involves parabolic on-site potential with rigid constraints and linear nearest-neighbor coupling. The rigid non-ideal impact…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
Lattice dynamics of rare-gas crystals is built on the base of adiabatic approximation when the deformation of electron shells of atoms of dipole and quadrupole types depending on nucleus shift and simultaneously arising Van-der-Vaals…
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…
Driven-dissipative light-matter systems can exhibit collective nonequilibrium phenomena due to loss and gain processes on the one hand and effective photon-photon interactions on the other hand. As generic example we study a bosonic lattice…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
Exact solutions for symmetric discrete breathers (DBs) are obtained in forced-damped linear chain with on-site vibro-impact constraints. The damping is related to inelastic impacts; the forcing may be chosen from broad class of periodic…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
We study the complex Ginzburg-Landau equation posed on possibly unbounded domains, including some singular and saturated nonlinear damping terms. This model interpolates between the nonlinear Schr{\"o}dinger equation and dissipative…
We investigate the dissipative dynamics of linear and nonlinear waves in harmonic traps by means of engineered complex non-Hermitian potentials. By combining an analytical mapping between real and complex Schr\"odinger equations with direct…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
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…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…