Related papers: Nonlinear dynamics of damped DNA systems with long…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
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…
Dynamics of DNA bubbles are of interest for both statistical physics and biology. We present exact solutions to the Fokker-Planck equation governing bubble dynamics in the presence of a long-range entropic interaction. The complete meeting…
By means of a modified Lugiato-Lefever equation model, we investigate the nonlinear dynamics of dissipative wave structures in coherently-driven Kerr cavities with a parabolic potential. The potential stabilizes system dynamics, leading to…
Discrete breathers with purely anharmonic short-range interaction potentials localize super-exponentially becoming compact-like. We analyze their spatial localization properties and their dynamical stability. Several branches of solutions…
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…
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 study the entanglement dynamics in the externally-driven single-mode Dicke model in the thermodynamic limit, when the field is in resonance with the atoms. We compute the correlations in the atoms-field ground state by means of the…
The dynamical evolution of a Bose-Einstein condensate trapped in a one-dimensional lattice potential is investigated theoretically in the framework of the Bose-Hubbard model. The emphasis is set on the far-from-equilibrium evolution in a…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
We investigate the dynamics of overdamped $D$-dimensional systems of particles repulsively interacting through short-ranged power-law potentials, $V(r)\sim r^{-\lambda}\;(\lambda/D>1)$. We show that such systems obey a non-linear diffusion…
We study the basepairing dynamics of DNA with repetitive sequences where local strand slippage can create, annihilate, and move bulge loops. Using an explicit theoretical model, we find a rich dynamical behavior as a function of an applied…
The paper studies the long time behavior of a system that describes the motion of a piece of elastic membrane driven by surface tension and inner air pressure. The system is a degenerate quasilinear hyperbolic one that involves the mean…
The quantum dynamics of two weakly coupled nonlinear oscillators is analytically and numerically investigated in the context of nonlinear dissipation. The latter facilitates the creation and preservation of non-classical steady states.…
The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
We present a numerical study of the dynamics of a non-ideal fluid subject to a density-dependent pseudo-potential characterized by a hierarchy of nested attractive and repulsive interactions. It is shown that above a critical threshold of…
We develop the theory of nonlinear localised modes (intrinsic localised modes or discrete breathers) in two-dimensional (2D) photonic crystal waveguides. We consider different geometries of the waveguides created by an array of nonlinear…
We have studied the dynamic evolution of the collective excitations in Bose-Einstein condensates in a deep optical lattice with tunable three-body interactions. Their dynamics is governed by a high order discrete nonlinear Schrodinger…