Related papers: Nonlinear waves in double-stranded DNA
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
Nonlinear waves are studied in a mixture of liquid and gas bubbles. Influence of viscosity and heat transfer is taken into consideration on propagation of the pressure waves. Nonlinear evolution equations of the second and the third order…
The formation of bubble defects of the double stranded DNA is treated according to the Lifshits theory of disordered chains. A molecule of the DNA is modelled on a harmonic lattice with nearest neighbour interaction, elastic constants being…
We here examine the nonlinear dynamics of artificial homogeneous DNA chain relying on the plain-base rotator model. It is shown that such dynamics can exhibit kink and antikink solitons of sine-Gordon type. In that respect we propose…
Nonlinear waves in a liquid with gas bubbles are studied. Higher order terms with respect to the small parameter are taken into account in the derivation of the equation for nonlinear waves. A nonlinear differential equation is derived for…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets…
In this work we generalize the models for nonlinear waves in a gas--liquid mixture taking into account an interphase heat transfer, a surface tension and a weak liquid compressibility simultaneously at the derivation of the equations for…
We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
We consider the dissipative dynamics of a qubit coupled to a nonlinear oscillator (NO) embedded in an Ohmic environment. By treating the nonlinearity up to first order and applying Van Vleck perturbation theory up to second order in the…
A theoretical and experimental investigation is presented on the intermodal coupling between the flexural vibration modes of a single clamped-clamped beam. Nonlinear coupling allows an arbitrary flexural mode to be used as a self-detector…
We consider the modulational instability of nonlinearly interacting two-dimensional waves in deep water, which are described by a pair of two-dimensional coupled nonlinear Schroedinger equations. We derive a nonlinear dispersion relation.…
The non-linear dynamics of driven oscillations in the size of a spherical bubble are mapped to the dynamics of a Newtonian particle in a potential within the incompressible liquid regime. The compressible liquid regime, which is important…
The instability and nonlinear evolution of directional ocean waves is investigated numerically by means of simulations of the governing kinetic equation for narrow-band surface waves. Our simulation results reveal the onset of the…
Cavitation and bubble dynamics are central concepts in engineering, the natural sciences, and the mathematics of fluid mechanics. Due to the nonlinear nature of their dynamics, the governing equations are not fully solvable. Here, the…
A fourth-order and a second-order nonlinear diffusion models in spectral space are proposed to describe gravitational wave turbulence in the approximation of strongly local interactions. We show analytically that the model equations satisfy…
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.…
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…