Related papers: Nonlinear waves in double-stranded DNA
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulation. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which…
Low-lying collective excitations in even-even vibrational and transitional nuclei may be described semi-classically as quadrupole running waves on the surface of the nucleus ("tidal waves"), and the observed vibrational-rotational behavior…
The propagation of ultrafast pulses in dispersion-engineered waveguides, exhibiting strong field confinement in both space and time, is a promising avenue towards single-photon nonlinearities in an all-optical platform. However, quantum…
Kinetics of dislocations is studied by means of computer simulation during intensive plastic deformation. The dynamical effect in the form of soliton-like wave of sharply disrupted interparticle bonds is observed. Along with it, micropores…
We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…
We demonstrate that nonlinearity plays a constructive role in supporting the robustness of dynamical localization in a model which is discrete, in one dimension and continuous in the orthogonal one. In the linear regime, time-periodic…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
We study a system consisting of a particle adsorbed on a carbon nanotube resonator. The particle is allowed to diffuse along the resonator, in order to enable study of e.g. room temperature mass sensing devices. The system is initialized in…
The internal motions of DNA immersed in bio-fluid are investigated. The interactions between the fragments of DNA and the surrounding bio-fluid are modeled using the gauge fluid lagrangian. In the model, the bio-fluid is coupled to the…
The nonlinear collisional dynamics of coupled driven plasma waves in the presence of background dissipation is studied analytically within kinetic theory. Sufficiently near marginal stability, phase space correlations are poorly preserved…
We study the nonlinear dynamics of a completely inhomogeneous DNA chain which is governed by a perturbed sine-Gordon equation. A multiple scale perturbation analysis provides perturbed kink-antikink solitons to represent open state…
We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day.…
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We show that long time distributions for the survival of DNA bubbles and the size autocorrelation function can be derived from…
The bubbles involved in sonochemistry and other applications of cavitation oscillate inertially. A correct estimation of the wave attenuation in such bubbly media requires a realistic estimation of the power dissipated by the oscillation of…
The oscillatory dynamics of nanoelectromechanical systems (NEMS) is at the heart of many emerging applications in nanotechnology. For common NEMS, such as beams and strings, the oscillatory dynamics is formulated using a dissipationless…
Using the very basic physics principles, we have studied the implications of quantum corrections to classical electrodynamics and the propagation of electromagnetic waves and pulses. The initial nonlinear wave equation for the…
We consider a non acoustic chain of harmonic oscillators with the dynamics perturbed by a random local exchange of momentum, such that energy and momentum are conserved. The macroscopic limits of the energy density, momentum and the…
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…