Related papers: Nonlinear waves in double-stranded DNA
A nonlinear dynamics of the thermal and electromagnetic instability of critical state in type II superconductors has been analysed taking into account effects of dissipation and dispersion. An existance of a nonlinear running waves…
The quantum dynamics of interacting bosons in a one-dimensional system is investigated numerically. We consider dissipative and conservative two-particle interactions, and integrate the master equation describing the system dynamics via a…
A model is presented for the characterization of dissipative effects on highly nonlinear waves in one-dimensional dry granular media. The model includes three terms: Hertzian, viscoelastic, and a term proportional to the square of the…
We demonstrate the stabilization of two-dimensional nonlinear wave patterns by means of a dissipative confinement potential. Our analytical and numerical analysis, based on the generalized dissipative Gross-Pitaevskii equation, makes use of…
In this work we explore how nonlinear modes described by a dispersive wave equation (in our example, the nonlinear Schrodinger equation) and localized in a few wells of a periodic potential can act analogously to a chain of coupled…
Modal methods are a long-standing approach to physical modelling synthesis. Extensions to nonlinear problems are possible, leading to coupled nonlinear systems of ordinary differential equations. Recent work in scalar auxiliary variable…
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single…
A novel third order nonlinear evolution equation governing the dynamics of high frequency electrostatic drift waves has been derived in the framework of a plasma fluid model in an inhomogeneous magnetized plasma. The linear dispersion…
The dynamics of many natural systems is dominated by non-linear waves propagating through the medium. We show that the dynamics of non-linear wave fronts with positive surface tension can be formulated as a gradient system. The variational…
Generation of an acoustic wave by two pump sound waves is studied in a three-phase marine sediment that consists of a solid frame and the pore water with air bubbles in it. To avoid shock-wave formation the interaction is considered in the…
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.…
We investigate bubble deformations in an homogeneous and isotropic turbulent flow by means of direct numerical simulations of a single bubble in turbulence. We examine interface deformations by decomposing the local radius into the…
We study the noisy dynamics of two coupled bistable modes of a nanomechanical beam. When de-coupled, each driven mode obeys the Duffing equation of motion, with a well-defined bistable region in the frequency domain. When both modes are…
We analyse transcriptional bursting within a stochastic non-equilibrium model which accounts for the coupling between the dynamics of DNA supercoiling and gene transcription. We find a clear signature of bursty transcription when there is a…
In a companion paper, a reduced model for propagation of acoustic waves in a cloud of inertial cavitation bubbles was proposed. The wave attenuation was calculated directly from the energy dissipated by a single bubble, the latter being…
The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We investigate the nonlinear dynamics of the Peyrard-Bishop DNA model taking into account site dependent inhomogeneities. By means of the multiple-scale expansion in the semi-discrete approximation, the dynamics is governed by the perturbed…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the…