Related papers: Nonlinear waves in double-stranded DNA
We develop a framework to solve a large class of linearly driven non-Hermitian quantum systems. Such a class of models in the Hermitian scenario is commonly known as multi-state Landau-Zener models. The non-hermiticity is due to the…
In the present work, we introduce a discrete formulation of the nonlinear Dirac equation in the form of a discretization of the Gross-Neveu model. The motivation for this discrete model proposal is both computational (near the continuum…
A new description of the dynamics of warped accretion discs is presented. A theory of fully nonlinear, slowly varying bending waves is developed, involving a proper treatment of viscous fluid dynamics but neglecting self-gravitation. The…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
The Weibel/filamentation instability is known to play a key role in the physics of weakly magnetized collisionless shock waves. From the point of view of high energy astrophysics, this instability also plays a crucial role because its…
The nonlinear interaction, due to quantum electrodynamical (QED) effects, between photons is investigated using a wave-kinetic description. Starting from a coherent wave description, we use the Wigner transform technique to obtain a set of…
The coupled-mode theory is developed for description of the nonlinear wave dynamics in binary optical lattices. The obtained equations of motion accurately describe nonlinear wave dynamics close to the band edges and in the gap of the…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
In this paper the travelling wave solutions in the adiabatic model with two-step chain branching reaction mechanism are investigated both numerically and analytically in the limit of equal diffusivity of reactant, radicals and heat. The…
Planar wave trains are traveling wave solutions whose wave profiles are periodic in one spatial direction and constant in the transverse direction. In this paper, we investigate the stability of planar wave trains in reaction-diffusion…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Inspired by creation of a fast exchange-only qubit (Medford et al., Phys. Rev. Lett., 111, 050501 (2013)), we develop a theory describing the nonlinear dynamics of two such qubits that are capacitively coupled, when one of them is driven…
The gravito-inertial waves propagating over a shellular baroclinic flow inside a rotating spherical shell are analysed using the Boussinesq approximation. The wave properties are examined by computing paths of characteristics in the…
We study theoretically the driven-dissipative dynamics of an array of two-level emitters, coupled to a single photonic mode, in the presence of disorder in the resonant frequencies. We introduce the notion of subradiant correlations in the…
This research was stimulated by the recent studies of damping solutions in dynamically stable spherical stellar systems. Using the simplest model of the homogeneous stellar medium, we discuss nontrivial features of stellar systems. Taking…
It appears that thermally activated DNA bubbles of different sizes play central roles in important genetic processes. Here we show that the probability for the formation of such bubbles is regulated by the number of soft AT pairs in…
We propose nonlinear semi-discrete and discrete models for the elastic energy induced by a finite systems of edge dislocations in two dimensions. Within the dilute regime, we analyze the asymptotic behavior of the nonlinear elastic energy,…
We propose a simple phenomenological model for describing the conformational dynamics of biopolymers via the nonlinearity-induced buckling and collapse (i.e. coiling up) instabilities. Taking into account the coupling between the internal…
We review the numerical modelling of the nonlinear pulsations of classical variable stars with hydrocodes that include the effects of turbulent convection. Despite their simplicity these turbulent convective recipes appear to remove many of…
The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path…