Related papers: Nonlinear dynamics of damped DNA systems with long…
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…
The dynamics of Bose-Einstein condensates trapped in a deep optical lattice is governed by a discrete nonlinear equation (DNL). Its degree of nonlinearity and the intersite hopping rates are retrieved from a nonlinear tight-binding…
We propose a dynamical model depicting the interactions between DNA and a specific binding protein involving long range transmissions. The dynamics rely on the coupling between Hydrogen bonds formed between DNA and protein and between the…
We analyze typical models which intend to describe (parts of) the dynamics of H-Bonds in DNA. We show that these models generically allow for nonlinear localized excitatons (NLEs) (discrete breathers). We especially study the scattering of…
We investigate the existence of spatially localised solutions, in the form of discrete breathers, in general damped and driven nonlinear lattice systems of coupled oscillators. Conditions for the exponential decay of the difference between…
We consider the links between nonlinear dynamics and thermodynamics in the framework of a simple nonlinear model for DNA. Two analyses of the phase transition, either with the transfer integral approach or by considering the instability of…
We propose a model for a chain of particles coupled by nonlinear springs in which each mass has an internal mass and all interactions are assumed to be nonlinear. We show how to construct an asymptotic solution of this system using multiple…
We study the dynamics of the discrete nonlinear Schr{\"o}dinger lattice initialized such that a very long transitory period of time in which standard Boltzmann statistics is insufficient is reached. Our study of the nonlinear system locked…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We propose a new simple model for DNA denaturation bases on the pendulum model of Englander\cite{A1} and the microscopic model of Peyrard {\it et al.},\cite{A3} so called "combined model". The main parameters of our model are: the coupling…
This work focuses on the study of time-periodic solutions, including breathers, in a nonlinear lattice consisting of elements whose contacts alternate between strain-hardening and strain-softening. The existence, stability, and bifurcation…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
We study long-time dynamics of a class of abstract second order in time evolution equations in a Hilbert space with the damping term depending both on displacement and velocity. This damping represents the nonlinear strong dissipation…
The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents…
We propose a nonlinear model derived from first principles, to describe bubble dynamics of DNA. Our model equations include a term derived from the dissipative effect of intermolecular vibrational modes. Such modes are excited by the…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We explore the dynamics of strongly localized periodic solutions (discrete solitons, or discrete breathers) in a finite one-dimensional chain of asymmetric vibro-impact oscillators. The model involves a parabolic on-site potential with…
We study the dynamics of discrete breathers -- spatially localized and time-periodic solutions -- inside the bandgap of a nonlinear honeycomb lattice where the dispersion landscape approaches a so-called semi-Dirac point in which the bands…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…