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As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify…
In the present paper we study the impact of dispersion and nonlinearity on DNA dynamics. We rely on the helicoidal Peyrard-Bishop model and use the fact that nonlinear DNA dynamics represents an interplay between nonlinearity and…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
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…
In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
Double stranded DNA chain is known to have nontrivial elasticity. We study the effect of this elasticity on the denaturation profile of DNA oligomer by constraining one base pair at one end of the oligomer to remain in unstretched (or…
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…
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…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
We show that the calculated DNA denaturation curves for finite (Peyrard-Bishop-Dauxois (PBD) chains are intrinsically undefined.
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we…
We present detailed molecular dynamics results for the displacement autocorrelation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
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…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…