Related papers: Solitons in Peyrard-Bishop model of DNA and the Re…
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…
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…
We use the helicoidal Peyrard-Bishop model of DNA in the current work. We solve a dynamical equation of motion using a continuum approximation, resulting in kink-solitary waves that travel along the chain. We demonstrate that, whereas…
A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous…
The non-perturbative renormalization-group approach is extended to lattice models, considering as an example a $\phi^4$ theory defined on a $d$-dimensional hypercubic lattice. Within a simple approximation for the effective action, we solve…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
A perturbative renormalization group method is used to obtain steady-state density profiles of a particle non-conserving asymmetric simple exclusion process. This method allows us to obtain a globally valid solution for the density profile…
The renormalization group method is applied to the study of discrete dynamical systems. As a particular example, the Henon map is considered as applied to describe the transverse betatron oscillations in a cyclic accelerator or storage ring…
We report on the nature of the thermal denaturation transition of homogeneous DNA as determined from a renormalisation group analysis of the Peyrard-Bishop-Dauxois model. Our approach is based on an analogy with the phenomenon of critical…
A proper version of the proto renormalization-group scheme is presented to derive amplitude equations in striped pattern formation with conserved and nonconserved order parameter. In the conserved case, the result preserves the conservation…
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…
The renormalization group has proven to be a very powerful tool in physics for treating systems with many length scales. Here we show how it can be adapted to provide a new class of algorithms for discrete optimization. The heart of our…
The renormalization method based on the Taylor expansion for asymptotic analysis of differential equations is generalized to difference equations. The proposed renormalization method is based on the Newton-Maclaurin expansion. Several basic…
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…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…
The renormalization group method is one of the singular perturbation methods used in the research of the asymptotic behavior of solution of ordinary differential equations. In this paper, the equation of VAN der Pol generalized oscillator…
We develop a renormalization group method to investigate synchronization clusters in a one-dimensional chain of nearest-neighbor coupled phase oscillators. The method is best suited for chains with strong disorder in the intrinsic…
Perturbative renormalization group theory is developed as a unified tool for global asymptotic analysis. With numerous examples, we illustrate its application to ordinary differential equation problems involving multiple scales, boundary…
For certain hierarchical structures, one can study the percolation problem using the renormalization-group method in a very precise way. We show that the idea can be also applied to two-dimensional planar lattices by regarding them as…
Soliton solutions are recovered as scale-invariant asymptotic states of vacuum inhomogeneous cosmologies using renormalization group method. The stability analysis of these states is also given.