Related papers: Generalized Poland-Scheraga denaturation model and…
We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
The paper deals with the homogenization of deformable porous media saturated by two-component electrolytes. The model relevant to the microscopic scale describes steady states of the medium while reflecting essential physical phenomena,…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We show that long time distributions for the survival of DNA bubbles and the size autocorrelation function can be derived from…
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…
The situation of the decay of the metastable phase on the several types of heterogeneous centers is described analytically. The total number of heterogeneous centers is supposed to be equal for different types. This description decomposes…
We consider a renewal process \tau={\tau_0,\tau_1,...} on the integers, where the law of \tau_i-\tau_{i-1} has a power-like tail P(\tau_i-\tau_{i-1}=n)=n^{-(\alpha+1)}L(n) with \alpha\ge0 and L(.) slowly varying. We then assign a random,…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
Results are presented for the phase separation process of a binary mixture subject to an uniform shear flow quenched from a disordered to a homogeneous ordered phase. The kinetics of the process is described in the context of the…
We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts…
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…
These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
The exact analytical solution of the degenerate Landau-Zener model, wherein two bands of degenerate energies cross in time, is presented. The solution is derived by using the Morris-Shore transformation, which reduces the fully coupled…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
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…
This survey offers an overview of recent advances in nonlocal phase transition problems, modeled by Ginzburg--Landau type energies of the form \[ \frac{1}{4}\iint_{\R^{2n}\setminus (\R^n \setminus \Omega)^2}…
We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models$\unicode{x2014}$oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes…
This article investigates the effect for random pinning models of long range power-law decaying correlations in the environment. For a particular type of environment based on a renewal construction, we are able to sharply describe the phase…
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…