Related papers: DNA denaturation bubbles at criticality
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
The present work is devoted to the study of the thermostability of native DNA during binding to TiO$_{2}$ nanoparticles (NPs) at various concentrations under conditions close to physiological (0.1 M Na $^+$, pH 7) using thermal denaturation…
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 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…
We study generic aspects of bubble dynamics in DNA under time dependent perturbations, for example temperature change, by mapping the associated Fokker-Planck equation to a quantum time-dependent Schroedinger equation with imaginary time.…
We investigate DNA breathing dynamics by suggesting and examining several different Brownian functionals associated with bubble lifetime and reactivity. Bubble dynamics is described as an overdamped random walk in the number of broken base…
The spontaneous formation of tiny bubbles in a liquid is at the root of the nucleation mechanism during the liquid-to-vapor transition of a metastable liquid. The smaller the bubbles the larger their probability to appear, and even for…
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
The denaturation of double-stranded DNA as function of force and temperature is discussed. At room temperature, sequence heterogeneity dominates the physics of single molecule force-extension curves starting about 7 piconewtons of below a…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
Near the melting transition the bending elastic constant, $\kappa$, an emergent property of double-stranded DNA (dsDNA), is shown not to follow the rod-like scaling for small length $N$. The reduction in $\kappa$ with temperature is…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Simple mechanical models of DNA play an important role in studying the dynamics of its open states. The main requirement when developing a DNA model is the correct selection of its effective potentials and parameters based on experimental…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
We developed a low-energy model that can be used at any time to describe the dynamics of DNA bubbles at temperatures below the melting point. The Schr\"odinger equation associated with this problem is solved in imaginary time with a quantum…