Related papers: DNA melting in poor solvent
We consider the phase behavior of two-dimensional ($2D$)system of particles with an isotropic core-softened potential introduced in our previous publications. As one can expect from the qualitative consideration for the three dimensional…
In the present paper, using a molecular dynamics simulation, we study a nature of melting of a two-dimensional ($2D$) system of classical particles interacting through a purely repulsive isotropic core-softened potential which is used for…
The viscosity of dilute and semidilute unentangled DNA solutions, in steady simple shear flow, has been measured across a range of temperatures and concentrations. For polystyrene solutions, measurements of viscosity have been carried out…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
The two-dimensional generalization of the Polyelectolite model of DNA is proposed. It is reduced to the boundary problem for nonlinear completely integrable equation $\sh$-Gordon. In the linearisible version the exact solution is…
The phase diagram of the prototypical two-dimensional Lennard-Jones system, while extensively investigated, is still debated. In particular, there are controversial results in the literature as concern the existence of the hexatic phase 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…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
We study the influence of quenched disorder on the two-dimensional melting behavior by using both video-microscopy of superparamagnetic colloidal particles and computer simulations of repulsive parallel dipoles. Quenched disorder is…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
The effects of ionic ordering in DNA water solutions are studied by conductivity experiments. The conductivity measurements are performed for the solutions of DNA with KCl salt in the temperature range from 28 to 70 C. Salt concentration…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
The melting-like transition in disordered sodium clusters Na_N, with N=92 and 142 is studied by using a first-principles constant-energy molecular dynamics simulation method. Na_142, whose atoms are distributed in two (surface and inner)…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
Two-dimensional melting is one of the most fascinating and poorly understood phase transitions in nature. Theoretical investigations often point to a two-step melting scenario involving unbinding of topological defects at two distinct…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
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…
We investigate the characteristics of two dimensional melting in simple atomic systems via isobaric-isothermal ($NPT$) and isochoric-isothermal ($NVT$) molecular dynamics simulations with special focus on the effect of the range of the…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
The cations, in form of salt, present in the solution containing DNA play a crucial role in the opening of two strands of DNA. We use a simple non linear model and investigate the role of these cations on the mechanical unzipping of DNA.…