Related papers: DNA melting in poor solvent
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
We investigate the role of bubble positioning in the force-induced melting of double-stranded DNA using two distinct approaches: Brownian Dynamics simulations and the Gaussian Network Model. We isolate the effect of bubble positioning by…
The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…
We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
The nature of the metal-insulator Mott transition at zero temperature has been discussed for a number of years. Whether it occurs through a quantum critical point or through a first order transition is expected to profoundly influence the…
We investigate two-species bosons in a two-dimensional square lattice by quantum Monte Carlo method. We show that the inter-species attraction and nearest-neighbor intra-species repulsion results in the pair-supersolid phase, where a…
A coarsened model for a binary system with limited miscibility of components is proposed; the system is described in terms of structural states in small parts of the material. The material is assumed to have two alternative types of…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
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…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
Two-dimensional (2D) solid-liquid transition (SLT)~\cite{Mermin1966Absence,Mermin1968Crystalline,Kosterlitz1972Long} concerns fundamental concepts of long-range correlations vital to magnetism, superconductivity, superfluidity, and…
We study the quantum melting of quasi-one-dimensional lattice models in which the dominant energy scale is given by a repulsive dipolar interaction. By constructing an effective low-energy theory, we show that the melting of crystalline…
We carry out extensive Monte Carlo simulations of the three-dimensional (3D) uniformly frustrated XY model with uncorrelated randomly perturbed couplings, as a model for the equilibrium behavior of an extreme type-II superconductor with…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
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…
The phase diagram of a water solution of DNA and oppositely charged spherical macroions is studied. DNA winds around spheres to form beads-on-a-string complexes resembling the chromatin 10 nm fiber. At small enough concentration of spheres…
We report a study of DNA (150 bp fragments) conformations in very low added salt $<0.05$mM, across wide DNA concentration range $0.0015\leq c \leq 8$~mM (bp). We found an intermediate DNA conformation in the region $0.05 < c < 1$~mM, by…
Monte Carlo or Molecular Dynamics calculations of surfaces of Lennard-Jones systems often indicate, apart from a gradual disordering of the surface called surface melting, the presence of a phase transition at the surface, but cannot…
The flux line lattice melting transition in two-dimensional pure and disordered superconductors is studied by a Monte Carlo simulation using the lowest Landau level approximation and quasi-periodic boundary condition on a plane. The…
There are strong evidences that the melting in two dimensions depends crucially on the form and range of the interaction potentials between particles. We study with Monte Carlo simulations the phase diagram and the melting of a monolayer of…