Related papers: Helix-coil Transition in Closed Circular DNA
We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…
Liquid-liquid phase transition of hydrogen is at the center of hydrogen phase diagram as a promising route towards emergent properties such as the Wigner-Huntington metallization, superconductivity, and superfluidity. Here we report a study…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
The Continuum Shell Model is an old but recently revived method that traverses the boundary between nuclear many-body structure and nuclear reactions. The method is based on the non-Hermitian energy-dependent effective Hamiltonian. The…
We have performed quantum molecular dynamics simulations for dense helium to study the nonmetal-to-metal transition at high pressures. We present new results for the equation of state and the Hugoniot curve in the warm dense matter region.…
We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
Radical recombination has been proposed to lead to the formation of complex organic molecules (COMs) in CO-rich ices in the early stages of star formation. These COMs can then undergo hydrogen addition and abstraction reactions leading to a…
The object of this study is the kinetic process of solid-liquid first-order phase transition - melting of carbon dioxide CS-I hydrate with various cavity occupation ratios. The work was done within a framework of study on the local…
The phase diagram of hydrogen is one of the most important challenges in high-pressure physics and astrophysics. Especially, the melting of dense hydrogen is complicated by dimer dissociation, metallization and nuclear quantum effect of…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
One-neutron halo nuclei, composed by a weakly-bound particle coupled to a core nucleus, are studied within a particle-plus-core model. A semi-microscopic method to generate the two-body Hamiltonian of such a system, including core…
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
We study the effect of temperature up to 1000K on the structure of dense molecular para-hydrogen and ortho-deuterium, using the path-integral Monte Carlo method. We find a structural phase transition from orientationally disordered…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…