Related papers: Duplex-single strand denaturing transition in DNA …
We consider layered superconductors with a flux lattice perpendicular to the layers and random columnar defects parallel to the magnetic field B. We show that the decoupling transition temperature Td, at which the Josephson coupling…
The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Using molecular dynamics simulations, we report phase separation in a 50:50 mixture of hot(active) and cold(passive) dumbbells which interact by Lennard-Jones potential. The ratio of the temperature difference between hot and cold dumbbells…
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…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
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…
Binary mixtures of lamellar colloids represented by hard platelets are studied within a generalization of the Zwanzig model for rods, whereby the square cuboids can take only three orientations along the $x$, $y$ or $z$ axes. The free…
Accurate knowledge of the thermodynamic properties of nucleic acids is crucial to predicting their structure and stability. To date most measurements of base-pair free energies in DNA are obtained in thermal denaturation experiments, which…
A new mean-field type theory is proposed to study order-disorder transitions (ODT) in block copolymers. The theory applies to both the weak segregation (WS) and the strong segregation (SS) regimes. A new energy functional is proposed…
We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
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 transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and…
We present a model for quark matter with a density dependent quark-quark (confining) potential, which allows to describe a deconfinement phase transition as the system evolves from a low density assembly of bound structures to a high…
We present a general framework to study the thermodynamic denaturation of double-stranded DNA under superhelical stress. We report calculations of position- and size-dependent opening probabilities for bubbles along the sequence. Our…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
X-ray and neutron powder diffraction data as a function of temperature are analyzed for the colossal dielectric constant material CaCu3Ti4O12. The local structure is studied using atomic pair distribution function analysis. No evidence is…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…