Related papers: Base pair fluctuations in helical models for nucle…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…
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…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
A method is proposed to select the suitable sets of potential parameters for a one-dimensional mesoscopic Hamiltonian model, first introduced to describe the DNA melting transition and later extended to investigate thermodynamic and…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
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…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
The thermodynamical stability of a set of circular double helical molecules is analyzed by path integral techniques. The minicircles differ only in \textit{i)} the radius and \textit{ii)} the number of base pairs ($N$) arranged along the…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
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…