Related papers: DNA entropic elasticity for short molecules attach…

We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…

In this paper, we present a theory to efficiently deal with mechanical properties of heterogeneous polymer chain in free space and the central problem is to evaluate the diffusion equation and orientation-orientation correlation function,…

The time-dependent transverse response of stiff polymers, represented as weakly-bending wormlike chains (WLCs), is well-understood on the linear level, where transverse degrees of freedom evolve independently from the longitudinal ones. We…

We show that the mechanical properties of a worm-like-chain (WLC) polymer, of contour length $L$ and persistence length $\l$ such that $t=L/\l\sim{\cal O}(1)$, depend both on the ensemble and the constraint on end-orientations. In the…

DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…

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…

It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large…

The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…

We calculate the equation of state of DNA under tension for the case that the DNA features loops. Such loops occur transiently during DNA condensation in the presence of multivalent ions or sliding cationic protein linkers. The…

A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…

We propose approximations for force-extension dependencies for the freely jointed chain (FJC) and worm-like chain (WLC) models as well as for extension-force dependence for the WLC model. Proposed expressions show less than 1% relative…

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 response of a semiflexible polyelectrolyte chain to stretching in the regimes of moderate and weak screening is studied theoretically, with a special focus on DNA experiments. By using the nonlinear Poisson--Boltzmann description of…

Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…

A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…

We obtain, using transfer matrix methods, the distribution function $P(R)$ of the end-to-end distance, the loop formation probability and force-extension relations in a model for short double-stranded DNA molecules. Accounting for the…

The quite recent technological rise in molecular biology allowed single molecule manipulation experiments, where molecule stretching plays a primary role. In order to understand the experimental data, it is felt the urge of some physical…

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…

DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…