Related papers: Strand diffusion-limited closure of denaturation b…
For the DNA denaturation transition in the presence of random contact energies, or equivalently the disordered wetting transition, we introduce a Strong Disorder Renewal Approach to construct the optimal contacts in each disordered sample…
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far,…
Conformational change of a DNA molecule is frequently observed in multiple biological processes and has been modelled using a chain of strongly coupled oscillators with a nonlinear bistable potential. While the mechanism and properties of…
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…
Diffusion in bidisperse Brownian hard-sphere suspensions is studied by Stokesian Dynamics (SD) computer simulations and a semi-analytical theoretical scheme for colloidal short-time dynamics, based on Beenakker and Mazur's method [Physica…
We present a theoretical study of single-stranded DNA under stretching. Within the proposed framework, the effects of basepairing on the mechanical response of the molecule can be studied in combination with an arbitrary underlying model of…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
Under constant applied force, the separation of double-stranded DNA into two single strands is known to proceed through a series of pauses and jumps. Given experimental traces of constant-force unzipping, we present a method whereby the…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…
We report a structural polymorphism of the S-DNA when a canonical B-DNA is stretched under different pulling protocols and provide a fundamental molecular understanding of the DNA stretching mechanism. Extensive all atom molecular dynamics…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
A simple Langevin approach is used to study stationary properties of the Peyrard-Bishop-Dauxois model for DNA, allowing known properties to be recovered in an easy way. Results are shown for the denaturation transition in homogeneous…
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately $100$ base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…