Related papers: Elasticity of a DNA chain dotted with bubbles unde…
The depinning of an elastic line in a random medium is studied via an extremal model. The latter gives access to the instantaneous depinning force for each successive conformation of the line. Based on conditional statistics the universal…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…
The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
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…
We have studied numerically the dynamics of a directed elastic string in a two-dimensional array of quenched random impurities. The string is driven by a constant transverse force and thermal fluctuations are neglected. There is a…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
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…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
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 studied the unzipping kinetics of single molecules of double-stranded DNA by pulling one of their two strands through a narrow protein pore. PCR analysis yielded the first direct proof of DNA unzipping in such a system. The time to unzip…
We present a dynamical model of DNA mechanical unzipping under the action of a force. The model includes the motion of the fork in the sequence-dependent landscape, the trap(s) acting on the bead(s), and the polymeric components of the…
We have recently suggested that the probability for the formation of thermally activated DNA bubbles is, to a very good approximation, proportional to the number of soft AT pairs over a length L(n) that depend on the size $n$ of the bubble…
We numerically examine the dynamics of a probe particle driven at a constant force through an assembly of particles with competing long-range repulsion and short-range attraction that forms a bubble or stripe state. In the bubble regime, we…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
A tribological system consisting of two contacting blocks has been considered. One of them is arranged between two springs, the other is driven periodically. The kinetics of the system has been studied in the boundary friction mode, when an…
We numerically examine the effect of thermal fluctuations on a first-order phase transition in 2+1 dimensions. By focusing on the expansion of a single bubble we are able to calculate changes in the bubble wall's velocity as well as changes…