Related papers: Stretching DNA in hard-wall potential channels
By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is…
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural…
The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
We analyze the diffusive transport of Brownian particles in narrow channels with periodically varying cross-section. The geometrical confinements lead to entropic barriers, the particle has to overcome in order to proceed in transport…
We study one-dimensional systems with random diagonal disorder but off-diagonal short-range correlations imposed by structural constraints. We find that these correlations generate effective conduction channels for finite systems. At a…
Predicting the macroscopic mechanical behavior of polymeric materials from the micro-structural features has remained a challenge for decades. Existing theoretical models often fail to accurately capture the experimental data, due to…
Linear chains of quantum scatterers are studied in the process of lengthening, which is treated and analysed as a discrete dynamical system defined over the manifold of scattering matrices. Elementary properties of such dynamics relate the…
We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
We develop a statistical model for a confined chain molecule based on a monomer grand canonical ensemble. The molecule is subject to an external chemical potential, a backbone interaction, and an attractive interaction between all monomers.…
We study macroscopic electrical or thermal conductivity of a composite made of straight or coiled nanowires suspended in poorly conducting medium. We assume that volume fraction of the wires is so large that spaces occupied by them overlap,…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
A phenomenological model based on the three-dimensional theory of nonlinear elasticity is developed to describe the phenomenon of overstretching in the force-extension curve for dsDNA. By using the concept of a material with multiple…
A rigorous theory of diffraction scattering from extended objects is proposed. The present theory is based on a multiple asymptotic expansion of an integral equation for the exact wave function in terms of the large parameters of the…
Macroscopic properties of heterogeneous media are frequently modelled by regular lattice models, which are based on a relatively small basic cluster of lattice sites. Here, we extend one of such models to any cluster's size kxk. We also…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We investigate the capacity of noisy frequency-based channels, motivated by DNA data storage in the short-molecule regime, where information is encoded in the frequency of items types rather than their order. The channel output is a…