Related papers: Self-avoiding worm-like chain model for dsDNA loop…
Recently Garel, Monthus and Orland (Europhys. Lett. v 55, 132 (2001)) considered a model of DNA denaturation in which excluded volume effects within each strand are neglected, while mutual avoidance is included. Using an approximate scheme…
The unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ is studied using Monte Carlo simulations. We obtain the dynamical order parameter, $Q$, defined as…
We compute the free energy of confinement ${\cal{F}}$ for a wormlike chain (WLC), with persistence length $l_p$, that is confined to the surface of a cylinder of radius $R$ under an external tension $f$ using a mean field variational…
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…
We study the effects of a power-law trapping potential on the scaling behaviour of the entanglement at the quantum critical point of one-dimensional (1D) lattice particle systems. We compute bipartite von Neumann and Renyi entropies in the…
We investigate the dynamic scaling properties of stochastic particle systems on a non-deterministic scale-free network. It has been known that the dynamic scaling behavior depends on the degree distribution exponent of the underlying…
We use an off - lattice bead - spring model of a self - avoiding polymer chain immersed in a 3-dimensional quenched random medium to study chain dynamics by means of a Monte - Carlo (MC) simulation. The chain center of mass mean-squared…
We investigate the symmetric Ashkin-Teller (AT) model on the triangular lattice in the antiferromagnetic two-spin coupling region ($J<0$). In the $J \rightarrow -\infty$ limit, we map the AT model onto a fully-packed loop-dimer model on the…
When the local intrinsic stiffness of a polymer chain varies over a wide range, one can observe both a crossover from rigid-rod-like behavior to (almost) Gaussian random coils and a further crossover towards self-avoiding walks in good…
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…
The loop gas approach to lattice field theory provides an alternative, geometrical description in terms of fluctuating loops. Statistical ensembles of random loops can be efficiently generated by Monte Carlo simulations using the worm…
Metropolis Monte Carlo simulation is used to investigate the elasticity of torsionally stressed double-stranded DNA, in which twist and supercoiling are incorporated as a natural result of base-stacking interaction and backbone bending…
We present a study of the bend angle distribution of semiflexible polymers of short and intermediate lengths within the wormlike chain model. This enables us to calculate the elastic response of a stiff molecule to a bending moment. Our…
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 mechanism and driving forces of chromosome segregation in the bacterial cell cycle of E. coli is one of the least understood events in its life cycle. Using principles of entropic repulsion between polymer loops confined in a cylinder,…
Using a highly efficient Monte Carlo algorithm, we are able to study the growth of coverage in a random sequential adsorption (RSA) of self-avoiding walk (SAW) chains for up to 10^{12} time steps on a square lattice. For the first time, the…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
By exploring a recent model [Palmeri, J., M. Manghi, and N. Destainville. 2007. Phys. Rev. Lett. 99:088103] where DNA bending elasticity, described by the wormlike chain model, is coupled to base-pair denaturation, we demonstrate that small…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…