相关论文: Self-avoiding worm-like chain model for dsDNA loop…

Using analytical approach and Monte-Carlo (MC) simulations, we study the elastic behaviour of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We…

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by…

The problem of reinforcement learning in an unknown and discrete Markov Decision Process (MDP) under the average-reward criterion is considered, when the learner interacts with the system in a single stream of observations, starting from an…

We investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to F^{\chi}, with \chi=(1-\nu)/\nu, where \nu is the well-known…

Bending of worm-like polymers carries an energy penalty which results in the appearance of a persistence length l such that the polymer is straight on length scales smaller than l and bends only on length scales larger than this length.…

Many biological systems exhibit multiscale dynamics, where some species occur in high copy numbers while others remain rare. This heterogeneity necessitates hybrid modelling approaches: deterministic models are computationally efficient but…

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…

Using Langevin dynamics simulations, we study the hysteresis in unzipping of longer double stranded DNA chains whose ends are subjected to a time dependent periodic force with frequency $\omega$ and amplitude $G$ keeping the other end…

We propose a new Monte Carlo algorithm for complex discrete distributions. The algorithm is motivated by the N-Fold Way, which is an ingenious event-driven MCMC sampler that avoids rejection moves at any specific state. The N-Fold Way can…

Recent measurements of the force versus extension curves in stretched single stranded DNA, under conditions where the hydrogen bonding between complementary bases is inhibited, provide a new handle for the study of self-avoiding effects in…

Polymer networks formed by cross linking flexible polymer chains are ubiquitous in many natural and synthetic soft-matter systems. Current micromechanics models generally do not account for excluded volume interactions except, for instance,…

The one-dimensional (1D) tight binding model with random nearest neighbor hopping is known to have a singularity of the density of states and of the localization length at the band center. We study numerically the effects of random long…

The entropy loss due to the formation of one or multiple loops in circular and linear DNA chains is calculated from a scaling approach in the limit of long chain segments. The analytical results allow to obtain a fast estimate for the…

We independently develop a simulation code following the previous dynamical Monte Carlo simulation of the diffusive shock acceleration under the isotropic scattering law during the scattering process, and the same results are obtained.…

The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…

Polydisperse brushes obtained by reversible radical chain polymerization reaction onto a solid substrate with surface-attached initiators, are studied by means of an off-lattice Monte Carlo algorithm of living polymers (LP). Various…

We propose a correlated spin-singlet-pairs wave function to describe the spin-gap phase of the one-dimensional $t-J$ model at low density. Adding a Jastrow factor with a variational parameter, $\nu$, first introduced by Hellberg and Mele,…

Clusters generated by the product-rule growth model of Achlioptas, D'Souza, and Spencer on a two-dimensional square lattice are shown to obey qualitatively different scaling behavior than standard (random growth) percolation. The threshold…

We introduce the concept of directed loops in stochastic series expansion and path integral quantum Monte Carlo methods. Using the detailed balance rules for directed loops, we show that it is possible to smoothly connect generally…

A polymer chain containing $N$ monomers confined in a finite cylindrical tube of diameter $D$ grafted at a distance $L$ from the open end of the tube may undergo a rather abrupt transition, where part of the chain escapes from the tube to…