相关论文: A simple model for DNA denaturation

We consider three different continuum polymer models, that all depend on a tunable parameter r that determines the strength of the excluded-volume interactions. In the first model chains are obtained by concatenating hard spherocylinders of…

The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…

Poland-Scheraga models were introduced to describe the DNA denaturation transition. We give a rigorous and refined discussion of a family of these models. We derive possible scaling functions in the neighborhood of the phase transition…

The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…

We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…

DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…

The Poland--Scheraga model, introduced in the 1970's, is a reference model to describe the denaturation transition of DNA. More recently, it has been generalized in order to allow for asymmetry in the strands lengths and in the formation of…

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…

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…

We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…

The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness…

We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…

It now becomes apparent that condensed DNA toroid which emerges in a poor solvent condition can be realised in the framework of the non-linear sigma model on a line segment. In fact, the classical solutions of the model, i.e., of the…

Force-induced structural transitions both in relatively random and in designed single-stranded DNA (ssDNA) chains are studied theoretically. At high salt conditions, ssDNA forms compacted hairpin patterns stabilized by base-pairing and…

We investigate the generalized Poland-Scheraga model, which is used in the bio-physical literature to model the DNA denaturation transition, in the case where the two strands are allowed to be non-complementary (and to have different…

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…

Deformation of single stranded DNA in translocation process before reaching the pore is investigated. By solving the Laplace equation in a suitable coordinate system and with appropriate boundary conditions, an approximate solution for the…

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal…

For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…