Related papers: Generalized Poland-Scheraga denaturation model and…
Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases,…
Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a…
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…
The distance distribution between complementary base pairs of the two strands of a DNA molecule is studied near the melting transition. Scaling arguments are presented for a generalized Poland-Scheraga type model which includes…
In Ref. [1] the author has recently established sharp large deviation principles for cumulative rewards associated with a discrete-time renewal model, supposing that each renewal involves a broad-sense reward taking values in a separable…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
We consider a general model of a disordered copolymer with adsorption. This includes, as particular cases, a generalization of the copolymer at a selective interface introduced by Garel et al. [Europhys. Lett. 8 (1989) 9--13], pinning and…
In these proceedings, we first summarize some general properties of phase transitions in the presence of quenched disorder, with emphasis on the following points: the need to distinguish typical and averaged correlations, the possible…
We have investigated the denaturation bubble life time for a homogeneous as well as for a heterogeneous DNA within a Poland-Scheraga model. It is shown that at criticality the bubble life time for a homogeneous DNA is finite provided that…
We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
We study the large deviations of additive quantities, such as energy or current, in stochastic processes with intermittent reset. Via a mapping from a discrete-time reset process to the Poland-Scheraga model for DNA denaturation, we derive…
We analyse the effects of the environment (solvent quality, presence of extended structures - crowded environment) that may have impact on the order of the transition between denaturated and bounded DNA states and lead to changes in the…
Mixed order phase transitions are transitions which have common features with both first order and second order transitions. I review some results obtained in the context of one of the prototypical models of mixed order transitions, the…
For the DNA denaturation transition in the presence of random contact energies, or equivalently the disordered wetting transition, we introduce a Strong Disorder Renewal Approach to construct the optimal contacts in each disordered sample…
We investigate the sharp asymptotic behavior at criticality of the large fluctuations of extensive observables in renewal models of statistical mechanics, such as the Poland-Scheraga model of DNA denaturation, the Fisher-Felderhof model of…
We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the…
We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA, that is clamped at one end. In particular, we quantify the…
We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid…