相关论文: Denaturation of Circular DNA: Supercoil Mechanism

The denaturation transition of circular DNA is studied within a Poland-Scheraga type approach, generalized to account for the fact that the total linking number (LK), which measures the number of windings of one strand around the other, is…

We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…

We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…

The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is…

We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops…

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 denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…

The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, 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…

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.…

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…

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…

We study a model for the denaturation transition of DNA in which the molecules are considered as composed of a sequence of alternating bound segments and denaturated loops. We take into account the excluded-volume interactions between…

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…

The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…

Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…

We perform an extensive numerical study of the disordered Poland-Scheraga (PS) model for DNA denaturation in which self-avoidance is completely taken into account. In complement to our previous work, we focus here on the finite size scaling…

We compare results of previous simulations of a simple model of DNA denaturation to the predictions of the Poland-Scheraga model. Concentrating on the critical region of the latter model we calculate both thermodynamic quantities and the…

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…