Related papers: Melting behavior and different bound states in thr…
The presence of a thermodynamic phase of a three-stranded DNA, namely, a mixed phase of bubbles of two bound strands and a single one, is established for large dimensions ($d\geq 5$) by using exact real space renormalization group (RG)…
A three-stranded DNA with short range base pairings only is known to exhibit a classical analog of the quantum Efimov effect, viz., a three chain bound state at the two chain melting point where no two are bound. By using a non-perturbative…
The base sequences of DNA contain the genetic code and to decode it a double helical DNA has to open its base pairs. Recent studies have shown that one can use a third strand to identify the base sequences without opening the double helix…
We study the melting of three-stranded DNA by using the real-space renormalization group and exact recursion relations. The prediction of an unusual Efimov-analog three-chain bound state, that appears at the critical melting of two-chain…
We show that there exists an Efimov-like three strand DNA bound state at the duplex melting point and it is described by a renormalization group limit cycle. A nonperturbative RG is used to obtain this result in a model involving short…
We define a generalised model for three-stranded DNA consisting of two chains of one type and a third chain of a different type. The DNA strands are modelled by random walks on the three-dimensional cubic lattice with different interactions…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
As sections of a strand duplexed DNA denature when exposed to high temperature, the excess linking number is taken up by the undenatured portions of the molecule. The mechanical energy that arises because of the overwinding of the…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
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…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
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…
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 mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
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 discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
Systems of three particles show a surprising feature in their bound state spectrum: a series of geometrically scaled states, known as Efimov states. These states have not yet been observed directly, but many recent experiments show indirect…