Unzipping DNA by force: thermodynamics and finite size behaviour

We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size scaling of thermodynamic quantities like the extensibility, the length of the unzipped segment of a Y-fork, the phase diagram can be recovered. We suggest that such procedures could be used to obtain the thermodynamic phase diagram from experiments on finite length DNA.Comment: 10 pages, accepted for publication in special issue of Journal of Physics: Condensed Matte

DNA sequence from the unzipping force? : one mutation problem

The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the zipped from the unzipped regions. We propose a comparison method (``differential force microscope'') to detect mutations. Two lattice models are treated as specific examples.Comment: 11 pages, 4 figures. Revised version with minor changes. Paragraph with discussion on experiments added. Accepted for publication in J. Phys. A as a Letter to the Edito

Helicase activity on DNA as a propagating front

We develop a propagating front analysis, in terms of a local probability of zipping, for the helicase activity of opening up a double stranded DNA (dsDNA). In a fixed-distance ensemble (conjugate to the fixed-force ensemble) the front separates the zipped and unzipped phases of a dsDNA and a drive acts locally around the front. Bounds from variational analysis and numerical estimates for the speed of a helicase are obtained. Different types of helicase behaviours can be distinguished by the nature of the drive.Comment: 5 pages, 5 eps figures; replaced by the published versio

Manipulating a single adsorbed DNA for a critical endpoint

We show the existence of a critical endpoint in the phase diagram of unzipping of an adsorbed double-stranded (ds) polymer like DNA. The competition of base pairing, adsorption and stretching by an external force leads to the critical end point. From exact results, the location of the critical end point is determined and its classical nature established.Comment: 6 pages, 5 figures, Published versio

A Constrained Tectonics Model for Coronal Heating

An analytical and numerical treatment is given of a constrained version of the tectonics model developed by Priest, Heyvaerts, & Title [2002]. We begin with an initial uniform magnetic field ${\bf B} = B_0 \hat{\bf z}$ that is line-tied at the surfaces $z = 0$ and $z = L$. This initial configuration is twisted by photospheric footpoint motion that is assumed to depend on only one coordinate ($x$) transverse to the initial magnetic field. The geometric constraints imposed by our assumption precludes the occurrence of reconnection and secondary instabilities, but enables us to follow for long times the dissipation of energy due to the effects of resistivity and viscosity. In this limit, we demonstrate that when the coherence time of random photospheric footpoint motion is much smaller by several orders of magnitude compared with the resistive diffusion time, the heating due to Ohmic and viscous dissipation becomes independent of the resistivity of the plasma. Furthermore, we obtain scaling relations that suggest that even if reconnection and/or secondary instabilities were to limit the build-up of magnetic energy in such a model, the overall heating rate will still be independent of the resistivity

Comment on " A simple model for DNA denaturation"

The replacment of mutual avoidance of polymers by a long-range interaction of the type proposed by Garel etal (Europhys. Lett. 55, 132 (2001), cond-mat/0101058) is inconsistent with the prevalent renormalization group arguments.Comment: 2 pages, Comment on Garel etal. Europhys. Lett 55, 132(2001) cond-mat/0101058. Appeared in Europhys Let

Helicase on DNA: A Phase coexistence based mechanism

We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.Comment: Revtex4. 5 pages. 4 figures. Published versio