8,488 research outputs found
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 that is
line-tied at the surfaces and . This initial configuration is
twisted by photospheric footpoint motion that is assumed to depend on only one
coordinate () 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
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