6,486 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
A Measure of data-collapse for scaling
Data-collapse is a way of establishing scaling and extracting associated
exponents in problems showing self-similar or self-affine characteristics as
e.g. in equilibrium or non-equilibrium phase transitions, in critical phases,
in dynamics of complex systems and many others. We propose a measure to
quantify the nature of data collapse. Via a minimization of this measure, the
exponents and their error-bars can be obtained. The procedure is illustrated by
considering finite-size-scaling near phase transitions and quite strikingly
recovering the exact exponents.Comment: 3 pages, revtex, 3 figures,2 in colour. Replaced by the proper
version - slightly longer and no mismatch of abstrac
Approach to equilibrium in adiabatically evolving potentials
For a potential function (in one dimension) which evolves from a specified
initial form to a different asymptotically, we study the
evolution, in an overdamped dynamics, of an initial probability density to its
final equilibeium.There can be unexpected effects that can arise from the time
dependence. We choose a time variation of the form
. For a , which is
double welled and a which is simple harmonic, we show that, in
particular, if the evolution is adiabatic, the results in a decrease in the
Kramers time characteristics of . Thus the time dependence makes
diffusion over a barrier more efficient. There can also be interesting
resonance effects when and are two harmonic potentials
displaced with respect to each other that arise from the coincidence of the
intrinsic time scale characterising the potential variation and the Kramers
time.Comment: This paper contains 5 page
Fast magnetic reconnection in laser-produced plasma bubbles
Recent experiments have observed magnetic reconnection in
high-energy-density, laser-produced plasma bubbles, with reconnection rates
observed to be much higher than can be explained by classical theory. Based on
fully kinetic particle simulations we find that fast reconnection in these
strongly driven systems can be explained by magnetic flux pile-up at the
shoulder of the current sheet and subsequent fast reconnection via two-fluid,
collisionless mechanisms. In the strong drive regime with two-fluid effects, we
find that the ultimate reconnection time is insensitive to the nominal system
Alfven time.Comment: 5 pages, 4 figures, accepted by Phys. Rev. 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
Supercriticality to subcriticality in dynamo transitions
Evidence from numerical simulations suggest that the nature of dynamo
transition changes from supercritical to subcritical as the magnetic Prandtl
number is decreased. To explore this interesting crossover we first use direct
numerical simulations to investigate the hysteresis zone of a subcritical
Taylor-Green dynamo. We establish that a well defined boundary exists in this
hysteresis region which separates dynamo states from the purely hydrodynamic
solution. We then propose simple dynamo models which show similar crossover
from supercritical to subcritical dynamo transition as a function of the
magnetic Prandtl number. Our models show that the change in the nature of
dynamo transition is connected to the stabilizing or de-stabilizing influence
of governing non-linearities.Comment: Version 3 note: Found a sign-error in an equation which propagated
further. Section 4 and Fig. 3,4,5 are updated in Version 3 (final form
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