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 $V_{i}(x)$ to a different $V_{f}(x)$ 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 $V(x,t)=V_{f}(x)+(V_{i}-V_{f})e^{-\lambda t}$. For a $V_{f}(x)$, which is double welled and a $V_{i}(x)$ 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 $V_{f}(x)$. Thus the time dependence makes diffusion over a barrier more efficient. There can also be interesting resonance effects when $V_{i}(x)$ and $V_{f}(x)$ 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