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

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

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

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

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

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

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

Reunion of Vicious Walkers: Results from ϵ\epsilon-Expansion -

The anomalous exponent, $\eta_{p}$, for the decay of the reunion probability of $p$ vicious walkers, each of length $N$, in $d$ $(=2-\epsilon)$ dimensions, is shown to come from the multiplicative renormalization constant of a $p$ directed polymer partition function. Using renormalization group(RG) we evaluate $\eta_{p}$ to $O(\epsilon^2)$. The survival probability exponent is $\eta_{p}/2$. For $p=2$, our RG is exact and $\eta_p$ stops at $O(\epsilon)$. For $d=2$, the log corrections are also determined. The number of walkers that are sure to reunite is 2 and has no $\epsilon$ expansion.Comment: No of pages: 11, 1figure on request, Revtex3,IP/BBSR/929

Dynamics of unbinding of polymers in a random medium

We have studied the aging effect on the dynamics of unbinding of a double stranded directed polymer in a random medium. By using the Monte Carlo dynamics of a lattice model in two dimensions, for which disorder is known to be relevant, the unbinding dynamics is studied by allowing the bound polymer to relax in the random medium for a waiting time and then allowing the two strands to unbind. The subsequent dynamics is formulated in terms of the overlap of the two strands and also the overlap of each polymer with the configuration at the start of the unbinding process. The interrelations between the two and the nature of the dependence on the waiting time are studied.Comment: 7 pages, latex, 3 figures, To appear in J. Chem. Phy

Dynamic phase transition in the conversion of B-DNA to Z-DNA

The long time dynamics of the conformational transition from B-DNA to Z-DNA is shown to undergo a dynamic phase transition. We obtained the dynamic phase diagram for the stability of the front separating B and Z. The instability in this front results in two split fronts moving with different velocities. Hence, depending on the system parameters a denatured state may develop dynamically eventhough it is thermodynamically forbidden. This resolves the current controversies on the transition mechanism of the B-DNA to Z-DNA.Comment: 5 pages, 4 figures. New version with correction of typos, new references, minor modifications in Fig 2, 3. To appear in EP