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

Ge growth on ion-irradiated Si self-affine fractal surfaces

We have carried out scanning tunneling microscopy experiments under ultrahigh vacuum condition to study the morphology of ultrathin Ge films eposited on pristine Si(100) and ion-irradiated Si(100) self-affine fractal surfaces. The pristine and the ion-irradiated Si(100) surface have roughness exponents of alpha=0.19+/-0.05 and alpha=0.82+/-0.04 respectively. These measurements were carried out on two halves of the same sample where only one half was ion-irradiated. Following deposition of a thin film of Ge (~6 A) the roughness exponents change to 0.11+/-0.04 and 0.99+/-0.06, respectively. Upon Ge deposition, while the roughness increases by more than an order of magnitude on the pristine surface, a smoothing is observed for the ion-irradiated surface. For the ion-irradiated surface the correlation length xi increases from 32 nm to 137 nm upon Ge deposition. Ge grows on Si surfaces in the Stranski-Krastanov or layer-plus-island mode where islands grow on a wetting layer of about three atomic layers. On the pristine surface the islands are predominantly of square or rectangular shape, while on the ion-irradiated surface the islands are nearly diamond shaped. Changes of adsorption behaviour of deposited atoms depending on the roughness exponent (or the fractal dimension) of the substrate surface are discussed.Comment: 5 pages, 2 figures and 1 tabl

Hydraulic Jump in One-dimensional Flow

In the presence of viscosity the hydraulic jump in one dimension is seen to be a first-order transition. A scaling relation for the position of the jump has been determined by applying an averaging technique on the stationary hydrodynamic equations. This gives a linear height profile before the jump, as well as a clear dependence of the magnitude of the jump on the outer boundary condition. The importance of viscosity in the jump formation has been convincingly established, and its physical basis has been understood by a time-dependent analysis of the flow equations. In doing so, a very close correspondence has been revealed between a perturbation equation for the flow rate and the metric of an acoustic white hole. We finally provide experimental support for our heuristically developed theory.Comment: 17 Pages, 8 Figures, 1 Table. To appear in European Physical Journal

Reunion of random walkers with a long range interaction: applications to polymers and quantum mechanics

We use renormalization group to calculate the reunion and survival exponents of a set of random walkers interacting with a long range $1/r^2$ and a short range interaction. These exponents are used to study the binding-unbinding transition of polymers and the behavior of several quantum problems.Comment: Revtex 3.1, 9 pages (two-column format), 3 figures. Published version (PRE 63, 051103 (2001)). Reference corrections incorporated (PRE 64, 059902 (2001) (E

Reduced magnetohydrodynamic theory of oblique plasmoid instabilities

The three-dimensional nature of plasmoid instabilities is studied using the reduced magnetohydrodynamic equations. For a Harris equilibrium with guide field, represented by \vc{B}_o = B_{po} \tanh (x/\lambda) \hat{y} + B_{zo} \hat{z}, a spectrum of modes are unstable at multiple resonant surfaces in the current sheet, rather than just the null surface of the polodial field $B_{yo} (x) = B_{po} \tanh (x/\lambda)$, which is the only resonant surface in 2D or in the absence of a guide field. Here $B_{po}$ is the asymptotic value of the equilibrium poloidal field, $B_{zo}$ is the constant equilibrium guide field, and $\lambda$ is the current sheet width. Plasmoids on each resonant surface have a unique angle of obliquity $\theta \equiv \arctan(k_z/k_y)$. The resonant surface location for angle $\theta$ is x_s = - \lambda \arctanh (\tan \theta B_{zo}/B_{po}), and the existence of a resonant surface requires $|\theta| < \arctan (B_{po} / B_{zo})$. The most unstable angle is oblique, i.e. $\theta \neq 0$ and $x_s \neq 0$, in the constant-$\psi$ regime, but parallel, i.e. $\theta = 0$ and $x_s = 0$, in the nonconstant-$\psi$ regime. For a fixed angle of obliquity, the most unstable wavenumber lies at the intersection of the constant-$\psi$ and nonconstant-$\psi$ regimes. The growth rate of this mode is $\gamma_{\textrm{max}}/\Gamma_o \simeq S_L^{1/4} (1-\mu^4)^{1/2}$, in which $\Gamma_o = V_A/L$, $V_A$ is the Alfv\'{e}n speed, $L$ is the current sheet length, and $S_L$ is the Lundquist number. The number of plasmoids scales as $N \sim S_L^{3/8} (1-\mu^2)^{-1/4} (1 + \mu^2)^{3/4}$.Comment: 9 pages, 8 figures, to be published in Physics of Plasma

Possible ferro-spin nematic order in NiGa2S4

We explore the possibility that the spin-1 triangular lattice magnet NiGa2 S4 may have a ferro-nematic ground state with no frozen magnetic moment but a uniform quadrupole moment. Such a state may be stabilized by biquadratic spin interactions. We describe the physical properties of this state and suggest experiments to help verify this proposal. We also contrast this state with a `non-collinear' nematic state proposed earlier by Tsunetsugu and Arikawa for NiGa2S4

Nonequilibrium tricriticality in one dimension

We show the existence of a nonequilibrium tricritical point induced by a repulsive interaction in one dimensional asymmetric exclusion process. The tricritical point is associated with the particle-hole symmetry breaking introduced by the repulsion. The phase diagram and the crossover in the neighbourhood of the tricritical point for the shock formation at one of the boundaries are determined.Comment: 6 pages; 4 figure