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

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

Analysis of a Three Phase Induction Motor Directly from Maxwell's Equations

The torque developed in a three phase AC squirrel cage motor is usually expressed in terms of resistances and reactances of the stator, the rotor, and the motor as a whole. We use Maxwell's equations to find the torque in terms of geometrical parameters. This allows us to estimate the torque developed by a motor without knowing the details of its circuitry

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

Current sheet formation and nonideal behavior at three-dimensional magnetic null points

The nature of the evolution of the magnetic field, and of current sheet formation, at three-dimensional (3D) magnetic null points is investigated. A kinematic example is presented which demonstrates that for certain evolutions of a 3D null (specifically those for which the ratios of the null point eigenvalues are time-dependent) there is no possible choice of boundary conditions which renders the evolution of the field at the null ideal. Resistive MHD simulations are described which demonstrate that such evolutions are generic. A 3D null is subjected to boundary driving by shearing motions, and it is shown that a current sheet localised at the null is formed. The qualitative and quantitative properties of the current sheet are discussed. Accompanying the sheet development is the growth of a localised parallel electric field, one of the signatures of magnetic reconnection. Finally, the relevance of the results to a recent theory of turbulent reconnection is discussed.Comment: to appear in Phys. Plasmas. A version with higher quality figures can be found at http://www.maths.dundee.ac.uk/~dpontin/ In this replacement version, typos have been corrected, and in addition references and some further discussion adde

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

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