Thermal and mechanical properties of a DNA model with solvation barrier

We study the thermal and mechanical behavior of DNA denaturation in the frame of the mesoscopic Peyrard- Bishop-Dauxois model with the inclusion of solvent interaction. By analyzing the melting transition of a homogeneous A-T sequence, we are able to set suitable values of the parameters of the model and study the formation and stability of bubbles in the system. Then, we focus on the case of the P5 promoter sequence and use the Principal Component Analysis of the trajectories to extract the main information on the dynamical behavior of the system. We find that this analysis method gives an excellent agreement with previous biological results.Comment: Physical Review E (in press

Non-equilibrium Effects in the Thermal Switching of Underdamped Josephson Junctions

We study the thermal escape problem in the low damping limit. We find that finiteness of the barrier is crucial for explaining the thermal activation results. In this regime low barrier non-equilibrium corrections to the usual theories become necessary. We propose a simple theoretical extension accounting for these non-equilibrium processes which agrees numerical results. We apply our theory to the understanding of switching current curves in underdamped Josephson junctions.Comment: 4 pages + 4 figure

Translocation of a polymer chain driven by a dichotomous noise

We consider the translocation of a one-dimensional polymer through a pore channel helped by a motor driven by a dichotomous noise with time exponential correlation. We are interested in the study of the translocation time, mean velocity and stall force of the system as a function of the mean driving frequency. We find a monotonous translocation time, in contrast with the mean velocity which shows a pronounced maximum at a given frequency. Interestingly, the stall force shows a nonmonotonic behavior with the presence of a minimum. The influence of the spring elastic constant to the mean translocation times and velocities is also presented.Comment: 11 pages, 7 figure

Numerical study of pattern formation in compliant surfaces scraped by a rigid tip

The emergence of surface patterns on the surfaces of compliant materials subject to plowing wear is a complex problem which can be quantitatively characterized, e.g., on polymer surfaces scraped by an atomic force microscope (AFM) tip. Here we explore the applicability of a phenomenological model recently introduced to describe this phenomenon. Based on the competition between the viscoplastic indentation and the elastic shear stress caused by the tip, the model is able to reproduce the wavy features (ripples) observed when the tip is scanned along a series of parallel lines. For low values of the driving velocity v and the spacing b between scan lines, the existence of dotted areas formed by variously oriented pit alignments is observed. Moreover, coexistence of rippled with dotted domains is also observed at suitable parameter values. The formation process of the ripples is also described in detail. The amplitude, period, and orientation of these features are estimated numerically for different values of v and b parameters. We have also revisited the formation of the wavy patterns formed when a single line is scanned, and derived an equation which correctly describes their period and depth, and the static friction as well. This equation is not applicable when several lines are scanned one after the other and the ripples emerge as result of a cooperative process which involves the scanning of several lines

Microwave photonics with Josephson junction arrays: Negative refraction index and entanglement through disorder

We study different architectures for a photonic crystal in the microwave regime based on superconducting transmission lines interrupted by Josephson junctions, both in one and two dimensions. A study of the scattering properties of a single junction in the line shows that the junction behaves as a perfect mirror when the photon frequency matches the Josephson plasma frequency. We generalize our calculations to periodic arrangements of junctions, demonstrating that they can be used for tunable band engineering, forming what we call a quantum circuit crystal. Two applications are discussed in detail. In a two-dimensional structure we demonstrate the phenomenon of negative refraction. We finish by studying the creation of stationary entanglement between two superconducting qubits interacting through a disordered media. © 2012 American Physical Society.This work was supported by Spanish Governement projects FIS2008-01240, FIS2009-10061, FIS2009-12773-C02-01, and FIS2011-25167 cofinanced by FEDER funds; CAM research consortium QUITEMAD; Basque Government Grants No. IT472-10, and No. UPV/EHU UFI 11/55; and PROMISCE, SOLID, and CCQED European projects.Peer Reviewe

Mode locking in discrete solition dynamics under ac forces

We present here analytical arguments and numerical evidence for the existence of net directional motion of highly discrete sine-Gordon kinks under ac forces of zero average. We have also characterized the depinning of the oscillating kink under those circumstances, and analyzed the instability mechanisms of the phase-locked running solutions. Possible experimental relevance of this phenomenon in circular arrays of Josephson junctions is discussed.Financial support from DGES (PB95-0797) and CICYT (MAT95-0325)Publicad

Equilibrium properties of a Josephson junction ladder with screening effects

In this paper we calculate the ground state phase diagram of a Josephson Junction ladder when screening field effects are taken into account. We study the ground state configuration as a function of the external field, the penetration depth and the anisotropy of the ladder, using different approximations to the calculation of the induced fields. A series of tongues, characterized by the vortex density $\omega$, is obtained. The vortex density of the ground state, as a function of the external field, is a Devil's staircase, with a plateau for every rational value of $\omega$. The width of each of these steps depends strongly on the approximation made when calculating the inductance effect: if the self-inductance matrix is considered, the $\omega=0$ phase tends to occupy all the diagram as the penetration depth decreases. If, instead, the whole inductance matrix is considered, the width of any step tends to a non-zero value in the limit of very low penetration depth. We have also analyzed the stability of some simple metastable phases: screening fields are shown to enlarge their stability range.Comment: 16 pp, RevTex. Figures available upon request at [email protected] To be published in Physical Review B (01-Dec-96

From Josephson junction metamaterials to tunable pseudo-cavities

arXiv:1305.4844v1The scattering through a Josephson junction (JJ) interrupting a superconducting line is revisited including power leakage. We also discuss how to make tunable and broadband resonant mirrors by concatenating junctions. As an application, we show how to construct cavities using these mirrors, thus connecting two research fields: JJ quantum metamaterials and coupled-cavity arrays. We finish by discussing the first nonlinear corrections to the scattering and their measurable effects. © 2013 IOP Publishing Ltd.This work was supported by Spanish government projects FIS2009-10061, and FIS2011-25167 conanced by FEDER funds. We thanks Aragon government support to group FENOL, CAM research consortium QUITEMAD and PROMISCE European project.Peer Reviewe

Anisotropy Effects in Atomic-Scale Friction

The static and kinetic friction experienced by a point mass elastically driven at different angles on surface lattices with square, hexagonal, and honeycomb symmetries are estimated by analytical and numeric calculations based on the Prandtl–Tomlinson (PT) model. Assuming a strong surface coupling, the anisotropy of static friction increases from 3.7 up to 46.3% when the density of packing of the surface atoms is reduced, but this is not the case for kinetic friction, the anisotropy of which is maximal on a square lattice. Although these results have not been supported by accurate experimental verifications so far, the PT model was successfully applied to interpret anisotropy effects in the friction force profiles measured, among other surfaces, on rectangular lattices with complex unit cells and on stepped crystal surfaces