arXiv subjects

J. J. Mazo

Publications and source records attributed to J. J. Mazo.

At least 19 recordsLinked to original sources

arXiv2017

Active translocation of a semiflexible polymer assisted by an ATP-based molecular motor

In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule binding and triggering the impulse, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at fixed temperature. The resulting dynamics shows a Michaelis-Menten translocation velocity that depends on the chain flexibility. The scaling behavior of the mean translocation time with the polymer length for different bending values is also investigated.

cond-mat.soft↗

arXiv2017

Pulse-coupled model of excitable elements on heterogeneous sparse networks

We study a pulse-coupled dynamics of excitable elements in uncorrelated scale-free networks. Regimes of self-sustained activity are found for homogeneous and inhomogeneous couplings, in which the system displays a wide variety of behaviors, including periodic and irregular global spiking signals, as well as coherent oscillations, an unexpected form of synchronization. Our numerical results also show that the properties of the population firing rate depend on the size of the system, particularly its structure and average value over time. However, a few straightforward dynamical and topological strategies can be introduced to enhance or hinder these global behaviors, rendering a scenario where signal control is attainable, which incorporates a basic mechanism to turn off the dynamics permanently. As our main result, here we present a framework to estimate, in the stationary state, the mean firing rate over a long time window and to decompose the global dynamics into average values of the inter-spike-interval of each connectivity group. Our approach provides accurate predictions of these average quantities when the network exhibits high heterogeneity, a remarkable finding that is not restricted exclusively to the scale-free topology.

q-bio.NC↗

arXiv2014

Breather decay into a vortex/anti-vortex pair in a Josephson Ladder

We present experimental evidence for a new behavior which involves discrete breathers and vortices in a Josephson Ladder. Breathers can be visualized as the creation and subsequent annihilation of vortex/anti-vortex pairs. An externally applied magnetic field breaks the vortex/anti-vortex symmetry and causes the breather to split apart. The motion of the vortex or anti-vortex creates multi-site breathers, which are always to one side or the other of the original breather depending on the sign of the applied field. This asymmetry in applied field is experimentally observed.

cond-mat.supr-con↗

arXiv2014

Lateral vibration effects in atomic-scale friction

The influence of lateral vibrations on the stick-slip motion of a nanotip elastically pulled on a flat crystal surface is studied by atomic force microscopy (AFM) measurements on a NaCl(001) surface in ultra-high vacuum. The slippage of the nanotip across the crystal lattice is anticipated at increasing driving amplitude, similarly to what is observed in presence of normal vibrations. This lowers the average friction force, as explained by the Prandtl-Tomlinson model with lateral vibrations superimposed at finite temperature. Nevertheless, the peak values of the lateral force, and the total energy losses, are expected to increase with the excitation amplitude, which may limit the practical relevance of this effect.

cond-mat.mes-hall↗

arXiv2014

Out-of-plane and in-plane actuation effects on atomic-scale friction

The influence of out-of-plane and in-plane contact vibrations and temperature on the friction force acting on a sharp tip elastically pulled on a crystal surface is studied using a generalized Prandtl- Tomlinson model. The average friction force is significantly lowered in a frequency range determined by the "washboard" frequency of the stick-slip motion and the viscous damping accompanying the tip motion. An approximately linear relation between the actuation amplitude and the effective corrugation of the surface potential is derived in the case of in-plane actuation, extending a similar conclusion for out-of-plane actuation. Temperature causes an additional friction reduction with a scaling relation in formal agreement with the predictions of reaction rate theory in absence of contact vibrations. In this case the actuation effects can be described by the effective energy or, more accurately, by introducing an effective temperature.

cond-mat.mes-hall↗

arXiv2013

From Josephson junction metamaterials to tunable pseudo-cavities

The scattering through a Josephson junction interrupting a superconducting line is revisited including power leakage. We discuss also 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 non-linear corrections to the scattering and their measurable effects.

quant-ph↗

arXiv2013

Thermal activation at moderate-to-high and high damping: finite barrier effects and force spectroscopy

We study the thermal escape problem in the moderate-to-high and high damping regime of a system with a parabolic barrier. We present a formula that matches our numerical results accounting for finite barrier effects, and compare it with previous works. We also show results for the full damping range. We quantitatively study some aspects on the relation between mean first passage time and the definition of a escape rate. To finish we apply our results and considerations in the framework of force spectroscopy problems. We study the differences on the predictions using the different theories and discuss the role of $γ\dot{F}$ as the relevant parameter at high damping.

cond-mat.stat-mech↗

arXiv2012

Surface defects and temperature on atomic friction

We present a theoretical study of the effect of surface defects on atomic friction in the stick-slip dynamical regime of a minimalistic model. We focus on how the presence of defects and temperature change the average properties of the system. We have identified two main mechanisms which modify the mean friction force of the system when defects are considered. As expected, defects change locally the potential profile and thus affect the friction force. But the presence of defects also changes the probability distribution function of the tip slip length and thus the mean friction force. We corroborated both effects for different values of temperature, external load, dragging velocity and damping. We show also a comparison of the effects of surface defects and surface disorder on the dynamics of the system.

cond-mat.mes-hall↗

arXiv2012

Non-adiabatic effects within a single thermally-averaged potential energy surface: Thermal expansion and reaction rates of small molecules

At non-zero temperature and when a system has low-lying excited electronic states, the ground-state Born--Oppenheimer approximation breaks down and the low-lying electronic states are involved in any chemical process. In this work, we use a temperature-dependent effective potential for the nuclei which can accomodate the influence of an arbitrary number of electronic states in a simple way, while at the same time producing the correct Boltzmann equibrium distribution for the electronic part. With the help of this effective potential, we show that thermally-activated low-lying electronic states can have a significant effect in molecular properties for which electronic excitations are oftentimes ignored. We study the thermal expansion of the Manganese dimer, Mn$_2$, where we find that the average bond length experiences a change larger than the present experimental accuracy upon the inclusion of the excited states into the picture. We also show that, when these states are taken into account, reaction rate constants are modified. In particular, we study the opening of the ozone molecule, O$_3$, and show that in this case the rate is modified as much as a 20% with respect to the ground-state Born--Oppenheimer prediction.

physics.chem-ph↗

arXiv2012

Mesoscopic Model for Free Energy Landscape Analysis of DNA sequences

A mesoscopic model which allows us to identify and quantify the strength of binding sites in DNA sequences is proposed. The model is based on the Peyrard-Bishop-Dauxois model for the DNA chain coupled to a Brownian particle which explores the sequence interacting more importantly with open base pairs of the DNA chain. We apply the model to promoter sequences of different organisms. The free energy landscape obtained for these promoters shows a complex structure that is strongly connected to their biological behavior. The analysis method used is able to quantify free energy differences of sites within genome sequences.

physics.bio-ph↗

arXiv2010

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.

cond-mat.supr-con↗

arXiv2008

Switching Current Measurements in Josephson Rings

We present switching current measurements in niobium-aluminum oxide-niobium underdamped Josephson rings. Underdamped Josephson rings display hysteretic current-voltage curves which can be characterized by their switching current, the value of applied current at which the junctions switch to the energy-gap voltage. The value of the switching current is strongly affected by temperature and by the presence of fluxons in the system. We observe a very small voltage (0.2 nV) across the ring prior to switching, indicating a low-velocity fluxon diffusion state before the jump to a full running state. In analogy with previous work on single junctions, we analyze the switching current data with the process of thermal activation over a dissipation barrier, where the system switches from a low velocity state to a high velocity state. We find that our data agrees qualitatively with this description, further supporting the observation of fluxon diffusion.

cond-mat.supr-con↗

arXiv2008

Thermal depinning of fluxons in discrete Josephson rings

We study the thermal depinning of single fluxons in rings made of Josephson junctions. Due to thermal fluctuations a fluxon can be excited from its energy minima and move through the array, causing a voltage across each junction. We find that for the initial depinning, the fluxon behaves as a single particle and follows a Kramers-type escape law. However, under some conditions this single particle description breaks down. At low values of the discreteness parameter and low values of the damping, the depinning rate is larger than the single particle result would suggest. In addition, for some values of the parameters the fluxon can undergo low-voltage diffusion before switching to the high-voltage whirling mode. This type of diffusion is similar to phase diffusion in a single junction, but occurs without frequency-dependent damping. We study the switching to the whirling state as well.

cond-mat.supr-con↗

arXiv2004

Multiple junction biasing of superconducting tunnel junction detectors

We describe a new biasing scheme for single photon detectors based on superconducting tunnel junctions. It replaces a single detector junction with a circuit of three junctions and achieves biasing of a detector junction at subgap currents without the use of an external magnetic field. The biasing occurs through the nonlinear interaction of the three junctions, which we demonstrate through numerical simulation. This nonlinear state is numerically stable against external fluctuations and is compatible with high fidelity electrical readout of the photon-induced current. The elimination of the external magnetic field potentially increases the capability of these types of photon detectors and eases constraints involved in the fabrication of large detector arrays.

cond-mat.supr-con↗

arXiv2001

Discrete Breathers in Josephson Ladders

We present a study of nonlinear localized excitations called discrete breathers in a superconducting array. These localized solutions were recently observed in Josephson-junction ladder arrays by two different experimental groups. We review the experiments made by Trias et al. We report the detection of different single-site and multi-site breather states and study the dynamics when changing the array bias current. By changing the temperature we can control the value of the damping (the Stewart-McCumber parameter) in the array, thus allowing an experimental study at different array parameters. We propose a simple DC circuit model to understand most of the features of the detected states. We have also compared this model and the experiments with simulations of the dynamics of the array. We show that the study of the resonances in the ladder and the use of harmonic balance techniques allow for understanding of most of the numerical results. We have computed existence diagrams of breather solutions in our arrays, found resonant localized solutions and described the localized states in terms of vortex and antivortex motion.

cond-mat↗

arXiv2000

Decoherence of the Superconducting Persistent Current Qubit

Decoherence of a solid state based qubit can be caused by coupling to microscopic degrees of freedom in the solid. We lay out a simple theory and use it to estimate decoherence for a recently proposed superconducting persistent current design. All considered sources of decoherence are found to be quite weak, leading to a high quality factor for this qubit.

cond-mat.mes-hall↗

arXiv1999

Depinning of kinks in a Josephson-junction ratchet array

We have measured the depinning of trapped kinks in a ratchet potential using a fabricated circular array of Josephson junctions. Our ratchet system consists of a parallel array of junctions with alternating cell inductances and junctions areas. We have compared this ratchet array with other circular arrays. We find experimentally and numerically that the depinning current depends on the direction of the applied current in our ratchet ring. We also find other properties of the depinning current versus applied field, such as a long period and a lack of reflection symmetry, which we can explain analytically.

cond-mat.supr-con↗

arXiv1999

A Superconducting Persistent Current Qubit

We present the design of a superconducting qubit that has circulating currents of opposite sign as its two states. The circuit consists of three nano-scale aluminum Josephson junctions connected in a superconducting loop and controlled by magnetic fields. The advantages of this qubit are that it can be made insensitive to background charges in the substrate, the flux in the two states can be detected with a SQUID, and the states can be manipulated with magnetic fields. Coupled systems of qubits are also discussed as well as sources of decoherence.

cond-mat↗