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

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.Comment: 10 pages, 10 figure

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.Comment: To appear in Physical Review

Intrinsically localized chaos in discrete nonlinear extended systems

The phenomenon of intrinsic localization in discrete nonlinear extended systems, i.e. the (generic) existence of discrete breathers, is shown to be not restricted to periodic solutions but it also extends to more complex (chaotic) dynamical behaviour. We illustrate this with two different forced and damped systems exhibiting this type of solutions: In an anisotropic Josephson junction ladder, we obtain intrinsically localized chaotic solutions by following periodic rotobreather solutions through a cascade of period-doubling bifurcations. In an array of forced and damped van der Pol oscillators, they are obtained by numerical continuation (path-following) methods from the uncoupled limit, where its existence is trivially ascertained, following the ideas of the anticontinuum limit.Comment: 6 pages, 6 figures, to appear in Europhysics Letter

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

A model for hand-over-hand motion of molecular motors

A simple flashing ratchet model in two dimensions is proposed to simulate the hand-over-hand motion of two head molecular motors like kinesin. Extensive Langevin simulations of the model are performed. Good qualitative agreement with the expected behavior is observed. We discuss different regimes of motion and efficiency depending of model parameters.Comment: 8 pages, Phys. Rev. E (in press

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.Comment: To appear in Applied Physics Letter

Mechanical Unfolding of a Simple Model Protein Goes Beyond the Reach of One-Dimensional Descriptions

We study the mechanical unfolding of a simple model protein. The Langevin dynamics results are analyzed using Markov-model methods which allow to describe completely the configurational space of the system. Using transition path theory we also provide a quantitative description of the unfolding pathways followed by the system. Our study shows a complex dynamical scenario. In particular, we see that the usual one-dimensional picture: free-energy vs end-to-end distance representation, gives a misleading description of the process. Unfolding can occur following different pathways and configurations which seem to play a central role in one-dimensional pictures are not the intermediate states of the unfolding dynamics.Comment: 10 pages, 6 figure