1,161 research outputs found
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
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
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
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
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