1,399 research outputs found
Finding mesoscopic communities in sparse networks
We suggest a fast method to find possibly overlapping network communities of
a desired size and link density. Our method is a natural generalization of the
finite- superparamegnetic Potts clustering introduced by Blatt, Wiseman, and
Domany (Phys. Rev. Lett. v.76, 3251 (1996) and the recently suggested by
Reichard and Bornholdt (Phys. Rev. Lett. v.93, 21870 (2004)) annealing of Potts
model with global antiferromagnetic term. Similarly to both preceding works,
the proposed generalization is based on ordering of ferromagnetic Potts model;
the novelty of the proposed approach lies in the adjustable dependence of the
antiferromagnetic term on the population of each Potts state, which
interpolates between the two previously considered cases. This adjustability
allows to empirically tune the algorithm to detect the maximum number of
communities of the given size and link density. We illustrate the method by
detecting protein complexes in high-throughput protein binding networks.Comment: 8 pages, 2 figure, typos corrected, 1 figure adde
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
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
Critical behavior of ferromagnetic pure and random diluted nanoparticles with competing interactions: variational and Monte Carlo approaches
The magnetic properties and critical behavior of both ferromagnetic pure and
metallic nanoparticles having concurrently atomic disorder, dilution and
competing interactions, are studied in the framework of an Ising model. We have
used both the free energy variational principle based on the Bogoliubov
inequality and Monte Carlo simulation. As a case of study for random diluted
nanoparticles we have considered the FeMnAl alloy
characterized for exhibiting, under bulk conditions, low temperature reentrant
spin glass (RSG) behavior and for which experimental and simulation results are
available. Our results allow concluding that the variational model is
successful in reproducing features of the particle size dependence of the Curie
temperature for both pure and random diluted particles. In this last case, low
temperature magnetization reduction was consistent with the same type of RSG
behavior observed in bulk in accordance with the Almeida-Thouless line at low
fields and a linear dependence of the freezing temperature with the reciprocal
of the particle diameter was also obtained. Computation of the correlation
length critical exponent yielded the values via Bogoliubov
and via Monte Carlo. This fact indicates that even though
thermodynamical models can be indeed used in the study of nanostructures and
they can reproduce experimental features, special attention must be paid
regarding critical behavior. From both approaches, differences in the
exponent with respect to the pure Ising model agree with Harris and Fisher
arguments.Comment: 11 pages, 11 figures. Submitted to Phys. Rev.
Active polymer translocation in the three-dimensional domain
In this work we study the translocation process of a polymer through a nanochannel where a time dependent force is acting. Two conceptually different types of driving are used: a deterministic sinusoidal one and a random telegraph noise force. The mean translocation time presents interesting resonant minima as a function of the frequency of the external driving. For the computed sizes, the translocation time scales with the polymer length according to a power law with the same exponent for almost all the frequencies of the two driving forces. The dependence of the translocation time with the polymer rigidity, which accounts for the persistence length of the molecule, shows a different low frequency dependence for the two drivings
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