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-$T$ 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 Fe$_{0.5}$Mn$_{0.1}$Al$_{0.4}$ 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 $\nu=0.926\pm 0.004$ via Bogoliubov and$\nu =0.71\pm 0.04$ 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 $\nu$ 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