Monte Carlo study of gating and selection in potassium channels

The study of selection and gating in potassium channels is a very important issue in modern biology. Indeed such structures are known in all types of cells in all organisms where they play many important functional roles. The mechanism of gating and selection of ionic species is not clearly understood. In this paper we study a model in which gating is obtained via an affinity-switching selectivity filter. We discuss the dependence of selectivity and efficiency on the cytosolic ionic concentration and on the typical pore open state duration. We demonstrate that a simple modification of the way in which the selectivity filter is modeled yields larger channel efficiency

Competitive nucleation in reversible Probabilistic Cellular Automata

The problem of competitive nucleation in the framework of Probabilistic Cellular Automata is studied from the dynamical point of view. The dependence of the metastability scenario on the self--interaction is discussed. An intermediate metastable phase, made of two flip--flopping chessboard configurations, shows up depending on the ratio between the magnetic field and the self--interaction. A behavior similar to the one of the stochastic Blume--Capel model with Glauber dynamics is found

Topology-Induced Critical Current Enhancement in Josephson Networks

We investigate the properties of Josephson junction networks with inhomogeneous architecture. The networks are shaped as "quare comb" planar lattices on which Josephson junctions link superconducting islands arranged in the plane to generate the pertinent topology. Compared to the behavior of reference linear arrays, the temperature dependencies of the Josephson currents of the branches of the network exhibit relevant differences. The observed phenomena evidence new and surprising behavior of superconducting Josephson arrays as well as remarkable similarities with bosonic junction arrays.Comment: improved figures (added magnetic pattern and single junction switching) some changes in the text and in the titl

Phase transitions for the cavity approach to the clique problem on random graphs

We give a rigorous proof of two phase transitions for a disordered system designed to find large cliques inside Erdos random graphs. Such a system is associated with a conservative probabilistic cellular automaton inspired by the cavity method originally introduced in spin glass theory.Comment: 36 pages, 4 figure

Phase ordering in chaotic map lattices with conserved dynamics

Dynamical scaling in a two-dimensional lattice model of chaotic maps, in contact with a thermal bath, is numerically studied. The model here proposed is equivalent to a conserved Ising model with coupligs which fluctuate over the same time scale as spin moves. When couplings fluctuations and thermal fluctuations are both important, this model does not belong to the class of universality of a Langevin equation known as model B; the scaling exponents are continuously varying with the temperature and depend on the map used. The universal behavior of model B is recovered when thermal fluctuations are dominant.Comment: 6 pages, 4 figures. Revised version accepted for publication on Physical Review E as a Rapid Communicatio

Superconducting properties of Nb thin films deposited on porous silicon templates

Porous silicon, obtained by electrochemical etching, has been used as a substrate for the growth of nanoperforated Nb thin films. The films, deposited by UHV magnetron sputtering on the porous Si substrates, inherited their structure made of holes of 5 or 10 nm diameter and of 10 to 40 nm spacing, which provide an artificial pinning structure. The superconducting properties were investigated by transport measurements performed in the presence of magnetic field for different film thickness and substrates with different interpore spacing. Perpendicular upper critical fields measurements present peculiar features such as a change in the H_c2(T) curvature and oscillations in the field dependence of the superconducting resistive transition width at H=1 Tesla. This field value is much higher than typical matching fields in perforated superconductors, as a consequence of the small interpore distance.Comment: accepted for publication on Journal of Applied Physic

Critical droplets in Metastable States of Probabilistic Cellular Automata

We consider the problem of metastability in a probabilistic cellular automaton (PCA) with a parallel updating rule which is reversible with respect to a Gibbs measure. The dynamical rules contain two parameters $\beta$ and $h$ which resemble, but are not identical to, the inverse temperature and external magnetic field in a ferromagnetic Ising model; in particular, the phase diagram of the system has two stable phases when $\beta$ is large enough and $h$ is zero, and a unique phase when $h$ is nonzero. When the system evolves, at small positive values of $h$, from an initial state with all spins down, the PCA dynamics give rise to a transition from a metastable to a stable phase when a droplet of the favored $+$ phase inside the metastable $-$ phase reaches a critical size. We give heuristic arguments to estimate the critical size in the limit of zero ``temperature'' ($\beta\to\infty$), as well as estimates of the time required for the formation of such a droplet in a finite system. Monte Carlo simulations give results in good agreement with the theoretical predictions.Comment: 5 LaTeX picture

Magnetic order in the Ising model with parallel dynamics

It is discussed how the equilibrium properties of the Ising model are described by an Hamiltonian with an antiferromagnetic low temperature behavior if only an heat bath dynamics, with the characteristics of a Probabilistic Cellular Automaton, is assumed to determine the temporal evolution of the system.Comment: 9 pages, 3 figure

Switching between dynamic states in intermediate-length Josephson junctions

The appearance of zero-field steps (ZFS’s) in the current-voltage characteristics of intermediate-length overlap-geometry Josephson tunnel junctions described by a perturbed sine-Gordon equation (PSGE) is associated with the growth of parametrically excited instabilities of the McCumber background curve (MCB). A linear stability analysis of a McCumber solution of the PSGE in the asymptotic linear region of the MCB and in the absence of magnetic field yields a Hill’s equation which predicts how the number, locations, and widths of the instability regions depend on the junction parameters. A numerical integration of the PSGE in terms of truncated series of time-dependent Fourier spatial modes verifies that the parametrically excited instabilities of the MCB evolve into the fluxon oscillations characteristic of the ZFS’s. An approximate analysis of the Fourier mode equations in the presence of a small magnetic field yields a field-dependent Hill’s equation which predicts that the major effect of such a field is to reduce the widths of the instability regions. Experimental measurements on Nb-NbxOy-Pb junctions of intermediate length, performed at different operating temperatures in order to vary the junction parameters and for various magnetic field values, verify the physical existence of switching from the MCB to the ZFS’s. Good qualitative, and in many cases quantitative, agreement between analytic, numerical, and experimental results is obtained