Kleinberg Navigation in Fractal Small World Networks

We study the Kleinberg problem of navigation in Small World networks when the underlying lattice is a fractal consisting of N>>1 nodes. Our extensive numerical simulations confirm the prediction that most efficient navigation is attained when the length r of long-range links is taken from the distribution P(r)~r^{-alpha}, where alpha=d_f, the fractal dimension of the underlying lattice. We find finite-size corrections to the exponent alpha, proportional to 1/(ln N)^2

Designer Nets from Local Strategies

We propose a local strategy for constructing scale-free networks of arbitrary degree distributions, based on the redirection method of Krapivsky and Redner [Phys. Rev. E 63, 066123 (2001)]. Our method includes a set of external parameters that can be tuned at will to match detailed behavior at small degree k, in addition to the scale-free power-law tail signature at large k. The choice of parameters determines other network characteristics, such as the degree of clustering. The method is local in that addition of a new node requires knowledge of only the immediate environs of the (randomly selected) node to which it is attached. (Global strategies require information on finite fractions of the growing net.

Diffusion-Limited Coalescence with Finite Reaction Rates in One Dimension

We study the diffusion-limited process $A+A\to A$ in one dimension, with finite reaction rates. We develop an approximation scheme based on the method of Inter-Particle Distribution Functions (IPDF), which was formerly used for the exact solution of the same process with infinite reaction rate. The approximation becomes exact in the very early time regime (or the reaction-controlled limit) and in the long time (diffusion-controlled) asymptotic limit. For the intermediate time regime, we obtain a simple interpolative behavior between these two limits. We also study the coalescence process (with finite reaction rates) with the back reaction $A\to A+A$, and in the presence of particle input. In each of these cases the system reaches a non-trivial steady state with a finite concentration of particles. Theoretical predictions for the concentration time dependence and for the IPDF are compared to computer simulations. P. A. C. S. Numbers: 82.20.Mj 02.50.+s 05.40.+j 05.70.LnComment: 13 pages (and 4 figures), plain TeX, SISSA-94-0

A Method of Intervals for the Study of Diffusion-Limited Annihilation, A + A --> 0

We introduce a method of intervals for the analysis of diffusion-limited annihilation, A+A -> 0, on the line. The method leads to manageable diffusion equations whose interpretation is intuitively clear. As an example, we treat the following cases: (a) annihilation in the infinite line and in infinite (discrete) chains; (b) annihilation with input of single particles, adjacent particle pairs, and particle pairs separated by a given distance; (c) annihilation, A+A -> 0, along with the birth reaction A -> 3A, on finite rings, with and without diffusion.Comment: RevTeX, 13 pages, 4 figures, 1 table. References Added, and some other minor changes, to conform with final for

Percolation in Hierarchical Scale-Free Nets

We study the percolation phase transition in hierarchical scale-free nets. Depending on the method of construction, the nets can be fractal or small-world (the diameter grows either algebraically or logarithmically with the net size), assortative or disassortative (a measure of the tendency of like-degree nodes to be connected to one another), or possess various degrees of clustering. The percolation phase transition can be analyzed exactly in all these cases, due to the self-similar structure of the hierarchical nets. We find different types of criticality, illustrating the crucial effect of other structural properties besides the scale-free degree distribution of the nets.Comment: 9 Pages, 11 figures. References added and minor corrections to manuscript. In pres

Facilitated diffusion of proteins on chromatin

We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.Comment: 4 pages, 4 figures, accepted versio

Hybrid method for simulating front propagation in reaction-diffusion systems

We study the propagation of pulled fronts in the $A \leftrightarrow A+A$ microscopic reaction-diffusion process using Monte Carlo (MC) simulations. In the mean field approximation the process is described by the deterministic Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation. In particular we concentrate on the corrections to the deterministic behavior due to the number of particles per site $\Omega$. By means of a new hybrid simulation scheme, we manage to reach large macroscopic values of $\Omega$ which allows us to show the importance in the dynamics of microscopic pulled fronts of the interplay of microscopic fluctuations and their macroscopic relaxation.Comment: 5 pages, 4 figure

Cluster approximation solution of a two species annihilation model

A two species reaction-diffusion model, in which particles diffuse on a one-dimensional lattice and annihilate when meeting each other, has been investigated. Mean field equations for general choice of reaction rates have been solved exactly. Cluster mean field approximation of the model is also studied. It is shown that, the general form of large time behavior of one- and two-point functions of the number operators, are determined by the diffusion rates of the two type of species, and is independent of annihilation rates.Comment: 9 pages, 7 figure

Target annihilation by diffusing particles in inhomogeneous geometries

The survival probability of immobile targets, annihilated by a population of random walkers on inhomogeneous discrete structures, such as disordered solids, glasses, fractals, polymer networks and gels, is analytically investigated. It is shown that, while it cannot in general be related to the number of distinct visited points, as in the case of homogeneous lattices, in the case of bounded coordination numbers its asymptotic behaviour at large times can still be expressed in terms of the spectral dimension $\widetilde {d}$, and its exact analytical expression is given. The results show that the asymptotic survival probability is site independent on recurrent structures ($\widetilde{d}\leq2$), while on transient structures ($\widetilde{d}>2$) it can strongly depend on the target position, and such a dependence is explicitly calculated.Comment: To appear in Physical Review E - Rapid Communication

Exact calculations of first-passage quantities on recursive networks

We present general methods to exactly calculate mean-first passage quantities on self-similar networks defined recursively. In particular, we calculate the mean first-passage time and the splitting probabilities associated to a source and one or several targets; averaged quantities over a given set of sources (e.g., same-connectivity nodes) are also derived. The exact estimate of such quantities highlights the dependency of first-passage processes with respect to the source-target distance, which has recently revealed to be a key parameter to characterize transport in complex media. We explicitly perform calculations for different classes of recursive networks (finitely ramified fractals, scale-free (trans)fractals, non-fractals, mixtures between fractals and non-fractals, non-decimable hierarchical graphs) of arbitrary size. Our approach unifies and significantly extends the available results in the field.Comment: 16 pages, 10 figure