Diffusion-Limited One-Species Reactions in the Bethe Lattice

We study the kinetics of diffusion-limited coalescence, A+A-->A, and annihilation, A+A-->0, in the Bethe lattice of coordination number z. Correlations build up over time so that the probability to find a particle next to another varies from \rho^2 (\rho is the particle density), initially, when the particles are uncorrelated, to [(z-2)/z]\rho^2, in the long-time asymptotic limit. As a result, the particle density decays inversely proportional to time, \rho ~ 1/kt, but at a rate k that slowly decreases to an asymptotic constant value.Comment: To be published in JPCM, special issue on Kinetics of Chemical Reaction

Exact mean first-passage time on the T-graph

We consider a simple random walk on the T-fractal and we calculate the exact mean time $\tau^g$ to first reach the central node $i_0$. The mean is performed over the set of possible walks from a given origin and over the set of starting points uniformly distributed throughout the sites of the graph, except $i_0$. By means of analytic techniques based on decimation procedures, we find the explicit expression for $\tau^g$ as a function of the generation $g$ and of the volume $V$ of the underlying fractal. Our results agree with the asymptotic ones already known for diffusion on the T-fractal and, more generally, they are consistent with the standard laws describing diffusion on low-dimensional structures.Comment: 6 page

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.

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

Fractal and Transfractal Recursive Scale-Free Nets

We explore the concepts of self-similarity, dimensionality, and (multi)scaling in a new family of recursive scale-free nets that yield themselves to exact analysis through renormalization techniques. All nets in this family are self-similar and some are fractals - possessing a finite fractal dimension - while others are small world (their diameter grows logarithmically with their size) and are infinite-dimensional. We show how a useful measure of "transfinite" dimension may be defined and applied to the small world nets. Concerning multiscaling, we show how first-passage time for diffusion and resistance between hub (the most connected nodes) scale differently than for other nodes. Despite the different scalings, the Einstein relation between diffusion and conductivity holds separately for hubs and nodes. The transfinite exponents of small world nets obey Einstein relations analogous to those in fractal nets.Comment: Includes small revisions and references added as result of readers' feedbac