Synchronization,stickiness effects and intermittent oscillations in coupled nonlinear stochastic networks

Long distance reactive and diffusive coupling is introduced in a spatially extended nonlinear stochastic network of interacting particles. The network serves as a substrate for Lotka-Volterra dynamics with 3rd order nonlinearities. If the network includes only local nearest neighbour interactions, the system organizes into a number of local asynchronous oscillators. It is shown that (a) Introduction of all-to-all coupling in the network leads the system into global, center-type, conservative oscillations as dictated by the mean-field dynamics. (b) Introduction of reactive coupling to the network leads the system to intermittent oscillations where the trajectories stick for short times in bounded regions of space, with subsequent jumps between different bounded regions. (c) Introduction of diffusive coupling to the system does not alter the dynamics for small values of the diffusive coupling p_diff, while after a critical value p_diff ^c the system synchronizes into a limit cycle with specific frequency, deviating non-trivially from the mean-field center-type behaviour. The frequency of the limit cycle oscillations depends on the reaction rates and on the diffusion coupling. The amplitude σ of the limit cycle depends on the control parameter p_diff.     

Detecting synchronization in coupled stochastic ecosystem networks

Instantaneous phase difference, synchronization index and mutual information are considered in order to detect phase transitions, collective behaviours and synchronization phenomena that emerge for different levels of diffusive and reactive activity in stochastic networks. The network under investigation is a spatial 2D lattice which serves as a substrate for Lotka-Volterra dynamics with 3rd order nonlinearities. Kinetic Monte Carlo simulations demonstrate that the system spontaneously organizes into a number of asynchronous local oscillators, when only nearest neighbour interactions are considered. In contrast, the oscillators can be correlated, phase synchronized and completely synchronized when introducing different interactivity rules (diffusive or reactive) for nearby and distant species. The quantitative measures of synchronization show that long distance diffusion coupling induces phase synchronization after a well defined transition point, while long distance reaction coupling induces smeared phase synchronization.     

Long- and Short-Range Correlations in Genome Organization

We study the size distribution of coding and non-coding regions in DNA sequences. For most organisms we observe that the size distribution P _c(S) of the coding regions of size S shows short range distribution, whereas the size distribution of the non-coding regions follows a power-law decay P _nc(S) S ^{–1 –} , with power exponents indicating clear long-range behavior. We argue, using the Generalized Central Limit Theorem, that the long-range distributions observed in the non-coding are related to the lower level clustering of purines and pyrimidines (1d islands) which follow similar long-range laws. We also address the question of clustering of coding segments in the two complementary strands of DNA. We observe a short-range clustering of coding regions in both strands, expressed by an exponential decay in the clustering size distribution. The decay exponent expresses the degree of short-range correlations and the deviation from random clustering.     

Entropy, free energy and phase transitions in the lattice Lotka-Volterra model

A thermodynamic approach is developed for reactive dynamic models restricted to substrates of arbitrary dimensions, including fractal substrates. The thermodynamic formalism is successfully applied to the lattice Lotka-Volterra (LLV) model of autocatalytic reactions on various lattice substrates. Different regimes of reactions described as phases, and phase transitions, are obtained using this approach. The predictions of thermodynamic theory confirm extensive numerical kinetic Monte Carlo simulations on square and fractal lattices. Extensions of the formalism to multispecies LLV models are also presented. This article was submitted by the authors in English.