Complex and unexpected dynamics in simple genetic regulatory networks

Peer reviewedPublisher PD

Synchronization in complex networks

Synchronization processes in populations of locally interacting elements are in the focus of intense research in physical, biological, chemical, technological and social systems. The many efforts devoted to understand synchronization phenomena in natural systems take now advantage of the recent theory of complex networks. In this review, we report the advances in the comprehension of synchronization phenomena when oscillating elements are constrained to interact in a complex network topology. We also overview the new emergent features coming out from the interplay between the structure and the function of the underlying pattern of connections. Extensive numerical work as well as analytical approaches to the problem are presented. Finally, we review several applications of synchronization in complex networks to different disciplines: biological systems and neuroscience, engineering and computer science, and economy and social sciences.Comment: Final version published in Physics Reports. More information available at http://synchronets.googlepages.com

Electronically--implemented coupled logistic maps

The logistic map is a paradigmatic dynamical system originally conceived to model the discrete-time demographic growth of a population, which shockingly, shows that discrete chaos can emerge from trivial low-dimensional non-linear dynamics. In this work, we design and characterize a simple, low-cost, easy-to-handle, electronic implementation of the logistic map. In particular, our implementation allows for straightforward circuit-modifications to behave as different one-dimensional discrete-time systems. Also, we design a coupling block in order to address the behavior of two coupled maps, although, our design is unrestricted to the discrete-time system implementation and it can be generalized to handle coupling between many dynamical systems, as in a complex system. Our findings show that the isolated and coupled maps' behavior has a remarkable agreement between the experiments and the simulations, even when fine-tuning the parameters with a resolution of $\sim 10^{-3}$. We support these conclusions by comparing the Lyapunov exponents, periodicity of the orbits, and phase portraits of the numerical and experimental data for a wide range of coupling strengths and map's parameters.Comment: 8 pages, 10 figure

Stability and chaos in coupled two-dimensional maps on Gene Regulatory Network of bacterium E.Coli

The collective dynamics of coupled two-dimensional chaotic maps on complex networks is known to exhibit a rich variety of emergent properties which crucially depend on the underlying network topology. We investigate the collective motion of Chirikov standard maps interacting with time delay through directed links of Gene Regulatory Network of bacterium Escherichia Coli. Departures from strongly chaotic behavior of the isolated maps are studied in relation to different coupling forms and strengths. At smaller coupling intensities the network induces stable and coherent emergent dynamics. The unstable behavior appearing with increase of coupling strength remains confined within a connected sub-network. For the appropriate coupling, network exhibits statistically robust self-organized dynamics in a weakly chaotic regime

Geometrical Properties of Coupled Oscillators at Synchronization

We study the synchronization of $N$ nearest neighbors coupled oscillators in a ring. We derive an analytic form for the phase difference among neighboring oscillators which shows the dependency on the periodic boundary conditions. At synchronization, we find two distinct quantities which characterize four of the oscillators, two pairs of nearest neighbors, which are at the border of the clusters before total synchronization occurs. These oscillators are responsible for the saddle node bifurcation, of which only two of them have a phase-lock of phase difference equals $\pm$$\pi$/2. Using these properties we build a technique based on geometric properties and numerical observations to arrive to an exact analytic expression for the coupling strength at full synchronization and determine the two oscillators that have a phase-lock condition of $\pm$$\pi$/2.Comment: accepted for publication in "Communications in Nonlinear Science and Numerical Simulations