Generalized synchronization mediated by a flat coupling between structurally nonequivalent chaotic systems.

Synchronization of chaotic systems is usually investigated for structurally equivalent systems typically coupled through linear diffusive functions. Here, we focus on a particular type of coupling borrowed from a nonlinear control theory and based on the optimal placement of a sensor-a device measuring the chosen variable-and an actuator-a device applying the actuating (control) signal to a variable's derivative-in the response system, leading to the so-called flat control law. We aim to investigate the dynamics produced by a response system that is flat coupled to a drive system and to determine the degree of generalized synchronization between them using statistical and topological arguments. The general use of a flat control law for getting generalized synchronization is discussed.

Unveiling the Connectivity of Complex Networks Using Ordinal Transition Methods.

Ordinal measures provide a valuable collection of tools for analyzing correlated data series. However, using these methods to understand information interchange in the networks of dynamical systems, and uncover the interplay between dynamics and structure during the synchronization process, remains relatively unexplored. Here, we compare the ordinal permutation entropy, a standard complexity measure in the literature, and the permutation entropy of the ordinal transition probability matrix that describes the transitions between the ordinal patterns derived from a time series. We find that the permutation entropy based on the ordinal transition matrix outperforms the rest of the tested measures in discriminating the topological role of networked chaotic Rössler systems. Since the method is based on permutation entropy measures, it can be applied to arbitrary real-world time series exhibiting correlations originating from an existing underlying unknown network structure. In particular, we show the effectiveness of our method using experimental datasets of networks of nonlinear oscillators.

Observability analysis and state reconstruction for networks of nonlinear systems.

We address the problem of retrieving the full state of a network of Rössler systems from the knowledge of the actual state of a limited set of nodes. The selection of nodes where sensors are placed is carried out in a hierarchical way through a procedure based on graphical and symbolic observability approaches applied to pairs of coupled dynamical systems. By using a map directly obtained from governing equations, we design a nonlinear network reconstructor that is able to unfold the state of non-measured nodes with working accuracy. For sparse networks, the number of sensor scales with half the network size and node reconstruction errors are lower in networks with heterogeneous degree distributions. The method performs well even in the presence of parameter mismatch and non-coherent dynamics and for dynamical systems with completely different algebraic structures like the Hindmarsch-Rose; therefore, we expect it to be useful for designing robust network control laws.

Using global modeling to unveil hidden couplings in small network motifs.

One of the main tasks in network theory is to infer relations among interacting elements. We propose global modeling as a tool to detect links between nodes and their nature. Various situations using small network motifs are investigated under the assumption that the variable to be measured at each node provides full observability when isolated. Such a choice ensures no intrinsic difficulties for getting a global model in the coupled situation. As a first step toward unveiling the coupling function in larger network motifs, we consider three different scenarios involving Rössler systems diffusively coupled, in a couple or embedded in a network, or parametrically forced. We show that the global modeling is able to determine not only the existence of an interaction but also its functional form, to retrieve the dynamics of the whole system, and to extract the equations governing the single node dynamics as if it was isolated.

Topological characterization versus synchronization for assessing (or not) dynamical equivalence.

Model validation from experimental data is an important and not trivial topic which is too often reduced to a simple visual inspection of the state portrait spanned by the variables of the system. Synchronization was suggested as a possible technique for model validation. By means of a topological analysis, we revisited this concept with the help of an abstract chemical reaction system and data from two electrodissolution experiments conducted by Jack Hudson's group. The fact that it was possible to synchronize topologically different global models led us to conclude that synchronization is not a recommendable technique for model validation. A short historical preamble evokes Jack Hudson's early career in interaction with Otto E. Rössler.

Synchronizability of nonidentical weakly dissipative systems.

Synchronization is a very generic process commonly observed in a large variety of dynamical systems which, however, has been rarely addressed in systems with low dissipation. Using the Rössler, the Lorenz 84, and the Sprott A systems as paradigmatic examples of strongly, weakly, and non-dissipative chaotic systems, respectively, we show that a parameter or frequency mismatch between two coupled such systems does not affect the synchronizability and the underlying structure of the joint attractor in the same way. By computing the Shannon entropy associated with the corresponding recurrence plots, we were able to characterize how two coupled nonidentical chaotic oscillators organize their dynamics in different dissipation regimes. While for strongly dissipative systems, the resulting dynamics exhibits a Shannon entropy value compatible with the one having an average parameter mismatch, for weak dissipation synchronization dynamics corresponds to a more complex behavior with higher values of the Shannon entropy. In comparison, conservative dynamics leads to a less rich picture, providing either similar chaotic dynamics or oversimplified periodic ones.

Graph-based unsupervised segmentation algorithm for cultured neuronal networks' structure characterization and modeling.

Large scale phase-contrast images taken at high resolution through the life of a cultured neuronal network are analyzed by a graph-based unsupervised segmentation algorithm with a very low computational cost, scaling linearly with the image size. The processing automatically retrieves the whole network structure, an object whose mathematical representation is a matrix in which nodes are identified neurons or neurons' clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocytochemistry techniques, our non invasive measures entitle us to perform a longitudinal analysis during the maturation of a single culture. Such an analysis furnishes the way of individuating the main physical processes underlying the self-organization of the neurons' ensemble into a complex network, and drives the formulation of a phenomenological model yet able to describe qualitatively the overall scenario observed during the culture growth.

Topological synchronization of chaotic systems.

A chaotic dynamics is typically characterized by the emergence of strange attractors with their fractal or multifractal structure. On the other hand, chaotic synchronization is a unique emergent self-organization phenomenon in nature. Classically, synchronization was characterized in terms of macroscopic parameters, such as the spectrum of Lyapunov exponents. Recently, however, we attempted a microscopic description of synchronization, called topological synchronization, and showed that chaotic synchronization is, in fact, a continuous process that starts in low-density areas of the attractor. Here we analyze the relation between the two emergent phenomena by shifting the descriptive level of topological synchronization to account for the multifractal nature of the visited attractors. Namely, we measure the generalized dimension of the system and monitor how it changes while increasing the coupling strength. We show that during the gradual process of topological adjustment in phase space, the multifractal structures of each strange attractor of the two coupled oscillators continuously converge, taking a similar form, until complete topological synchronization ensues. According to our results, chaotic synchronization has a specific trait in various systems, from continuous systems and discrete maps to high dimensional systems: synchronization initiates from the sparse areas of the attractor, and it creates what we termed as the 'zipper effect', a distinctive pattern in the multifractal structure of the system that reveals the microscopic buildup of the synchronization process. Topological synchronization offers, therefore, a more detailed microscopic description of chaotic synchronization and reveals new information about the process even in cases of high mismatch parameters.

Introduction to focus issue: mesoscales in complex networks.

Although the functioning of real complex networks is greatly determined by modularity, the majority of articles have focused, until recently, on either their local scale structure or their macroscopical properties. However, neither of these descriptions can adequately describe the important features that complex networks exhibit due to their organization in modules. This Focus Issue precisely presents the state of the art on the study of complex networks at that intermediate level. The reader will find out why this mesoscale level has become an important topic of research through the latest advances carried out to improve our understanding of the dynamical behavior of modular networks. The contributions presented here have been chosen to cover, from different viewpoints, the many open questions in the field as different aspects of community definition and detection algorithms, moduli overlapping, dynamics on modular networks, interplay between scales, and applications to biological, social, and technological fields.

Node differentiation dynamics along the route to synchronization in complex networks.

Synchronization has been the subject of intense research during decades mainly focused on determining the structural and dynamical conditions driving a set of interacting units to a coherent state globally stable. However, little attention has been paid to the description of the dynamical development of each individual networked unit in the process towards the synchronization of the whole ensemble. In this paper we show how in a network of identical dynamical systems, nodes belonging to the same degree class, differentiate in the same manner, visiting a sequence of states of diverse complexity along the route to synchronization independently on the global network structure. In particular, we observe, just after interaction starts pulling orbits from the initially uncoupled attractor, a general reduction of the complexity of the dynamics of all units being more pronounced in those with higher connectivity. In the weak-coupling regime, when synchronization starts to build up, there is an increase in the dynamical complexity, whose maximum is achieved, in general, first in the hubs due to their earlier synchronization with the mean field. For very strong coupling, just before complete synchronization, we found a hierarchical dynamical differentiation with lower degree nodes being the ones exhibiting the largest complexity departure. We unveil how this differentiation route holds for several models of nonlinear dynamics, including toroidal chaos and how it depends on the coupling function. This study provides insights to understand better strategies for network identification or to devise effective methods for network inference.

Neuronal circuits on a chip for biological network monitoring.

Cultured neuronal networks (CNNs) are a robust model to closely investigate neuronal circuits' formation and monitor their structural properties evolution. Typically, neurons are cultured in plastic plates or, more recently, in microfluidic platforms with potentially a wide variety of neuroscience applications. As a biological protocol, cell culture integration with a microfluidic system provides benefits such as accurate control of cell seeding area, culture medium renewal, or lower exposure to contamination. The objective of this report is to present a novel neuronal network on a chip device, including a chamber, fabricated from PDMS, vinyl and glass connected to a microfluidic platform to perfuse the continuous flow of culture medium. Network growth is compared in chips and traditional Petri dishes to validate the microfluidic chip performance. The network assessment is performed by computing relevant topological measures like the number of connected neurons, the clustering coefficient, and the shortest path between any pair of neurons throughout the culture's life. The results demonstrate that neuronal circuits on a chip have a more stable network structure and lifespan than developing in conventional settings, and therefore this setup is an advantageous alternative to current culture methods. This technology could lead to challenging applications such as batch drug testing of in vitro cell culture models. From the engineering perspective, a device's advantage is the chance to develop custom designs more efficiently than other microfluidic systems.

Network-based features for retinal fundus vessel structure analysis.

Retinal fundus imaging is a non-invasive method that allows visualizing the structure of the blood vessels in the retina whose features may indicate the presence of diseases such as diabetic retinopathy (DR) and glaucoma. Here we present a novel method to analyze and quantify changes in the retinal blood vessel structure in patients diagnosed with glaucoma or with DR. First, we use an automatic unsupervised segmentation algorithm to extract a tree-like graph from the retina blood vessel structure. The nodes of the graph represent branching (bifurcation) points and endpoints, while the links represent vessel segments that connect the nodes. Then, we quantify structural differences between the graphs extracted from the groups of healthy and non-healthy patients. We also use fractal analysis to characterize the extracted graphs. Applying these techniques to three retina fundus image databases we find significant differences between the healthy and non-healthy groups (p-values lower than 0.005 or 0.001 depending on the method and on the database). The results are sensitive to the segmentation method (manual or automatic) and to the resolution of the images.

Nonlinear graph-based theory for dynamical network observability.

A faithful description of the state of a complex dynamical network would require, in principle, the measurement of all its d variables, an infeasible task for high dimensional systems due to practical limitations. However the network dynamics might be observable from a reduced set of measured variables but how to reliably identify the minimum set of variables providing full observability still remains an unsolved problem. In order to tackle this issue from the Jacobian matrix of the governing equations, we construct a pruned fluence graph in which the nodes are the state variables and the links represent only the linear dynamical interdependences after having ignored the nonlinear ones. From this graph, we identify the largest connected subgraphs with no outgoing links in which every node can be reached from any other node in the subgraph. In each one of them, at least one node must be measured to correctly monitor the state of the system in a d-dimensional reconstructed space. Our procedure is here tested by investigating large-dimensional reaction networks. Our results are validated by comparing them with the determinant of the observability matrix which provides a rigorous assessment of the system's observability.

A symbolic network-based nonlinear theory for dynamical systems observability.

When the state of the whole reaction network can be inferred by just measuring the dynamics of a limited set of nodes the system is said to be fully observable. However, as the number of all possible combinations of measured variables and time derivatives spanning the reconstructed state of the system exponentially increases with its dimension, the observability becomes a computationally prohibitive task. Our approach consists in computing the observability coefficients from a symbolic Jacobian matrix whose elements encode the linear, nonlinear polynomial or rational nature of the interaction among the variables. The novelty we introduce in this paper, required for treating large-dimensional systems, is to identify from the symbolic Jacobian matrix the minimal set of variables (together with their time derivatives) candidate to be measured for completing the state space reconstruction. Then symbolic observability coefficients are computed from the symbolic observability matrix. Our results are in agreement with the analytical computations, evidencing the correctness of our approach. Its application to efficiently exploring the dynamics of real world complex systems such as power grids, socioeconomic networks or biological networks is quite promising.

Adaptive control of dynamical synchronization on evolving networks with noise disturbances.

In real-world networked systems, the underlying structure is often affected by external and internal unforeseen factors, making its evolution typically inaccessible. An adaptive strategy was introduced for maintaining synchronization on unpredictably evolving networks [Sorrentino and Ott, Phys. Rev. Lett. 100, 114101 (2008)PRLTAO0031-900710.1103/PhysRevLett.100.114101], which yet does not consider the noise disturbances widely existing in networks' environments. We provide here strategies to control dynamical synchronization on slowly and unpredictably evolving networks subjected to noise disturbances which are observed at the node and at the communication channel level. With our strategy, the nodes' coupling strength is adaptively adjusted with the aim of controlling synchronization, and according only to their received signal and noise disturbances. We first provide a theoretical analysis of the control scheme by introducing an error potential function to seek for the minimization of the synchronization error. Then, we show numerical experiments which verify our theoretical results. In particular, it is found that our adaptive strategy is effective even for the case in which the dynamics of the uncontrolled network would be explosive (i.e., the states of all the nodes would diverge to infinity).

Observability coefficients for predicting the class of synchronizability from the algebraic structure of the local oscillators.

Understanding the conditions under which a collective dynamics emerges in a complex network is still an open problem. A useful approach is the master stability function-and its related classes of synchronization-which offers a necessary condition to assess when a network successfully synchronizes. Observability coefficients, on the other hand, quantify how well the original state space of a system can be observed given only the access to a measured variable. The question is therefore pertinent: Given a generic dynamical system (represented by a state variable x) and given a generic measure on it h(x) (which may be either an observation of an external agent, or an output function through which the units of a network interact), are classes of synchronization and observability actually related to each other? We explicitly address this issue, and show a series of nontrivial relationships for networks of different popular chaotic systems (Rössler, Lorenz, and Hindmarsh-Rose oscillators). Our results suggest that specific dynamical properties can be evoked for explaining the classes of synchronizability.

Unidirectional mechanism for reentrant activity generation in excitable media.

A closed excitable pathway with one point-to-point connection is used to generate a rotating wave both in experiments using the photosensitive Belousov-Zhabotinsky system and numerically with an Oregonator reaction-diffusion model. By varying the excitability and geometrical properties of the medium, propagation can be made unidirectional or bidirectional, giving rise, respectively, to the existence or not of sustained reentrant activity in a closed excitable track.

Emergence of small-world anatomical networks in self-organizing clustered neuronal cultures.

In vitro primary cultures of dissociated invertebrate neurons from locust ganglia are used to experimentally investigate the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. At all the different stages of the culture's development, identification of neurons' and neurites' location by means of a dedicated software allows to ultimately extract an adjacency matrix from each image of the culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main network's characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graph's micro- and meso-scale properties emerge. Finally, we identify the main physical processes ruling the culture's morphological transformations, and embed them into a simplified growth model qualitatively reproducing the overall set of experimental observations.

Targeting the dynamics of complex networks.

We report on a generic procedure to steer (target) a network's dynamics towards a given, desired evolution. The problem is here tackled through a Master Stability Function approach, assessing the stability of the aimed dynamics, and through a selection of nodes to be targeted. We show that the degree of a node is a crucial element in this selection process, and that the targeting mechanism is most effective in heterogeneous scale-free architectures. This makes the proposed approach applicable to the large majority of natural and man-made networked systems.

Unveiling protein functions through the dynamics of the interaction network.

Protein interaction networks have become a tool to study biological processes, either for predicting molecular functions or for designing proper new drugs to regulate the main biological interactions. Furthermore, such networks are known to be organized in sub-networks of proteins contributing to the same cellular function. However, the protein function prediction is not accurate and each protein has traditionally been assigned to only one function by the network formalism. By considering the network of the physical interactions between proteins of the yeast together with a manual and single functional classification scheme, we introduce a method able to reveal important information on protein function, at both micro- and macro-scale. In particular, the inspection of the properties of oscillatory dynamics on top of the protein interaction network leads to the identification of misclassification problems in protein function assignments, as well as to unveil correct identification of protein functions. We also demonstrate that our approach can give a network representation of the meta-organization of biological processes by unraveling the interactions between different functional classes.