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The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
The evolution of cooperation in networked systems helps to understand the dynamics in social networks, multi-agent systems, and biological species. The self-persistence of individual strategies is common in real-world decision making. The…
Many biological systems dynamically rearrange their components through a sequence of configurations in order to perform their functions. Such dynamic processes have been studied using network models that sequentially retrieve a set of…
What can we learn from the collective dynamics of a complex network about its interaction topology? Taking the perspective from nonlinear dynamics, we briefly review recent progress on how to infer structural connectivity (direct…
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates its own expression. The nonlinear coupling…
We propose new direction to understanding evolutionary dynamics of complex networks using two different types of collaboration networks: academic collaboration networks; and, disaster collaboration networks. The results show that academic…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Over the last two decades, network science has greatly advanced our understanding of how the collective behaviors of a complex system emerge from the interactions among its basic units. Multiplex networks, i.e. networks with many layers,…
Sensory mechanisms in biology, from cells to humans, have the property of adaptivity, whereby the response produced by the sensor is adapted to the overall amplitude of the signal; reducing the sensitivity in the presence of strong…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
Humans and other animals often follow the decisions made by others because these are indicative of the quality of possible choices, resulting in `social response rules': observed relationships between the probability that an agent will make…
We explore the interplay between the protein-protein interactions network and the expression of the interacting proteins. It is shown that interacting proteins are expressed in significantly more similar cellular concentrations. This is…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…
Detecting the interactions of genetic compounds like genes, SNPs, proteins, metabolites, etc. can potentially unravel the mechanisms behind complex traits and common genetic disorders. Several methods have been taken into consideration for…
This paper deals with a new model for clonal network dynamics. We describe in detail this model and derive special equations governing immune system dynamics based on the general gradient type principles that can be inherent to a wide class…
We introduce the concept of network susceptibilities quantifying the response of the collective dy- namics of a network to small parameter changes. We distinguish two types of susceptibilities: vertex susceptibilities and edge…
Recent studies on the evolutionary dynamics of the Prisoner's Dilemma game in scale-free networks have demonstrated that the heterogeneity of the network interconnections enhances the evolutionary success of cooperation. In this paper we…
The relation between network structure and dynamics is determinant for the behavior of complex systems in numerous domains. An important long-standing problem concerns the properties of the networks that optimize the dynamics with respect…
Power grid networks, as well as neuronal networks with synaptic plasticity, describe real-world systems of tremendous importance for our daily life. The investigation of these seemingly unrelated types of dynamical networks has attracted…