Related papers: Modular Gene Dynamics and Network Theory at Mesosc…
Random Boolean networks have been used widely to explore aspects of gene regulatory networks. A modified form of the model through which to systematically explore the effects of increasing the number of gene states has previously been…
The biological processes of cellular decision making and differentiation involve a plethora of signalling pathways and gene regulatory circuits. These networks, in their turn, exhibit a multitude of motifs playing crucial parts in…
In this study, we performed comprehensive morphological investigations of the spontaneous formations of effective network structures among elements in coupled logistic maps, specifically with a delayed connection change. Our proposed model…
Interconnected ensembles of biological entities are perhaps some of the most complex systems that modern science has encountered so far. In particular, scientists have concentrated on understanding how the complexity of the interacting…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
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…
We study the synchronization of coupled dynamical systems on a variety of networks. The dynamics is governed by a local nonlinear map or flow for each node of the network and couplings connecting different nodes via the links of the…
Gene regulatory networks arise in all living cells, allowing the control of gene expression patterns. The study of their topology has revealed that certain subgraphs of interactions or "motifs" appear at anomalously high frequencies. We ask…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
We investigate the behavior of a simple majority dynamics on networks of agents whose interaction topology exhibits a community structure. By leveraging recent advancements in the analysis of dynamics, we prove that, when the states of the…
Temporal networks model how the interaction between elements in a complex system evolve over time. Just like complex systems display collective dynamics, here we interpret temporal networks as trajectories performing a collective motion in…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Characterizing the emergence of chaotic dynamics of complex networks is an essential task in nonlinear science with potential important applications in many fields such as neural control engineering, microgrid technologies, and ecological…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
Motivation: Since susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and…
Across all scales of the physical world, dynamical systems can often be usefully represented as abstract networks that encode the system's units and inter-unit interactions. Understanding how physical rules shape the topological structure…
Adaptive networks appear in many biological applications. They combine topological evolution of the network with dynamics in the network nodes. Recently, the dynamics of adaptive networks has been investigated in a number of parallel…
This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…
Most complex systems are nonlinear, relying on emergent behavior from interacting subsystems, often characterized by oscillatory dynamics. Collective oscillatory behavior is essential for the proper functioning of many real world systems.…