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In neural information processing, an input modulates neural dynamics to generate a desired output. To unravel the dynamics and underlying neural connectivity enabling such input-output association, we proposed an exactly soluble…
Natural, social, and artificial multi-agent systems usually operate in dynamic environments, where the ability to respond to changing circumstances is a crucial feature. An effective collective response requires suitable information…
We formulate a reduction theory that describes the response of an oscillator network as a whole to external forcing applied nonuniformly to its constituent oscillators. The phase description of multiple oscillator networks coupled weakly is…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
We address the issue of the effects of considering a network of contacts on the emergence of cooperation on social dilemmas under myopic best response dynamics. We begin by summarizing the main features observed under less intellectually…
In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…
We study the role of connectivity on the linear and nonlinear elastic behavior of amorphous systems using a two-dimensional random network of harmonic springs as a model system. A natural characterization of these systems arises in terms of…
Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology,…
Systems composed of distinct complex networks are present in many real-world environments, from society to ecological systems. In the present paper, we propose a network model obtained as a consequence of interactions between two species…
Zero-one biochemical reaction networks play key roles in cell signalling such as signalling pathways regulated by protein phosphorylation. Multistability of reaction networks is a crucial dynamics feature enabling decision-making in cells.…
Understanding the structural complexity and predictability of complex networks is a central challenge in network science. Although recent studies have revealed a relationship between compression-based entropy and link prediction…
Here we propose a new approach to modeling gene expression based on the theory of random dynamical systems (RDS) that provides a general coupling prescription between the nodes of any given regulatory network given the dynamics of each node…
We show that the resolution of social dilemmas on random graphs and scale-free networks is facilitated by imitating not the strategy of better performing players but rather their emotions. We assume sympathy and envy as the two emotions…
Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
Competition between synapses arises in some forms of correlation-based plasticity. Here we propose a game theory-inspired model of synaptic interactions whose dynamics is driven by competition between synapses in their weak and strong…
Control of the living cell functions with remarkable reliability despite the stochastic nature of the underlying molecular networks -- a property presumably optimized by biological evolution. We here ask to what extent the property of a…
Most existing works on physical-layer (PHY) cooperation (beyond routing) focus on how to best use a given, static relay network--while wireless networks are anything but static. In this paper, we pose a different set of questions: given…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…