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Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…

Complex network infrastructure systems for power-supply, communication, and transportation support our economical and social activities, however they are extremely vulnerable against the frequently increasing large disasters or attacks.…

Many real-world multilayer systems such as critical infrastructure are interdependent and embedded in space with links of a characteristic length. They are also vulnerable to localized attacks or failures, such as terrorist attacks or…

There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…

Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…

The class of weakly acyclic games, which includes potential games and dominance-solvable games, captures many practical application domains. In a weakly acyclic game, from any starting state, there is a sequence of better-response moves…

We studied in silico effects of structural stress in Mycoplasma pneumoniae, a genome-reduced model bacterial organism, by tracking the damage propagating on its metabolic network after a deleterious perturbation. First, we analyzed failure…

Highly connected recurrent neural networks often produce chaotic dynamics, meaning their precise activity is sensitive to small perturbations. What are the consequences for how such networks encode streams of temporal stimuli? On the one…

A dynamic model for failures in biological organisms is proposed and studied both analytically and numerically. Each cell in the organism becomes dead under sufficiently strong stress, and is then allowed to be healed with some probability.…

The transcriptional regulation of gene expression is orchestrated by complex networks of interacting genes. Increasing evidence indicates that these transcriptional regulatory networks (TRNs) in bacteria have an inherently hierarchical…

Many systems on our planet are known to shift abruptly and irreversibly from one state to another when they are forced across a "tipping point," such as mass extinctions in ecological networks, cascading failures in infrastructure systems,…

Network science is already making an impact on the study of complex systems and offers a promising variety of tools to understand their formation and evolution (1-4) in many disparate fields from large communication networks (5,6),…

Weakly acyclic games generalize potential games and are fundamental to the study of game theoretic control. In this paper, we present a generalization of weakly acyclic games, and we observe its importance in multi-agent learning when…

This paper studies network resilience against structured additive perturbations to its topology. We consider dynamic networks modeled as linear time-invariant systems subject to perturbations of bounded energy satisfying specific sparsity…

Many real world complex systems such as infrastructure, communication and transportation networks are embedded in space, where entities of one system may depend on entities of other systems. These systems are subject to geographically…

We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into…

Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…

Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…

Central nodes are critical in establishing structural connectivity in a complex network. Attacking such nodes can create real havoc in a complex system. We propose attack strategies based on four types of centers, namely betweenness center,…

Fractional killing in response to drugs is a hallmark of non-genetic cellular heterogeneity. Yet how individual lineages evade drug treatment, as observed in bacteria and cancer cells, is not quantitatively understood. We analyse a…