Related papers: Knockouts, Robustness and Cell Cycles
When three species compete cyclically in a well-mixed, stochastic system of $N$ individuals, extinction is known to typically occur at times scaling as the system size $N$. This happens, for example, in rock-paper-scissors games or…
A characteristic property of networks is their ability to propagate influences, such as infectious diseases, behavioral changes, and failures. An especially important class of such contagious dynamics is that of cascading processes. These…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
We study networked control of non-linear systems where system states and tentative plant input sequences are transmitted over unreliable communication channels. The sequences are calculated recursively by using a pre-designed nominally…
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…
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Deterministic and stochastic Boolean network models are build for the dynamics of negative feedback loops of the p53 pathways. It is shown that the main function of the negative feedback in the p53 pathways is to keep p53 at a low steady…
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable solutions of the generated Boolean…
Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Motor systems show an overall robustness, but because they are highly nonlinear, understanding how they achieve robustness is difficult. In many rhythmic systems, robustness against perturbations involves response of both the shape and the…
Networks in nature rarely function in isolation but instead interact with one another with a form of a network of networks (NoN). A network of networks with interdependency between distinct networks contains instability of abrupt collapse…
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.…
With increasingly ambitious initiatives such as GENI and FIND that seek to design the future Internet, it becomes imperative to define the characteristics of robust topologies, and build future networks optimized for robustness. This paper…
The existence of inter-dependence between multiple networks imparts an additional scale of complexity to such systems often referred to as `network of networks' (NON). We have investigated the robustness of NONs to random breakdown of their…
Network controllability robustness reflects how well a networked dynamical system can maintain its controllability against destructive attacks. This paper investigates the network controllability robustness from the perspective of a…
While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…
Networks with a given degree distribution may be very resilient to one type of failure or attack but not to another. The goal of this work is to determine network design guidelines which maximize the robustness of networks to both random…
The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks,…