Related papers: Computationally Checking if a Reaction Network is …
Much attention has been focused in recent years on the following algebraic problem arising from applications: which chemical reaction networks, when taken with mass-action kinetics, admit multiple positive steady states? The interest behind…
Networks are useful descriptions of the structure of many complex systems. Unsurprisingly, it is thus important to analyze the robustness of networks in many scientific disciplines. In applications in communication, logistics, finance,…
In citation networks, the activity of papers usually decreases with age and dormant papers may be discovered and become fashionable again. To model this phenomenon, a competition mechanism is suggested which incorporates two factors:…
Many physical systems--from mechanical lattices and electrical circuits to biological tissues and architected metamaterials--can be understood as networks transmitting physical quantities. We present a unified mathematical framework for…
The spatially distributed reaction networks are indispensable for the understanding of many important phenomena concerning the development of organisms, coordinated cell behavior, and pattern formation. The purpose of this brief discussion…
Multiplex networks are a powerful framework for representing systems with multiple types of interactions among a common set of entities. Understanding their structure requires statistical tools capturing higher-order cross-layer…
We investigate the stochastic resonance phenomenon in a physical system based on a tunnel diode. The experimental control parameters are set to allow the control of the frequency and amplitude of the deterministic modulating signal over an…
We study expanding circle maps interacting in a heterogeneous random network. Heterogeneity means that some nodes in the network are massively connected, while the remaining nodes are only poorly connected. We provide a probabilistic…
We apply the linear response theory developed in \cite{Ruelle} to analyze how a periodic signal of weak amplitude, superimposed upon a chaotic background, is transmitted in a network of non linearly interacting units. We numerically compute…
Stochastic chemical processes are described by the chemical master equation satisfying the law of mass-action. We first ask whether the dual master equation, which has the same steady state as the chemical master equation, but with inverted…
We present a computational procedure to characterize the signs of sensitivities of steady states to parameter perturbations in chemical reaction networks.
In systems and synthetic biology, much research has focused on the behavior and design of single pathways, while, more recently, experimental efforts have focused on how cross-talk (coupling two or more pathways) or inhibiting molecular…
This paper studies the observability radius of network systems, which measures the robustness of a network to perturbations of the edges. We consider linear networks, where the dynamics are described by a weighted adjacency matrix, and…
The power of networks manifests itself in a highly non-linear amplification of a number of effects, and their weakness - in propagation of cascading failures. The potential systemic risk effects can be either exacerbated or mitigated,…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
Dynamical system models of complex biochemical reaction networks are usually high-dimensional, nonlinear, and contain many unknown parameters. In some cases the reaction network structure dictates that positive equilibria must be unique for…
Robustness is an observable property for which a chemical reaction network (CRN) can maintain its functionalities despite the influence of different perturbations. In general, to verify whether a network is robust, it is necessary to…
The monotone duality problem is defined as follows: Given two monotone formulas f and g in iredundant DNF, decide whether f and g are dual. This problem is the same as duality testing for hypergraphs, that is, checking whether a hypergraph…
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,…
Molecular networks guide the biochemistry of a living cell on multiple levels: its metabolic and signalling pathways are shaped by the network of interacting proteins, whose production, in turn, is controlled by the genetic regulatory…