Related papers: Computationally Checking if a Reaction Network is …
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…
A central issue in the study of large complex network systems, such as power grids, financial networks, and ecological systems, is to understand their response to dynamical perturbations. Recent studies recognize that many real networks…
This work considers the robustness of uncertain consensus networks. The first set of results studies the stability properties of consensus networks with negative edge weights. We show that if either the negative weight edges form a cut in…
Sensitivity studies the network response to perturbations. We consider local perturbations of the concentrations of metabolites at an equilibrium. We investigate the responses in the network, both of the metabolite concentrations and of the…
Chemical reaction network theory provides powerful tools for rigorously understanding chemical reactions and the dynamical systems and differential equations that represent them. A frequent issue with mathematical analyses of these networks…
In both natural and engineered systems, communication often occurs dynamically over networks ranging from highly structured grids to largely disordered graphs. To use, or comprehend the use of, networks as efficient communication media…
In this paper we study a model of weighted network formation. The bilateral interaction is modeled as a Tullock contest game with the possibility of a draw. We describe stable networks under different concepts of stability. We show that a…
Nonextensivity is foreseeable in network ensembles, as heterogeneous interactions generally exist in complex networked systems that need to be described by network ensembles. But this nonextensivity has not been literatured proved yet. In…
Steady states are frequently used to investigate the long-term behaviors of (bio)-chemical systems. Recently, there has been a growing interest in network-based approaches due to their efficiency in deriving parametrizations of positive…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
In many application domains, networks are observed with node-level features. In such settings, a common problem is to assess whether or not nodal covariates are correlated with the network structure itself. Here, we present four novel…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…
The network density matrix formalism allows for describing the dynamics of information on top of complex structures and it has been successfully used to analyze from system's robustness to perturbations to coarse graining multilayer…
Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches…
Given a resistive electrical network, we would like to determine whether all the resistances (edges) in the network are working, and if not, identify which edge (or edges) are faulty. To make this determination, we are allowed to measure…
Analyzing nonlinear conformational relaxation dynamics in elastic networks corresponding to two classical motor proteins, we find that they respond by well-defined internal mechanical motions to various initial deformations and that these…
Reaction networks are a general framework widely used in modeling diverse phenomena in different science disciplines. The dynamical process of a reaction network endowed with mass-action kinetics is a mass-action system as an ODE defined by…
Networks are universally considered as complex structures of interactions of large multi-component systems. In order to determine the role that each node has inside a complex network, several centrality measures have been developed. Such…
A central issue in complex networks is tolerance to random failures and intentional attacks. Current literature emphasizes the dichotomy between networks with a power-law node connectivity distribution, which are robust to random failures…