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The stability of ecosystems as well as the relation between topology and dynamics on multilayer networks are important questions that are usually discussed in separate communities. Here, we combine these two topics by investigating the…
Robust Bayesian inference is the calculation of posterior probability bounds given perturbations in a probabilistic model. This paper focuses on perturbations that can be expressed locally in Bayesian networks through convex sets of…
In systems biology new ways are required to analyze the large amount of existing data on regulation of cellular processes. Recent work can be roughly classified into either dynamical models of well-described subsystems, or coarse-grained…
We simulate the evolution of a protein-like sequence subject to point mutations, imposing conservation of the ground state, thermodynamic stability and fast folding. Our model is aimed at describing neutral evolution of natural proteins. We…
We investigate how nonlinearity and topological disorder affect the energy relaxation of local kicks in coarse-grained network models of proteins. We find that nonlinearity promotes long-range, coherent transfer of substantial energy to…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Many real world networks are characterized by adaptive changes in their topology depending on the dynamic state of their nodes. Here we study epidemic dynamics in an adaptive network, where susceptibles are able to avoid contact with…
Distress propagation occurs in connected networks, its rate and extent being dependent on network topology. To study this, we choose economic production networks as a paradigm. An economic network can be examined at many levels: linkages…
Given a reaction-diffusion system interacting via a complex network, we propose two different techniques to modify the network topology while preserving its dynamical behaviour. In the region of parameters where the homogeneous solution…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
By employing the adaptive network simulation method, we demonstrate that the ensemble-averaged stress caused by a local force for packings of frictionless rigid beads is concentrated along rays whose slope is consistent with unity: forces…
In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
The properties of certain networks are determined by hidden variables that are not explicitly measured. The conditional probability (propagator) that a vertex with a given value of the hidden variable is connected to k of other vertices…
We study the effects of network topology on the response of networks of coupled discrete excitable systems to an external stochastic stimulus. We extend recent results that characterize the response in terms of spectral properties of the…
A fundamental question regarding biological transport networks is the interplay between the network development or reorganization and the flows it carries. We use Physarum polycephalum, a true slime mould with a transport network which…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
Disease awareness in infection dynamics can be modeled with adaptive contact networks whose rewiring rules reflect the attempt by susceptibles to avoid infectious contacts. Simulations of this type of models show an active phase with…
Diffusion of information, behavioral patterns or innovations follows diverse pathways depending on a number of conditions, including the structure of the underlying social network, the sensitivity to peer pressure and the influence of…