Related papers: Network architectural conditions for prominent and…

We study the emergence and coherence of stochastic oscillations in star networks of excitable elements in which peripheral nodes receive independent random inputs. A biophysical model of a distal branch of sensory neuron in which peripheral…

Homeostasis is a running theme in biology. Often achieved through feedback regulation strategies, homeostasis allows living cells to control their internal environment as a means for surviving changing and unfavourable environments. While…

The activity generated by an ensemble of neurons is affected by various noise sources. It is a well-recognised challenge to understand the effects of noise on the stability of such networks. We demonstrate that the patterns of activity…

Adaptation to environmental change is a common property of biological systems. Cells initially respond to external changes in the environment, but after some time, they regain their original state. By considering an element consisting of…

Ergodicity and output controllability have been shown to be fundamental concepts for the analysis and synthetic design of closed-loop stochastic reaction networks, as exemplified by the use of antithetic integral feedback controllers. In…

Adaptation plays a fundamental role in shaping the structure of a complex network and improving its functional fitting. Even when increasing the level of synchronization in a biological system is considered as the main driving force for…

Many natural systems are organized as networks, in which the nodes (be they cells, individuals or populations) interact in a time-dependent fashion. The dynamic behavior of these networks depends on how these nodes are connected, which can…

We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcation to a state where a stable fixed point…

Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more…

We consider how to connect a set of disjoint networks to optimize the performance of the resulting composite network. We quantify this performance by the coherence of the composite network, which is defined by an $H_2$ norm of the system.…

Shortcuts in a regular architecture affect the information transport through the system due to the severe decrease in average path length. A fundamental new perspective in terms of pattern formation is the destabilizing effect of…

A perturbative method is developed for calculating the effects of recurrent synaptic interactions between neurons embedded in a network. A series expansion is constructed that converges for networks with noisy membrane potential and weak…

Many natural, complex systems are remarkably stable thanks to an absence of feedback acting on their elements. When described as networks, these exhibit few or no cycles, and associated matrices have small leading eigenvalues. It has been…

We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…

Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…

Networks of model neurons with balanced recurrent excitation and inhibition produce irregular and asynchronous spiking activity. We extend the analysis of balanced networks to include the known dependence of connection probability on the…

We analyze transport on a graph with multiple constraints and where the weight of the edges connecting the nodes is a dynamical variable. The network dynamics results from the interplay between a nonlinear function of the flow, dissipation,…

The paper investigates the synchronization of a network of identical linear state-space models under a possibly time-varying and directed interconnection structure. The main result is the construction of a dynamic output feedback coupling…

Cancer invasion and metastasis depend on angiogenesis. The cellular processes (growth, migration, and apoptosis) that occur during angiogenesis are tightly regulated by signaling molecules. Thus, understanding how cells synthesize multiple…

The purpose of this paper is trifold -- to serve as an instructive resource and a reference catalog for biologically plausible modeling with i) conductance-based models, coupled with ii) strength-varying slow synapse models, culminating in…