Related papers: A dynamic logic method for determining behaviors o…

This paper considers the problem of detecting topology variations in dynamical networks. We consider a network whose behavior can be represented via a linear dynamical system. The problem of interest is then that of finding conditions under…

Key network motifs searching in complex networks is one of the crucial aspects of network analysis. There has been a series of insightful findings and valuable applications for various scenarios through the analysis of network structures.…

We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…

Oscillations arise in many real-world systems and are associated with both functional and dysfunctional states. Whether a network can oscillate can be estimated if we know the strength of interaction between nodes. But in real-world…

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,…

We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors…

Recent experimental results based on multi-electrode and imaging techniques have reinvigorated the idea that large neural networks operate near a critical point, between order and disorder. However, evidence for criticality has relied on…

Cellular mechanism-of-action is of fundamental concern in many biological studies. It is of particular interest for identifying the cause of disease and learning the way in which treatments act against disease. However, pinpointing such…

We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental…

To find interesting structure in networks, community detection algorithms have to take into account not only the network topology, but also dynamics of interactions between nodes. We investigate this claim using the paradigm of…

Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously…

Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…

We consider steady states of dynamics that have an underlying network structure. We study how a steady state responds to small perturbations in the network parameters and how this sensitivity is connected to the network structure. We…

We study classes of dynamical systems that can be obtained by constructing recursive networks with monotone Boolean functions. Stack filters in nonlinear signal processing are special cases of such systems. We show an analytical connection…

A circuit architecture is proposed and implemented for a dynamical network composed of a type of hybrid chaotic oscillator based on Unstable Dissipative Systems (UDS). The circuit architecture allows selecting a network topology with its…

Natural and technological networks exhibit dynamics that can lead to complex cooperative behaviors, such as synchronization in coupled oscillators and rhythmic activity in neuronal networks. Understanding these collective dynamics is…

The identification of the limiting factors in the dynamical behavior of complex systems is an important interdisciplinary problem which often can be traced to the spectral properties of an underlying network. By deriving a general relation…

Chemical reaction networks in living cells maintain precise control over thousands of metabolites despite operating far from equilibrium under constant perturbations. While mass action kinetics accurately describe the underlying dynamics,…

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…