Related papers: Effective connectivity determines the critical dyn…
Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context specific and dynamic in…
A new probabilistic network construction system, DYNASTY, is proposed for diagnostic reasoning given variables whose probabilities change over time. Diagnostic reasoning is formulated as a sequential stochastic process, and is modeled using…
The collective dynamics of a network of coupled excitable systems in response to an external stimulus depends on the topology of the connections in the network. Here we develop a general theoretical approach to study the effects of network…
Many situations in physics, biology, and engineering consist of the transport of some physical quantity through a network of narrow channels. The ability of a network to transport such a quantity in every direction can be described by the…
Biological information processing is often carried out by complex networks of interconnected dynamical units. A basic question about such networks is that of reliability: if the same signal is presented many times with the network in…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…
Standard Random Boolean Networks display an order-disorder phase transition. We add to the standard Random Boolean Networks a disconnection rule which couples the control and order parameters. By this way, the system is driven to the…
Applying the mathematical circulation theory of Markov chains, we investigate the synchronized stochastic dynamics of a discrete network model of yeast cell-cycle regulation where stochasticity has been kept rather than being averaged out.…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
Individual heterogeneity is a key characteristic of many real-world systems, from organisms to humans. However its role in determining the system's collective dynamics is typically not well understood. Here we study how individual…
We consider the goal of predicting how complex networks respond to chronic (press) perturbations when characterizations of their network topology and interaction strengths are associated with uncertainty. Our primary result is the…
Networks with only central force interactions are floppy when their average connectivity is below an isostatic threshold. Although such networks are mechanically unstable, they can become rigid when strained. It was recently shown that the…
A mechanism for self-organization of the degree of connectivity in model neural networks is studied. Network connectivity is regulated locally on the basis of an order parameter of the global dynamics which is estimated from an observable…
The vicinity of phase transitions selectively amplifies weak stimuli, yielding optimal sensitivity to distinguish external input. Along with this enhanced sensitivity, enhanced levels of fluctuations at criticality reduce the specificity of…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
The relationship between network topology and system dynamics has significant implications for unifying our understanding of the interplay among metabolic, gene-regulatory, and ecosystem network architecures. Here we analyze the stability…
Synchronization of networked oscillators is known to depend fundamentally on the interplay between the dynamics of the graph's units and the microscopic arrangement of the network's structure. For non identical elements, the lack of…
Analytical studies of network epidemiology almost exclusively focus on the extreme situations where the time scales of network dynamics are well separated (longer or shorter) from that of epidemic propagation. In realistic scenarios,…
Functional connectivity is a fundamental property of neural networks that quantifies the segregation and integration of information between cortical areas. Due to mathematical complexity, a theory that could explain how the parameters of…