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The presence of noise in non linear dynamical systems can play a constructive role, increasing the degree of order and coherence or evoking improvements in the performance of the system. An example of this positive influence in a biological…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
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…
Engineering genetic networks to be both predictable and robust is a key challenge in synthetic biology. Synthetic circuits must reliably function in dynamic, stochastic and heterogeneous environments, and simple circuits can be studied to…
Deterioration in the dynamical activities may come up naturally or due to environmental influences in a massive portion of biological and physical systems. Such dynamical degradation may have outright effect on the substantive network…
Biochemical computing attempts to process information with biomolecules and biological objects. In this work we review our results on analysis and optimization of single biochemical logic gates based on enzymatic reactions, and a network of…
Recurrent networks of dynamic elements frequently exhibit emergent collective oscillations, which can display substantial regularity even when the individual elements are considerably noisy. How noise-induced dynamics at the local level…
We consider weighted coupled cell networks, that is networks where the interactions between any two cells have an associated weight that is a real valued number. Weighted networks are ubiquitous in real-world applications. We consider a…
Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical…
Highly connected recurrent neural networks often produce chaotic dynamics, meaning their precise activity is sensitive to small perturbations. What are the consequences for how such networks encode streams of temporal stimuli? On the one…
We investigate how correlations between the diversity of the connectivity of networks and the dynamics at their nodes affect the macroscopic behavior. In particular, we study the synchronization transition of coupled stochastic phase…
Varied sensory systems use noise in order to enhance detection of weak signals. It has been conjectured in the literature that this effect, known as stochastic resonance, may take place in central cognitive processes such as the memory…
We study the oscillatory behaviour of a gene regulatory network with interlinked positive and negative feedback loop. Frequency and amplitude are two important properties of oscillation. Studied network produces two different modes of…
We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
We introduce noisy beeping networks, where nodes have limited communication capabilities, namely, they can only emit energy or sense the channel for energy. Furthermore, imperfections may cause devices to malfunction with some fixed…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
The sensitivity (i.e. dynamic response) of complex networked systems has not been well understood, making difficult to predict whether new macroscopic dynamic behavior will emerge even if we know exactly how individual nodes behave and how…
Entrainment of randomly coupled oscillator networks by periodic external forcing applied to a subset of elements is numerically and analytically investigated. For a large class of interaction functions, we find that the entrainment window…
We consider the influence of local noise on a generalized network of populations having positive and negative feedbacks. The population dynamics at the nodes is nonlinear, typically chaotic, and allows cessation of activity if the…