Related papers: Towards the Understanding of Stability Puzzles in …
The problem of reliability of the dynamics in biological regulatory networks is studied in the framework of a generalized Boolean network model with continuous timing and noise. Using well-known artificial genetic networks such as the…
Natural systems are remarkably robust and resilient, maintaining essential functions despite variability, uncertainty, and hostile conditions. Understanding these nonlinear, dynamic behaviours is challenging because such systems involve…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
In adaptive dynamical networks, the dynamics of the nodes and the edges influence each other. We show that we can treat such systems as a closed feedback loop between edge and node dynamics. Using recent advances on the stability of…
A stochastic model of excitatory and inhibitory interactions which bears universality traits is introduced and studied. The endogenous component of noise, stemming from finite size corrections, drives robust inter-nodes correlations, that…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
Dynamics in biological networks are in general robust against several perturbations. We investigate a coupled map network as a model motivated by gene regulatory networks and design systems which are robust against phenotypic perturbations…
Diverse biological networks exhibit universal features distinguished from those of random networks, calling much attention to their origins and implications. Here we propose a minimal evolution model of Boolean regulatory networks, which…
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…
The use of available disturbance predictions within a nominal model predictive control formulation is studied. The main challenge that arises is the loss of recursive feasibility and stability guarantees when a persistent disturbance is…
We develop a framework to discuss stability of epigenetic states as first exit problems in dynamical systems with noise. We consider in particular the stability of the lysogenic state of the lambda prophage, which is known to exhibit…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
This paper investigates the robustness of NLP against perturbed word forms. While neural approaches can achieve (almost) human-like accuracy for certain tasks and conditions, they often are sensitive to small changes in the input such as…
The dynamic instability of the living systems and the "superposition" of different forms of randomness are viewed as a component of the contingently increasing organization of life along evolution. We briefly survey how classical and…
Understanding the relationship between complexity and stability in large dynamical systems -- such as ecosystems -- remains a key open question in complexity theory which has inspired a rich body of work developed over more than fifty…
Motivated by questions in biology, we investigate the stability of equilibria of the dynamical system $\mathbf{x}^{\prime}=P(t)\nabla f(x)$ which arise as critical points of $f$, under the assumption that $P(t)$ is positive semi-definite.…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
The characterization of plasticity, robustness, and evolvability, an important issue in biology, is studied in terms of phenotypic fluctuations. By numerically evolving gene regulatory networks, the proportionality between the phenotypic…
Inside living cells are complex mixtures of thousands of components. It is hopeless to try to characterise all the individual interactions in these mixtures. Thus, we develop a statistical approach to approximating them, and examine the…