Corpus ID: 231648073

Effective connectivity determines the critical dynamics of biochemical networks

@inproceedings{Manicka2021EffectiveCD,
  title={Effective connectivity determines the critical dynamics of biochemical networks},
  author={Santosh Manicka and Manuel Marques-Pita and Luis Mateus Rocha},
  year={2021}
}
Living systems operate in a critical dynamical regime—between order and chaos—where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established structural theory of criticality uses automata network connectivity and node bias (to be on or off) as tuning parameters. This parsimony in the number of parameters needed sometimes leads to uncertain predictions about the dynamical regime of both random and systems biology models of… Expand

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References

SHOWING 1-10 OF 69 REFERENCES
From topology to dynamics in biochemical networks.
TLDR
Finite, scale-free networks, characterized by a wide distribution in the number of inputs per element, may provide a source of order in living cells, and are shown to be more ordered than either the Poisson or delta function networks below the critical point. Expand
Gene expression dynamics in the macrophage exhibit criticality
TLDR
Using global gene expression data from macrophages stimulated with a variety of Toll-like receptor agonists, it is found that macrophage dynamics are indeed critical, providing the most compelling evidence to date for this general principle of dynamics in biological systems. Expand
Morphogenesis at criticality
TLDR
It is argued that, as expected from the thermodynamic case, genetic regulatory networks should exhibit behaviors near criticality that are independent of most molecular details, and that the different signatures are related in ways predicted by theory. Expand
Eukaryotic cells are dynamically ordered or critical but not chaotic.
TLDR
Using the Boolean approach, this work shows what it believes to be the first direct evidence that the underlying genetic network of HeLa cells appears to operate either in the ordered regime or at the border between order and chaos but does not appear to be chaotic. Expand
Ensembles, dynamics, and cell types: Revisiting the statistical mechanics perspective on cellular regulation.
TLDR
Ensembles of random Boolean networks whose dynamical attractors model cell types whose generic properties predict essential features of cell differentiation are discussed, and prospects for new research lines for Boolean networks as a base model for systems biology are shown. Expand
Control of complex networks requires both structure and dynamics
TLDR
This work studies Boolean network ensembles of network motifs as well as three models of biochemical regulation, demonstrating that structure-only methods both undershoot and overshoot the number and which sets of critical variables best control the dynamics of these models. Expand
Dynamical Criticality: Overview and Open Questions
TLDR
The authors review the main contributions concerning dynamics and information processing at the edge of chaos, and illustrate the main achievements in the study of critical dynamics in biological systems. Expand
Genetic networks with canalyzing Boolean rules are always stable.
TLDR
The results indicate that for single cells, the dynamics should become more stable with evolution, and there are hints that genetic networks acquire broader degree distributions with evolution. Expand
Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions
We explore the connection between order/chaos in Boolean networks and the naturally occurring fraction of canalizing functions in such systems. This fraction turns out to give a very clear indicationExpand
Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms
TLDR
The results show that the gene transcription networks reported for S. cerevisiae, E. coli, and B. subtilis indeed operate close to criticality, and suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that the authors observe around us. Expand
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