Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Taming out-of-equilibrium dynamics on interconnected networks.

ABSTRACT: A wide variety of social, biological or technological systems can be described as processes taking place on networked structures in continuous interaction with other networks. We propose here a new methodology to describe, anticipate and manage, in real time, the out-of-equilibrium dynamics of processes that evolve on interconnected networks. This goal is achieved through the full analytical treatment of the phenomenology and its reduction to a two-dimensional flux diagram, allowing us to predict at every time step the dynamical consequences of modifying the links between the different ensembles. Our results are consistent with real data and the methodology can be translated to clustered networks and/or interconnected networks of any size, topology or origin, from the struggle for knowledge on innovation structures to international economic relations or disease spreading on social groups.

SUBMITTER: Buldu JM

PROVIDER: S-EPMC6874616 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Taming out-of-equilibrium dynamics on interconnected networks.

Buldú Javier M JM Pablo-Martí Federico F Aguirre Jacobo J

Nature communications 20191122 1

A wide variety of social, biological or technological systems can be described as processes taking place on networked structures in continuous interaction with other networks. We propose here a new methodology to describe, anticipate and manage, in real time, the out-of-equilibrium dynamics of processes that evolve on interconnected networks. This goal is achieved through the full analytical treatment of the phenomenology and its reduction to a two-dimensional flux diagram, allowing us to predic ...[more]

PMID: 31757969

Similar Datasets

Interphase human chromosome exhibits out of equilibrium glassy dynamics.

Project description:Fingerprints of the three-dimensional organization of genomes have emerged using advances in Hi-C and imaging techniques. However, genome dynamics is poorly understood. Here, we create the chromosome copolymer model (CCM) by representing chromosomes as a copolymer with two epigenetic loci types corresponding to euchromatin and heterochromatin. Using novel clustering techniques, we establish quantitatively that the simulated contact maps and topologically associating domains (TADs) for chromosomes 5 and 10 and those inferred from Hi-C experiments are in good agreement. Chromatin exhibits glassy dynamics with coherent motion on micron scale. The broad distribution of the diffusion exponents of the individual loci, which quantitatively agrees with experiments, is suggestive of highly heterogeneous dynamics. This is reflected in the cell-to-cell variations in the contact maps. Chromosome organization is hierarchical, involving the formation of chromosome droplets (CDs) on genomic scale, coinciding with the TAD size, followed by coalescence of the CDs, reminiscent of Ostwald ripening.

| S-EPMC6082855 | biostudies-other

Emergence of metastable state dynamics in interconnected cortical networks with propagation delays.

Project description:The importance of the large number of thin-diameter and unmyelinated axons that connect different cortical areas is unknown. The pronounced propagation delays in these axons may prevent synchronization of cortical networks and therefore hinder efficient information integration and processing. Yet, such global information integration across cortical areas is vital for higher cognitive function. We hypothesized that delays in communication between cortical areas can disrupt synchronization and therefore enhance the set of activity trajectories and computations interconnected networks can perform. To evaluate this hypothesis, we studied the effect of long-range cortical projections with propagation delays in interconnected large-scale cortical networks that exhibited spontaneous rhythmic activity. Long-range connections with delays caused the emergence of metastable, spatio-temporally distinct activity states between which the networks spontaneously transitioned. Interestingly, the observed activity patterns correspond to macroscopic network dynamics such as globally synchronized activity, propagating wave fronts, and spiral waves that have been previously observed in neurophysiological recordings from humans and animal models. Transient perturbations with simulated transcranial alternating current stimulation (tACS) confirmed the multistability of the interconnected networks by switching the networks between these metastable states. Our model thus proposes that slower long-range connections enrich the landscape of activity states and represent a parsimonious mechanism for the emergence of multistability in cortical networks. These results further provide a mechanistic link between the known deficits in connectivity and cortical state dynamics in neuropsychiatric illnesses such as schizophrenia and autism, as well as suggest non-invasive brain stimulation as an effective treatment for these illnesses.

| S-EPMC3812055 | biostudies-other

Breathing synchronization in interconnected networks.

Project description:Global synchronization in a complex network of oscillators emerges from the interplay between its topology and the dynamics of the pairwise interactions among its numerous components. When oscillators are spatially separated, however, a time delay appears in the interaction which might obstruct synchronization. Here we study the synchronization properties of interconnected networks of oscillators with a time delay between networks and analyze the dynamics as a function of the couplings and communication lag. We discover a new breathing synchronization regime, where two groups appear in each network synchronized at different frequencies. Each group has a counterpart in the opposite network, one group is in phase and the other in anti-phase with their counterpart. For strong couplings, instead, networks are internally synchronized but a phase shift between them might occur. The implications of our findings on several socio-technical and biological systems are discussed.

| S-EPMC3836035 | biostudies-literature

Polarity, cell division, and out-of-equilibrium dynamics control the growth of epithelial structures.

Project description:The growth of a well-formed epithelial structure is governed by mechanical constraints, cellular apico-basal polarity, and spatially controlled cell division. Here we compared the predictions of a mathematical model of epithelial growth with the morphological analysis of 3D epithelial structures. In both in vitro cyst models and in developing epithelial structures in vivo, epithelial growth could take place close to or far from mechanical equilibrium, and was determined by the hierarchy of time-scales of cell division, cell-cell rearrangements, and lumen dynamics. Equilibrium properties could be inferred by the analysis of cell-cell contact topologies, and the nonequilibrium phenotype was altered by inhibiting ROCK activity. The occurrence of an aberrant multilumen phenotype was linked to fast nonequilibrium growth, even when geometric control of cell division was correctly enforced. We predicted and verified experimentally that slowing down cell division partially rescued a multilumen phenotype induced by altered polarity. These results improve our understanding of the development of epithelial organs and, ultimately, of carcinogenesis.

| S-EPMC3812962 | biostudies-literature

Fluctuation-response inequality out of equilibrium.

Project description:We present an approach to response around arbitrary out-of-equilibrium states in the form of a fluctuation-response inequality (FRI). We study the response of an observable to a perturbation of the underlying stochastic dynamics. We find that the magnitude of the response is bounded from above by the fluctuations of the observable in the unperturbed system and the Kullback-Leibler divergence between the probability densities describing the perturbed and the unperturbed system. This establishes a connection between linear response and concepts of information theory. We show that in many physical situations, the relative entropy may be expressed in terms of physical observables. As a direct consequence of this FRI, we show that for steady-state particle transport, the differential mobility is bounded by the diffusivity. For a "virtual" perturbation proportional to the local mean velocity, we recover the thermodynamic uncertainty relation (TUR) for steady-state transport processes. Finally, we use the FRI to derive a generalization of the uncertainty relation to arbitrary dynamics, which involves higher-order cumulants of the observable. We provide an explicit example, in which the TUR is violated but its generalization is satisfied with equality.

| S-EPMC7104339 | biostudies-literature

Navigability of interconnected networks under random failures.

Project description:Assessing the navigability of interconnected networks (transporting information, people, or goods) under eventual random failures is of utmost importance to design and protect critical infrastructures. Random walks are a good proxy to determine this navigability, specifically the coverage time of random walks, which is a measure of the dynamical functionality of the network. Here, we introduce the theoretical tools required to describe random walks in interconnected networks accounting for structure and dynamics inherent to real systems. We develop an analytical approach for the covering time of random walks in interconnected networks and compare it with extensive Monte Carlo simulations. Generally speaking, interconnected networks are more resilient to random failures than their individual layers per se, and we are able to quantify this effect. As an application--which we illustrate by considering the public transport of London--we show how the efficiency in exploring the multiplex critically depends on layers' topology, interconnection strengths, and walk strategy. Our findings are corroborated by data-driven simulations, where the empirical distribution of check-ins and checks-out is considered and passengers travel along fastest paths in a network affected by real disruptions. These findings are fundamental for further development of searching and navigability strategies in real interconnected systems.

| S-EPMC4060702 | biostudies-literature

2D pn junctions driven out-of-equilibrium.

Project description:The pn junction is a fundamental electrical component in modern electronics and optoelectronics. Currently, there is a great deal of interest in the two-dimensional (2D) pn junction. Although many experiments have demonstrated the working principle, there is a lack of fundamental understanding of its basic properties and expected performances, in particular when the device is driven out-of-equilibrium. To fill the current gap in understanding, we investigate the electrostatics and electronic transport of 2D lateral pn junctions. To do so we implement a physics-based simulator that self-consistently solves the 2D Poisson's equation coupled to the drift-diffusion and continuity equations. Notably, the simulator takes into account the strong influence of the out-of-plane electric field through the surrounding dielectric, capturing the weak screening of charge carriers. Supported by simulations, we propose a Shockley-like equation for the ideal current-voltage (J-V) characteristics, in full analogy to the bulk junction after defining an effective depletion layer (EDL). We also discuss the impact of recombination-generation processes inside the EDL, which actually produce a significant deviation with respect to the ideal behavior, consistently with experimental data. Moreover, we analyze the capacitances and conductance of the 2D lateral pn junction. Based on its equivalent circuit we investigate its cut-off frequency targeting RF applications. To gain deeper insight into the role played by material dimensionality, we benchmark the performances of single-layer MoS2 (2D) lateral pn junctions against those of the Si (3D) junction. Finally, a practical discussion on the short length 2D junction case together with the expected impact of interface states has been provided. Given the available list of 2D materials, this work opens the door to a wider exploration of material-dependent performances.

| S-EPMC9419719 | biostudies-literature

A network of networks approach for modeling interconnected brain tissue-specific networks.

Project description:MotivationRecent sequence-based analyses have identified a lot of gene variants that may contribute to neurogenetic disorders such as autism spectrum disorder and schizophrenia. Several state-of-the-art network-based analyses have been proposed for mechanical understanding of genetic variants in neurogenetic disorders. However, these methods were mainly designed for modeling and analyzing single networks that do not interact with or depend on other networks, and thus cannot capture the properties between interdependent systems in brain-specific tissues, circuits and regions which are connected each other and affect behavior and cognitive processes.ResultsWe introduce a novel and efficient framework, called a 'Network of Networks' approach, to infer the interconnectivity structure between multiple networks where the response and the predictor variables are topological information matrices of given networks. We also propose Graph-Oriented SParsE Learning, a new sparse structural learning algorithm for network data to identify a subset of the topological information matrices of the predictors related to the response. We demonstrate on simulated data that propose Graph-Oriented SParsE Learning outperforms existing kernel-based algorithms in terms of F-measure. On real data from human brain region-specific functional networks associated with the autism risk genes, we show that the 'Network of Networks' model provides insights on the autism-associated interconnectivity structure between functional interaction networks and a comprehensive understanding of the genetic basis of autism across diverse regions of the brain.Availability and implementationOur software is available from https://github.com/infinite-point/GOSPEL.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC6735868 | biostudies-literature

Out-of-equilibrium phonons in gated superconducting switches.

Project description:Recent experiments have suggested that superconductivity in metallic nanowires can be suppressed by the application of modest gate voltages. The source of this gate action has been debated and either attributed to an electric-field effect or to small leakage currents. Here we show that the suppression of superconductivity in titanium nitride nanowires on silicon substrates does not depend on the presence or absence of an electric field at the nanowire, but requires a current of high-energy electrons. The suppression is most efficient when electrons are injected into the nanowire, but similar results are obtained when electrons are passed between two remote electrodes. This is explained by the decay of high-energy electrons into phonons, which propagate through the substrate and affect superconductivity in the nanowire by generating quasiparticles. By studying the switching probability distribution of the nanowire, we also show that high-energy electron emission leads to a much broader phonon energy distribution compared with the case where superconductivity is suppressed by Joule heating near the nanowire.

| S-EPMC8885403 | biostudies-literature

Topological localization in out-of-equilibrium dissipative systems.

Project description:In this paper, we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We consider two physically disparate systems: stochastic networks governed by microscopic single-particle dynamics, and collections of driven interacting particles described by coarse-grained hydrodynamic theory. We derive our results by mapping to well-known electronic models and exploiting the resulting correspondence between a bulk topological number and the spectrum of dissipative modes localized at the boundary. For the Markov networks, we report a general procedure to uncover the topological properties in terms of the transition rates. For the active fluid on a substrate, we introduce a topological interpretation of fluid dissipative modes at the edge. In both cases, the presence of dissipative couplings to the environment that break time-reversal symmetry are crucial to ensuring topological protection. These examples constitute proof of principle that notions of topological protection do indeed extend to dissipative processes operating out of equilibrium. Such topologically robust boundary modes have implications for both biological and synthetic systems.

| S-EPMC6166820 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data