arXiv subjects

Astero Provata

Publications and source records attributed to Astero Provata.

At least 19 recordsLinked to original sources

arXiv2026

Adaptive transitions in FitzHugh-Nagumo networks with Hebb-Oja coupling rules

Adaptive coupling in networks of interacting neurons has gained recent attention due to the many applications both in biological and in artificial neural networks, where adaptive coupling or synaptic plasticity is considered as a key factor in learning processes. In the present study, we apply adaptive connectivity rules in networks of interacting FitzHugh-Nagumo oscillators. Adaptive coupling, here, is realized via Hebbian learning adjusted by the Oja rule to prevent the network link weights from growing without bounds. Numerical investigations demonstrate that during the adaptation process the FitzHugh-Nagumo network undergoes adaptive transitions realizing traveling waves, synchronized states and chimera states transiting through various multiplicities. These transitions become more evident when the time scales governing the coupling dynamics are much slower than the ones governing the nodal dynamics (nodal potentials). Namely, when the coupling time scales are slow, the network has the time to realize and demonstrate different synchronization regimes before reaching the final steady state. The transitions can be observed not only in the spacetime plots but also in the abrupt changes of the average coupling weights as the network evolves in time. Regarding the asymptotic coupling distributions, we show that the limiting average coupling strength follows an inverse power law with respect to the Oja parameter (also called "forgetting" parameter) which balances the learning growth. We also report abrupt transitions in the asymptotic coupling strengths when the parameter related to adaptive coupling crosses from fast to slow time scales. These findings are in line with previous studies on spiking neural networks.

nlin.PS↗

arXiv2025

Synchronization transitions in spiking networks with adaptive coupling

Adaptive link sizes is a major breakthrough step in evolving networks and is now considered as an essential process both in biological and artificial neural networks. In adaptive networks the link weights change in time and, in brain dynamics, these changes are controlled by the potential variations of the pre- and post-synaptic neurons. In particular, in biological neural networks the adaptivity of the links (synapses) was first addressed by D. Hebb who proposed the rule that neurons which fire together wire together. In the present study, we explore the effects of adaptive linking in networks where hybrid synchronization patterns (solitaries, chimeras and bump states) are observed in the absence of adaptivity (i.e., for constant coupling strengths). The network consists of Leaky Integrate-and-Fire (LIF) neurons coupled nonlocally in a 1D ring geometry. The adaptivity follows the Hebbian principle adjusted by the Oja rule to avoid unbounded increase of the coupling strengths. Our results indicate that, for negative coupling strengths, the adaptive LIF network may transit through chimera state regimes with different multiplicity, provided that the time scales governing the link dynamics are relatively small compared to the time scales of the potential evolution. Moreover, the size of the coherent and incoherent domains of the chimera and their multiplicity change following the average coupling strength in the network. Similar results are shown for the case of bump states: for positive coupling strengths, the adaptive LIF network transits through states of different number of active and subthreshold domains. The size and number of these domains also follow the evolution of the average coupling strength. Such transient effects are suppressed when the time scales governing the link adaptive dynamics become of the same order as the time scales governing the potential dynamics.

nlin.AO↗

arXiv2024

Multistable Synaptic Plasticity induces Memory Effects and Cohabitation of Chimera and Bump States in Leaky Integrate-and-Fire Networks

Chimera states and bump states are collective synchronization phenomena observed independently (at different parameter regions) in networks of coupled nonlinear oscillators. And while chimera states are characterized by coexistence of coherent and incoherent domains, bump states consist of active domains operating on a silent background. Multistable plasticity in the network connections originates from brain dynamics and is based on the idea that neural cells may transmit inhibitory or excitatory signals depending on various factors, such as local connectivity, influence of neighboring cells etc. During the system/network integration, the link weights adapt and, in the case of multistability, they may organize in coexisting excitatory and/or inhibitory domains. Here, we explore the influence of bistable plasticity on collective synchronization states and we numerically demonstrate that the dynamics of the linking may give rise to co-existence of bump-like and chimera-like states simultaneously in the network. In the case of bump and chimera co-existence, confinement effects are developed: the different domains stay localized and do not travel around the network. Memory effects are also reported in the sense that the final spatial arrangement of the coupling strengths reflects some of the local properties of the initial link distribution. For the quantification of the system's spatial and temporal features, the global and local entropy functions are employed as measures of the network organization, while the average firing rates account for the network evolution and dynamics.

nlin.CD↗

arXiv2024

An Extensive Study of Two-Node McCulloch-Pitts Networks

Networks with two nodes are previously grouped into either two classes (mutually interactive, master-slave) or five classes (mutualism, competition, predator-prey, commensalism, amensalism). By allowing self-loops, the number of signed regulatory graphs increases to 39. We provide a complete summary of dynamical behaviors of the 39 two-node McCulloch-Pitts models when the link weights are constrained to three values [$-1$,0,$+1$] and Boolean node variables. Depending on whether the Boolean values are [$-1,1$] (bipolar) or [0,1] (binary), we show that the dynamics could also be different with the same signed regulatory graphs. We demonstrate that slight variations in the McCulloch-Pitts model (called variants) may lead to fundamentally different dynamics. We study the full model space and three kinds of robustness or stability: a) of a rule against parameter change on its overall dynamics, b) for a given state against parameter change on its final state, and c) against an initial state change on its final state. All these stability properties are loosely related to a model's limiting dynamics, with the fixed-point rules to be more stable in the first two types of robustness, but less stable in the third robustness type. These analyses pave the way towards a better understanding of a minimum complex system.

cs.SI↗

arXiv2024

Range-Limited Heaps' Law for Functional DNA Words in the Human Genome

Heaps' or Herdan's law is a linguistic law describing the relationship between the vocabulary/dictionary size (type) and word counts (token) to be a power-law function. Its existence in genomes with certain definition of DNA words is unclear partly because the dictionary size in genome could be much smaller than that in a human language. We define a DNA word as a coding region in a genome that codes for a protein domain. Using human chromosomes and chromosome arms as individual samples, we establish the existence of Heaps' law in the human genome within limited range. Our definition of words in a genomic or proteomic context is different from other definitions such as over-represented k-mers which are much shorter in length. Although an approximate power-law distribution of protein domain sizes due to gene duplication and the related Zipf's law is well known, their translation to the Heaps' law in DNA words is not automatic. Several other animal genomes are shown herein also to exhibit range-limited Heaps' law with our definition of DNA words, though with various exponents. When tokens were randomly sampled and sample sizes reach to the maximum level, a deviation from the Heaps' law was observed, but a quadratic regression in log-log type-token plot fits the data perfectly. Investigation of type-token plot and its regression coefficients could provide an alternative narrative of reusage and redundancy of protein domains as well as creation of new protein domains from a linguistic perspective.

q-bio.GN↗

arXiv2023

Amplitude chimeras and bump states with and without frequency entanglement: a toy model

When chaotic oscillators are coupled in complex networks a number of interesting synchronization phenomena emerge. Notable examples are the frequency and amplitude chimeras, chimera death states, solitary states as well as combinations of these. In a previous study [Journal of Physics: Complexity, 2020, 1(2), 025006], a toy model was introduced addressing possible mechanisms behind the formation of frequency chimera states. In the present study a variation of the toy model is proposed to address the formation of amplitude chimeras. The proposed oscillatory model is now equipped with an additional 3rd order equation modulating the amplitude of the network oscillators. This way, the single oscillators are constructed as bistable in amplitude and depending on the initial conditions their amplitude may result in one of the two stable fixed points. Numerical simulations demonstrate that when these oscillators are nonlocally coupled in networks, they organize in domains with alternating amplitudes (related to the two fixed points), naturally forming amplitude chimeras. A second extension of this model incorporates nonlinear terms merging amplitude together with frequency, and this extension allows for the spontaneous production of composite amplitude-and-frequency chimeras occurring simultaneously in the network. Moreover the extended model allows to understand the emergence of bump states via the continuous passage from chimera states, when both fixed point amplitudes are positive, to bump states when one of the two fixed points vanishes. The proposed mechanisms of creating domains with variable amplitudes and/or frequencies provide a generic scenario for understanding the formation of the complex synchronization phenomena observed in networks of coupled nonlinear and chaotic oscillators.

nlin.AO↗

arXiv2022

From Turing patterns to chimera states in the 2D Brusselator model

The Brusselator has been used as a prototype model for autocatalytic reactions, and in particular for the Belouzov- Zhabotinsky reaction. When coupled at the diffusive limit, the Brusselator undergoes a Turing bifurcation resulting in the formation of classical Turing patterns, such as spots, stripes and spirals in 2 spatial dimensions. In the present study we use generic nonlocally coupled Brusselators and show that in the limit of the coupling range R->1 (diffusive limit), the classical Turing patterns are recovered, while for intermediate coupling ranges and appropriate parameter values chimera states are produced. This study demonstrates how the parameters of a typical nonlinear oscillator can be tuned so that the coupled system passes from spatially stable Turing structures to dynamical spatiotemporal chimera states.

nlin.CD↗

arXiv2020

Revisiting the Neutral Dynamics Derived Limiting Guanine-Cytosine Content Using the Human De Novo Point Mutation Data

We revisit the topic of human genome guanine-cytosine content under neutral evolution. For this study, the de novo mutation data within human is used to estimate mutational rate instead of using base substitution data between related species. We then define a new measure of mutation bias which separate the de novo mutation counts from the background guanine-cytosine content itself, making comparison between different datasets easier. We derive a new formula for calculating limiting guanine-cytosine content by separating CpG-involved mutational events as an independent variable. Using the formula when CpG-involved mutations are considered, the guanine-cytosine content drops less severely in the limit of neutral dynamics. We provide evidence, under certain assumptions, that an isochore-like structure might remain as a limiting configuration of the neutral mutational dynamics.

q-bio.GN↗

arXiv2019

Chimera states formed via a two-level synchronization mechanism

Chimera states, which consist of coexisting synchronous and asynchronous domains in networks of coupled oscillators, are in the focus of attention for over a decade. Although chimera morphology and properties have been investigated in a number of models, the mechanism responsible for their formation is still not well understood. To shed light in the chimera producing mechanism, in the present study we introduce an oscillatory model with variable frequency governed by a 3rd order equation. In this model single oscillators are constructed as bistable and depending on the initial conditions their frequency may result in one of the two stable fixed points, $ω_l$ and $ω_h $ (two-level synchronization). Numerical simulations demonstrate that these oscillators organize in domains with alternating frequencies, when they are nonlocally coupled in networks. In each domain the oscillators synchronize, sequential domains follow different modes of synchronization and the border elements between two consecutive domains form the asynchronous domains. We investigate the influence of the frequency coupling constant and of the coupling range on the chimera morphology and we show that the chimera multiplicity decreases as the coupling range increases. The frequency spectrum is calculated in the coherent and incoherent domains of this model. In the coherent domains single frequencies ($ω_l$ or $ω_h$) are observed, while in the incoherent domains both $ω_l$ and $ω_h$ as well as their superpositions appear. This mechanism of creating domains of alternating frequencies offers a reasonable generic scenario for chimera state formation.

nlin.CD↗

arXiv2018

Quantifying Local Randomness in Human DNA and RNA Sequences Using Erdos Motifs

In 1932, Paul Erdos asked whether a random walk constructed from a binary sequence can achieve the lowest possible deviation (lowest discrepancy), for the sequence itself and for all its subsequences formed by homogeneous arithmetic progressions. Although avoiding low discrepancy is impossible for infinite sequences, as recently proven by Terence Tao, attempts were made to construct such sequences with finite lengths. We recognize that such constructed sequences (we call these "Erdos sequences") exhibit certain hallmarks of randomness at the local level: they show roughly equal frequencies of subsequences, and at the same time exclude the trivial periodic patterns. For the human DNA we examine the frequency of a set of Erdos motifs of length-10 using three nucleotides-to-binary mappings. The particular length-10 Erdos sequence is derived by the length-11 Mathias sequence and is identical with the first 10 digits of the Thue-Morse sequence, underscoring the fact that both are deficient in periodicities. Our calculations indicate that: (1) the purine (A and G)/pyridimine (C and T) based Erdos motifs are greatly underrepresented in the human genome, (2) the strong(G and C)/weak(A and T) based Erdos motifs are slightly overrepresented, (3) the densities of the two are negatively correlated, (4) the Erdos motifs based on all three mappings being combined are slightly underrepresented, and (5) the strong/weak based Erdos motifs are greatly overrepresented in the human messenger RNA sequences.

q-bio.GN↗

arXiv2018

Constructive approach to limiting periodic orbits with exponential and power law dynamics

In dynamical systems limit cycles arise as a result of a Hopf bifurcation, after a control parameter has crossed its critical value. In this study we present a constructive method to produce dissipative dynamics which lead to stable periodic orbits as time grows, with predesigned transient dynamics. Depending on the construction method a) the limiting orbit can be a regular circle, an ellipse or a more complex closed orbit and b) the approach to the limiting orbit can follow an exponential law or a power law. This technique allows to design nonlinear models of dynamical systems with desired (exponential or power law) relaxation properties.

nlin.CD↗

arXiv2017

Chimera patterns in two-dimensional networks of coupled neurons

We discuss synchronization patterns in networks of FitzHugh-Nagumo and Leaky Integrate-and-Fire oscillators coupled in a two-dimensional toroidal geometry. Common feature between the two models is the presence of fast and slow dynamics, a typical characteristic of neurons. Earlier studies have demonstrated that both models when coupled nonlocally in one-dimensional ring networks produce chimera states for a large range of parameter values. In this study, we give evidence of a plethora of two-dimensional chimera patterns of various shapes including spots, rings, stripes, and grids, observed in both models, as well as additional patterns found mainly in the FitzHugh-Nagumo system. Both systems exhibit multistability: For the same parameter values, different initial conditions give rise to different dynamical states. Transitions occur between various patterns when the parameters (coupling range, coupling strength, refractory period, and coupling phase) are varied. Many patterns observe in the two models follow similar rules. For example the diameter of the rings grows linearly with the coupling radius.

nlin.AO↗

arXiv2015

Fractal and multifractal analysis of PET-CT images of metastatic melanoma before and after treatment with ipilimumab

PET/CT with F-18-Fluorodeoxyglucose (FDG) images of patients suffering from metastatic melanoma have been analysed using fractal and multifractal analysis to assess the impact of monoclonal antibody ipilimumab treatment with respect to therapy outcome. Our analysis shows that the fractal dimensions which describe the tracer dispersion in the body decrease consistently with the deterioration of the patient therapeutic outcome condition. In 20 out-of 24 cases the fractal analysis results match those of the medical records, while 7 cases are considered as special cases because the patients have non-tumour related medical conditions or side effects which affect the results. The decrease in the fractal dimensions with the deterioration of the patient conditions (in terms of disease progression) are attributed to the hierarchical localisation of the tracer which accumulates in the affected lesions and does not spread homogeneously throughout the body. Fractality emerges as a result of the migration patterns which the malignant cells follow for propagating within the body (circulatory system, lymphatic system). Analysis of the multifractal spectrum complements and supports the results of the fractal analysis. In the kinetic Monte Carlo modelling of the metastatic process a small number of malignant cells diffuse throughout a fractal medium representing the blood circulatory network. Along their way the malignant cells engender random metastases (colonies) with a small probability and, as a result, fractal spatial distributions of the metastases are formed similar to the ones observed in the PET/CT images. In conclusion, we propose that fractal and multifractal analysis has potential application in the quantification of the evaluation of PET/CT images to monitor the disease evolution as well as the response to different medical treatments.

physics.med-ph↗

arXiv2015

Controlling Chimera States - The influence of excitable units

We explore the influence of a block of excitable units on the existence and behavior of chimera states in a nonlocally coupled ring-network of FitzHugh-Nagumo elements. The FitzHugh-Nagumo system, a paradigmatic model in many fields from neuroscience to chemical pattern formation and nonlinear electronics, exhibits oscillatory or excitable behavior depending on the values of its parameters. Until now, chimera states have been studied in networks of coupled oscillatory FitzHugh-Nagumo elements. In the present work, we find that introducing a block of excitable units into the network may lead to several interesting effects. It allows for controlling the position of a chimera state as well as for generating a chimera state directly from the synchronous state.

nlin.PS↗

arXiv2015

Chimera states in population dynamics: networks with fragmented and hierarchical connectivities

We study numerically the development of chimera states in networks of nonlocally coupled oscillators whose limit cycles emerge from a Hopf bifurcation. This dynamical system is inspired from population dynamics and consists of three interacting species in cyclic reactions. The complexity of the dynamics arises from the presence of a limit cycle and four fixed points. When the bifurcation parameter increases away from the Hopf bifurcation the trajectory approaches the heteroclinic invariant manifolds of the fixed points producing spikes, followed by long resting periods. We observe chimera states in this spiking regime as a coexistence of coherence (synchronization) and incoherence (desynchronization) in a one-dimensional ring with nonlocal coupling, and demonstrate that their multiplicity depends both on the system and the coupling parameters. We also show that hierarchical (fractal) coupling topologies induce traveling multichimera states. The speed of motion of the coherent and incoherent parts along the ring is computed through the Fourier spectra of the corresponding dynamics.

nlin.CD↗

arXiv2014

Robustness of chimera states for coupled FitzHugh-Nagumo oscillators

Chimera states are complex spatio-temporal patterns that consist of coexisting domains of spatially coherent and incoherent dynamics. This counterintuitive phenomenon was first observed in systems of identical oscillators with symmetric coupling topology. Can one overcome these limitations? To address this question, we discuss the robustness of chimera states in networks of FitzHugh-Nagumo oscillators. Considering networks of inhomogeneous elements with regular coupling topology, and networks of identical elements with irregular coupling topologies, we demonstrate that chimera states are robust with respect to these perturbations, and analyze their properties as the inhomogeneities increase. We find that modifications of coupling topologies cause qualitative changes of chimera states: additional random links induce a shift of the stability regions in the system parameter plane, gaps in the connectivity matrix result in a change of the multiplicity of incoherent regions of the chimera state, and hierarchical geometry in the connectivity matrix induces nested coherent and incoherent regions.

nlin.AO↗

arXiv2012

Coupled Intermittent Maps Modelling the Statistics of Genomic Sequences: A Network Approach

The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range correlation features which are observed in the genomic sequences of higher eucaryotes. A weighted network approach to symbolic sequences is introduced and it is shown that coupled intermittent polynomial maps produce degree and link size distributions with power law exponents similar to the ones observed in real genomes. The proposed network approach to symbolic sequences is generic and can be applied to any symbol sequence (artificial or natural).

cond-mat.stat-mech↗

arXiv2011

Multifractal analysis of nonhyperbolic coupled map lattices: Application to genomic sequences

Symbolic sequences generated by coupled map lattices (CMLs) can be used to model the chaotic-like structure of genomic sequences. In this study it is shown that diffusively coupled Chebyshev maps of order 4 (corresponding to a shift of 4 symbols) very closely reproduce the multifractal spectrum $D_q$ of human genomic sequences for coupling constant $α=0.35\pm 0.01$ if $q>0$. The presence of rare configurations causes deviations for $q<0$, which disappear if the rare event statistics of the CML is modified. Such rare configurations are known to play specific functional roles in genomic sequences serving as promoters or regulatory elements.

nlin.CD↗