arXiv subjects

A. Provata

Publications and source records attributed to A. Provata.

16 recordsLinked to original sources

arXiv2024

Mechanisms for bump state localization in two-dimensional networks of leaky Integrate-and-Fire neurons

Networks of nonlocally coupled leaky Integrate-and-Fire neurons exhibit a variety of complex collective behaviors, such as partial synchronization, frequency or amplitude chimeras, solitary states and bump states. In particular, the bump states consist of one or many regions of asynchronous elements within a sea of subthreshold (quiescent) elements. The asynchronous domains travel in the network in a direction predetermined by the initial conditions. In the present study we investigate the occurrence of bump states in networks of leaky Integrate-and-Fire neurons in two-dimensions using nonlocal toroidal connectivity and we explore possible mechanisms for stabilizing the moving asynchronous domains. Our findings indicate that I) incorporating a refractory period can effectively anchor the position of these domains in the network, and II) the switching off of some randomly preselected nodes (i.e., making them permanently idle/inactive) can likewise contribute to stabilizing the positions of the asynchronous domains. In particular, in case II for large values of the coupling strength and a large percentage of idle elements, all nodes acquire different fixed (frozen) values in the quiescent region and oscillations cease throughout the network due to self-organization. For the special case of stationary bump states, we propose an analytical approach to predict their properties. This approach is based on the self-consistency argument and is valid for infinitely large networks. Case I is of particular biomedical interest in view of the importance of refractoriness for biological neurons, while case II can be biomedically relevant when designing therapeutic methods for stabilizing moving signals in the brain.

q-bio.NC↗

arXiv2022

Scattering-induced splitting of solitons in the discrete NLS equation with saturable nonlinearity

We study systematically the scattering of solitons on localized impurities in the discrete nonlinear Schr\"odinger (DNLS) equation with a saturable nonlinearity. We show that, apart from the generic scenario of the outcome of the scattering process, namely the emergence of a reflected and a transmitted soliton, other effects can occur. In particular, it is found that, in the case of an attractive impurity, a soliton trapped at the impurity can coexist with the reflected and transmitted ones. This effect, which resembles the behaviour of a quantum particle interacting with a narrow impurity, has not previously reported for discrete setting. Parameter regimes are explored for determining soliton splitting on the impurity with special attention to equal soliton splitting.

nlin.PS↗

arXiv2020

Structural anomalies in brain networks induce dynamical pacemaker effects

Dynamical effects on healthy brains and brains affected by tumor are investigated via numerical simulations. The brains are modeled as multilayer networks consisting of neuronal oscillators, whose connectivities are extracted from Magnetic Resonance Imaging (MRI) data. The numerical results demonstrate that the healthy brain presents chimera-like states where regions with high white matter concentrations in the direction connecting the two hemispheres act as the coherent domain, while the rest of the brain presents incoherent oscillations. To the contrary, in brains with destructed structure traveling waves are produced initiated at the region where the tumor is located. These areas act as the pacemaker of the waves sweeping across the brain. The numerical simulations are performed using two neuronal models: a) the FitzHugh-Nagumo model and b) the Leaky Integrate-and-Fire model. Both models give consistent results regarding the chimera-like oscillations in healthy brains and the pacemaker effect in the tumorous brains. These results are considered as a starting point for further investigation in the detection of tumors with small sizes before becoming discernible on the MRI recordings, as well as in tumor development and evolution.

nlin.AO↗

arXiv2020

Chimera states in ring-star network of Chua circuits

We investigate the emergence of amplitude and frequency chimera states in ring-star networks consisting of identical Chua circuits connected via nonlocal diffusive, bidirectional coupling. We first identify single-well chimera patterns in a ring network under nonlocal coupling schemes. When a central node is added to the network, forming a ring-star network, the central node acts as the distributor of information, increasing the chances of synchronization. Numerical simulations show that the radial coupling strength $k$ between the central and the peripheral nodes acts as an order parameter leading from a lower to a higher frequency domain. The transition between the domains takes place for intermediate coupling values, $0.5 <k< 2$, where the frequency chimera states prevail. The transition region (width and boundaries) depends on the Chua oscillator parameters and the network specifics. Potential applications of star connectivity can be found in the control of Chua networks and in other coupled chaotic dynamical systems. By adding one central node and without further modifications to the individual network parameters it is possible to entrain the system to lower or higher frequency domains as desired by the particular applications.

nlin.AO↗

arXiv2018

Synchronization patterns in LIF Neural Networks: Merging Nonlocal and Diagonal Connectivity

The effects of nonlocal and reflecting connectivities have been previously investigated in coupled Leaky Integrate-and-Fire (LIF) elements, which assimilate the exchange of electrical signals between neurons. In this work we investigate the effect of diagonal coupling inspired by findings in brain neuron connectivity. Multi-chimera states are reported both for the simple diagonal and combined nonlocal-diagonal connectivities and we determine the range of optimal parameter regions where chimera states appear. Overall, the measures of coherence indicate that as the coupling range increases (below all-to-all coupling) the emergence of chimera states is favoured and the mean phase velocity deviations between coherent and incoherent regions become more prominent. A number of novel synchronization phenomena are induced as a result of the combined connectivity. We record that for coupling strengths $σ< 1$ the synchronous regions have mean phase velocities lower than the asynchronous, while the opposite holds for $σ> 1$. In the intermediate regime, $σ\sim 1$, the oscillators have common mean phase velocity (i.e., are frequency-locked) but different phases (i.e., they are phase-asynchronous). Solitary states are recorded for small values of the coupling strength, which grow into chimera states as the coupling strength increases.We determine parameter values where the combined effects of nonlocal-diagonal coupling generate chimera states with two different levels of synchronous domains mediated by asynchronous regions.

nlin.PS↗

arXiv2018

Three-dimensional chimera patterns in networks of spiking neuron oscillators

We study the stable spatiotemporal patterns that arise in a 3D network of neuron oscillators, whose dynamics is described by the Leaky Integrate-and-Fire (LIF) model. More specifically, we investigate the form of the chimera states induced by a 3D coupling matrix with nonlocal topology. The observed patterns are in many cases direct generalizations of the corresponding 2D patterns, e.~g. spheres, layers and cylinder grids. We also find cylindrical and "cross-layered" chimeras that do not have an equivalent in 2D systems. Quantitative measures are calculated, such as the ratio of synchronized and unsynchronized neurons as a function of the coupling range, the mean phase velocities and the distribution of neurons in mean phase velocities. Based on these measures the chimeras are categorized in two families. The first family of patterns is observed for weaker coupling and exhibits higher mean phase velocities for the unsynchronized areas of the network. The opposite holds for the second family where the unsynchronized areas have lower mean phase velocities. The various measures demonstrate discontinuities, indicating criticality as the parameters cross from the first family of patterns to the second.

cond-mat.dis-nn↗

arXiv2016

Chimeras in Leaky Integrate-and-Fire Neural Networks: Effects of Reflecting Connectivities

The effects of nonlocal and reflecting connectivity are investigated in coupled Leaky Integrate-and-Fire (LIF) elements, which assimilate the exchange of electrical signals between neurons. Earlier investigations have demonstrated that non-local and hierarchical network connectivity often induces complex synchronization patterns and chimera states in systems of coupled oscillators. In the LIF system we show that if the elements are non-locally linked with positive diffusive coupling in a ring architecture the system splits into a number of alternating domains. Half of these domains contain elements, whose potential stays near the threshold, while they are interrupted by active domains, where the elements perform regular LIF oscillations. The active domains move around the ring with constant velocity, depending on the system parameters. The idea of introducing reflecting non-local coupling in LIF networks originates from signal exchange between neurons residing in the two hemispheres in the brain. We show evidence that this connectivity induces novel complex spatial and temporal structures: for relatively extensive ranges of parameter values the system splits in two coexisting domains, one domain where all elements stay near-threshold and one where incoherent states develop with multileveled mean phase velocity distribution.

nlin.PS↗

arXiv2015

Multi-chimera states in the Leaky Integrate-and-Fire model

We study the dynamics of identical leaky integrate-and-fire neurons with symmetric non-local coupling. Upon varying control parameters (coupling strength, coupling range, refractory period) we investigate the system's behaviour and highlight the formation of chimera states. We show that the introduction of a refractory period enlarges the parameter region where chimera states appear and affects the chimera multiplicity.

nlin.AO↗

arXiv2013

Abstract Phase-space Networks Describing Reactive Dynamics

An abstract network approach is proposed for the description of the dynamics in reactive processes. The phase space of the variables (concentrations in reactive systems) is partitioned into a finite number of segments, which constitute the nodes of the abstract network. Transitions between the nodes are dictated by the dynamics of the reactive process and provide the links between the nodes. These are weighted networks, since each link weight reflects the transition rate between the corresponding states-nodes. With this construction the network properties mirror the dynamics of the underlying process and one can investigate the system properties by studying the corresponding abstract network. As a working example the Lattice Limit Cycle (LLC) model is used. Its corresponding abstract network is constructed and the transition matrix elements are computed via Kinetic (Dynamic) Monte Carlo simulations. For this model it is shown that the degree distribution follows a power law with exponent -1, while the average clustering coefficient $c(N)$ scales with the network size (number of nodes) $N$ as $c(N)\sim N^{-ν}, ν\simeq 1.46$. The computed exponents classify the LLC abstract reactive network into the scale-free networks. This conclusion corroborates earlier investigations demonstrating the formation of fractal spatial patterns in LLC reactive dynamics due to stochasticity and to the clustering of homologous species. The present construction of abstract networks (based on the partition of the phase space) is generic and can be implemented with appropriate adjustments in many dynamical systems and in time series analysis.

cond-mat.stat-mech↗

arXiv2013

DNA viewed as an out-of-equilibrium structure

The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a low order Markov chain of order up to $r=6$. Although detailed balance seems to hold at the level of purine-pyrimidine notation it fails when all four basepairs are considered, suggesting spatial asymmetry and irreversibility. Furthermore, the block entropy does not increase linearly with the block size, reflecting the long range nature of the correlations in the human genomic sequences. To probe locally the spatial structure of the chain we study the exit distances from a specific symbol, the distribution of recurrence distances and the Hurst exponent, all of which show power law tails and long range characteristics. These results suggest that human DNA can be viewed as a non-equilibrium structure maintained in its state through interactions with a constantly changing environment. Based solely on the exit distance distribution accounting for the nonequilibrium statistics and using the Monte Carlo rejection sampling method we construct a model DNA sequence. This method allows to keep all long range and short range statistical characteristics of the original sequence. The model sequence presents the same characteristic exponents as the natural DNA but fails to capture point-to-point details.

q-bio.GN↗

arXiv2013

Effective Mean Field Approach to Kinetic Monte Carlo Simulations in Limit Cycle Dynamics with Reactive and Diffusive Rewiring

The dynamics of complex reactive schemes is known to deviate from the Mean Field (MF) theory when restricted on low dimensional spatial supports. This failure has been attributed to the limited number of species-neighbours which are available for interactions. In the current study, we introduce effective reactive parameters, which depend on the type of the spatial support and which allow for an effective MF description. As working example the Lattice Limit Cycle dynamics is used, restricted on a 2D square lattice with nearest neighbour interactions. We show that the MF steady state results are recovered when the kinetic rates are replaced with their effective values. The same conclusion holds when reactive stochastic rewiring is introduced in the system via long distance reactive coupling. Instead, when the stochastic coupling becomes diffusive the effective parameters no longer predict the steady state. This is attributed to the diffusion process which is an additional factor introduced into the dynamics and is not accounted for, in the kinetic MF scheme.

nlin.PS↗

arXiv2006

Coarse graining the Cyclic Lotka-Volterra Model: SSA and local maximum likelihood estimation

When the output of an atomistic simulation (such as the Gillespie stochastic simulation algorithm, SSA) can be approximated as a diffusion process, we may be interested in the dynamic features of the deterministic (drift) component of this diffusion. We perform traditional scientific computing tasks (integration, steady state and closed orbit computation, and stability analysis) on such a drift component using a SSA simulation of the Cyclic Lotka-Volterra system as our illustrative example. The results of short bursts of appropriately initialized SSA simulations are used to fit local diffusion models using Ait-Sahalia's transition density expansions \cite{ait2,aitECO,aitVEC} in a maximum likelihood framework. These estimates are then coupled with standard numerical algorithms (such as Newton-Raphson or numerical integration routines) to help design subsequent SSA experiments. A brief discussion of the validity of the local diffusion approximation of the SSA simulation (a jump process) is included.

cond-mat.stat-mech↗

arXiv2005

Non-extensive Trends in the Size Distribution of Coding and Non-coding DNA Sequences in the Human Genome

We study the primary DNA structure of four of the most completely sequenced human chromosomes (including chromosome 19 which is the most dense in coding), using Non-extensive Statistics. We show that the exponents governing the decay of the coding size distributions vary between $5.2 \le r \le 5.7$ for the short scales and $1.45 \le q \le 1.50$ for the large scales. On the contrary, the exponents governing the decay of the non-coding size distributions in these four chromosomes, take the values $2.4 \le r \le 3.2$ for the short scales and $1.50 \le q \le 1.72$ for the large scales. This quantitative difference, in particular in the tail exponent $q$, indicates that the non-coding (coding) size distributions have long (short) range correlations. This non-trivial difference in the DNA statistics is attributed to the non-conservative (conservative) evolution dynamics acting on the non-coding (coding) DNA sequences.

q-bio.GN↗

arXiv2004

Statistical analysis of Gene and Intergenic DNA Sequences

Much of the on-going statistical analysis of DNA sequences is focused on the estimation of characteristics of coding and non-coding regions that would possibly allow discrimination of these regions. In the current approach, we concentrate specifically on genes and intergenic regions. To estimate the level and type of correlation in these regions we apply various statistical methods inspired from nonlinear time series analysis, namely the probability distribution of tuplets, the Mutual Information and the Identical Neighbour Fit. The methods are suitably modified to work on symbolic sequences and they are first tested for validity on sequences obtained from well--known simple deterministic and stochastic models. Then they are applied to the DNA sequence of chromosome 1 of {\em arabidopsis thaliana}. The results suggest that correlations do exist in the DNA sequence but they are weak and that intergenic sequences tend to be more correlated than gene sequences. The use of statistical tests with surrogate data establish these findings in a rigorous statistical manner.

q-bio.GN↗

arXiv2003

Reactive dynamics on fractal sets: anomalous fluctuations and memory effects

We study the effect of fractal initial conditions in closed reactive systems in the cases of both mobile and immobile reactants. For the reaction $A+A\to A$, in the absence of diffusion, the mean number of particles $A$ is shown to decay exponentially to a steady state which depends on the details of the initial conditions. The nature of this dependence is demonstrated both analytically and numerically. In contrast, when diffusion is incorporated, it is shown that the mean number of particles $ $ decays asymptotically as $t^{-d_f/2}$, the memory of the initial conditions being now carried by the dynamical power law exponent. The latter is fully determined by the fractal dimension $d_f$ of the initial conditions.

cond-mat.stat-mech↗

arXiv2003

Nonextensivity of the cyclic Lattice Lotka Volterra model

We numerically show that the Lattice Lotka-Volterra model, when realized on a square lattice support, gives rise to a {\it finite} production, per unit time, of the nonextensive entropy $S_q= \frac{1- \sum_ip_i^q}{q-1}$ $(S_1=-\sum_i p_i \ln p_i)$. This finiteness only occurs for $q=0.5$ for the $d=2$ growth mode (growing droplet), and for $q=0$ for the $d=1$ one (growing stripe). This strong evidence of nonextensivity is consistent with the spontaneous emergence of local domains of identical particles with fractal boundaries and competing interactions. Such direct evidence is for the first time exhibited for a many-body system which, at the mean field level, is conservative.

cond-mat↗