Synergistic effect of repulsive inhibition in synchronization of excitatory networks

Breathing and switching cyclops states in Kuramoto networks with higher-mode coupling

Cyclops states are intriguing cluster patterns observed in oscillator networks, including neuronal ensembles. The concept of cyclops states formed by two distinct, coherent clusters and a solitary oscillator was introduced by Munyaev et al. [Phys. Rev. Lett. 130, 107201 (2023)0031-900710.1103/PhysRevLett.130.107201], where we explored the surprising prevalence of such states in repulsive Kuramoto networks of rotators with higher-mode harmonics in the coupling. This paper extends our analysis to understand the mechanisms responsible for destroying the cyclops' states and inducing dynamical patterns called breathing and switching cyclops states. We first analytically study the existence and stability of cyclops states in the Kuramoto-Sakaguchi networks of two-dimensional oscillators with inertia as a function of the second coupling harmonic. We then describe two bifurcation scenarios that give birth to breathing and switching cyclops states. We demonstrate that these states and their hybrids are prevalent across a wide coupling range and are robust against a relatively large intrinsic frequency detuning. Beyond the Kuramoto networks, breathing and switching cyclops states promise to strongly manifest in other physical and biological networks, including coupled theta neurons.

Stability and synchronization in neural network with delayed synaptic connections

In this paper, we investigate the stability of the synchronous state in a complex network using the master stability function technique. We use the extended Hindmarsh-Rose neuronal model including time delayed electrical, chemical, and hybrid couplings. We find the corresponding master stability equation that describes the whole dynamics for each coupling mode. From the maximum Lyapunov exponent, we deduce the stability state for each coupling mode. We observe that for electrical coupling, there exists a mixing between stable and unstable states. For a good setting of some system parameters, the position and the size of unstable areas can be modified. For chemical coupling, we observe difficulties in having a stable area in the complex plane. For hybrid coupling, we observe a stable behavior in the whole system compared to the case where these couplings are considered separately. The obtained results for each coupling mode help to analyze the stability state of some network topologies by using the corresponding eigenvalues. We observe that using electrical coupling can involve a full or partial stability of the system. In the case of chemical coupling, unstable states are observed whereas in the case of hybrid interactions a full stability of the network is obtained. Temporal analysis of the global synchronization is also done for each coupling mode, and the results show that when the network is stable, the synchronization is globally observed, while in the case when it is unstable, its nodes are not globally synchronized.

Cyclops States in Repulsive Kuramoto Networks: The Role of Higher-Order Coupling

Repulsive oscillator networks can exhibit multiple cooperative rhythms, including chimera and cluster splay states. Yet, understanding which rhythm prevails remains challenging. Here, we address this fundamental question in the context of Kuramoto-Sakaguchi networks of rotators with higher-order Fourier modes in the coupling. Through analysis and numerics, we show that three-cluster splay states with two distinct coherent clusters and a solitary oscillator are the prevalent rhythms in networks with an odd number of units. We denote such tripod patterns cyclops states with the solitary oscillator reminiscent of the Cyclops' eye. As their mythological counterparts, the cyclops states are giants that dominate the system's phase space in weakly repulsive networks with first-order coupling. Astonishingly, the addition of the second or third harmonics to the Kuramoto coupling function makes the cyclops states global attractors practically across the full range of coupling's repulsion. Beyond the Kuramoto oscillators, we show that this effect is robustly present in networks of canonical theta neurons with adaptive coupling. At a more general level, our results suggest clues for finding dominant rhythms in repulsive physical and biological networks.

Beyond the Bristol book: Advances and perspectives in non-smooth dynamics and applications

Non-smooth dynamics induced by switches, impacts, sliding, and other abrupt changes are pervasive in physics, biology, and engineering. Yet, systems with non-smooth dynamics have historically received far less attention compared to their smooth counterparts. The classic "Bristol book" [di Bernardo et al., Piecewise-smooth Dynamical Systems. Theory and Applications (Springer-Verlag, 2008)] contains a 2008 state-of-the-art review of major results and challenges in the study of non-smooth dynamical systems. In this paper, we provide a detailed review of progress made since 2008. We cover hidden dynamics, generalizations of sliding motion, the effects of noise and randomness, multi-scale approaches, systems with time-dependent switching, and a variety of local and global bifurcations. Also, we survey new areas of application, including neuroscience, biology, ecology, climate sciences, and engineering, to which the theory has been applied.

When multilayer links exchange their roles in synchronization

Real world networks contain multiple layers of links whose interactions can lead to extraordinary collective dynamics, including synchronization. The fundamental problem of assessing how network topology controls synchronization in multilayer networks remains open due to serious limitations of the existing stability methods. Towards removing this obstacle, we propose an approximation method which significantly enhances the predictive power of the master stability function for stable synchronization in multilayer networks. For a class of saddle-focus oscillators, including Rössler and piecewise linear systems, our method reduces the complex stability analysis to simply solving a set of linear algebraic equations. Using the method, we analytically predict surprising effects due to multilayer coupling. In particular, we prove that two coupling layers-one of which would alone hamper synchronization and the other would foster it-reverse their roles when used in a multilayer network. We also analytically demonstrate that increasing the size of a globally coupled layer, that in isolation would induce stable synchronization, makes the multilayer network unsynchronizable.

Stability of rotatory solitary states in Kuramoto networks with inertia

Solitary states emerge in oscillator networks when one oscillator separates from the fully synchronized cluster and oscillates with a different frequency. Such chimera-type patterns with an incoherent state formed by a single oscillator were observed in various oscillator networks; however, there is still a lack of understanding of how such states can stably appear. Here, we study the stability of solitary states in Kuramoto networks of identical two-dimensional phase oscillators with inertia and a phase-lagged coupling. The presence of inertia can induce rotatory dynamics of the phase difference between the solitary oscillator and the coherent cluster. We derive asymptotic stability conditions for such a solitary state as a function of inertia, network size, and phase lag that may yield either attractive or repulsive coupling. Counterintuitively, our analysis demonstrates that (1) increasing the size of the coherent cluster can promote the stability of the solitary state in the attractive coupling case and (2) the solitary state can be stable in small-size networks with all repulsive coupling. We also discuss the implications of our stability analysis for the emergence of rotatory chimeras.

Unbalanced clustering and solitary states in coupled excitable systems

We discover the mechanisms of emergence and the link between two types of symmetry-broken states, the unbalanced periodic two-cluster states and solitary states, in coupled excitable systems with attractive and repulsive interactions. The prevalent solitary states in non-locally coupled arrays, whose self-organization is based on successive (order preserving) spiking of units, derive their dynamical features from the corresponding unbalanced cluster states in globally coupled networks. Apart from the states with successive spiking, we also find cluster and solitary states where the interplay of excitability and local multiscale dynamics gives rise to so-called leap-frog activity patterns with an alternating order of spiking between the units. We show that the noise affects the system dynamics by suppressing the multistability of cluster states and by inducing pattern homogenization, transforming solitary states into patterns of patched synchrony.

Collective behavior in a two-layer neuronal network with time-varying chemical connections that are controlled by a Petri net

In this paper, we propose and study a two-layer network composed of a Petri net in the first layer and a ring of coupled Hindmarsh-Rose neurons in the second layer. Petri nets are appropriate platforms not only for describing sequential processes but also for modeling information circulation in complex systems. Networks of neurons, on the other hand, are commonly used to study synchronization and other forms of collective behavior. Thus, merging both frameworks into a single model promises fascinating new insights into neuronal collective behavior that is subject to changes in network connectivity. In our case, the Petri net in the first layer manages the existence of excitatory and inhibitory links among the neurons in the second layer, thereby making the chemical connections time-varying. We focus on the emergence of different types of collective behavior in the model, such as synchronization, chimeras, and solitary states, by considering different inhibitory and excitatory tokens in the Petri net. We find that the existence of only inhibitory or excitatory tokens disturbs the synchronization of electrically coupled neurons and leads toward chimera and solitary states.

A taxonomy of seizure dynamotypes

Seizures are a disruption of normal brain activity present across a vast range of species and conditions. We introduce an organizing principle that leads to the first objective Taxonomy of Seizure Dynamics (TSD) based on bifurcation theory. The ‘dynamotype’ of a seizure is the dynamic composition that defines its observable characteristics, including how it starts, evolves and ends. Analyzing over 2000 focal-onset seizures from multiple centers, we find evidence of all 16 dynamotypes predicted in TSD. We demonstrate that patients’ dynamotypes evolve during their lifetime and display complex but systematic variations including hierarchy (certain types are more common), non-bijectivity (a patient may display multiple types) and pairing preference (multiple types may occur during one seizure). TSD provides a way to stratify patients in complement to present clinical classifications, a language to describe the most critical features of seizure dynamics, and a framework to guide future research focused on dynamical properties.

Epileptic seizures have been recognized for centuries. But it was only in the 1930s that it was realized that seizures are the result of out-of-control electrical activity in the brain. By placing electrodes on the scalp, doctors can identify when and where in the brain a seizure begins. But they cannot tell much about how the seizure behaves, that is, how it starts, stops or spreads to other areas. This makes it difficult to control and prevent seizures. It also helps explain why almost a third of patients with epilepsy continue to have seizures despite being on medication.

Saggio, Crisp et al. have now approached this problem from a new angle using methods adapted from physics and engineering. In these fields, “dynamics research” has been used with great success to predict and control the behavior of complex systems like electrical power grids. Saggio, Crisp et al. reasoned that applying the same approach to the brain would reveal the dynamics of seizures and that such information could then be used to categorize seizures into groups with similar properties. This would in effect create for seizures what the periodic table is for the elements.

Applying the dynamics research method to seizure data from more than a hundred patients from across the world revealed 16 types of seizure dynamics. These “dynamotypes” had distinct characteristics. Some were more common than others, and some tended to occur together. Individual patients showed different dynamotypes over time. By constructing a way to classify seizures based on the relationships between the dynamotypes, Saggio, Crisp et al. provide a new tool for clinicians and researchers studying epilepsy.

Previous clinical tools have focused on the physical symptoms of a seizure (referred to as the phenotype) or its potential genetic causes (genotype). The current approach complements these tools by adding the dynamotype: how seizures start, spread and stop in the brain. This approach has the potential to lead to new branches of research and better understanding and treatment of seizures.

Synchronizability of directed networks: The power of non-existent ties

The understanding of how synchronization in directed networks is influenced by structural changes in network topology is far from complete. While the addition of an edge always promotes synchronization in a wide class of undirected networks, this addition may impede synchronization in directed networks. In this paper, we develop the augmented graph stability method, which allows for explicitly connecting the stability of synchronization to changes in network topology. The transformation of a directed network into a symmetrized-and-augmented undirected network is the central component of this new method. This transformation is executed by symmetrizing and weighting the underlying connection graph and adding new undirected edges with consideration made for the mean degree imbalance of each pair of nodes. These new edges represent "non-existent ties" in the original directed network and often control the location of critical nodes whose directed connections can be altered to manipulate the stability of synchronization in a desired way. In particular, we show that the addition of small-world shortcuts to directed networks, which makes "non-existent ties" disappear, can worsen the synchronizability, thereby revealing a destructive role of small-world connections in directed networks. An extension of our method may open the door to studying synchronization in directed multilayer networks, which cannot be effectively handled by the eigenvalue-based methods.

Synchronization of Rulkov neuron networks coupled by excitatory and inhibitory chemical synapses

This paper takes into account a neuron network model in which the excitatory and the inhibitory Rulkov neurons interact each other through excitatory and inhibitory chemical coupling, respectively. Firstly, for two or more identical or non-identical Rulkov neurons, the existence conditions of the synchronization manifold of the fixed points are investigated, which have received less attention over the past decades. Secondly, the master stability equation of the arbitrarily connected neuron network under the existence conditions of the synchronization manifold is discussed. Thirdly, taking three identical Rulkov neurons as an example, some new results are presented: (1) topological structures that can make the synchronization manifold exist are given, (2) the stability of synchronization when different parameters change is discussed, and (3) the roles of the control parameters, the ratio, as well as the size of the coupling strength and sigmoid function are analyzed. Finally, for the chemical coupling between two non-identical neurons, the transversal system is given and the effect of two coupling strengths on synchronization is analyzed.

When two wrongs make a right: synchronized neuronal bursting from combined electrical and inhibitory coupling

Synchronized cortical activities in the central nervous systems of mammals are crucial for sensory perception, coordination and locomotory function. The neuronal mechanisms that generate synchronous synaptic inputs in the neocortex are far from being fully understood. In this paper, we study the emergence of synchronization in networks of bursting neurons as a highly non-trivial, combined effect of electrical and inhibitory connections. We report a counterintuitive find that combined electrical and inhibitory coupling can synergistically induce robust synchronization in a range of parameters where electrical coupling alone promotes anti-phase spiking and inhibition induces anti-phase bursting. We reveal the underlying mechanism, which uses a balance between hidden properties of electrical and inhibitory coupling to act together to synchronize neuronal bursting. We show that this balance is controlled by the duty cycle of the self-coupled system which governs the synchronized bursting rhythm.This article is part of the themed issue 'Mathematical methods in medicine: neuroscience, cardiology and pathology'.

Spontaneous symmetry breaking due to the trade-off between attractive and repulsive couplings

Spontaneous symmetry breaking is an important phenomenon observed in various fields including physics and biology. In this connection, we here show that the trade-off between attractive and repulsive couplings can induce spontaneous symmetry breaking in a homogeneous system of coupled oscillators. With a simple model of a system of two coupled Stuart-Landau oscillators, we demonstrate how the tendency of attractive coupling in inducing in-phase synchronized (IPS) oscillations and the tendency of repulsive coupling in inducing out-of-phase synchronized oscillations compete with each other and give rise to symmetry breaking oscillatory states and interesting multistabilities. Further, we provide explicit expressions for synchronized and antisynchronized oscillatory states as well as the so called oscillation death (OD) state and study their stability. If the Hopf bifurcation parameter (λ) is greater than the natural frequency (ω) of the system, the attractive coupling favors the emergence of an antisymmetric OD state via a Hopf bifurcation whereas the repulsive coupling favors the emergence of a similar state through a saddle-node bifurcation. We show that an increase in the repulsive coupling not only destabilizes the IPS state but also facilitates the reentrance of the IPS state.

Finishing monkeypox genomes from short reads: assembly analysis and a neural network method

BACKGROUND

Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses, the emergence of monkeypox outbreaks in humans and the need to monitor potential malicious release of smallpox virus requires development of methods for rapid virus identification. Whole-genome sequencing (WGS) is an emergent technology with increasing application to the diagnosis of diseases and the identification of outbreak pathogens. But "finishing" such a genome is a laborious and time-consuming process, not easily automated. To date the large, complete poxvirus genomes have not been studied comprehensively in terms of applying WGS techniques and evaluating genome assembly algorithms.

RESULTS

To explore the limitations to finishing a poxvirus genome from short reads, we first analyze the repetitive regions in a monkeypox genome and evaluate genome assembly on the simulated reads. We also report on procedures and insights relevant to the assembly (from realistically short reads) of genomes. Finally, we propose a neural network method (namely Neural-KSP) to "finish" the process by closing gaps remaining after conventional assembly, as the final stage in a protocol to elucidate clinical poxvirus genomic sequences.

CONCLUSIONS

The protocol may prove useful in any clinical viral isolate (regardless if a reference-strain sequence is available) and especially useful in genomes confounded by many global and local repetitive sequences embedded in them. This work highlights the feasibility of finishing real, complex genomes by systematically analyzing genetic characteristics, thus remedying existing assembly shortcomings with a neural network method. Such finished sequences may enable clinicians to track genetic distance between viral isolates that provides a powerful epidemiological tool.

Imperfect traveling chimera states induced by local synaptic gradient coupling

In this paper, we report the occurrence of chimera patterns in a network of neuronal oscillators, which are coupled through local, synaptic gradient coupling. We discover a new chimera pattern, namely the imperfect traveling chimera state, where the incoherent traveling domain spreads into the coherent domain of the network. Remarkably, we also find that chimera states arise even for one-way local coupling, which is in contrast to the earlier belief that only nonlocal, global, or nearest-neighbor local coupling can give rise to chimera state; this find further relaxes the essential connectivity requirement of getting a chimera state. We choose a network of identical bursting Hindmarsh-Rose neuronal oscillators, and we show that depending upon the relative strength of the synaptic and gradient coupling, several chimera patterns emerge. We map all the spatiotemporal behaviors in parameter space and identify the transitions among several chimera patterns, an in-phase synchronized state, and a global amplitude death state.

Effects of self-coupling and asymmetric output on metastable dynamical transient firing patterns in arrays of neurons with bidirectional inhibitory coupling

Metastable dynamical transient patterns in arrays of bidirectionally coupled neurons with self-coupling and asymmetric output were studied. First, an array of asymmetric sigmoidal neurons with symmetric inhibitory bidirectional coupling and self-coupling was considered and the bifurcations of its steady solutions were shown. Metastable dynamical transient spatially nonuniform states existed in the presence of a pair of spatially symmetric stable solutions as well as unstable spatially nonuniform solutions in a restricted range of the output gain of a neuron. The duration of the transients increased exponentially with the number of neurons up to the maximum number at which the spatially nonuniform steady solutions were stabilized. The range of the output gain for which they existed reduced as asymmetry in a sigmoidal output function of a neuron increased, while the existence range expanded as the strength of inhibitory self-coupling increased. Next, arrays of spiking neuron models with slow synaptic inhibitory bidirectional coupling and self-coupling were considered with computer simulation. In an array of Class 1 Hindmarsh-Rose type models, in which each neuron showed a graded firing rate, metastable dynamical transient firing patterns were observed in the presence of inhibitory self-coupling. This agreed with the condition for the existence of metastable dynamical transients in an array of sigmoidal neurons. In an array of Class 2 Bonhoeffer-van der Pol models, in which each neuron had a clear threshold between firing and resting, long-lasting transient firing patterns with bursting and irregular motion were observed.

The role of asymmetrical and repulsive coupling in the dynamics of two coupled van der Pol oscillators

A system of two asymmetrically coupled van der Pol oscillators has been studied. We show that the introduction of a small asymmetry in coupling leads to the appearance of a "wideband synchronization channel" in the bifurcational structure of the parameter space. An increase of asymmetry and transition to repulsive interaction leads to the formation of multistability. As the result, the tip of the Arnold's tongue widens due to the formation of folds defined by saddle-node bifurcation curves for the limit cycles on the torus.

Chimera states in bursting neurons

We study the existence of chimera states in pulse-coupled networks of bursting Hindmarsh-Rose neurons with nonlocal, global, and local (nearest neighbor) couplings. Through a linear stability analysis, we discuss the behavior of the stability function in the incoherent (i.e., disorder), coherent, chimera, and multichimera states. Surprisingly, we find that chimera and multichimera states occur even using local nearest neighbor interaction in a network of identical bursting neurons alone. This is in contrast with the existence of chimera states in populations of nonlocally or globally coupled oscillators. A chemical synaptic coupling function is used which plays a key role in the emergence of chimera states in bursting neurons. The existence of chimera, multichimera, coherent, and disordered states is confirmed by means of the recently introduced statistical measures and mean phase velocity.