arXiv subjects

Hiroshi Kori

Publications and source records attributed to Hiroshi Kori.

At least 55 records · Page 3Linked to original sources

arXiv2016

A Simple Generic Model of Cellular Polarity Alignment: Derivation and Analysis

Ordered polarity alignment of a cell population plays a vital role in biology, such as in hair follicle alignment and asymmetric cell division. Here, we propose a theoretical framework for the understanding of generic dynamical properties of polarity alignment in interacting cellular units, where each cell is described by a reaction-diffusion system and the cells further interact with one another through their proximal surfaces. The system behavior is shown to be strongly dependent on geometric properties such as cell alignment and cell shape. Using a perturbative method under the assumption of weak coupling between cells, we derive a reduced model in which each cell is described by just one variable, the phase. The reduced model resembles an XY model but contains novel terms that possesses geometric information, which enables the understanding of the geometric dependencies as well as the effects of external signal and noise. The model is simple, generic, and analytically and numerically tractable, and is therefore expected to facilitates studies on cellular polarity alignment in various nonequilibrium systems.

nlin.PS↗

arXiv2016

Energetics of synchronization in coupled oscillators rotating on circular trajectories

We derive a concise and general expression of the energy dissipation rate for coupled oscillators rotating on circular trajectories by unifying the nonequilibrium aspects with the nonlinear dynamics via stochastic thermodynamics. In the framework of phase oscillator models, it is known that the even and odd parts of the coupling function express the effect on collective and relative dynamics, respectively. We reveal that the odd part always decreases the dissipation upon synchronization, while the even part yields a characteristic square-root change of the dissipation near the bifurcation point whose sign depends on the specific system parameters. We apply our theory to hydrodynamically coupled Stokes spheres rotating on circular trajectories that can be interpreted as a simple model of synchronization of coupled oscillators in a biophysical system. We show that the coupled Stokes spheres gain the ability to do more work on the surrounding fluid as the degree of phase synchronization increases.

nlin.AO↗

arXiv2016

Synchronization failure caused by interplay between noise and network heterogeneity

We investigate synchronization in complex networks of noisy phase oscillators. We find that, while too weak a coupling is not sufficient for the whole system to synchronize, too strong a coupling induces a nontrivial type of phase slip among oscillators, resulting in synchronization failure. Thus, an intermediate coupling range for synchronization exists, which becomes narrower when the network is more heterogeneous. Analyses of two noisy oscillators reveal that nontrivial phase slip is a generic phenomenon when noise is present and coupling is strong. Therefore, the low synchronizability of heterogeneous networks can be understood as a result of the difference in effective coupling strength among oscillators with different degrees; oscillators with high degrees tend to undergo phase slip while those with low degrees have weak coupling strengths that are insufficient for synchronization.

nlin.AO↗

arXiv2015

Exponential system-size dependence of the lifetime of transient spiral chaos in excitable and oscillatory media

Excitable media can develop spiral chaos, in which the number of spirals changes chaotically with time. Depending on parameter values in dynamical equations, spiral chaos may permanently persist or spontaneously arrive at a steady state after a transient time, referred to as the lifetime. Previous numerical studies have demonstrated that the lifetime of transient spiral chaos increases exponentially with system size to a good approximation. In this study, using the fact that the number of spirals obeys a Gaussian distribution, we provide a general expression for the system size dependence of the lifetime for large system sizes, which is indeed exponential. We confirm that the expression is in good agreement with numerically obtained lifetimes for both excitable and oscillatory media with parameter sets near the onset of transient chaos. The expression we develop for the lifetime is expected to be useful for predicting lifetimes in large systems.

nlin.CD↗

arXiv2015

Reentrant transition in coupled noisy oscillators

We report on a novel type of instability observed in a noisy oscillator unidirectionally coupled to a pacemaker. Using a phase oscillator model, we find that, as the coupling strength is increased, the noisy oscillator lags behind the pacemaker more frequently and the phase slip rate increases, which may not be observed in averaged phase models such as the Kuramoto model. Investigation of the corresponding Fokker-Planck equation enables us to obtain the reentrant transition line between the synchronized state and the phase slip state. We verify our theory using the Brusselator model, suggesting that this reentrant transition can be found in a wide range of limit cycle oscillators.

nlin.AO↗

arXiv2014

Clustering in Globally Coupled Oscillators Near a Hopf Bifurcation: Theory and Experiments

A theoretical analysis is presented to show the general occurrence of phase clusters in weakly, globally coupled oscillators close to a Hopf bifurcation. Through a reductive perturbation method, we derive the amplitude equation with a higher order correction term valid near a Hopf bifurcation point. This amplitude equation allows us to calculate analytically the phase coupling function from given limit-cycle oscillator models. Moreover, using the phase coupling function, the stability of phase clusters can be analyzed. We demonstrate our theory with the Brusselator model. Experiments are carried out to confirm the presence of phase clusters close to Hopf bifurcations with electrochemical oscillators.

nlin.AO↗

arXiv2013

Coarse-grained description of general oscillator networks

We propose a novel and systematic method for coarse-graining oscillator networks described by phase equations. Our coarse-graining method enables us to obtain the closed coarse-grained equations for a few effective eigenmodes, which is based on the eigenvalue problem of the linearized system around the phase-locked solution and a nonlinear transformation. We demonstrate our method by applying it to oscillator dynamics on a random graph, which exhibits a saddle-node bifurcation at the bifurcation point.

nlin.AO↗

arXiv2013

Period Variability of Coupled Noisy Oscillators

Period variability, quantified by the standard deviation (SD) of the cycle-to-cycle period, is investigated for noisy phase oscillators. We define the checkpoint phase as the beginning/end point of one oscillation cycle and derive an expression for the SD as a function of this phase. We find that the SD is dependent on the checkpoint phase only when oscillators are coupled. The applicability of our theory is verified using a realistic model. Our work clarifies the relationship between period variability and synchronization from which valuable information regarding coupling can be inferred.

physics.bio-ph↗

arXiv2012

Formation of feedforward networks and frequency synchrony by spike-timing-dependent plasticity

Spike-timing-dependent plasticity (STDP) with asymmetric learning windows is commonly found in the brain and useful for a variety of spike-based computations such as input filtering and associative memory. A natural consequence of STDP is establishment of causality in the sense that a neuron learns to fire with a lag after specific presynaptic neurons have fired. The effect of STDP on synchrony is elusive because spike synchrony implies unitary spike events of different neurons rather than a causal delayed relationship between neurons. We explore how synchrony can be facilitated by STDP in oscillator networks with a pacemaker. We show that STDP with asymmetric learning windows leads to self-organization of feedforward networks starting from the pacemaker. As a result, STDP drastically facilitates frequency synchrony. Even though differences in spike times are lessened as a result of synaptic plasticity, the finite time lag remains so that perfect spike synchrony is not realized. In contrast to traditional mechanisms of large-scale synchrony based on mutual interaction of coupled neurons, the route to synchrony discovered here is enslavement of downstream neurons by upstream ones. Facilitation of such feedforward synchrony does not occur for STDP with symmetric learning windows.

q-bio.NC↗

arXiv2012

Traveling and pinned fronts in bistable reaction-diffusion systems on network

Traveling fronts and stationary localized patterns in bistable reaction-diffusion systems have been broadly studied for classical continuous media and regular lattices. Analogs of such non-equilibrium patterns are also possible in networks. Here, we consider traveling and stationary patterns in bistable one-component systems on random Erdös-Rényi, scale-free and hierarchical tree networks. As revealed through numerical simulations, traveling fronts exist in network-organized systems. They represent waves of transition from one stable state into another, spreading over the entire network. The fronts can furthermore be pinned, thus forming stationary structures. While pinning of fronts has previously been considered for chains of diffusively coupled bistable elements, the network architecture brings about significant differences. An important role is played by the degree (the number of connections) of a node. For regular trees with a fixed branching factor, the pinning conditions are analytically determined. For large Erdös-Rényi and scale-free networks, the mean-field theory for stationary patterns is constructed.

nlin.PS↗

arXiv2011

Structure of Cell Networks Critically Determines Oscillation Regularity

Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously oscillatory cells. Such biological rhythms have notable periodicity despite the internal and external noise present in each cell. Previous experimental studies indicate that the regularity of oscillatory dynamics is enhanced when noisy oscillators interact and become synchronized. This effect, called the collective enhancement of temporal precision, has been studied theoretically using particular assumptions. In this study, we propose a general theoretical framework that enables us to understand the dependence of temporal precision on network parameters including size, connectivity, and coupling intensity; this effect has been poorly understood to date. Our framework is based on a phase oscillator model that is applicable to general oscillator networks with any coupling mechanism if coupling and noise are sufficiently weak. In particular, we can manage general directed and weighted networks. We quantify the precision of the activity of a single cell and the mean activity of an arbitrary subset of cells. We find that, in general undirected networks, the standard deviation of cycle-to-cycle periods scales with the system size $N$ as $1/\sqrt{N}$, but only up to a certain system size $N^*$ that depends on network parameters. Enhancement of temporal precision is ineffective when $N>N^*$. We also reveal the advantage of long-range interactions among cells to temporal precision.

q-bio.CB↗

arXiv2010

Dynamics-based centrality for general directed networks

Determining the relative importance of nodes in directed networks is important in, for example, ranking websites, publications, and sports teams, and for understanding signal flows in systems biology. A prevailing centrality measure in this respect is the PageRank. In this work, we focus on another class of centrality derived from the Laplacian of the network. We extend the Laplacian-based centrality, which has mainly been applied to strongly connected networks, to the case of general directed networks such that we can quantitatively compare arbitrary nodes. Toward this end, we adopt the idea used in the PageRank to introduce global connectivity between all the pairs of nodes with a certain strength. Numerical simulations are carried out on some networks. We also offer interpretations of the Laplacian-based centrality for general directed networks in terms of various dynamical and structural properties of networks. Importantly, the Laplacian-based centrality defined as the stationary density of the continuous-time random walk with random jumps is shown to be equivalent to the absorption probability of the random walk with sinks at each node but without random jumps. Similarly, the proposed centrality represents the importance of nodes in dynamics on the original network supplied with sinks but not with random jumps.

physics.soc-ph↗

arXiv2010

Collective fluctuations in networks of noisy components

Collective dynamics result from interactions among noisy dynamical components. Examples include heartbeats, circadian rhythms, and various pattern formations. Because of noise in each component, collective dynamics inevitably involve fluctuations, which may crucially affect functioning of the system. However, the relation between the fluctuations in isolated individual components and those in collective dynamics is unclear. Here we study a linear dynamical system of networked components subjected to independent Gaussian noise and analytically show that the connectivity of networks determines the intensity of fluctuations in the collective dynamics. Remarkably, in general directed networks including scale-free networks, the fluctuations decrease more slowly with the system size than the standard law stated by the central limit theorem. They even remain finite for a large system size when global directionality of the network exists. Moreover, such nontrivial behavior appears even in undirected networks when nonlinear dynamical systems are considered. We demonstrate it with a coupled oscillator system.

physics.bio-ph↗

arXiv2010

Synchronization Transition of Identical Phase Oscillators in a Directed Small-World Network

We numerically study a directed small-world network consisting of attractively coupled, identical phase oscillators. While complete synchronization is always stable, it is not always reachable from random initial conditions. Depending on the shortcut density and on the asymmetry of the phase coupling function, there exists a regime of persistent chaotic dynamics. By increasing the density of shortcuts or decreasing the asymmetry of the phase coupling function, we observe a discontinuous transition in the ability of the system to synchronize. Using a control technique, we identify the bifurcation scenario of the order parameter. We also discuss the relation between dynamics and topology and remark on the similarity of the synchronization transition to directed percolation.

cond-mat.dis-nn↗

arXiv2010

Phase synchronization between collective rhythms of globally coupled oscillator groups: noiseless non-identical case

Phase synchronization between collective oscillations exhibited by two weakly interacting groups of non-identical phase oscillators with internal and external global sinusoidal coupling of the groups is analyzed theoretically. Coupled amplitude equations describing the collective oscillations of the oscillator groups are obtained by using the Ott-Antonsen ansatz, and then coupled phase equations for the collective oscillations are derived by phase reduction of the amplitude equations. The collective phase coupling function, which determines the dynamics of macroscopic phase differences between the groups, is calculated analytically. It is demonstrated that the groups can exhibit effective anti-phase collective synchronization even if the microscopic external coupling between individual oscillator pairs belonging to different groups is in-phase, and similarly effective in-phase collective synchronization in spite of microscopic anti-phase external coupling between the groups.

nlin.AO↗

arXiv2010

Phase synchronization between collective rhythms of globally coupled oscillator groups: noisy identical case

We theoretically investigate collective phase synchronization between interacting groups of globally coupled noisy identical phase oscillators exhibiting macroscopic rhythms. Using the phase reduction method, we derive coupled collective phase equations describing the macroscopic rhythms of the groups from microscopic Langevin phase equations of the individual oscillators via nonlinear Fokker-Planck equations. For sinusoidal microscopic coupling, we determine the type of the collective phase coupling function, i.e., whether the groups exhibit in-phase or anti-phase synchronization. We show that the macroscopic rhythms can exhibit effective anti-phase synchronization even if the microscopic phase coupling between the groups is in-phase, and vice versa. Moreover, near the onset of collective oscillations, we analytically obtain the collective phase coupling function using center-manifold and phase reductions of the nonlinear Fokker-Planck equations.

nlin.AO↗

arXiv2010

Noise-Induced Synchronization of a Large Population of Globally Coupled Nonidentical Oscillators

We study a large population of globally coupled phase oscillators subject to common white Gaussian noise and find analytically that the critical coupling strength between oscillators for synchronization transition decreases with an increase in the intensity of common noise. Thus, common noise promotes the onset of synchronization. Our prediction is confirmed by numerical simulations of the phase oscillators as well as of limit-cycle oscillators.

nlin.AO↗

arXiv2009

Impact of hierarchical modular structure on ranking of individual nodes in directed networks

Many systems, ranging from biological and engineering systems to social systems, can be modeled as directed networks, with links representing directed interaction between two nodes. To assess the importance of a node in a directed network, various centrality measures based on different criteria have been proposed. However, calculating the centrality of a node is often difficult because of the overwhelming size of the network or the incomplete information about the network. Thus, developing an approximation method for estimating centrality measures is needed. In this study, we focus on modular networks; many real-world networks are composed of modules, where connection is dense within a module and sparse across different modules. We show that ranking-type centrality measures including the PageRank can be efficiently estimated once the modular structure of a network is extracted. We develop an analytical method to evaluate the centrality of nodes by combining the local property (i.e., indegree and outdegree of nodes) and the global property (i.e., centrality of modules). The proposed method is corroborated with real data. Our results provide a linkage between the ranking-type centrality values of modules and those of individual nodes. They also reveal the hierarchical structure of networks in the sense of subordination (not nestedness) laid out by connectivity among modules of different relative importance. The present study raises a novel motive of identifying modules in networks.

physics.soc-ph↗