arXiv subjects

Takashi Shimada

Publications and source records attributed to Takashi Shimada.

At least 19 recordsLinked to original sources

arXiv2026

Enhanced robustness of evolving systems with bipartite topology

Evolving open systems, in which new entities are continually introduced and those turning unfit go extinct, exhibit a phase transition between a diverging phase, where the system size grows indefinitely, and a finite phase, where it remains bounded. We show that imposing a bipartite interaction topology alone leaves this transition unchanged when the two partitions are introduced with equal initial connectivity. In contrast, when the initial degrees are asymmetric, the robustness of the system is markedly enhanced such that the transition shifts to higher connectivity and the diverging phase persists even when both initial degrees individually exceed the critical point of the corresponding unstructured system. In addition, we find a re-entrant transition, i.e. a return to the diverging phase as asymmetry is increased while the initial degree of one of the partitions is fixed, making it lying entirely outside the original mean-field picture. An extended mean-field analysis identifies the origin of these effects such that in the asymmetric regime, a feedback between the bipartite handshaking constraint and different extinction rates drives the mean degree of emergent network far above the initially assigned connectivity. This degree elevation suppresses extinction probabilities across the community while simultaneously concentrating extinctions among recently introduced, low-degree nodes. The interplay of these two effects constitutes a simple and universal robustness mechanism for evolving systems with asymmetric bipartite structure.

nlin.AO↗

arXiv2026

Cross-feeding yields high-dimensional chaos and coexistence of species beyond exclusion principle

Species interactions through cross-feeding via leakage and uptake of chemicals are important in microbial communities, and play an essential role in the coexistence of diverse species. Here, we study a simple dynamical model of a microbial community in which species interact by competing for the uptake of common metabolites that are leaked by other species. The model includes coupled dynamics of species populations and chemical concentrations in the medium, allowing for a variety of uptake and leakage networks among species. Depending on the structure of these networks, the system exhibits different attractors, including fixed points, limit cycles, low-dimensional chaos, and high-dimensional chaos. In the fixed-point and limit-cycle cases, the number of coexisting species is bounded by the number of exchangeable chemicals, consistent with the well-known competitive exclusion principle. In contrast, in the low-dimensional chaotic regime, the number of coexisting species exhibits noticeable but limited excess over this limit. Remarkably, in the high-dimensional chaotic regime, a much larger number of species beyond this limit coexist persistently over time. In this case, the rank-abundance distribution is broader than exponential, as often observed in real ecosystems. The population dynamics displays intermittent switching among quasi-stationary states, while the chemical dynamics explore most of the high dimensions. We find that such high-dimensional chaos is ubiquitous when the number of uptake chemicals is moderately larger than the number of leaked chemicals. Our results identify high-dimensional chaos with intermittent switching as a generic dynamical mechanism that stabilizes coexistence in interacting systems. We discuss its relevance to sustaining diverse microbial communities with leak-uptake cross-feeding.

physics.bio-ph↗

arXiv2026

Convergence criteria for self-consistent measures in bipartite networks

Many quantities that characterize network elements are defined in an explicit form and calculated directly from the network structure; examples of include several centrality measures like degree, closeness, or betweenness. However, there are also implicitly defined quantitative measures, which are usually calculated iteratively, in a self-consistent manner, like PageRank or countries' fitness / products' complexity relations. The iteration algorithms involve calculations over the entire network; therefore, their convergence properties depend on the structure of the network. Here, we focus on investigating self-consistently defined quantities in bipartite networks of two sets of nodes where the quantities in one set are determined by the quantities in the other set and vice versa. We derive an explicit convergence criterion for iterations of these quantities and describe two different approaches to improve the convergence properties. In the first one, we identify "problematic nodes" that can be removed or merged while in the second one, we introduce a regularization scheme and show how to estimate the regularization parameter.

physics.soc-ph↗

arXiv2025

Exact cluster dynamics of indirect reciprocity in complete graphs

Heider's balance theory emphasizes cognitive consistency in assessing others, as is expressed by ``The enemy of my enemy is my friend.'' At the same time, the theory of indirect reciprocity provides us with a dynamical framework to study how to assess others based on their actions as well as how to act toward them based on the assessments. Well known are the ``leading eight'' from L1 to L8, the eight norms for assessment and action to foster cooperation in social dilemmas while resisting the invasion of mutant norms prescribing alternative actions. In this work, we begin by showing that balance is equivalent to stationarity of dynamics only for L4 and L6 (stern judging) among the leading eight. Stern judging reflects an intuitive idea that good merits reward whereas evil warrants punishment. By analyzing the dynamics of Stern Judging in complete graphs, we prove that this norm almost always segregates the graph into two mutually hostile groups as the graph size grows. We then compare L4 with stern judging: The only difference of L4 is that a good player's cooperative action toward a bad one is regarded as good. This subtle difference transforms large populations governed by L4 to a ``paradise'' where cooperation prevails and positive assessments abound. Our study thus helps us understand the relationship between individual norms and their emergent consequences at a population level, shedding light on the nuanced interplay between cognitive consistency and segregation dynamics.

physics.soc-ph↗

arXiv2025

Controlling sternness in judging a good person who helps the bad

Recent studies on indirect reciprocity with private assessment on complete graphs suggest the possibility that one can continuously modulate the degree of segregation by controlling how to judge a good person helping a bad one. A well-known social norm called L6 judges it as bad, which eventually segregates the society into two antagonistic clusters, but if it is judged as good, the system reaches paradise where everyone likes each other. In this work, we numerically study this transition between segregation and paradise in two different settings. Firstly, in a uniform population of size $N$ where everyone regards such a donor as good with probability $p$ and bad with $1-p$, we observe paradise when $Np$ is sufficiently greater than $O(1)$. In contrast, in a heterogeneous setting where only $k$ individuals judge such a donor as good, the size difference of the clusters increases almost linearly as $k$ increases, so paradise can only be reached as $k \to N$ in a large population. Therefore, when an urgent change is needed to overcome the segregation due to L6, a small change in each and every individual's behavior is more efficient than a radical change in a fraction of the population.

physics.soc-ph↗

arXiv2025

Indirect reciprocity as a dynamics for weak balance

A social network is often divided into many factions. People are friends within each faction, while they are enemies of the other factions, and even my enemy's enemy is not necessarily my friend. This configuration can be described in terms of a weak form of structural balance. Although weak balance explains a number of real social networks, which dynamical rule achieves it has remained relatively unexplored. In this work, we show that the answer can be found in the field of indirect reciprocity, which assumes that people assess each other's behavior and choose how to behave to others based on the assessment according to a social norm. We begin by showing that weak structural balance is equivalent to stationarity when the rule is given by a norm called `judging'. By analyzing its cluster dynamics of merging, fission, and migration induced by assessment error in complete graphs, we obtain the cluster size distribution in a steady state, which shows the coexistence of a giant cluster and smaller ones. This study suggests that indirect reciprocity can provide insight into the interplay between a norm that individuals abide by and the macroscopic group structure in society.

physics.soc-ph↗

arXiv2024

Simple measures to capture the robustness and the plasticity of soil microbial communities

Soil microbial communities are known to be robust against perturbations such as nutrition inputs, which appears as an obstacle for the soil improvement. On the other hand, its adaptable aspect has been also reported. Here we propose simple measures for these seemingly contradicting features of soil microbial communities, robustness and plasticity, based on the distribution of the populations. The first measure is the similarity in the population balance, i.e. the shape of the distribution function, which is found to show resilience against the nutrition inputs. The other is the similarity in the composition of the species measured by the rank order of the population, which shows an adaptable response during the population balance is recovering. These results clearly show that the soil microbial system is robust (or, homeostatic) in its population balance, while the composition of the species is rather plastic and adaptable.

q-bio.PE↗

arXiv2024

Characterizing limit order books in call auctions of a stock market

Statistical and dynamical characters of stock markets have been extensively studied, which now is providing the firm basis for econophysics and its application as ``stylized facts''. However, most of those studies are for markets under the continuous auction, i.e. trades are executed sequentially. There has been less research on another major type of auction, call auctions, where orders are accumulated and those are executed at once in the final moment. This study focuses on the structure of the limit order books of stocks under the call auctions. Using the data of all stocks listed in the Tokyo Stock Exchange, we find that the shape of the limit order books in call auctions are well fitted by a simple functional form of hyperbolic tangent. From the fitting, we define the ``median spread'' and the ``width'' of limit orders. The ratio of the ``width'' to the ``median spread'' of most stocks are found to be similar, indicating that the execution ratio (the trading volume relative to the total number of orders) are nearly equal among them. Furthermore, the deviation in this ratio from the majority is found to be a good indicator for finding the stocks of the companies making outstanding profit. Our results demonstrate that those parameters of the structure of the limit order book well characterizes the states of the market under call auctions.

physics.soc-ph↗

arXiv2023

A simple model of edit activity in Wikipedia

A simple dynamical model of collective edit activity of Wikipedia articles and their content evolution is introduced. Based on the recent empirical findings, each editor in the model is characterized by an ability to make content edit, i.e., improving the article by adding content and a tendency to make maintenance edit, i.e., dealing with formal aspects and maintaining the edit flow. In addition, each article is characterized by a level of maturity as compared to a potential quality needed to comprehensively cover its topic. This model is found to reproduce the basic structure of the bipartite network between editors and articles of Wikipedia. Furthermore, the relation between the model parameters of editors and articles and the metrics of those calculated from the emergent network turns out to be robust, i.e. depending only on the rate of the introduction of new articles to the editing activity. This results provides us a way to relate observations in the real data to the hidden characteristics of editors and articles. For the nestedness of the networks, systems with weighted parameter distribution gives better match to the empirical one. This suggests the importance of high-dimensional nature of the ability of editors and quality of articles in the real system.

physics.soc-ph↗

arXiv2022

Invasion and Interaction Determine Population Composition in an Open Evolving System

It is well-known that interactions between species determine the population composition in an ecosystem. Conventional studies have focused on fixed population structures to reveal how interactions shape population compositions. However, interaction structures are not fixed, but change over time due to invasions. Thus, invasion and interaction play an important role in shaping communities. Despite its importance, however, the interplay between invasion and interaction has not been well explored. Here, we investigate how invasion affects the population composition with interactions in open evolving systems considering generalized Lotka-Volterra-type dynamics. Our results show that the system has two distinct regimes. One is characterized by low diversity with abrupt changes of dominant species in time, appearing when the interaction between species is strong and invasion slowly occurs. On the other hand, frequent invasions can induce higher diversity with slow changes in abundances despite strong interactions. It is because invasion happens before the system reaches its equilibrium, which drags the system from its equilibrium all the time. All species have similar abundances in this regime, which implies that fast invasion induces regime shift. Therefore, whether invasion or interaction dominates determines the population composition.

q-bio.PE↗

arXiv2021

Ecology in the digital world of Wikipedia

Wikipedia, a paradigmatic example of online knowledge space is organized in a collaborative, bottom-up way with voluntary contributions, yet it maintains a level of reliability comparable to that of traditional encyclopedias. The lack of selected professional writers and editors makes the judgement about quality and trustworthiness of the articles a real challenge. Here we show that a self-consistent metrics for the network defined by the edit records captures well the character of editors' activity and the articles' level of complexity. Using our metrics, one can better identify the human-labeled high-quality articles, e.g., "featured" ones, and differentiate them from the popular and controversial articles. Furthermore, the dynamics of the editor-article system is also well captured by the metrics, revealing the evolutionary pathways of articles and diverse roles of editors. We demonstrate that the collective effort of the editors indeed drives to the direction of article improvement.

physics.soc-ph↗

arXiv2021

Balanced-imbalanced transitions in indirect reciprocity dynamics on networks

Here we investigate the dynamics of indirect reciprocity on networks, a type of social dynamics in which the attitude of individuals, either cooperative or antagonistic, toward other individuals changes over time by their actions and mutual monitoring. We observe an absorbing state phase transition as we change the network's link or edge density. When the edge density is either small or large enough, opinions quickly reach an absorbing state, from which opinions never change anymore once reached. In contrast, if the edge density is in the middle range the absorbing state is not reached and the state keeps changing thus being active. The result shows a novel effect of social networks on spontaneous group formation.

physics.soc-ph↗

arXiv2020

On the relation between active population and infection rate of COVID-19

The relation between the number of passengers in the main stations and the infection rate of COVID19 in Tokyo is empirically studied. Our analysis based on conventional compartment model suggests: 1) Average time from the true day of infection to the day the infections are reported is about $15$ days. 2) The scaling relation between the density of active population and the infection rate suggests that the increase of infection rate is linear to the active population rather than quadratic, as that is assumed in the conventional SIR model. 3) Notable deviations from the overall scaling relation seems to correspond to the change of the peoples's behavior in response to the public announcements of action regulation.

physics.soc-ph↗

arXiv2018

Temporal inactivation enhances robustness in an evolving system

We study the robustness of an evolving system that is driven by successive inclusions of new elements or constituents with $m$ random interactions to older ones. Each constitutive element in the model stays either active or is temporarily inactivated depending upon the influence of the other active elements. If the time spent by an element in the inactivated state reaches $T_W$, it gets extinct. The phase diagram of this dynamic model as a function of $m$ and $T_W$ is investigated by numerical and analytical methods and as a result both growing (robust) as well as non-growing (volatile) phases are identified. It is also found that larger time limit $T_W$ enhances the system's robustness against the inclusion of new elements, mainly due to the system's increased ability to reject "falling-together" type attacks. Our results suggest that the ability of an element to survive in an unfavorable situation for a while, either as a minority or in a dormant state, could improve the robustness of the entire system.

nlin.AO↗

arXiv2017

Enhanced robustness of evolving open systems by the bidirectionality of interactions between elements

Living organisms, ecosystems, and social systems are examples of complex systems in which robustness against inclusion of new elements is an essential feature. A recently proposed simple model has revealed a general mechanism by which such systems can become robust against inclusion of elements with random interactions when the elements have a moderate number of links. This happens as a result of two opposing effects such that while the inclusion of elements with more interactions makes each individual element more robust against disturbances, it also increases the net impact of the loss of any element in the system. The interaction is, however, in many systems often intrinsically bidirectional like for mutual symbiosis, competition in ecology, and the action-reaction law of Newtonian mechanics, etc. This study reports the strong reinforcement effect of the bidirectionality of the interactions on the robustness of evolving systems. We show that the system with purely bidirectional interactions can grow with two-fold average degree, in comparison with the purely unidirectional system. This drastic shift of the transition point comes from the reinforcement of each node, not from a change in structure of the emergent system. For systems with partially bidirectional interactions we find that the area of the growing phase gets expanded. In the dense interaction regime, there exists an optimum proportion of bidirectional interactions for the growth rate at around $1/3$. In the sparsely connected systems, small but finite fraction of bidirectional links can change the system's behaviour from non-growing to growing behaviour.

nlin.AO↗

arXiv2016

The effect of laziness in chasers in group chase and escape model

The effect of laziness in the group chase and escape problem is studied using a simple model. The laziness is introduced as random walks in two ways: uniformly and in a "division of labor" way. It is shown that, while the former is always ineffective, the latter can improve the efficiency of catching, through the formation of pincer attack configuration by diligent and lazy chasers.

nlin.AO↗

arXiv2016

Order-disorder transition in repulsive self-propelled particle systems

We study the collective dynamics of repulsive self-propelled particles. The particles are governed by coupled equations of motion that include polar self-propulsion, damping of velocity and of polarity, repulsive particle-particle interaction, and deterministic dynamics. Particle dynamics simulations show that the collective coherent motion with large density fluctuations spontaneously emerges from a disordered, isotropic state. In the parameter region where the rotational damping of polarity is strong, the systems undergoes an abrupt shift to the absorbing ordered state after a waiting period in the metastable disordered state. In order to obtain a simple understanding of the mechanism underlying the collective behavior, we analyze binary particle scattering process. We show that this approach correctly predicts the order-disorder transition at dilute limit. The same approach is expanded for finite densities, although it disagrees with the result from many-particle simulations due to many-body correlations and density fluctuations.

cond-mat.stat-mech↗

arXiv2015

Splash Detail Due to Grain Incident on Granular Bed

Using the discrete element method (DEM), we study the splash processes induced by the impact of a grain on two types of granular beds, namely, randomly packed and FCC-structured beds.Good correspondence is obtained between our numerical results and the findings of previous experiments, and it is demonstrated that the packing structure of the granular bed strongly affects the splash process.The mean ejection angle for the randomly packed bed is consistent with previous experimental results. The FCC-structured bed yields a larger mean ejection angle; however, the latter result has not been confirmed experimentally. Furthermore, the ejection angle distributions and the vertical ejection speeds for individual grains vary depending on the relative timing at which the grains are ejected after the initial impact. Obvious differences are observed between the distributions of grains ejected during the earlier and later splash periods: the form of the vertical ejection speed distribution varies from a power-law form to a lognormal form with time, and more than 80\% of the kinetic energy of all ejected grains is used for earlier ejected grains.

cond-mat.soft↗