arXiv subjects

Tatsuo Shibata

Publications and source records attributed to Tatsuo Shibata.

18 recordsLinked to original sources

arXiv2025

A geometric framework for curvature-dependent collective behavior of polar active agents on curved surfaces

In biological systems, active agents such as actomyosin and cells move and interact on curved surfaces, exhibiting diverse phenomena. These observations have motivated studies of how curvature shapes their collective behavior. Here, using a geometric framework, a minimal model is presented for interacting active agents on curved surfaces with Vicsek-like polar alignment. A transition between disordered and ordered states occurs on spheres as well as on oblate and prolate spheroids. As the deviation from sphericity increases, the transition point shifts to higher alignment strengths, and swarming localizes to an equatorial belt away from the poles, indicating that curvature heterogeneity influences the emergence of the polar-ordered state.

cond-mat.soft↗

arXiv2025

Emergence of chiral multi-armed spirals in an open system of migrating cells under continuous cell supply

Chirality organize living and active matter systems into striking collective states, yet the principles that govern chiral ordering in open systems, where elements are continuously added or removed, remain unclear. A mutant strain of Dictyostelium discoideum deficient in chemotaxis (KI cells) forms centimeter-scale, clockwise multi-armed spirals. Each arm is a traveling band produced by short-range alignment interactions and guided by a polar-ordered rotating core that encircles the cell source. A subtle clockwise bias in the single-cell migration is amplified by collective ordering into tissue-scale chirality. To uncover the minimal ingredients, we developed an open chiral Vicsek model and identified intrinsic chirality and continuous cell supply as the key factors. Our study establishes a general route by which weak microscopic chirality and sustained material flux generate macroscopic chiral order, offering new insight into chiral patterning in multicellular behaviors.

cond-mat.soft↗

arXiv2023

Scaling-up Memristor Monte Carlo with magnetic domain-wall physics

By exploiting the intrinsic random nature of nanoscale devices, Memristor Monte Carlo (MMC) is a promising enabler of edge learning systems. However, due to multiple algorithmic and device-level limitations, existing demonstrations have been restricted to very small neural network models and datasets. We discuss these limitations, and describe how they can be overcome, by mapping the stochastic gradient Langevin dynamics (SGLD) algorithm onto the physics of magnetic domain-wall Memristors to scale-up MMC models by five orders of magnitude. We propose the push-pull pulse programming method that realises SGLD in-physics, and use it to train a domain-wall based ResNet18 on the CIFAR-10 dataset. On this task, we observe no performance degradation relative to a floating point model down to an update precision of between 6 and 7-bits, indicating we have made a step towards a large-scale edge learning system leveraging noisy analogue devices.

cs.ET↗

arXiv2023

Pattern formation and the mechanics of a motor-driven filamentous system confined by rigid membranes

Pattern formation and the mechanics of a mixture of actin filaments and myosin motors that is confined by a rigid membrane is investigated. By using a coarse-grained molecular dynamics model, we demonstrate that the competition between the depletion force and the active force of the motors gives rise to actin accumulation in the membrane vicinity. The resulting actomyosin structure exerts pressure on the membrane, that, due to nematic alignment of the filaments, converges to a constant for large motor active force. The results are independent of filament length and membrane curvature, indicating the universality of this phenomenon. Thus, this study proposes a novel mechanism by which the compounds of the cytoskeleton can self-organize into a higher-order structure.

cond-mat.soft↗

arXiv2022

Non-monotonic fluidization generated by fluctuating edge tensions in confluent tissues

In development and homeostasis, multi-cellular systems exhibit spatial and temporal heterogeneity in their biochemical and mechanical properties. Nevertheless, it remains unclear how spatiotemporally heterogeneous forces affect the dynamical and mechanical properties of confluent tissue. To address this question, we study the dynamical behavior of the two-dimensional cellular vertex model for epithelial monolayers in the presence of fluctuating cell-cell interfacial tensions, which is a biologically relevant source of mechanical spatiotemporal heterogeneity. In particular, we investigate the effects of the amplitude and persistence time of fluctuating tension on the tissue dynamics. We unexpectedly find that the long-time diffusion constant describing cell rearrangements depends non-monotonically on the persistence time, while it increases monotonically as the amplitude increases. Our analysis indicates that at low and intermediate persistence times tension fluctuations drive motion of vertices and promote cell rearrangements, while at the highest persistence times the tension in the network evolves so slowly that rearrangements become rare.

cond-mat.soft↗

arXiv2019

Collective cell migration of epithelial cells driven by chiral torque generation

Various multicellular tissues show chiral morphology. Experimental studies have shown this can originate from cell chirality. However, no theory has been proposed to connect the cellular chiral torque and multicellular chiral morphogenesis. We propose a model of confluent tissue dynamics with cellular chiral torque. We found that cells migrate unidirectionally under a gradient of cellular chiral torque. While the migration speed varies depending on the tissue's mechanical parameters, it is scaled solely by a structural order parameter for liquid-to-solid transition in confluent tissues.

cond-mat.soft↗

arXiv2016

Enhancing the blocking temperature of perpendicular-exchange biased Cr2O3 thin films using spacer and buffer layers

In this study, we investigated the effect of spacer and buffer layers on the blocking temperature TB of the perpendicular exchange bias of thin Cr2O3 films, and revealed a high TB of 260 K for 20-nm-thick Cr2O3 thin films. By inserting a Ru spacer layer between the Cr2O3 and Co films and changing the spacer thickness, we controlled the magnitude of the exchange bias and TB. By comparing the TB values of the 20-nm-thick Cr2O3 films on Pt and alpha-Fe2O3 buffers, we investigated the lattice strain effect on the TB. We show that higher TB value can be obtained using an alpha-Fe2O3 buffer, which is likely because of the lattice-strain-induced increase of Cr2O3 magnetic anisotropy.

cond-mat.mtrl-sci↗

arXiv2013

Relevance of intracellular polarity to accuracy of eukaryotic chemotaxis

Chemotactic cells establish cell polarity in the absence of external guidance cues. Such self-organized polarity is induced by spontaneous symmetry breaking in the intracellular activities, which produces an emergent memory effect associated with slow-changing mode. Therefore, spontaneously established polarity should play a pivotal role in efficient chemotaxis. In this study, we develop a model of chemotactic cell migration that demonstrates the connection between intracellular polarity and chemotactic accuracy. Spontaneous polarity formation and gradient sensing are described by a stochastic differential equation. We demonstrate that the direction of polarity persists over a characteristic time that is predicted to depend on the chemoattractant concentration. Next, we theoretically derive the chemotactic accuracy as a function of both the gradient sensing ability and the characteristic time of polarity direction. The results indicate that the accuracy can be improved by the polarity. Furthermore, the analysis of chemotactic accuracy suggests that accuracy is maximized at some optimal responsiveness to extracellular perturbations. To obtain the model parameters, we studied the correlation time of random cell migration in cell tracking analysis of Dictyostelium cells. As predicted, the persistence time depended on the chemoattractant concentration. From the fitted parameters, we inferred that polarized Dictyosteium cells can respond optimally to a chemical gradient. Chemotactic accuracy was almost 10 times larger than can be achieved by non-polarized gradient sensing. Using the obtained parameter values, we show that polarity also improves the dynamic range of chemotaxis.

q-bio.CB↗

arXiv2005

Nonequilibrium pattern formation in chiral Langmuir monolayers with transmembrane flows

Nonequilibrium Langmuir monolayers including a fraction of chiral molecules and subject to transmembrane flow are considered. The flow induces coherent collective precession of chiral molecules. Our theoretical study shows that splay interactions in this system lead to spatial redistribution of chiral molecules and formation of spiral waves and target patterns observed in experiments.

cond-mat.soft↗

arXiv2002

Coupled map gas: structure formation and dynamics of interacting motile elements with internal dynamics

A model of interacting motile chaotic elements is proposed. The chaotic elements are distributed in space and interact with each other through interactions depending on their positions and their internal states. As the value of a governing parameter is changed, the model exhibits successive phase changes with novel pattern dynamics, including spatial clustering, fusion and fission of clusters and intermittent diffusion of elements. We explain the manner in which the interplay between internal dynamics and interaction leads to this behavior by employing certain quantities characterizing diffusion, correlation, and the information cascade of synchronization. Keywords: collective motion, coupled map system, interacting motile elements

nlin.AO↗

arXiv2000

A generalization of Clausius inequality for processes between nonequilibrium steady states in chemical reaction systems

We investigate nonequilibrium chemical reaction systems from the view point of steady state thermodynamics proposed by Oono and Paniconi [Prog. Theor. Phys. Suppl. 130, 29 (1998)]. The concentrations of some compounds are operated by an external system, so that a transition from a steady state to other steady state takes place. We show that an analogue of Clausius inequality holds macroscopically for the operation processes. This implies that the second law of thermodynamics can be generalized, including nonequilibrium steady states.

cond-mat.stat-mech↗

arXiv2000

Energetics of Open Systems and Chemical Potential From Micro-Dynamics Viewpoints

We present the energetic aspect of open systems which may exchange particles with their environments. Our attention shall be paid to the scale that the motion of the particles is described by the classical Langevin dynamics. Along a particular realization of the stochastic process, we study the energy transfer into the open system from the environments. We are able to clarify how much energy each particle carries when it enters or leaves the system. On the other hand, the chemical potential should be considered as the concept in macro scale, which is relevant to the free energy potential with respect to the number of particles. Keywords: open systems, stochastic energetics, chemical potential

cond-mat.stat-mech↗

arXiv1998

Noiseless Collective Motion out of Noisy Chaos

We consider the effect of microscopic external noise on the collective motion of a globally coupled map in fully desynchronized states. Without the external noise a macroscopic variable shows high-dimensional chaos distinguishable from random motion. With the increase of external noise intensity, the collective motion is successively simplified. The number of effective degrees of freedom in the collective motion is found to decrease as $-\log{σ^2}$ with the external noise variance $σ^2$. It is shown how the microscopic noise can suppress the number of degrees of freedom at a macroscopic level.

chao-dyn↗

arXiv1998

Collective Chaos

An algorithm to characterize collective motion is presented, with the introduction of ``collective Lyapunov exponent'', as the orbital instability at a macroscopic level. By applying the algorithm to a globally coupled map, existence of low-dimensional collective chaos is confirmed, where the scale of (high-dimensional) microscopic chaos is separated from the macroscopic motion, and the scale approaches zero in the thermodynamic limit. pacs:05.45+b,05.90+m,64.60.Cn

chao-dyn↗

arXiv1998

On the Tongue-Like Bifurcation Structures of the Mean-Field Dynamics in a Network of Chaotic Elements

Collective behavior is studied in globally coupled maps. Several coherent motions exist, even in fully desynchronized state. To characterize the collective behavior, we introduce scaling transformation of parameter, and detect the tongue-like structure of collective motions in parameter space. Such collective motion is supported by the separation of time scale, given by the self-consistent relationship between the collective motion and chaotic dynamics of each element. It is shown that the change of collective motion is related with the window structure of a single one-dimensional map. Formation and collapse of regular collective motion are understood as the internal bifurcation structure. Coexistence of multiple attractors with different collective behaviors is also found in fully desynchronized state. 05.45+b,05.90+m,87.10+e Keywords: Globally coupled map, Mean field dynamics, Collective motion

chao-dyn↗

arXiv1997

Brownian Motors driven by Particle Exchange

We extend the Langevin dynamics so that particles can be exchanged with a particle reservoir. We show that grand canonical ensembles are realized at equilibrium and derive the relations of thermodynamics for processes between equilibrium states. As an application of the proposed evolution rule, we devise a simple model of Brownian motors driven by particle exchange. KEYWORDS: Langevin Dynamics, Thermodynamics, Open Systems

cond-mat.stat-mech↗

arXiv1997

Equilibrium Chemical Engines

An equilibrium reversible cycle with a certain engine to transduce the energy of any chemical reaction into mechanical energy is proposed. The efficiency for chemical energy transduction is also defined so as to be compared with Carnot efficiency. Relevance to the study of protein motors is discussed. KEYWORDS: Chemical thermodynamics, Engine, Efficiency, Molecular machine.

cond-mat.soft↗

arXiv1996

Heterogeneity Induced Order in Globally Coupled Chaotic Systems

Collective behavior is studied in globally coupled maps with distributed nonlinearity. It is shown that the heterogeneity enhances regularity in the collective dynamics. Low-dimensional quasiperiodic motion is often found for the mean-field, even if each element shows chaotic dynamics. The mechanism of this order is due to the formation of an internal bifurcation structure, and the self-consistent dynamics between the structures and the mean-field. Keywords: Globally Coupled Map with heterogeneity, Collective behavior

chao-dyn↗