arXiv subjects

Kazumasa A. Takeuchi

Publications and source records attributed to Kazumasa A. Takeuchi.

At least 19 recordsLinked to original sources

arXiv2026

Near-field Hydrodynamics Disentangles Angular Correlations in Confined Active Suspensions

Spatial confinement profoundly impacts the transport and self-organization of active matter across diverse biological systems. While the collective orders in confined active matter have been extensively characterized, how geometric constraints reshape near-field flows and the resulting inter-particle correlations remains largely unexplored. In this study, we combine experiments and hydrodynamic simulations to investigate inter-particle correlations within quasi-two-dimensional Chlamydomonas reinhardtii suspensions. We reveal two disentangled modes characterizing cell pairs: a dipolar mode and an entrainment mode, which exhibit a density- and distance-dependent competition. Combining single-cell flow field analysis, hydrodynamic simulations, and active-passive mixtures, we link these two modes to singular hydrodynamics and lubrication-induced entrainment. Our results demonstrate that spatiotemporal correlations in confined active matter are fundamentally rooted in the interplay of these two hydrodynamic mechanisms.

cond-mat.soft↗

arXiv2026

Various phases of active matter emerging from bacteria and their implications

In this perspective article, we discuss bacterial populations as a model system of active matter. It allows for the exploration and characterization of various phases of active matter and brings rich implications for both physics and biology. Specifically, we focus on active gas, active liquid, active glass and active liquid crystal states observed in bacterial populations and describe how these differ from their thermal counterparts. A few future directions are also discussed that will deepen the physical interest in active matter as a new type of material, with its implications for several life phenomena observed in bacterial populations and other biological systems.

cond-mat.soft↗

arXiv2026

Symmetry-Informed Term Filtering for Continuum Equation Discovery

Discovering governing equations, whether manually or by data-driven methods, has been central in physics and related areas. Since governing equations are typically constrained by a set of symmetries, using symmetry constraints to restrict terms is usually the first step in manually formulating a governing equation, but it often becomes intractable for complex systems with high-order derivatives or multiple fields. When a data-driven method is used, on the other hand, imposing physical constraints such as symmetries typically requires manual preprocessing or computationally expensive iterative procedures. Here, we propose an algebraic filtering method that enumerates all symmetry-allowed terms for continuum equations within a finite candidate space. By treating symmetry generators as linear operators on the candidate space, we reduce the problem of enforcing both discrete and continuous symmetries to solving a set of linear kernel equations. The solution yields a provably complete list of permitted terms. We demonstrate the method's effectiveness by identifying invariant terms for systems with dihedral symmetry and recovering the governing equations for the Toner--Tu and Kardar--Parisi--Zhang systems, including higher-order terms useful for extending known models. The method provides a systematic way to obtain a symmetry-allowed search space for data-driven equation discovery, e.g., the sparse identification of nonlinear dynamics method.

cond-mat.stat-mech↗

arXiv2026

Population dynamics simulations of large deviations for three subclasses of the Kardar-Parisi-Zhang universality class

Recent theoretical studies have gradually deepened our understanding of the one-dimensional (1D) Kardar-Parisi-Zhang (KPZ) universality class even in the large deviation regime, but numerical methods for studying KPZ large deviations remain limited. Here we implement a method based on the population dynamics algorithm for studying large deviations of time-integrated local currents in the totally asymmetric simple exclusion process (TASEP), which is a pragmatic model in the 1D KPZ class. Carrying out simulations for the three representative initial conditions, namely step, flat, and stationary ones, we not only confirm theoretical predictions available for the step case, but also characterize large deviations for the flat and stationary cases which have not been investigated before. We reveal in particular an unexpected robustness of the deeply negative large deviation regime with respect to different initial conditions. We attribute this robustness to the spontaneous formation of a wedge shape in interface profile. Our population dynamics approach may serve as a versatile method for studying large deviations in the KPZ class numerically and, potentially, even experimentally.

cond-mat.stat-mech↗

arXiv2026

Designing topological edge states in bacterial active matter

Topology provides a unifying framework for understanding robust transport through protected edge states arising from nontrivial wavenumber topology. Extending these concepts to active matter, however, remains largely unexplored experimentally, with realizations limited to systems composed of chiral active particles. Here, we realize topological edge states in dense bacterial suspension, which represents a prototypical active matter system, using microfabricated geometrical structures with nontrivial wavenumber topology. Inspired by previous theoretical studies, we constructed a directional kagome network composed of ratchet-shaped channels that induce unidirectional bacterial flow. In this network, we found clear edge localization of bacterial density. A steady-state analysis based on the bacterial transport model and experimentally measured velocity field reveals how the characteristic collective flow generates edge localization. The model also uncovers the topological origin of the observed edge states. By tuning the geometry of the microfabricated networks, we identified directional channel design and network chirality as the key design features essential for the emergence of the edge state. Our results pave the way for establishing a control and design principle of topological transport in such active matter systems.

cond-mat.soft↗

arXiv2025

Partial yet definite emergence of the Kardar-Parisi-Zhang class in isotropic spin chains

Integrable spin chains with a continuous non-Abelian symmetry, such as the one-dimensional isotropic Heisenberg model, show superdiffusive transport with little theoretical understanding. Although recent studies reported a surprising connection to the Kardar-Parisi-Zhang (KPZ) universality class in that case, this view was most recently questioned by discrepancies in full counting statistics. Here, by combining extensive numerical simulations of classical and quantum integrable isotropic spin chains with a framework developed by exact studies of the KPZ class, we characterize various two-point quantities that remain hitherto unexplored in spin chains, and find full agreement with KPZ scaling laws without adjustable parameters. This establishes the partial emergence of the KPZ class in integrable isotropic spin chains. Moreover, we reveal that the KPZ scaling laws are intact in the presence of an energy current, under the appropriate Galilean boost required by the propagation of spacetime correlation.

cond-mat.stat-mech↗

arXiv2024

Rigidity transition of a highly compressible granular medium

A wide range of disordered materials, from biological to geological assemblies, feature discrete elements undergoing large shape changes. How significant geometrical variations at the microscopic scale affect the response of the assembly, in particular rigidity transitions, is an ongoing challenge in soft matter physics. However, the lack of a model granular-like experimental system featuring large and versatile particle deformability impedes advances. Here, we explore the oscillatory shear response of a sponge-like granular assembly composed of highly compressible elastic rings. We highlight a progressive rigidity transition, switching from a yielded phase to a solid one by increasing density or decreasing shear amplitude. The rearranging yielded state consists of crystal clusters separated by melted regions; in contrast, the solid state remains amorphous and absorbs all imposed shear elastically. We rationalize this transition by uncovering an effective, attractive shear force between rings that emerges from a friction-geometry interplay. If friction is sufficiently high, the extent of the contacts between rings, captured analytically by elementary geometry, controls the rigidity transition.

cond-mat.soft↗

arXiv2024

Smectic-like bundle formation of planktonic bacteria upon nutrient starvation

Bacteria aggregate through various intercellular interactions to build biofilms, but the effect of environmental changes thereupon remains largely unexplored. Here, by using an experimental device that overcomes past difficulties, we observed the collective response of Escherichia coli aggregates against dynamic changes in the growth condition. We discovered that nutrient starvation caused bacterial cells to arrange themselves into bundle-shaped clusters, developing a structure akin to that of smectic liquid crystal. The degree of the smectic-like bundle order was evaluated by a deep learning approach. Our experiments suggest that both the depletion attraction by extracellular polymeric substances and the growth arrest are essential for the bundle formation. Since these effects of nutrient starvation at the single-cell level are common to many bacterial species, bundle formation might also be common collective behavior that bacterial cells may exhibit under harsh environments.

physics.bio-ph↗

arXiv2024

Vortex reversal is a precursor of confined bacterial turbulence

Active turbulence, or chaotic self-organized collective motion, is often observed in concentrated suspensions of motile bacteria and other systems of self-propelled interacting agents. To date, there is no fundamental understanding of how geometrical confinement orchestrates active turbulence and alters its physical properties. Here, by combining large-scale experiments, computer modeling, and analytical theory, we have discovered a generic sequence of transitions occurring in bacterial suspensions confined in cylindrical wells of varying radii. With increasing the well's radius, we observed that persistent vortex motion gives way to periodic vortex reversals, four-vortex pulsations, and then well-developed active turbulence. Using computational modeling and analytical theory, we have shown that vortex reversal results from the nonlinear interaction of the first three azimuthal modes that become unstable with the radius increase. The analytical results account for our key experimental findings. To further validate our approach, we reconstructed equations of motion from experimental data. Our findings shed light on the universal properties of confined bacterial active matter and can be applied to various biological and synthetic active systems.

cond-mat.soft↗

arXiv2024

Emergence of bacterial glass

Densely packed, motile bacteria can adopt collective states not seen in conventional, passive materials. These states remain in many ways mysterious, and their physical characterization can aid our understanding of natural bacterial colonies and biofilms as well as materials in general. Here, we overcome challenges associated with generating uniformly growing, large, quasi-two-dimensional bacterial assemblies by a membrane-based microfluidic device and report the emergence of glassy states in two-dimensional suspension of Escherichia coli. As the number density increases by cell growth, populations of motile bacteria transition to a glassy state, where cells are packed and unable to move. This takes place in two steps, the first one suppressing only the orientational modes and the second one vitrifying the motion completely. Characterizing each phase through statistical analyses and investigations of individual motion of bacteria, we find not only characteristic features of glass such as rapid slowdown, dynamic heterogeneity and cage effects, but also a few properties distinguished from those of thermal glass. These distinctive properties include the spontaneous formation of micro-domains of aligned cells with collective motion, the appearance of an unusual signal in the dynamic susceptibility, and the dynamic slowdown with a density dependence generally forbidden for thermal systems. Our results are expected to capture general characteristics of such active rod glass, which may serve as a physical mechanism underlying dense bacterial aggregates.

cond-mat.stat-mech↗

arXiv2024

Approach and rotation of reconnecting topological defect lines in liquid crystal

Topological defects are a universal concept across many disciplines, such as crystallography, liquid-crystalline physics, low-temperature physics, cosmology, and even biology. In nematic liquid crystals, topological defects called disclinations have been widely studied. For their three-dimensional (3D) dynamics, however, only recently have theoretical approaches dealing with fully 3D configurations been reported. Further, recent experiments have observed 3D disclination line reconnections, a phenomenon characteristic of defect line dynamics, but detailed discussions were limited to the case of approximately parallel defects. In this study, we focus on the case of two disclination lines that approach at finite angles and lie in separate planes, a more fundamentally 3D reconnection configuration. Observing and analyzing such reconnection events, we find the square-root law of the distance between disclinations and the decrease of the inter-disclination angle over time. We compare the experimental results with theory and find qualitative agreement on the scaling of distance and angle with time, but quantitative disagreement on distance and angle relative mobilities. To probe this disagreement, we derive the equations of motion for systems with reduced twist constant and also carry out simulations for this case. These, together with the experimental results, suggest that deformations of disclinations may be responsible for the disagreement.

cond-mat.soft↗

arXiv2024

Phase-ordering kinetics in the Allen-Cahn (Model A) class: universal aspects elucidated by electrically-induced transition in liquid crystals

The two-dimensional (2d) Ising model is the statistical physics textbook example for phase transitions and their kinetics. Quenched through the Curie point with Glauber rates, the late-time description of the ferromagnetic domain coarsening finds its place at the scalar sector of the Allen-Cahn (Model A) class. Resisting exact results sought since Lifshitz's account in 1962, central quantities in 2d Model A $-$ most scaling exponents and correlation functions $-$ remain known up to approximate theories whose disparate outcomes urge experimental assessment. Here, we perform such assessment from a comprehensive study of the coarsening of 2d twisted nematic liquid crystals whose kinetics is induced by a super-fast switching from a spatiotemporally chaotic state to a two-phase concurrent, equilibrium one. Tracking the dynamics via optical microscopy, we firstly show the sharp evidence of well-established Model A aspects, such as the dynamic exponent $z=2$ and the dynamic scaling hypothesis, to then move forward. We confirm the Bray-Humayun theory for Porod's regime describing intradomain length scales of spatial correlators, and show that their nontrivial decay beyond that regime is captured in a free-from-parameter fashion by Gaussian theories. These paradigmatic theories, however, do not perform well for time-related Model A statistics. We reveal that the collapsed form of two-time correlators is best accounted for by the local scaling invariance theory, along with the Fisher-Huse conjecture. We also suggest the true value for the local persistence exponent, in disfavour of Gaussian models, and extract a universal fractal dimension for the morphology of persistence clusters that is notably close to the golden ratio. Given its accuracy and possibilities, this experimental setup may work as a prototype to address universality issues in the realm of nonequilibrium systems.

cond-mat.stat-mech↗

arXiv2023

Route to turbulence via oscillatory states in polar active fluid under confinement

We report a novel route to active turbulence, observed in numerical simulations of a polar active fluid model under confinement. To deal with large-scale computations with arbitrary geometries, we developed a GPU-based scheme that can be used for any boundary shape in a unified manner. For the circular confinement, as the radius was increased, we found a series of transitions first from a single stationary vortex to an oscillating pair of vortices, then through reentrant transitions between oscillatory and chaotic dynamics before finally reaching the active turbulence. The first transition turned out to be hysteretic, with the emergence of the oscillatory state consistent with the subcritical Hopf bifurcation. In dumbbell-shaped boundaries composed of two overlapping circles, we observed a transition comparable to the ferromagnetic-antiferromagnetic vortex-order transition reported in previous experiments, but the transition point turned out to show a qualitatively different geometry dependence.

cond-mat.stat-mech↗

arXiv2022

Scaling and spontaneous symmetry restoring of topological defect dynamics in liquid crystal

Topological defects -- locations of local mismatch of order -- are a universal concept playing important roles in diverse systems studied in physics and beyond, including the universe, various condensed matter systems, and recently, even life phenomena. Among these, liquid crystal has been a platform for studying topological defects via visualization, yet it has been a challenge to resolve three-dimensional structures of dynamically evolving singular topological defects. Here, we report a direct confocal observation of nematic liquid crystalline defect lines, called disclinations, relaxing from an electrically driven turbulent state. We focus in particular on reconnections, characteristic of such line defects. We find a scaling law for in-plane reconnection events, by which the distance between reconnecting disclinations decreases by the square root of time to the reconnection. Moreover, we show that apparently asymmetric dynamics of reconnecting disclinations is actually symmetric in a comoving frame, in marked contrast to the two-dimensional counterpart whose asymmetry is established. We argue, with experimental supports, that this is because of energetically favorable symmetric twist configurations that disclinations take spontaneously, thanks to the topology that allows for rotation of the winding axis. Our work illustrates a general mechanism of such spontaneous symmetry restoring that may apply beyond liquid crystal, which can take place if topologically distinct asymmetric defects in lower dimensions become homeomorphic in higher dimensions and if the symmetric intermediate is energetically favorable.

cond-mat.soft↗

arXiv2022

Tilt-induced polar order and topological defects in growing bacterial populations

Rod-shaped bacteria, such as Escherichia coli, commonly live forming mounded colonies. They initially grow two-dimensionally on a surface and finally achieve three-dimensional growth. While it was recently reported that three-dimensional growth is promoted by topological defects of winding number $+1/2$ in populations of motile bacteria, how cellular alignment plays a role in non-motile cases is largely unknown. Here, we investigate the relevance of topological defects in colony formation processes of non-motile E. coli populations, and found that both $\pm 1/2$ topological defects contribute to the three-dimensional growth. Analyzing the cell flow in the bottom layer of the colony, we observe that $+1/2$ defects attract cells and $-1/2$ defects repel cells, in agreement with previous studies on motile cells, in the initial stage of the colony growth. However, later, cells gradually flow toward $-1/2$ defects as well, exhibiting a sharp contrast to the existing knowledge. By investigating three-dimensional cell orientations by confocal microscopy, we find strong vertical tilting of cells near the defects. Crucially, this leads to the emergence of a polar order in the otherwise nematic two-dimensional cell orientation. We extend the theory of active nematics by incorporating this polar order and the vertical tilting, which successfully explains the influx toward $-1/2$ defects in terms of a polarity-induced force. Our work reveals that three-dimensional cell orientations may result in drastic changes in properties of active nematics, especially those of topological defects, which may be generically relevant in active matter systems driven by cellular growth instead of self-propulsion.

cond-mat.soft↗

arXiv2022

Active colloid with externally induced periodic bipolar motility and its cooperative motion

Active matter physics has been developed with various types of self-propelled particles, including those with polar and bipolar motility and beyond. However, the bipolar motions experimentally realized so far have been either random along the axis or periodic at intrinsic frequencies. Here we report another kind of bipolar active particles, whose periodic bipolar self-propulsion is set externally at a controllable frequency. We used Quincke rollers -- dielectric particles suspended in a conducting liquid driven by an electric field -- under an AC electric field instead of the usually used DC field. Reciprocating motion of a single particle at the external frequency was observed experimentally and characterized theoretically as stable periodic motion. Experimentally, we observed not only the reciprocating motion but also non-trivial active Brownian particle (ABP)-like persistent motion in a long time scale. This resulted in a Lorentzian spectrum around zero frequency, which is not accounted for by a simple extension of the conventional model of Quincke rollers to the AC field. It was found that ABP-like motion can be reproduced by considering the top-bottom asymmetry in the experimental system. Moreover, we found a rotational diffusion coefficient much larger than the thermal one, as also reported in previous experiments, which may have resulted from roughness of the electrode surface. We also found self-organized formation of small clusters, such as doublets and triplets, and characterized cooperative motion of particles therein. The AC Quincke rollers reported here may serve as a model experimental system of bipolar active matter, which appears to deserve further investigations.

cond-mat.soft↗

arXiv2021

Scale invariance of cell size fluctuations in starving bacteria

In stable environments, cell size fluctuations are thought to be governed by simple physical principles, as suggested by recent findings of scaling properties. Here, by developing a microfluidic device and using E. coli, we investigate the response of cell size fluctuations against starvation. By abruptly switching to non-nutritious medium, we find that the cell size distribution changes but satisfies scale invariance: the rescaled distribution is kept unchanged and determined by the growth condition before starvation. These findings are underpinned by a model based on cell growth and cell cycle. Further, we numerically determine the range of validity of the scale invariance over various characteristic times of the starvation process, and find the violation of the scale invariance for slow starvation. Our results, combined with theoretical arguments, suggest the relevance of the multifork replication, which helps retaining information of cell cycle states and may thus result in the scale invariance.

q-bio.CB↗

arXiv2021

Initial perturbation matters: implications of geometry-dependent universal Kardar-Parisi-Zhang statistics for spatiotemporal chaos

Infinitesimal perturbations in various systems showing spatiotemporal chaos (STC) evolve following the power laws of the Kardar-Parisi-Zhang (KPZ) universality class. While universal properties beyond the power-law exponents, such as distributions and correlations, and their geometry dependence, are established for random growth and related KPZ systems, the validity of these findings to deterministic chaotic perturbations is unknown. Here we fill this gap between stochastic KPZ systems and deterministic STC perturbations by conducting extensive simulations of a prototypical STC system, namely the logistic coupled map lattice. We show that the perturbation interfaces, defined by the logarithm of the modulus of the perturbation vector components, exhibit the universal, geometry-dependent statistical laws of the KPZ class, despite the deterministic nature of STC. We demonstrate that KPZ statistics for three established geometries arise for different initial profiles of the perturbation, namely point (local), uniform, and "pseudo-stationary" initial perturbations, the last being the statistically stationary state of KPZ interfaces given independently of the Lyapunov vector. This geometry dependence lasts until the KPZ correlation length becomes comparable to the system size. Thereafter, perturbation vectors converge to the unique Lyapunov vector, showing characteristic meandering, coalescence, and annihilation of borders of piece-wise regions that remain different from the Lyapunov vector. Our work implies that the KPZ universality for stochastic systems generally characterizes deterministic STC perturbations, providing new insights for STC, such as the universal dependence on initial perturbation and beyond.

nlin.CD↗