arXiv subjects

Takuji Ishikawa

Publications and source records attributed to Takuji Ishikawa.

17 recordsLinked to original sources

arXiv2026

Self-organised structures in mixed active-passive suspensions due to hydrodynamic interactions

Microswimmers in suspension exhibit collective swimming behaviour, forming various self-organised structures including ordered, aggregated, and turbulent-like structures. When mixed with passive particles phase-separation is known to occur, but due to the difficulty of accurately handling many-body hydrodynamic interactions, the formation of self-organised structures in mixed suspensions has remained unexplored so far. In this study, we investigate the dynamics of mixed dense suspensions of spherical bottom-heavy squirmers and obstacle spheres using Stokesian dynamics in three dimensions, taking hydrodynamic interactions into account. The results show that without an external orientating mechanism the formation of orientational order is in general disturbed by the presence of passive spheres. An initially phase-separated state is metastable for neutral or puller squirmers at high packing densities. When the squirmers are bottom-heavy, phase-separation can occur dynamically in some cases, notably a fibrillar kind of separation for neutral squirmers and pullers at medium densities. We also observed a novel form of lamellar phase-separation for pullers at high densities with strong bottom-heaviness, with a sandwich-like structure consisting of a layer of passive particles pushed by a layer of swimmers, followed by a gap. These results indicate that microstructure and particle transport undergo significant changes depending on the type of swimmer, highlighting the importance of hydrodynamic interactions. These insights allow for a deeper understanding of the behaviour of active particles in complex fluids and to control them using external torques.

physics.flu-dyn↗

arXiv2025

Pure hydrodynamic instabilities in active jets of "puller" microalgae

Active fluids can develop spontaneous flow instabilities and complex patterns. However, spatio-temporal control of active particles has remained challenging, despite its relevance in biological and applied contexts. Here, we harnessed phototaxis to steer millions of swimming ``puller" Chlamydomonas reinhardtii algae to create active jets and control both pearling and buckling instabilities through the preferential orientation of the cells. Our experiments, supported by a full analytical model and simulations, confirm long-standing predictions that self-generated flows can lead to jet destabilization. Our results further indicate that pullers can behave analogously to pushers when their orientation is properly tuned, and demonstrate how light enables efficient control of active fluids.

cond-mat.soft↗

arXiv2025

Hydrodynamic Instabilities of Active Jets

Using a combination of theory, experiments, and numerical simulations, we investigate the stability of coherent structures in a suspension of strongly aligned active swimmers. We show that a dilute jet of pullers undergoes a pearling instability, while a jet of pushers exhibits a helical (or, in two dimensions, zigzag) instability. We further characterise the nonlinear evolution of these instabilities, deriving exact and approximate solutions for the spreading and mutual attraction of puller clusters, as well as the wavelength coarsening of the helical instability. Our theoretical predictions closely match the experimentally observed wavelengths, timescales, and flow fields in suspensions of photophobic algae, as well as results from direct numerical simulations. These findings reveal the intrinsic instability mechanisms of aligned active suspensions and demonstrate that coherent structures can be destabilised by the flows they generate.

cond-mat.soft↗

arXiv2024

The Architecture of Sponge Choanocyte Chambers Maximizes Mechanical Pumping Efficiency

Sponges, the basalmost members of the animal kingdom, exhibit a range of complex architectures in which microfluidic channels connect multitudes of spherical chambers lined with choanocytes, flagellated filter-feeding cells. Choanocyte chambers can possess scores or even hundreds of such cells, which drive complex flows entering through porous walls and exiting into the sponge channels. One of the mysteries of the choanocyte chamber is its spherical shape, as it seems inappropriate for inducing directional transport since many choanocyte flagella beat in opposition to such a flow. Here we combine direct imaging of choanocyte chambers in living sponges with computational studies of many-flagella models to understand the connection between chamber architecture and directional flow. We find that those flagella that beat against the flow play a key role in raising the pressure inside the choanocyte chamber, with the result that the mechanical pumping efficiency, calculated from the pressure rise and flow rate, reaches a maximum at a small outlet opening angle. Comparison between experimental observations and the results of numerical simulations reveal that the chamber diameter, flagellar wave number and the outlet opening angle of the freshwater sponge $E. muelleri$, as well as several other species, are related in a manner that maximizes the mechanical pumping efficiency. These results indicate the subtle balances at play during morphogenesis of choanocyte chambers, and give insights into the physiology and body design of sponges.

cond-mat.soft↗

arXiv2023

Swimming, Feeding and Inversion of Multicellular Choanoflagellate Sheets

The recent discovery of the striking sheet-like multicellular choanoflagellate species $Choanoeca~flexa$ that dynamically interconverts between two hemispherical forms of opposite orientation raises fundamental questions in cell and evolutionary biology, as choanoflagellates are the closest living relatives of animals. It similarly motivates questions in fluid and solid mechanics concerning the differential swimming speeds in the two states and the mechanism of curvature inversion triggered by changes in the geometry of microvilli emanating from each cell. Here we develop fluid dynamical and mechanical models to address these observations and show that they capture the main features of the swimming, feeding, and inversion of $C.~flexa$ colonies.

cond-mat.soft↗

arXiv2023

Self-organisation of spermatozoa in bulk suspensions via unsteady elastohydrodynamic interactions

We developed a mechanical model of spermatozoal swimming in bulk suspensions. We traced the spatiotemporal elastohydrodynamic interactions and found that spermatozoa engaged in self-organisation: flagellar undulatory motion generated a stable polar order. Conventional microswimmer theories use time-averaged stress fields to predict that the cellular structure is unstable. However, our present results reveal a novel self-organisation mechanism attributable to unsteady hydrodynamic interactions. We thus contribute to the theory of active soft matter dynamics.

physics.flu-dyn↗

arXiv2022

Instability of an active fluid jet

The breakup of a fluid jet into droplets has long fascinated natural scientists, with early research dating back to the 19th century. Infinitesimal perturbations to a jet grow because of surface tension, which eventually leads to breakup of the jet into droplets (Rayleigh-Plateau instability). Although this classical phenomenon has long been studied, it is not clear how it is modified when the fluid is replaced by an active fluid. In this study, we investigate instabilities of a jet of an active fluid. The active fluid is modelled by a suspension of microswimmers that propel themselves by generating surface tangential velocities, i.e. squirmers. The squirmers are assumed to be bottom-heavy and heavier than the surrounding fluid, so that a downward jet of the active fluid self-assembles under gravity. Hydrodynamic interactions between squirmers are computed using the Stokesian dynamics method, in which near-field hydrodynamics are accurately calculated. We find that jets of active fluids are unstable, with different unstable modes between pullers and pushers. For an active fluid of pullers, the jet breaks up into droplets in a varicose manner reminiscent of a Newtonian fluid. For pushers, on the other hand, the jet buckles and undergoes a waving (sinuous) instability. The physical mechanisms for these two instabilities can be understood by an inspection of the stress fields in the jets and parametric study reveals the importance of hydrodynamic interactions in the instabilities. Although both gravity and bottom-heaviness play an essential role in realizing the downward jet, their influence on the instability is found to be limited. Our findings help reveal new features of the collective properties of active fluids.

physics.flu-dyn↗

arXiv2020

Stability of dancing Volvox

Biflagellate algal cells of the genus Volvox form spherical colonies that propel themselves, vertically upwards in still fluid, by the coordinated beating of thousands of flagella, that also cause the colonies to rotate about their vertical axes. When they are swimming in a chamber of finite depth, pairs (or more) of Volvox carteri colonies were observed by Drescher et al. [Phys. Rev. Lett. 102, 168101 (2009)] to exhibit hydrodynamic bound states when they are close to a rigid horizontal boundary. When the boundary is above, the colonies are attracted to each other and orbit around each other in a `waltz'; when the boundary is below they perform more complex `minuet' motions. These dances are simulated in the present paper, using a novel `spherical squirmer' model of a colony in which, instead of a time-independent but $θ$-dependent tangential velocity being imposed on the spherical surface (radius $a$; $θ$ is the polar angle), a time-independent and uniform tangential shear stress is applied to the fluid on a sphere of radius $(1+ε)a, ε\ll 1$, where $εa$ represents the length of the flagella. The fluid must satisfy the no-slip condition on the sphere at radius $a$. In addition to the shear stress, the motions depend on two dimensionless parameters that describe the effect of gravity on a colony: $F_g$, proportional to the ratio of the sedimentation speed of a non-swimming colony to its swimming speed, and $G_{bh}$, that represents the fact that colonies are bottom-heavy...

physics.flu-dyn↗

arXiv2019

Motility and Phototaxis of $Gonium$, the Simplest Differentiated Colonial Alga

Green algae of the $Volvocine$ lineage, spanning from unicellular $Chlamydomonas$ to vastly larger $Volvox$, are models for the study of the evolution of multicellularity, flagellar dynamics, and developmental processes. Phototactic steering in these organisms occurs without a central nervous system, driven solely by the response of individual cells. All such algae spin about a body-fixed axis as they swim; directional photosensors on each cell thus receive periodic signals when that axis is not aligned with the light. The flagella of $Chlamydomonas$ and $Volvox$ both exhibit an adaptive response to such signals in a manner that allows for accurate phototaxis, but in the former the two flagella have distinct responses, while the thousands of flagella on the surface of spherical $Volvox$ colonies have essentially identical behaviour. The planar 16-cell species $Gonium~pectorale$ thus presents a conundrum, for its central 4 cells have a $Chlamydomonas$-like beat that provide propulsion normal to the plane, while its 12 peripheral cells generate rotation around the normal through a $Volvox$-like beat. Here, we combine experiment, theory, and computations to reveal how $Gonium$, perhaps the simplest differentiated colonial organism, achieves phototaxis. High-resolution cell tracking, particle image velocimetry of flagellar driven flows, and high-speed imaging of flagella on micropipette-held colonies show how, in the context of a recently introduced model for $Chlamydomonas$ phototaxis, an adaptive response of the peripheral cells alone leads to photo-reorientation of the entire colony. The analysis also highlights the importance of local variations in flagellar beat dynamics within a given colony, which can lead to enhanced reorientation dynamics.

cond-mat.soft↗

arXiv2018

Asymmetry in cilia configuration induces hydrodynamic phase locking

To gain insight into the nature of biological synchronization at the microscopic scale, we here investigate the hydrodynamic synchronization between conically rotating objects termed nodal cilia. A mechanical model of three rotating cilia is proposed with consideration of variation in their shapes and geometrical arrangement. We conduct numerical estimations of both near-field and far-field hydrodynamic interactions, and apply a conventional averaging method for weakly coupled oscillators. In the non-identical case, the three cilia showed stable locked-phase differences around $\pm π/2$. However, such phase locking also occurred with three identical cilia when allocated in a triangle except for the equilateral triangle. The effects of inhomogeneity in cilia shapes and geometrical arrangement on such asymmetric interaction is discussed to understand the role of biological variation in synchronization via hydrodynamic interactions.

cond-mat.soft↗

arXiv2017

Active particles in periodic lattices

Both natural and artificial small-scale swimmers may often self-propel in environments subject to complex geometrical constraints. While most past theoretical work on low-Reynolds number locomotion addressed idealised geometrical situations, not much is known on the motion of swimmers in heterogeneous environments. As a first theoretical model, we investigate numerically the behaviour of a single spherical micro-swimmer located in an infinite, periodic body-centred cubic lattice consisting of rigid inert spheres of the same size as the swimmer. Running a large number of simulations we uncover the phase diagram of possible trajectories as a function of the strength of the swimming actuation and the packing density of the lattice. We then use hydrodynamic theory to rationalise our computational results and show in particular how the far-field nature of the swimmer (pusher vs. puller) governs even the behaviour at high volume fractions.

physics.flu-dyn↗

arXiv2016

Decoherence and the Branching of Chaos-less Classical Trajectory

This study was started to know mysterious classicality of nuclei. This time, I found a new rule for decoherence. I used a model without chaos. As a result, it was shown that not only the intersection of classical trajectories but also branching of classical trajectories are needed for decoherence. In other words, it was shown that interactions between a main system and environments have to make enough branchings of classical trajectories of the main system for decoherence.

quant-ph↗

arXiv2016

Decoherence in Sub-Systems of an Isolated System and the Disappearance of Quantum Multiverse

This study was started to know mysterious classicality of nuclei. Using three particles model without external environments, it is found that decisions of respective state of three particles by decoherence are not simultaneous. Furthermore, in this model, wave function of total three body system collapses spontaneously without any external environments. Therefore we may able to insist that a wavefunction of our universe has already collapsed spontaneously without any external observer, because of the same mechanism with this model.

quant-ph↗

arXiv2013

Asymmetric Rotational Stroke in Mouse Node Cilia during Left-Right Determination

Clockwise rotational movement of isolated single cilia in mice embryo was investigated in vivo. The movement generates leftward fluid flow in the node cavity and plays an important role in left-right determination. The leftward unidirectional flow results from tilting of the rotational axis of the cilium to posterior side. Because of the no-slip boundary condition at the cell surface, the upper stroke away from the boundary generates leftward flow, and the lower stroke close to the boundary generates slower rightward flow. By combining computational fluid dynamics with experimental observations, we demonstrate that the leftward stroke can be more effective than expected for cases in which cilia tilting alone is considered with the no-slip condition under constant driving force. Our results suggest that the driving force is asymmetric and that it is determined by the tilting angle and open angle of the rotating cilia. Specifically, it is maximized in the leftward stroke when the cilia moves comparatively far from the boundary.

q-bio.TO↗

arXiv2013

Orientational order in concentrated suspensions of spherical microswimmers

We use numerical simulations to probe the dynamics of concentrated suspensions of spherical microswimmers interacting hydrodynamically. Previous work in the dilute limit predicted orientational instabilities of aligned suspensions for both pusher and puller swimmers, which we confirm computationally. Unlike previous work, we show that isotropic suspensions of spherical swimmers are also always unstable. Both types of initial conditions develop long-time polar order, of a nature which depends on the hydrodynamic signature of the swimmer but very weakly on the volume fraction up to very high volume fractions.

cond-mat.soft↗

arXiv2009

Study of Quantum Decoherence in a Finite System -- Three Schroedinger Cats and Crossing of Classical Orbits

Nuclei are rather classical systems in a sense. In the old days, their phenomena were roughly explained in classical rules such as the liquid drop model. This fact may be understood that when we see an finite quantum many body system like nucleus, though which is a group of quantum mechanical particles, its any collective degree of freedom has any classicality. Getting a classicality does not depend on spatial scales of objects. It is made by a phenomenon called Quantum Decoherence. We have studied about Quantum Decoherence in a finite system as nucleus. In this paper, at the harmonic three body problem (3 Schroedinger cats), it is shown that one degree of freedom as a sub-system would get classicality because of the other two degrees of freedom. Therefore we can assume that a nuclear collective degree of freedom would get classicality when it couples with any other internal degrees of freedom. In this paper, we also note that there is some relationship between the Quantum Decoherence and Crossing of classical orbits in 3 Schroedinger cats model.

quant-ph↗

arXiv2009

Dancing Volvox: Hydrodynamic Bound States of Swimming Algae

The spherical alga Volvox swims by means of flagella on thousands of surface somatic cells. This geometry and its large size make it a model organism for studying the fluid dynamics of multicellularity. Remarkably, when two nearby Volvox swim close to a solid surface, they attract one another and can form stable bound states in which they "waltz" or "minuet" around each other. A surface-mediated hydrodynamic attraction combined with lubrication forces between spinning, bottom-heavy Volvox explains the formation, stability and dynamics of the bound states. These phenomena are suggested to underlie observed clustering of Volvox at surfaces.

cond-mat.soft↗