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Ryoichi Yamamoto

Publications and source records attributed to Ryoichi Yamamoto.

At least 37 records · Page 2Linked to original sources

Spontaneous Spatiotemporal Ordering of Shape Oscillations Enhances Cell Migration

The migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence collective properties. Here we demonstrate, using numerical simulations, that the interplay of directed motion, shape oscillations, and excluded volume enables cells to locally "synchronize" their motion and thus enhance collective migration. Our model captures elongation and contraction of crawling ameboid cells controlled by an internal clock with a fixed period, mimicking the internal cycle of biological cells. We show that shape oscillations are crucial for local rearrangements that induce ordering of internal clocks between neighboring cells even in the absence of signaling and regularization. Our findings reveal a novel, purely physical mechanism through which the internal dynamics of cells influences their collective behavior, which is distinct from well known mechanisms like chemotaxis, cell division, and cell-cell adhesion.

physics.bio-ph↗

Modeling the Mechanosensitivity of Fast-Crawling Cells on Cyclically Stretched Substrates

The mechanosensitivity of cells, which determines how they are able to respond to mechanical signals received from their environment, is crucial for the functioning of all biological systems. In experiments, cells placed on cyclically stretched substrates have been shown to reorient in a direction that depends not only on the type of cell, but also on the mechanical properties of the substrate, and the amplitude and rate of stretching. However, the underlying biochemical and mechanical mechanisms responsible for this realignment are still not completely understood. In this study, we introduce a computational model for fast crawling on cyclically stretched substrates that accounts for the sub-cellular processes responsible for the cell shape and motility, as well as the coupling to the substrate through the focal adhesion sites. In particular, we focus on the role of the focal adhesion dynamics, and show that the reorientation under cyclic stretching is strongly dependent on the frequency, as has been observed experimentally. Furthermore, we show that an asymmetry during the loading and unloading phases of the stretching, whether coming from the response of the cell itself, or from the stretching protocol, can be used to selectively align the cells in either the parallel or perpendicular directions.

physics.bio-ph↗

Mechanics of cell crawling by means of force-free cyclic motion

The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the cell cyclically in time, together with periodic alternation of adhesive characters at the interface between the cell and the substrate. Here the key model parameters are the phase shifts between the elongation of the actuator and the alternation of the adhesion of the two elements. We emphasize that the phase shifts determine not only the efficiency of the crawling motion but also its direction.

cond-mat.soft↗

Hydrodynamic synchronization of externally driven colloids

The collective dynamics of externally driven $N_{\rm p}$-colloidal systems ($1\le N_{\rm p}\le 4$) in a confined viscous fluid have been investigated using three-dimensional direct numerical simulations with fully resolved hydrodynamics. The dynamical modes of collective particle motion are studied by changing the particle Reynolds number {as determined by the strength of the external driving force} and the confining wall distance. For a system with $N_{\rm p}= 3$, we found that at a critical Reynolds number, a dynamical mode transition occurs from the doublet-singlet mode to the triplet mode, which has not been reported experimentally. The dynamical mode transition was analyzed in detail from the following two viewpoints: (1) spectrum analysis of the time evolution of a tagged particle velocity and (2) the relative acceleration of the doublet cluster with respect to the singlet particle. For a system with $N_{\rm p}=4$, we found similar dynamical mode transitions from the doublet-singlet-singlet mode to the triplet-singlet mode and further to the quartet mode.

cond-mat.soft↗

Hydrodynamic alignment of microswimmers in pipes

We investigate the dynamics of model microswimmers under confinement, in cylindrical geometries, by means of three dimensional direct numerical calculations with fully resolved hydrodynamics. Such swimmers are known to show collective alignment in bulk, and we confirmed that similar alignment can be observed even in pipes, although the volume fraction dependency shows qualitative differences. By comparing the structural information, we investigated the cause of such differences. We found an order/disorder phase transition for a specific type of swimmers, as the size of the pipe becomes comparable to the size of the swimmers. Such dynamics are found not to depend on the geometry of confinement.

cond-mat.soft↗

Do hydrodynamically assisted binary collisions lead to orientational ordering of microswimmers?

We have investigated the onset of collective motion in systems of model microswimmers, by performing a comprehensive analysis of the binary collision dynamics using three dimensional direct numerical simulations (DNS) with fully resolved hydrodynamics. From this data, we have constructed a simplified binary collision model (BCM) which accurately reproduces the collective behavior obtained from the DNS for most cases. Thus, we show that global alignment can mostly arise solely from binary collisions. Although the agreement between both models (DNS and BCM) is not perfect, the parameter range in which notable differences appear is also that for which strong density fluctuations are present in the system (where pseudo-sound mound can be observed[1]).

physics.flu-dyn↗

Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibition

Contact inhibition plays a crucial role in the motility of cells, the process of wound healing, and the formation of tumors. By mimicking the mechanical motion of calls crawling on a substrate using a pseudopod, we constructed a minimal model for migrating cells which gives rise to contact inhibition of locomotion (CIL) naturally. The model cell consists of two disks, one in the front (a pseudopod) and the other one in the back (cell body), connected by a finitely extensible spring. Despite the simplicity of the model, the cells' collective behavior is highly nontrivial, depending on the shape of cells and whether CIL is enabled or not. Cells with a small front circle (i.e. a narrow pseudopod) form immobile colonies. In contrast, cells with a large front circle (i.e. such as a lamellipodium) exhibit coherent migration without any explicit alignment mechanism being present in the model. This suggests that crawling cells often exhibit broad fronts because it helps them avoid clustering. Upon increasing the density, the cells develop density waves which propagate against the direction of cell migration and finally arrest at higher densities.

cond-mat.soft↗

Purely hydrodynamic origin for swarming of swimming particles

Three-dimensional simulations with fully resolved hydrodynamics are performed to study the collective motion of model swimmers in confinement. We show that certain swimming mechanisms can lead to traveling wave-like collective motion even without any direct alignment mechanism. It is also shown that by varying the swimming mechanism, this collective motion can be suppressed, contrary to the perception that hydrodynamic effects are completely screened at high volume fraction. From an analysis of bulk systems, it is shown that this traveling wave-like motion, which can be characterized as a pseudo-acoustic mode, is mainly due to the intrinsic swimming property of the particles.

cond-mat.soft↗

Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication

The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal flow behaviors of complex fluids. In this method, the molecular dynamics simulations are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum- transport equations. This method is applied to the lubrication of a polymeric liquid composed of short chains with ten beads between parallel plates. The rheological properties and conformation of polymer chains coupled with the local viscous heating are investigated with a non-dimensional parameter, i.e., the Nahme-Griffith number, which is defined by the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer chains occur with a rapid temperature rise when the Nahme-Griffith number exceeds unity. The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains and heat generation under shear flows.

cond-mat.soft↗

Direct numerical simulations of rigid body dispersions. I. Mobility/Friction tensors of assemblies of spheres

An improved formulation of the Smoothed Profile method is introduced to perform direct numerical simulations of arbitrary rigid body dispersions in a Newtonian host solvent. Previous implementations of the method were restricted to spherical particles, severely limiting the types of systems that could be studied. The validity of the method is carefully examined by computing the friction/mobility tensors for a wide variety of geometries and comparing them to reference values obtained from accurate solutions to the Stokes-Equation.

cond-mat.soft↗

Propagation of hydrodynamic interactions between particles in a compressible fluid

Hydrodynamic interactions are transmitted by viscous diffusion and sound propagation: the temporal evolution of hydrodynamic interactions by both mechanisms is studied by direct numerical simulation in this paper. The hydrodynamic interactions for a system of two particles in a fluid are estimated by the velocity correlation of the particles. In an incompressible fluid, hydrodynamic interactions propagate instantaneously at the infinite speed of sound, followed by the temporal evolution of viscous diffusion. On the other hand, in a compressible fluid, sound propagates at a finite speed, which affects the temporal evolution of the hydrodynamic interactions by the order of magnitude relation between the time scales of viscous diffusion and sound propagation. The hydrodynamic interactions are characterized by introducing the ratio of these time scales as an interactive compressibility factor.

cond-mat.soft↗

Velocity relaxation of a particle in a confined compressible fluid

The velocity relaxation of an impulsively forced spherical particle in a fluid confined by two parallel plane walls is studied using a direct numerical simulation approach. During the relaxation process, the momentum of the particle is transmitted in the ambient fluid by viscous diffusion and sound wave propagation, and the fluid flow accompanied by each mechanism has a different character and affects the particle motion differently. Because of the bounding walls, viscous diffusion is hampered, and the accompanying shear flow is gradually diminished. However, the sound wave is repeatedly reflected and spreads diffusely. As a result, the particle motion is governed by the sound wave and backtracks differently in a bulk fluid. The time when the backtracking of the particle occurs changes non-monotonically with respect to the compressibility factor and is minimized at the characteristic compressibility factor. This factor depends on the wall spacing, and the dependence is different at small and large wall spacing regions based on the different mechanisms causing the backtracking.

physics.flu-dyn↗

Hydrodynamic Interactions of Self-Propelled Swimmers

The hydrodynamic interactions of a suspension of self-propelled particles are studied using a direct numerical simulation method which simultaneously solves for the host fluid and the swimming particles. A modified version of the "Smoothed Profile" method (SPM) is developed to simulate microswimmers as squirmers, which are spherical particles with a specified surface-tangential slip velocity between the particles and the fluid. This simplified swimming model allows one to represent different types of propulsion (pullers and pushers) and is thus ideal to study the hydrodynamic interactions among swimmers. We use the SPM to study the diffusive behavior which arises due to the swimming motion of the particles, and show that there are two basic mechanisms responsible for this phenomena: the hydrodynamic interactions caused by the squirming motion of the particles, and the particle-particle collisions. This dual nature gives rise to two distinct time- and length- scales, and thus to two diffusion coefficients, which we obtain by a suitable analysis of the swimming motion. We show that the collisions between swimmers can be interpreted in terms of binary collisions, in which the effective collision radius is reduced due to the collision dynamics of swimming particles in viscous fluids. At short time-scales, the dynamics of the swimmer is analogous to that of an inert tracer particle in a swimming suspension, in which the diffusive motion is caused by fluid-particle collisions. Our results, along with the simulation method we have introduced, will allow us to gain a better understanding of the complex hydrodynamic interactions of self-propelled swimmers.

cond-mat.soft↗

Acoustic wave propagation through a supercooled liquid: A normal mode analysis

The mechanism of acoustic wave propagation in supercooled liquids is not yet fully understood since the vibrational dynamics of supercooled liquids are strongly affected by their amorphous inherent structures. In this paper, the acoustic wave propagation in a supercooled model liquid is studied by using normal mode analysis. Due to the highly disordered inherent structure, a single acoustic wave is decomposed into many normal modes in broad frequency range. This causes the rapid decay of the acoustic wave and results in anomalous wavenumber dependency of the dispersion relation and the rate of attenuation.

cond-mat.dis-nn↗

Direct numerical simulation of dispersed particles in a compressible fluid

We present a direct numerical simulation method for investigating the dynamics of dispersed particles in a compressible solvent fluid. The validity of the simulation is examined by calculating the velocity relaxation of an impulsively forced spherical particle with a known analytical solution. The simulation also gives information about the fluid motion, which provides some insight into the particle motion. Fluctuations are also introduced by random stress, and the validity of this case is examined by comparing the calculation results with the fluctuation-dissipation theorem.

cond-mat.soft↗

Mechanical Responses and Stress Fluctuations of a Supercooled Liquid in a Sheared Non-Equilibrium State

A steady shear flow can drive supercooled liquids into a non-equilibrium state. Using molecular dynamics simulations under steady shear flow superimposed with oscillatory shear strain for a probe, non-equilibrium mechanical responses are studied for a model supercooled liquid composed of binary soft spheres. We found that even in the strongly sheared situation, the supercooled liquid exhibits surprisingly isotropic responses to oscillating shear strains applied in three different components of the strain tensor. Based on this isotropic feature, we successfully constructed a simple two-mode Maxwell model that can capture the key features of the storage and loss moduli, even for highly non-equilibrium state. Furthermore, we examined the correlation functions of the shear stress fluctuations, which also exhibit isotropic relaxation behaviors in the sheared non-equilibrium situation. In contrast to the isotropic features, the supercooled liquid additionally demonstrates anisotropies in both its responses and its correlations to the shear stress fluctuations. Using the constitutive equation (a two-mode Maxwell model), we demonstrated that the anisotropic responses are caused by the coupling between the oscillating strain and the driving shear flow. We measured the magnitude of this violation in terms of the effective temperature. It was demonstrated that the effective temperature is notably different between different components, which indicates that a simple scalar mapping, such as the concept of an effective temperature, oversimplifies the true nature of supercooled liquids under shear flow. An understanding of the mechanism of isotropies and anisotropies in the responses and fluctuations will lead to a better appreciation of these violations of the FDT, as well as certain consequent modifications to the concept of an effective temperature.

cond-mat.soft↗

2D Lattice Liquid Models

A family of novel models of liquid on a 2D lattice (2D lattice liquid models) have been proposed as primitive models of soft-material membrane. As a first step, we have formulated them as single-component, single-layered, classical particle systems on a two-dimensional surface with no explicit viscosity. Among the family of the models, we have shown and constructed two stochastic models, a vicious walk model and a flow model, on an isotropic regular lattice and on the rectangular honeycomb lattice of various sizes. In both cases, the dynamics is governed by the nature of the frustration of the particle movements. By simulations, we have found the approximate functional form of the frustration probability, and peculiar anomalous diffusions in their time-averaged mean square displacements in the flow model. The relations to other existing statistical models and possible extensions of the models are also discussed.

cond-mat.soft↗

Dynamic rheology of a supercooled polymer melt in non-uniform oscillating flows in rapidly oscillating plates

The dynamic rheology of a polymer melt composed of short chains with ten beads between rapidly oscillating plates is investigated for various oscillation frequencies by using the hybrid simulation of the molecular dynamics and computational fluid dynamics. In the rapidly oscillating plates, non-uniform boundary layer flows are generated over the plate due to inertia of the fluid, and the local rheological properties of the melt are spatially varied according to the local flow fields. Far from the plate, the local strain decreases as the oscillation frequency increases such that the dynamic rheology deviates from the linear moduli at the low oscillation frequencies rather than high oscillation frequencies. On the contrary, near the plate, the local strain rate increases with the oscillation frequency such that the shear thinning is enhanced at high oscillation frequencies. In close vicinity to the plate, the dynamic viscosity is mostly independent of the oscillation frequency, and the shear thinning behavior becomes similar to that observed in steady shear flows. Non-linear rheological properties are also investigated by the spectrum analysis and the Lissajous-Bowditch curve. It is found that the fractional amplitude of the higher harmonics to the linear harmonics is suppressed within the boundary layer due to the non-slip boundary on the oscillating plate. We also find that the melt exhibits inter-cycle shear thinning between different positions but exhibits intra-cycle shear thickening at a fixed position in the vicinity of the plate.

cond-mat.soft↗