arXiv subjects

Shigeyuki Komura

Publications and source records attributed to Shigeyuki Komura.

At least 37 records · Page 2Linked to original sources

arXiv2024

Time-correlation functions of stochastic three-sphere micromachines

We discuss and compare the statistical properties of two stochastic three-sphere micromachines, i.e., odd micromachine and thermal micromachine. We calculate the steady state time-correlation functions for these micromachines and decompose them into the symmetric and antisymmetric parts. In both cases, the cross-correlation between the two spring extensions has an antisymmetric part, which is a direct consequence of the broken time-reversal symmetry. For the odd micromachine, the antisymmetric part of the correlation function is proportional to the odd elasticity, whereas it is proportional to the temperature difference between the two edge spheres for the thermal micromachine. The entropy production rate and the Green-Kubo relations for the two micromachines are also obtained. Comparing the results of the two models, we argue an effective odd elastic constant of the thermal micromachine. The effective odd elasticity of the thermal micromachine is proportional to the temperature difference among the spheres, which causes an internal heat flow and leads to directional locomotion in the presence of hydrodynamic interactions.

cond-mat.stat-mech↗

arXiv2024

Field Theory of Active Brownian Particles with Dry Friction

We present a field theoretic approach to capture the motion of a particle with dry friction for one- and two-dimensional diffusive particles, and further expand the framework for two-dimensional active Brownian particles. Starting with the Fokker-Planck equation and introducing the Hermite polynomials as the corresponding eigen-functions, we obtain the actions and propagators. Using a perturbation expansion, we calculate the effective diffusion coefficient in the presence of both wet and dry frictions in a perturbative way via the Green-Kubo relation. We further compare the analytical result with the numerical simulation. Our result can be used to estimate the values of dry friction coefficient in experiments.

cond-mat.stat-mech↗

arXiv2024

Statistical formulation of Onsager-Machlup variational principle

Onsager's variational principle (OVP) provides us with a systematic way to derive dynamical equations for various soft matter and active matter. By reformulating the Onsager-Machlup variational principle (OMVP), which is a time-global principle, we propose a new method to incorporate thermal fluctuations. To demonstrate the utility of the statistical formulation of OMVP (SOMVP), we obtain the diffusion constant of a Brownian particle embedded in a viscous fluid only by maximizing the modified Onsager-Machlup integral for the surrounding fluid. We also apply our formulation to a Brownian particle in a steady shear flow, which is a typical example of a non-equilibrium system. Possible extensions of our formulation to internally driven active systems are discussed.

cond-mat.soft↗

arXiv2024

Emergence of odd elasticity in a microswimmer using deep reinforcement learning

We use the Deep Q-Network with reinforcement learning to investigate the emergence of odd elasticity in an elastic microswimmer model. For an elastic microswimmer, it is challenging to obtain the optimized dynamics due to the intricate elastohydrodynamic interactions. However, our machine-trained model adopts a novel transition strategy (the waiting behavior) to optimize the locomotion. For the trained microswimmers, we evaluate the performance of the cycles by the product of the loop area (called non-reciprocality) and the loop frequency, and show that the average swimming velocity is proportional to the performance. By calculating the force-displacement correlations, we obtain the effective odd elasticity of the microswimmer to characterize its non-reciprocal dynamics. This emergent odd elasticity is shown to be closely related to the loop frequency of the cyclic deformation. Our work demonstrates the utility of machine learning in achieving optimal dynamics for elastic microswimmers and introduces post-analysis methods to extract crucial physical quantities such as non-reciprocality and odd elasticity.

cond-mat.soft↗

arXiv2023

Non-reciprocal Phase Separations with Non-conserved Order Parameters

We numerically investigate the phase separation dynamics of the non-reciprocal Allen-Cahn model in which two non-conserved order parameters are coupled. The system exhibits several dynamical patterns such as the randomly oscillating phase and the spiral phase as well as the homogeneously oscillating phase. Topological defects in the spirals are either bound or unbound depending on the non-reciprocality. The traveling stripe pattern is also found when the diffusion constants are highly asymmetric and the non-reciprocality is small.

cond-mat.soft↗

arXiv2023

Generalized Three-Sphere Microswimmers

Among several models for microswimmers, the three-sphere microswimmer proposed by Najafi and Golestanian captures the essential mechanism for the locomotion of a microswimmer in a viscous fluid. Owing to its simplicity and flexibility, the original three-sphere model has been extended and generalized in various ways to discuss new swimming mechanisms of microswimmers. We shall provide a systematic and concise review of the various extensions of the three-sphere microswimmers that have been developed by the present authors. In particular, we shall discuss the following seven cases; elastic, thermal, odd, autonomous three-sphere microswimmers; two interacting ones; and those in viscoelastic and structured fluids. The well-known Purcell's scallop theorem can be generalized for stochastic three-sphere microswimmers and also for the locomotion in viscoelastic and structured fluids.

cond-mat.soft↗

arXiv2023

Odd elasticity of a catalytic micromachine

We perform numerical simulations of a model micromachine driven by catalytic chemical reactions. Our model includes a mechano-chemical coupling between the structural variables and the nonequilibrium variable describing the catalytic reactions. The time-correlation functions of the structural variables are calculated and further analyzed in terms of odd Langevin dynamics. We obtain the effective odd elastic constant that manifests the broken time-reversal symmetry of a catalytic micromachine. Within the simulation, we separately estimate the quantity called nonreciprocality and show that its behavior is similar to that of the odd elasticity.Our approach suggests a new method to extract the nonequilibrium properties of a micromachine only by measuring its structural dynamics.

cond-mat.soft↗

arXiv2023

Pair dynamics of active force dipoles in an odd-viscous fluid

We discuss the lateral dynamics of two active force dipoles, which interact with each other via hydrodynamic interactions in a thin fluid layer that is active and chiral. The fluid layer is modeled as a two-dimensional (2D) compressible fluid with an odd viscosity, while the force dipole (representing an active protein or enzyme) induces a dipolar flow. Taking into account the momentum decay in the 2D fluid, we obtain analytically the mobility tensor that depends on the odd viscosity and includes nonreciprocal hydrodynamic interactions. We find that the particle pair shows spiral behavior due to the transverse flow induced by the odd viscosity. When the magnitude of the odd viscosity is large as compared with the shear viscosity, two types of oscillatory behaviors are seen. One of them can be understood as arising from closed orbits in dynamical systems, and its circular trajectories are determined by the ratio between the magnitude of the odd viscosity and the force dipole. In addition, the phase diagrams of the particle dipolar angles are obtained numerically. Our findings reveal that the nonreciprocal response leads to complex dynamics of active particles embedded in an active fluid with odd viscosity.

cond-mat.soft↗

arXiv2023

Simulations of Odd Microswimmers

We perform numerical simulations of odd microswimmers consisting of three spheres and two odd springs. To describe the hydrodynamic interaction, both the Oseen-type and the Rotne-Prager-Yamakawa (RPY)-type mobilities are used. For the Oseen-type mobility, the simulation results quantitatively reproduce the asymptotic expression of the average velocity. For the RPY-type mobility, on the other hand, the average velocity is smaller than that of the Oseen-type mobility and the deviation is more pronounced for larger spheres. We also perform simulations of microswimmers having different sphere sizes and show that the average velocity becomes smaller than that of the equal size case. The size of the middle sphere plays an important role in determining the average velocity.

cond-mat.soft↗

arXiv2023

Onsager's variational principle for nonreciprocal systems with odd elasticity

Using Onsager's variational principle, we derive dynamical equations for a nonequilibrium active system with odd elasticity. The elimination of the extra variable that is coupled to the nonequilibrium driving force leads to the nonreciprocal set of equations for the material coordinates. The obtained nonreciprocal equations manifest the physical origin of the odd elastic constants that are proportional to the nonequilibrium force and the friction coefficients. Our approach offers a systematic and consistent way to derive nonreciprocal equations for active matter in which the time-reversal symmetry is broken.

cond-mat.soft↗

arXiv2022

Universality in the dynamics of vesicle translocation through a hole

We analyze the translocation process of a spherical vesicle, made of membrane and incompressible fluid, through a hole smaller than the vesicle size, driven by pressure difference $ΔP$. We show that such a vesicle shows certain universal characteristics which is independent of the details of the membrane elasticity; (i) there is a critical pressure $ΔP_{\rm c}$ below which no translocation occurs, (ii) $ΔP_{\rm c}$ decreases to zero as the vesicle radius $R_0$ approaches the hole radius $a$, satisfying the scaling relation $ΔP_{\rm c} \sim (R_0 - a)^{3/2}$, and (iii) the translocation time $τ$ diverges as $ΔP$ decreases to $ΔP_{\rm c}$, satisfying the scaling relation $τ\sim (ΔP -ΔP_{\rm c})^{-1/2}$.

cond-mat.soft↗

arXiv2022

Lateral response of a layered material with interlayer friction

We investigate the mechanical properties of a layered material with interlayer friction. We propose a model that contains lateral elasticity and interlayer friction to obtain the response function both in the Fourier and real spaces. By investigating how the internal deformation is laterally induced due to the applied surface displacement, we find that it is transmitted into the material with an apparent phase difference. We also obtain the effective complex modulus of the layered material and show that it exhibits an intermediate power-law behavior in the low-frequency regime. Our result can be used to estimate the internal deformation of layered materials that exist on various different scales.

cond-mat.soft↗

arXiv2022

Time-correlation functions for odd Langevin systems

We investigate the statistical properties of fluctuations in active systems that are governed by non-symmetric responses. Both an underdamped Langevin system with an odd resistance tensor and an overdamped Langevin system with an odd elastic tensor are studied. For a system in thermal equilibrium, the time-correlation functions should satisfy time-reversal symmetry and the anti-symmetric parts of the correlation functions should vanish. For the odd Langevin systems, however, we find that the anti-symmetric parts of the time-correlation functions can exist and that they are proportional to either the odd resistance coefficient or the odd elastic constant. This means that the time-reversal invariance of the correlation functions is broken due to the presence of odd responses in active systems. Using the short-time asymptotic expressions of the time-correlation functions, one can estimate an odd elastic constant of an active material such as an enzyme or a motor protein.

cond-mat.soft↗

arXiv2022

Nonequilibrium Transport Induced by Biological Nanomachines

Biological nanomachines are nanometer-size macromolecular complexes that catalyze chemical reactions in the presence of substrate molecules. The catalytic functions carried out by such nanomachines in the cytoplasm, and biological membranes are essential for cellular metabolism and homeostasis. During catalytic reactions, enzymes undergo conformational changes induced by substrate binding and product release. In recent years, these conformational dynamics have been considered to account for the nonequilibrium transport phenomena such as diffusion enhancement, chemotaxis, and substantial change in rheological properties, which are observed in biological systems. In this review article, we shall give an overview of the recent theoretical and experimental investigations that deal with nonequilibrium transport phenomena induced by biological nanomachines such as enzymes or proteins.

cond-mat.soft↗

arXiv2022

Odd Viscosity in Chiral Passive Suspensions

Prior studies have revealed that nonzero odd viscosity is an essential property for chiral active fluids. Here we report that such an odd viscosity also exists in suspensions of non-active or non-externally-driven but chirally-shaped particles. Computational simulations are carried out for monolayers of dense ratchets in simple shear and planar extensional flows. The contact between two ratchets can be either frictionless or infinitely-frictional, depending on their teeth and sliding directions at the contact point. Our results show that the ratchet suspension has the intermediate shear/extensional viscosity as compared with the suspensions of smooth and gear-like particles. Meanwhile, the ratchet suspensions show nonzero even and odd components of the first normal stress coefficient, which indicates the mixed feature of conventional complex fluids and chiral viscous fluids.

cond-mat.soft↗

arXiv2022

Emergent Stripes of Active Rotors in Shear Flows

The shear-induced self-organization of active rotors into stripy aggregates is studied by carrying out computational simulations. The rotors, modeled by monolayers of frictional spheres, develop to stripy microstructures only when they counterrotate with respect to the vorticity of the imposed shear flow. The average width of the stripes is demonstrated to be linearly dependent on the relative intensity of active torque to the shear rate. By giving insight into three collective particle behaviors, i.e., shear-induced diffusion, rotation-induced rearrangement, and edge flows, we explain the mechanisms of formation of the particle stripes. Additionally, the rheological result shows the dependence of shear and rotational viscosities on the active torque direction and the oddness of the normal stress response. By exhibiting a collective phenomenon of active rotors, our study paves the way to understanding chiral active matter.

cond-mat.soft↗

arXiv2021

The Onsager-Machlup Integral for Non-reciprocal Systems with Odd Elasticity

The variational principle of the Onsager-Machlup integral is used to describe the stochastic dynamics of a micromachine, such as an enzyme, characterized by odd elasticity. The obtained most probable path is found to become non-reciprocal in the presence of odd elasticity and is further related to the entropy production.

cond-mat.soft↗

arXiv2021

Hydrodynamic lift of a two-dimensional liquid domain with odd viscosity

We discuss hydrodynamic forces acting on a two-dimensional liquid domain that moves laterally within a supported fluid membrane in the presence of odd viscosity. Since active rotating proteins can accumulate inside the domain, we focus on the difference in odd viscosity between the inside and outside of the domain. Taking into account the momentum leakage from a two-dimensional incompressible fluid to the underlying substrate, we analytically obtain the fluid flow induced by the lateral domain motion, and calculate the drag and lift forces acting on the moving liquid domain. In contrast to the passive case without odd viscosity, the lateral lift arises in the active case only when the in/out odd viscosities are different. The in/out contrast in the odd viscosity leads to nonreciprocal hydrodynamic responses of an active liquid domain.

cond-mat.soft↗