arXiv subjects

Yuto Hosaka

Publications and source records attributed to Yuto Hosaka.

34 records · Page 2Linked to original sources

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↗

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↗

arXiv2021

Odd Microswimmer

We propose a model for a thermally driven microswimmer in which three spheres are connected by two springs with odd elasticity. We demonstrate that the presence of odd elasticity leads to the directional locomotion of the stochastic microswimmer.

cond-mat.soft↗

arXiv2021

Non-reciprocal response of a two-dimensional fluid with odd viscosity

We discuss the linear hydrodynamic response of a two-dimensional active chiral compressible fluid with odd viscosity. The viscosity coefficient represents broken time-reversal and parity symmetries in the 2D fluid and characterizes the deviation of the system from a passive fluid. Taking into account the hydrodynamic coupling to the underlying bulk fluid, we obtain the odd viscosity-dependent mobility tensor, which is responsible for the non-reciprocal hydrodynamic response to a point force. Furthermore, we consider a finite-size disk moving laterally in the 2D fluid and demonstrate that the disk experiences a non-dissipative lift force in addition to the dissipative drag one.

physics.flu-dyn↗

arXiv2020

Autonomous elastic microswimmer

A model of an autonomous three-sphere microswimmer is proposed by implementing a coupling effect between the two natural lengths of an elastic microswimmer. Such a coupling mechanism is motivated by the previous models for synchronization phenomena in coupled oscillator systems. We numerically show that a microswimmer can acquire a nonzero steady state velocity and a finite phase difference between the oscillations in the natural lengths. These velocity and phase difference are almost independent of the initial phase difference. There is a finite range of the coupling parameter for which a microswimmer can have an autonomous directed motion. The stability of the phase difference is investigated both numerically and analytically in order to determine its bifurcation structure.

cond-mat.soft↗

arXiv2020

Mechanochemical enzymes and protein machines as hydrodynamic force dipoles: The active dimer model

Mechanochemically active enzymes change their shapes within every turnover cycle. Therefore, they induce circulating flows in the solvent around them and behave as oscillating hydrodynamic force dipoles. Because of non-equilibrium fluctuating flows collectively generated by the enzymes, mixing in the solution and diffusion of passive particles within it are expected to get enhanced. Here, we investigate the intensity and statistical properties of such force dipoles in the minimal active dimer model of a mechanochemical enzyme. In the framework of this model, novel estimates for hydrodynamic collective effects in solution and in lipid bilayers under rapid rotational diffusion are derived, and available experimental and computational data is examined.

cond-mat.soft↗

arXiv2020

Irreversibility and entropy production of a thermally driven micromachine

We discuss the non-equilibrium properties of a thermally driven micromachine consisting of three spheres which are in equilibrium with independent heat baths characterized by different temperatures. Within the framework of a linear stochastic Langevin description, we calculate the time-dependent average irreversibility that takes a maximum value for a finite time. This time scale is roughly set by the spring relaxation time. The steady-state average entropy production rate is obtained in terms of the temperatures and the friction coefficients of the spheres. The average entropy production rate depends on thermal and/or mechanical asymmetry of a three-sphere micromachine. We also obtain the center of mass diffusion coefficient of a thermally driven three-sphere micromachine as a function of different temperatures and friction coefficients. With the results of the total entropy production rate and the diffusion coefficient, we finally discuss the efficiency of a thermally driven micromachine.

cond-mat.stat-mech↗

arXiv2019

Shear viscosity of two-state enzyme solutions

We discuss the shear viscosity of a Newtonian solution of catalytic enzymes and substrate molecules. The enzyme is modeled as a two-state dimer consisting of two spherical domains connected with an elastic spring. The enzymatic conformational dynamics is induced by the substrate binding and such a process is represented by an additional elastic spring. Employing the Boltzmann distribution weighted by the waiting times of enzymatic species in each catalytic cycle, we obtain the shear viscosity of dilute enzyme solutions as a function of substrate concentration and its physical properties. The substrate affinity distinguishes between fast and slow enzymes, and the corresponding viscosity expressions are obtained. Furthermore, we connect the obtained viscosity with the diffusion coefficient of a tracer particle in enzyme solutions.

cond-mat.soft↗

arXiv2019

Non-equilibrium probability flux of a thermally driven micromachine

We discuss the non-equilibrium statistical mechanics of a thermally driven micromachine consisting of three spheres and two harmonic springs [Y. Hosaka et al., J. Phys. Soc. Jpn. 86, 113801 (2017)]. We obtain the non-equilibrium steady state probability distribution function of such a micromachine and calculate its probability flux in the corresponding configuration space. The resulting probability flux can be expressed in terms of a frequency matrix that is used to distinguish between a non-equilibrium steady state and a thermal equilibrium state satisfying detailed balance. The frequency matrix is shown to be proportional to the temperature difference between the spheres. We obtain a linear relation between the eigenvalue of the frequency matrix and the average velocity of a thermally driven micromachine that can undergo a directed motion in a viscous fluid. This relation is consistent with the scallop theorem for a deterministic three-sphere microswimmer.

cond-mat.stat-mech↗

arXiv2018

Three-disk microswimmer in a supported fluid membrane

A model of three-disk micromachine swimming in a quasi two-dimensional supported membrane is proposed. We calculate the average swimming velocity as a function of the disk size and the arm length. Due to the presence of the hydrodynamic screening length in the quasi two-dimensional fluid, the geometric factor appearing in the average velocity exhibits three different asymptotic behaviors depending on the microswimmer size and the hydrodynamic screening length. This is in sharp contrast with a microswimmer in a three-dimensional bulk fluid that shows only a single scaling behavior. We also find that the maximum velocity is obtained when the disks are equal-sized, whereas it is minimized when the average arm lengths are identical. The intrinsic drag of the disks on the substrate does not alter the scaling behaviors of the geometric factor.

cond-mat.soft↗

arXiv2017

Thermally Driven Elastic Micromachines

We discuss the directional motion of an elastic three-sphere micromachine in which the spheres are in equilibrium with independent heat baths having different temperatures. Even in the absence of prescribed motion of springs, such a micromachine can gain net motion purely because of thermal fluctuations. A relation connecting the average velocity and the temperatures of the spheres is analytically obtained. This velocity can also be expressed in terms of the average heat flows in the steady state. Our model suggests a new mechanism for the locomotion of micromachines in nonequilibrium biological systems.

cond-mat.soft↗

arXiv2017

Elastic three-sphere microswimmer in a viscous fluid

We discuss the dynamics of a generalized three-sphere microswimmer in which the spheres are connected by two elastic springs. The natural length of each spring is assumed to undergo a prescribed cyclic change. We analytically obtain the average swimming velocity as a function of the frequency of the cyclic change in the natural length. In the low-frequency region, the swimming velocity increases with the frequency and its expression reduces to that of the original three-sphere model by Najafi and Golestanian. In the high-frequency region, conversely, the average velocity decreases with increasing the frequency. Such a behavior originates from the intrinsic spring relaxation dynamics of an elastic swimmer moving in a viscous fluid.

cond-mat.soft↗

arXiv2017

Lateral diffusion induced by active proteins in a biomembrane

We discuss the hydrodynamic collective effects due to active protein molecules that are immersed in lipid bilayer membranes and modeled as stochastic force dipoles. We specifically take into account the presence of the bulk solvent which surrounds the two-dimensional fluid membrane. Two membrane geometries are considered: the free membrane case and the confined membrane case. Using the generalized membrane mobility tensors, we estimate the active diffusion coefficient and the drift velocity as a function of the size of a diffusing object. The hydrodynamic screening lengths distinguish the two asymptotic regimes of these quantities. Furthermore, the competition between the thermal and non-thermal contributions in the total diffusion coefficient is characterized by two length scales corresponding to the two membrane geometries. These characteristic lengths describe the crossover between different asymptotic behaviors when they are larger than the hydrodynamic screening lengths.

cond-mat.soft↗