arXiv subjects

Shigeyuki Komura

Publications and source records attributed to Shigeyuki Komura.

At least 73 records · Page 4Linked to original sources

arXiv2018

Thermal and active fluctuations of a compressible bilayer vesicle

We discuss thermal and active fluctuations of a compressible bilayer vesicle by using the results of hydrodynamic theory for vesicles. Coupled Langevin equations for the membrane deformation and the density fields are employed to calculate the power spectral density matrix of membrane fluctuations. Thermal contribution is obtained by means of the fluctuation dissipation theorem, whereas active contribution is calculated from exponentially decaying time correlation functions of active random forces. We obtain the total power spectral density as a sum of thermal and active contributions. An apparent response function is further calculated in order to compare with the recent microrheology experiment on red blood cells. An enhanced response is predicted in the low-frequency regime for non-thermal active fluctuations.

cond-mat.soft↗

arXiv2018

Kosmotropic effect leads to LCST decrease in thermoresponsive polymer solutions

We study the phenomena of decrease in lower critical solution temperature (LCST) with addition of kosmotropic (order-making) cosolvents in thermoresponsive polymer solutions. A combination of explicit solvent coarse-grained simulations and mean-field theory has been employed. The polymer-solvent LCST behavior in the theoretical models have been incorporated through the Kolomeisky-Widom solvophobic potential. Our results illustrate how the decrease in the LCST can be achieved by the reduction in the bulk solvent energy with addition of cosolvent. It is shown that this effect of cosolvent is weaker with increase in polymer hydrophilicity which can explain the absence of LCST decrease in PDEA, water and methanol systems. The coarse-grained nature of the models indicates that a mean energetic representation of the system is sufficient to understand the phenomena of LCST decrease.

cond-mat.soft↗

arXiv2017

Permeation through a lamellar stack of lipid mixtures

We study material transport and permeation through a lamellar stack of multi-component lipid membranes by performing Monte Carlo simulations of a stacked two-dimensional Ising model in presence of permeants. In the model, permeants are transported through the stack via in-plane lipid clusters, which are inter-connected in the vertical direction. These clusters are formed transiently by concentration fluctuations of the lipid mixture, and the permeation process is affected, especially close to the critical temperature of the binary mixture. We show that the permeation rate decays exponentially as function of temperature and permeant lateral size, whereas the dependency on the characteristic waiting time obeys a stretched exponential function. The material transport through such lipid clusters can be significantly affected around physiological temperatures.

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

Coexistences of lamellar phases in ternary surfactant solutions

We theoretically investigate the coexistences of lamellar phases both in binary and ternary surfactant solutions. The previous free energy of a lamellar stack is extended to take into account the translational entropy of membrane segments. The obtained phase diagram for binary surfactant solutions (surfactant/water mixtures) shows a phase separation between two lamellar phases and also exhibits a critical point. For lamellar phases in ternary surfactant solutions (surfactant/surfactant/water mixtures), we explore possible phase behaviors and show that the phase diagrams exhibit various three-phase regions as well as two-phase regions in which different lamellar phases coexist. We also find that finite surface tension suppresses undulation fluctuations of membranes and leads to a wider three-phase and two-phase coexistence regions.

cond-mat.soft↗

arXiv2017

Dynamics of a Bilayer Membrane Coupled to a Two-dimensional Cytoskeleton: Scale Transfers of Membrane Deformations

We theoretically investigate the dynamics of a floating lipid bilayer membrane coupled with a two-dimensional cytoskeleton network, taking into explicitly account the intermonolayer friction, the discrete lattice structure of the cytoskeleton, and its prestress. The lattice structure breaks lateral continuous translational symmetry and couples Fourier modes with different wavevectors. It is shown that within a short time interval a long-wavelength deformation excites a collection of modes with wavelengths shorter than the lattice spacing. These modes relax slowly with a common renormalized rate originating from the long-wavelength mode. As a result, and because of the prestress, the slowest relaxation is governed by the intermonolayer friction. Reversely, and most interestingly, forces applied at the scale of the cytoskeleton for a sufficiently long time can cooperatively excite large-scale modes.

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↗

arXiv2017

Anomalous diffusion in viscoelastic media with active force dipoles

With the use of the "two-fluid model", we discuss anomalous diffusion induced by active force dipoles in viscoelastic media. Active force dipoles, such as proteins and bacteria, generate non-thermal fluctuating flows that lead to a substantial increment of the diffusion. Using the partial Green's function of the two-fluid model, we first obtain passive (thermal) two-point correlation functions such as the displacement cross-correlation function between the two point particles separated by a finite distance. We then calculate active (non-thermal) one-point and two-point correlation functions due to active force dipoles. The time correlation of a force dipole is assumed to decay exponentially with a characteristic time scale. We show that the active component of the displacement cross-correlation function exhibits various crossovers from super-diffusive to sub-diffusive behaviors depending on the characteristic time scales and the particle separation. Our theoretical results are intimately related to the microrheology technique to detect fluctuations in non-equilibrium environment.

cond-mat.soft↗

arXiv2017

Swimmer-microrheology

We discuss a locomotion of a three-sphere microswimmer in a viscoelastic medium and propose a new type of active microrheology. We derive a relation which connects average swimming velocity and frequency-dependent viscosity of the surrounding medium. In this relation, the viscous contribution can exist only when the time-reversal symmetry is broken, whereas the elastic contribution is present only when the structural symmetry of the swimmer is broken. The Purcell's scallop theorem breaks down for a three-sphere swimmer in a viscoelastic medium.

cond-mat.soft↗

arXiv2017

Localization and diffusion of tracer particles in viscoelastic media with active force dipoles

Optical tracking in vivo experiments reveal that diffusion of particles in biological cells is strongly enhanced in the presence of ATP and the experimental data for animal cells could previously be reproduced within a phenomenological model of a gel with myosin motors acting within it [EPL 110, 48005 (2015)]. Here, the two-fluid model of a gel is considered where active macromolecules, described as force dipoles, cyclically operate both in the elastic and the fluid components. Through coarse-graining, effective equations of motions for tracer particles displaying local deformations and local fluid flows are derived. The equation for deformation tracers coincides with the earlier phenomenological model and thus confirms it. For flow tracers, diffusion enhancement caused by active force dipoles in the fluid component, and thus due to metabolic activity, is found. The latter effect may explain why ATP-dependent diffusion enhancement could also be observed in bacteria that lack molecular motors in their skeleton or when the activity of myosin motors was chemically inhibited.

cond-mat.soft↗

arXiv2016

Relaxation dynamics of a compressible bilayer vesicle containing highly viscous fluid

We study the relaxation dynamics of a compressible bilayer vesicle with an asymmetry in the viscosity of the inner and outer fluid medium. First we explore the stability of the vesicle free energy which includes a coupling between the membrane curvature and the local density difference between the two monolayers. Two types of instabilities are identified: a small wavelength instability and a larger wavelength instability. Considering the bulk fluid viscosity and the inter-monolayer friction as the dissipation sources, we next employ Onsager's variational principle to derive the coupled equations both for the membrane and the bulk fluid. The three relaxation modes are coupled to each other due to the bilayer and the spherical structure of the vesicle. Most importantly, a higher fluid viscosity inside the vesicle shifts the cross-over mode between the bending and the slipping to a larger value. As the vesicle parameters approach toward the unstable regions, the relaxation dynamics is dramatically slowed down, and the corresponding mode structure changes significantly. In some limiting cases, our general result reduces to the previously obtained relaxation rates.

cond-mat.soft↗

arXiv2016

Budding Transition of Asymmetric Two-component Lipid Domains

We propose a model that accounts for the budding transition of asymmetric two-component lipid domains, where the two monolayers (leaflets) have different average compositions controlled by independent chemical potentials. Assuming a coupling between the local curvature and local lipid composition in each of the leaflets, we discuss the morphology and thermodynamic behavior of asymmetric lipid domains. The membrane free-energy contains three contributions: the bending energy, the line tension, and a Landau free-energy for a lateral phase separation. Within a mean-field treatment, we obtain various phase diagrams containing fully budded, dimpled, and flat states as a function of the two leaflet compositions. The global phase behavior is analyzed, and depending on system parameters, the phase diagrams include one-phase, two-phase and three-phase regions. In particular, we predict various phase coexistence regions between different morphologies of domains, which may be observed in multi-component membranes or vesicles.

cond-mat.soft↗

arXiv2016

Spherically symmetric solvent is sufficient to explain lower critical solution temperature in polymer solutions

We study the lower critical solution temperature (LCST) in thermoresponsive polymer solutions by means of a coarse grained single polymer chain simulation and a theoretical approach. The simulation model includes solvent explicitly and thus accounts for solvent interactions and entropy directly. The theoretical model consists of a single chain polymer in an implicit solvent where the effect of solvent is included through the intra-polymer solvophobic potential proposed by Kolomeisky and Widom. Our results indicate that the LCST behavior is determined by the competition between the mean energy difference between the bulk and bound solvent, and the entropy loss due to the bound solvent. At low temperatures, solvent molecules are bound to the polymer and the solvophobicity of the polymer is screened, resulting in a coiled state. At high temperatures the entropy loss due to bound solvent offsets the energy gain due to binding which causes the solvent molecules to unbind, leading to the collapse of the polymer chain to a globular state. Furthermore, the coarse grained nature of these models indicates that mean interaction energies are sufficient to explain LCST in comparison to specific solvent structural arrangements.

cond-mat.soft↗

arXiv2016

Phase diagrams and ordering in charged membranes: Binary mixtures of charged and neutral lipids

We propose a model describing the phase behavior of two-component membranes consisting of binary mixtures of electrically charged and neutral lipids. We take into account the structural phase transition (main-transition) of the hydrocarbon chains, and investigate the interplay between this phase transition and the lateral phase separation. The presence of charged lipids significantly affects the phase behavior of the multi-component membrane. Due to the conservation of lipid molecular volume, the main-transition temperature of charged lipids is lower than that of neutral ones. Furthermore, as compared with binary mixtures of neutral lipids, the membrane phase separation in binary mixtures of charged lipids is suppressed, in accord with recent experiments. We distinguish between two types of charged membranes: mixtures of charged saturated lipid/neutral unsaturated lipid and a second case of mixtures of neutral saturated lipid/charged unsaturated lipid. The corresponding phase behavior is calculated and shown to be very different. Finally, we discuss the effect of added salt on the phase separation and the temperature dependence of the lipid molecular area.

cond-mat.soft↗

arXiv2016

Dynamics of a membrane interacting with an active wall

Active motions of a biological membrane can be induced by non-thermal fluctuations that occur in the outer environment of the membrane. We discuss the dynamics of a membrane interacting hydrodynamically with an active wall that exerts random velocities on the ambient fluid. Solving the hydrodynamic equations of a bound membrane, we first derive a dynamic equation for the membrane fluctuation amplitude in the presence of different types of walls. Membrane two-point correlation functions are calculated for three different cases; (i) a static wall, (ii) an active wall, and (iii) an active wall with an intrinsic time scale. We focus on the mean squared displacement (MSD) of a tagged membrane describing the Brownian motion of a membrane segment. For the static wall case, there are two asymptotic regimes of MSD ($\sim t^{2/3}$ and $\sim t^{1/3}$) when the hydrodynamic decay rate changes monotonically. In the case of an active wall, the MSD grows linearly in time ($\sim t$) in the early stage, which is unusual for a membrane segment. This linear-growth region of the MSD is further extended when the active wall has a finite intrinsic time scale.

cond-mat.soft↗

arXiv2016

Nano-domain formation in charged membranes: Beyond Debye-Huckel approximation

We investigate the microphase separation in a membrane composed of charged lipid, by taking into account explicitly the electrostatic potential and the ion densities in the surrounding solvent. While the overall (membrane and solvent) charge neutrality is assumed, the membrane can have a non-zero net charge. The static structure factor in the homogeneous state is analytically obtained without using the Debye-Huckel approximation and is found to have a peak at an intermediate wave number. For a binary membrane composed of anionic and neutral lipids, the characteristic wave number corresponds to a scale from several to tens of nanometers. Our numerical calculation further predicts the existence of nano-domains in charged membranes.

cond-mat.soft↗

arXiv2016

Relaxation dynamics of two-component fluid bilayer membranes

We theoretically investigate the relaxation dynamics of a nearly-flat binary lipid bilayer membrane by taking into account the membrane tension, hydrodynamics of the surrounding fluid, inter-monolayer friction and mutual diffusion in each monolayer. We find that two relaxation modes associated with the mutual diffusion appear in addition to the three previously discussed relaxation modes reflecting the bending and compression of the membrane. Because of the symmetry, only one of the two diffusive mode is coupled to the bending mode. The two diffusive modes are much slower than the bending and compression modes in the entire realistic wave number range. This means that the long time relaxation behavior is dominated by the mutual diffusion in binary membranes. The two diffusive modes become even slower in the vicinity of the unstable region towards phase separation, while the other modes are almost unchanged. In short time scales, on the other hand, the lipid composition heterogeneity induces in-plane compression and bending of the bilayer.

cond-mat.soft↗