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Hiroshi Noguchi

Publications and source records attributed to Hiroshi Noguchi.

At least 73 records · Page 4Linked to original sources

Effects of anchored flexible polymers on mechanical properties of model biomembranes

We have studied biomembranes with grafted polymer chains using a coarse-grained membrane simulation, where a meshless membrane model is combined with polymer chains. We focus on the polymer-induced entropic effects on mechanical properties of membranes. The spontaneous curvature and bending rigidity of the membranes increase with increasing polymer density. Our simulation results agree with the previous theoretical predictions.

physics.bio-ph↗

Structure formation in binary mixtures of lipids and detergents: Self-assembly and vesicle division

Self-assembly dynamics in binary surfactant mixtures and structure changes of lipid vesicles induced by detergent solution are studied using coarse-grained molecular simulations. Disk-shaped micelles, the bicelles, are stabilized by detergents surrounding the rim of a bilayer disk of lipids. The self-assembled bicelles are considerably smaller than bicelles formed from vesicle rupture, and their size is determined by the concentrations of lipids and detergents and the interactions between the two species. The detergent-adsorption induces spontaneous curvature of the vesicle bilayer and results in vesicle division into two vesicles or vesicle rupture into worm-like micelles. The division occurs mainly via the inverse pathway of the modified stalk model. For large spontaneous curvature of the monolayers of the detergents, a pore is often opened, thereby leading to vesicle division or worm-like micelle formation.

cond-mat.soft↗

Structure formation in binary mixtures of surfactants: vesicle opening-up to bicelles and octopus-like micelles

Micelle formation in binary mixtures of surfactants is studied using a coarse-grained molecular simulation. When a vesicle composed of lipid and detergent types of molecules is ruptured, a disk-shaped micelle, the bicelle, is typically formed. It is found that cup-shaped vesicles and bicelles connected with worm-like micelles are also formed depending on the surfactant ratio and critical micelle concentration. The obtained octopus shape of micelles agree with those observed in the cryo-TEM images reported in [S. Jain and F. S. Bates, Macromol. 37, 1511 (2004).]. Two types of connection structures between the worm-like micelles and the bicelles are revealed.

cond-mat.soft↗

Line tension of branching junctions of bilayer membranes

Branching of bilayer membranes appear in the inverted hexagonal phase as well as in metastable states of the lamellar phase such as membrane fusion intermediates. A method for estimating the line tension of the branching junction is proposed for molecular simulations. The line tension is calculated from the pressure tensor of equiangularly branched membranes. The simulation results agree very well with the theoretical prediction of Hamm and Kozlov's tilt model. The transition between the lamellar and inverted hexagonal phases is also investigated using the tilt model.

cond-mat.soft↗

Measurement of the bending rigidity and spontaneous curvature of fluid membranes in simulations

Several numerical methods for measuring the bending rigidity and the spontaneous curvature of fluid membranes are studied using two types of meshless membrane models. The bending rigidity is estimated from the thermal undulations of planar and tubular membranes and the axial force of tubular membranes. We found a large dependence of its estimate value from the thermal undulation analysis on the upper-cutoff frequency q_{cut} of the least squares fit. The inverse power-spectrum fit with an extrapolation to q_{cut} -> 0 yields the smallest estimation error among the investigated methods. The spontaneous curvature is estimated from the axial force of tubular membranes and the average curvature of bent membrane stripes. The results of these methods show good agreement with each other.

cond-mat.soft↗

Anisotropic surface tension of buckled fluid membrane

Solid sheets and fluid membranes exhibit buckling under lateral compression. Here, it is revealed that fluid membranes have anisotropic buckling surface tension contrary to solid sheets. Surprisingly, the surface tension perpendicular to the buckling direction shows stronger dependence than that parallel to it. Our theoretical predictions are supported by numerical simulations of a meshless membrane model. This anisotropic tension can be used to measure the membrane bending rigidity. It is also found phase synchronization occurs between multilayered buckled membranes.

cond-mat.soft↗

Solvent-free coarse-grained lipid model for large-scale simulations

A coarse-grained molecular model, which consists of a spherical particle and an orientation vector, is proposed to simulate lipid membrane on a large length scale. The solvent is implicitly represented by an effective attractive interaction between particles. A bilayer structure is formed by orientation-dependent (tilt and bending) potentials. In this model, the membrane properties (bending rigidity, line tension of membrane edge, area compression modulus, lateral diffusion coefficient, and flip-flop rate) can be varied over broad ranges. The stability of the bilayer membrane is investigated via droplet-vesicle transition. The rupture of the bilayer and worm-like micelle formation can be induced by an increase in the spontaneous curvature of the monolayer membrane.

cond-mat.soft↗

Dynamic Modes of Red Blood Cells in Oscillatory Shear Flow

The dynamics of red blood cells (RBCs) in oscillatory shear flow was studied using differential equations of three variables: a shape parameter, the inclination angle $θ$, and phase angle $ϕ$ of the membrane rotation. In steady shear flow, three types of dynamics occur depending on the shear rate and viscosity ratio. i) tank-treading (TT): $ϕ$ rotates while the shape and $θ$ oscillate. ii) tumbling (TB): $θ$ rotates while the shape and $ϕ$ oscillate. iii) intermediate motion: both $ϕ$ and $θ$ rotate synchronously or intermittently. In oscillatory shear flow, RBCs show various dynamics based on these three motions. For a low shear frequency with zero mean shear rate, a limit-cycle oscillation occurs, based on the TT or TB rotation at a high or low shear amplitude, respectively. This TT-based oscillation well explains recent experiments. In the middle shear amplitude, RBCs show an intermittent or synchronized oscillation. As shear frequency increases, the vesicle oscillation becomes delayed with respect to the shear oscillation. At a high frequency, multiple limit-cycle oscillations coexist. For a high mean shear rate with small shear oscillation, the shape and $θ$ oscillate in the TT motion but only one attractor exists even at high shear frequencies. The measurement of these oscillatory modes is a promising tool for quantifying the viscoelasticity of RBCs and synthetic capsules.

cond-mat.soft↗

Dynamic Modes of Microcapsules in Steady Shear Flow: Effects of Bending and Shear Elasticities

The dynamics of microcapsules in steady shear flow was studied using a theoretical approach based on three variables: The Taylor deformation parameter $α_{\rm D}$, the inclination angle $θ$, and the phase angle $ϕ$ of the membrane rotation. It is found that the dynamic phase diagram shows a remarkable change with an increase in the ratio of the membrane shear and bending elasticities. A fluid vesicle (no shear elasticity) exhibits three dynamic modes: (i) Tank-treading (TT) at low viscosity $η_{\rm {in}}$ of internal fluid ($α_{\rm D}$ and $θ$ relaxes to constant values), (ii) Tumbling (TB) at high $η_{\rm {in}}$ ($θ$ rotates), and (iii) Swinging (SW) at middle $η_{\rm {in}}$ and high shear rate $\dotγ$ ($θ$ oscillates). All of three modes are accompanied by a membrane ($ϕ$) rotation. For microcapsules with low shear elasticity, the TB phase with no $ϕ$ rotation and the coexistence phase of SW and TB motions are induced by the energy barrier of $ϕ$ rotation. Synchronization of $ϕ$ rotation with TB rotation or SW oscillation occurs with integer ratios of rotational frequencies. At high shear elasticity, where a saddle point in the energy potential disappears, intermediate phases vanish, and either $ϕ$ or $θ$ rotation occurs. This phase behavior agrees with recent simulation results of microcapsules with low bending elasticity.

cond-mat.soft↗

Dynamics of Fluid Vesicles in Flow through Structured Microchannels

The dynamics of fluid vesicles is studied under flow in microchannels, in which the width varies periodically along the channel. Three types of flow instabilities of prolate vesicles are found. For small quasi-spherical vesicles -- compared to the average channel width -- perturbation theory predicts a transition from a state with orientational oscillations of a fixed prolate shape to a state with shape oscillations of symmetrical ellipsoidal or bullet-like shapes with increasing flow velocity. Experimentally, such orientational oscillations are observed during the slow migration of a vesicle towards the centerline of the channel. For larger vesicles, mesoscale hydrodynamics simulations and experiments show similar symmetric shape oscillation at reduced volumes $V^* \gtrsim 0.9$. However, for non-spherical vesicles with $V^* \lesssim 0.9$, shapes are found with two symmetric or a single asymmetric tail.

cond-mat.soft↗

Dynamics of Fluid Vesicles in Oscillatory Shear Flow

The dynamics of fluid vesicles in oscillatory shear flow was studied using differential equations of two variables: the Taylor deformation parameter and inclination angle $θ$. In a steady shear flow with a low viscosity $η_{\rm {in}}$ of internal fluid, the vesicles exhibit steady tank-treading motion with a constant inclination angle $θ_0$. In the oscillatory flow with a low shear frequency, $θ$ oscillates between $\pm θ_0$ or around $θ_0$ for zero or finite mean shear rate $\dotγ_{\rm m}$, respectively. As shear frequency $f_γ$ increases, the vesicle oscillation becomes delayed with respect to the shear oscillation, and the oscillation amplitude decreases. At high $f_γ$ with $\dotγ_{\rm m}=0$, another limit-cycle oscillation between $θ_0-π$ and $-θ_0$ is found to appear. In the steady flow, $θ$ periodically rotates (tumbling) at high $η_{\rm {in}}$, and $θ$ and the vesicle shape oscillate (swinging) at middle $η_{\rm {in}}$ and high shear rate. In the oscillatory flow, the coexistence of two or more limit-cycle oscillations can occur for low $f_γ$ in these phases. For the vesicle with a fixed shape, the angle $θ$ rotates back to the original position after an oscillation period. However, it is found that a preferred angle can be induced by small thermal fluctuations.

cond-mat.soft↗

Swinging and Synchronized Rotations of Red Blood Cells in Simple Shear Flow

The dynamics of red blood cells (RBCs) in simple shear flow was studied using a theoretical approach based on three variables: a shape parameter, the inclination angle $θ$, and phase angle $ϕ$ of the membrane rotation. At high shear rate and low viscosity contrast of internal fluid, RBCs exhibit tank-treading motion, where $ϕ$ rotates with swinging oscillation of shape and $θ$. At low shear rate, tumbling motion occurs and $θ$ rotates. In the middle region between these two phases, it is found that synchronized rotation of $ϕ$ and $θ$ with integer ratios of the frequencies occurs in addition to intermittent rotation. These dynamics are robust to the modification of the potential of the RBC shape and membrane rotation. Our results agree well with recent experiments.

cond-mat.soft↗

Dynamical regimes and hydrodynamic lift of viscous vesicles under shear

The dynamics of two-dimensional viscous vesicles in shear flow, with different fluid viscosities $η_{\rm in}$ and $η_{\rm out}$ inside and outside, respectively, is studied using mesoscale simulation techniques. Besides the well-known tank-treading and tumbling motions, an oscillatory swinging motion is observed in the simulations for large shear rate. The existence of this swinging motion requires the excitation of higher-order undulation modes (beyond elliptical deformations) in two dimensions. Keller-Skalak theory is extended to deformable two-dimensional vesicles, such that a dynamical phase diagram can be predicted for the reduced shear rate and the viscosity contrast $η_{\rm in}/η_{\rm out}$. The simulation results are found to be in good agreement with the theoretical predictions, when thermal fluctuations are incorporated in the theory. Moreover, the hydrodynamic lift force, acting on vesicles under shear close to a wall, is determined from simulations for various viscosity contrasts. For comparison, the lift force is calculated numerically in the absence of thermal fluctuations using the boundary-integral method for equal inside and outside viscosities. Both methods show that the dependence of the lift force on the distance $y_{\rm {cm}}$ of the vesicle center of mass from the wall is well described by an effective power law $y_{\rm {cm}}^{-2}$ for intermediate distances $0.8 R_{\rm p} \lesssim y_{\rm {cm}} \lesssim 3 R_{\rm p}$ with vesicle radius $R_{\rm p}$. The boundary-integral calculation indicates that the lift force decays asymptotically as $1/[y_{\rm {cm}}\ln(y_{\rm {cm}})]$ far from the wall.

cond-mat.soft↗

Membrane simulation models from nm to $μ$m scale

Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are relatively more coarse-grained and efficient for simulating large bilayer membranes. On a $μ$m scale, the molecular details are typically negligible and the membrane can be described as a continuous curved surface. The theoretical models for fluid and elastic membranes with mesh or meshless discretizations are presented. As examples of applications, the dynamics of vesicles in flows, vesicle formation, and membrane fusion are presented.

cond-mat.soft↗

Transport coefficients of off-lattice mesoscale-hydrodynamics simulation techniques

The viscosity and self-diffusion constant of particle-based mesoscale hydrodynamic methods, multi-particle collision dynamics (MPC) and dissipative particle dynamics (DPD), are investigated, both with and without angular-momentum conservation. Analytical results are derived for fluids with an ideal-gas equation of state and a finite-time-step dynamics, and compared with simulation data. In particular, the viscosity is derived in a general form for all variants of the MPC method. In general, very good agreement between theory and simulations is obtained.

cond-mat.soft↗

Relevance of angular momentum conservation in mesoscale hydrodynamics simulations

The angular momentum is conserved in fluids with a few exceptions such as ferrofluids. However it can be violated locally in fluid simulations to reduce computational costs. The effects of this violation are investigated using a particle-based simulation method, multi-particle collision dynamics, which can switch on or off angular-momentum conservation. To this end, we study circular Couette flows between concentric and eccentric cylinders, where non-physical torques due to the lack of the angular-momentum conservation are found whereas the velocity field is not affected. In addition, in simulations of fluids with different viscosities in contact and star polymers in solvent, incorrect angular velocities occur. These results quantitatively agree with the theoretical predictions based on the macroscopic stress tensor.

cond-mat.soft↗

Transport coefficients of dissipative particle dynamics with finite time step

The viscosity and self-diffusion constant of a mesoscale hydrodynamic method, dissipative particle dynamics (DPD), are investigated. The viscosity of DPD with finite time step, including the Lowe-Anderson thermostat, is derived analytically for the ideal-gas equation of state and phenomenologically for systems with soft repulsive potentials. The results agree well with numerical data. The scaling of the local relative velocity in molecular dynamics simulations is shown to be useful to obtain faster diffusion than for the DPD thermostat.

cond-mat.soft↗

Swinging and Tumbling of Fluid Vesicles in Shear Flow

The dynamics of fluid vesicles in simple shear flow is studied using mesoscale simulations of dynamically-triangulated surfaces, as well as a theoretical approach based on two variables, a shape parameter and the inclination angle, which has no adjustable parameters. We show that between the well-known tank-treading and tumbling states, a new ``swinging'' state can appear. We predict the dynamic phase diagram as a function of the shear rate, the viscosities of the membrane and the internal fluid, and the reduced vesicle volume. Our results agree well with recent experiments.

cond-mat.soft↗