arXiv subjects

Hiroshi Noguchi

Publications and source records attributed to Hiroshi Noguchi.

At least 37 records · Page 2Linked to original sources

arXiv2022

Membrane shape deformation induced by curvature-inducing proteins consisting of chiral crescent binding and intrinsically disordered domains

Curvature-inducing proteins containing a Bin/Amphiphysin/Rvs domain often have intrinsically disordered domains. Recent experiments have shown that these disordered chains enhance curvature sensing and generation. Here, we report on the modification of protein-membrane interactions by disordered chains using meshless membrane simulations. The protein and bound membrane are modeled together as a chiral crescent protein rod with two excluded-volume chains. As the chain length increases, the repulsion between them reduces the cluster size of the proteins. It induces spindle-shaped vesicles and a transition between arc-shaped and circular protein assemblies in a disk-shaped vesicle. For flat membranes, an intermediate chain length induces many tubules owing to the repulsion between the protein assemblies, whereas longer chains promote perpendicular elongation of tubules. Moreover, protein rods with zero rod curvature and sufficiently long chains stabilize the spherical buds. For proteins with a negative rod curvature, an intermediate chain length induces a rugged membrane with branched protein assemblies, whereas longer chains induce the formation of tubules with periodic concave-ring structures.

cond-mat.soft↗

arXiv2022

Binding of anisotropic curvature-inducing proteins onto membrane tubes

Bin/Amphiphysin/Rvs superfamily proteins and other curvature-inducing proteins have anisotropic shapes and anisotropically bend biomembrane. Here, we report how the anisotropic proteins bind the membrane tube and are orientationally ordered using mean-field theory including an orientation-dependent excluded volume. The proteins exhibit a second-order or first-order nematic transition with increasing protein density depending on the radius of the membrane tube. The tube curvatures for the maximum protein binding and orientational order are different and varied by the protein density and rigidity. As the external force along the tube axis increases, a first-order transition from a large tube radius with low protein density to a small radius with high density occurs once, and subsequently, the protein orientation tilts to the tube-axis direction. When an isotropic bending energy is used for the proteins with an elliptic shape, the force-dependence curves become symmetric and the first-order transition occurs twice. This theory quantitatively reproduces the results of meshless membrane simulation for short proteins, whereas deviations are seen for long proteins owing to the formation of protein clusters.

cond-mat.soft↗

arXiv2021

Binding of thermalized and active membrane curvature-inducing proteins

Membrane phase behavior induced by the binding of curvature-inducing proteins is studied by a combination of analytical and numerical approaches. In thermal equilibrium under the detailed balance between binding and unbinding, the membrane exhibits three phases: an unbound uniform flat phase (U), a bound uniform flat phase (B), and a separated/corrugated phase (SC). In the SC phase, the bound proteins form hexagonally-ordered bowl-shaped domains. The transitions between the U and SC phases and between the B and SC phases are second order and first order, respectively. At a small spontaneous curvature of the protein or high surface tension, the transition between B and SC phases becomes continuous. Moreover, a first-order transition between the U and B phases is found at zero spontaneous curvature driven by the Casimir-like interactions between rigid proteins. Furthermore, nonequilibrium dynamics is investigated by the addition of active binding and unbinding at a constant rate. The active binding and unbinding processes alter the stability of the SC phase.

cond-mat.soft↗

arXiv2021

Effects of gas-liquid phase transitions on soundwave propagation: A molecular dynamics study

To understand ultrasonic cavitation, it is imperative to analyze the effects of the gas-liquid phase transitions on soundwave propagation. Since current methods based on fluid dynamics offer limited information, it is imperative to carry out further research on this phenomenon. In this study, we investigated the effects of cavitation and near-critical fluid on soundwaves using the molecular dynamics (MD) simulations of Lennard-Jones fluids. In the first-order liquid-to-gas transition region (far from the critical point), the waveform does not continuously change with the temperature and source oscillation amplitude owing to the discontinuous change in the density due to the phase transition. Meanwhile, in the continuous transition region (crossing near the critical point), the waveform continuously varies with temperature regardless of the amplitudes because phase separation is not involved in this region. The density fluctuations increase as the amplitude increases; however, it does not affect the waveform. Thus, we clarified that the first-order and continuous transitions have different impacts on soundwaves. Moreover, we determined the acoustic characteristics, such as attenuation and nonlinear parameters, by comparing the results of the numerical solution of Burgers' equation and MD simulation. Burgers' equation clearly describes the soundwave phenomenon until phase separation or bubble formation occurs. In the continuous transition region, the attenuation parameters tend to diverge, reflecting a critical anomaly trend. We observed the bubbles move forward with the oscillation of their radii owing to their interaction with the soundwaves. This is the first direct observation of the interaction using MD simulations.

physics.flu-dyn↗

arXiv2021

Binding of curvature-inducing proteins onto tethered vesicles

A tethered vesicle, which consists of a cylindrical membrane tube and a spherical vesicle, is produced by a mechanical force that is experimentally imposed by optical tweezers and a micropipette. This tethered vesicle is employed for examining the curvature sensing of curvature-inducing proteins. In this study, we clarify how the binding of proteins with a laterally isotropic spontaneous curvature senses and generates the membrane curvatures of the tethered vesicle using mean-field theory and meshless membrane simulation. The force-dependence curves of the protein density in the membrane tube and the tube curvature are reflection symmetric and point symmetric, respectively, from the force point, in which the tube has a sensing curvature. The bending rigidity and spontaneous curvature of the bound proteins can be estimated from these force-dependence curves. First-order transitions can occur between low and high protein densities in the tube at both low and high force amplitudes. The simulation results of the homogeneous phases agree very well with the theoretical predictions. In addition, beaded-necklace-like tubes with microphase separation are found in the simulation.

cond-mat.soft↗

arXiv2021

Vesicle budding induced by binding of curvature-inducing proteins

Vesicle budding induced by protein binding that generates an isotropic spontaneous curvature is studied using a mean-field theory. Many spherical buds are formed via protein binding. As the binding chemical potential increases, the proteins first bind to the buds and then to the remainder of the vesicle. For a high spontaneous curvature and/or high bending rigidity of the bound membrane, it is found that a first-order transition occurs between a small number of large buds and a large number of small buds. These two states coexist around the transition point. The proposed scheme is simple and easily applicable to many interaction types, so we investigate the effects of inter-protein interactions, the protein-insertion-induced changes in area, the variation of the saddle-splay-modulus, and the area-difference-elasticity energy. The differences in the preferred curvatures for curvature sensing and generation are also clarified.

cond-mat.soft↗

arXiv2021

Reaction-Diffusion Waves Coupled with Membrane Curvature

The reaction-diffusion waves of proteins are known to be involved in fundamental cellular functions, such as cell migration, cell division, and vesicular transportation. In some of these phenomena, pattern formation on the membranes is induced by the coupling between membrane deformation and the reaction-diffusion system through curvature-inducing proteins that bend the biological membranes. Although the membrane shape and the dynamics of the curvature-inducing proteins affect each other in these systems, the effect of such mechanochemical feedback loops on the waves has not been studied in detail. In this study, reaction-diffusion waves coupled with membrane deformation are investigated using simulations combining a dynamically triangulated membrane model with the Brusselator model extended to include the effect of membrane curvature. It is found that the propagating wave patterns change into nonpropageting patterns and spiral wave patterns due to the mechanochemical effects. Moreover, the wave speed is positively or negatively correlated with the local membrane curvature depending on the spontaneous curvature and bending rigidity. In addition, self-oscillation of the vesicle shape occurs, associated with the reaction-diffusion waves of curvature-inducing proteins. This agrees with the experimental observation of liposomes with a reconstituted Min system, which plays a key role in the cell division of Escherichia coli. The findings of this study demonstrate the importance of mechanochemical coupling in biological phenomena.

cond-mat.soft↗

arXiv2021

Effects of polymers on the cavitating flow around a cylinder: A Large-scale molecular dynamics analysis

The cavitation flow of linear-polymer solutions around a cylinder is studied by performing a large-scale molecular dynamics simulation. The addition of polymer chains remarkably suppresses the cavitation. The polymers are stretched into a linear shape near the cylinder and entrained in the vortex behind the cylinder. As the polymers stretch, the elongational viscosity increases, which suppresses the vortex formation. Furthermore, the polymers exhibit an entropic elasticity owing to the stretching. This elastic energy increases the local temperature, which inhibits the cavitation inception. These effects of polymers result in the dramatic suppression of cavitation.

physics.flu-dyn↗

arXiv2021

On multiplier systems and theta functions of half-integral weight for the Hilbert modular group $\mathrm{SL}_2(\mathfrak{o})$

Let $F$ be a totally real number field and $\mathfrak{o}$ the ring of integers of $F$. We study theta functions which are Hilbert modular forms of half-integral weight for the Hilbert modular group $\mathrm{SL}_2(\mathfrak{o})$. We obtain an equivalent condition that there exists a multiplier system of half-integral weight for $\mathrm{SL}_2(\mathfrak{o})$. We determine the condition of $F$ that there exists a theta function which is a Hilbert modular form of half-integral weight for $\mathrm{SL}_2(\mathfrak{o})$. The theta function is defined by a sum on a fractional ideal $\mathfrak{a}$ of $F$.

math.NT↗

arXiv2020

Virtual bending method to calculate bending rigidity, saddle-splay modulus, and spontaneous curvature of thin fluid membrane

A method to calculate the bending rigidity $κ$, saddle-splay modulus $\barκ$, and spontaneous curvature $C_0$ of a fluid membrane is proposed. Virtual work for the bending deformations into cylindrical and spherical shapes is calculated for a flat membrane. This method does not require a force decomposition, unlike the existing stress-profile method. The first derivative of the deformation gives $κC_0$ and is a discrete form of the first moment of the stress profile. The second derivatives give $κ$ and $\barκ$, and include the variance terms of the first derivatives, which are not accounted for in the stress-profile method. This method is examined for a solvent-free meshless membrane model and a dissipative-particle-dynamics two-bead amphiphilic molecular model. It is concluded that $κ$ and $\barκ$ of a thin membrane can be accurately calculated, whereas for a thick membrane or one with an explicit solvent, a further extension to include the volume-fluctuation effects is required for an accurate estimation. The amplitude of the volume-fluctuation effects can be evaluated using the parameter dependence in the present method.

cond-mat.soft↗

arXiv2020

Pattern Formation in Reaction-Diffusion System on Membrane with Mechanochemical Feedback

Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently, chemical reaction propagation has been experimentally observed in plasma membranes. Thus, it is important to understand how the reaction-diffusion dynamics are modified on deformable curved membranes. Here, we investigated nonequilibrium pattern formation on vesicles induced by mechanochemical feedback between membrane deformation and chemical reactions, using dynamically triangulated membrane simulations combined with the Brusselator model. We found that membrane deformation changes stable patterns relative to those that occur on a non-deformable curved surface, as determined by linear stability analysis. We further found that budding and multi-spindle shapes are induced by Turing patterns, and we also observed the transition from oscillation patterns to stable spot patterns. Our results demonstrate the importance of mechanochemical feedback in pattern formation on deforming membranes.

physics.bio-ph↗

arXiv2020

Molecular Dynamics Simulation of Soundwave Propagation in a Simple Fluid

A molecular dynamics (MD) simulation was performed to study the propagation of soundwaves in a fluid. Soundwaves are generated by a sinusoidally oscillating wall and annihilated by a locally applied Langevin thermostat near the opposite wall. The waveform changes from sinusoidal to sawtooth with increasing wave amplitude. For low-frequency sounds, the simulation results show very good agreement with Burgers equation without any fitting parameters. In contrast, for highfrequency sounds, significant deviations are obtained because of acoustic streaming. The speed of sound can be directly determined from the Fourier transform of a waveform with high accuracy. Although obtaining the attenuation rate directly from the simulation results is difficult because of the nonlinear effects of the wave amplitude, it can be estimated via Burgers equation. The results demonstrate that MD simulations are a useful tool for the quantitative analysis of soundwaves.

physics.flu-dyn↗

arXiv2019

Effects of Cavitation on Karman Vortex Behind Circular-Cylinder Arrays

The effects of cavitation on the flow around a circular-cylinder array are studied by using a molecular dynamics simulation. Cavitation significantly affects on vortex shedding characteristics. As the cavitation develops,the vibration acting on the cylinders decreases and eventually disappears. The further cavitation development generates a longer vapor region next to the cylinders, and the vortex streets are formed at further positions from the cylinders. The neighboring Karman vortexes are synchronized in the antiphase in the absence of the cavitation. This synchronization is weakened by the cavitation, and an asymmetric wake mode can be induced. These findings help mechanical designs of fluid machinery that include cylinder arrays.

physics.flu-dyn↗

arXiv2019

Detachment of fluid membrane from substrate and vesiculation

The detachment dynamics of a fluid membrane with an isotropic spontaneous curvature from a flat substrate are studied by using meshless membrane simulations. The membrane is detached from an open edge leading to vesicle formation. With strong adhesion, the competition between the bending and adhesion energies determines the minimum value of the spontaneous curvature for the detachment. In contrast, with weak adhesion, a detachment occurs at smaller spontaneous curvatures due to the membrane thermal undulation. When parts of the membrane are pinned on the substrate, the detachment becomes slower and a remained membrane patch forms straight or concave membrane edges. The edge undulation induces vesiculation of long strips and disk-shaped patches. Therefore, membrane rolling is obtained only for membrane strips shorter than the wavelength for deformation into unduloid. This suggests that the rolling observed for Ca$^{2+}$-dependent membrane-binding proteins, annexins A3, A4, A5, and A13, results from by the anisotropic spontaneous curvature induced by the proteins.

cond-mat.soft↗

arXiv2019

Cup-to-vesicle transition of a fluid membrane with spontaneous curvature

The disk-to-vesicle transition of a fluid membrane with no spontaneous curvature is well described by the competition between edge line and curvature energies. However, the transition of asymmetric membranes with spontaneous curvatures is not yet understood. In this study, the shape of the fluid membrane patch with a constant spontaneous curvature and its closing transition to a vesicle is investigated using theory and meshless membrane simulations. It is confirmed that the (meta)stable and transient membranes are well approximated by spherical caps. The membrane Gaussian modulus can be estimated from the cup shape of membrane patches as well as from the transition probability, although the latter estimate gives slightly smaller negative values. Furthermore, the self-assembly dynamics of membranes are presented, in which smaller vesicles are formed at higher spontaneous curvatures, higher edge line tension, and lower density.

cond-mat.soft↗

arXiv2019

Finite-Size Effects on Karman Vortex in Molecular Dynamics Simulation

The characteristics of the Karman vortex generated by a molecular dynamics (MD) simulation exhibit strong finite-size effects, and MD can only reproduce the experimental results qualitatively. Here, we seek the simulation conditions for quantitatively reproduce the vortex shedding frequency. We found that the finite-size effects are mainly caused by the interference of vortices and the nonuniformity of the fluid viscosity coefficient.

physics.flu-dyn↗

arXiv2019

Angular-momentum conservation in discretization of Navier-Stokes equation for viscous fluids

Although the Navier-Stokes equation (NSE) is derived under angular-momentum conservation (AMC), numerical simulation methods often lack it. Here, we reveal that AMC violations result from implementation of the degenerated viscous terms of NSE. To maintain AMC, these degenerated terms must be separately integrated in accordance with their stress origins. As observed in particle-based hydrodynamics methods, the violation causes artificial rotations in multi-component fluids with different viscosities. At the interface between two fluids or with a mobile solid object, AMC must be satisfied, whereas AMC can be neglected in bulk fluids. We also clarify that the condition for constant fluid rotation as a rigid body in a container rotating at a constant speed is not the AMC of the stresses, but the invariance of the viscous forces under a global rotation. To confirm our theory, we simulated the circular laminar flows of single- and binary-component fluids using two-dimensional Lagrangian finite volume methods. The results show excellent agreement with the analytical predictions for fluids with and without AMC.

physics.comp-ph↗

arXiv2018

Shape transition from elliptical to cylindrical membrane tubes induced by chiral crescent-shaped protein rods

Proteins often form chiral assembly structures on a biomembrane. However, the role of the chirality in the interaction with an achiral membrane is poorly understood. Here, the differential behavior between chiral and achiral crescent-shaped protein rods was investigated using meshless membrane simulations. The achiral rods deformed the membrane tube into an elliptical shape by stabilizing the edges of the ellipse. In contrast, the chiral rods formed a helical assembly that generated a cylindrical membrane tube with a constant radius in addition to the elliptical tube. This helical assembly could be further stabilized by the direct side-to-side attraction between the protein rods. These results agree with experimental findings of the constant radius of membrane tubules induced by the Bin/Amphiphysin/Rvs (BAR) superfamily proteins.

cond-mat.soft↗