Masako Takasu

Fusion pathways of vesicles: A Brownian dynamics simulation

We studied the fusion dynamics of vesicles using a Brownian dynamics simulation. Amphiphilic molecules spontaneously form vesicles with a bilayer structure. Two vesicles come into contact and form a stalk intermediate, in which a necklike structure only connects the outer monolayers, as predicted by the stalk hypothesis. We have found a new pathway of pore opening from stalks at high temperature: the elliptic stalk bends and contact between the ends of the arc-shaped stalk leads to pore opening. On the other hand, we have clarified that the pore-opening process at low temperature agrees with the modified stalk model: a pore is induced by contact between the inner monolayers inside the stalk.

Adhesion of nanoparticles to vesicles: A Brownian dynamics simulation

We studied the interaction of bilayer vesicles and adhesive nanoparticles using a Brownian dynamics simulation. The nanoparticles are simple models of proteins or colloids. The adhering nanoparticle induces the morphological change of the vesicle: budding, formation of two vesicles in which only outer monolayers are connected, and fission. We also show that the nanoparticle promotes the fusion process: fusion-pore opening from a stalk intermediate, a neck-like structure that only connects outer monolayers of two vesicles. The nanoparticle bends the stalk, and induces the pore opening.

Inverted micelle formation of cell-penetrating peptide studied by coarse-grained simulation: Importance of attractive force between cell-penetrating peptides and lipid head group

Arginine-rich peptide and Antennapedia are cell-penetrating peptides (CPPs) which have the ability to permeate plasma membrane. Deformation of the plasma membrane with CPPs is the key to understand permeation mechanism. We investigate the dynamics of CPP and the lipid bilayer membrane by coarse-grained simulation. We found that the peptide makes inverted micelle in the lipid bilayer membrane, when the attractive potential between the peptide and lipid heads is strong. The inverted micelle is formed to minimize potential energy of the peptide. For vesicle membrane, the peptide moves from the outer vesicle to the inner vesicle through the membrane. The translocation of the peptide suggests inverted micelle model as a possible mechanism of CPPs.

Multicanonical Monte Carlo Simulation of a Polymer with Stickers

We study the temperature dependence of the behavior of a polymer chain with stickers by using multicanonical Monte Carlo simulations. For our two-dimensional model, we performed equilibrium calculations and obtained physical quantities at low temperatures. We calculated the radius of gyration and the end-to-end distance and found that those quantities drastically change between the temperature k T / u 0 =0.1 and 0.2. As the temperature is lowered, the value of the exponent ν becomes slightly smaller than the high temperature case. We also investigated the distribution of gyration radius and winding angle.

Monte Carlo Simulation of Quantum Heisenberg Magnets on the Triangular Lattice

2) a systematic method for Monte Carlo simulation of quantum systems. There have been reported many studies using this method to investigate various quantum systems. 3 ) The essence of the method is to approximate the partition function with the use of the generalized Trotter formula exp(-S

Dynamics of DNA in entangled polymer solutions: An anisotropic friction model

C)~[ITexp (-SJljn)]n, (1) j

The isotropic–nematic transition and the phase separation of the tobacco mosaic virus particles with polysaccharide

We studied the electrophoretic behavior of DNA chains in linear-polymer solutions using Brownian dynamics with an anisotropic friction model in a three-dimensional space and projected on the x axis. For the three-dimensional model with a chain segment equal to 1/8 of the Kuhn length, a chain migrates with U-shaped conformation with low anisotropy of friction. With high anisotropy of friction, a chain always migrates with linear-shaped conformation with high segment-density regions, which remain at the same positions in space. This migration mode agrees with the observation of DNA in highly entangled solutions [Ueda et al., Biophys. Chem. 71, 113 (1998)]. The projection model also reproduces the linear-shaped motion. We clarified that the essential conditions for linear shaped motion are the sufficient chain length of DNA, the small mesh size, and strong confinement by entanglement with solvent polymers.

Characterization of gels by Monte Carlo method using a model of radical polymerization with cross linkers

The isotropic–nematic transition of the tobacco mosaic virus (TMV) particles by polysaccharide is related to a high inhibitory activity against TMV infection. We study the process of the isotropic–nematic transition of the TMV particles as a function of the polysaccharide concentration by Monte Carlo simulations in three-dimensional continuous space. In these simulations, we simplify the TMV particles and the polysaccharide molecules as the hard spherocylinders and semirigid chains, respectively, and we assume the simple interactions for the TMV particles and the polysaccharide chains. In our simulation, with increasing concentration of the polysaccharide the homogeneously dispersed TMV particles begin to segregate without orientational ordering, that is isotropic phase separation, and then transform to the nematic state of the TMV particles. The isotropic–nematic transition is caused by simple interactions such as the excluded volume effect, and the complicated biological interaction is not necessary.

Linear-Shaped Motion of DNA in Entangled Polymer Solutions under a Steady Field

In this paper, we propose some physical quantities for characterizing gels. Polymer networks (gels) were investigated by Monte Carlo method using a model of free-radical cross-linked polymerization in a continuous system. The distributions of the degree of polymerization for clusters in this simulation are in good qualitative agreement with experimental results. Linkers can be classified into two types according to their role in the network: One forms a simple closed loop within a polymer, and another forms polymer clusters. Their respective amounts and ratios are examined with regard to changes in the distribution of the degree of polymerization.

The Distribution of the Gyration Radius of a Model of Ionomer Studied by Multicanonical Monte Carlo Simulation

We studied the electrophoretic behavior of DNA chains in linear-polymer solutions using Brownian dynamics with an anisotropic friction tensor. We simulated the linear-shaped motion of DNA observed in highly entangled solutions [Ueda et al.: Biophys. Chem. 71 (1998) 113] using a model with a chain segment equal to 1/4 of the persistence length. A linear conformation is seen for a chain with high segment-density regions, which remain at the same positions in space, with a high anisotropy of friction, while a U-shaped conformation is seen for a chain with a low anisotropy of friction.