Takenobu Nakamura

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The characterization of the medium-range (MRO) order in amorphous materials and its relation to the short-range order is discussed. A new topological approach to extract a hierarchical structure of amorphous materials is presented, which is robust against small perturbations and allows us to distinguish it from periodic or random configurations. This method(More)
A lipid assembly composed of a finite number of lipid molecules can have multiple metastable structures. Using a series of coarse-grained molecular dynamics simulations, we evaluate the free energy profile for the transformation of a small vesicle to a disk-like structure called a bicelle. This free energy is found to be lower than that predicted from(More)
This article proposes a topological method that extracts hierarchical structures of various amorphous solids. The method is based on the persistence diagram (PD), a mathematical tool for capturing shapes of multiscale data. The input to the PDs is given by an atomic configuration and the output is expressed as 2D histograms. Then, specific distributions(More)
A new method is proposed to estimate the bending rigidity of lipid membranes from molecular dynamics simulations. An external cylindrical guiding potential is used to impose a sinusoidal deformation to a planar membrane. The bending rigidity is obtained from the mean force acting on the cylinder by calibrating against a discretized Helfrich model that(More)
Measurement of energy dissipation in small nonequilibrium systems is generally a difficult task. Recently, Harada and Sasa [Phys. Rev. Lett. 95, 130602 (2005)] derived an equality relating the energy dissipation rate to experimentally accessible quantities in nonequilibrium steady states described by the Langevin equation. Here, we show an experimental test(More)
A numerical method is proposed for evaluating the curvature dependency of elastic parameters of a spherical vesicle based on a calculation of the pressure profile across the membrane. The proposed method is particularly useful for small unilamellar vesicles (SUVs), in which the internal structure of the membrane is asymmetric owing to the high curvature. In(More)
We study the time-correlation function of a density field in two-dimensional driven diffusive systems within the framework of fluctuating hydrodynamics. It is found that the time correlation exhibits power-law behavior in an intermediate time regime in the case that the fluctuation-dissipation relation is violated and that the power-law exponent depends on(More)
We study many interacting Brownian particles under a tilted periodic potential. We numerically measure the linear response coefficient of the density field by applying a slowly varying potential transversal to the tilted direction. In equilibrium cases, the linear response coefficient is related to the intensity of density fluctuations in a universal(More)
We propose a novel method for computing the pressure tensor along the radial axis of a molecular system with spherical symmetry. The proposed method uses the slice averaged pressure to improve the numerical stability and precision significantly. Simplified expressions of the local pressure are derived for a conventional molecular force field including(More)
We study the statistical properties of many Brownian particles under the influence of both a spatially homogeneous driving force and a periodic potential with period l in a two-dimensional space. In particular, we focus on two asymptotic cases lint<<l and lint>>l , where lint represents the interaction length between two particles. We derive fluctuating(More)