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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)

- Takenobu Nakamura, Wataru Shinoda
- The Journal of chemical physics
- 2013

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)

- Shoichi Toyabe, Hong-Ren Jiang, Takenobu Nakamura, Yoshihiro Murayama, Masaki Sano
- Physical review. E, Statistical, nonlinear, and…
- 2007

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)

- Takenobu Nakamura, Wataru Shinoda, Tamio Ikeshoji
- The Journal of chemical physics
- 2011

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)

- Takenobu Nakamura, Shin-Ichi Sasa
- Physical review. E, Statistical, nonlinear, and…
- 2008

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)

- Takenobu Nakamura, Michio Otsuki, Shin-ichi Sasa
- Physical review. E, Statistical, nonlinear, and…
- 2005

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)

- Seiji Tsuzuki, Toshihiko Mandai, +8 authors Masayoshi Watanabe
- Physical chemistry chemical physics : PCCP
- 2017

The interactions of glymes with alkali or alkaline earth metal cations depend strongly on the metal cations. For example, the stabilization energies (Eform) calculated for the formation of cation-triglyme (G3) complexes with Li+, Na+, K+, Mg2+, and Ca2+ at the MP2/6-311G** level were -95.6, -66.4, -52.5, -255.0, and -185.0 kcal mol-1, respectively, and… (More)

- Takenobu Nakamura, Shuhei Kawamoto, Wataru Shinoda
- Computer Physics Communications
- 2015

An accurate and efficient algorithm for calculating the 3D pressure field has been developed and implemented in the open-sourcemolecular dynamics package, LAMMPS. Additionally, an algorithm to compute the pressure profile along the radial direction in spherical coordinates has also been implemented. The latter is particularly useful for systems showing a… (More)

- Takenobu Nakamura, Shin-ichi Sasa
- Physical review. E, Statistical, nonlinear, and…
- 2006

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)

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