Faculty Profiles - Shinoda Wataru

Papers - Shinoda Wataru

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Molecular dynamics study on mechanism of selective permeation of water through aquaporin-1

Shinoda W, Tateno M, Ohfuku Y, Mikami M

Seibutsu Butsuri 41 S178 2001

Molecular dynamics study of structure and dynamics of lipid bilayer in the liquid crystal phase Reviewed

W Shinoda, S Okazaki

ELECTROCHEMISTRY 68 ( 2 ) 129 - 133 2000.2

Parallel molecular dynamics simulation: implementation of PVM for a lipid membrane Reviewed

ZW Fang, ADJ Haymet, W Shinoda, S Okazaki

COMPUTER PHYSICS COMMUNICATIONS 116 ( 2-3 ) 295 - 310 1999.2

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

This paper describes a parallel algorithm for Molecular Dynamics simulation of a lipid membrane using the isothermal-isobaric ensemble. A message-passing paradigm is adopted for interprocessor communications using PVM3 (Parallel Virtual Machine). A data decomposition technique is employed for the parallelization of the calculation of intermolecular forces. The algorithm has been tested both on distributed memory architecture (DEC Alpha 500 workstation dusters) and shared memory architecture (SGI Powerchallenge with 20 R10000 processors) for a dipalmitoylphosphatidylcholine (DPPC) lipid bilayer consisting of 32 DPPC molecules and 928 water molecules. For each architecture, we measure the execution time with average work load, and the optimal number of processors for the current simulation. Some dynamical quantities are presented for a 2 ns simulation obtained with 5 processors on DEC Alpha 500 workstations. Our results show that the code is extremely efficient on 5-8 processors, and a useful addition to other major computational resources. (C) 1999 Published by Elsevier Science B.V.

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Other Link： http://orcid.org/0000-0002-3388-9227

Molecular dynamics study on electrostatic properties of a lipid bilayer: Polarization, electrostatic potential, and the effects on structure and dynamics of water near the interface Reviewed

W Shinoda, M Shimizu, S Okazaki

JOURNAL OF PHYSICAL CHEMISTRY B 102 ( 34 ) 6647 - 6654 1998.8

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER CHEMICAL SOC

Electrostatic properties of the dipalmitoylphosphatidylcholine bilayer in water have been investigated on the basis of molecular dynamics calculations in the isothermal-isobaric ensemble. Analysis of the long-time trajectory of partial charges on the atoms showed that polarization of the total system has an anisotropic fluctuation; the component along the bilayer normal was I order of magnitude smaller than that parallel to the bilayer plane, the polarization of lipid being canceled out mostly by that of water along the bilayer normal. A positive electrostatic potential was observed inside the membrane. The potential was found to vary in two steps across the interface; the first gradient comes from the preferential orientation of the ester group, and the second one is attributed to asymmetrical solvation of water around the phosphate group. Slower reorientation of the dipole projected on the bilayer normal was found than that on the bilayer plane. Dynamics of water near the headgroup was strongly influenced by the hydrogen bonding with the phosphate group.

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Other Link： http://orcid.org/0000-0002-3388-9227

A Voronoi analysis of lipid area fluctuation in a bilayer Reviewed

W Shinoda, S Okazaki

JOURNAL OF CHEMICAL PHYSICS 109 ( 4 ) 1517 - 1521 1998.7

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER INST PHYSICS

Membrane area fluctuation of the lipid bilayer has been investigated based upon two-dimensional Voronoi tessellation analysis for the centers of mass of the lipid molecules projected on the bilayer plane. Long-time trajectories of the molecules used in the analysis have been generated by molecular dynamics calculations. The single-molecular area defined by Voronoi polygon showed a broad Gaussian distribution, from which area distribution of the membrane composed of N lipid molecules may satisfactorily be predicted. The fluctuation was found to be caused mainly by thermal motions of the alkyl chains. The number of gauche conformation and alkyl chain length was strongly correlated to the molecular area. Head group motions, however, showed little contribution to the fluctuation. Geometry of Voronoi polygons and the number of nearest neighbor molecules showed rather broad distribution due to the thermal fluctuation. This is in contrast to the structure found in the ripple, gel, and crystal phases. Formation of large pores in the membrane was also investigated. (C) 1998 American Institute of Physics.

DOI： 10.1063/1.476702

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Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics Reviewed

W Shinoda, N Namiki, S Okazaki

JOURNAL OF CHEMICAL PHYSICS 106 ( 13 ) 5731 - 5743 1997.4

Language：English Publishing type：Research paper (scientific journal) Publisher：AMER INST PHYSICS

Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such as atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence to the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in the bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (C) 1997 American Institute of Physics.

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MOLECULAR-DYNAMICS SIMULATION OF THE DIPALMITOYLPHOSPHATIDYLCHOLINE (DPPC) LIPID BILAYER IN THE FLUID-PHASE USING THE NOSE-PARRINELLO-RAHMAN NPT ENSEMBLE Reviewed

W SHINODA, T FUKADA, S OKAZAKI, OKADA, I

CHEMICAL PHYSICS LETTERS 232 ( 3 ) 308 - 312 1995.1

Language：English Publishing type：Research paper (scientific journal) Publisher：ELSEVIER SCIENCE BV

A dipalmitoylphosphatidylcholine (DPPC) bilayer could successfully be simulated in the Nose-Parrinello-Rahman NPT ensemble from an arbitrarily generated crystal-like initial configuration. The initial condition dependence may be small and various artefacts, which were found in molecular dynamics calculations with rectangular cells, could be avoided.

DOI： 10.1016/0009-2614(94)01352-V

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