Faculty Profiles - Shinoda Wataru

MISC - Shinoda Wataru

Division display 41 - 60 of about 65 ／ All the affair displays >>

COLL 372-Theory of nanoparticle self-assembly at oil/water interfaces: The role of curvature

Steven O. Nielsen, Preston B. Moore, Wataru Shinoda, Robert J. B. Kalescky, Chi-cheng Chiu

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 235 2008.4

23pTG-4 Electronic band structure of polyicosahedral Si nanowire

Nishio K., Ozaki T., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan 63 ( 1 ) 804 - 804 2008.2

22aRL-1 The shear hysteresis in the lamellar phase by dissipative particle dynamics

Nakamura Takenobu, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan 62 ( 2 ) 366 - 366 2007.8

COLL 26-Coarse-grained molecular simulation of surfactant self-assembly

Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 2007.8

COMP 384-Multiproperty parametrization of a coarse grained model for proteins

Russell DeVane, Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 2007.8

COMP 258-Multi-terascale molecular modeling of biological systems

Russell DeVane, Wataru Shinoda, Jerome Henin, Matteo Dal Peraro, Axel Kohlmeyer, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 2007.8

21aTG-5 Molecular dynamics simulation of polyicosahedral Si nanowire formation

Nishio K., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan 62 ( 1 ) 919 - 919 2007.2

ナノとバイオ領域における膜科学高度含フッ素リン脂質液晶膜の創製と特性化

馬場照彦, 高井克毅, 高木俊之, 金森敏幸, 篠田渉, 齋藤大明, 三上益弘

膜シンポジウム ( 18 ) 41 - 44 2006.10

Molecular dynamics simulations of self-organized polyicosahedral Si nanowire

Kengo Nishio, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF CHEMICAL PHYSICS 125 ( 7 ) 074712-1-074712-4 2006.8

Language：English Publisher：AMER INST PHYSICS

A novel polyicosahedral nanowire is spontaneously formed in a series of annealing molecular dynamics simulations of liquid Si inside a nanopore of 1.36 nm in diameter. The polyicosahedral Si nanowire is stable even in a vacuum up to about 77% of the melting temperature of bulk Si. Our structural energy calculations reveal that the polyicosahedral nanowire is energetically advantageous over the pentagonal one for a wire whose diameter is less than 6.02 nm, though the latter has been recently proposed as the lowest energy wire. These results suggest the possibility of the formation of a new stable polyicosahedral Si nanowire. (c) 2006 American Institute of Physics.

DOI： 10.1063/1.2337291

Web of Science

researchmap

28aXJ-5 Molecular dynamics simulation of the icosahedral Si nano cluster formation

Nishio K., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan 61 ( 1 ) 877 - 877 2006.3

28pPSB-39 Calculation of free energy of a water molecule in a lipid bilayer using overlapping method

Shinoda Keiko, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan 61 ( 1 ) 370 - 370 2006.3

Molecular dynamics simulation of icosahedral Si quantum dot formation from liquid droplets

K Nishio, T Morishita, W Shinoda, M Mikami

PHYSICAL REVIEW B 72 ( 24 ) 245321-1-4 2005.12

Language：English Publisher：AMERICAN PHYSICAL SOC

The present paper reports on molecular dynamics simulations of the formation process of Si quantum dots (Si QDs). Icosahedral Si QDs are formed spontaneously by freezing 274-, 280-, and 323-atom Si droplets. We find that the initialization of pentagonal channels leads into the overall icosahedral structure. We also study the melting behavior of the 280-atom icosahedral Si QD. We find that the melting point is reduced more than 15% compared with that of bulk Si. A possible approach to synthesize icosahedral Si QDs is discussed. The formation of the icosahedral structure could be expected in other systems characterized by tetrahedral bonding network.

DOI： 10.1103/PhysRevB.72.245321

Web of Science

researchmap

Intermolecular interaction between the pendant chain of perfluorinated ionomer and methanol

S Urata, J Irisawa, A Takada, S Tsuzuki, W Shinoda, M Mikami

JOURNAL OF FLUORINE CHEMISTRY 126 ( 9-10 ) 1312 - 1320 2005.10

Language：English Publisher：ELSEVIER SCIENCE SA

A comparison between water and methanol on the interaction with a pendant chain model for perfluorosulfonic ionomers (PFI), CF3OCF2CF2SO3-, was made by using molecular orbital calculation. Intermolecular interaction energy (E-int) of the most stable complex for CF3OCF2CF2SO3- + CH3OH, where methanol associates with sulfonic acid group, is -10.38 kcal/mol at the MP2/aug-cc-pVDZ//B3LYP/631 + G* level, and it is almost the same with that of CF3OCF2CF2SO3- + H2O complex (-10.58 kcal/mol). Since an association of methanol to the sulfonic acid group is quite advantageous in energy, it is expected that, similarly to water, methanol would likely populate around the acidic site. On the contrary, according to a systematic E-int analysis for 500 random configurations, dissimilar distribution of E-int was observed for methanol compared with water. This is because methyl group substitution reduces oxygen surface area and causes more attractive dispersion energy with CF3OCF2CF2SO3- by about 1.0 kcal/mol on average compared with water. To see how the difference in the interaction energy affects the solvation structure of methanol and water to the PFI, molecular dynamics simulations of a CF3OCF2CF2SO3- molecule in methanol solutions have also been carried out at the methanol concentration of 10-90 mol%. Consequently, water probably associates with the sulfonic acid group-pushing methanol close to hydrophobic sites. It was also observed that methanol molecule tends to point its methyl group toward the solute at hydrophobic sites. These results demonstrated that methanol should locate in the vicinity of hydrophobic site compared with water due to methyl group substitution. (c) 2005 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.jfluchem.2005.07.004

Web of Science

researchmap

Molecular dynamics study of the methanol effect on the membrane morphology of perfluorosulfonic ionomers

S Urata, J Irisawa, A Takada, W Shinoda, S Tsuzuki, M Mikami

JOURNAL OF PHYSICAL CHEMISTRY B 109 ( 36 ) 17274 - 17280 2005.9

Language：English Publisher：AMER CHEMICAL SOC

The membranes of a perfluorosulfonic acid polymer swollen in 10-80 wt % methanol solution were investigated to elucidate the methanol effect on their morphologies, such as size of the solvent cluster, solvent location, and polymer structure, by using isothermal-isobaric molecular dynamics simulations. In higher methanol concentrations, we found less-spherical solvent aggregation and a more spread polymer structure because of the ampholytic nature of methanol. The partial radial distribution functions between solvent oxygen and fluorocarbons, which are composed of the main chain, clearly show that methanol is located closer to the polymer matrix than water. On the other hand, water is preferentially located in the vicinity of an acidic headgroup, SO3-, compared with methanol, although both have similar attractive interaction energies to the acidic group. Furthermore, we discussed solvent dynamics and hydrogen bonding between sulfonic oxygen and solvent O-H groups.

DOI： 10.1021/jp052647h

Web of Science

CiNii Article

researchmap

24aYW-5 Molecular Dynamics study on the freezing phenomena of Ar confined in nanopores

Nishio K., Shinoda W., Morishita T., Mikami M.

Meeting abstracts of the Physical Society of Japan 60 ( 1 ) 347 - 347 2005.3

Molecular dynamics simulation of swollen membrane of perfluorinated ionomer

S Urata, J Irisawa, A Takada, W Shinoda, S Tsuzuki, M Mikami

JOURNAL OF PHYSICAL CHEMISTRY B 109 ( 9 ) 4269 - 4278 2005.3

Language：English Publisher：AMER CHEMICAL SOC

Molecular dynamics simulations of the swollen membrane of perfluorinated ionomer, which is composed of poly(tetrafluoroethylene) backbones and perfluosulfonic pendant side chains, have been undertaken to analyze the static and dynamic properties of the water and the side chain in the membrane. The calculations were carried out for four different water contents, 5, 10, 20 and 40 wt %, at 358.15 K and 0.1 MPa. The results are summarized as follows: (1) The sulfonic acid is the unique site to which water molecules can bind, and the other sites in the pendant side chain have no bound water even at high water concentration. (2) Sulfonic acids aggregate in the short range within 4.6-7.7 Angstrom despite the electrostatic repulsion between them. In such aggregates, a water molecule bridges two sulfonic acids. (3) Pendant side chains prefer to orient perpendicular to the hydrophilic/hydrophobic interface, and long-range correlation of side chain orientations is observed at 20 and 40 wt % water uptake membranes. (4) In a low water uptake membrane, the dynamics of water is substantially restricted due to strong attractive interactions with acidic sites. In contrast, at high water content, even the water locating near the sulfonic acid is relatively mobile. The short residence time of the bound water reveals that such water can frequently exchange position with relatively free water, which locates in the center of water cluster, in highly swollen membranes.

DOI： 10.1021/jp046434o

Web of Science

CiNii Article

researchmap

15aTA-13 Molecular dynamics simulation of an ether-linked lipid bilayer

Shinoda Keiko, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan 59 ( 2 ) 311 - 311 2004.8

Intermolecular interaction between the pendant chain of perfluorinated ionomer and water

S Urata, J Irisawa, A Takada, S Tsuzuki, W Shinoda, M Mikami

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 6 ( 13 ) 3325 - 3332 2004.7

Language：English Publisher：ROYAL SOC CHEMISTRY

The intermolecular interaction energies between a water molecule and four models of pendant chains for perfluorinated ionomers, such as CF3OCF2CF2SO3H, CF3OCF2CF2SO3-, CF3CF2CF2COOH, CF3CF2CF2COO-, were analyzed by using a molecular orbital calculation. In order to investigate a variety of configurations.. five hundred random configurations that water and monomer contact at their van der Waals surfaces were generated for each system. We employed an empirical correction method for dispersion energy defined by the equation E-disp = -f(d)(R)C6R-6, so as to reduce the computational costs. The C-6 coefficients of this equation were optimized to reproduce the energies obtained at the MP2/aug-cc-pVDZ level of calculations, and then overall intermolecular interaction energies (E-int = E-HF+E-disp) were evaluated as a summation of E-disp and intermolecular interaction energy at the HF/aug-cc-pVDZ level (E-HF). From these analyses, we obtained the following conclusions. (1) The ether oxygen in the pendant chain cannot bind with water strongly due to fluorination. (2) De-protonations of sulfonic and carboxylic acids extend the region where water molecules sufficiently bind with pendant chains, and this effect would cause rich water absorption when these pendant chains form membranes. Therefore, the degree of proton disassociation would be one of the key factors for the water sorption ratio and membrane morphology. (3) The binding energy of the optimized configuration for CF3CF2CF2COO- + H2O is about 2.5 kcal mol(-1) larger than that for the CF3OCF2CF2SO3-+H2O system because of the larger electron negativities of the oxygen atoms on deprotonated carboxylic acid compared with those on the sulfonic acid.

DOI： 10.1039/b316395d

Web of Science

CiNii Article

researchmap

水の比熱:経路積分分子動力学法による研究

篠田渉, 志賀基之

分子シミュレーション討論会講演要旨集 18th 2004

経路積分分子動力学法による比熱の精密計算

志賀基之, 篠田渉

分子構造総合討論会講演要旨集(CD-ROM) 2004 2004

　 PREV - NEXT 　

< Shinoda Wataru >

MISC - Shinoda Wataru