研究者詳細 - 篠田　渉

28aXJ-5 20面体Siナノクラスターの形成シミュレーション(28aXJ 微粒子・クラスタ・結晶成長,領域9(表面・界面,結晶成長))

西尾憲吾, 森下徹也, 篠田渉, 三上益弘

日本物理学会講演概要集 61 ( 1 ) 877 - 877 2006年3月

28pPSB-39 Overlapping法による膜を透過する水分子の自由エネルギー計算(28pPSB 領域12ポスターセッション(ソフトマター,化学物理,生物物理),領域12(ソフトマター物理,化学物理,生物物理))

篠田恵子, 篠田渉, 三上益弘

日本物理学会講演概要集 61 ( 1 ) 370 - 370 2006年3月

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年12月

記述言語：英語出版者・発行元：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

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年10月

記述言語：英語出版者・発行元：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

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年9月

記述言語：英語出版者・発行元：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

24aYW-5 分子動力学シミュレーションによるナノ細孔内Arの凝固過程の研究(過冷却液体,領域12(ソフトマター物理,化学物理,生物物理))

西尾憲吾, 篠田渉, 森下徹也, 三上益弘

日本物理学会講演概要集 60 ( 1 ) 347 - 347 2005年3月

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年3月

記述言語：英語出版者・発行元：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

15aTA-13 古細菌膜モデルとしてのエーテル型脂質二重層膜の分子動力学シミュレーション(生物物理, 領域 12)

篠田恵子, 篠田渉, 三上益弘

日本物理学会講演概要集 59 ( 2 ) 311 - 311 2004年8月

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年7月

記述言語：英語出版者・発行元：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

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年

温度と応力を制御した分子動力学法による粒界すべりの研究

志賀基之, 篠田渉

分子シミュレーション討論会講演要旨集 18th 2004年

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年

Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency

W Shinoda, M Mikami

JOURNAL OF COMPUTATIONAL CHEMISTRY 24 ( 8 ) 920 - 930 2003年6月

記述言語：英語出版者・発行元：JOHN WILEY & SONS INC

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermalisobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL. (C) 2003 Wiley Periodicals, Inc.

DOI： 10.1002/jcc.10249

分子動力学法による温度とストレスの制御とその応用

志賀基之, 篠田渉, 三上益弘, 蕪木英雄

分子構造総合討論会講演要旨集(CD-ROM) 2003 2003年

大規模系のための汎用分子動力学統合システムTACPACK2000の開発その3 システム化技術

南多善, 森川良忠, 小川浩, 田中真悟, 寺倉清之, 増田裕寿, 三井崇志, 佐々木幹夫, 三上益弘, 篠田渉, 劉子敬, 川田正晃, 池庄司民夫

情報化学討論会講演要旨集 0 ( 0 ) J25 - J25 2001年

出版者・発行元：公益社団法人日本化学会・情報化学部会

The TACPACK2000 system consists of general purpose molecular dynamics simulators for large scale system of complicated materials such as biopolymer, organic crystal, liquid crystal, polymers, semiconductor, metal and alloy and ceramics and integration system for the simulators. In this presentation, the systematization technologies of the integration system are described. In the database management technology, we have developed the new technology using XML(eXtensible Markup Language) to control uniformly the data composed of molecular structure, crystal structure , potential and pseudopotential function etc. Also in the plug-in function, we have developed the software technologies for program restoration / deletion function to this system, compilation linkage functions of the program and automatic generation function of parameters input screen.

DOI： 10.11547/ciqs2001.tokusi.0.J25.0