投稿者: 博佐藤

[Published online Journal of Computer Chemistry, Japan Vol.19, 8-17, by J-STAGE]
<Title:> 系列二分決定グラフを用いたタンパク質配列モチーフの多重表現
<Author(s):> 大和　康平, 加藤　博明, 桂樹　哲雄, 高橋　由雅
<Corresponding author E-Mill:> kato(at)hiroshima-cmt.ac.jp
<Abstract:> 本稿では，系列二分決定グラフ(SeqBDD)を用いたタンパク質配列モチーフの多重表現とそのモチーフ検索への応用について述べる．SeqBDDは，複数の文字列のような配列集合の圧縮表現である．本研究では，SeqBDDのための二つのアルゴリズムを開発した．一つ目は，対応するモチーフのアミノ酸配列を表現するSeqBDDを構築するためのもので，二つ目は状態遷移を追加することにより，SeqBDDのための決定性有限オートマトン(DFA)に相当するオートマトンを構築するためのものである．性能評価のために，マトリクスメタロプロテアーゼ(MMP)ファミリーにおいて保存されている三つのドメインを，UniProtKB/Swiss-Prot (Rel. 2017_09)から得られた555,594の全てのアミノ酸配列に対して検索した．PROSITEパターンを使用した同様の検索結果と比較して，本手法は，適合率，再現率，およびF値において良好な結果を示した．
<Keywords:> sequence binary decision diagram, Aho-Corasick algorithm, multiple representation, sequence motif, motif search
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/1/19_2019-0028/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 1-7, by J-STAGE]
<Title:> カルサイト・ハイドロキシアパタイト結晶表面とペプチドのFMO相互作用解析
<Author(s):> 畑田　崚, 加藤　幸一郎, 奥脇　弘次, 福澤　薫, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> カルサイトとその表面に特異的に吸着する DDGSDD モチーフの複合系，ハイドロキシアパタイトとESQES モチーフの複合系を対象に，フラグメント分子軌道法 (FMO 法) に基づく Pair Interaction Energy Decomposition Analysis (PIEDA) 解析を用いて，結晶-ペプチド間の相互作用エネルギーの成分解析を行った．さらに，PIEDA解析の結果や結晶-残基間の距離，残基の構造的特徴を特徴量として残基-結晶間の相互作用エネルギーの重回帰分析を行った．これらの結果を両複合系で比較したところ，カルサイト系では残基と近距離のフラグメントとの相互作用が，ハイドロキシアパタイト系では残基-結晶表面間の距離が，残基-結晶間相互作用において最も寄与が大きい特徴量であることが分かった．
<Keywords:> Biomineral, Fragment molecular orbital method, PIEDA analysis, Multiple regression
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/1/19_2019-0030/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> カルサイト・ハイドロキシアパタイト結晶表面とペプチドのFMO相互作用解析
<Author(s):> 畑田　崚, 加藤　幸一郎, 奥脇　弘次, 福澤　薫, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> カルサイトとその表面に特異的に吸着する DDGSDD モチーフの複合系，ハイドロキシアパタイトとESQES モチーフの複合系を対象に，フラグメント分子軌道法 (FMO 法) に基づく Pair Interaction Energy Decomposition Analysis (PIEDA) 解析を用いて，結晶-ペプチド間の相互作用エネルギーの成分解析を行った．さらに，PIEDA解析の結果や結晶-残基間の距離，残基の構造的特徴を特徴量として残基-結晶間の相互作用エネルギーの重回帰分析を行った．これらの結果を両複合系で比較したところ，カルサイト系では残基と近距離のフラグメントとの相互作用が，ハイドロキシアパタイト系では残基-結晶表面間の距離が，残基-結晶間相互作用において最も寄与が大きい特徴量であることが分かった．
<Keywords:> Biomineral, Fragment molecular orbital method, PIEDA analysis, Multiple regression
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2019-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 259-262, by J-STAGE]
<Title:> A Molecular Dynamics Study on Alumina/Carbon Nanotube Composite: How Does Annealing Affect Mechanical Properties?
<Author(s):> Yixin SU, Jing ZHANG, Qian CHEN, Yang WANG, Narumasa MIYAZAKI, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp
<Abstract:> Carbon nanotube (CNT) is conventionally expected to reinforce ceramic matrix like alumina. Previous experiments show that processing conditions such as annealing have positive effect on mechanical properties of the alumina/CNT composite. However, the reinforcing mechanism by annealing is not fully understood yet. For further improving the performance of alumina/CNT composite, this study aims to understand the reinforcing mechanism by annealing from the atomic scale with reactive molecular dynamics simulations. We conduct tensile simulations on pure alumina, non-annealed and annealed alumina/CNT composites, and then analyze the mechanical properties of the three models. Consequently, we find out that annealing enhances the interfacial interactions between alumina and CNT and reduces the interfacial slippage, so that the annealed CNT is more stretched than the non-annealed CNT, finally resulting in an improvement of the mechanical performance of composite.
<Keywords:> Carbon nanotubes, Ceramic matrix composites, Elastic properties, Reactive molecular dynamics simulations
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2020-0001/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 257-258, by J-STAGE]
<Title:> Conversion Reaction of Polyoxometalates from Anderson Structure to Keggin Structure
<Author(s):> Teruyoshi YAMAKAWA, Kazuo EDA, Toshiyuki OSAKAI, Takahito NAKAJIMA
<Corresponding author E-Mill:> 181s225s(at)stu.kobe-u.ac.jp
<Abstract:> Aiming at developing synthetic methods of new Keggin-type polyoxometalates (POMs) that can mediate proton-conjugated multi-electron transfer reactions useful for efficient regeneration of fuels, we have investigated the reaction routes from Anderson-type POMs to Keggin-type POMs. The POM systems with various kinds of heteroatoms as their central cations were calculated using the Nudged Elastic Band (NEB) method as well as the first-principles electronic structure method. The effects of the heteroatoms on the reaction routes have been discussed.
<Keywords:> Polyoxometalates, Polyoxotungstates, NEB
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0039/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 254-256, by J-STAGE]
<Title:> アントラセン-ウレア誘導体の励起状態プロトン移動における蛍光挙動に関する解析
<Author(s):> 小野澤　周, 松井　亨, 西村　賢宣,, 守橋　健二
<Corresponding author E-Mill:> matsui(at)chem.tsukuba.ac.jp
<Abstract:> We investigated the hydrogen bonding interaction between the anion and nitrogen atom of the urea derivative nPUA (n = 1, 2, 9, where n is the substituted position of the parent anthracene) to examine a proton transfer reaction in the complex in the excited state, which is known as excited-state intermolecular proton transfer (ESPT). We revealed the details of the hydrogen bonding interaction between an anthracene-urea derivative and an acetate anion in the excited state by taking advantage of TD-DFT calculation.
<Keywords:> Density functional theory, Excited state, Proton transfer, Fluorescence, Molecular orbitals
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0050/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 248-250, by J-STAGE]
<Title:> 粒子法とBohm形式による量子波束の電子状態計算
<Author(s):> 廣野　史明, 岩沢　美佐子, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> 18t0014(at)cis.k.hosei.ac.jp
<Abstract:> In order to describe the time evolution of the electronic state, we have developed a new method, using the particle method with the Bohmian, to solve the time-dependent Schr dinger equation. The method has been applied to the time-dependent coherent state for a harmonic potential, whose analytical solutions are well-known. To evaluate this method, the ground state is evolved to estimate the excited state, and we follow the dynamic dipole moment as the linear responses of the system under externally applied perturbations in real time. From the polarizability obtained as the Fourier transform of the dipole moment, we calculate the optical strength function. As a result, a single peak is observed, which was exactly expected from the analytical solution. We recognize that the method is quite valid for the time dependent electronic structure calculation.
<Keywords:> Symmetric smoothed particle hydrodynamics, Bohmian, Harmonic potential, Wave packet, Dipole moment, Optical strength function
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0048/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 251-253, by J-STAGE]
<Title:> Surface Adsorption Model Calculation Database and Its Application to Activity Prediction of Heterogeneous Catalysts
<Author(s):> Masato KOBAYASHI, Haruka ONODA, Yusuke KURODA, Tetsuya TAKETSUGU
<Corresponding author E-Mill:> k-masato(at)sci.hokudai.ac.
<Abstract:> The surface adsorption model calculation database, which we are constructing from systematic quantum chemical calculations, is reported. The database can be utilized to analyze heterogeneous catalytic reactions. As an application, we predicted the experimental catalytic activity for the methane steam reforming reaction with this database by using the sparse modeling techniques.
<Keywords:> Calculation database, Catalytic reaction, Methane steam reforming, Conversion rate, Sparse modeling
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0053/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.6, -, by J-STAGE]
<Title:> QM- and ONIOM-Molecular Dynamics Studies of the S_N2 Reaction. How Does the Rare Event Take Place?
<Author(s):> Toshiaki MATSUBARA
<Corresponding author E-Mill:> matsubara(at)kanagawa-u.ac.jp
<Abstract:> A model S_N2 reaction of 2-chlorobutane with OH^– is examined from the dynamical point of view by means of the molecular dynamics (MD) methods. The reactions are simulated in both the gas phase and the water solvent by the QM- and the ONIOM-MD methods, respectively. The MD simulations show that a migration of the kinetic energy between the atoms generated by the fluctuation of the kinetic energy of the atoms triggers the reaction. When some requirements of the velocity vector with a certain direction of the specific atoms participating in the reaction are satisfied by the migration of the kinetic energy, the substrate is led to the transition state and then to the product in turn. The time required to pass the transition state becomes shorter in the water solvent compared to the case of the gas phase, which shows that the reaction proceeds more quickly in the water solvent. Another pattern of the requirement of the velocity vector with a certain direction of the specific atoms for the reaction, which makes the reaction rate faster, is also found at a higher temperature in the water solvent.
<Keywords:> Molecular dynamics simulation, SN2 reaction, Requirement for the reaction, Solvent effect
<URL:> https://www.jstage.jst.go.jp/article/jccjie/6/0/6_2019-0006/_html

[Published online Journal of Computer Chemistry, Japan Vol.18, 244-247, by J-STAGE]
<Title:> 分子動力学法を用いた水/xNa₂O-(1-x)SiO₂ (x=0~0.5)ガラス界面の構造解析
<Author(s):> 星野　圭祐, 澤口　直哉
<Corresponding author E-Mill:> 18042073(at)mmm.muroran-it.ac.jp
<Abstract:> Weathering of glass is a problem because it degrades the optical performance of the glass. The weathering occurs when the glass has been contacted with water in the long-term. In this work, a water/glass interface model was prepared and molecular dynamics simulation was performed to investigate the structure and properties near the water/glass interface. The broken surface of the glass network at near the interface was confirmed by the distribution change of the Qⁿ species, and it suggests that the sodium ions are trapped by the destabilized glass surface structure.
<Keywords:> Molecular dynamics, Sodium silicate glasses, Water, Glass structure, Interface structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/5/18_2019-0052/_article/-char/ja/