月別: 2021年4月

[Published online Journal of Computer Chemistry, Japan Vol.19, 164-166, by J-STAGE]
<Title:> 人工知能を用いた打音試験による片状及び球状黒鉛鋳鉄の材質判定
<Author(s):> 篠原　美月, 内田　希, 岩見　祐貴, 平本　雄一, 加藤　雅也, 菅野　利猛
<Corresponding author E-Mill:> mitsuki_shinohara(at)gmail.com
<Abstract:> Tapping test is an inspection method that determines the presence or absence of abnormality in a specimen based on the difference in the sound when tapping a material. This method is used to inspect buildings and railway vehicles. It is considered that this method can be used for quality evaluation of cast iron. However, although the tapping test has the advantage of being able to be performed non-destructively and simply, it also has the disadvantage of requiring a worker who can distinguish sounds. In order to solve this problem, we introduced a neural network and studied whether it is possible to judge the quality of cast iron by learning the tapping sound of cast iron.
<Keywords:> Flake graphite cast iron, Spheroidal graphite cast iron, Neural network, Tapping test
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 167-168, by J-STAGE]
<Title:> 人工知能による片状黒鉛鋳鉄の黒鉛組織の判定
<Author(s):> 池原　瑞生, 内田　希, 岩見　祐貴, 加藤　雅也, 菅野　利猛
<Corresponding author E-Mill:> s183195(at)stn.nagaokaut.ac.jp
<Abstract:> The graphite structure of flake graphite cast iron is classified into 5 types of A,B,C,D,E or 6 types including chill. In usually, type A is good quality and type D is poor quality. As the proportion of D-type graphite increases, the tensile strength decreases.Inspection of graphite structure is one of the quality evaluations. However, there is no method for numerically determining the graphite structure of flake graphite cast iron. In this study, we created an AI that determines 6 types of graphite structure from A to chill using a Convolutional Neural Network (CNN).The created AI judged the graphite structure photographs that not used for learning with an average correct answer rate of 97.5%. In addition, when the graphite structure of one sample was analyzed by AI, it was confirmed numerically that the graphite structure deteriorated.
<Keywords:> Convolutional Neural Network, Flake graphite cast iron, Graphite structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0017/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 169-171, by J-STAGE]
<Title:> 位相幾何的データ分析によるブロックコポリマー準安定構造の自由エネルギー推定
<Author(s):> 本武　陽一, 山中　貞人, 青柳　岳司, 大西　立顕, 福水　健次
<Corresponding author E-Mill:> mototake(at)ism.ac.jp
<Abstract:> Block copolymers with repulsive sub-chains form a variety of domain structures called microphase-separated structures. Most microphase-separated structures have a periodic patterned structure while in a stable state. On the other hand, metastable states with an acyclic structure and sufficiently long lifetimes are often observed around the configuration space of the periodic structures. In this study, we focused on the double gyroid structure a type of microphase-separated structure and built a model to predict free energy using topological data analysis (TDA), which has recently proven useful for analyzing acyclic compound structures such as the amorphous structure of glass. The model obtained can predict the free energy of the metastable state of the double-gyroid structure using persistent homology, which is one of the features of TDA.
<Keywords:> topological data analysis, Persistent homology, Double-gyroid, Microphase separation, Block copolymers
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0009/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 151-153, by J-STAGE]
<Title:> Ni-ZSM-5によるメタノール酸化反応の理論的研究
<Author(s):> 田中　靖也, Mahyuddin　Muhammad Haris, 塩田　淑仁, 吉澤　一成
<Corresponding author E-Mill:> s.tanaka(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> Ni-ZSM-5 is a promising catalyst for the conversion of methane to methanol. In many methane oxidation catalysts, the problem is that the oxidation reaction continues after methane oxidation (over-oxidation). The ease of over-oxidation is an important factor in evaluating the performance of methane oxidation catalysts. In the present study, we performed density functional theory (DFT) calculation to evaluate the two reaction pathways for the oxidation of methanol to formaldehyde by Ni-ZSM-5. DFT calculations indicated that the activation energies for the C-H bond cleavage are more than 40 kcal/mol in the reaction pathways. After methane oxidation the second step reaction corresponding to the methanol oxidation by [Ni-O-Ni]²⁺ is unlikely to occur.
<Keywords:> Keyword Methanol, Formaldehyde, Over-oxidation, Ni-ZSM-5, DFT calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0004/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, -, by J-STAGE]
<Title:> Performance Research of Clustering Methods for Detecting State Transition Trajectories in Hemoglobin
<Author(s):> Kei TAKAMI, Yukichi KITAMURA, Masataka NAGAOKA
<Corresponding author E-Mill:> kitamura.yuhkichi(at)shizuoka.ac.jp
<Abstract:> The time-series clustering method is one of unsupervised machine learning techniques that classify time-series data. In this article, we applied three methods to the clustering analysis for 200 molecular dynamics (MD) trajectories of human adult hemoglobin (HbA), and have reported their clustering performances for detecting the T-R state transition trajectories (Traj_T-R). By compared with their silhouette indices, we have discussed the proper clustering conditions.
<Keywords:> Keyword Time-series clustering method, Dynamic time warping distance, Silhouette analysis, Hemoglobin, Allostery regulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 158-160, by J-STAGE]
<Title:> ヘテロ原子を含んだ単分子接合の導電性に関するグラフ理論的研究
<Author(s):> 岡澤　一樹, 辻　雄太, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> Single-molecule junctions have unique electron transport properties that are not found in solids or polymers. Graph theoretical approaches have been used to predict whether conductivity in single-molecule junctions. In this paper, the change in single-molecule conductivity when carbon atoms in alternant hydrocarbons are replaced with heteroatoms is investigated by using the graph-theoretic path-counting method. The results predicted by graph theory are consistent with those obtained by using nonequilibrium Green’s function combined with the H ckel method.
<Keywords:> Heteroatom-containing single-molecular junction, π-conjugated system, Graph theory, H ckel method
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0013/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 161-163, by J-STAGE]
<Title:> 分子動力学シミュレーションによる嗅覚受容体タンパク質mOR-EGと香り分子オイゲノールの結合解析
<Author(s):> 岡本　千怜, 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> Molecular dynamics (MD) simulations were used to analyze the effect of the odorant molecule eugenol on the olfactory receptor protein mOR-EG and the dynamic correlation between amino acid residues around the binding site due to ligand binding. When eugenol hydrogen-bonded with Ser 113 of mOR-EG, the dynamic correlation with amino acid residues 213-218 on the adjacent α-helix increased within 10 ps. In particular, the correlation between Ser 113 and Leu 217 showed characteristic oscillations between 10 ps and 30 ps. The correlation with Leu 217 shifted toward residues closer to the G protein over time. Correlation with amino acids on the other side of the membrane was also observed, suggesting the contribution of collective protein motion
<Keywords:> Molecular dynamics simulation, Olfactory receptor, Membrane protein, Dynamical cross correlation
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 133-135, by J-STAGE]
<Title:> 計算化学を用いた新規メタン水酸化触媒の提案
<Author(s):> 池田　京, Mahyuddin　Muhammad Haris, 塩田　淑仁, 吉澤　一成
<Corresponding author E-Mill:> kazunari(at)ms.ifoc.kyushu-u.ac.jp
<Abstract:> Motivated by a recent study on light-induced solar cell that Iridium-oxo complex over WO₃ electrode catalyze water oxidation reaction, we investigated the methane hydroxylation reaction by the same complex. Herein we focused on the closed-shell singlet state reaction due to the no-radical intermediate mechanism although this reaction is energetically unfavored reaction. Using intrinsic bond orbital analysis, we found that the C H bond cleavage reaction proceed via the hydride transfer mechanism. From the view point of orbital interaction between σ orbital (C H bond in methane) and π* orbital (Ir=O bond in Ir complex), we demonstrated that the reactivity of the methane hydroxylation reaction in the closed shell singlet state depends on the energy level of π* orbital.
<Keywords:> DFT calculation, Methane hydroxylation, Iridium-oxo complex, IBO analysis, Orbital interaction
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 139-141, by J-STAGE]
<Title:> Reactive Molecular Dynamics Simulation on Friction-induced Chemical Reactions of SiC in Water Environments
<Author(s):> Masayuki KAWAURA, Yang WANG, Yusuke OOTANI, Nobuki OZAWA, Momoji KUBO
<Corresponding author E-Mill:> momoji(at)imr.tohoku.ac.jp
<Abstract:> Silicon carbide (SiC) exhibits super low friction in water environments. It has been well noticed that this super low friction property is caused by the generated lubricating layers through friction-induced chemical reactions. However, the chemical reactions at the friction interface have not been well clarified because it is difficult to observe the tribological processes at the friction interface in experiments. In the present study, we simulated the friction processes of SiC/SiC in water environments using reactive molecular dynamics simulations. It is interesting to observe that the hydrolysis reactions of Si-C and Si-Si bonds occurred, and however, the chemical reactions of C-C bonds hardly occur, indicating that Si atoms are preferentially oxidized and C atoms are not. The oxidation of Si atoms in SiC generates colloidal silica lubricating layers at the friction interface, being responsible for the super low friction of SiC.
<Keywords:> Molecular Dynamics, Friction, Wear, Silicon Carbide, Water Lubrication
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0010/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.19, 146-148, by J-STAGE]
<Title:> β-LiAlSiO₄結晶の温度変化シミュレーション
<Author(s):> 藤田　和希, 澤口　直哉
<Corresponding author E-Mill:> nasawa(at)mmm.muroran-it.ac.jp
<Abstract:> Anisotropic low-thermal expansion of β-LiAlSiO₄ crystal was reproduced by MD calculation applying a potential model of a spherically symmetric two-body interatomic interaction. From the correlation between the Si-O-Al angle and the Si-Al distance in the c-axis direction, the expansion of a-axis and the contract of c-axis brings the split of Si-O-Al angle distribution. At the same time, the stable position of Li⁺ ion sites also changed. This suggests the cation position also important in the mechanism of low-thermal expansion observed in silicate materials.
<Keywords:> Molecular dynamics, Beta-eucryptite, Thermal expansion, Bonding angle distribution
<URL:> https://www.jstage.jst.go.jp/article/jccj/19/4/19_2021-0012/_article/-char/ja/