月別: 2021年11月

[Published online Journal of Computer Chemistry, Japan Vol.20, 100-102, by J-STAGE]
<Title:> 3次元畳み込みニューラルネットワークの転移学習を用いたブロック共重合体の応力ひずみ曲線予測
<Author(s):> 川口　裕靖, 伊藤　真利子, 青柳　岳司, 大西　立顕
<Corresponding author E-Mill:> hironobukawaguchi(at)rikkyo.ac.jp
<Abstract:> The simulation to obtain stress-strain curves of block copolymers requires large computational resources. As an alternative to simulation, a method for high-throughput prediction of stress-strain curves using a three-dimensional convolutional neural network has been reported. In this study, we incorporated shortcut coupling into the neural network and performed pre-training and transfer learning in a step-by-step manner to successfully predict the stress-strain curve with high accuracy while reducing the training cost.
<Keywords:> Block copolymers, Microphase separation, Stress-strain curve, Deep learning, 3D convolutional neural network
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 89-91, by J-STAGE]
<Title:> エラストマーの一軸伸長における重み付きネットワーク構造の変化
<Author(s):> 伊藤　真利子, 天本　義史, 大西　立顕
<Corresponding author E-Mill:> marikoito.rnu1(at)gmail.com
<Abstract:> Previous studies on elastomers have revealed that the physical property of elastomers can be affected by the topological feature of their network structure. In the paper, for the simulation data of construction and elongation of elastomers, we analyzed the weighted network structure of each elastomer, where each node is a crosslinking point and the distance between crosslinking points is incorporated into the weight of a link. We derived centrality of each link based on the idea of closeness centrality in complex networks. We found that how the centrality of each node changes during elongation was significantly affected by the concentration under which crosslinking reaction was carried out, implicating that the weighted network structure of elastomer changed differently according to the reaction concentration.
<Keywords:> Elastomers, Network polymer, Complex networks, Weighted network, Closeness centrality
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 103-105, by J-STAGE]
<Title:> ランダムフォレストを用いた結晶性高分子のX線散乱回折データの解析
<Author(s):> 髙橋　数冴, 天本　義史, 菊武　裕晃, 伊藤　真利子, 高原　淳, 大西　立顕
<Corresponding author E-Mill:> takaha5.26(at)gmail.com
<Abstract:> Crystalline polymers have a hierarchical structure in which polymer chains are folded. Although each hierarchical structure strongly affects the physical properties of crystalline polymers, it is hard to describe the relationship between the formation conditions, crystal structure and physical properties. We used Random Forest regression to comprehensively investigate the relationship between these features of polylactic acid (PLA), a biodegradable crystalline polymer. It was suggested that important features for mechanical property and biodegradability, where the trade-off relationship between them is a significant issue of PLA, are related to the different level crystal structures. This shows that it is possible to use Random Forest for complex prediction of crystalline polymer properties to search for important forming conditions and crystal structures.
<Keywords:> Random Forest, Importance, Crystalline polymers, Polylactic acid, X-ray diffraction and scattering
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 97-99, by J-STAGE]
<Title:> ヘモグロビンのアロステリック制御に関するデータ科学的研究
<Author(s):> 田中　美帆, 高橋　由芽, 高見　慧, 北村　勇吉, 長岡　正隆
<Corresponding author E-Mill:> kitamura.yuhkichi(at)shizuoka.ac.jp
<Abstract:> In this letter, we investigated the contribution of bridging hydrogen bonds (BHB) via Cl^– on the T-R transition of human adult hemoglobin (HbA). We applied the time-series clustering method to time-series data of the αβ dimer rotation angle φ and the total number of the BHBs. Compared with the above two results, we have concluded that Cl^–-BHBs do not significantly contribute to the structural regulation of HbA.
<Keywords:> Keyword Hemoglobin, Allostery regulation, Chloride ion, Bridging hydrogen bond, Time-series clustering method
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0045/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 92-93, by J-STAGE]
<Title:> FMO結晶エネルギーを用いた結晶構造予測の高精度化
<Author(s):> 内海　洋平, 梅田　大貴, 奥脇　弘次, 小畑　繁昭, 中山　尚史, 後藤　仁志, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> k-fukuzawa(at)hoshi.ac.jp
<Abstract:> The aim of this study is to improve the accuracy of crystal structure prediction for Target XXIII, which was the target of the 6th Crystal Structure Prediction Blind Test (CSP6), by using the fragment molecular orbital (FMO) method. The intermolecular interaction analysis revealed that the dispersion interaction is stronger than the electrostatic interaction in all crystal polymorphs. In our method, the three correct structures included in the predicted structures were located within the top five. Furthermore, it was possible to evaluate the stability of polymorphs by the difference of intramolecular hydrogen bonds.
<Keywords:> Polymorphism, Crystal structure prediction, CONFLEX, Fragment molecular orbital method, ABINI-MP
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0041/_article/-char/ja/