カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.8, -, by J-STAGE]
<Title:> Analyses of Optical Gains and Oscillation Wavelengths for Quantum Cascade Lasers Using the Nonequilibrium Green’s Function Method
<Author(s):> Hirotaka TANIMURA, Shigeyuki TAKAGI, Tsutomu KAKUNO, Rei HASHIMOTO, Kei KANEKO, Shinji SAITO
<Corresponding author E-Mill:> takagisgyk(at)stf.teu.ac.jp
<Abstract:> We have succeeded in improving the gain of the base quantum cascade laser (QCL) through experiments and device simulations using the nonequilibrium Green’s function (NEGF) method, and we investigate the factor that increases the gain by reducing the thickness of the barrier by 10%. Specifically, we analyzed the minibands (Wannier Stark states), density of states (DOS), and electron density that contribute to the emission. The results show that the gain enhancement is due to the increase in the electron density of the quantum wells in the active region and the increase in the oscillator strength between the minibands that contribute to the emission. Quantum mechanical calculation like the NEGF method is very effective for mesoscopic systems such as the active layer of QCL.
<Keywords:> Nonequilibrium Green’s function, Quantum cascade laser, Optical gain, Electroluminescence, Current voltage characteristic, Oscillation wavelength, Density of states, Electron density, Oscillator strength
<URL:> https://www.jstage.jst.go.jp/article/jccjie/8/0/8_2021-0024/_html

[Published online Journal of Computer Chemistry, Japan Vol.20, 123-125, by J-STAGE]
<Title:> マイクロ波帯の交番電磁界印加における分子運動のシミュレーション
<Author(s):> 杉山　順一, 米谷　慎
<Corresponding author E-Mill:> sugiyama-j(at)aist.go.jp
<Abstract:> Molecular dynamics calculations were performed to consider the peculiarities of microwave chemistry. The temperature rise curve obtained without using the parameters of permittivity and conductivity showed the rise due to the traveling energy in addition to the accumulation of thermal energy in the periodic application of the electric field. We showed that the non-thermal effects of microwave chemistry might be caused by this traveling energy.
<Keywords:> Microwave heating, Molecular dynamics, Traveling energy, Conductive loss, Dielectric loss
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0035/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 106-111, by J-STAGE]
<Title:> 機械学習QSARの整数計画法に基づく逆解析法
<Author(s):> 仁 永持, 見深 朱, Naveed Ahmed AZAM, 和也 原口, 亮 趙, 達也 阿久津
<Corresponding author E-Mill:> nag(at)amp.i.kyoto-u.ac.jp
<Abstract:> We have developed a novel framework for inferring a chemical graph. Given an ANN that maps a feature vector x = f ( G ) of a chemical graph G to a predicted value η ( x ) of a chemical property to G, we formulate an integer program that simulates the functions f and η. Given a target value y*, we can infer a chemical graph G such that η ( f ( G ) ) = y * by solving the integer program.
<Keywords:> Machine learning, Integer programming, Chemical graphs, QSAR/QSPR, Molecular design
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0030/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 112-115, by J-STAGE]
<Title:> 数学・数理科学からのアプローチによる分子動力学計算
<Author(s):> 深作　亮也, 溝口　佳寛, 檜貝　信一
<Corresponding author E-Mill:> higai(at)ark-i.com
<Abstract:> In the present report, we introduce our new three approaches based on the mathematics / mathematical sciences to the classical molecular dynamics calculations; 1) the approach by the analytical mechanics instead of the classical mechanics; 2) the approach to the periodic boundary condition by the torus model; 3) the approach by the mathematics-based programming substituting for the procedural (imperative) programming. Then, we found that these approaches are very effective to make calculations simpler, more compact, steadier, and firmer. Thus, it was concluded that the mathematical / mathematical scientific approaches are the promising ones to overcome various problems that we confront in the computational chemistry.
<Keywords:> Analytical mechanics, Periodic boundary condition, Torus model, Mathematics-based programming, Molecular dynamics calculations
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 116-118, by J-STAGE]
<Title:> デジタルアニーラ前処理空間探索と拡張アンサンブル法による環状ペプチド分子の高速安定構造探索
<Author(s):> 谷田　義明, 佐藤　博之, 眞鍋　敏夫, 島　千絵子
<Corresponding author E-Mill:> tanida.yoshiaki(at)fujitsu.com
<Abstract:> Cyclization generally stabilizes the bioactive conformation of the peptide and increases its affinity for the target. However, since cyclic peptides frequently adopt multiple conformations in solution, the structural information is not fully understood in experiments, and the relationship between structure and function is not well understood. We demonstrate the practical possibilities of using a combination of a special purpose computing engine (Digital Annealer) and REST2 (replica exchange with solute tempering) simulation in “ab initio” structure prediction of macrocyclic peptides.
<Keywords:> Macrocyclic peptide, Digital Annealer, Lattice protein model, REST2, Structure prediction, Cluster analysis
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0036/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 119-122, by J-STAGE]
<Title:> DSSC用のトリフェニルアミンドナーベース有機色素におけるベンゾチアジアゾールを補助置換基とした時の効果の解析
<Author(s):> 山崎　直人, 野村　泰志, 森川　大
<Corresponding author E-Mill:> nomuray(at)shinshu-u.ac.jp
<Abstract:> It has been reported that the introduction of a 2, 1, 3-benzothiadiazole (BTD) into an organic dye used in dye sensitized solar cells (DSSC) makes its conversion efficiency improve. In this study, we examine the effects of BTD’s from viewpoints of its number and position, for DSSC with triphenylamine (TPA) as a donor moiety and cyanoacrylic acid (CA) as an acceptor one. And it is found that the best optical response was obtained when only one BTD was introduced on the side of the acceptor moiety.
<Keywords:> Organic dyes, Dye sensitized solar cells, Conjugation order, Optoelectronic properties, Benzothiadiazole
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.20, 94-96, by J-STAGE]
<Title:> HSP90とコシャペロンp23複合体の安定性に関するシミュレーション研究
<Author(s):> 松倉　里紗, 宮下　尚之
<Corresponding author E-Mill:> miya(at)waka.kindai.ac.jp
<Abstract:> Heat Shock Protein 90 (HSP90) has been known as one of the molecular chaperone proteins, and it supports the correct folding of client proteins. It has been getting attention as the target protein for an anti-cancer drug because the client proteins sometimes include the critical proteins of progressing cancer. In the HSP90 chaperon cycle, several co-chaperones and substrates interact with HSP90 in turn. In this study, we focused on the interaction between HSP90 and p23, which is one of the co-chaperones. After the HSP90 dimer forms the closed conformation, the p23 and ATP bind to the HSP90. However, the detailed interaction among them has not been clear yet. To clear the mechanism of the interaction among HSP90, ATP, and p23, we performed the all-atom molecular dynamics simulations of ATP bound/unbound HSP90 with/without p23. We found that the domain swapping in HSP90 closed conformation is essential for the stable binding between HSP90 and p23, and the ATP binding supports the stability of the HSP90 and p23 complex.
<Keywords:> Molecular Dynamics Simulation, Co-chaperone, Heat Shock Protein 90, Chaperone cycle, Computational Biophysics
<URL:> https://www.jstage.jst.go.jp/article/jccj/20/3/20_2021-0044/_article/-char/ja/

[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/