月別: 2015年9月

[Published online Journal of Computer Chemistry, Japan14, 71-73, by J-STAGE]
<Title:> 最大エントロピー法による発光吸収スペクトルの解析
<Author(s):> 遠越　光輝, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> 14t0007(at)cis.k.hosei.ac.jp

<Abstract:> The maximum entropy method (MEM) is one of the key techniques for spectral analysis. The main feature is to describe spectra in low frequency with short time-series data. We adopted MEM to analyze the spectrum from the dipole moment obtained by the time-dependent density functional theory (TDDFT) calculation in real time, which is intensively studied and applied to computing optical properties. In the MEM analysis, we proposed that we use the concatenated data set made from several-times repeated raw data and the phase shift. We have applied this technique to the spectral analysis of the TDDFT dipole moment of oligo-fluorene with n=8. As a result, higher resolution can be obtained without any peak shift due to the phase jump. The peak position is in good agreement with that of FT with just raw data. The efficiency and the characteristic feature of this technique are presented in this paper.
<Keywords:> Real-time, Time-dependent density functional theory, Maximum entropy method, Fourier transform, Dipole moment
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan14, 80-82, by J-STAGE]
<Title:> 複数結合ポーズ系の標準自由エネルギー計算
<Author(s):> 谷田　義明, 松浦　東

<Abstract:> We have applied alchemical free energy calculation of theophylline with an RNA aptamer with one or more ligand docking poses. We find that the predicted binding affinity strongly depends on the anchor’s position at the receptor using only distance restraints; it means that a ligand is trapped at the other metastable states during the decoupling process. We also demonstrate that the binding affinity of a fragment-like molecule such as theophylline to the receptor is obtained by phase space decomposition with orientational restraints.
<Keywords:> 結合自由エネルギー, 標準状態, フラグメント, 創薬, アルケミカル変換法
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0029/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0048] Published online by J-STAGE
<Title:> “Maizo”-chemistry Project: toward Molecular- and Reaction Discovery from Quantum Mechanical Global Reaction Route Mappings
<Author(s):> Hiroko Satoh, Tomohiro Oda, Kumiyo Nakakoji, Takeaki Uno, Satoru Iwata, Koichi Ohno
<Corresponding author E-Mill:> hsatoh(at)nii.ac.jp<Abstract:> We have launched a project called “Maizo”-chemistry, which is aimed toward molecular- and reaction discovery based on big data of quantum mechanical global reaction route mappings. The global reaction data includes equilibrium structures (EQs), dissociation channels (DCs), and transition structures (TSs), which are automatically calculated by a global search on a potential energy surface using the GRRM (global reaction route mapping) method. Applications to molecular- and synthesis design are an important part of the project. Machine learning and visualization techniques as well as chemoinformatics methods are essential to acquire useful information from the large reaction data space. We describe here a software system, RMapViewer, which we have developed to visualize and analyze the GRRM outputs.
<Keywords:> Maizo-chemistry project, Global reaction route mapping (GRRM), Database, Quantum chemical calculation, RMapViewer, Minimum energy path
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0048/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0041] Published online by J-STAGE
<Title:> OpenFMOにおける4中心クーロン相互作用項計算のGPGPU化の試み
<Author(s):> 梅田　宏明, 塙　敏博, 庄司　光男, 朴　泰祐, 重田　育照
<Corresponding author E-Mill:> umeda(at)ccs.tsukuba.ac.jp<Abstract:> GPU acceleration of four-center (4C) inter-fragment Coulomb interaction term (IFC) for OpenFMO, a fragment molecular orbital calculation program, has been implemented and its performance was examined. FMO calculation has two time-consuming steps: Fock matrix construction and IFC calculation, and in our previous letter, it was reported that the former is successfully accelerated with our GPU-enable code. The 4C-IFC calculation is the core part of the latter and its code is similar to that of Fock matrix construction. In this letter, we briefly describe the GPU-accelerated 4C-IFC calculation routine, and report a performance benchmark for GPU-accelerated FMO calculation. The GPU-accelerated program shows 3.3× speedups from CPU only FMO-HF/6-31G (d) calculation for 642 atomic protein on 8 nodes of HA-PACS base cluster.
<Keywords:> GPGPU, FMO, Inter-fragment Coulomb interaction, Molecular orbital calculation, Performance benchmark
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0041/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0040] Published online by J-STAGE
<Title:> Parallel Performance Analysis for Electronic Structure Calculation of Metal Nanoparticles
<Author(s):> Takayoshi Ishimoto, Yuichi Inadomi, Hiroaki Honda, Michihisa Koyama
<Corresponding author E-Mill:> ishimoto(at)ifrc.kyushu-u.ac.jp<Abstract:> Electronic structure calculation is necessary for metal nanoparticles composed of more than 1000 atoms to understand the intrinsic physical and chemical properties of nanoparticles. In this study, we analyzed the parallel performance of electronic structure calculation for metal nanoparticles by using the Vienna Ab-initio Simulation Package (VASP) program with large-scale computational resources. We found that VASP is suitable for the large-scale electronic structure calculation because the parallelization efficiency improved with increasing metal nanoparticle size (Pd405, Pd807, and Pd1289).
<Keywords:> Metal nanoparticle, Density functional theory, Parallel efficiency, Large-scale calculation, Computational time
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0040/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0038] Published online by J-STAGE
<Title:> 積分で定義される関数の高精度数値計算法：量子力学の数値解析から数学・数値解析へのフィードバック
<Author(s):> 石川　英明
<Corresponding author E-Mill:> UHI91261(at)nifty.com<Abstract:> We applied a method for calculating indefinite integrals developed for atomic structure calculations to mathematical functions defined by integrals and obtained highly accurate results. The method is simple and has wide applicability. Examples of application are, elementary transcendental functions such as exponential, logarithmic, and arctangent functions, then error function, Fresnel integrals, exponential, cosine, and sine integrals, and incomplete gamma functions.
<Keywords:> method, numerical calculation, integral, mathematical functions, high accuracy
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0038/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0036] Published online by J-STAGE
<Title:> xNa2O-(1-x) SiO2 ガラスに適用する原子間相互作用の考察
<Author(s):> 山本　優也, 澤口　, 佐々木　眞
<Corresponding author E-Mill:> 14042074(at)mmm.muroran-it.ac.jp<Abstract:> The interatomic potential for a wide composition range of sodium silicate glasses was proposed by first-principles calculation. Point charge was set for each glass composition on the basis of population analysis of the alkali silicate crystals by using the density functional theory. The potential parameters were obtained from the energy surface of the SiO2+ model by using the molecular orbital method. The molecular dynamics simulation using the new interatomic potential showed improved structures of sodium silicate glasses.
<Keywords:> Molecular dynamics, Interatomic potential, First-principles calculation, Sodium silicate glasses, Glass structure
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0036/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0032] Published online by J-STAGE
<Title:> 放射性plume 軌跡のためのシミュレータ開発
<Author(s):> 青山　智夫, 若月　泰孝
<Corresponding author E-Mill:> aoyama.tomoo(at)gmail.com<Abstract:> Under nuclear power plant accident, by the ventilation of containment vessel, suspended particulate matter (SPM) is emitted; it attracts radioactive compounds, and the plume diffuses in air. It soaks into the human body. We are required to run away from the invisible plumes. The routes do not exist at any time. We recognize status soon, and should select priority persons to escape from there. We code a real-time plume tracer, which reads 4D-winds of Meso Scale Model (MSM), calculates time-development of plumes. The precision for reach time of plumes is 3?5 min, inner 8 km points from emission.
<Keywords:> radioactive substance, movement of SPM, accident prediction, air contamination
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0032/_article/-char/ja/

Journal of Computer Chemistry, Japan [No.2015-0034] Published online by J-STAGE
<Title:> 分子動力学法理解のためのExcelを用いた授業実践と量子力学への応用
<Author(s):> 成島　和男, 岩武　澄, 川上　侑作
<Corresponding author E-Mill:> narushim(at)ube-k.ac.jp<Abstract:> The author is confident that knowledge of electronic materials and molecular simulation will become indispensable for future students of electrical and electronic engineering majors.This paper presents an approach for an introductory lesson on molecular simulation just inaugurated by the author. Specifically, the first step of molecular simulation was incorporated into the lecture “The Basic Theory of Optical Property.” This lesson was taught using spreadsheets (Excel; Microsoft Corp.), which are familiar and easily used software for students. Comments by students after the lesson included the following; “Abstract contents were well understood through exercises,” and “The significance of simulations was abundantly clear.” Consequently, the author believes that effects anticipated from this lesson (the objective of this lesson) were attained to a good degree.
<Keywords:> Molecular Simulation Education, Oligomer, Photoirradiation, Compton effect, Tunnel Effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/14/3/14_2015-0034/_article/-char/ja/