Journal of Computer Chemistry, Japan
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Volume 12 , Issue 2
Showing 1-11 articles out of 11 articles from the selected issue
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  • Toru YAGI, Junko KAMBE, Hiroshi ISHIKAWA, Eiko NAKAYAMA, Umpei NAGASHI ...
    Volume 12 (2013) Issue 2 Pages 87-94
    Released: June 30, 2013
    [Advance publication] Released: February 14, 2013
    JOURNALS FREE ACCESS
    The annular eclipse occurred in the southeast of Japan for 5 min on May 21 2012 7:32, we measured the change in ambient dose rate by using Geiger-Muller counters at three locations, which were Nagareyama, Hino, and Setagaya in Tokyo district.We calculate the frequency spectrum of the observations, and find the spectrum has two distributions. Time scale of the higher-frequency is 2∼2.6 min. We execute an inverse Fourier transformation for the higher-frequency part, and reproduce the change of ambient dose rate. It suggests a phenomenon like scintillation in secondary cosmic ray. It subsides after a delay of more than 5∼22 min from the time of maximum eclipse servings, and then, it scintillates again. We believe the scintillation relates with the solar wind because of the delay time.
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  • Kimichika FUKUSHIMA
    Volume 12 (2013) Issue 2 Pages 95-100
    Released: June 30, 2013
    [Advance publication] Released: June 08, 2013
    JOURNALS FREE ACCESS
    This article investigates the relationship between the characteristic radii from an anion nucleus, by comparing RSP (the Shannon−Prewitt anion radius based on Pauling's theory with Goldschmidt's experimental data) with Req, at which the charge densities of one anion and cation respectively are equal in the interatomic region in an ionic crystal. Calculations were performed via the SIWB (surrounding or solid Coulomb-potential-induced well for basis set) method reported previously using the discrete variational (DV) molecular orbital method in a density functional theory (DFT) scheme. Numerical basis atomic orbitals were derived via the method introduced by the present author in a previous paper, in which a spherically symmetric well potential generated by the crystal Coulomb potential was added solely to the potential for electrons within the anion radius on the isolated anion. The radius Req for the well radius was determined to satisfy the conditions that the input value of the well radius for the anion coincides with the output value of Req after sequential repetitions. The analysis also obtained the radius Rmin, where the sum of the above two charge densities takes the minimum. It was clear that Req is relatively similar to the Shannon−Prewitt anion radius.
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  • Yosuke KATAOKA, Yuri YAMADA
    Volume 12 (2013) Issue 2 Pages 101-108
    Released: June 30, 2013
    [Advance publication] Released: May 10, 2013
    JOURNALS FREE ACCESS
    Equations of state (EOS) are proposed for a system consisting of a perfect solid and a perfect liquid made up of single spherical molecules. The Lennard–Jones interaction is assumed for this system. Molecular dynamics simulations are performed to determine the temperature and density dependences of the internal energy and pressure. The internal energy term in the EOS is the sum of the average kinetic and potential energies at 0 K and the temperature-dependent potential energy. The temperature-dependent term of the average potential energy is assumed to be a linear function of the temperature and its coefficient is expressed as a polynomial of the number density. The pressure is expressed in a similar way, where the pressure satisfies the thermodynamic EOS. The equilibrium condition is solved numerically for the phase equilibrium of argon. The Gibbs energy gives a reasonable transition pressure for three-phase equilibrium in argon. The thermodynamic properties at low pressures have significant temperature dependences.
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  • Jun KAWAKAMI, Hiroko KAKINAMI, Noriyuki MATSUSHIMA, Akio NAKANE, Haruo ...
    Volume 12 (2013) Issue 2 Pages 109-112
    Released: June 30, 2013
    [Advance publication] Released: April 24, 2013
    JOURNALS FREE ACCESS
    Tryptanthrin (T) and eight of its monosubstituted derivatives (T2NH2, T2Cl, T2Br, T2NO2, T8OMe, T8Me, T8F, and T8Br) were synthesized, and their antimicrobial activities were investigated against a fungus (Malassezia furfur) and a gram-positive bacterium (methicillin-resistant staphylococcus aureus, MRSA). Antimicrobial activities of these derivatives were influenced by the substituents on tryptanthrin, with the halogen-substituted tryptanthrin derivatives (T2Cl, T2Br, T8F, and T8Br) showing the highest potency against M. furfur and MRSA. Therefore, semiempirical molecular orbital calculations (PM3) were performed on T and its eight derivatives to investigate the cause of the differences in their antimicrobial activities. The results of the calculations showed that antimicrobial activities could be related to the electrophilicity of the carbonyl carbon of the five-membered ring.
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  • Takuya KISHIO, Hiromasa KANEKO, Kimito FUNATSU
    Volume 12 (2013) Issue 2 Pages 113-121
    Released: June 30, 2013
    [Advance publication] Released: May 18, 2013
    JOURNALS FREE ACCESS
    In experimental design for functional molecules, materials or products, complicated relationships exist between various experimental parameters and objective physical and chemical properties. Regression analysis with experimental data are a useful way for understanding those relationships. A constructed regression model can be used to effectively search for functional products. However, although those products can be found in domains out of existing data, the predictive ability of the model tends to be low in regions where data density is low, and new candidates whose predicted values of a property are unreliable will not achieve desired values of the property. Therefore to search for new candidates in appropriate extrapolation domains, we consider the probability that a new candidate will have intended values of a property and the reliability of a predicted value of the property for the candidate. The probability is calculated from a predicted value and its prediction error estimated by using the gaussian process model, and the reliability is based on data density calculated with the one-class support vector machine (OCSVM) model. The proposed method is applied to simulation data and aqueous solubility data, and the efficiency of the method could be confirmed.
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  • Toru YAGI, Junko KAMBE, Eiko NAKAYAMA, Umpei NAGASHIMA, Tomoo AOYAMA
    Volume 12 (2013) Issue 2 Pages 122-132
    Released: June 30, 2013
    [Advance publication] Released: June 24, 2013
    JOURNALS FREE ACCESS
    We discuss the half-life of radioactive substances in the environment, define the residence half-life, and derive the calculation method. The residence half-life is an index to represent migrations of radioactive compounds. It becomes positive or negative for the evaluation periods. To examine the index, we calculate the residence half-lives of Fukushima and Tokyo prefectures by using published ambient dose rates. Through the calculations, low and high frequency phenomena hidden in the change of ambient dose rate are separated by Fourier transformation and the inverse one. From the low-frequency component, we calculated plural residence half-lives for a continuous period, i.e., residence half-life function. The function shows that radioactive substances migrated, as the flow of air increases together with the advent of spring.
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  • Hiroyuki TERAMAE, Yuya ITO, Umpei NAGASHIMA
    Volume 12 (2013) Issue 2 Pages 133-137
    Released: June 30, 2013
    [Advance publication] Released: June 24, 2013
    JOURNALS FREE ACCESS
    Approximating its surface with Ptn (n =1–4) cluster, the singlet state potential surface for the dissociation and absorption of H2 molecule on the Pt surface is studied at the RHF/LANL2DZ level. For Pt1-Pt3, it is not possible to find the potential surface for the dissociation and absorption of H2 molecule. On the other hand, the potential surface for the dissociation and absorption of H2 molecule is found with the tetrahedral Pt4 cluster. At least four Pt atoms are necessary to represent the the dissociation and absorption of H2 molecule.
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Technical Paper
  • Toru YAGI, Junko KAMBE, Eiko NAKAYAMA, Umpei NAGASHIMA, Tomoo AOYAMA
    Volume 12 (2013) Issue 2 Pages 138-144
    Released: June 30, 2013
    [Advance publication] Released: February 14, 2013
    JOURNALS FREE ACCESS
    From airplanes, we find a black mist that diffuses in upper layer of the troposphere, and discover cumulus wrapped around dark fog. They indicate contamination of the upper atmosphere layer. We recognize the fact from 2007.To research the air pollution, we observed scattering light of the atmosphere on Marishiten peak 2872 m in Mt. Norikura, from September 14 to 15 2011. We conclude that the atmosphere over 3 km is still clean; however, a black mist layer spreads in the free atmosphere gradually. We believe that it is a pre-signal of the long distance movement of air-pollution.
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  • Yuichi INADOMI, Jun MAKI, Hiroaki HONDA, Toshiya TAKAMI, Taizo KOBAYAS ...
    Volume 12 (2013) Issue 2 Pages 145-155
    Released: June 30, 2013
    [Advance publication] Released: May 18, 2013
    JOURNALS FREE ACCESS
    The performance tuning of parallel fragment molecular orbital (FMO) program (OpenFMO) was done to carry out massively parallel FMO calculations effectively on K computer, which is one of the fastest super computers in the world. In this tuning, we focused on the load-balancing of each small-scale molecular orbital calculation for monomer and dimer. To maintain the load-balance for each process, we used the dynamic load-balancing technique with the global counter, and the global counter was implemented using a de facto standard parallelization library such as MPI and OpenMP to keep the portability of our code.In our implementation of the global counter, one thread in each group is used as the master thread of global counter which doesn't calculate molecular integrals, it is required that thread support of MPI_THREAD_SERIALIZED level, and three kinds of codes be provided depending on the kind of the thread as shown in Figure 3, Figure 4 and Figure 5.As a result of applying the dynamic load-balancing using our global counter, the load of molecular integral calculation for each process was well-balanced in each small-scale calculation (see Figure 7 lower), and the parallelization efficiency of the molecular integral part became very high (94% in 256 parallel execution, see Figure 8, "molecular integral part"). On the other hand, it was observed that the parallelization efficiency of the SCF part was so bad, that it caused efficiency lowering of calculations of the monomer electronic structure (see Figure 8). The results of large-scale performance evaluation showed that high efficiency (93%) of coarse grained parallelization was achieved in 20480 parallel executions using the Intel Xeon PC cluster (see Figure 8 and Figure 9) and the elapsed time of the FMO calculation for a large molecule (16,764 atoms) was only 30 min.
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