Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Volume 8, Issue 1
Displaying 1-6 of 6 articles from this issue
General Papers
  • Masato KOBAYASHI, Tomoko AKAMA, Hiromi NAKAI
    2009 Volume 8 Issue 1 Pages 1-12
    Published: March 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: November 25, 2008
    JOURNAL FREE ACCESS
    The divide-and-conquer (DC) linear-scaling electronic structure method has been applied mainly to pure density functional theory (DFT) or semi-empirical molecular orbital (MO) calculations. The authors have applied the DC method to the Hartree-Fock (HF) and hybrid DFT calculations and confirmed its reliability and efficiency. In addition, they have developed a linear-scaling post-HF algorithm using subsystem orbitals obtained from DC-HF calculation by virtue of the idea of energy density analysis (EDA) and have shown its efficiency by applying it to second-order perturbation (MP2) and coupled-cluster (CCSD) calculations. In our group, these methods are implemented in the GAMESS quantum chemistry program and can easily be executed by slightly modifying the standard input file. In this paper, we describe the implementation and capabilities of our DC program on GAMESS and report the method to execute and the results of the calculations.
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  • Tomoo AOYAMA, Junko KAMBE, Umpei NAGASHIMA, Eiko NAKAYAMA
    2009 Volume 8 Issue 1 Pages 13-22
    Published: January 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: December 12, 2008
    JOURNAL FREE ACCESS
    Meteorological phenomena, yellow sand and haze are caused by suspended particulate matter (SPM) in the atmosphere. We measured the density when the phenomena occurred. We show that there is a meso-structure in the SPM distribution; and the distributive representation function is different from the yellow sand in the case of boundary surfaces of the atmosphere.
    We devised an SPM visualizing method to watch the details of the meso-structure, which was by using a digital single-lens reflex camera. On use of the method, the yellow sand phenomena have the following characters.
    1. The distribution has a high density center and the shape of the fringe is not decided. Occasionally, an unstable cloud was generated in the fringe.
    2. Estimating the upper limit of the yellow sand from the cloud, we obtain the altitude (about 600m).
    3. The yellow sand subsiding in the sea has two layers which are the main body and diffused haze.
    We applied the method to the haze and got the following:
    1. The detailed flow in the atmosphere is described by the scattering of SPM particles. Thus, the SPM is a tracer to detect the atmospheric flow.
    2. The three-dimensional structure of the atmosphere is estimated by the RGB resolution image of the scattering pictures qualitatively.
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  • Yosuke KATAOKA, Yuri YAMADA
    2009 Volume 8 Issue 1 Pages 23-30
    Published: March 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: December 22, 2008
    JOURNAL FREE ACCESS
    The Gibbs free energies of proton-ordered ices were estimated by molecular dynamics simulations. The ordered structures were obtained using NTV ensemble molecular dynamics of cells with small numbers of molecules, where the cut off distance for short range interaction was 1.4×10-9 m. The internal energy and volume were obtained by NTp molecular dynamics simulations at T = 1 K for each type of ice, where the cut off distance for short range interaction was half of the unit cell and the Ewald method was used to determine coulombic interaction. The infinite number limits in the internal energies of each ice type at T = 1 K were estimated. The enthalpy temperature dependence was calculated and the low temperature limit was estimated to obtain the Gibbs free energy at low temperatures. Phase transition pressures obtained were satisfactory when compared with the experimental results, at least qualitatively.
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  • Hiroyuki TERAMAE, Kazushige OHTAWARA
    2009 Volume 8 Issue 1 Pages 31-40
    Published: March 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: January 19, 2009
    JOURNAL FREE ACCESS
    The Hamiltonian Algorithm combined with ab initio molecular orbital calculation is applied to the optimization of molecular structure. In order to carry out an optimization within a reasonable time frame even in the systems of many atoms, we perform parallel processing of the two-electron integrals by personal computer (PC) cluster consisting of 8 CPU's with Pentium 4 (3.0GHz) processor. We attempt to clear up the relation between the computation time and the number of CPU's focusing particularly on the reduction of the elapsed time. The computation time for single-point 3-21G calculations of the molecules of minor tranquilizer drugs having the benzodiazepin or the thienodiazepin backbone are measured. In the calculation of flutoplazepam (1:C19H16ClFN2O), the acceleration ratio of the CPU time and the elapsed time are 4.1 and 4.3 with 4 CPU's, 7.9 and 42.1 with 8 CPU's, respectively. Increasing the number of CPU's achieves an extensive improvement of the elapsed time more than the number of the CPU's used, because calculated two-electron integrals are able to be buffered on the memory of the PC cluster. The number of CPU's needed to buffer the two-electron integrals is estimated through a series of the calculations of the glycine oligomers.
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  • Ikuo KURISAKI, Hirofumi WATANABE, Shigenori TANAKA
    2009 Volume 8 Issue 1 Pages 41-50
    Published: March 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: March 06, 2009
    JOURNAL FREE ACCESS
    The RNA-binding proteins (RBPs) can recognize and bind their target RNAs specifically according to RNA sequences and/or 3D structures, and can thus express their functions. One of the RBPs, Pumilio, has an RNA-binding domain, Puf domain, in the C-terminal region, which recognizes the RNA sequence (Figure 1) and the 2' hydroxyl group in ribose. The Puf domain consists of 8 tandem modules (Figure 2) and forms the complexes with RNA containing specific sequences (Figure 3). Further, RNA base mutational experiments suggest that each base in the sequence differs in the contribution to the binding free energy of Puf domain-RNA complex formation. In this study, we employ molecular dynamics (MD) simulation to quantitatively estimate the contribution of each base and amino acid to complex stabilization. We analyze the MD trajectory of Puf domain-RNA complex system and calculate the frequencies of hydrogen bond formation at the Puf domain-RNA interface (Figures 6, 7). We also calculate the enthalpy term of the binding free energy of Puf domain-RNA complex, decompose it into enthalpy per residue (Figure 8), and compare the contributions of each amino acid and RNA base. From these analyses, we conclude that each base does not uniquely contribute to the stabilization of the complex and that amino acid residues around the binding interface are key factors of stabilization in Puf domain.
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Technical Paper
  • Hiroshi ABE, Umpei NAGASHIMA
    2009 Volume 8 Issue 1 Pages 51-58
    Published: March 15, 2009
    Released on J-STAGE: March 15, 2009
    Advance online publication: February 02, 2009
    JOURNAL FREE ACCESS
    A real-time visual molecular dynamics simulator, Molecula Numerica is developed. The simulator is designed with modern object-oriented and template meta-programming techniques and is developed with C++. The software is supposed to run most effectively on typical high-end personal computers, which are expected to have multi-cored CPU with SIMD co-processors, and to have a high-end graphic board with high speed BUS. The software adopts multi-platform GUI library and standard libraries so as to be able to run on popular operating systems such as Microsoft Windows, MacOS X or the others. The software can deal with both single-site atoms and multi-site molecules. The multi-site molecules are dealt with as a rigid model. The governing equation of rotational motion of rigid molecules is the quaternion-based equation. The atoms/molecules are defined as C++ Classes. The force calculations between any two of the Classes are defined separated from their class definition using double dispatch mechanism of C++. The mechanism reduces the code-maintenance cost yielded by adding new force models. As an example of simulation, a scene of dissolving salts into water is shown. The executables of the software are available free of charge for MacOS X and for MS Windows.
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