List of Research Output | FY 2006

Papers, peer-reviewed conference proceedings etc.

【Computer Science Research and Development Office】

Y. Shu, K. Furuta “An Inference Method of Team Situation Awareness Based on Mutual Awareness, Cognition” Technology and Work, Vol.7, No.4 PP.272-287
A. Nishida “Wave propagation properties of frame structures; Formulation for three-dimensional frame structures” JSME International Journal (Series B), Vol.49, No.2 PP.360-367
N. Aiba, S. Tokuda, T. Ishizawa, M. Okamoto “Extension of the Newcomb equation into the vacuum for the stability analysis of tokamak edge plasmas” Computer Physics Communications, Vol.175, No.4 PP.269-289

【Simulation Technology Research and Development Office】

M. Machida and S. Sakai “Unified theory for magnetic and electric field coupling in multistacked Josephson junctions” Physical Review B, Vol.70, No.14 PP.144520_1-144520_6
M. Machida and T. Koyama “Structure of a quantized vortex near the BCS-BEC crossover in atomic fermi gas” Physical Review Letters, Vol.94, No.14 PP.14041_1-14041_4
G. J. Carty, M. Machida and D. P. Hampshire “Numerical studies on the effect of normal-metal coatings on the magnetization characteristics of type-II superconductors” Physical Review B, Vol.71, No.14 PP.144507_1-144507_9
A. Hayashi, M. Shiga and M. Tachikawa “Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH₄⁺…BeH₂” Chemical Physics Letters, Vol.410 PP.54-58
M. Tachikawa and M. Shiga “Geometrical H/D isotope effect on hydrogen bonds in charged water clusters” Journal of the American Chemical Society, Vol.127, No.34 PP.11908-11909
M. Machida “Effects of edge boundaries on Josephson vortices in finite-size layered high-T_c superconductors” Physical Review Letters, Vol.96, No.9 PP.097002_1-097002_4
M. Machida, S. Yamada, Y. Ohashi and H. Matsumoto “Reply to comment on “Novel superfluidity in a trapped gas of fermi atoms with repulsive interaction loaded on an optical lattice”” Physical Review Letters Vol.95, No.21 PP.218902_1-218902_5
K. Ebihara “Dynamical pressure anisotropy in liquid-gas model of lattice-gas” International Journal of Modern Physics C, Vol.17, No.1 PP.53-64
F. Shimizu, S. Ogata and J. Li “Yield point of metallic glass” Acta Materialia, Vol.54, No.16 PP.4293-4298
K. Ebihara and H. Kaburaki “Lattice boltzmann simulation of solution chemistry for crevice corrosion” Mathematics and Computers in Simulation, Vol.72 PP.117-123
K. Muraoka et al. “A Model for striation formation in ac PDP discharges” Journal of Physics D; Applied Physics, Vol.39 No.10 PP.2135-2139
M. Machida and T. Koyama “Time-dependent ginzburg-landau theory for atomic fermi gasses near the BCS-BEC crossover” Physical Review A, Vol.74 No.3 PP.033603_1-033603_6
M. Machida, Y. Ohashi and T. Koyama “Microscopic structure of a quantized vortex core in atomic fermi gases” Physical Review A, Vol.74 No.2 PP.023621_1-023621_5
T. Kuchitsu, M. Tachikawa and M. Shiga “Attosecond electron dynamics with linear combination of floating Gaussian type basis function” Chemical Physics Letters, Vol.433 PP.193-198
A. Hayashi, M. Shiga and M. Tachikawa “H/D isotope effect on the dihydrogen bond of NH₄⁺･BeH₂ by ab initio path integral molecular dynamics simulation” Journal of Chemical Physics, Vol.125 No.20 PP.204310_1-204310_7
M. Yamaguchi, M. Shiga and H. Kaburaki “Grain boundary decohesion by sulfur segregation in ferromagnetic iron and nickel; A First-principles study” Materials Transactions, Vol.47 No.11 PP.2682-2689
M. Machida et al. “Direct numerical simulations for non-equilibrium superconducting dynamics and related neutron detection in MgB₂” Physica C, Vol.426-431 No.1 PP.169-173
M. Machida et al. “Josephson half-quantized vortices in long square π junctions around d-dot” Physica C, Vol.426-431 No.2 PP.1566-1571
M. Machida et al. “Direct numerical simulation on non-equilibrium superconducting dynamics after neutron capture in MgB₂ superconductor” Nuclear Instruments and Methods in Physics Research A, Vol.559 No.2 PP.594-596
M. Machida, T. Koyama and Y. Ohashi “Vortex structure from BCS to BEC Superfluid” Physica C, Vol.437-438 PP.190-194
S. Yamada, T. Imamura and M. Machida “16.447 Tflops and 159-billion-dimensional exact-diagonalization for trapped fermion-hubbard model on the earth simulator” Proceedings of International Conference for High Performance Computing, Networking and Storage (SC '05) (CD-ROM)
S. Ogata et al. (F. Shimizu) “Atomistic simulation of shear localization in Cu-Zr bulk metallic glass” Intermetallics, Vol.14 PP.1033-1037
M. Machida et al. “On-site pairing and microscopic inhomogeneneity in confined lattice fermion systems” Physical Review A, Vol.74, No.5 PP.053621_1-053621_6
T. Kadoyoshi et al. “Molecular dynamics study on the formation of stacking fault tetrahedra and unfaulting of Frank loop in FCC metals” Acta Materialia (in press, Available online 7 March 2007)
A. Hayashi, M. Shiga and M. Tachikawa “H/D isotope effect of dihydrogen bond by ab initio path integral molecular dynamics simulation” Molecular Simulation, Vol.74, No.1-2 PP.185-188
M. Shiga and M. Tachikawa “Ab initio quantum mechanical/molecular mechanical molecular dynamics using multiple-time-scale approach and perturbation theory” Molecular Simulation, Vol.74, No.1-2 PP.174-184
T. Watanabe “Oscillation and rotation of levitated liquid droplet” Proceedings of European Conference on Computational Fluid Dynamics (ECCOMAS CFD 2006) (CD-ROM)
M. Machida, T. Koyama and Y. Ohashi “Vortex microscopic structure in BCS to BEC fermi superfluids” Physica C, Vol.460-462, No.1 PP.275-276
M. Machida and T. Koyama “Collective dynamics of macroscopic quantum tunneling in layered high-T_c superconductors” Superconductor Science and Technology, Vol.20, No.2 PP.S23-S27
M. Machida and T. Koyama “Collective macroscopic tunneling in intrinsic josephson junctions” Physica C, Vol.460-462, No.1 PP.289-292
S. Yamada et al. “Strong pairing and microscopic inhomogeneity of lattice fermion systems” Physica C, Vol.463-465, PP.103-106
M. Machida and T. Koyama “Theory for collective macroscopic tunneling in high-T_c intrinsic Josephson junctions” Physica C Vol.463-465, PP.84-88
K. Yura et al. “Alternative splicing in human transcriptome; Functional and structural influence on proteins” Gene, Vol.380, No.2 PP.63-71
J. Takeda et al. “Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs” Nucleic Acids Research, Vol.34, No.14 PP.3917-3928
K. Yura, S. Yamaguchi and M. Go “Coverage of whole proteome by structural genomics observed through protein homology modeling database” Journal of Structural and Functional Genomics, Vol.7, No.2 PP.65-76
A. Matsumoto and W. K. Olson “Effects of sequence, cyclization, and superhelical stress on the internal motions of DNA” Normal Mode Analysis; Theory and Applications to Biological and Chemical Systems PP.187-211
O. T. P. Kim, K. Yura and N. Go “Amino acid residue doublet propensity in the protein-RNA interface and its application to RNA interface prediction” Nucleic Acids Research, Vol.34, No.22 PP.6450-6460
H. Ishida et al. “Conformational analysis of the structure of ribosome fit into electron microscopy density maps with normal mode analyses and molecular dynamics simulations” Proceeding of 16th International Microscopy Congress
A. Matsumoto and W. K. Olson “Predicted effects of local conformational coupling and external restraints on the torsional properties of single DNA molecules” Multiscale Modeling & Simulation, Vol.5 No.4 PP.1227-1247
M. Go, K. Yura and M. Shionyu “Contribution of computational biology and structural genomics to understand genome and transcriptome” Proceedings of International Symposium on Frontiers of Computational Science, PP.75-80

Talks at international and Japanese conferences

【Computer Science Research and Development Office】

Y. Idomura “Large scale simulations of turbulent fusion plasmas” 21st International Supercomputer Conference (ISC 2006)
N. Kushida et al. “Interoperability establishment between UNICORE and ITBL” 9th HLRS Metacomputing and Grid Workshop/10th Anniversary of HLRS
J. Suzuki (T. Aoyagi et al.) “Object oriented data analysis environment for neutron scattering” 6th New Opportunities for Better User Group Software (NOBUGS 2006)
R. Tian “Part/component-based large-scale finite element analysis; Discontinuous meshes stitching up” 7th World Congress on Computational Mechanics (WCCM-2006)
N. Nakajima et al. “Deployment of computational science in nuclear engineering and science with HPC and network technology” International Conference for High Performance Computing, Networking, Storage and Analysis (SC '06)
M. Ida “On the transition frequencies of acoustically coupled gas bubbles” 2006 APS Division of Fluid Dynamics 59th Annual Meeting (DFD '06)

【Simulation Technology Research and Development Office】

J. Li, F. Shimizu, S. Ogata and H. Kaburaki “Approaching the universal yield point of bulk metallic glasses from molecular dynamics simulations” 135th Annual Meeting & Exhibition (TMS 2006)
M. Shiga and M. Tachikawa “Accelerating combined quantum mechanical/molecular mechanical molecular dynamics using multiple-time-scale approach combined with perturbation theory” Symposium on Progress and Future Prospects in Molecular Dynamics Simulation
H. Kaburaki et al. “Microscopic simulations on the hardening and embrittlement of materials” International Symposium on Fusion Reactor Materials Development
T. Suzudo et al. “Three-dimensional meso-scale Monte-Carlo simulation of the growth of bubbles” International Symposium on Fusion Reactor Materials Development
M. Shiga “Accelerating QM/MM molecular dynamics using multiple-time-scale approach and perturbation theory” Gordon Research Conference on Computational Chemistry
M. Machida “Confinement effects for Josephson vortices in layered high-T_c superconductors” International Workshop on Mesoscopic Superconductivity and Magnetism (MesoSuperMag 2006)
M. Yamaguchi, Y. Nishiyama, H. Kaburaki “Iron grain boundary decohesion by phosphorous segregation; A First-principles study” 13th Meeting of the International Group on Radiation Damage Mechanisms in Pressure Vessel Steels (IGRDM-13)
S. Yamada et al. “High-performance computing for exact numerical approaches to quantum many-body problems on the earth simulator” International Conference for High Performance Computing, Networking, Storage and Analysis (SC '06)
J. Li, F. Shimizu and S. Ogata “Size effects in metallic glass” Materials Research Society 2006 Fall Meeting
M. Machida “Numerical simulations for Abrikosov and Josephson vortices” International Autumn Seminar on Nanoscience and Engineering in Superconductivity for Young Scientists
M. Yamaguchi et al. “The Effects of various segregated solutes on the embrittlement of bcc Fe grain boundaries by the first-principles calculation” Materials Research Society 2006 Fall Meeting
T. Suzudo, H. Kaburaki and M. Itakura “Mesoscopic simulation of fuel-material behaviors under irradiation; A Computer modeling on the bubble growth in UO₂ fuel” New Cross-over Project Workshop-3
J. Li, F. Shimizu and S. Ogata “Yield point of metallic glass” 136th Annual Meeting & Exhibition (TMS 2007)
F. Shimizu, S. Ogata and J. Li “Large-scale molecular dynamics simulation of shear band propagation in metallic glass” 136th Annual Meeting & Exhibition (TMS 2007)
O. T. P. Kim, K. Yura and N. Go “Structure-based bioinformatics analyses and a prediction method of protein-RNA interfaces” 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress
M. Shionyu et al. “Systematic detection of protein regions affected by alternative splicing” 20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress
A. Matsumoto “Predicted effects of local conformational coupling and external restraints on the torsional properties of single DNA molecules” 5th East Asian Biophysics Symposium & 44th Annual Meeting of the Biophysical Society of Japan
O. Kim, K. Yura and N. Go “Computational analyses of amino acid residue propensity in protein-RNA interfaces and prediction methods for the interfaces” 5th East Asian Biophysics Symposium & 44th Annual Meeting of the Biophysical Society of Japan
K. Nakamura, K. Yura and N. Go “Prediction of metal-binding sites from high-throughput metalloproteomics data” Pacific Symposium on Biocomputing 2007 (PSB 2007)
A. Matsumoto “Structural analysis of ribosome based on the elastic network normal mode analysis” Biophysical Society 51th Annual Meeting

Research reports, technical reports and periodical articles

M. Machida, T. Koyama “Vortex structure and dynamics in fermi superfluids; From weakly BCS to strongly-coupled BEC superfluid” Proceedings of Ryukoku Workshop on Mathematical Aspects of Pattern Formation and Dynamics in Dissipative Systems
O. Hazama, Y. Suzuki, H. Matsubara, Tian, R., A. Nishida, M. Tani, N. Nakajima “Towards construction of a numerical testbed for nuclear power plants” Proceedings of 7th MpCCI User Forum
M. Yamaguchi, Y. Nishiyama, M. Shiga, H. Kaburaki, H. Matsuzawa “Impurity-induced decohesion in iron grain boundary; A First-principles study” Proceedings of 3rd International Conference on Multiscale Materials Modeling
K. Shinohara, Y. Okuda, S. Ito, N. Nakajima, M. Ida “Shape optimization using an adjoint variable method in ITBL grid environment” Proceedings of 14th International Conference on Nuclear Engineering (ICONE-14) (CD-ROM)
Y. Suzuki et al. “Interoperability between UNICORE and ITBL” Proceedings of 7th International Meeting on High Performance Computing for Computational Science (VECPAR’ 06)/Workshop on Computational Grids and Clusters (WCGC’06) (CD-ROM)