List of Research Output | FY 2008

Papers, peer-reviewed conference proceedings etc.

【Computer Science Research and Development Office】

＜Research papers＞

Y. Suzuki et al. “Development of three-dimensional virtual plant vibration simulator on grid computing environment ITBL-IS/AEGIS" Journal of Power and Energy Systems(Internet), Vol.3, No.1 PP.60-71
T. Watanabe “Numerical simulation of oscillations and rotations of a free liquid droplet using the level set method” Computers & Fluids, Vol.37, No.2 PP.91-98
T. Watanabe “Zero frequency shift of an oscillating-rotating liquid droplet” Physics Letters A, Vol.372, No.4 PP.482-485
N. Kushida and Y. Okuda “Optimization of the parallel finite element method for the earth simulator” Journal of Computational Science and Technology (Internet), Vol.2, No.1 PP.81-91
M. Ida “Bubble-bubble interaction; A Potential source of cavitation noise” Physical Review E, Vol.79, No.1 PP.016307_1-016307_7
M. Ida, T. Naoe and M. Futakawa “On the effect of microbubble injection on cavitation bubble dynamics in liquid mercury” Nuclear Instruments and Methods in Physics Research A, Vol.600, No.2 PP.367-375
T. Yamada et al. “Proposal of vibration table in an extended world by grid computing technology for assembled structures” Theoretical and Applied Mechanics Japan, Vol.57 PP.81-87
K. Shinohara et al. (M. Ida and N. Nakajima) “Shape optimization using adjoint variable method for reducing drag in Stokes flow” International Journal for Numerical Methods in Fluids, Vol.58, No.2 PP.119-159

＜Peer-reviewed conference proceedings＞

Y. Suzuki et al. “Research and development of fusion grid infrastructure based on Atomic Energy Grid InfraStructure(AEGIS)” Fusion Engineering and Design, Vol.83, No.2-3 PP.511-515
Y. Suzuki et al. “Development of three-dimensional virtual plant vibration simulator on grid computing environment ITBL-IS/AEGIS” Proceedings of 16th International Conference on Nuclear Engineering (ICONE-16) (CD-ROM)
Y. Suzuki et al. “Interoperation between Atomic Energy Grid Infrastructure(AEGIS) and other grids” High Performance Computing on Vector Systems 2008, PP.65-77
N. Kushida et al. “Toward an international sparse linear algebra expert system by interconnecting the ITBL Computational Grid with the Gri d-TLSE platform” Proceedings of 8th International Meeting on High Performance Computing for Computational Science (VECPAR ’08) (CD-ROM), PP.424-429
Y. Tsujita et al. (Y. Suzuki and H. Kimura) “Building an application-specific grid computing environment using ITBL for nuclear material engineering” Proceedings of 16th International Conference on Nuclear Engineering (ICONE-16) (CD-ROM)
Y. Caniou, N. Kushida and N. Teshima “Implementing interoperability between the AEGIS and DIET GridRPC middleware to build an international sparse linear algebra expert system” Proceedings of 2nd International Conference on Advanced Engineering Computing and Applications in Sciences (ADVCOMP 2008) (CD-ROM), PP.205-210
T. Watanabe “Parallel computations of droplet oscillations” Proceedings of International Conference on Parallel Computational Fluid Dynamics (ParCFD 2007) (CD-ROM)
C. Kino et al. “Development of cognitive methodology based data analysis system” High Performance Computing on Vector Systems 2008, PP.89-97

【Simulation Technology Research and Development Office】

＜Research papers＞

M. Machida et al. “Correlation effects on atom-density profiles of one-and two-dimensional polarized atomic fermi gases loaded on an optical lattice” Physical Review A, Vol.77, No.5 PP.053614_1-053614_8
M. Machida, M. Okumura and S. Yamada “Stripe formation in fermionic atoms on a two-dimensional optical lattice inside a box trap; Density-matrix renormalization-group studies for the repulsive Hubbard model with open boundary conditions” Physical Review A, Vol.77, No.4 PP.043601_1-043601_6
M. Okumura et al. “Hole localization in the one-dimensional doped anderson-hubbard model ” Physical Review Letters, Vol.101, No.1 PP.016407_1-016407_4
H. Kaburaki et al. “Dynamical thermal conductivity of argon crystal” Journal of Applied Physics, Vol.102, No.4 PP.043514_1-043514_6
Y. Nagai et el. (N. Hayashi) “Kramer-Pesch approximation for analyzing field-angle-resolved measurements made in unconventional superconductors; A Calculation of the zero-energy density of states” Physical Review Letters, Vol.101, No.9 PP.097001_1-097001_4
K. Suzuki, M. Shiga and M. Tachikawa “Temperature and isotope effects on water cluster ions with path integral molecular dynamics based on the fourth order Trotter expansion” Journal of Chemical Physics, Vol.129, No.144 PP.144310_1-144310_8
T. Takayanagi et al. (M. Shiga) “Molecular dynamics simulations of small glycine-(H₂0)_n (n=2-7) clusters on semiempirical PM6 potential energy surfaces” Journal of Molecular Structure (THEOCHEM), Vol.869, No.1-3 PP.29-36
H. Motegi et al. (M. Shiga) “Path-integral molecular dynamics simulations of BeO embedded in helium clusters; Formation of the stable HeBeO complex” Chemical Physics, Vol.354, No.1-3 PP.38-43
T. Nishio et el. (N. Hayashi) “Superconducting Pb island nanostructures studied by scanning tunneling microscopy and spectroscopy” Physical Review Letters, Vol.101, No.16 PP.167001_1-167001_4
Y. Nagai et al. (N. Hayashi, N. Nakai, H. Nakamura, M. Okumura and M. Machida) “Nuclear magnetic relaxation and superfluid density in Fe-pnictide superconductors; An Anisotropic ±s-wave scenario” New Journal of Physics (Internet), Vol.10, No.10 PP.103026_1-103026_17
A. Ramasubramaniam et al. (M. Itakura) “Effect of atomic scale plasticity on hydrogen diffusion in iron; Quantum mechanically informed and on-the-fly kinetic Monte Carlo simulations” Journal of Materials Research, Vol.23, No.10 PP.2757-2773
M. Kamaya and M. Itakura “Simulation for intergranular stress corrosion cracking based on a three-dimensional polycrystalline model” Engineering Fracture Mechanics, Vol.76, No.3 PP.386-401
T. Ichinomiya et al. (M. Itakura) “Temperature accelerated dynamics study of migration process of oxygen defects in UO₂” Journal of Nuclear Materials, Vol.384, No.3 PP.315-321
A. Matsumoto et al. “Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis” Biophysical Journal, Vol.95, No.6 PP.2895-2908
C. Yamasaki et al. (K. Yura) “The H-Invitational Database (H-InvDB); A Comprehensive annotation resource for human genes and transcripts” Nucleic Acids Research, Vol.36, Database PP.D793-D799
A. Srinivasan et al. (A. Matsumoto) “Properties of the nucleic-acid bases in free and Watson-Crick hydrogen-bonded states; Computational insights into the sequence-dependent features of double-helical DNA” Biophysical Reviews, Vol.1, No.1 PP.13-20

＜Peer-reviewed conference proceedings＞

M. Okumura, S. Yamada and M. Machida “DMRG studies for 1-D random Hubbard chain close to the half-filling” Journal of Physics and Chemistry of Solids, Vol.69, No.12 PP.3324-3326
S. Yamada et al. “On-site pairing interaction and quantum coherence in strongly correlated systems” Journal of Physics and Chemistry of Solids, Vol.69, No.12 PP.3395-3397
N. Hayashi et al. “Josephson effect between conventional and non-centrosymmetric superconductors” Journal of Physics and Chemistry of Solids, Vol.69, No.12 PP.3225-3227
N. Hayashi et al. “Josephson effect between conventional and Rashba superconductors” Physica C, Vol.486, No.7-10 PP.844-847
S. Yamada, M. Okumura and M. Machida “Parallel computing of directly-extended density-matrix renormalization group to two-dimensional strongly correlated quantum systems” Proceedings of IASTED International Conference on Parallel and Distributed Computing and Networks (PDCN 2008), PP.175-180
S. Yamada, M. Okumura and M. Machida “High performance computing for eigenvalue solver in density-matrix renormalization group method; Parallelization of the hamiltonian matrix-vector multiplication” Proceedings of 8th International Meeting on High Performance Computing for Computational Science (VECPAR ’08) (CD-ROM), PP.448-454
M. Machida et al. “Quantum synchronization effects in intrinsic Josephson junctions” Physica C, Vol.468, No.7-10 PP.689-694
S. Yamada et al. “Vortex core structure in strongly correlated superfluidity” Physica C, Vol.468, No.15-20 PP.1237-1240
M. ltakura et al. “Multi-scale modeling of crack propagation” High Performance Computing on Vector Systems 2008, PP.145-152
M. Okumura et al. “Hole localization in strongly correlated and disordered systems; DMRG studies for 1-D and 3-leg ladder random Hubbard models” Physica C, Vol.468, No.15-20 PP.1241-1244

Talks at international and Japanese conferences

【Computer Science Research and Development Office】

N. Nakajima et al. “Deployment of nuclear science simulations and IT infrastructure” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
G. Kim et al. “Hybrid method combining atomic model and continuum” International Conference on Quantum Simulators and Design 2008 (QSD 2008)
Y. Suzuki et al. “Cerebral methodology based computing for estimating validity of simulation results” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
H. Takemiya et al. “Using heterogeneous multi-core processors for MHD stability analysis” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
N. Teshima et al. “AEGIS; Atomic Energy Grid InfraStructure” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
A. Nishida, M. Kondo “Towards our French-Japan collaboration” 2nd Meeting of REDIMPS
A. Nishida et al. “Wave propagation analysis of three-dimensional frame structures” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
N. Kushida et al. “AEGIS-DIET interconnection using message translation” International Conference for High Performance Computing, Networking, Storage and Analysis (SC ’08)
T. Yamada “Construction of vibration table in an extended world for safety assessment of nuclear power plants” 9th Teraflop Workshop

【Simulation Technology Research and Development Office】

S. Yamada et al. “Tera-flops quantum simulation for superconducting nano-device; High-performance eigenvalue solver on the earth simulator” 7th Teraflop Workshop
S. Yamada et al. “High performance computing for eigenvalue solver to coupled Josephson junctions on the earth simulator” 3rd Asian-Pacific Congress on Computational Mechanics (APCOM ’07) & 11th International Conference on Enhancement and Promotion of Computational Method in Engineering and Science (EPMESC-11)
N. Hayashi “Josephson effect between conventional and Rashba superconductors” Workshop on Non-centrosymmetric Superconductors
M. Machida “Quantum synchronization and electromagnetic wave emission in intrinsic Josephson junctions” International Conference on Theoretical Physics (Dubna Nano-2008)
M. Machida “Quantum dynamics, synchronization, and electromagnetic wave emission in intrinsic Josephson junctions” 6th International Symposium on Intrinsic Josephson Effect and Plasma Oscillations in High-Tc Superconductors (Plasma 2008)
T. Shiga “Ab initio path integral molecular dynamics using ONIOM method” World Association of Theoretical and Computational Chemists Conference 2008 (WATOC 2008)
T. Shiga “Ab initio path integral molecular dynamics simulations; Nuclear quantum effect” 11th Asian Workshop on First-Principles Electronic Structure Calculations (ASIAN-11)
M.Itakura et al. “Coupled simulation of grain boundary decohesion and hydrogen segregation” 4th International Conference on Multiscale Materials Modeling (MMM 2008)
N.Hayashi “New theoretical method for analyzing the field-angle-dependent measurements made in unconventional superconductors” Joint ESF-JSPS International Workshop on Nanostructured Superconductors; From fundamentals to applications
M. Okumura, S. Yamada and M. Machida “Ground states of cold neutral fermions in 2-dimensional optical lattices; Effects of strong correlation in square and triangular lattices” 21th International Conference on Atomic Physics (ICAP 2008)
H. Nakamura et al. “Effects of magnetic ordering on phonon spectra in iron-based superconductors; First principle calculation and theoretical analysis” American Physical Society 2009 March Meeting
M. Okumura et al. “Magnetizm localization and hole localization in fermionic atoms loaded on optical lattice” American Physical Society 2009 March Meeting
N. Nakai, N. Hayashi and M. Machida “TDGL simulation for the driven vortex-latice in an amorphous superconductor” International Workshop on Nanostructured Superconductors: From fundamentals to applications
M. Okumura et al. “Spin and charge dynamics in atomic fermions loaded on optical lattice" American Physical Society 2009 March Meeting
M. Okumura, S. Yamada and M. Machida “Parallelized DMRG studies for atomic Fermi gas loaded on optical lattice” Supercomputing in Solid State Physics 2009
M. Yamada and H. Kaburaki “First principles calculation on iron grain boundary embrittlement due to impurity segregation” IEA Fusion Modeling Meeting
H. Kaburaki et al. “Modeling of the mechanism of delayed fracture initiation” NIMS Conference 2008
T. Suzudo, M. Itakura and H. Kaburaki “Modeling study of grain sub-division observed at high burnup nuclear fuel” 4th International Conference on Multiscale Materials Modeling (MMM 2008)
A. Matsumoto “Structural analysis of ribosome based on the elastic network normal mode analysis and fitting technique” Japan-UK symposium on conformational changes in proteins and nucleic acids which constitute biological macro-molecules
A. Matsumoto and H. Ishida “Structural analysis of ribosome based on the elastic network normal mode analysis and fitting technique” 6th Asian Biophysics Association (ABA) Symposium / 27th Hong Kong Society of Neuroscience Annual Meeting

Research reports, technical reports and periodical articles

T. Watanabe “Oscillation frequency and deformation of levitated droplets” Proceedings of 22nd International Congress of Theoretical and Applied Mechanics (ICTAM 2008) (CD-ROM)
N. Nakajima et al. “A Large scale simulation for impact and blast loading issues” Proceedings of International Symposium on Structures under Earthquake, Impact, and Blast Loading 2008
O. Hazama et al. “Integrated framework for simulating behaviors of nuclear power plants under earthquakes” Proceedings of 9th MpCCI User Forum
A. Nishida “Impact analysis of three-dimensional frame structures; An Application for piping structures of a nuclear power plant” Proceedings of International Symposium on Structures under Earthquake, Impact, and Blast Loading 2008