Papers from MSS Project †

↑

FY2010 (04/2010-03/2011) †

↑

Original Papers (Refereed) †

  1. Takahiro Murashima, Takashi Taniguchi, Ryoichi Yamamoto, and Shugo Yasuda, "Multiscale Simulations for Polymeric Flow", to be submitted.

  2. Takahiro Murashima, Takashi Taniguchi, "Multiscale Simulation of History Dependent Flow in Polymer Melt", submitted.

  3. Masayuki Uranagase and Ryoichi Yamamoto, "Electrostatic potential around a charged colloidal particle in an electrolyte solution with ion strong coupling," submitted.

  4. H. Mizuno and R. Yamamoto, "Dynamical heterogeneity in a highly supercooled liquid: Its correlation length, intensity, and lifetime", submitted.

  5. S. Yasuda and R. Yamamoto, "Dynamic rheology of a supercooled polymer melt in non-uniform oscillating flows in rapidly oscillating plates", submitted.

  6. K. Takahashi, T. Narumi, and K. Yasuoka, "Cutoff radius effect of the isotropic periodic sum method for polar molecules in a bulk1 water system", Molec. Simul., (in print).

  7. H. Kobayashi and R. Yamamoto, "Implementation of Lees-Edwards periodic boundary conditions for direct numerical simulations of particle dispersions under shear flow", J. Chem. Phys., (in print).

  8. Saeed Jafari, Ryoichi Yamamoto, and Mohamad Rahnama "Lattice-Boltzmann method combined with smoothed-profile method for particulate suspensions", Phys. Rev. E, (in print).

  9. K. Takahashi, T. Narumi, and K. Yasuoka, "Cutoff radius effect of isotropic periodic sum method in homogeneous system. II . Water", J. Chem. Phys., 133, 014109(2010).
    [DOI : 10.1063/1.3462241 ]

  10. H. J. Myung, R. Sakamaki, K. J. Oh, T. Narumi, K. Yasuoka, and S. Lee, "Accelerating molecular dynamics simulation using graphics processing unit", Bulletin of the Korean Chemical Society, 31, 3639(2010).
    [DOI: 10.5012/bkcs.2010.31.12.3639 ]

  11. T. Narumi, K. Yasuoka, M. Taiji, F. Zerbetto, and S. Hoefinger, "Fast Calculation of Electrostatic Potentials on the GPU or the ASIC MD-GRAPE-3", Computer Journal, (2010) on line. [DOI : 10.1093/comjnl/bxq079 ]

  12. N. Arai, K. Yasuoka, T. Koishi, and T. Ebisuzaki, "Asymmetric Brownian motor driven by bubble formation in a hydrophobic channel", ACS Nano, 4, 5905(2010).
    [DOI : 10.1021/nn101855d ]

  13. Hideyuki. Mizuno and Ryoichi. Yamamoto, "Lifetime of dynamical heterogeneity in a highly supercooled liquid", Phys.Rev.E, 82,030501(R)(2010).
    [DOI: 10.1103/PhysRevE.82.030501 ]

  14. Takuya Iwashita, Takuya Kumagai and Ryoichi Yamamoto, "A direct numerical simulation method for complex modulus of particle dispersions", Eur. Phys. J. E, 32, 357-363 (2010).
    [DOI: 10.1140/epje/i2010-10638-7 ]

  15. Hideki Kobayashi and Ryoichi Yamamoto, "Tumbling motion of a single chain in shear flow: a crossover from Brownian to non-Brownian behavior", Phys.Rev.E, 81, 041807 (2010).
    [DOI: 10.1103/PhysRevE.81.041807 ]

  16. Takahiro Murashima, Takashi Taniguchi, "Multiscale Lagrangian Fluid Dynamics Simulation for Polymeric Fluid", J. Polym. Sci. B, 48, 886-893 (2010).
    [DOI: 10.1002/polb.21975 ]

  17. Yuichi Masubuchi, Takashi Uneyama, Hiroshi Watanabe, G.iovanni Ianniruberto, Francesci Greco, and Giuseppe Marrucci, "Structure of entangled polymer network from primitive chain network simulations", J. Chem. Phys. 132, [134902]1 - 8 (2010).
    [DOI: 10.1063/1.3370346]

  18. Kenji Furuichi, Chisato Nonomura, Yuichi Masubuchi and Hiroshi Watanabe, "Chain contraction and nonlinear stress damping in primitive chain network simulations", J Chem Phys, 133, [174902]1-10 (2010).
    [DOI: 10.1063/1.3502681]
↑

Review, Proceedings, etc †

  1. 増渕雄一，”高分子成形加工の分子シミュレーション”，日本機械学会計算力学部門ニュースレター（CMD News Letter）44, 14-15 (2010)

  2. 増渕雄一，"高分子の高速分子シミュレーション法"．アンサンブル（分子シミュレーション研究会誌），12(1), 2 - 7 (2010)

  3. 増渕雄一，"溶融体基本特性（研究総覧）", 成形加工, 22(7), 358-361 (2010).
↑

FY2009 (04/2009-03/2010) †

↑

Original Papers (Refereed) †

  1. Yasuya Nakayama, Kang. Kim, and Ryoichi Yamamoto, "Direct simulation of flowing colloidal dispersions by smoothed profile method", Advanced Powder Technology 21, 206–211 (2010).
    [DOI: 10.1016/j.apt.2009.11.011 ]

  2. Shugo Yasuda and Ryoichi Yamamoto, "Multiscale modeling and simulation for polymer melt flows between parallel plates", Phys. Rev. E 81, 036308 (2010).
    [DOI: 10.1103/PhysRevE.81.036308 ]

  3. T. Iwashita and R. Yamamoto, "Direct numerical simulations for non-Newtonian rheology of concentrated particle dispersions", Phys. Rev. E 80, 061402 (2009)
    [DOI: 10.1103/PhysRevE.80.061402]

  4. Takahiro Murashima and Takashi Taniguchi, "Multiscale Lagrangian Fluid Dynamics Simulation for Polymeric Fluid", J. Pol. Sci. Part B, 48, pp. 886-893 (2010)
    [DOI:10.1002/polb.21975]

  5. R. Yamamoto, Y. Nakayama, and K. Kim, "Smoothed profile method to simulate colloidal particles in complex fluids", Int. J. Mod. Phys. C, 20, 1457-1465 (2009).
    [DOI: 10.1142/S0129183109014515]

  6. Yuichi Masubuchi, Kenji Furuichi, Kazushi Horio, Takashi Uneyama, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Primitive chain network simulations for entangled DNA solutions", J. Chem. Phys. 131, 114906, (2009)
    [DOI: doi:10.1063/1.3225994]

  7. Satoru Okuda, Yasuhiro. Inoue, Yuichi Masubuchi, Takashi Uneyama and Masaki Hojo, "Wall boundary model for primitive chain network simulations", J. Chem. Phys. 130(21), 214907, (2009).
    [DOI: doi:10.1063/1.3140941]

  8. Takashi Uneyama, Yuichi Masubuchi, Kazushi Horio, Yumi Matsumiya, Hiroshi Watanabe, Jai A. Pathak, C. Michael Roland, "A theoretical analysis of rheodielectric response of type-A polymer chains", J. Polym. Sci. B: Polym. Phys., 47(11), 1039-1057, (2009)
    [DOI: doi:10.1002/polb.21708]

  9. Yuichi Masubuchi, Takashi Uneyama, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco and Giuseppe Marrucci, "Primitive Chain Network Simulations of Conformational Relaxation for Individual Molecules in the Entangled State. II. Retraction from Stretched States", Nihon Reoroji Gakkaishi (J. Soc. Rheol. Japan), 37 (2), 65-68 (2009).
    [DOI: doi:10.1678/rheology.37.65]

  10. Takashi Uneyama, "Coarse-Grained Brownian Dynamics Simulations for Symmetric Diblock Copolymer Melts Based on the Soft Dumbbell Model", Nihon Reoroji Gakkaishi (J. Soc. Rheol. Japan), 37 (2), 81-90 (2009).
    [DOI: doi:10.1678/rheology.37.81]

  11. Shugo Yasuda and Ryoichi Yamamoto, "Rheological properties of polymer melt between rapidly oscillating plates: an application of multiscale modeling", EPL 86, 18002 (2009).
    [DOI: 10.1209/0295-5075/86/18002]

  12. Takuya Iwashita, Yasuya Nakayama, and Ryoichi Yamamoto, "Velocity autocorrelation function of fluctuating particles in incompressible fluids, -Toward direct numerical simulation of particle dispersions-", Prog. Theor. Phys. Suppl. 178, 86-91 (2009).
    [DOI: 10.1143/PTPS.178.86 ]

  13. E. Dushanov, Kh. Kholmurodov, G. Aru, V. Korenkov, W. Smith, Y. Ohno, T. Narumi, G. Morimoto, M. Taiji, and K. Yasuoka, "JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures", Physics of Particles and Nuclei Letters, 6(3), 251, (2009).
    [DOI: 10.1134/S154747710903011X ]

  14. Narumi, T., Yasuoka, K., Taiji, M., and Höfinger, S., "Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach", J. Comput Chem., 30, 2351(2009).
    [DOI: 10.1002/jcc.21257 ]

  15. Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., and Yasuoka, K. , "Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence Computer Physics Communications", Comput. Phys. Commun., 180, 2066(2009).
    [DOI: 10.1016/j.cpc.2009.06.009 ]

  16. 坂牧隆司，成見哲，泰岡顕治，"グラフィックカードを用いた水表面張力の高速分子動力学シミュレーション", 情報処理学会論文誌　コンピューティングシステム，2(2), 89-97, (2009)．

  17. Yuichi Masubuchi, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, " Primitive Chain Network Simulations for Particle Dispersed Polymers ", International Journal of Polymers and Technologies, 1(1), 17-21, (2009).

  18. 増渕雄一，"プリミティブチェーンネットワークシミュレーションによる高分子材料の応力緩和挙動の予測", 日本ゴム協会誌，82(11), 459-463 (2009)
↑

Review, Proceedings, etc †

  1. Tsuyoshi Hamada, Rio Yokota, Keigo Nitadori, Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Kiyoshi Oguri, "42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence", Proceedings of the SC2009, USB memory, Portland, USA, (2009). [DOI: 10.1145/1654059.1654123 ]

  2. 安田修悟，山本量一， "ソフトマターのマルチスケールシミュレーション：高分子溶液の流動解析への応用"， プラズマ・核融合学会誌 85-09, 607 (2009).
↑

FY2008 (04/2008-03/2009) †

↑

Original Papers (Refereed) †


  1. Takuya Iwashita and Ryoichi Yamamoto, "Short-time motion of Brownian particles in a shear flow", Phys. Rev. E 79, 031401 (2009).

  2. Shugo Yasuda and Ryoichi Yamamoto, "A Model for Hybrid Simulations of Molecular Dynamics and Computational Fluid Dynamics", Phys. Fluids 20, 113101 (2008). [DOI: 10.1063/1.3003218]

  3. Tetsu Narumi, Shun Kameoka, Makoto Taiji, and Kenji Yasuoka, "Accelerating Molecular Dynamics Simulation on PLAYSTATION 3 Platform using "Virtual-GRAPE" Programming Model, SIAM Journal on Scientific Computing, 30, 3108-3125 (2008). [DOI: 10.1137/070692054 ]

  4. Yasuya Nakayama, Kang Kim and Ryoichi Yamamoto, "Smoothed Profile Method for Direct Simulation of Flowing (Charged) Colloids in Solvents", AES Technical Reviews International Journal of Nano and Advanced Engineering Materials, 1, 21-28 (2008).

  5. Toshiki Mima, Tetsu Narumi, Shun Kameoka, and Kenji Yasuoka, "Cell size dependence of orientational order of uniaxial liquid", Molecular Simulation, 34, 761-773(2008). [DOI: 10.1080/08927020802256058 ]

  6. Ryoichi Yamamoto, Kang Kim, Yasuya Nakayama, Kunimasa Miyazaki, David R. Reichman, "On the Role of Hydrodynamic Interactions in Colloidal Gelation", J. Phys. Soc. Jpn., 77, 084804 (2008).

  7. Yuichi Masubuchi, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Primitive Chain Network Simulations for Bidisperse Linear Polymers", Int. J. Nano Adv. Eng. Mat., Part A. 1(1), 35-40 (2008).

  8. Quan Chen, Yumi Matsumiya, Yuichi Masubuchi, Hiroshi Watanabe, and Tadashi Inoue, "Component Dynamics in Polyisoprene/Poly(4-tert-butylstyrene) Miscible Blends," Macromolecules, 41, 8694-8711, (2008) [DOI: doi:10.1021/ma8013417]

  9. Kenji Furuichi, Chisato Nonomura, Yuichi Masubuchi, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Entangled polymer orientation and stretch under large step shear deformations in primitive chain network simulations," Rheologica Acta, 47, 591-599, (2008) [DOI: doi:10.1007/s00397-008-0258-3]

  10. Yuichi Masubuchi, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Comparison among Slip-Link Simulations of Bidisperse Linear Polymer Melts," Macromolecules, 41, 8275-8280, (2008) [DOI: doi:10.1021/ma800954q]

  11. Yuichi Masubuchi, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Primitive chain network simulations of conformational relaxation for individual molecules in the entangled state," NIHON REOROJI GAKKAISHI (J. Soc. Rheol. Jpn.) , 36, 181-185, (2008) [DOI: doi:10.1678/rheology.37.65]

  12. Takatoshi Yaoita, Takeharu Isaki, Yuichi Masubuchi, Hiroshi Watanabe, Giovanni Ianniruberto, Francesco Greco, and Giuseppe Marrucci, "Statics, linear, and nonlinear dynamics of entangled polystyrene melts simulated through the primitive chain network model," J Chem Phys, 128, 154901 (2008) [DOI: doi:10.1063/1.2899653]

  13. Noriyoshi Arai, Kenji Yasuoka, X. C. Zeng, "Self-Assembly of Surfactants and Polymorphic Transition in Nanotubes", J. Am. Chem. Soc., 130, 7916-7920 (2008). [DOI: 10.1021/ja7108739 ]

  14. Yasuya Nakayama, Kang Kim and Ryoichi Yamamoto, "Simulating (electro) hydrodynamic effects in colloidal dispersions: smoothed profile method", Eur. Phys. J. E, 26, 361-368 (2008).

  15. Takuya Iwashita, Yasuya Nakayama, and Ryoichi Yamamoto, "A numerical model for Brownian particles fluctuating in incompressible fluids", J. Phys. Soc. Jpn., 77, 074007, (2008).
↑

Review, Proceedings, etc †


  1. Tetsu Narumi, Tsuyoshi Hamada, Keigo Nitadori, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka, "High-Performance Quasi Double-Precision Method using Single-Precision Hardware for Molecular Dynamics Simulations with GPUs", Proceedings of HPC Asia 2009, Kaohsiung, Taiwan, in press.

  2. Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka, "Overheads in Accelerating Molecular Dynamics Simulations with GPUs", Proceedings of the 9th International Conference on Parallel and Distributed Computing, Applications, and Technologies　(PDCAT’08), pp. 143-150, Dunedin, New Zealand, (2008). [DOI: 10.1109/PDCAT.2008.68 ]

  3. 名嘉山祥也, 金鋼, 岩下拓哉, 山本量一, "コロイド分散系の直接数値シミュレーション", 九州大学応用力学研究所研究集会報告「乱流現象及び多自由度系の動力学、構造と統計法則」19ME-S7. (2008).
↑

FY2007 (04/2007-03/2008) †

↑

Original Papers (Refereed) †


  1. M. Moriya, K. Oogo, Y. Masubuchi and T. Asakura, "Flow analysis of aqueous solution of silk fibroin in the spinneret of Bombyx mori silkworm by combination of viscosity measurement and finite element method calculation", Polymer, 49(4), 952-956 (2008) [DOI: doi:10.1016/j.polymer.2007.12.032]

  2. Y. Masubuchi, G. Ianniruberto, F. Greco and G. Marrucci, "Unit of molecular weight, stress and time of the primitive chain network simulations for polymer melts ", J. Non-newtonian Fluid Mech., 149 (1-3), 87-92 (2008). [DOI: doi:10.1016/j.jnnfm.2007.02.014]

  3. Noriyoshi Arai, Kenji Yasuoka, Yuichi Masubuchi, "Spontaneous self-assembly process for threadlike micelles", J. Chem. Phys., 126, 244905 (2007). [DOI: 10.1063/1.2747240 ]

  4. N. Hosono, Y. Masubuchi, H. Furukawa and T. Watanabe, "A molecular dynamics simulation study on polymer networks of end-linked flexible or rigid chains", J. Chem. Phys., 127, 164905, (2007) [DOI: doi:10.1063/1.2790007]

  5. Kazuaki Takahashi, Kenji Yasuoka, and Tetsu Narumi, "Cutoff radius effect of isotropic periodic sum method for transport coefficients of Lennard-Jones liquid", J. Chem. Phys., 127, 114511 (2007). [DOI: 10.1063/1.2775929 ]

  6. Ryoichi Yamamoto, Kang Kim, and Yasuya Nakayama, "Strict simulations of non-equilibrium dynamics of colloids", Colloids and Surfaces A: Physicochemical and Engineering Aspects, 311, 42-47 (2007).
↑

Review, Proceedings, etc †


  1. 山本量一, "コロイド系のハイブリッドシミュレーション", 高分子, 56, 1001 (2007).

  2. 山本量一, "荷電コロイド分散系の計算機シミュレーション", セラミックス, 43, 77-86 (2008).

  3. 山本量一, 米谷慎, 奥薗透, 福田順一, "液晶の計算機シミュレーション", 液晶, 11, 259-266 (2007).

  4. 名嘉山祥也, 金鋼, 山本量一, "コロイド分散系の直接数値シミュレーション", ケミカルエンジニヤリング, 52, 340-345 (2007).

  5. Y. Nakayama, K. Kim and R. Yamamoto, "Smoothed Profile Method for Direct Simulation of Flowing (Charged) Colloids in Solvents", Proceedings of AES - ATEMA First International Conference(2007) pp.277-284 (2007).
↑

FY2006 (10/2006-03/2007) †

↑

Original Papers (Refereed) †


  1. 名嘉山祥也, 金鋼, 山本量一, "Smoothed Profile 法によるコロイド系の直接数値シミュレーション", 粉体工学会誌, 44, 191-197 (2007).

  2. Ryoichi Yamamoto, Kim kang, and Yasuya Nakayama, "KAPSEL: Kyoto Advanced Particle Simulator for ELectrohydrodynamics -Toward Direct Numerical Simulations of Colloidal Dispersions-", KONA, 24, 167-182 (2006).
↑

Review, Proceedings, etc †


  1. 金鋼, 名嘉山祥也, 山本量一, "荷電コロイド分散系の直接数値シミュレーション -KAPSELの原理と操作-", 粉体工学会誌, 44, 28-36 (2007).