#include(jp/Papers,notitle)


* Publications from the MSS project [#mda18fc0]

//** FY2011 (04/2011-03/2012) [#z10e9daf]

//*** Original Papers (Refereed) [#gaf14110]

//*** Review, Proceedings, etc [#b81bb8eb]

//** FY2010 (04/2010-03/2011) [#x152e680]

//*** Original Papers (Refereed) [#g3cc0241]

//*** Review, Proceedings, etc [#pd2b1d07]

** FY2009 (04/2009-03/2010) [#r73ed7af]
+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) 
+Shugo Yasuda and Ryoichi Yamamoto, "Multiscale modeling and simulation for polymer melt flows between parallel plates", [[arXiv0909.2466>http://arxiv.org/abs/0909.2466]] (preprint).
+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).
+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)
//
+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).
//
+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).
//
+ Shugo Yasuda and Ryoichi Yamamoto, "Rheological properties of polymer melt between rapidly oscillating plates: an application of multiscale modeling", EPL ''86'', 18002 (2009).
//
+ 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). 
//
+ 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).
//
+ 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).
//

** FY2008 (04/2008-03/2009) [#ib11127f]

+ Takuya Iwashita and Ryoichi Yamamoto,
"Short-time motion of Brownian particles in a shear flow",
Phys. Rev. E ''79'', 031401 (2009).
//
+ Shugo Yasuda and Ryoichi Yamamoto,
"A Model for Hybrid Simulations of Molecular Dynamics and Computational Fluid Dynamics",
Phys. Fluids ''20'', 113101 (2008).
// 
+ 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). 
//
+ 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).
 
+ Toshiki Mima, Tetsu Narumi, Shun Kameoka, and Kenji Yasuoka, "Cell size dependence of orientational order of uniaxial liquid", Molecular Simulation, 34, 761-773(2008).
 
+ 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).
 
+ 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).
 
+ 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)
 
+ 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)
 
+ 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)
 
+ 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)
 
+ 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)
 
+ Noriyoshi Arai, Kenji Yasuoka, X. C. Zeng, "Self-Assembly of Surfactants and Polymorphic Transition in Nanotubes", J. Am. Chem. Soc., ''130'',  7916-7920 (2008).
 
+ 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).
//
+ Takuya Iwashita, Yasuya Nakayama, and Ryoichi Yamamoto,
"A numerical model for Brownian particles fluctuating in incompressible fluids", 
J. Phys. Soc. Jpn., ''77'', 074007, (2008). 
//
+ 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.
+ 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).


** FY2007 (04/2007-03/2008) [#q9f7aa23]

+ 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)
 
+ 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), 8792 (2008).
 
+ Noriyoshi Arai, Kenji Yasuoka, Yuichi Masubuchi, "Spontaneous self-assembly process for threadlike micelles", J. Chem. Phys., ''126'', 244905 (2007).
 
+ 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)
 
+ 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).
 
+ 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). 
//
+ 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) [#n663ac3d]
. 
+ Ryoichi Yamamoto, Kim kang, and Yasuya Nakayama, "[[KAPSEL: Kyoto Advanced Particle Simulator for ELectrohydrodynamics -Toward Direct Numerical Simulations of Colloidal Dispersions-:http://www.kona.or.jp/search/24_167.pdf]]", KONA, ''24'', 167-182 (2006).