Publication List †

↑

Publication List of RY †

↑

Refereed Papers †

Future

2023

130
T. Kobayashi, G. Jung, Y. Matsuoka, Y. Nakayama, J. J. Molina, and R. Yamamoto,
Direct numerical simulations of a microswimmer in a viscoelastic fluid,
Soft Matter 19, 7109–7121 (2023). [http://dx.doi.org/10.1039/D3SM00600J]
129
S. K. Schnyder, J. J. Molina, R. Yamamoto, and M. S. Turner,
Rational social distancing policy during epidemics with limited healthcare capacity,
PLOS Comput. Biol. 19, e1011533 (2023). [http://dx.doi.org/10.1371/journal.pcbi.1011533]
128
S. K. Schnyder, J. J. Molina, R. Yamamoto, and M. S. Turner,
Rational social distancing in epidemics with uncertain vaccination timing,
PLoS One 18, e0288963 (2023). [http://dx.doi.org/10.1371/journal.pone.0288963]
127
K. Sankaewtong, J. J. Molina, M. S. Turner, and R. Yamamoto,
Learning to swim efficiently in a nonuniform flow field,
Phys. Rev. E 107, 065102 (2023). [http://dx.doi.org/10.1103/PhysRevE.107.065102]
126
C. Feng, J. J. Molina, and R. Yamamoto,
Dynamics of a Model Microswimmer in the Vicinity of a Liquid Droplet,
J. Phys. Soc. Japan 92, 074802 (2023). [http://dx.doi.org/10.7566/JPSJ.92.074802]
125
C. Feng, J. J. Molina, M. S. Turner, and R. Yamamoto,
Dynamics of microswimmers near a liquid–liquid interface with viscosity difference,
Phys. Fluids 35, 051903 (2023). [http://dx.doi.org/10.1063/5.0148008]
124
S. Imamura, K. Sawaki, J. J. Molina, M. S. Turner, and R. Yamamoto,
Collective Motion of Quincke Rollers with Fully Resolved Hydrodynamics,
Adv. Theory Simulations 6, 2200683 (2023). [http://dx.doi.org/10.1002/adts.202200683]
123
M. Uzair, M. D. Qasim, M. A. Bhatti, A. A. Zaidi, J. J. Molina, R. Yamamoto, A. Hamid,
Direct numerical simulations of isolated rigid particles; Validation of smooth profile method,
Powder Technol. 418, 118280 (2023). [http://dx.doi.org/10.1016/j.powtec.2023.118280]

2022

122
J. Li, S. K. Schnyder, M. S. Turner, and R. Yamamoto,
Competition between cell types under cell cycle regulation with apoptosis,
Phys. Rev. Res. 4, 033156 (2022). [http://dx.doi.org/10.1103/PhysRevResearch.4.033156]
121
K. Kanayama, T. Hoshino, and R. Yamamoto,
Relation between dynamic heterogeneities observed in scattering experiments and four-body correlations,
Phys. Rev. Res. 4, L022006 (2022). [http://dx.doi.org/10.1103/PhysRevResearch.4.L022006]
120
M. Tarama, K. Mori, and R. Yamamoto,
Mechanochemical subcellular-element model of crawling cells,
Front. Cell Dev. Biol. 10, 118280 (2022). [http://dx.doi.org/10.3389/fcell.2022.1046053]
119
C. Feng, J. J. Molina, M. S. Turner, and R. Yamamoto,
Dynamics of microswimmers near a soft penetrable interface,
Phys. Rev. Res. 4, 043202 (2022). [http://dx.doi.org/10.1103/PhysRevResearch.4.043202]

2021

118
J. Li, S. K. Schnyder, M. S. Turner, and R. Yamamoto,
Role of the Cell Cycle in Collective Cell Dynamics,
Phys. Rev. X 11, 031025 (2021). [http://dx.doi.org/10.1103/PhysRevX.11.031025]
117
R. Yamamoto, J. J. Molina, and Y. Nakayama,
Smoothed profile method for direct numerical simulations of hydrodynamically interacting particles,
Soft Matter 16, 4226–4253 (2021). [http://dx.doi.org/10.1039/D0SM02210A]

2020

116
Federico Fadda, John Jairo Molina, and Ryoichi Yamamoto,
Dynamics of a chiral swimmer sedimenting on a flat plate,
Phys. Rev. E 101, 052608 (2020). [http://dx.doi.org/10.1103/PhysRevE.101.052608]
115
Simon K. Schnyder, John J. Molina, and Ryoichi Yamamoto,
Control of cell colony growth by contact inhibition,
Scientific Report 10, 6713-6726 (2020). [http://dx.doi.org/10.1038/s41598-020-62913-z]
114
Gregory Lecrivain, Taisa B. Pacheco, Ryoichi Yamamoto, Uwe Hampel, and Takashi Taniguchi,
Eulerian/Lagrangian formulation for the elasto-capillary deformation of a flexible fibre,
J. Comput. Phys. 409, 109324-109339 (2020). [http://dx.doi.org/10.1016/j.jcp.2020.109324]
113
N. Arai, S. Watanabe, M. T. Miyahara, R. Yamamoto, U. Hampel, and G. Lecrivain,
Direct observation of the attachment behavior of hydrophobic colloidal particles onto a bubble surface,
Soft Matter 16, 695–702 (2020). [http://dx.doi.org/10.1039/C9SM01787A]
112
A. Hamid, A.B. Arshad, S. Mehdi, M.D. Qasim, A. Ullah, J.J. Molina, R. Yamamoto,
A numerical study of sedimentation of rod like particles using smooth profile method,
Int. J. Multiph. Flow 127, 103263-103273 (2020). [http://dx.doi.org/10.1016/j.ijmultiphaseflow.2020.103263]

2019

111
Matteo Campoa, Simon K. Schnyderc, John J. Molinad, Thomas Speck and Ryoichi Yamamoto,
Spontaneous Spatiotemporal Ordering of Shape Oscillations Enhances Cell Migration,
Soft Matter 15, 4939-4946 (2019). [http://dx.doi.org/10.1039/C9SM00526A]
110
John J. Molina, Ryoichi Yamamoto,
Mechanosensitivity of Crawling Cells under Periodically Stretching Substrates,
Soft Matter 15, 683 (2019). [http://dx.doi.org/10.1039/C8SM01903G]

2018

109
Gregory Lecrivain, Yuki Kotani, Ryoichi Yamamoto, Uwe Hampel, and Takashi Taniguchi,
A diffuse interface model to simulate the rise of a fluid droplet across a cloud of particles,
Physical Review Fluids 3, 094002 (2018). [http://dx.doi.org/10.1103/PhysRevFluids.3.094002]
108
Chunyu Shih, John J. Molina, and Ryoichi Yamamoto,
Field-induced dipolar attraction between like-charged colloids,
Soft Matter 12, 914-924 (2018). [http://dx.doi.org/10.1039/C8SM00395E]
107
M. Shakeel, A. Hamid, A. Ullah, J. J. Molina, and R. Yamamoto,
Direct Numerical Simulations of Correlated Settling particles,
J. Phys. Soc. Japan 87, 064402 (2018). [http://dx.doi.org/10.7566/JPSJ.87.064402]
106
Mitsusuke Tarama and Ryoichi Yamamoto,
Mechanics of cell crawling by means of force-free cyclic motion,
J. Phys. Soc. Japan 87, 044803 (2018). [http://dx.doi.org/10.7566/JPSJ.87.044803]
105
Norihiro Oyama, Kosuke Teshigawara, John J. Molina, Ryoichi Yamamoto, and Takashi Taniguchi,
Reynolds-number-dependent dynamical transitions on hydrodynamic synchronization modes of externally driven colloids,
Phys. Rev. E 97, 032611 (2018). [http://dx.doi.org/10.1103/PhysRevE.97.032611]

2017

104
Norihiro Oyama, John J. Molina, and Ryoichi Yamamoto,
Do hydrodynamically assisted binary collisions lead to orientational ordering of microswimmers?
Eur. Phys. J. E 40, 95 (2017). [http://dx.doi.org/10.1140/epje/i2017-11586-4]
103
Norihiro Oyama, John J. Molina, and Ryoichi Yamamoto,
Simulations of model micro-swimmers with fully resolved hydrodynamics,
J. Phys. Soc. Jpn., 86, 101008 (2017). [http://dx.doi.org/10.7566/JPSJ.86.101008]
102
Gregory Lecrivain, Ryoichi Yamamoto, Uwe Hampel, and Takashi Taniguchi,
Direct numerical simulation of an arbitrarily shaped particle at a fluidic interface,
Phys. Rev. E 95, 063107 (2017). [http://dx.doi.org/10.1103/PhysRevE.95.063107]
101
Samia Mehdi, Adnan Hamid, Atta Ullah, and Ryoichi Yamamoto,
Microstructure of Rod like Sedimenting Particles: Direct Numerical Simulations,
14th International Bhurban Conference on Applied Sciences and Technology (IBCAST), 622-626 (2017). [http://dx.doi.org/10.1109/IBCAST.2017.7868115]
100
Simon K. Schnyder, Yuki Tanaka, John J. Molina, and Ryoichi Yamamoto,
Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibition,
Scientific Reports 7, 5163 (2017). [http://dx.doi.org/10.1038/s41598-017-05321-0]

2016

99
Gregory Lecrivain, Ryoichi Yamamoto, Uwe Hampel, and Takashi Taniguchi,
Direct numerical simulation of a single particle attachment on a stationary immersed bubble,
Phys. Fluids 28, 083301 (2016). [http://dx.doi.org/10.1063/1.4960627]
98
Norihiro Oyama, John J. Molina, Ryoichi Yamamoto,
Purely hydrodynamic origin for swarming of swimming particles,
Phys. Rev. E 93, 043114 (2016). [http://dx.doi.org/10.1103/PhysRevE.93.043114]
97
John J. Molina, Kotaro Otomura, Hayato Shiba, Hideki Kobayashi, Masaki Sano, and Ryoichi Yamamoto,
Rheological evaluation of colloidal dispersions using the smooth profile method: formulation and applications,
J. Fluid Mech. 792, 590-619 (2016). [http://dx.doi.org/10.1017/jfm.2016.78]
96
Shugo Yasuda and Ryoichi Yamamoto,
Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates,
Computers and Fluids 124, 185-189 (2016). [http://dx.doi.org/10.1016/j.compfluid.2015.05.018]

2015

95
Chunyu Shih, John J. Molina, and Ryoichi Yamamoto,
Dynamic polarization of a charged colloid in an oscillating electric field,
Molec. Phys. 113, 2511-2522 (2015). [http://dx.doi.org/10.1080/00268976.2015.1059510]
94
Andrew J. Dunleavy, Karoline Wiesner, Ryoichi Yamamoto, and C. Patrick Royall,
Mutual information reveals multiple structural relaxation mechanisms in a model glassformer,
Nature Communications 6, 6089 (2015). [http://dx.doi.org/10.1038/ncomms7089]
93
Gregory Lecrivain, Giacomo Petrucci, Uwe Hampel and Ryoichi Yamamoto,
Attachment of solid elongated particles on the surface of a stationary gas bubble,
Int. J. Multiphase Flow 71, 83-93 (2015). [http://dx.doi.org/10.1016/j.ijmultiphaseflow.2015.01.002]
92
Shugo Yasuda and Ryoichi Yamamoto,
Multiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plate,
Molec. Simulation 41, 1002-1005 (2015). [http://dx.doi.org/10.1080/08927022.2014.951639]
91
Adnan Hamid, John J. Molina, and Ryoichi Yamamoto,
Simulation studies of microstructure of colloids in sedimentation,
Molec. Simulation 41, 968-973 (2015). [http://dx.doi.org/10.1080/08927022.2014.929124]

2014

90
Shugo Yasuda and Ryoichi Yamamoto,
Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication,
Phys. Rev. X 4, 041011 (2014). [http://dx.doi.org/10.1103/PhysRevX.4.041011]
89
Adnan Hamid, John J. Molina, and Ryoichi Yamamoto,
Direct Numerical Simulations of Sedimenting Spherical Particles at Finite Reynolds Number,
RSC Advances 4, 53681-53693 (2014). [http://dx.doi.org/10.1039/C4RA11025K]
88
Chunyu Shih and Ryoichi Yamamoto,
Dynamic Electrophoresis of Charged Colloids in an Alternating Electric Field,
Phys. Rev. E 89, 062317 (2014). [http://dx.doi.org/10.1103/PhysRevE.89.062317]
87
John J. Molina and Ryoichi Yamamoto,
Diffusion of colloidal particles in swimming suspensions,
Molec. Phys. 112, 1389-1397 (2014). [http://dx.doi.org/10.1080/00268976.2014.903004]

2013

86
John J. Molina and Ryoichi Yamamoto,
Direct numerical simulations of rigid body dispersions. I. Mobility/Friction tensors of assemblies of spheres,
J. Chem. Phys. 139, 234105 (2013). [http://dx.doi.org/10.1063/1.4844115]
85
Adnan Hamid, John J. Molina, and Ryoichi Yamamoto,
Sedimentation of non-Brownian spheres at high volume fraction,
Soft Matter 9, 10056-10068 (2013). [http://dx.doi.org/10.1039/c3sm50748c]
84
Rei Tatsumi and Ryoichi Yamamoto,
Velocity relaxation of a particle in a confined compressible fluid,
J. Chem. Phys. 138, 184905 (2013). [http://dx.doi.org/10.1063/1.4804186]
83
John J. Molina, Yasuya Nakayama, and Ryoichi Yamamoto,
Hydrodynamic interactions of self-propelled swimmers,
Soft Matter 9, 4923-4936 (2013). [http://dx.doi.org/10.1039/c3sm00140g]
82
Rei Tatsumi and Ryoichi Yamamoto,
Propagation of hydrodynamic interactions between particles in a compressible fluid,
Phys. Fluids 25, 046101 (2013). [http://dx.doi.org/10.1063/1.4802038]
81
Hideyuki Mizuno and Ryoichi Yamamoto,
General constitutive model for supercooled liquids: Anomalous transverse wave propagation,
Phys. Rev. Lett. 110, 095901 (2013). [http://dx.doi.org/10.1103/PhysRevLett.110.095901]
80
Adnan Hamid and Ryoichi Yamamoto,
Direct numerical simulations of anisotropic diffusion of spherical particles in sedimentation,
Phys. Rev. E 87, 022310 (2013). [http://dx.doi.org/10.1103/PhysRevE.87.022310]
79
Adnan Hamid and Ryoichi Yamamoto,
Sedimentation at Finite Peclet Number: Direct Numerical Simulation,
AIP Conf. Proc. 1518, 444-447 (2013). [http://dx.doi.org/10.1063/1.4794612]
78
Adnan Hamid and Ryoichi Yamamoto,
Anisotropic velocity fluctuations and particle diffusion in sedimentation,
J. Phys. Soc. Jpn. 82, 024004 (2013). [http://dx.doi.org/10.7566/JPSJ.82.024004]
77
Takahiro Murashima, Shugo Yasuda, Takashi Taniguchi, and Ryoichi Yamamoto,
Multiscale modeling for polymeric flow: Particle-fluid bridging scale methods,
J. Phys. Soc. Jpn. 82, 012001 (2013). [http://dx.doi.org/10.7566/JPSJ.82.012001]

2012

76
Yuki Matsuoka, Tomonori Fukasawa, Ko Higashitani, and Ryoichi Yamamoto,
Effect of hydrodynamic interactions on rapid Brownian coagulation of colloidal dispersions,
Phys. Rev. E 86, 051403 (2012). [http://dx.doi.org/10.1103/PhysRevE.86.051403]
75
Yuki Matsuoka, Hideyuki Mizuno, and Ryoichi Yamamoto,
Acoustic wave propagation through a supercooled liquid: A normal mode analysis,
J. Phys. Soc. Jpn. 81, 124602 (2012). [http://dx.doi.org/10.1143/JPSJ.81.124602]
74
Yukitaka Ishimoto, Takahiro Murashima, Takashi Taniguchi, and Ryoichi Yamamoto,
Two-dimensional lattice liquid models,
Phys. Rev. E 86, 031124 (2012). [http://dx.doi.org/10.1103/PhysRevE.86.031124]
73
Rei Tatsumi and Ryoichi Yamamoto,
Direct numerical simulation of dispersed particles in a compressible fluid,
Phys. Rev. E 85, 066704 (2012). [http://dx.doi.org/10.1103/PhysRevE.85.066704]
72
Hideyuki Mizuno and Ryoichi Yamamoto,
Mechanical Responses and Stress Fluctuations of a Strongly Sheared Supercooled Liquid,
Eur. Phys. J. E 35, 29 (2012). [http://dx.doi.org/10.1140/epje/i2012-12029-6]
71
Hideyuki Mizuno and Ryoichi Yamamoto,
Dynamical heterogeneity in a highly supercooled liquid under a sheared situation,
J. Chem. Phys. 136, 084505 (2012). [http://dx.doi.org/10.1063/1.3688227]
70
Masayuki Uranagase, Takashi Taniguchi, and Ryoichi Yamamoto,
Electrostatic potential around a charged colloidal particle in an electrolyte solution with ion strong coupling,
J. Phys. Soc. Jpn. 81 024803 (2012). [http://dx.doi.org/10.1143/JPSJ.81.024803]

2011

69
Hideki Kobayashi and Ryoichi Yamamoto,
Re-entrant transition in the shear viscosity of dilute rigid rod dispersions,
Phys. Rev. E 84 051404 (2011). [http://dx.doi.org/10.1103/PhysRevE.84.051404]
68
Hideyuki Mizuno and Ryoichi Yamamoto,
Dynamical heterogeneity in a highly supercooled liquid: Its correlation length, intensity, and lifetime,
Phys. Rev. E 84, 011506 (2011). [http://dx.doi.org/10.1103/PhysRevE.84.011506]
67
Shugo Yasuda and Ryoichi Yamamoto,
Dynamic rheology of a supercooled polymer melt in non-uniform oscillating flows in rapidly oscillating plates,
Phys. Rev. E 84, 031501 (2011). [http://dx.doi.org/10.1103/PhysRevE.84.031501]
66
Hideki Kobayashi and Ryoichi Yamamoto,
Implementation of Lees-Edwards periodic boundary conditions for direct numerical simulations of particle dispersions under shear flow,
J. Chem. Phys. 134, 064110 (2011). [http://dx.doi.org/10.1063/1.3537974]
65
Saeed Jafari, Ryoichi Yamamoto, and Mohamad Rahnama,
Lattice-Boltzmann method combined with smoothed-profile method for particulate suspensions,
Phys. Rev. E 83, 026702 (2011). [http://dx.doi.org/10.1103/PhysRevE.83.026702]

2010

64
Hideyuki Mizuno and Ryoichi Yamamoto,
Lifetime of dynamical heterogeneity in a highly supercooled liquid,
Phys. Rev. E 82, 030501 (2010). [http://dx.doi.org/10.1103/PhysRevE.82.030501]
63
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). [http://dx.doi.org/10.1140/epje/i2010-10638-7]
62
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). [http://dx.doi.org/10.1103/PhysRevE.81.041807]
61
Yasuya Nakayama, Kang Kim, and Ryoichi Yamamoto,
Direct simulation of flowing colloidal dispersions by smoothed profile method,
Advanced Powder Technology 21, 206–211 (2010). [http://dx.doi.org/10.1016/j.apt.2009.11.011]
60
Shugo Yasuda and Ryoichi Yamamoto,
Multiscale modeling and simulation for polymer melt flows between parallel plates,
Phys. Rev. E 81, 036308 (2010). [http://dx.doi.org/10.1103/PhysRevE.81.036308]

2009

59
Takuya Iwashita and Ryoichi Yamamoto,
Direct numerical simulations for non-Newtonian rheology of concentrated particle dispersions,
Phys. Rev. E 80, 061402 (2009). [http://dx.doi.org/10.1103/PhysRevE.80.061402]
58
Ryoichi Yamamoto, Yasuya Nakayama, and Kang Kim,
Smoothed profile method to simulate colloidal particles in complex fluids,
Int. J. Mod. Phys. C 20, 1457-1465 (2009). [http://dx.doi.org/10.1142/S0129183109014515]
57
Shugo Yasuda and Ryoichi Yamamoto,
Rheological properties of polymer melt between rapidly oscillating plates: an application of multiscale modeling,
EPL 86, 18002 (2009). [http://dx.doi.org/10.1209/0295-5075/86/18002]
56
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). [http://dx.doi.org/10.1143/PTPS.178.86]
55
Takuya Iwashita and Ryoichi Yamamoto,
Short-time motion of Brownian particles in a shear flow,
Phys. Rev. E 79, 031401 (2009). [http://dx.doi.org/10.1103/PhysRevE.79.031401]

2008

54
Shugo Yasuda and Ryoichi Yamamoto,
A Model for Hybrid Simulations of Molecular Dynamics and Computational Fluid Dynamics,
Phys. Fluids 20, 113101 (2008). [http://dx.doi.org/10.1063/1.3003218]
53
Ryoichi Yamamoto, Kang Kim, Yasuya Nakayama, K. Miyazaki, and D.R. Reichman,
On the role of hydrodynamic interactions in colloidal gelation,
J. Phys. Soc. Jpn. 77, 084804 (2008). [http://dx.doi.org/10.1143/JPSJ.77.084804]
52
Takuya Iwashita, Yasuya Nakayama, and Ryoichi Yamamoto,
A numerical model for Brownian particles fluctuating in incompressible fluids,
J. Phys. Soc. Jpn. 77, 074007, (2008). [http://dx.doi.org/10.1143/JPSJ.77.074007]
51
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). [http://dx.doi.org/10.1140/epje/i2007-10332-y]

2007

50
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). [http://dx.doi.org/10.1016/j.colsurfa.2007.08.041]

2006

49
Ryoichi Yamamoto, Kang Kim, and Yasuya Nakayama,
KAPSEL: Kyoto Advanced Particle Simulator for ELectrohydrodynamics: Toward Direct Numerical Simulations of Colloidal Dispersions,
KONA 24, 167-182 (2006). [http://dx.doi.org/10.14356/kona.2006019]
48
Kang Kim, Yasuya Nakayama, and Ryoichi Yamamoto,
Direct Numerical Simulations of Electrophoresis,
Phys. Rev. Lett. 96, 208302 (2006). [http://dx.doi.org/10.1103/PhysRevLett.96.208302]
47
Kang Kim, Yasuya Nakayama, and Ryoichi Yamamoto,
Simulating electrohydrodynamics in charged colloidal dispersions: A smoothed profile method,
AIP Conf. Proc. 832, 251-256 (2006). [http://dx.doi.org/10.1063/1.2204501]
46
Yasuya Nakayama, Kang Kim, and Ryoichi Yamamoto,
Hydrodynamic effects in colloidal dispersions studied by a new efficient direct simulation,
AIP Conf. Proc. 832, 245-250 (2006). [http://dx.doi.org/10.1063/1.2204500]
45
Ryoichi Yamamoto,
Supercooled Liquids under Shear: Computational Approach,
Computer Simulation Studies in Condensed Matter Physics XVI; Ed. D.P. Landau, S.P Lewis, and H.B. Schuttler (Springer, Berlin, 2006) p.61-73. [http://dx.doi.org/10.1007/3-540-26565-1_6]

2005

44
Kang Kim and Ryoichi Yamamoto,
Efficient simulations of charged colloidal dispersions: A density functional approach,
Macromol. Theory Simul. 14, 278-284 (2005). [http://dx.doi.org/10.1002/mats.200400068]
43
Yasuya Nakayama and Ryoichi Yamamoto,
A Simulation Method to Resolve Hydrodynamic Interactions in Colloidal Dispersions,
Phys. Rev. E 71, 036707 (2005). [http://dx.doi.org/10.1103/PhysRevE.71.036707]
42
Ryoichi Yamamoto, Yasuya Nakayama, and Kang Kim,
A Method to Resolve Hydrodynamic Interactions in Colloidal Dispersions,
Comp. Phys. Comm. 169, 301-304 (2005). [http://dx.doi.org/10.1016/j.cpc.2005.03.067]
41
Kang Kim, Yasuya Nakayama, and Ryoichi Yamamoto,
A Smoothed Profile Method for Simulating Charged Colloidal Dispersions,
Comp. Phys. Comm. 169, 104-106 (2005). [http://dx.doi.org/10.1016/j.cpc.2005.03.024]
40
Toshiyuki Hamanaka, Ryoichi Yamamoto, and Akira Onuki,
Molecular Dynamics Simulation of Heat-Conducting Near-Critical Fluids,
Phys. Rev. E 71, 011507 (2005). [http://dx.doi.org/10.1103/PhysRevE.71.011507]

2004

39
Ryoichi Yamamoto and Akira Onuki,
Entanglements in a quiescent and sheared polymer melt,
Phys. Rev. E 70, 041801 (2004). also selected for the October 15, 2004 issue of Virtual Journal of Biological Physics Research. [http://dx.doi.org/10.1103/PhysRevE.70.041801]
38
Kunimasa Miyazaki, David R. Reichman, and Ryoichi Yamamoto,
Supercooled Liquids under Shear: Theory and Simulation,
Phys. Rev. E 70, 011501 (2004). [http://dx.doi.org/10.1103/PhysRevE.70.011501]
37
Ryoichi Yamamoto, Yasuya Nakayama, and Kang Kim,
A Smooth Interface Method for Simulating Colloidal Dispersions,
J. Phys.; Condens. Matt. 16, S1945-S1955 (2004). [http://dx.doi.org/10.1088/0953-8984/16/19/007]
36
Kunimasa Miyazaki, Ryoichi Yamamoto, and David R. Reichman,
Supercooled Liquids under Shear: A Mode-Coupling Approach,
AIP Conf. Proc. 708, 635-638. (2004). [http://dx.doi.org/10.1063/1.1764242]
35
Ryoichi Yamamoto, Kunimasa Miyazaki, and David R. Reichman,
Supercooled Liquids under Shear: Computational Approach,
AIP Conf. Proc. 708, 717-718 (2004). [http://dx.doi.org/10.1063/1.1764277]

2002

34
Ryoichi Yamamoto and Akira Onuki,
Dynamics and Rheology of a supercooled polymer melt in shear flow,
J. Chem. Phys. 117 2359-2367 (2002). [http://dx.doi.org/10.1063/1.1488589]

2001

33
Ryoichi Yamamoto,
Simulating particle dispersions in nematic liquid-crystal solvents,
Phys. Rev. Lett. 87, 075502 (2001). [http://dx.doi.org/10.1103/PhysRevLett.87.075502]
32
Walter Kob, C. Brangian, T. Stuehn, and Ryoichi Yamamoto,
Equilibrating glassy systems with parallel tempering,
Computer Simulation Studies in Condensed Matter Physics XIII; Ed. D.P. Landau, S.P Lewis, and H.B. Schuttler (Springer, Berlin, 2001) p.153-166. [http://dx.doi.org/10.1007/978-3-642-56577-9_18]

2000

31
Ryoichi Yamamoto and Kang Kim,
Heterogeneity and finite size effects in the dynamics of supercooled liquids,
J. Phys. IV France 10, 15-20 (2000). [http://dx.doi.org/10.1051/jp4:2000703]
30
Ryoichi Yamamoto and Akira Onuki,
Dynamics of Highly Supercooled Liquids far from Equilibrium,
J. Phys.; Cond. Matt. 12, 6323-6334 (2000). [http://dx.doi.org/10.1088/0953-8984/12/29/304]
29
Ryoichi Yamamoto and Walter Kob,
Replica-exchange molecular dynamics simulation for supercooled liquids,
Phys. Rev. E 61, 5473-5476 (2000). [http://dx.doi.org/10.1103/PhysRevE.61.5473]
28
Ryoichi Yamamoto and Akira Onuki,
Dynamics and Rheology of a Supercooled Polymer Melt,
AIP Conf. Proc. 519, 151-157 (2000). [http://dx.doi.org/10.1063/1.1291531]
27
Ryoichi Yamamoto and Akira Onuki,
Dynamics and Rheology of a Supercooled Polymer Melt,
Prog. Theor. Phys. Suppl. 138, 336-341 (2000). [http://dx.doi.org/10.1143/PTPS.138.336]
26
Kang Kim and Ryoichi Yamamoto,
Apparent finite-size effect in the dynamics of supercooled liquids,
Phys. Rev. E 61, R41-R44 (2000). [http://dx.doi.org/10.1103/PhysRevE.61.R41]

1999

25
Ryoichi Yamamoto and Akira Onuki,
Large scale long-lived heterogeneity in the dynamics of supercooled liquids,
Int. J. Mod. Phys. C 10, 1553-1561 (1999). [http://dx.doi.org/10.1142/S0129183199001339]
24
Hideki Tanaka and Ryoichi Yamamoto, Kenichiro Koga, and Xiao C. Zeng,
Can thin disk-like ice clusters be more stable than compact droplet-like ice clusters?
Chem. Phys. Lett. 304, 378-384 (1999). [http://dx.doi.org/10.1016/S0009-2614(99)00293-6]
23
Ryoichi Yamamoto and Xiao C. Zeng,
Molecular dynamics study of a phase-separating binary fluid mixture under shear flow,
Phys. Rev. E 59, 3223-3230 (1999). [http://dx.doi.org/10.1103/PhysRevE.59.3223]
22
Ryoichi Yamamoto and Akira Onuki,
Dynamics of Highly Supercooled Liquids,
AIP Conf. Proc. 469, 476-483 (1999). [http://dx.doi.org/10.1063/1.58529]

1998

21
Ryoichi Yamamoto and Akira Onuki,
Heterogeneous Diffusion in Highly Supercooled Liquids,
Phys. Rev. Lett. 81, 4915-4018 (1998). [http://dx.doi.org/10.1103/PhysRevLett.81.4915]
20
Ryoichi Yamamoto and Akira Onuki,
Dynamics of Highly Supercooled Liquids; Heterogeneity, Rheology, and Diffusion,
Phys. Rev. E 58, 3515-3529 (1998). [http://dx.doi.org/10.1103/PhysRevE.58.3515]
19
Akira Onuki and Ryoichi Yamamoto,
Kinetic Heterogeneities and Nonlinear Rheology of Highly Supercooled Liquids,
J. Non-cryst. Solid. 235-237, 34-40 (1998). [http://dx.doi.org/10.1016/S0022-3093(98)00558-4]

1997

18
Ryoichi Yamamoto and Akira Onuki,
Nonlinear Rheology of a Highly Supercooled Liquid,
EPL 40, 61-66 (1997). [http://dx.doi.org/10.1209/epl/i1997-00419-1]
17
Ryoichi Yamamoto and Akira Onuki,
Kinetic Heterogeneities in a Highly Supercooled Liquid,
J. Phys. Soc. Jpn. 66, 2545-2548 (1997). [http://dx.doi.org/10.1143/JPSJ.66.2545]
16
Ryoichi Yamamoto, M. Kano, and Yoji Kawamoto,
Computer simulation of ionic conduction in ZrF_4-BaF_2 glass, II. Normal mode analysis,
J. Phys.: Cond. Matt. 9, 5157-5166 (1997). [http://dx.doi.org/10.1088/0953-8984/9/24/014]
15
Akira Onuki, Ryoichi Yamamoto, and Takashi Taniguchi,
Viscoelastic effects and shear-induced phase separation in polymer solutions in polymer solutions,
Progr. Colloid. Polym. Sci. 106, 150-157 (1997). [http://dx.doi.org/10.1007/BFb0111049]
14
Akira Onuki, Ryoichi Yamamoto, and Takashi Taniguchi,
Phase separation in polymer solutions induced by shear,
J. Phys. II France 7, 295-304 (1997). [http://dx.doi.org/10.1051/jp2:1997126]

1996

13
Sigenobu Matsuo, Y. Mizuguchi, Yoshiyuki Tanaka, Hironobu Kubota, and Ryoichi Yamamoto,
Volumetric properties of mixtures of 1,4-dioxane and water at high pressures,
Int. J. Thermophys. 17, 441-454 (1996). [http://dx.doi.org/10.1007/BF01443402]
12
Ryoichi Yamamoto and Koichiro Nakanishi,
Computer simulation of vapor-liquid phase separation,
Molec. Simulation 16, 119-126 (1996). [http://dx.doi.org/10.1080/08927029608024066]

1995

11
Ryoichi Yamamoto, T. Kobayashi, and Yoji Kawamoto,
Computer simulation of ionic conduction in ZrF_4-BaF_2 glass,
J. Phys.: Cond. Matt. 7, 8557-8567 (1995). [http://dx.doi.org/10.1088/0953-8984/7/45/011]
10
Masahide Takahashi, Ryoichi Yamamoto, Ryoji Kanno, and Yoji Kawamoto,
Molecular dynamics simulation of Er^{3+}-doped chlorofluorozirconate glasses,
J. Phys.; Cond. Matt. 7, 4583-4592 (1995). [http://dx.doi.org/10.1088/0953-8984/7/24/001]
9
Ryoichi Yamamoto, Osamu Kitao, and Koichiro Nakanishi,
Can the van der Waals loop vanish?, Effect of domain size,
Molec. Phys. 84, 757-768 (1995). [http://dx.doi.org/10.1080/00268979500100521]
8
Ryoichi Yamamoto, Osamu Kitao, and Koichiro Nakanishi,
Monte Carlo Simulation of Fluoro Propane,
Fluid Phase Equilibria 104, 349-361 (1995). [http://dx.doi.org/10.1016/0378-3812(94)02660-S]
7
Ryoichi Yamamoto and Koichiro Nakanishi,
Computer simulation of vapor-liquid phase separation in two- and three-dimensional fluids. II. Domain structure,
Phys. Rev. B 51, 2715-2722 (1995). [http://dx.doi.org/10.1103/PhysRevB.51.2715]

1994

6
Ryoichi Yamamoto, Hideki Tanaka, Koichiro Nakanishi, and Xiao C. Zeng,
Can the van der Waals loop vanish?, Effect of surface free energy,
Chem. Phys. Lett. 231, 401-406 (1994). [http://dx.doi.org/10.1016/0009-2614(94)01268-7]
5
Ryoichi Yamamoto and Koichiro Nakanishi,
Computer simulation of vapor-liquid phase separation in two- and three-dimensional fluids. Growth law of domain size,
Phys. Rev. B 49, 14958-14966 (1994). [http://dx.doi.org/10.1103/PhysRevB.49.14958]
4
Ryoichi Yamamoto, Osamu Kitao, and Koichiro Nakanishi,
Intermolecular Interaction of Fluoro Propanes,
Molec. Simulation 12, 383-391 (1994). [http://dx.doi.org/10.1080/08927029408023045]
3
Sigenobu Matsuo, Ryoichi Yamamoto, Hironobu Kubota, and Yoshiyuki Tanaka,
Volumetric Properties of Mixtures of Fluoroalcohols and Water at High Pressures,
Int. J. Thermophys. 15, 245-259 (1994). [http://dx.doi.org/10.1007/BF01441585]

1993

2
Sigenobu Matsuo, Ryoichi Yamamoto, Yoshiyuki Tanaka, and Hironobu Kubota,
Viscosity of Mixtures of Fluoroalcohols and Water at High Pressures,
Int. J. Thermophys. 14, 835-849 (1993). [http://dx.doi.org/10.1007/BF00502111]
1
Ryoichi Yamamoto, Sigenobu Matsuo, and Yoshiyuki Tanaka,
Thermal Conductivity of Halogenated Ethanes, HFC-134a, HCFC-123 and HCFC-141b,
Int. J. Thermophys. 14, 79-90 (1993). [http://dx.doi.org/10.1007/BF00522663]
↑

Books †

  1. John. J. Molina, Ryoichi Yamamoto,
    Chapter 8 of "Computer Simulation of Polymeric Materials: Applications of the OCTA System", (Springer, 2016) ISBN:978-9811008146 [http://dx.doi.org/10.1007/978-981-10-0815-3]

  2. Kang Kim, Yasuya Nakayama, and Ryoichi Yamamoto,
    Chapters 8 and 9 of "Electrical Phenomena at Interfaces and Biointerfaces: Fundamentals and Applications in Nano-, Bio-, and Environmental Sciences" (Wiley, 2012) ISBN:978-0470582558 [http://dx.doi.org/10.1002/9781118135440.ch8] [http://dx.doi.org/10.1002/9781118135440.ch9]

  3. Ryoichi Yamamoto,
    Section 5.25.6 of "Powder Technology Handbook, 4th Edition", (CRC Press, 2019) ISBN 9781138739222
↑

Proceedings, etc. †

  1. Ryoichi Yamamoto, John J. Molina, and Rei Tatsumi,
    Simulating colloids and self-propelled particles with fully resolved hydrodynamics using the smoothed profile method (SPM),
    Proceedings for the "Workshop on Hybrid Particle-Continuum Methods in Computational Materials Physics" (Jülich, Germany, 4-7 March 2013) p.11-24. "ISBN:978-3-89336-849-5"

  2. Shugo Yasuda and Ryoichi Yamamoto,
    Multiscale simulation for polymer melt flows in parallel plates,
    MMM2010 Conference Proceedings, 659--662 (2010).

  3. Yasuya Nakayama, Kang Kim and Ryoichi Yamamoto,
    Smoothed Profile Method for Direct Simulation of Flowing (Charged) Colloids in Solvents,
    AES Technical Reviews　Part A: International Journal of Nano and Advanced Engineering Materials 1, 21-28 (2008). [http://aix1.uottawa.ca/~yhaddad/AESTR_About.htm]

  4. Ryoichi Yamamoto, Yasuya Nakayama, and Kang Kim,
    A Smoothed Profile Method for Colloidal Dispersions,
    Advances in Science and Technology 43, 3rd International Conference "Computational Modeling and Simulation of Materials" Part B, Ed. P. Vincenzini and A. Lami (Techna Group Srl, Faenza - Italy, 2004) p.27-32. "ISBN:8886538464"

  5. Yasuya Nakayama and Ryoichi Yamamoto,
    Resolving the Hydrodynamic Interaction in Particle Suspensions,
    Advances in Science and Technology 43, 3rd International Conference "Computational Modeling and Simulation of Materials" Part B, Ed. P. Vincenzini and A. Lami (Techna Group Srl, Faenza - Italy, 2004) p.77-84. "ISBN:8886538464"

  6. Kang Kim and Ryoichi Yamamoto,
    Simulation Study of Charged Colloidal Particles in Electrolyte Solutions,
    Advances in Science and Technology 43, 3rd International Conference "Computational Modeling and Simulation of Materials" Part B, Ed. P. Vincenzini and A. Lami (Techna Group Srl, Faenza - Italy, 2004) p.33-40. "ISBN:8886538464"

  7. Ryoichi Yamamoto and Akira Onuki,
    Dynamics of Highly Supercooled Liquids under Shear,
    Proceedings of the Complex Liquids Symposium, Ed. F. Yonezawa (World Scientific, Singapore, 1998) p.242-257 "ISBN:981023631X"

  8. Akira Onuki and Ryoichi Yamamoto,
    Nonlinear Rheology of Highly Supercooled Liquids,
    Proceedings of the 2nd Tohwa University International Meeting "Statistical Physics" Ed. M.Tokuyama and I.Oppenheim (World Scientific, Singapore, 1998) p.26-29. "ISBN:9810233795"

  9. Yoshiyuki Tanaka, S. Matsuo, C. Takata, and Ryoichi Yamamoto,
    Thermal Conductivity of Environmentally Acceptable Alternatives to Fully Halogenated Chlorofluorocarbones,
    Proc. China-Japan Chem. Eng. Conf. (Tianjin, China, 1991) p.80-87.
↑

Articles in Japanese †

  1. 山本量一，
    第1章 粒子の性質と測定 1.10 単一粒子の運動と拡散 1.10.3 Brown運動, 粉体工学会誌 56, 272-277, (2019). [http://dx.doi.org/10.4164/sptj.56.272]

  2. 山本量一，
    アクティブマターのモデリング：水中を泳ぐ微生物／基板上で遊走・増殖する細胞, 分子シミュレーション研究会会誌"アンサンブル"，20, 173-178, (2018).

  3. 山本量一，
    特集「アクティブマターの物理学」, 分子シミュレーション研究会会誌"アンサンブル"，20, 148, (2018).

  4. 山本量一 ，John J. MOLINA ，Simon K. SCHNYDER,
    細胞と組織に対する力学的モデルの構築, 生物物理, 58 (3)，159-162 (2018). [http://dx.doi.org/10.2142/biophys.58.159]

  5. 山本 量一, Molina John J., Schneider Simon K.,
    基板上で遊走•増殖する細胞集団のモデリング, Journal of Computer Chemistry, Japan, 17, 14-19 (2018). [https://doi.org/10.2477/jccj.2018-0003]

  6. 山本 量一,
    力学的モデルによる細胞の集団運動のシミュレーション, 生産研究, 69, 253-260 (2017). [http://dx.doi.org/10.11188/seisankenkyu.69.253]

  7. 山本量一，大山倫弘，John J. MOLINA，Simon K. SCHNYDER，
    ソフトマターのモデリング：非平衡系・生物系への挑戦, "化学工学"（会誌），Vol.81, 282-285 (2017). PDF

  8. 安田修悟, 山本量一，
    Synchronized Molecular Dynamics 法による高分子潤滑の解析, 分子シミュレーション研究会会誌"アンサンブル"，17, 30-34, (2015).

  9. 安田修悟, 村島隆浩, 谷口貴志, 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, 日本シミュレーション学会誌, 31, 23-27, (2012).

  10. 谷口貴志, 山本量一,
    "解説：ソフトマターのマルチスケールシミュレーション", 日本物理學會誌, 67, 317-324, (2012).

  11. 山本量一,
    ソフトマターの多階層/相互接続シミュレーション, 「マルチスケール・マルチフィジックス現象の統合シミュレーション」 科学技術振興機構 (ISBN 978-4-9904860-3-7 C0040)

  12. 村島隆浩, 安田修悟, 谷口貴志, 山本量一,
    "ソフトマターの多階層・相互接続シミュレーション―高分子メルト のマルチスケールモデル―", 工業材料, 60, 27-30, (2012).

  13. 安田修悟, 山本量一,
    振動境界層流れにおける高分子液体の動的レオロジー特性, 分子シミュレーション研究会会誌"アンサンブル", 13, 105 (2011).

  14. 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, 607-610 (2009). "CiNii"

  15. 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).

  16. 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). "CiNii"

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

  18. 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). "CiNii"

  19. 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). "CiNii"

  20. 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). "CiNii"

  21. 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). "CiNii"

  22. 山本量一, 小貫明,
    ガラスの非平衡ダイナミクス， 日本物理學會誌, 60, 603-609 (2005). "CiNii"

  23. 山本量一, 小貫明,
    ガラス・過冷却液体における動的不均一性, 高圧力学会誌, 9, 134-141 (1999). "CiNii"

  24. 山本量一, 中西浩一郎,
    1994年の化学：シミュレーションによるフラーレン生成過程の解明, 化学, 49, 66-67 (1994). "CiNii"

  25. 松尾成信, 田中嘉之, 田谷智, 山本量一,
    混合気体の熱伝導率 −（HFC 32 + HFC125）系−, 熱物性, 8, 207-212 (1994).

  26. 山本量一, 北尾修, 中西浩一郎,
    プロパン系フロン代替物質の分子シミュレーション, JCPE Newsletter, 4, 4-15 (1993).
↑

Books in Japanese †

  1. 山本量一，John J. Molina，
    第６章, 「増補版　高分子材料シミュレーション -OCTA活用事例集」公益社団法人新化学技術推進協会 (編)，ISBN:978-4873266879（化学工業日報社, 2017）

  2. 山本量一，John J. Molina，
    第６章, 「高分子材料シミュレーション -OCTA活用事例集」公益社団法人新化学技術推進協会 (編)，ISBN:978-4873266381（化学工業日報社, 2014）

  3. 金鋼, 名嘉山祥也, 山本量一,
    2.23.3.3, 2.23.3.4, 「粉体工学ハンドブック」粉体工学会（編）, ISBN:978-4-254-25267-5（朝倉書店, 2014)

  4. 「マルチスケール・マルチフィジックス現象の統合シミュレーション」山本量一（編）ISBN:978-4-9904860-3-7 C0040 (科学技術振興機構, 2012)