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安藤 嘉倫

安藤 嘉倫 (ANDOH, Yoshimichi) 0000-0001-5027-4120

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305-0047 茨城県つくば市千現1-2-1 [アクセス]
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[論文] | [書籍] | [会議録] | [口頭発表] | [その他の文献] | [公開特許出願]

論文 TSV

2023
  1. Yoshimichi Andoh, Shin-ichi Ichikawa, Tatsuya Sakashita, Kazushi Fujimoto, Noriyuki Yoshii, Tetsuro Nagai, Zhiye Tang, Susumu Okazaki. An exa-scale high-performance molecular dynamics simulation program: MODYLAS. The Journal of Chemical Physics. 158 [19] (2023) 194803 10.1063/5.0144361
2021
  1. Yoshimichi Andoh, Shin‐ichi Ichikawa, Tatsuya Sakashita, Noriyuki Yoshii, Susumu Okazaki. Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations.. Journal of Computational Chemistry. 42 [15] (2021) 1073-1087 10.1002/jcc.26524
2020
  1. Yoshimichi Andoh, Shiho Hayakawa, Susumu Okazaki. Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets. The Journal of Chemical Physics. 153 [3] (2020) 035105 10.1063/5.0012676
  2. Yoshimichi Andoh, Noriyuki Yoshii, Susumu Okazaki. Extension of the fast multipole method for the rectangular cells with an anisotropic partition tree structure. Journal of Computational Chemistry. 41 [14] (2020) 1353-1367 10.1002/jcc.26180
  3. Noriyuki Yoshii, Yoshimichi Andoh, Susumu Okazaki. Fast multipole method for three‐dimensional systems with periodic boundary condition in two directions. Journal of Computational Chemistry. 41 [9] (2020) 940-948 10.1002/jcc.26141
2019
  1. Yoshimichi ANDOH, Susumu OKAZAKI. All-atom Molecular Dynamics Simulation Study ofSelf-assemblies of Amphiphilic Molecules in Solution 水溶液中の両親媒性分子集団系の全原子分子動力学シミュレーション. Oleoscience. 19 [11] (2019) 447-453 10.5650/oleoscience.19.447 Open Access
  2. Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki. Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation. Langmuir. 35 [33] (2019) 10877-10884 10.1021/acs.langmuir.9b01607
  3. Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki. Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ′), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied by X-ray Diffraction and Molecular Dynamics Simulation. Langmuir. 35 [27] (2019) 9011-9019 10.1021/acs.langmuir.9b01199
2018
  1. Yoshimichi Andoh, Sakiho Kitou, Susumu Okazaki. Difference in molecular mechanisms governing changes in membrane properties of phospholipid bilayers induced by addition of nonionic and zwitterionic surfactants. Journal of Molecular Liquids. 271 (2018) 933-941 10.1016/j.molliq.2018.09.018
  2. Noriyuki Yoshii, Yoshimichi Andoh, Susumu Okazaki. Pressure tensor for electrostatic interaction calculated by fast multipole method with periodic boundary condition. Journal of Computational Chemistry. 39 [19] (2018) 1192-1199 10.1002/jcc.25179
  3. Yoshimichi Andoh, Soichiro Suzuki, Satoshi Ohshima, Tatsuya Sakashita, Masao Ogino, Takahiro Katagiri, Noriyuki Yoshii, Susumu Okazaki. A thread-level parallelization of pairwise additive potential and force calculations suitable for current many-core architectures. The Journal of Supercomputing. 74 [6] (2018) 2449-2469 10.1007/s11227-018-2272-2
2017
  1. Yoshimichi Andoh, Siti Nor Syafawani Mohamed, Sakiho Kitou, Susumu Okazaki. Structural ordering of lipid bilayers induced by surfactant molecules with small hydrophilic head group. Molecular Simulation. 43 [13-16] (2017) 1247-1255 10.1080/08927022.2017.1319061
  2. Yoshimichi Andoh, Noriyuki Yoshii, Atsushi Yamada, Susumu Okazaki. Evaluation of atomic pressure in the multiple time-step integration algorithm. Journal of Computational Chemistry. 38 [10] (2017) 704-713 10.1002/jcc.24731
  3. Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Takata, Susumu Okazaki, Yasuhiro Uozumi. Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Using Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations. Chemistry - A European Journal. 23 [6] (2017) 1291-1298 10.1002/chem.201603494
  4. Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Takata, Susumu Okazaki, Yasuhiro Uozumi. Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations. Chemistry - A European Journal. 23 [6] (2017) 1209 10.1002/chem.201605213
  5. Go Hamasaka, Tsubasa Muto, Yoshimichi Andoh, Kazushi Fujimoto, Kenichi Kato, Masaki Takata, Susumu Okazaki, Yasuhiro Uozumi. Cover Picture: Detailed Structural Analysis of a Self-Assembled Vesicular Amphiphilic NCN-Pincer Palladium Complex by Using Wide-Angle X-Ray Scattering and Molecular Dynamics Calculations (Chem. Eur. J. 6/2017). Chemistry - A European Journal. 23 [6] (2017) 1207 10.1002/chem.201605178
2016
  1. Yoshimichi Andoh, Noriyuki Aoki, Susumu Okazaki. Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas. The Journal of Chemical Physics. 144 [8] (2016) 085104 10.1063/1.4942159
2015
  1. Yoshimichi Andoh, Shun Muraoka, Susumu Okazaki. Molecular dynamics study of changes in physico-chemical properties of DMPC lipid bilayers by addition of nonionic surfactant C12E10. Molecular Simulation. 41 [10-12] (2015) 955-960 10.1080/08927022.2014.928707
  2. Noriyuki Yoshii, Yoshimichi Andoh, Kazushi Fujimoto, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki. MODYLAS: A highly parallelized general-purpose molecular dynamics simulation program. International Journal of Quantum Chemistry. 115 [5] (2015) 342-348 10.1002/qua.24841
2014
  1. Y. Andoh, N. Yoshii, A. Yamada, K. Fujimoto, H. Kojima, K. Mizutani, A. Nakagawa, A. Nomoto, S. Okazaki. All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution. The Journal of Chemical Physics. 141 [16] (2014) 165101 10.1063/1.4897557
  2. Takuma Yagasaki, Masakazu Matsumoto, Yoshimichi Andoh, Susumu Okazaki, Hideki Tanaka. Dissociation of Methane Hydrate in Aqueous NaCl Solutions. The Journal of Physical Chemistry B. 118 [40] (2014) 11797-11804 10.1021/jp507978u
  3. Takuma Yagasaki, Masakazu Matsumoto, Yoshimichi Andoh, Susumu Okazaki, Hideki Tanaka. Effect of Bubble Formation on the Dissociation of Methane Hydrate in Water: A Molecular Dynamics Study. The Journal of Physical Chemistry B. 118 [7] (2014) 1900-1906 10.1021/jp412692d
2013
  1. Yoshimichi Andoh, Noriyuki Yoshii, Kazushi Fujimoto, Keisuke Mizutani, Hidekazu Kojima, Atsushi Yamada, Susumu Okazaki, Kazutomo Kawaguchi, Hidemi Nagao, Kensuke Iwahashi, Fumiyasu Mizutani, Kazuo Minami, Shin-ichi Ichikawa, Hidemi Komatsu, Shigeru Ishizuki, Yasuhiro Takeda, Masao Fukushima. MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms. Journal of Chemical Theory and Computation. 9 [7] (2013) 3201-3209 10.1021/ct400203a
  2. Yoshimichi Andoh, Susumu Okazaki, Ryuichi Ueoka. Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1828 [4] (2013) 1259-1270 10.1016/j.bbamem.2013.01.005
2012
  1. Yoshimichi Andoh, Kimiko Oono, Susumu Okazaki, Ichiro Hatta. A molecular dynamics study of the lateral free energy profile of a pair of cholesterol molecules as a function of their distance in phospholipid bilayers. The Journal of Chemical Physics. 136 [15] (2012) 155104 10.1063/1.4704740
  2. Y. Andoh, T. Ito, S. Okazaki. An application of improved force field to fully hydrated DPPC and POPC bilayers in a tensionless NPT ensemble: a test of CHARMM 27-based new force field by Högberg et al.. Molecular Simulation. 38 [5] (2012) 414-418 10.1080/08927022.2010.548385
2009
  1. Hiroshi Kuramochi, Yoshimichi Andoh, Noriyuki Yoshii, Susumu Okazaki. All-Atom Molecular Dynamics Study of a Spherical Micelle Composed of N-Acetylated Poly(ethylene glycol)−Poly(γ-benzyll-glutamate) Block Copolymers: A Potential Carrier of Drug Delivery Systems for Cancer. The Journal of Physical Chemistry B. 113 [46] (2009) 15181-15188 10.1021/jp906155z
2007
  1. Yoshimichi Andoh, Kenji Kurahashi, Hiroshi Sakuma, Kenji Yasuoka, Kazue Kurihara. Anisotropic molecular clustering in liquid ethanol induced by a charged fully hydroxylated silicon dioxide (SiO2) surface. Chemical Physics Letters. 448 [4-6] (2007) 253-257 10.1016/j.cplett.2007.10.008
  2. Y. Andoh, K. Yasuoka. Molecular understanding of dynamical properties of the vapor/ethanol-aqueous-solution interface. Molecular Simulation. 33 [1-2] (2007) 139-145 10.1080/08927020601075337
2006
  1. Yoshimichi Andoh, Kenji Yasuoka. Hydrogen-Bonded Clusters on the Vapor/Ethanol-Aqueous-Solution Interface. The Journal of Physical Chemistry B. 110 [46] (2006) 23264-23273 10.1021/jp061150k
2005
  1. Yoshimichi Andoh, Kenji Yasuoka. Two-Dimensional Supercritical Behavior of an Ethanol Monolayer:  A Molecular Dynamics Study. Langmuir. 21 [23] (2005) 10885-10894 10.1021/la051384f

書籍 TSV

2019
  1. Y. Andoh, N. Yoshii, J. Jung, Y. Sugita. Acceleration of Classical Molecular Dynamics Simulations. The Art of High Performance Computing for Computational Science, Vol. 2. Springer Singapore, 2019 10.1007/978-981-13-9802-5_5

会議録 TSV

2019
  1. Satoshi Ohshima, Soichiro Suzuki, Tatsuya Sakashita, Masao Ogino, Takahiro Katagiri, Yoshimichi Andoh. Performance Evaluation of the MODYLAS Application on Modern Multi-core and Many-Core Environments. 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW). (2019) 10.1109/ipdpsw.2019.00129

口頭発表 TSV

2023
  1. 安藤 嘉倫, 名倉 和彦, 中西 尚志, 袖山 慶太郎. 分子動力学計算と機械学習による機能性分子液体材料の特異な粘性挙動の解明. 第37回分子シミュレーション討論会. 2023
2022
  1. 安藤 嘉倫. MODYLAS講習会. HPCアプリケーション講習会. 2022 招待講演
2021
  1. 安藤 嘉倫. OpenMP SIMDディレクテブ挿入による第一原理計算プログラムCONQUESTの高速化II:gemmコードとの性能比較. 第35回分子シミュレーション討論会. 2021
2020
  1. 安藤 嘉倫. OpenMP SIMD ディレクテブ挿入による第一原理計算プログラムCONQUESTの高速化. 第34回分子シミュレーション討論会. 2020
  2. ANDOH, Yoshimichi. Large-scale molecular dynamics simulations of biomolecular assemblies. Frontiers of Computational Physics from meV to MeV. 2020 招待講演

その他の文献 TSV

2023
  1. 安藤 嘉倫. 分子動力学計算の大規模並列化のための技術 1. アンサンブル. 25 [1] (2023) 46-51
  2. 安藤 嘉倫. 分子動力学計算の大規模並列化のための技術 2. アンサンブル. 25 [2] (2023) 149-157
  3. 安藤 嘉倫. 分子動力学計算の大規模並列化のための技術 3. アンサンブル. 25 [3] (2023) 223-230

公開特許出願 TSV

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