2014: [1] M. Fukuda, Y. Komatsu, H. Yamada, R. Morikawa, T. Miyakawa, M. Takasu, S. Akanuma, and A. Yamagishi, Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation, Mol. Sim. 40 (2014) 498-503.

[2] T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, and, H. Nagao, Analysis of Water Molecules around GTP in Hras-GTP Complex and GDP in Hras-GDP Complex by Molecular Dynamics Simulations, Mol. Phys. 112 (2014) 526-532.

[3] T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, T. Kawaguchi, H. Saito, H. Nagao, Network of Water Molecules Around Guanine Nucleotide in the Hras-GTP and -GDP Complexes by MD Simulations, JPS Conf. Proc. 1(2014) 016006.

[4] R. Morikawa, M. Tamakoshi, T. Miyakawa, M. Takasu, Numerical Simulation of the Twitching Motility of Bacterium Crawling on a Solid Surface, JPS Conf. Proc. 1 (2014) 016019.

[5] Y. Hirata, Y. Komatsu, M. Fukuda, H. Yamada, T. Miyakawa, R. Morikawa, S. Akanuma, A. Yamagishi, M. Takasu, Coarse-Grained Molecular Dynamics Simulation of IPMDH Proteins, JPS Conf. Proc.1 (2014) 016010.

[6] H. Yamada, M. Fukuda, T. Miyakawa, R. Morikawa, M. Takasu, Conformation Analysis of Peptides Derived from Laminin Alpha 1?2 Chain Using Molecular Dynamics Simulation, JPS Conf. Proc. 1(2014) 016016.

[7] M. Fukuda, H. Yamada, R. Morikawa, T. Miyakawa, M. Takasu, S. Akanuma, A. Yamagishi, Computer Simulation Analysis of the Protein Binding Interfaces that Form a 4-Helix Bundle Motif, JPS Conf. Proc. 1(2014) 016020.

[8] M. Kaburagi, M. Fukuda, H. Yamada, T. Miyakawa, R. Morikawa, M. Takasu, Takamitsu A. Kato, Mitsuru Uesaka, Molecular Dynamics Simulation of Telomere and TRF1, JPS Conf. Proc. 1(2014) 016018.

[9] M. Rusmerryani, M. Takasu, K. Kawaguchi, H. Saito, H. Nagao, Protein?Protein Interactions of Azurin Complex by Coarse-Grained Simulations with a G?-Like Model, JPS Conf. Proc.1 (2014) 012054.

[10] H. Saito, M. Iwayama, K. Kawaguchi, T. Mizukami, T. Miyakawa, M. Takasu, H. Nagao, Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction, JPS Conf. Proc.1 (2014) 012053.

[11] Y. Fukasawa, J. Kumai, F. Katagiri, Y. Kikkawa, K. Hozumi, M. Nomizu,　S. Mori, H. Yamada, M. Fukuda, T. Miyakawa, R. Morikawa and M. Takasu, Conformation Analysis of the A2G80 Peptide Derived from Laminin α2 Chain by Molecular Dynamics Simulation, Peptide Science (2014), 289-292.

[12] S. Mori, H. Yamada, M. Fukuda, Y. Fukasawa, T. Miyakawa, R. Morikawa, M. Takasu, T. Watanabe, Structure Analysis of GLP-1 by Molecular Dynamics Simulation, Peptide Science (2014), 285-288.

2013: [1] H. Yamada, T. Miyakawa, R. Morikawa, F. Katagiri, K. Hozumi, Y. Kikkawa, M. Nomizu, and M. Takasu, Molecular Dynamics Simulations of Peptides Derived from Laminin Alpha 2 Chain Peptide Science 2012, Jap. Peptide Soc. (2013) 339-342.

[2] R. Morikawa, T. Miyakawa, M. Tamakoshi and M. Takasu, Simulation study of bacterial colonies formed by the twitching motility: the effect of slingshot-like motions of bacteria on the colony edge, AIP Conf. Proc. 1518 (2013) 590-593.

[3] T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and H. Nagao, A Molecular Dynamics Study of Hras-GTP and GDP Complexes: the Properties of Water Molecules around Guanine Nucleotide, AIP Conf. Proc., 1518 (2013) 594-597..

[4] M. Fukuda, Y. Komatsu, R. Morikawa, T. Miyakawa, M. Takasu1, S. Akanuma1, and A. Yamagishi, Simulation Study of Protein-protein Interfaces Based on the 4-helix Bundle Structure, AIP Conf. Proc., 1518 (2013) 606-609.

[5] M. Rusmerryani, M. T. Pakpahan, M. Nishimura, M. Takasu, K. Kawaguchi, H. Saito and H. Nagao, Transition State Analysis of Azurin via Go-like Model, AIP Conf. Proc., 1518 (2013) 641-644.

[6] K. Kawaguchi, H. Takagi, M. Takasu, H. Saito and H. Nagao, Molecular Dynamics Studies of Hsp90 with ADP: Protein-ligand Binding Dynamics, AIP Conf. Proc.,1518 (2013) 637-640.

[7] R. Fujimori, Y. Komatsu, M. Fukuda, T. Miyakawa, R. Morikawa and M. Takasu, Analysis of the Histone Protein Tail and DNA in Nucleosome Using Molecular Dynamics Simulation, AIP Conf. Proc.1518 (2013) 602-605.

[8] T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, T. Mizukami, K. Kawaguchi, H. Saito, and, H. Nagao, Molecular Dynamics Simulations of the Hras-GTP Complex and the Hras-GDP Complex, Int. J. Quant. Chem., 113, (2013) 2333-2337. (One of the figures appeared on the cover of issue 21, vol. 113 of Int. J. Quant. Chem.)

[9] Y. Kawaguchi, Y. Yang, N. Kawashiri, K. Shiraishi, M. Takasu, I. Narumi, K. Satoh, H. Hashimoto, K. Nakagawa, Yoshiaki Tanigawa, Y. Momoki, M. Tanabe, T. Sugino, Y. Takahashi, Y. Shimizu, S. Yoshida, K. Kobayashi, S. Yokobori, A. Yamagishi, The Possible Interplanetary Transfer of Microbes: Assessing the Viability of Deinococcus spp. under the ISS Environmental Conditions for Performing Exposure Experiments of Microbes in the Tanpopo Mission, Orig. Life Evol. Biosph. 43 (2013) 411-428.

[10] T. Miyakawa, R. Morikawa, M. Takasu, A. Dobashi, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao, Analysis of Water Molecules in the Hras-GTP and GDP Complexes with Molecular Dynamics Simulations, Prog. Theor. Chem. Phys. 27, (2013) 351-360.

2012: [1] H. Yamada, Y. Komatsu, T. Miyakawa, R. Morikawa, F. Katagiri, K. Hozumi, Y. Kikkawa, M. Nomizu, and M. Takasu, Conformation Analysis of Loop Region Peptides in the Laminin Alpha Chain LG4 Modules by Molecular Dynamics Simulations, Peptide Science 2011, Jap. Peptide Soc. (2012) 201-204.

[2] S. Kawamoto, T. Miyakawa, M. Takasu, R. Morikawa, T. Oda, H. Saito, S. Futaki and H. Nagao, Cell Penetrating Peptide Induces Various Deformations of Lipid Bilayer Membrane: Inverted Micelle, Double Bilayer and Trans-membrane, Int. J. Quant. Chem 112 (2012)178-183.

[3] H. Saito, T. Mizukami, S. Kawamoto, T. Miyakawa, M. Iwayama, M. Takasu, H. Nagao, Molecular Dynamics Studies of Lipid Bilayer with Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match, Int. J. Quant. Chem.112 (2012)161-170

[4] T. Mizukami, H. Saito, S. Kawamoto, T. Miyakawa, M. Iwayama, M. Takasu, H. Nagao, Solvation Effect of the Structural Change of a Globular Protein: a Molecular Dynamics Study, Int. J. Quant. Chem.112 (2012)344-350.

[5] S. Kawamoto, M. Takasu, T. Miyakawa, R. Morikawa, T. Oda, S. Futaki and H. Nagao, Binding of Tat Peptides on DOPC and DOPG Lipid Bilayer Membrane Studied by Molecular Dynamics Simulation, Mol. Sim. 38 (2012) 366-368

[6] K. Fujiwara, K. Horiuchi, S. Goryoda, Y. Hashidume, N. Horiguchi, T. Miyakawa, M. Takasu, and M. Aoki, Observation of Cell-size Variation under Environmental Stress by Fluorescence Correlation Spectroscopy without Objective Image Magnification, J. Environ. Sci. Eng. A 1 (2012) 364-370

[7] K. Kawaguchi, H. Takagi, M. Iwayama, M. Nishimura, T. Miyakawa, H. Saito, M. Takasu and H. Nagao, Molecular Dynamics Analyses of the Dissociation Process of ADP from Hsp90, Int. J. Quant. Chem.112 (2012) 3791-3795.

[8] H. Saito, M. Iwayama, H. Takagi, M. Nishimura, T. Miyakawa, K. Kawaguchi, M. Takasu, T. Mizukami and H. Nagao, Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile, Int. J. Quant. Chem. 112 (2012) 3834-3839.

[9] Y. Komatsu, M. Fukuda, H. Yamada, S. Kawamoto, T. Miyakawa, R. Morikawa, M. Takasu, S. Yokojima S. Akanuma, A. Yamagishi: Constructing Protein Nano-Fiber and Estimation of the Electronic State Around Metal Ions, Int. J. Quant. Chem. 112 (2012) 3750-3755

[10] S. Kawamoto, M. Takasu, T. Miyakawa, R. Morikawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda: Free Energy of Cell-penetrating Peptide through Lipid Bilayer Membrane: Coarse-Grained Model Simulation, Prog. Theor. Chem. Phys. 26 (2012) 503-511.
[11] Y. Komatsu, H. Yamada, S. Kawamoto, M. Fukuda, T. Miyakawa, R. Morikawa, M. Takasu, S. Akanuma, A. Yamagishi: Designing the Binding Surface of Proteins to Construct Nano-Fibers, Prog. Theor. Chem. Phys. 26 (2012) 555-567.

[12] T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, T. Mizukami, K. Kawaguchi, H. Saito and H. Nagao: The Potentials of the Atoms around Mg2+ in the H-ras GTP and GDP Complexes, Prog. Theor. Chem. Phys. 26 (2012) 525-543.

2011: [1] S. Kawamoto, M. Takasu, T. Miyakawa, R. Morikawa, T.Oda, S. Futaki and H. Nagao, Inverted Micelle Formation of Cell-penetrating Peptide Studied by Coarse-grained Simulation: Importance of Attractive Force Between Cell-penetrating Peptides and Lipid Head Group, J. Chem. Phys 134, (2011) 095103 (1-6).

[2] T. Miyakawa, K. Fujiwara, K. Takahashi, K. Horiuchi, R. Morikawa, M. Takasu, Theoretical Evaluation of the Correlation Time of the E. coli Detected in the Stationary flow, J. Tokyo Univ. Pharm. and Life Sci. 14 (2011) 13-17.

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