Kanazawa University Graduate School of Natural Science and Technology, Computational Science Course

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List of Pablication

in 2017

1. K. Kawaguchi, S. Nakagawa, I. Kurniawan, K. Kodama, M.S. Arwansyah, and H. Nagao, “A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer", Mol. Phys. 116,649-657 (2018) [doi]
2. S. Nakagawa, I. Kurniawan, K. Kodama, M.S. Arwansyah, K. Kawaguchi, H. Nagao, “Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect", Mol. Phys. 116,666-677 (2018) [doi]

in 2016

1. K. Kawaguchi, S. Nakagawa, S. Kinoshita, M. Wada, H. Saito, and H. Nagao, “A simple coarse-grained model for interacting protein complex”, Mol. Phys.,115,587-597 (2017) [doi]

in 2014

1. K. Kawaguchi, H. Saito, and H. Nagao, “Decomposition analysis of free energy profile for Hsp90-ADP association”, Mol. Sim., 42 (2015) 896.
2. M. Iwayama, I. Kurniawan, K. Kawaguchi, H. Saito, and H. Nagao, “A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules”, Mol. Sim., 41 (2015) 10.

in 2013

1. K. Kawaguchi, H. Saito and H. Nagao, "Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation", JPS Conference Proceedings, 1, 012056, (2014). [doi]
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, 526-532, (2014). [doi]

in 2012

1. K. Kawaguchi, H. Saito, S. Okazaki and H. Nagao, "Moolecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90", Chem. Phys. Lett., 588 , 226-230, (2013). [doi]
2. T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and H. Nagao, "Moolecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex", Int. J. Quant. Chem., 113 , 2333-2337, (2013). [doi]

in 2012

1. T. Mizukami, H. Saito, S. Kawamoto, T. Miyakawa, M. Iwayama, M. Takasu and H. Nagao, "Solvation Effect on the Structural Change of a Globular Protein: A Molecular Dynamics Study", Int. J. Quant. Chem., 112, 344-350, (2012).　 [doi]
2. H. Saito, T. Mizukami, S. Kawamoto, T. Miyakawa, M. Iwayama, M. Takasu and 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, 161-170, (2012).　[doi]

in 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, 095103-095108, (2011).　[doi]
2. H. Saito and W. Shinoda, "Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study", J.Phys.Chem.B, 115, 15241-15250, (2011). [doi]

in 2010

1. H. Saito, N. Matubayasi, K. Nishikawa and H. Nagao, "Hydration property of globular proteins: An analysis of solvation free energy by energy representation method", Chem. Phys. Lett., 497, 218-222, (2010).　[doi]
2. Y. Hashimoto, Masako Takasu, Shuhei Kawamoto, Tatsuki Oda, Hidemi Nagao, T. Sakai and U. Chung "Structure and dynamics of tetra-PEG gel by Brownian dynamics", Trans. Mat. Res. Soc. Japan, 35, 547-553, (2010).
   

in 2009

1. T. Ohta, Y. Hagiwara, J. Kang, K. Nishikawa, T. Yamamoto, H. Nagao and M. Tateno, "Evaluation of Electronic and Geometrical Properties of the Blue Copper Site in Fully Solvated Azurin by QM/MM Hybrid Calculations Using a New Interface Program Connecting QM and MM Engines", J. Comput. Theor. Nanosci, 6, 2648-2655, (2009).　[doi]
2. P. Acep, T. Yamamoto, K. Nishikawa, H. Nagao and K. Nishikawa, "Effects of Salty Water and Temperature on Shape Fluctuations of a Few Correlated Phospholipids", Prog. Theor. Phys. Supplement, 178, 187-192, (2009).　[doi]

in 2008

1. T.V.B. Phung, K. Nishikawa and H. Nagao, "Theoretical Studies on Stable Structure and Noncollinear Magnetism of Aluminum Clusters", AIP Conference Proceedings, 1046, 64-67, (2008).　[doi]
2. A. Purqon, A. Sugiyama, H. Nagao, M. Takasu and K. Nishikawa, "Geometrical Classification of Spagetti-Like Nanoclusters", AIP Conference Proceedings, 982, 331-336, (2008).　[doi]

in 2007

1. T. Oda, K. Sugimori, H. nagao, I. Hamada, S. Kagayama, M. Geshi, H. Nagara, K. Kusakabe and N. Suzuki, "Oxygen at high pressures: a theoretical approach to monoatomic phases", J. Phys.: Condents. Matter, 19, 365211, (2007).　[doi]
2. A. Purqon, A. Sugiyama, H. Nagao and K. Nishikawa, "Aperture, symmetry, isotropy, and compactness analysis and their correlation in spaghetti-like nanostructure dynamics", Chem. Phys. Lett, 443, 356-363, (2007).　[doi]

in 2006

1. D.H. Chi, N.T. Cuong, N.A. Tuan, Y-T. Kim, H.T. Bao, T. Mitani, T. Ozaki and H. Nagao, "Electronic structures of Pt clusters adsorbed on (5, 5) single wall carbon nanotube", Chem. Phys. Lett, 432 ,213-217, (2006).　[doi]
2. A. Sugiyama, Y Takamatsu, K. Nishikawa, H. Nagao and K. Nishikawa, "Docking Stability and Electronic Structure of Azurin-Cytochrome c₅₅₁ Complex System", Int. J. Quant. Chem, 106, 3071-3078, (2006).　[doi]

in 2005

1. T. Ito, K. Sugimori, H. Nagao and K. Nishikawa, "Laser control of singlet-triplet transition in molecules by light-induced potentials", Proceedings of Regional Symposium on Chemical Engineering 2005, 131-135, (2005).
2. H. Nagao and H. Kawabe, "Theoretical Studies on Effective Interactions in Two-Band System", Int. J. Quant. Chem, 105, 571-579, (2005).　[doi]

in 2004

1. H. Nagao, "Theoretical Studies on Many-Band Effects in Superconductivity and Magnetism", Int. J. Quant. Chem, 100, 867-876, (2004).　[doi]
2. T. Ito, T. Yoshimoto, Y. Ohta, H. Kawabe, H. Nagao and K. Nishikawa, "Formulation and Numerical Approach to Molecular Systems by the Green Function Method without Born-Oppenheimer AApproximation II: Nucleus-Electron Correlation", Int. J. Quant. Chem, 100, 918-926, (2004).　[doi]

in 2003

1. K. Yamaguchi, T. Kawakami, T. Taniguchi, S. Nakano, Y. Kitagawa, H. Nagao, T. Ohsaku and R. Takeda, "Theoretical studies of molecule-based magnetic conductors", Polyhedron, 22, 2077-2090, (2003).　[doi]
2. Y. Yamaguchi , M, Nakano, H. Nagao, M. Okumura, S. Yamanaka, T. Kawakami, D. yamaki, M, Nishino, Y. Shigeta, Y. Kitagawa, Y. Takano, M. Takahara and R. Takeda, "Spin and Pseudo Spins in Theoretical Chemistry. A Unified View for Superposed and Entangled Quantum Systems", B. Kor. Chem. Soc., 24, 864-880, (2003).　[doi]

in 2002

1. K. Nishikawa, Y. Ohta, T. Yoshimoto, T. Saito, K. Nishi and H. Nagao, "Laser control of proton motion in malonaldehyde molecule", J. Mol. Struct., 615, 13-22, (2002).　[doi]
2. H. Nagao, S.P. Kruchinin, A.M. Yaremko and K. Yamaguchi, "MULTIBAND SUPERCONDUCTIVITY", Int. J. Mod. Phys B., 16, 3419-3428, (2002).　[doi]

in 2001

1. K. Kinugawa, H. Nagao and K. Ohta, "A semiclassical approach to the dynamics of many-body Bose/Fermi systems by the path integral centroid molecular dynamics", J. Chem. Phys, 114, 1454-1466, (2001).　[doi]
2. K. Kinugawa, H. Nagao and K. Ohta, "A path integral centroid molecular dynamcis method for Bose and Fermi statistics", J. Mol. Liq, 90, 11-20, (2001). 　[doi]

in 2000

1. T. Soda, Y. Kitagawa, T. Onishi, Y. Takano, Y. Shigeta, H. Nagao, Y. Yoshioka and K. Yamaguchi, "Ab initio computations of effective exchange integrals for H-H, H-He-H and Mn₂O₂ complex: comparision of broken-symmetry approaches", Chem. Phys. Lett, 319, 223-230, (2000).　[doi]
2. H. Nagao, M. Nishino, Y. Shigeta, T. Soda, Y. Kitagawa, T. Onishi, Y. Yoshioka and K. Yamaguchi, "Theoretical studies on effective spin interactions, spin alignments and macroscopic spin tunneling in polynuclear manganese and related complexes and their mesoscopic clusters", Coordination Chemistry Review, 198, 265-295, (2000).　[doi]

in 1999/h4>

1. S. Yamada, M. Nakano, H. Nagao, and K.Yamaguchi, "Electron Correlation and Structure Dependecies of the Second Hyperpolarizability of Ethylene", Int. J. Quant. Chem, 71, 177-184, (1999).　[doi]
2. M. Nakano, S. Yamada, H. Nagao, and K. Yamaguchi, "Numerical Coupled Liouville Approach: Application to Second Hyperpolarizability of Molecular Aggregate", Int. J. Quant. Chem, 71, 295-306, (1999).　[doi]

more>>

3. H. Nagao, S. Yamanaka, M. Nishino, Y. Yoshioka and K. Yamaguchi, "Theoretical studies on the magnetic quantum tunneling rates in Mn Clusters by the path integral method", Chem. Phys. Lett, 302, 418-424, (1999).　[doi]
4. K. Yamaguchi, S. Yamanaka, M. Nishino, Y. Takano, Y. Kitagawa, H. Nagao, and Y.Yoshioka, "Symmetry and broken symmetries in molecular orbital descriptions of unstable Molecules II. Alignment, flustration and tunneling of Spins in mesoscopic molecular magnets", Theor. Chem. Acc, 102, 328-345, (1999).　[doi]
5. K. Kinugawa, H. Nagao, and K. Ohta, "Path integral centroid molecular dynamics method for Bose and Fermi statistics : formalism and simulation", Chem. Phys. Lett, 307, 187-197, (1999).　[doi]
6. H. Nagao, M. Nakano, Y. Shigeta, and K. Yamaguchi, "Quantum Phase Dynamics of Interaction between Photon Field and Magnetic System: Effects of Magnetic Quantum Tunnelling", Optical Review, 6, 227-231, (1999).　[doi]
7. Y. Shigeta, T. Kawakami, H. Nagao, and K. Yamaguchi, "Theoretical studies of magnetization by ab initio path integral method", Synthetic Metals, 103, 1989-1990, (1999).　[doi]
8. D. Yamaki, H. Nagao, M. Nakano, Y. Yoshioka, and K. Yamaguchi, "Visualization of two-body electron-densities and wavefunctions for several molecules", Synthetic Metals, 103, 2002-2003, (1999).　[doi]
9. H. Nagao, H. Kawabe, Y. Shigeta, M. Nishino, M. Mitani, and K. Yamaguchi, "Theoretical studies on anomalous phases in model plane systems of libeh₃", Synthetic Metals, 103, 2651-2652, (1999).　[doi]
10. Y. Shigeta, S. Yamada, H. Nagao, M. Nakano, K. Ohta, and K. Yamaguchi, "Theoretical study on polarizability of ethylene by path intergal method", Synthetic Metals, 101, 513, (1999).　[doi]
11. Y. Shigeta, H. Nagao, K. Nishikawa, and K. Yamaguchi, "A formulation and numerical approach to molecular systems by the Green function method without the Born-Oppenheimer approximation", J. Chem. Phys, 111, 6171-6179, (1999).　[doi]
12. M. Nishino, H. Nagao, Y. Yoshioka, and K. Yamaguchi, "Dynamics of Magnetization for a System (S=3) with Strong Uniaxial Magnetocrystalline Anisotropy", Molecular Crystals and Liquid Crystals Science and Technology. Secton A. Molecular Crystals and Liquid Crystals, 335, 593-602, (1999).　[doi]
13. H. Nagao, M. Mitani, M. Nishino, Y. Shigeta, Y. Yoshioka, and K. Yamaguchi, "Theoretical Studies on Anomalous Phases in Molecular Systems with External Field: Possibility of Photo-Induced Superconductivity", Int. J. Quant. Chem, 75, 549-561, (1999).　[doi]
14. D. Yamaki, Y. Kitagawa, H. Nagao, M. Nakano, Y. Yoshioka, and K. Yamaguchi, "Visualization of Two-Body Electron Densities and Wave Functions of Magnetic Molecules", Int. J. Quant. Chem., 75, 645-654, (1999).　[doi]
15. Y. Shigeta, H. Nagao, K. Nishikawa, and K. Yamaguchi, "Density Functional Theory without the Born-Oppenheimer Approximation. II. Green Function Techniques", Int. J. Quant. Chem, 75, 875-883, (1999).　[doi]
16. Y. Shigeta, T. Kawakami, H. Nagao, and K. Yamaguchi, "A theoretical study of spin level crossing induced by an external magnetic field of ring molecule magnet models", Chem. Phys. Lett, 315, 441-445, (1999).　[doi]

close

in 1998

1. Y. Shigeta, Y. Ozaki, K. Kodama, H. Nagao, H. Kawabe, and K. Nishikawa, "Nonadiabatic Molecular Theory and its Application. II. Water Molecule", Int. J. Quant. Chem, 69, 629-637, (1998).　[doi]
2. Y. Shigeta, H. Takahashi, S. Yamanaka, M. Mitani, H. Nagao, and K. Yamaguchi, "Density Functional Theory Without the Born-Oppenheimer Approximation and its Application", Int. J. Quant. Chem., 70, 659-669, (1998).　[doi]

in 1997

1. M. Nakano, H. Nagao, and K. Yamaguchi, "Many-electron hyperpolarizability density analysis: Application to the dissociation process of one-dimensional H₂s", Phys. Rev. A, 55, 1503-1513, (1997).　[doi]
2. H. Nagao, M. Nakano, S. Yamada, K. Ohta, and K. Yamaguchi, "Theoretical study on the second hyperpolarizability of H₃⁺ system by path integral method", Synthetic Metals, 85, 1159-1160, (1997).　[doi]

in 1996

1. M. Nakano, Y. Matsuzaki, H. Nagao, S. Yamada, I. Shigemoto, and K. Yamaguchi, "Damping wave packet approach: a calculation method of nonperturbative nonlinear optical susceptibilities including effects of nuclear motion at finite temperatures", Chem. Phys. Lett., 258, 307-315, (1996).　[doi]
2. H. Nagao, H. Kawabe, T. Kawakami, M. Okumura, W. Mori, K. Nishikawa, and K. Yamaguchi, "Calculation of Magnetization by Path Integral Method I", Molecular Crystals and Liquid Crystals Science and Technology. Section A. Molecular Crystals and Liquid Crystals, 286, 171-176, (1996).　[doi]

Society Award

in 2018