Peer-reviewed papers

  1. "Ab initio CASSCF/MRSDCI study of the CuCH2 cluster",
    Y. Mochizuki*, K. Tanaka, K. Ohno, H. Tatewaki, and S. Yamamoto, Chem. Phys. Lett. , 152 (1988) 457-463.
  2. "Electronic structure of CO adsorbed on small Cu clusters: Theoretical study on excited states",
    Y. Mochizuki*, K. Tanaka, K. Ohno, and H. Tatewaki, Phys. Rev. B , 39 (1989) 11907-11913.
  3. "A theoretical study of the bent form of CuO2",
    Y. Mochizuki*, U. Nagashima, S. Yamamoto, and H. Kashiwagi, Chem. Phys. Lett. , 164 (1989) 225-230.
  4. "Electronic structure of the linear form of OCuO",
    Y. Mochizuki*, K. Tanaka, and H. Kashiwagi, Chem. Phys. , 151 (1991) 11-20.
  5. "Electronic structure of lower singlet states of binuclear copper acetate monohydrate",
    K. Ogasawara, Y. Mochizuki, T. Noro, and K. Tanaka, Can. J. Chem. , 70 (1992) 393-398.
  6. "A theoretical study of the CuOH molecule",
    Y. Mochizuki*, T. Takada, and A. Murakami, Chem. Phys. Lett. , 185 (1991) 535-543.
  7. "Thoretical study of the gallium chloride molecules and its interaction with arsenic dangling bonds",
    Y. Mochizuki*, T. Takada, and A. Usui, Phys. Rev. B , 47 (1993) 13420-13431.
  8. "New concerted mechanism of the Cl-removal reaction induced by H2 in chloride atomic layer epitaxy",
    Y. Mochizuki*, T. Takada, and A. Usui, Jpn. J. Appl. Phys. , 32 (1993) L197-L199.
  9. "Theoretical study of the Cl desorption reaction induced by H2 in the chloride atomic layer epitaxy",
    Y. Mochizuki*, T. Takada, T. Sakuma, S. Handa, C. Sasaoka, and A. Usui, J. Cryst. Growth , 135 (1994) 259-268.
  10. "Theoretical study of As2 desorption from the Ga dangling-bond site",
    Y. Mochizuki*, T. Takada, C. Sasaoka, A. Usui, E. Miyoshi, and Y. Sakai, Phys. Rev. B , 49 (1994) 4658-4667.
  11. "Theoretical studies on the chloride ALE process",
    Y. Mochizuki*, T. Takada, and A. Usui, Appl. Surf. Sci. , 82/83 (1994) 200-207.
  12. "Theoretical study on the direct reaction between AsH3 and surface-adsorbed GaCl",
    Y. Mochizuki*, A. Usui, S. Handa, and T. Takada, J. Cryst. Growth , 148 (1995) 96-105.
  13. "On the reaction scheme for Ti/TiN chemical vapor deposition (CVD) process using TiCl4",
    Y. Mochizuki*, Y. Okamoto, A. Ishitani, K. Hirose, and T. Takada, Jpn. J. Appl. Phys. , 34 (1995) L326-L329.
  14. "Generalized doubly symbolic formulation for integral-driven direct configuration interaction method",
    Y. Mochizuki*, N. Nishi, Y. Hirahara, and T. Takada, Theor. Chim. Acta , 93 (1996) 211-233.
  15. "Theoretical Study of the Surface Reaction Mechanism of GaN with HCl",
    Y. Okamoto, T. Takada, and Y. Mochizuki, Jpn. J. Appl. Phys. , 35 (1996) L1641-L1643.
  16. "Computational study of the spectroscopic constants of the ground state of the As2 molecule",
    Y. Mochizuki* and K. Tanaka, Chem. Phys. Lett. , 274 (1997) 264-268.
  17. "A CSF-based multireference coupled pair approximation III - An application to F2, As2, and As2+ ",
    K. Tanaka and Y. Mochizuki, Theor. Chem. Acc. , 98 (1997) 165-170.
  18. "Theoretical investigation on the GaH molecule and its positive ion",
    Y. Mochizuki* and K. Tanaka, Theor. Chem. Acc. , 99 (1998) 88-94.
  19. "Theoretical study of the spectroscopic constants of low-lying states of Ga2",
    T. K. Ghosh, K. Tanaka, and Y. Mochizuki, J. Mol. Struct. ( Theochem ) , 451 (1998) 61-71.
  20. "Theoretical investigation on the GaF molecule and its positive ion",
    Y. Mochizuki* and K. Tanaka, Theor. Chem. Acc. , 101 (1999) 257-261.
  21. "Theoretical spectroscopic constants of the GaN molecule",
    Y. Mochizuki* and K. Tanaka, Theor. Chem. Acc. , 101 (1999) 292-296.
  22. "Multireference coupled-pair approximation study of the CuSi molecule",
    M. Tomonari, Y. Mochizuki, and K. Tanaka, Theor. Chem. Acc. , 101 (1999) 332-335.
  23. "A thoretical investigation of sulphur K-shell X-ray absorption of cysteine",
    Y. Mochizuki*, H. Agren, L. G. M. Pettersson, and V. Carravetta, Chem. Phys. Lett. , 309 (1999) 241-248.
  24. "HF-STEX and RASSCF calculations on nitrogen K-shell X-ray absorption of purine base and its derivative",
    Y. Mochizuki*, H. Koide, T. Imamura, and H. Takemiya, J.Synchrotron Rad., 8 (2001) 1003-1005.
  25. "Polarizability of silicon clusters",
    Y. Mochizuki* and H. Agren, Chem. Phys. Lett. , 336 (2001) 451-456.
  26. "Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions",
    Y. Mochizuki* and H. Tatewaki, Chem. Phys. , 273 (2001) 135-148.
  27. "Modification of nonrelativistic Gaussian basis sets for relativistic calculations",
    H. Tatewaki, Y. Mochizuki, T. Koga, and J. Karwowski, J. Chem. Phys. , 115 (2001) 9160-9164.
  28. "Size, order and dimensional relations for silicon cluster polarizabilities",
    B. Jansik, B. Schimmelpfennig, P. Norman, Y. Mochizuki, Y. Luo, and H. Agren, J. Phys. Chem. A , 106 (2002) 395-399.
  29. "Vectorization of Direct Fock Matrix Construction in DIRAC-DHF Calculations",
    Y. Mochizuki*, M. Matsumura, T. Yokura, Y. Hirahara, and T. Imamura, J. Nucl. Sci. Tech. , 39 (2002) 195-199.
  30. "On the electronic structure of Cm(H2O)n3+ (n=1,2,4,6) by all electron Dirac-Hartree-Fock calculations",
    Y. Mochizuki* and H. Tatewaki, J. Chem. Phys. , 116 (2002) 8838-8842.
  31. "Four-component relativistic calculations on the mono-ammine complexes of trivalent f0, f7, and f14 ions",
    Y. Mochizuki* and Y. Okamoto, Chem. Phys. Lett. , 359 (2002) 331-336.
  32. "Ab initio MO studies on the hydration of trivalent curium ion",
    Y. Mochizuki*, H. Tatewaki, and Y. Okamoto J. Nucl. Sci. Tech. , Supplement 3 (2002) 418-421.
  33. "Comments on relativistic basis sets",
    H. Tatewaki and Y. Mochizuki, Theor. Chem. Acc. , 109 (2003) 40-42.
  34. "On the electronic structures of Th4+ and Ac3+ hydrate models",
    Y. Mochizuki* and S. Tsushima, Chem. Phys. Lett. , 372 (2003) 114-120.
  35. "Theoretical study of hydrolysis reactions of tetravalent thorium ion",
    Y. Okamoto, Y. Mochizuki, and S. Tsushima, Chem. Phys. Lett. , 373 (2003) 213-217.
  36. "On the electronic structure of CmFn (n=1-4) by all-electron Dirac-Hartree-Fock calculations",
    Y. Mochizuki* and H. Tatewaki, J. Chem. Phys. , 118 (2003) 9201-9207.
  37. "Prolapses in four-component relativistic Gaussian basis sets",
    H. Tatewaki, T. Koga, and Y. Mochizuki, Chem. Phys. Lett. , 375 (2003) 399-405.
  38. "Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution",
    S. Tsushima, T. X. Yang, Y. Mochizuki, and Y. Okamoto, Chem. Phys. Lett. , 375 (2003) 204-212.
  39. "Comparative study of dehydrogenation of methanol at Pt(111)/water and Pt(111)/vacuum interfaces",
    Y. Okamoto, O. Sugino, Y. Mochizuki, T. Ikeshoji, and Y. Morikawa, Chem. Phys. Lett. , 377 (2003) 236-242.
  40. "A parallelized integral-direct second-order Moeller-Plesset perturbation theory method with a fragment molecular orbital scheme",
    Y. Mochizuki*, T. Nakano, S. Koikegami, S. Tanmori, Y. Abe, U. Nagashima, and K. Kitaura, Theor. Chem. Acc., 112 (2004) 442-452.
  41. "Large scale MP2 calculations with fragment molecular orbital scheme",
    Y. Mochizuki*, S. Koikegami, T. Nakano, S. Amari, and K. Kitaura, Chem. Phys. Lett. , 396 (2004) 473-479.
  42. "Configuration interaction singles method with multilayer fragment molecular orbital scheme",
    Y. Mochizuki*, S. Koikegami, S. Amari, K. Segawa, K. Kitaura, and T. Nakano, Chem. Phys. Lett. , 406 (2005) 283-288.
  43. "A size-extensive modification of super-CI for orbital relaxation",
    Y. Mochizuki*, Chem. Phys. Lett. , 410 (2005) 165-171.
  44. "A configuration analysis for fragment interaction",
    Y. Mochizuki*, K. Fukuzawa, A. Kato, S. Tanaka, K. Kitaura, and T. Nakano, Chem. Phys. Lett. , 410 (2005) 247-253.
  45. "Dynamic polarizability calculation with fragment molecular orbital scheme",
    Y. Mochizuki*, T. Ishikawa, K. Tanaka, H. Tokiwa, T. Nakano, and S. Tanaka, Chem. Phys. Lett. , 418 (2006) 418-422.
  46. "VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening",
    S. Amari, M. Aizawa, J. Zhang, K. Fukuzawa, Y. Mochizuki, Y. Iwasawa, K. Nakata, H. Chuman, and T. Nakano, J. Chem. Inf. Model. , 46 (2006) 221-230.
  47. "Intra- and Inter-molecular Interactions between Cyclic-AMP Receptor Protein and DNA: Ab initio Fragment Molecular Orbital Study",
    K. Fukuzawa, Y. Komeiji, Y. Mochizuki, A. Kato, T. Nakano, and S. Tanaka, J. Comp. Chem. , 27 (2006) 948-960.
  48. "Molecular Interactions Between Estrogen Receptor and Its Ligand Studied by the Ab Initio Fragment Molecular Orbital Method",
    K. Fukuzawa, Y. Mochizuki, S. Tanaka, K. Kitaura, and T. Nakano, J. Phys. Chem. B, 110 (2006) 16102-16110 (errata, 110 (2006) 24276).
  49. "Fragment molecular orbital calculations on large scale systems containing heavy metal atom",
    T. Ishikawa, Y. Mochizuki*, T. Nakano, S. Amari, H. Mori, H. Honda, T. Fujita, H. Tokiwa, S. Tanaka, Y. Komeiji, K. Fukuzawa, K. Tanaka, and E. Miyoshi, Chem. Phys. Lett., 427 (2006) 159-165.
  50. "Application of fragment molecular orbital scheme to silicon-containing systems",
    T. Ishikawa, Y. Mochizuki*, K. Imamura, T. Nakano, H. Mori, H. Tokiwa, K. Tanaka, E. Miyoshi, and S. Tanaka, Chem. Phys. Lett., 430 (2006) 361-366.
  51. "A graphical symmetric group approach for a spin adapted full configuration interaction",
    K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, and H. Tokiwa, Theor. Chem. Acc., 117 (2007) 397-405.
  52. "Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme",
    Y. Mochizuki*, K. Tanaka, K. Yamashita, T. Ishikawa, T. Nakano, S. Amari, K. Segawa, T. Murase, H. Tokiwa, and M. Sakurai, Theor. Chem. Acc., 117 (2007) 541-553.
  53. "Fragment molecular orbital calculations on red fluorescent protein (DsRed)",
    Y. Mochizuki*, T. Nakano, S. Amari, T. Ishikawa, K. Tanaka, M. Sakurai, and S. Tanaka, Chem. Phys. Lett., 433 (2007) 360-367.
  54. "A fully quantum mechanical simulation study on the lowest n-pi* state of hydrated formaldehyde",
    Y. Mochizuki*, Y. Komeiji, T. Ishikawa, T. Nakano, and H. Yamataka, Chem. Phys. Lett., 437 (2007) 66-72.
  55. "Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator: Roles of Helix12 in the Coactivator Binding Mechanism",
    M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, J. Phys. Chem. B, 111 (2007) 3525-3533.
  56. "Modification for spin-adapted version of configuration interaction singles with perturbative doubles",
    Y. Mochizuki* and K. Tanaka, Chem. Phys. Lett., 443 (2007) 389-397.
  57. "Fragment interaction analysis based on local MP2",
    T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, H. Tokiwa, S. Tanaka, and K. Tanaka, Theor. Chem. Acc., 118 (2007) 937-945.
  58. "Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method",
    I. Kurisaki, K. Fukuzawa, Y. Komeiji, Y. Mochizuki, T. Nakano, J. Imada, A. Chmielewski, S. M. Rothstein, H. Watanabe, and S. Tanaka, Biophys. Chem., 130 (2007) 1-9.
  59. "Application of the fragment molecular orbital method for determination of atomic charges on polypeptides",
    Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, S. Tanaka, and K. Ebina, Chem. Phys. Lett., 449 (2007) 329-335.
  60. "On Fluorescence Mechanism of Green Fluorescent Protein",
    E. B. Starikov, I. Panas, Y. Mochizuki, S. Tanaka, Y. Luo, and H. Agren, Biophys. Rev. Lett., 2 (2007) 221-227.
  61. "Multi-reference calculations of nitric oxide dimer",
    N. Taguchi, Y. Mochizuki*, T. Ishikawa, and K. Tanaka, Chem. Phys. Lett., 451 (2008) 31-36 [Fig.1 was adopted as the front cover figure of the corresponding issue].
  62. "A practical use of self-energy shift for the description of orbital relaxation",
    Y. Mochizuki*, Chem. Phys. Lett., 453 (2008) 109-116.
  63. "Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator. Part II: Influence of Mutations in Transcriptional Activation Function 2 Activating Domain Core on the Molecular Interactions",
    M. Ito, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, J. Phys. Chem. A, 112 (2008) 2702-2712.
  64. "How does an SN2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion",
    M. Sato, H. Yamataka, Y. Komeiji, Y. Mochizuki, T. Ishikawa, and T. Nakano, J. Amer. Chem. Soc., 130 (2008) 2396-2397.
  65. "Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method",
    T. Iwata, K. Fukuzawa, K. Nakajima, S. Aida-Hyugaji, Y. Mochizuki H. Watanabe, and S. Tanaka, Comp. Bio. Chem., 32 (2008) 198-211.
  66. "Large scale FMO-MP2 calculations on a massively parallel-vector computer",
    Y. Mochizuki*, K. Yamashita, T. Murase, T. Nakano, K. Fukuzawa, K. Takematsu, H. Watanabe, and S. Tanaka, Chem. Phys. Lett., 457 (2008) 396-403.
  67. An application of fragment interaction analysis based on local MP2",
    T. Ishikawa, Y. Mochizuki, S. Amari, T. Nakano, S. Tanaka, and K. Tanaka, Chem. Phys. Lett., 463 (2008) 189-194.
  68. "Ab Initio Fragment Molecular Orbital Study of Molecular Interactions in Liganded Retinoid X Receptor: Specification of Residues with Roles of Ligand Inducible Information Transmission",
    M. Ito, K. Fukuzawa, T. Ishikawa, Y. Mochizuki, T. Nakano, and S. Tanaka, J. Phys. Chem. B , 112 (2008) 12081-12094.
  69. "Fragment Molecular Orbital method based Molecular Dynamics (FMO-MD) as a simulator for chemical reactions in explicit solvation",
    Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, and T. Nakano, J. Comp. Chem. , 30 (2009) 40-50.
  70. "Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Toward an improvement of force fields used for classical molecular dynamics simulations",
    Y. Okiyama, H. Watanabe, K. Fukuzawa, T. Nakano, Y. Mochizuki, T. Ishikawa, K. Ebina, and S. Tanaka, Chem. Phys. Lett., 467 (2009) 417-423.
  71. "Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD), a quantum simulation tool for large molecular systems",
    Y. Komeiji, Y. Mochizuki, T. Nakano, and D. G. Fedorov, J. Mole. Struct. (Theochem) , 898 (2009) 2-7.
  72. "Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits)",
    N. Taguchi, Y. Mochizuki*, T. Nakano, S. Amari, K. Fukuzawa, T. Ishikawa, M. Sakurai, and S. Tanaka, J. Phys. Chem. B , 113 (2009) 1153-1161.
  73. "Ab Initio Quantum-Chemical Study on Emission Spectra of Bioluminescent Luciferases by Fragment Molecular Orbital Method",
    A. Tagami, N. Ishibashi, D. Kato, N. Taguchi, Y. Mochizuki, H. Watanabe, M. Ito, and S. Tanaka, Chem. Phys. Lett., 472 (2009) 118-123.
  74. "Application of Dyson-corrected second-order perturbation theories",
    Y. Mochizuki*, Chem. Phys. Lett., 472 (2009) 143-148.
  75. "Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding",
    K. Takematsu, K. Fukuzawa, K. Omagari, S. Nakajima, K. Nakajima, Y. Mochizuki, T. Nakano, H. Watanabe, and S. Tanaka, J. Phys. Chem. B , 113 (2009) 4991-4994.
  76. "Accuracy of fragmentation in ab initio calculations of hydrated sodium",
    T. Fujita, K. Fukuzawa, Y. Mochizuki, T. Nakano, and S. Tanaka, Chem. Phys. Lett., 478 (2009) 295-300.
  77. "Three-body expansion and generalized dynamic fragmentation improve the Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD)",
    Y. Komeiji, Y. Mochizuki, and T. Nakano, Chem. Phys. Lett., 484 (2010) 380-386.
  78. "Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion",
    T. Fujiwara, Y Mochizuki*, Y. Komeiji, Y. Okiyama, H. Mori, T. Nakano, and E. Miyoshi, Chem. Phys. Lett., 490 (2010) 41-45.
  79. "Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach",
    Y. Okiyama, T. Nakano, K. Yamashita, Y. Mochizuki, N. Taguchi, and S. Tanaka, Chem. Phys. Lett., 490 (2010) 84-89 [Graphical Abstract was adopted as the front cover figure of the corresponding issue].
  80. "Flexible Ligand Recognition of Peroxisome Proliferator-Activated Receptor-γ (PPARγ)",
    K. Yamagishi, K. Yamamoto, Y. Mochizuki, T. Nakano, S. Yamada, and H. Tokiwa, Bio. Med. Chem. Lett., 20 (2010) 3344-3347.
  81. "Theoretical study of hydration models of trivalent rare-earth ions using model core potentials",
    T. Fujiwara, H. Mori, Y. Mochizuki, H. Tatewaki, and E. Miyoshi, J. Mol. Struct. (THEOCHEM), 949 (2010) 28-35.
  82. " Does Amination of Formaldehyde Proceeds through Zwitterionic Intermediate in Water? FMO-MD Simulations by using Constraint Dynamics ",
    M. Sato, H. Yamataka, Y. Mochizuki, Y. Komeiji, and T. Nakano, Chem. Eur. J., 16 (2010) 6430-6433.
  83. "Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA)",
    Y. Mochizuki*, K. Yamashita, K. Fukuzawa, K. Takematsu, H. Watanabe, N. Taguchi, Y. Okiyama, M. Tsuboi, T. Nakano, and S. Tanaka, Chem. Phys. Lett., 493 (2010) 346-352.
  84. "Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system",
    I. Kurisaki, K. Fukuzawa, T. Nakano, Y. Mochizuki, H. Watanabe, and S. Tanaka, J. Mol. Struct. (THEOCHEM), 962 (2010) 45-55.
  85. "Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins",
    N. Taguchi, Y. Mochizuki*, T. Nakano, Chem. Phys. Lett., 504 (2011) 76-82.
  86. "Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient",
    Y. Mochizuki*, T. Nakano, Y. Komeiji, K. Yamashita, Y. Okiyama, H. Yoshikawa, and H. Yamataka, Chem. Phys. Lett., 504 (2011) 95-99.
  87. "Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations",
    A. Yoshioka, K. Fukuzawa, Y. Mochizuki, K. Yamashita, T. Nakano, Y. Okiyama, E. Nobusawa, K. Nakajimah, and S. Tanaka, J. Mol. Gr. Mod., 30 (2011) 110-119.
  88. "Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme",
    Y. Okiyama K. Fukuzawa H. Yamada, Y. Mochizuki, T. Nakano, and S. Tanaka, Chem. Phys. Lett., 509 (2011) 67-71.
  89. "4f-in-core model core potentials for trivalent lanthanides",
    T. Fujiwara, H. Mori, Y. Mochizuki, Y. Osanai, and E. Miyoshi, Chem. Phys. Lett., 510 (2011) 261-266.
  90. "Higher-order correlated calculations based on fragment molecular orbital scheme",
    Y. Mochizuki*, K. Yamashita, T. Nakano, Y. Okiyama, K. Fukuzawa, N. Taguchi, and S. Tanaka, Theor. Chem. Acc., 130 (2011) 515-530.
  91. "Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation",
    A. Yoshioka, K. Takematsu, I. Kurisaki, K. Fukuzawa, Y. Mochizuki, T. Nakano, E. Nobusawa, K. Nakajima, and S. Tanaka, Theor. Chem. Acc., 130 (2011) 1197-1202.
  92. "Development of the four-body corrected fragment molecular orbital (FMO4) method",
    T Nakano, Y. Mochizuki*, K. Yamashita, C. Watanabe, K. Fukuzawa, K. Segawa, Y. Okiyama, T. Tsukamoto, and S. Tanaka, Chem. Phys. Lett., 523 (2012) 128-133.
  93. "Excited state calculation for free-base and metalloporphyrins with the partially renormalized polarization propagator approach",
    M. Saitow, Y. Mochizuki, Chem. Phys. Lett., 525-526 (2012) 144-149.
  94. "Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD)",
    H. Mori, N. Hirayama, Y. Komeiji, Y. Mochizuki, Comp. Theor. Chem., 986 (2012) 30-34.
  95. "Partial geometry optimization with FMO-MP2 gradient: application to TrpCage",
    T. Tsukamoto, Y. Mochizuki*, N. Watanabeb, K. Fukuzawa, and T. Nakano, Chem. Phys. Lett., 535 (2012) 157-162.
  96. "Recent advances in fragment molecular orbital-based molecular dynamics (FMO-MD) simulations",
    Y. Komeiji, Y. Mochizuki, T. Nakano, and H. Mori, Intech - Open Access Publisher, (2012) (Click Here)
  97. "FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics",
    M. Sato, H. Yamataka, Y. Komeiji, and Y. Mochizuki, Chem. Eur. J., 18 (2012) 9714-9721.
  98. "Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects",
    T. Fujita, S. Tanaka, T. Fujiwara, M. Kusa, Y. Mochizuki, and M. Shiga, Comp. Theor. Chem., 997 (2012) 7-13.
  99. "Importance of spin-orbit coupling effect and solvent effect in electronic 3 transition assignments of PtII complexes: In the case of cis/trans-[PtIICl2(NH3)2]",
    H. Mori, R. Kojima, Y. Mochizuki, W. Uenohara, I. Umezawa, N. Matsushita, J. Mol. Struct., 1035 (2013) 218-223.
  100. "Modeling of peptide - silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations",
    Y. Okiyama, T. Tsukamoto, C. Watanabe, K. Fukuzawa, S. Tanaka, and Y. Mochizuki*, Chem. Phys. Lett., 566 (2013) 25-31.
  101. "Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design",
    C. Watanabe, K. Fukuzawa, Y. Okiyama, T. Tsukamoto, A. Kato, S. Tanaka, Y. Mochizuki, and T. Nakano, J. Mol. Gr. Mod., 41 (2013) 31-42.
  102. "Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides",
    Y. Komeiji, T. Fujiwara, Y. Okiyama, Y. Mochizuki, ChemBio Informatics J. 13 (2013) 45-57.
  103. "Improved description of the orbital relaxation effect by practical use of the self-energy",
    M. Saitow, T. Ida, and Y. Mochizuki, Intern. J. Quant. Chem. 114 (2014) 577-586.
  104. "Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy",
    K. Fukuzawa, C. Watanabe, I. Kurisaki, N. Taguchi, Y. Mochizuki, T. Nakano, S. Tanaka, and Y. Komeiji, Comp. Theor. Chem. 1034 (2014) 7-16.
  105. "Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems",
    S. Tanaka*, Y. Mochizuki*, Y. Komeiji, Y. Okiyama, and K. Fukuzawa, Phys. Chem. Chem. Phys., 16 (2014) 10310-10344.
  106. "Interaction energy analysis on specific binding of influenza virushemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change",
    S. Anzaki, C. Watanabe, K. Fukuzawa, Y. Mochizuki, and S. Tanaka, J. Mol. Gr. Mod., 53 (2014) 48-58.
  107. "Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion",
    Y. Kato, T. Fujiwara, Y. Komeiji, T. Nakano, H. Mori, Y. Okiyama, and Y. Mochizuki*, ChemBio Informatics J. 14 (2014) 1-13.
  108. "Optimal damping algorithm for unrestricted Hartree-Fock calculations",
    J. Yamamoto and Y. Mochizuki*, ChemBio Informatics J. 14 (2014) 14-33.
  109. "Explicit solvation modulates intra- and inter-molecular interactions within DNA: electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method",
    K. Fukuzawa, I. Kurisaki, C. Watanabe, Y. Okiyama, Y. Mochizuki, S. Tanaka, and Y. Komeiji, Comp. Theo. Chem. 1054 (2015) 29-37.
  110. "Hydration effects on enzyme-substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method",
    H. Ando, Y. Shigeta, T. Baba, C. Watanabe, Y. Okiyama, Y. Mochizuki, and M. Nakano, Mol. Phys., 113 (2015) 319-326.
  111. "Modeling of hydroxyapatite - peptide interaction based on fragment molecular orbital method",
    K. Kato, K. Fukuzawa, and Y. Mochizuki*, Chem. Phys. Lett., 629 (2015) 58-64.
  112. "Reversible Structural Changes Accompanying the Two-Electron Redox Reaction of Pt(tacn) (tacn: 1,4,7-triazacyclononane) Complexes",
    T. Wada, K. Enami, R. Kojima, T. Okada, Y. Ishikawa, Y. Miyazato, E. Horn, and Y. Mochizuki, Bull. Chem. Soc. Jpn. 88 (2015) 1230-1237. (Selected Paper)
  113. "Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method",
    K. Tokuda, C. Watanabe, Y. Okiyama, Y. Mochizuki, K. Fukuzawa, and Yuto Komeiji, J. Mol. Graphics Model. 69 (2016) 144-153.
  114. "Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Moeller-Plesset perturbation (MP2.5) scheme",
    H. Yamada, Y. Mochizuki*, K. Fukuzawa, Y. Okiyama, and Y. Komeiji, Comp. Theor. Chem. 1101 (2017) 46-54.
  115. "Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane",
    H. Doi, K. Okuwaki, Y. Mochizuki, T. Ozawa, K. Yasuoka, Chem. Phys. Lett. 684 (2017) 427-432.
  116. "Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation",
    Y. Komeiji, Y. Okiyama, Y. Mochizuki, and K. Fukuzawa, ChemBio Informatics J., 17 (2017) 72-84.
  117. "Fragment Molecular Orbital-based Parameterization Procedure for Mesoscopic Structure Prediction of Polymeric Materials",
    K. Okuwaki, Y. Mochizuki*, H. Doi, and T. Ozawa, J. Phys. Chem. B 122 (2018) 338-347.
  118. "Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations",
    S. Saitou, J. Iijima, M. Fujimoto, Y. Mochizuki*, K. Okuwaki, H. Doi, and Y. Komeiji, ChemBio Informatics J. 18 (2018) 58-69.
  119. "Development of the Fragment Molecular Orbital Method for Calculating Non-local Excitations in Large Molecular Systems",
    T. Fujita, and Y. Mochizuki, J. Phys. Chem. A 122 (2018) 3886-3898.
  120. "Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: Implementation and DNA Study",
    Y. Okiyama, T. Nakano, C. Watanabe, K. Fukuzawa, Y. Mochiuzki, and S. Tanaka, J. Phys. Chem. B 122 (2018) 4457-4471.
  121. "A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions",
    H. Doi, K. Okuwaki, T. Naitou, S. Saitou, and Y. Mochizuki*, ChemBio Informatics J. 18 (2018) 70-85.
  122. "RI-MP3 calculations of biomolecules based on the fragment molecular orbital method",
    T. Ishikawa, K. Sakakura, Y. Mochizuki, J. Comp. Chem., 39 (2018) 1970-1978.
  123. "Interaction between a single-stranded DNA and a binding protein viewed by the fragment molecular orbital method",
    Y. Komeiji, Y. Okiyama, Y. Mochizuki, and K. Fukuzawa, Bull. Chem. Soc. Jpn., 91 (2018) 1596-1605.
  124. "Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method",
    T. Nakano, K. Fukuzawa, Y. Okiyama, C. Watanabe, Y. Komeiji, and Y. Mochizuki, ChemBio Informatics J., 18 (2018) 119-122.
  125. "Theoretical Analyses on Water Cluster Structures in Polymer Electrolyte Membrane by Using Dissipative Particle Dynamics Simulations with Fragment Molecular Orbital Based Effective Parameters",
    K. Okuwaki, Y. Mochizuki*, H. Doi, S. Kawada, T. Ozawa, and K. Yasuoka, RSC Adv., 8 (2018) 34582-34595 (Open Access).
  126. "Development of analysis toolkit to visualize interaction energies generated by fragment molecular orbital calculations",
    T. Tokiwa, S. Nakano, Y. Yamamoto, T. Ishikawa, S. Ito, K. Fukuzawa, Y. Mochizuki, H. Tokiwa, F. Misaizu, and Y. Shigeta, J. Chem. Inform. Model., 59 (2019) 25-30.
  127. "Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies",
    Y. Okiyama, C. Watanabe, K. Fukuzawa, Y. Mochiuzki, T. Nakano, and S. Tanaka, J. Phys. Chem. B, 123 (2019) 957-973 [This article obtained the cover image of issue].
  128. "Destabilization of DNA through interstrand crosslinking by UO22+",
    A. Rossberg, T. Abe, K. Okuwaki, A. Barkleit, K. Fukuzawa, T. Nakano, Y. Mochizuki, and S. Tsushima, Chem. Comm., 55 (2019) 2015-2018 [This article obtained the cover image of issue].
  129. "Cm3+/ Eu3+ Induced Structural, Mechanistic and Functional Implications for Calmodulin",
    B. Drobot, M. Schmidt, Y. Mochizuki, T. Abe, K. Okuwaki, F. Brulfert, S. Falke, S. A. Samsonov, Y. Komeiji, C. Betzel, T. Stumpf, J. Raff, and S. Tsushima, Phys. Chem. Chem. Phys., 21 (2019) 21213-21222 [This article obtained the inside cover image of issue and selected as a 2019 Hot Paper].
  130. "Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method",
    K. Kato, K. Fukuzawa, and Y. Mochizuki, Jpn. J. Appl. Phys., 58 (2019) 120906.
  131. "Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations",
    K. Okuwaki, H. Doi, K. Fukuzawa, and Y. Mochizuki*, Appl. Phys. Express, 13 (2020) 017002-1-4 (Open Access).
  132. "Stabilization Mechanism of Non-fibrillar Amyloid-β Oligomer Involved with Hydrophobic Core Obtained by Dissipative Particle Dynamics",
    R. Kawai, S. Chiba, K. Okuwaki, R. Kanada, H. Doi, M. Ono, Y. Mochizuki, and Y. Okuno, ACS Chem. Neuroscience, 11 (2020) 385-394.
  133. "FMO-MD simulations of (NH3)32 cluster: effect of electron correlation",
    M. Ninomiya, H. Doi, Y. Matsumoto, Y. Mochizuki, and Y. Komeiji, Bull. Chem. Soc. Jpn., 93 (2020) 553-560.
  134. "Fragmentation at sp2 carbon in fragment molecular orbital (FMO) method",
    Y. Akinaga, K. Kato, T. Nakano, K. Fukuzawa, and Y. Mochizuki, J. Comp. Chem., 41 (2020) 1416-1420.
  135. "Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7)",
    R. Hatada, K. Okuwaki, Y. Mochizuki*, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama and S. Tanaka, J. Chem. Inform. Model., 60 (2020) 3593-3602 (Open Access).
  136. "Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery",
    H. Tanaka, T. Takahashi, M. Konishi, N. Takata, M. Gomi. D. Shirane, R. Miyama, S. Hagiwara, Y. Yamasaki, Y. Sakurai, K. Ueda, K. Higashi, K. Moribe, E. Shinsho, R. Nishida, K. Fukuzawa, E. Yonemochi, K. Okuwaki, Y. Mochizuki, Y. Nakai, K. Tange. H. Yoshioka. S. Tamagawa, and H. Akita, Adv. Funct. Mater., 30 (2020) 1910575 (Open Access).
  137. "Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method",
    Y. Okiyama, T. Nakano, C. Watanabe, K. Fukuzawa, Y. Komeiji, K. Segawa, and Yuji Mochizuki, Bull. Chem. Soc. Jpn., 94 (2021) 91-96 (Open Access).
  138. "Interaction analyses on SARS-CoV-2 spike protein based on fragment molecular orbital calculations",
    K. Akisawa, R. Hatada, K. Okuwaki, Y. Mochizuki*, K. Fukuzawa, Y. Komeiji, and S. Tanaka, RSC Adv., 11 (2021) 3272-3279 (Open Access).
  139. "Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining of molecular dynamics simulation and fragment molecular orbital calculation",
    R. Hatada, K. Okuwaki, K. Akisawa, Y. Mochizuki*, Y. Handa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and S. Tanaka, Appl. Phys. Express 14 (2021) 027003-1-5 (Open Access).
  140. "Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals",
    Y. Okiyama, Y. Mochizuki, M. Yamanaka, and S. Tanaka, J. Phys. Soc. Jpn., 90 (2021) 064301-1-14 (Open Access).
  141. "Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method",
    S. Tanaka, S. Tokutomi, R. Hatada,, K. Okuwaki, K. Akisawa, K. Fukuzawa, Y. Komeiji, Y. Okiyama, and Y. Mochizuki, J. Phys. Chem. B, 125 (2021) 6501-6512.
  142. "Fragment Molecular Orbital Based Interaction Analyses on Complexes Between SARS-CoV-2 RBD Variants and ACE2",
    K. Akisawa, R. Hatada, K. Okuwaki, S. Kitahara, Y. Tachino, Y. Mochizuki*, Y. Komeiji, and S. Tanaka, Jpn. J. Appl. Phys., 60 (2021) 090901-1-5 (Open Access).
  143. "Interaction Analysis on SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity",
    T. Ishikawa, H. Ozono, K. Akisawa, R. Hatada, K. Okuwaki, and Y. Mochizuki, J. Chem. Phys. Lett., 12 (2021) 11267-11272.
  144. "Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins on the basis of fragment molecular orbital method",
    K. Okuwaki, K. Akisawa, R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, and S. Tanaka, Appl. Phys. Express, 15 (2021) 017001-1-9 (Open Access & Selected as a spotlight article).
  145. "Variational quantum eigensolver simulations with the multireference unitary coupled cluster ansatz: a case study of the C2v quasi-reaction pathway of beryllium insertion into a H2 molecule",
    K. Sugusaki, T. Kato, Y. Minato, K. Okuwaki, and Y. Mochizuki, Phys. Chem. Chem. Phys., 24 (2022) 8439-8452 (Open Access).
  146. "Practical computational chemistry course for a comprehensive understanding of organic, inorganic, and physical chemistry: from molecular interactions to chemical reactions",
    N. Kuroki, Y. Mochizuki, and H. Mori, J. Chem. Educ., 100 (2023) 647-654 (Open Access).
  147. "Lattice folding simulation of peptide by quantum computation",
    R. Saito, K. Okuwaki, Y. Mochizuki*, R. Nagai, T. Kato, K. Sugisaki, and Y. Minato, J. Comp. Chem. Jpn. Inter. Ed., 9 (2023) ID:2022-0036 (1-6) (Open Access).
  148. "Bifurcated hydrogen bonds in a peptide crystal unveiled by X-ray diffraction and polarized Raman spectroscopy",
    K. Motai, N. Koishihara, T. Narimatsu, H. Ohtsu, M. Kawano, K. Akisawa, K. Okuwaki, T. Mori, J.-S. Kim, Y. Mochizuki, and Y. Hayamizu, Cryst. Growth Design, 23 (2023) 4556-4561 & 6988 (Open Access).
  149. "Machine learning to improve efficiency of non-empirical interaction parameter for dissipative particle dynamics (DPD) simulation",
    H. Doi, S. Matsuoka, K. Okuwaki, R. Hatada, S. Minami, R. Suhara, and Y. Mochizuki, Jpn. J. Appl. Phys., 62 (2023) 070901-1-6.
  150. "Bayesian phase difference estimation algorithm for direct calculation of fine structure splitting: accelerated simulation of relativistic and quantum many-body effects",
    K. Sugisaki, V. S. Prasannaa, S. Ohshima, T. Katagiri, Y. Mochizuki, B. K. Sahoo, and B. P. Das, Electr. Struct., 5 (2023) 035006-1-10 (Open Access).
  151. "Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set",
    Y. Tachino, K. Okuwaki, H. Doi, K. Akisawa, and Y. Mochizuki*, Jpn. J. Appl. Phys., 62 (2023) 090902-1-6 (Open Access).
  152. "Development of Reverse Mapping System Bridging Dissipative Particle Dynamics and Fragment Molecular Orbital Calculation",
    K. Okuwaki, H. Doi, T. Ozawa, and Y. Mochizuki*, Jpn. J. Appl. Phys., 62 (2023) 110902-1-4 (Open Access).
  153. "Enhancement of energy decomposition analysis in fragment molecular orbital calculations",
    S. Matsuoka, S. Sakakura, Y. Akinaga, K. Akisawa, K. Okuwaki, H. Doi, and Y. Mochizuki*, J. Comp. Chem., 45 (2024) 898-902.
  154. "Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations",
    Y. Handa, K. Okuwaki, Y. Kawashima, R. Hatada, Y. Mochizuki, Y. Komeiji, S. Tanaka, T. Furuishi, E. Yonemochi, T. Honma, and K. Fukuzawa, J. Phys. Chem. B, 128 (2024) 2249-2265.
  155. "Towards tailoring hydrophobic interaction with uranyl(VI) oxygen for C-H activation",
    S. Tsushima, J. Kretzschmar, H. Doi, K. Okuwaki, M. Kaneko, Y. Mochizuki, and K. Takao, Chem. Comm., 60 (2024) 4769-4772 (Open Access) [This article obtained the inside cover image of issue].

Proceedings

  1. "Theoretical study of the electronic structure of CO adsorbed on small Cu clusters",
    K. Tanaka, Y. Mochizuki, T. Kawaguchi, K. Ohno, and H. Tatewaki, in Microclusters: Proceedings of the first NEC symposium, Vol.4 of Springer Series in Materials Science , (1986) 82-86.
  2. "High scalability inherent in the ab initio molecular orbital method",
    Y. Hirahara, Y. Mochizuki, A. Yamamoto, H. Nakada, M. Tsuchiya, and T. Takada, in PDSC' 95 : Proceedings of the international symposium on parallel and distributed supercomputing, Fukuoka, Japan , (1995 Sep. 26-28) 277-284.
  3. "AMOSSWEB: ab initio molecular orbital calculation service system in the world-wide web environment",
    Y. Mochizuki, A. Yamamoto, Y. Hirahara, N. Okamoto, K. Nishizawa, Y. Okamoto, S. Handa, T. Sakuma, H. Nakada, T. Sano, K. Tsuda, and T. Takada, in Proceedings of the Cenju Workshop joined to HPC Asia 97 at Soul, Korea , (1997 Apr. 28) 92-96.
  4. "Ab initio FMO-MD Method Reimplemented and Applied to Pure Water",
    Y. Komeiji, T. Ishikawa, Y. Mochizuki, H. Yamataka, and T. Nakano, in Computation in Modern Science and Engineering - Proc. ICCMSE2007 (Simos, T. E, Maroulis, G., eds, AIP) , (2007) 1261-1264.
  5. "Groebner basis technique for algebraic formulas in electron correlation theories",
    T. Osoekawa, N. Shinohara, Y. Mochizuki, and K. Yokoyama, Proceeding of the 10th International Conference on Computational Science and Its Applications (ICCSA-2010), (2010) 17-23.
  6. "Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptide",
    T. Fujita, M. Kusa, T. Fujiwara, Y. Mochizuki, and S. Tanaka, In Advances in Quantum Monte Carlo, Ch. 15, 2012, ACS Symposium Series, 1094 (2012) 187-199.
  7. "Fragment molecular orbital-based molecular dynamics study on hydrated Ln(III) ions",
    T. Fujiwara, H. Mori, Y. Komeiji, and Y. Mochizuki*, CSW2014, JPS-Conf. Series 5 (2015) 011001-1-8.

Books

  1. Japanese translation of "Modern Quantum Chemistry" as "新しい量子化学 (上下)", 大野公男, 阪井健男, 望月祐志, (1987, 東京大学出版会).
  2. "Multireference Coupled Pair Approximation: A State-Universal Approach of a CEPA Type Variant of MRSDCI",
    K. Tanaka, T. Sakai, and Y. Mochizuki, in Recent Advances in Multireference Methods , edited by K. Hirao, (1999 World Scientific Publishing) 95-130.
  3. "Developments and Applications of ABINIT-MP Software Based on the Fragment Molecular Orbital Method",
    T. Nakano, Y. Mochizuki, K. Fukuzawa, S. Amari and S. Tanaka in Modern Methods for Theoretical Physical Chemistry of Biopolymers , edited by E. B. Starikov, S. Tanaka, and J. P. Lewis, (2006, Elsevier B.V., Amsterdam, The Netherlands) 39-52.
  4. "プログラムで実践する生体分子量子化学計算", 分担執筆, 佐藤文俊・中野達也・望月祐志 編, (2008年10月刊、森北出版).
  5. "Excited states of photoactive proteins by configuration interaction studies",
    Y. Mochizuki*, N. Taguchi, T. Nakano, and S. Tanaka &
    "Developments of FMO methodology and graphical user interface in ABINIT-MP",
    T. Nakano, Y. Mochizuki, A. Kato, K. Fukuzawa, T. Ishikawa, S. Amari, I. Kurisaki, and S. Tanaka &
    "Application of FMO method to specific molecular recognition of bio-macromolecules",
    K. Fukuzawaa, Y. Mochizuki, T. Nakano, and S. Tanaka, in The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems, edited by K. Kitaura and D. G. Fedorov (2009, Boca Raton, CRC press).
  6. "フラグメント分子軌道法と分子動力学シミュレーション", 望月祐志, 古明地勇人, 『レアメタル・希少金属リサイクル技術の最先端』（フロンティア出版, 2011） pp.187-204.
  7. "FMO計算によるマルチスケールシミュレーション手法の開発と材料開発への応用", 望月祐志, 奥脇弘次, 土居英男, 小沢拓, 『マテリアルズ・インフォマティクスによる材料開発と活用事例』（技術情報協会, 2019） pp.237-245.
  8. Recent Advances of the Fragment Molecular Orbital Method - Enhanced Performance and Applicability
    Y. Mochizuki (main editor), S. Tanaka & K. Fukuzawa (sub editors), (January 2021, Springer).
  9. "The ABINIT-MP Program",
    Y. Mochizuki*, T. Nakano, K. Sakakura, Y. Okiyama, H. Watanabe, K. Kato, Y. Akinaga, S. Sato, J. Yamamoto, K. Yamashita, T. Murase, T. Ishikawa, Y. Komeiji, Y. Kato, N. Watanabe, T. Tsukamoto, H. Mori, K. Okuwaki, S. Tanaka, A. Kato, C. Watanabe, and K. Fukuzawa (pp. 53-67) &
    "Modeling of Solid and Surface",
    K. Kato, A. Hashimoto, E. Tamiya, K. Fukuzawa, Y. Ishikawa, and Y. Mochizuki (pp. 407-424) &
    "Extension to Multiscale Simulations",
    K. Okuwaki, T. Ozawa, and Y. Mochizuki (pp. 529-546), in Recent Advances of the Fragment Molecular Orbital Method - Enhanced Performance and Applicability, (January 2021, Springer).

Sundries

  1. "Development of integral transformation modules for correlated calculations",
    Y. Mochizuki and U. Nagashima, J. Comp. Chem. Jpn., 3 (2004) 1-12 (in Japanese).
  2. Private review (in Japanese) "米欧日の量子化学ソフトウェアの現状と今後の展望", 望月祐志, (2004年5月 初: 10月 改). 『21世紀の産業革命　コンピュータ・シミュレーション（戦略的基盤ソフトウェア産業応用推進協議会編）』, 2005, アドバンスソフト刊 5.1.4節に収録.
  3. "量子化学計算（FMO法）",
    中野達也, 望月祐志, 甘利真司, 福澤薫, 東京大学情報基盤センター『スーパーコンピューティングニュース』, Vol.8 (2006) 63-74.
  4. "BioStation Viewer：生体高分子の相互作用解析と可視化",
    加藤昭史, 福澤薫, 望月祐志, 甘利真司, 中野達也, 可視化情報学会誌, 26 (2006) 124-129.
  5. "エストロゲン受容体のアミノ酸変異によるエストラジオール結合エネルギーの変化",
    前田紘輔, Alexander Schug, 渡邉博文, 福澤薫, 望月祐志, 中野達也, 田中成典, J. Comp. Chem. Jpn., 6 (2007) 33-46.
  6. "Frontier Simulation Software for Industrial Science",
    Makoto Tsubokura, Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Kenji Yamagishi, Hiroaki Tokiwa, Tatsuya Nakano, Takenori Yamamoto, and Takahisa Ohno, Annual Report of the Earth Simulator Center April 2005 - March 2006, (2007) 299-304.
  7. "フラグメント分子軌道法に基づいた生体巨大分子の電子状態計算の現状と今後の展望"【査読有】,
    中野達也, 望月祐志, 甘利真司, 小林将人, 福澤薫, 田中成典, J. Comp. Chem. Jpn., 6 (2007) 173-184.
  8. "フラグメント分子軌道法による生体高分子の応用計算"【査読有】,
    福澤薫, 中野達也, 加藤昭史, 望月祐志, 田中成典, J. Comp. Chem. Jpn., 6 (2007) 185-198.
  9. "フラグメント分子軌道法によるホタルルシフェラーゼの発光特性に関する理論的研究"【査読有】,
    田上歩, 石橋延裕, 加藤太一郎, 田口尚貴, 望月祐志, 渡邉博文, 伊藤三香, 田中成典, J. Comp. Aided Chem. 9 (2008) 47-54.
  10. "Continuous multipole methodによるfragment molecular orbital法の高速化"【査読有】,
    中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 渡邊千鶴, 福澤薫, 田中成典, 望月祐志, J. Comp. Aided Chem., 13 (2012) 44-50.
  11. "計算科学ロードマップ白書", FMO関係部分-執筆, 望月祐志*, (2012). (PDF)
  12. "FMO法における電子相関計算", 望月祐志*, 日本化学会・情報部会誌, 31 (2013) 64-72. (PDF)
  13. "フラグメント分子軌道法によるインフルエンザウイルス表面タンパク質の大規模量子化学計算",
    福澤薫, 望月祐志, 中野達也, 田中成典, CBI学会誌, 1 (2013) 25-31.
  14. "Structure-based drug designを指向した新規フラグメント分割法に基づく4体補正フラグメント分子軌道(FMO4)計算",
    渡邉千鶴, 福澤薫, 沖山佳生, 望月祐志, 塚本貴志, 加藤昭史, 田中成典, 中野達也, CBI学会誌, 1 (2013) 32-41.
  15. "Cartesian Gaussianの積分の初期積分の計算",
    中野達也, 山下勝美, 瀬川勝智, 沖山佳生, 望月祐志, CBI学会誌, 1 (2013) 42-46.
  16. "計算科学ロードマップ白書 第二版", FMO関係部分-執筆, 望月祐志*, (2014). (PDF)
  17. "フラグメント分子軌道法を用いたspin-component-scaled MP2法に基づくタンパク－リガンド相互作用クラスター解析",
    甘利真司, 望月祐志, 加藤昭史, 福澤薫, 渡邉千鶴, 沖山佳生, 田中成典, 中野達也, CBI学会誌 2 (2014) 17-25.
  18. "相互作用エネルギー成分分割解析機能PIEDAの実装とタンパク質-リガンド間の相互作用解析"【査読有】,
    塚本貴志, 加藤幸一郎, 加藤昭史, 中野達也, 望月祐志, 福澤薫, J. Com. Chem. Jpn., 14 (2015) 1-9.
  19. "赤色蛍光タンパク質 DsRed の色素部周辺における水分子ならびに隣接アミノ酸残基の構造の励起エネルギーへの影響評価"【査読有】,
    坂口正貴, 望月祐志*, 渡邉千鶴, 福澤薫, J. Comp. Chem. Jpn., 14 (2015) 155-163.
  20. "ペプトイド類のフラグメント分子軌道計算"【査読有】,
    川田修太郎, 坂口正貴, 米倉伊吹, 奥脇弘次, 望月祐志, 福澤薫, J. Comp. Chem. Jpn.,15 (2016) 51-52.
  21. "化学・生命科学系の理学教育における3Dプリンタの活用事例"【査読有】,
    望月祐志*, 中村昇太, 山中正浩, 山田康之, 工藤光子, 常盤広明, 川上勝, 北本俊二, J. Com. Chem. Jpn., 15 (2016) 65-67.
  22. "C5Ch5およびC6Ch6 (Ch=S, Se, Te)の分子構造と芳香族性の評価"【査読有】,
    川田修太郎, 望月祐志*, 中野克洋, J. Comp. Chem. Jpn., 15 (2016) 87-91.
  23. "Intel Xeon Phi上でのSMASHによる並列化DFT計算の性能評価"【査読有】,
    齊藤天菜，望月祐志*，山崎大，石村和也, J. Comp. Chem. Jpn. 15 (2016) 92-96.
  24. "散逸粒子動力学におけるシリカ－脂質膜界面付近の水の取扱い"【査読有】,
    土居英男, 奥脇弘次, 望月祐志, 小沢拓, J. Comp. Chem. Jpn. 16 (2017) 28-31.
  25. "フラグメント分子軌道(FMO)計算の結果の自動解析の試み"【依頼】,
    望月祐志*, 奥沢明, 計算工学学会誌, 22 (2017) 3539-3542.
  26. "計算科学ロードマップ白書 第三版", FMO＆DPD関係部分-執筆, 望月祐志*, (2017). (HP)
  27. "ベンゼンを基本骨格に持つ正イオン内包ペプトイドの理論的計算"【査読有】,
    川田修太郎, 袴田真由, 望月祐志, J. Comp. Chem. Jpn., 16 (2017) 77-79.
  28. "Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試み"【査読有】,
    中野達也, 望月祐志*, 福澤薫, 沖山佳生, 渡邉千鶴, J. Comp. Aided Chem., 18 (2017) 143-148.
  29. "FMOプログラムABINIT-MPの開発状況と機械学習との連携"【査読有】,
    望月祐志*, 坂倉耕太, 秋永宜伸, 加藤幸一郎, 渡邊啓正, 沖山佳生, 中野達也, 古明地勇人,奥沢明, 福澤薫, 田中成典, J. Comp. Chem. Jpn., 16 (2017) 119-122.
  30. "散逸粒子動力学(DPD)プログラムCAMUSの新規開発と性能評価"【査読有】,
    土居英男, 齊藤天菜, 奥脇弘次, 内藤貴充, 望月祐志, J. Comp. Chem. Jpn., 16 (2017) 126-128.
  31. "フラグメント分子軌道(FMO)法を用いた散逸粒子動力学シミュレーションのための有効相互作用パラメータ算出の自動化フレームワーク"【査読有】,
    奥脇弘次, 土居英男, 望月祐志, J. Comp. Chem. Jpn., 17 (2018) 102-109 [2018年度 日本コンピュータ化学会論文賞(吉田賞)].
  32. "AIを活用した流体解析シミュレーション技術の開発",
    小杉範仁, 近藤修司, 秋永宜伸、望月祐志, 機械設計, 2018年7月号, 62 (2018) 42-46.
  33. "X線小角散乱と散逸粒子動力学法を用いた脂質膜およびベシクル形成メカニズムの解明"【査読有】,
    新庄永治, 奥脇弘次, 土居英男, 望月祐志, 古石誉之, 福澤薫, 米持悦生, J. Comp. Chem. Jpn., 17 (2018) 172-179.
  34. "大学初年度向け化学教育のためのScratchプログラムの開発"【査読有】,
    満野仁美, 中川知樹, 土居英男, 望月祐志*, J. Comp. Chem. Jpn., 17 (2018) 111-112.
  35. "FMO計算-粗視化シミュレーション連携手法の開発と応用"【査読有】,
    奥脇弘次, 土居英男, 望月祐志, 小沢拓, 泰岡顕治, 福澤薫, J. Comp. Chem. Jpn., 17 (2018) 144-146
  36. "FMOプログラムABINIT-MPのOakForest-PACS上での多層並列化と性能評価"【査読有】,
    渡邊啓正, 佐藤伸哉, 坂倉耕太, 齊藤天菜, 望月祐志, J. Comp. Chem. Jpn., 17 (2018) 147-149.
  37. "Bond detached atom (BDA)を共有しているフラグメント間の相互作用エネルギーの補正に関する試みII：ラジカル開裂補正"【査読有】,
    中野達也, 望月祐志, 福澤薫, 沖山佳生, 渡邉千鶴, J. Comp. Aided Chem., 20 (2019) 1-6.
  38. "(ワークショップ報告書) 科学技術未来戦略ワークショップ報告書 みんなの量子コンピューター ～情報・数理・物理で拓く新しい量子アプリ～／CRDS-FY2018-WR-09",
    望月祐志 (量子化学関係でコミット). (HP)
  39. "機械学習によるテキスト処理ツールの開発と応用"【査読有】,
    亘理結香, 奥脇弘次, 望月祐志*, J. Comp. Chem. Jpn., 18 (2019) 123-125.
  40. "Scratchを経由する機械学習教材の開発の試み"【査読有】,
    満野仁美, 奥脇弘次, 伊藤雅仁, 望月祐志*, J. Comp. Chem. Jpn., 18 (2019) 126-128.
  41. "ABINIT-MP Openシリーズの最新の開発状況について"【査読有】,
    望月祐志*, 秋永宜伸, 坂倉耕太, 渡邊啓正, 加藤幸一郎, 渡辺尚貴, 奥脇弘次, 中野達也, 福澤薫, J. Comp. Chem. Jpn., 18 (2019) 129-131.
  42. "転移学習と生成ネットワークの試行事例"【査読有】,
    伊藤雅仁, 篠嶋友也, 望月祐志*, 秋永宜伸, 小杉範仁, J. Comp. Chem. Jpn., 18 (2019) 132-135.
  43. "深層学習とシミュレーションの連携事例"【依頼】,
    伊藤雅仁, 遠藤克浩, 望月祐志*, 泰岡顕治*, 計算工学学会誌, 24 (2019) 3983-3987.
  44. "カルサイト・ハイドロキシアパタイト結晶表面とペプチドのFMO相互作用解析"【査読有】,
    畑田崚, 加藤幸一郎, 奥脇弘次, 福澤薫, 望月祐志, J. Comp. Chem. Jpn., 19 (2020) 1-7.
  45. "新型コロナウイルスのタンパク質に対するフラグメント分子軌道計算による解析事例 "【依頼】,
    望月祐志*, 応用物理学会 特設コラム, (2021). (HP)
  46. "フラグメント分子軌道（FMO）法、ならびに散逸粒子動力学（DPD）シミュレーションとの連携"【依頼&査読有】,
    望月祐志*, 奥脇弘次, 応用物理学会誌, 89 (2020) 566-572.
  47. "新型コロナウイルスタンパク質のフラグメント分子軌道計算"【依頼】,
    望月祐志*, 現代化学, 596 (2020) 34-35.
  48. "新型コロナウイルスのタンパク質に関するフラグメント分子軌道計算の事例"【依頼】,
    望月祐志*, 奥脇弘次, 計算工学学会誌, 26 (2021) 4204-4209.
  49. "FMOプログラムABINIT-MPの整備状況2020"【査読有】,
    望月祐志*, 坂倉耕太, 渡邊啓正, 奥脇弘次, 加藤幸一郎, 渡辺尚貴, 沖山佳生, 福澤薫, 中野達也, J. Comp. Chem. Jpn., 19 (2020) 142-145.
  50. "種々の科学データにおける機械学習を用いた分析の試み"【査読有】,
    奥脇弘次, 増田淳希, 柿沼紗也果, 長谷川貴一, 水野寛哉, 満野仁美, 伊藤雅仁, 藤方玲衣, 望月祐志, J. Comp. Chem. Jpn., 19 (2020) A21-A24.
  51. "FMOプログラムABINIT-MPの整備状況2021"【査読有】,
    望月祐志*, 中野達也, 佐藤伸哉, 坂倉耕太, 渡邊啓正, 奥脇弘次, 大島聡史, 片桐孝洋, J. Comp. Chem. Jpn., 20 (2021) 132-136.
  52. "量子コンピュータを利用したタンパク質の畳み込みモデル"【査読有】,
    齊藤瑠偉, 奥脇弘次, 望月祐志*, 永井隆太郎, 加藤拓己, 杉﨑研司, 湊雄一郎, J. Comp. Chem. Jpn., 21 (2022) 39-42.
  53. "量子アプリケーション"【依頼】,
    杉﨑研司, 望月祐志, 映像情報メディア学会誌, 77 (2023) 43-48.
  54. "FMOプログラムABINIT-MPの整備状況2022"【査読有】,
    望月祐志*, 中野達也, 坂倉耕太, 渡邊啓正, 佐藤伸哉, 奥脇弘次, 秋澤和輝, 土居英男, 大島聡史，片桐孝洋, J. Comp. Chem. Jpn., 21 (2022) 106-110.
  55. "「富岳」時代のフラグメント分子軌道計算"【依頼】,
    望月祐志*, 「化学」, 78 (2023年8月号) 12-15.
  56. "タンパク質に関するFMO-DPD シミュレーション用パラメータ算定と試行"【査読有】,
    太刀野雄介, 土居英男, 奥脇弘次, 平野秀典, 望月祐志*, J. Comp. Chem. Jpn., 22 (2023) 15-17.
  57. "計算科学ロードマップ2023", FMO関係部分-執筆と取り纏め, 望月祐志*, (2023). (HP)
  58. "FMOプログラムABINIT-MPの整備状況2023"【査読有】,
    望月祐志*, 中野達也, 坂倉耕太, 奥脇弘次, 土居英男, 加藤季広, 滝沢寛之, 成瀬彰, 大島聡史, 星野哲也, 片桐孝洋, J. Comp. Chem. Jpn., 23 (2024) 4-8.