Large-scale FMO-MP2 calculations of the spike protein droplet model Peer-reviewed International journal

Hideo Doi, Tatsuya Nakano, Kota Sakakura, Kazuki Akisawa, Koji Okuwaki, Yoshinori Hirano, Eiji Yamamoto, Kenji Yasuoka, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki

J. Comp. Chem.46   e70052   5 2 2025

Geometry Optimization Using the Frozen Domain and Partial Dimer Approaches in the Fragment Molecular Orbital Method: Implementation, Benchmark, and Applications to Protein Ligand-Binding Sites Peer-reviewed

Koji Okuwaki, Naoki Watanabe, Koichiro Kato, Chiduru Watanabe, Naofumi Nakayama, Akifumi Kato, Yuji Mochizuki, Tatsuya Nakano, Teruki Honma, Kaori Fukuzawa

Journal of Chemical Information and Modeling64 ( 24 ) 9449 - 9458   2 12 2024

Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital-based Molecular Dynamics (FMO-MD) Simulation Peer-reviewed

Tatsuya NAKANO, Yoshio OKIYAMA, Katsunori SEGAWA, Yoshiro SAITO, Yuji MOCHIZUKI, Yuto KOMEIJI

Journal of Computer Chemistry, Japan -International Edition10 ( 2023-0038 ) 1 - 8   10 2024

DPD simulation to reproduce lipid membrane microdomains based on fragment molecular orbital calculations Peer-reviewed

Hideo Doi, Yushi Osada, Yusuke Tachino, Koji Okuwaki, Melvin Wei Shern Goh, Ryugo Tero, Yuji Mochizuki

Applied Physics Express17   055001   5 2024

Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme Peer-reviewed International journal

Kenji Sugisaki, Tatsuya Nakano, Yuji Mochizuki

J. Comp. Chem.45   2204 - 2213   5 2024

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 Peer-reviewed International journal

Yuma Handa, Koji Okuwaki, Yusuke Kawashima, Ryo Hatada, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka, Takayuki Furuishi, Etsuo Yonemochi, Teruki Honma, Kaori Fukuzawa

The Journal of Physical Chemistry B128 ( 10 ) 2249 - 2265   4 3 2024

Towards tailoring hydrophobic interaction with uranyl(VI) oxygen for C-H activation Peer-reviewed International journal

Satoru Tsushima, Jérôme Kretzschmar, Hideo Doi, Koji Okuwaki, Masashi Kaneko, Yuji Mochizuki, Koichiro Takao

Chem. Comm.60   4769 - 4772   3 2024

Enhancement of energy decomposition analysis in fragment molecular orbital calculations Peer-reviewed International journal

Sota Matsuoka, Kota Sakakura, Yoshinobu Akinaga, Kazuki Akisawa, Koji Okuwaki, Hideo Doi, Yuji Mochizuki

J. Comp. Chem.45   898 - 902   3 2024

Development of reverse mapping system bridging dissipative particle dynamics and fragment molecular orbital calculation Peer-reviewed

Koji Okuwaki, Hideo Doi, Taku Ozawa, Yuji Mochizuki

Japanese Journal of Applied Physics62 ( 11 ) 110902   23 10 2023

Bayesian phase difference estimation algorithm for direct calculation of fine structure splitting: accelerated simulation of relativistic and quantum many-body effects Peer-reviewed

Kenji Sugisaki, Srinivasa Prasannaa, Satoshi Ohshima, Takahiro Katagiri, Yuji Mochizuki, Bijaya Kumar Sahoo, Bhanu Pratap Das

Electronic Structure5 ( 3 ) 035006   12 9 2023

Dissipative particle dynamics simulation for peptoid nanosheet with non-empirical parameter set Peer-reviewed

Yusuke Tachino, Koji Okuwaki, Hideo Doi, Kazuki Akisawa, Yuji Mochizuki

Japanese Journal of Applied Physics62 ( 9 ) 090902   23 8 2023

Machine learning to improve efficiency of non-empirical interaction parameter for dissipative particle dynamics (DPD) simulation Peer-reviewed

Hideo Doi, Sota Matsuoka, Koji Okuwaki, Ryo Hatada, Soujiro Minami, Ryosuke Suhara, Yuji Mochizuki

Japanese Journal of Applied Physics62 ( 7 ) 070901   7 7 2023

Bifurcated Hydrogen Bonds in a Peptide Crystal Unveiled by X-ray Diffraction and Polarized Raman Spectroscopy Peer-reviewed

Kazunori Motai, Nao Koishihara, Takuma Narimatsu, Hiroyoshi Ohtsu, Masaki Kawano, Yuki Wada, Kazuki Akisawa, Koji Okuwaki, Takehiko Mori, Ji-Seon Kim, Yuji Mochizuki, Yuhei Hayamizu

Crystal Growth & Design23 ( 6 ) 4556 - 4561   10 5 2023

Practical Computational Chemistry Course for a Comprehensive Understanding of Organic, Inorganic, and Physical Chemistry: From Molecular Interactions to Chemical Reactions Peer-reviewed International journal

Nahoko Kuroki, Yuji Mochizuki, Hirotoshi Mori

J. Chem. Educ.100 ( 2 ) 647 - 654   4 1 2023

Lattice Folding Simulation of Peptide by Quantum Computation Peer-reviewed

Rui SAITO, Koji OKUWAKI, Yuji MOCHIZUKI, Ryutaro NAGAI, Takumi KATO, Kenji SUGISAKI, Yuichiro MINATO

Journal of Computer Chemistry, Japan -International Edition9 ( 2022 ) 2036   2023

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 Peer-reviewed International journal

Kenji Sugisaki, Takumi Kato, Yuichiro Minato, Koji Okuwaki, Yuji Mochizuki

Phys. Chem. Chem. Phys.24   8439 - 8452   15 3 2022

Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method Peer-reviewed

K. Okuwaki, K. Akisawa, R. Hatada, Y. Mochizuki, K. Fukuzawa, Y. Komeiji, S. Tanaka

Applied Physics Express15   017001   24 12 2021

Interaction Analysis on the SARS-CoV-2 Spike Protein Receptor Binding Domain Using Visualization of the Interfacial Electrostatic Complementarity Peer-reviewed

Takeshi Ishikawa, Hiroki Ozono, Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki

J. Phys. Chem. Lett.12   11267 - 11272   12 11 2021

Fragment Molecular Orbital Based Interaction Analyses on Complexes Between SARS-CoV-2 RBD Variants and ACE2 Peer-reviewed

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Shun Kitahara, Yusuke Tachino, Yuji Mochizuki, Yuto Komeiji, Shigenori Tanaka

Jpn. J. Appl. Phys.60 ( 9 ) 090901   13 8 2021

Towards Accurate Description of Chemical Reaction Energetics by Using Variational Quantum Eigensolver: A Case Study of the C2v Quasi-Reaction Pathway of Beryllium Insertion to H2 Molecule

Kenji Sugisaki, Takumi Kato, Yuichiro Minato, Koji Okuwaki, Yuji Mochizuki

    25 6 2021

Dynamical Cooperativity of Ligand-Residue Interactions Evaluated with the Fragment Molecular Orbital Method Peer-reviewed

Shigenori Tanaka, Shusuke Tokutomi, Ryo Hatada,, Koji Okuwaki, Kazuki Akisawa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki

J. Phys. Chem. B125 ( 24 ) 6501 - 6512   14 6 2021

Density-Matrix Based Scheme of Basis Selection for Linear Combination of Fragment Molecular Orbitals Peer-reviewed International journal

Yoshio Okiyama, Yuji Mochizuki, Masanori Yamanaka, Shigenori Tanaka

J. Phys. Soc. Jpn.90 ( 6 ) 064301 - 064301   5 2021

分子動力学計算とFMO計算を用いたSARS-CoV-2メインプロテアーゼと既存薬との結合性予測

半田 佑磨, 川嶋 裕介, 畑田 崚, 奥脇 弘次, 望月 祐志, 古明地 勇人, 田中 成典, 本間 光貴, 古石 誉之, 福澤 薫, 米持 悦生

日本薬学会年会要旨集141年会   27V04 - am12S   3 2021

Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations Peer-reviewed International journal

Kazuki Akisawa, Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

RSC Advances11 ( 6 ) 3272 - 3279   14 1 2021

Statistical interaction analyses between SARS-CoV-2 main protease and inhibitor N3 by combining molecular dynamics simulation and fragment molecular orbital calculation Peer-reviewed

Ryo Hatada, Koji Okuwaki, Kazuki Akisawa, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Applied Physics Express14   027003   1 2021

Extension to Multiscale Simulations Invited

Koji Okuwaki, Taku Ozawa, Yuji Mochizuki

Recent Advances of the Fragment Molecular Orbital Method   529 - 546   1 2021

Modeling of Solid and Surface

Koichiro Kato, Aya Hashimoto, Eiichi Tamiya, Kaori Fukuzawa, Yuichiro Ishikawa, Yuji Mochizuki

Recent Advances of the Fragment Molecular Orbital Method   407 - 424   1 2021

The ABINIT-MP Program Invited

Yuji Mochizuki, Tatsuya Nakano, Kota Sakakura, Yoshio Okiyama, Hiromasa Watanabe, Koichiro Kato, Yoshinobu Akinaga, Shinya Sato, Jun-inchi Yamamoto, Katsumi Yamashita, Tadashi Murase, Takeshi Ishikawa, Yuto Komeiji, Yuji Kato, Naoki Watanabe, Takashi Tsukamoto, Hirotoshi Mori, Koji Okuwaki, Shigenori Tanaka, Akifumi Kato, Chiduru Watanabe, Kaori Fukuzawa

Recent Advances of the Fragment Molecular Orbital Method   53 - 67   1 2021

Acceleration of Environmental Electrostatic Potential Using Cholesky Decomposition with Adaptive Metric (CDAM) for Fragment Molecular Orbital (FMO) Method Peer-reviewed

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuto Komeiji, Katsunori Segawa, Yuji Mochizuki

Bull. Chem. Soc. Jpn.94 ( 1 ) 91 - 96   1 2021

Fragment Molecular Orbital Based Interaction Analyses on COVID-19 Main Protease - Inhibitor N3 Complex (PDB ID: 6LU7). Peer-reviewed International journal

Ryo Hatada, Koji Okuwaki, Yuji Mochizuki, Yuma Handa, Kaori Fukuzawa, Yuto Komeiji, Yoshio Okiyama, Shigenori Tanaka

Journal of chemical information and modeling60 ( 7 ) 3593 - 3602   25 6 2020

Self-Degradable Lipid-Like Materials Based on "Hydrolysis accelerated by the intra-Particle Enrichment of Reactant (HyPER)" for Messenger RNA Delivery Peer-reviewed

Hiroki Tanaka, Tatsunari Takahashi, Manami Konishi, Nae Takata, Masaki Gomi, Daiki Shirane, Ryo Miyama, Shinya Hagiwara, Yuki Yamasaki, Yu Sakurai, Keisuke Ueda, Kenjirou Higashi, Kunikazu Moribe, Eiji Shinsho, Ruka Nishida, Kaori Fukuzawa, Etsuo Yonemochi, Koji Okuwaki, Yuji Mochizuki, Yuta Nakai, Kota Tange, Hiroki Yoshioka, Shinya Tamagawa, Hidetaka Akita

ADVANCED FUNCTIONAL MATERIALS30 ( 34 ) 1910575-1 - 1910575-17   6 2020

小角X線散乱と分子シミュレーションを融合したDOPC/Cholesterol二重膜の物性解析

新庄 永治, 西田 瑠花, 奥脇 弘次, 望月 祐志, 古石 誉之, 福澤 薫, 米持 悦生

日本薬学会年会要旨集140年会   27Y - pm04S   3 2020

Fragmentation at sp2 carbon in fragment molecular orbital (FMO) method Peer-reviewed

Yoshinobu Akinaga, Kouichiro Kato, Tatsuya Nakano, Kaori Fukuzawa, Yuji Mochizuki

J. Comp. Chem.41   1416 - 1420   3 2020

Ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of (NH3)32 cluster: effects of electron correlation Peer-reviewed

Moeko Ninomiya, Hideo Doi, Yoshiteru Matsumoto, Yuji Mochizuki, Yuto Komeiji

Bulletin of the Chemical Society of Japan93 ( 4 ) 553 - 560   2 2020

Interaction Analyses between Calcite/Apatite and Peptides by Fragment Molecular Orbital Method Peer-reviewed

Ryo HATADA, Kouichiro KATO, Koji OKUWAKI, Kaori FUKUZAWA, Yuji MOCHIZUKI

Journal of Computer Chemistry, Japan19 ( 1 ) 1 - 7   2020

Stabilization Mechanism for a Nonfibrillar Amyloid β Oligomer Based on Formation of a Hydrophobic Core Determined by Dissipative Particle Dynamics Peer-reviewed

Ryoko Kawai, Shuntaro Chiba, Koji Okuwaki, Ryo Kanada, Hideo Doi, Masahiro Ono, Yuji Mochizuki, Yasushi Okuno

ACS Chemical Neuroscience20 ( 11 ) 385 - 394   1 2020

Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations Peer-reviewed

Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

Applied Physics Express13   017002   1 2020

Interaction between calcite and adsorptive peptide analyzed by fragment molecular orbital method Peer-reviewed

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

Japanese Journal of Applied Physics58 ( 12 ) 120906 - 120906   1 12 2019

Reduction of Orbital Space for Molecular Orbital Calculations with Quantum Computation Simulator for Educations

Yuji Mochizuki Koji Okuwaki Takumi Kato Yuichiro Minato

ChemRxiv   9 2019

Cm3+/Eu3+ induced structural, mechanistic and functional implications for calmodulin Peer-reviewed

Björn Drobot, Moritz Schmidt, Yuji Mochizuki, Takaya Abe, Koji Okuwaki, Florian Brulfert, Sven Falke, Sergey A. Samsonov, Yuto Komeiji, Christian Betzel, Thorsten Stumpf, Johannes Raff, Satoru Tsushima

Phys. Chem. Chem. Phys.21 ( 38 ) 21213 - 21222   8 2019

物性測定とFMO-DPD法による脂質微粒子の構造解析 Peer-reviewed

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

日本DDS学会学術集会プログラム予稿集35回   135 - 135   6 2019

小角X線散乱測定とFMO-DPDシミュレーションによる脂質/Cholesterol混合二重膜における物性の解析 Peer-reviewed

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

日本薬学会年会要旨集139年会 ( 4 ) 80 - 80   3 2019

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies Peer-reviewed

Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

The Journal of Physical Chemistry B123 ( 5 ) 957 - 973   7 2 2019

Destabilization of DNA through interstrand crosslinking by UO22+ Peer-reviewed

Andr{\'{e } } Rossberg, Takaya Abe, Koji Okuwaki, Astrid Barkleit, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Satoru Tsushima

Chemical Communications55 ( 14 ) 2015 - 2018   2 2019

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 Peer-reviewed

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 ( 4 ) 172 - 179   1 2019

A Radical Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA) Peer-reviewed

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry20 ( 0 ) 1 - 6   2019

Development of an Analysis Toolkit, AnalysisFMO, to Visualize Interaction Energies Generated by Fragment Molecular Orbital Calculations Peer-reviewed

Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, Yasuteru Shigeta

Journal of Chemical Information and Modeling59 ( 1 ) 25 - 30   1 2019

Deeper Level Parallelization and Performance Evaluation ofFMO Program ABINIT-MP on Oakforest-PACS Invited Peer-reviewed

MOCHIZUKI Yuji

J. Comp. Chem. Jpn.17   147 - 149   11 2018

Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method Peer-reviewed

Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

Bulletin of the Chemical Society of Japan91 ( 11 ) 1596 - 1605   11 2018

<b>Accuracy of Dimer-ES Approximation on Fragment Molecular Orbital (FMO) Method</b><b> </b> Peer-reviewed

Tatsuya Nakano, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe, Yuto Komeiji, Yuji Mochizuki

Chem-Bio Informatics Journal18 ( 0 ) 119 - 122   5 10 2018

Theoretical Analyses on Water Cluster Structures in Polymer Electrolyte Membrane by Using Dissipative Particle Dynamics Simulations with Fragment Molecular Orbital Based Effective Parameters Peer-reviewed

Okuwaki Koji, Mochizuki Yuji, Doi Hideo, Kawada Shutaro, Ozawa Taku, Yasuoka Kenji

RSC Advances8 ( 60 ) 34582 - 34595   10 2018

RI-MP3 calculations of biomolecules based on the fragment molecular orbital method Peer-reviewed

Journal of Computer Chemistry, Japan39   1970 - 1978   9 2018

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62   42 - 46   7 2018

A portable code for dissipative particle dynamics (DPD) simulations with additional specific interactions Peer-reviewed

Okuwaki Koji, Naito Takamitsu, Saitou Sona, Mochizuki Yuji, other

Chem-Bio Informatics Journal   6 2018

Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study Peer-reviewed

Yoshio Okiyama, Tatsuya Nakano, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

The Journal of Physical Chemistry B122 ( 16 ) 4457 - 4471   26 4 2018

Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems Peer-reviewed

Takatoshi Fujita, Yuji Mochizuki

Journal of Physical Chemistry A122 ( 15 ) 3886 - 3898   19 4 2018

Development and Performance Evaluation of a Simulation Code for Dissipative Particle Dynamics (DPD) CAMUS Peer-reviewed

Doi Hideo, Saitou Sona, Okuwaki Koji, Naito Takamitsu, Mochizuki Yuji

Journal of Computer Chemistry, Japan16 ( 5 ) 126   2 2018

An automated framework to evaluate effective interactionparameters for dissipative particle dynamics simulations basedon the fragment molecular orbital (FMO) method Peer-reviewed

Okuwaki Koji, Doi Hideo, Mochizuki Yuji

Journal of Computer Chemistry, Japan17 ( 2 ) 102   2 2018

Fragment Molecular Orbital Based Parametrization Procedure for Mesoscopic Structure Prediction of Polymeric Materials Peer-reviewed

Koji Okuwaki, Yuji Mochizuki, Hideo Doi, Taku Ozawa

Journal of Physical Chemistry B122 ( 1 ) 338 - 347   11 1 2018

FMO計算-粗視化シミュレーション連携手法の開発と応用 Peer-reviewed

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   144 - 146   2018

大学初年度向け化学教育のためのScratchプログラムの開発 Peer-reviewed

満野仁美, 中川知樹, 土居英男, 望月祐志

J. Comp. Chem. Jpn.17   111 - 112   2018

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 Peer-reviewed

奥脇弘次, 土居英男, 望月祐志

J. Comp. Chem. Jpn.17   102 - 109   2018

Application of tensorflow to recognition of visualized results of fragment molecular orbital (FMO) calculations Peer-reviewed

Sona Saitou, Jun Iijima, Mayu Fujimoto, Yuji Mochizuki, Koji Okuwaki, Hideo Doi, Yuto Komeiji

Chem-Bio Informatics Journal18   58 - 69   1 1 2018

Development and Application of FMO Calculation − DPD Simulation Conbination Scheme Peer-reviewed

Okuwaki Koji, Doi Hideo, Mochizuki Yuji, Ozawa Taku, Yasuoka Kenji, Fukuzawa Kaori

Journal of Computer Chemistry, Japan17 ( 3 ) 144   2018

Formation Mechanism of Lipid Membrane and Vesicle Using Small Angle X-ray Scattering and Dissipative Particle Dynamics (DPD) Method Peer-reviewed

Eiji Shinsho, Koji Okuwaki, Hideo Doi, Yuji Mochizuki, Takayuki Furuishi, Kaori Fukuzawa, Etsuo Yonemochi

JOURNAL OF COMPUTER CHEMISTRY-JAPAN17 ( 4 ) 172 - 179   2018

Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane Peer-reviewed

Hideo Doi, Koji Okuwaki, Yuji Mochizuki, Taku Ozawa, Kenji Yasuoka

CHEMICAL PHYSICS LETTERS684   427 - 432   9 2017

Theoretical Calculations on Cation-capturing ofMacrocyclic Peptoid with Phenyl Rings in Main Chain Peer-reviewed

Kawada Shutaro, Hakamata Mayu, Mochizuki Yuji

Journal of Computer Chemistry, Japan16 ( 3 ) 77   8 2017

A New Treatment for Water near the Interface between Lipid Membrane and Silica in Dissipative Particle Dynamics Simulation Peer-reviewed

Doi Hideo, Okuwaki Koji, Mochizuki Yuji, Ozawa Taku

Journal of Computer Chemistry, Japan16 ( 1 ) 28   4 2017

Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme Peer-reviewed

Haruka Yamada, Yuji Mochizuki, Kaori Fukuzawa, Yoshio Okiyama, Yuto Komeiji

Computational and Theoretical Chemistry1101   46 - 54   2 2017

Current Status of ABINIT-MP as a FMO Program and Related Works with Machine Learning Peer-reviewed

Yuji MOCHIZUKI, Kota SAKAKURA, Yoshinobu AKINAGA, Kouichiro KATO, Hiromasa WATANABE, Yoshio OKIYAMA, Tatsuya NAKANO, Yuto KOMEIJI, Akira OKUSAWA, Kaori FUKUZAWA, Shigenori TANAKA

Journal of Computer Chemistry, Japan16 ( 5 ) 119 - 122   2017

A Preliminary Study of Correction for Inter Fragment Interaction Energy (IFIE) between Fragments Sharing Bond Detached Atom (BDA) Peer-reviewed

Tatsuya Nakano, Yuji Mochidzuki, Kaori Fukuzawa, Yoshio Okiyama, Chiduru Watanabe

Journal of Computer Aided Chemistry18 ( 0 ) 143 - 148   2017

Theoretical Calculations on Cation-capturing ofMacrocyclic Peptoid with Phenyl Rings in Main Chain Peer-reviewed

KAWADA Shutaro, HAKAMATA Mayu, MOCHIZUKI Yuji

Journal of Computer Chemistry, Japan16   77 - 79   2017

フラグメント分子軌道(FMO)計算の結果の自動解析の試み

望月祐志, 奥沢明

計算工学22   3539 - 3542   2017

A New Treatment for Water near the Interface between Lipid Membrane and Silica in Dissipative Particle Dynamics Simulation Peer-reviewed

DOI Hideo, OKUWAKI Koji, MOCHIZUKI Yuji, OZAWA Taku

Journal of Computer Chemistry, Japan16   28 - 31   2017

Explicit solvation of a single-stranded DNA, a binding protein, and their complex: a suitable protocol for fragment molecular orbital calculation Peer-reviewed

Yuto Komeij, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

Chem-Bio Informatics Journal17 ( 0 ) 72 - 84   2017

Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor Peer-reviewed

Sona SAITOU, Yuji MOCHIZUKI, Yutaka YAMAZAKI, Kazuya ISHIMURA

Journal of Computer Chemistry, Japan15 ( 4 ) 92 - 96   11 2016

Evaluations of Molecular Structure and Aromaticity of C5Ch5 and C6Ch6 (Ch=S, Se, Te) Peer-reviewed

KAWADA Syuutaro, MOCHIZUKI Yuji, NAKANO Katsuhiro

Journal of Computer Chemistry, Japan15 ( 4 ) 87 - 91   11 2016

Practical Usages Of 3D-printer for Scientific Education of Chemistry and Biology Peer-reviewed

    10 2016

Fragment Molecular Orbital (FMO) Calculations of Peptoids Peer-reviewed

KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori

Journal of Computer Chemistry, Japan15 ( 3 ) 51 - 52   10 2016

Hydration of ligands of influenza virus neuraminidase studied by the fragment molecular orbital method Peer-reviewed

Kana Tokuda, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa, Yuto Komeiji

Journal of Molecular Graphics and Modelling69   144 - 153   9 2016

Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor Peer-reviewed

Sona SAITOU, Yuji MOCHIZUKI, Yutaka YAMAZAKI, Kazuya ISHIMURA

Journal of Computer Chemistry, Japan15 ( 4 ) 92 - 96   2016

Evaluations of Molecular Structure and Aromaticity of C₅Ch₅ and C₆Ch₆ (Ch=S, Se, Te) Peer-reviewed

KAWADA Syuutaro, MOCHIZUKI Yuji, NAKANO Katsuhiro

Journal of Computer Chemistry, Japan15 ( 4 ) 87 - 91   2016

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 Peer-reviewed

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. Comp. Chem. Jpn.15   65 - 67   2016

Fragment Molecular Orbital (FMO) Calculations of Peptoids Peer-reviewed

KAWADA Shutaro, SAKAGUCHI Masataka, YONEKURA Ibuki, OKUWAKI Kouji, MOCHIZUKI Yuji, FUKUZAWA Kaori

Journal of Computer Chemistry, Japan15 ( 3 ) 51 - 52   2016

Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy Peer-reviewed

坂口正貴, 望月祐志, 望月祐志, 渡邉千鶴, 福澤薫, 福澤薫

Journal of Computer Chemistry, Japan (Web)14 ( 5 )   12 2015

Reversible Structural Changes Accompanying the Two-Electron Redox Reaction of Pt(tacn) (tacn: 1,4,7-triazacyclononane) Complexes Peer-reviewed

Tohru Wada, Koki Enami, Ryohei Kojima, Tomoki Okada, Yuki Ishikawa, Yuji Miyazato, Ernst Horn, Yuji Mochizuki

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN88 ( 9 ) 1230 - 1237   9 2015

Modeling of hydroxyapatite-peptide interaction based on fragment molecular orbital method Peer-reviewed

Koichiro Kato, Kaori Fukuzawa, Yuji Mochizuki

CHEMICAL PHYSICS LETTERS629   58 - 64   6 2015

ペプチド結合における新規フラグメント分割方法の検証および精度評価

坂口正貴, 福澤薫, 渡邉千鶴, 望月祐志

日本化学会講演予稿集95th ( 2 ) 231   11 3 2015

Explicit solvation modulates intra- and inter-molecular interactions within DNA: Electronic aspects revealed by the ab initio fragment molecular orbital (FMO) method Peer-reviewed

Kaori Fukuzawa, Ikuo Kurisaki, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Shigenori Tanaka, Yuto Komeiji

Computational and Theoretical Chemistry1054   29 - 37   2 2015

Effects of Water Molecules and Configurations of Neighboring Amino Acid Residues Surrounding DsRed Chromophore on Its Excitation Energy Peer-reviewed

坂口正貴, 望月祐志, 望月祐志, 渡邉千鶴, 福澤薫, 福澤薫

Journal of Computer Chemistry, Japan (Web)14 ( 5 ) 155 - 163   2015

Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems Peer-reviewed

Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan14 ( 1 ) 1 - 9   2015

Fragment Molecular Orbital-Based Molecular Dynamics Study on Hydrated Ln (III) Ions Peer-reviewed

Fujiwara Takayuki, Mori Hirotoshi, Komeiji Yuto, Mochizuki Yuji

Proceedings of Computational Science Workshop 2014 (CSW2014)   011001   2015

Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems Peer-reviewed

Takayuki TSUKAMOTO, Koichiro KATO, Akifumi KATO, Tatsuya NAKANO, Yuji MOCHIZUKI, Kaori FUKUZAWA

Journal of Computer Chemistry, Japan14 ( 1 ) 1 - 9   2015

Optimal damping algorithm for unrestricted Hartree-Fock calculations Peer-reviewed

Jun-Ichi Yamamoto, Yuji Mochizuki

Chem-Bio Informatics Journal14   14 - 33   13 9 2014

Interaction energy analysis on specific binding of influenza virus hemagglutinin to avian and human sialosaccharide receptors: Importance of mutation-induced structural change Peer-reviewed

Satoshi Anzaki, Chiduru Watanabe, Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka

JOURNAL OF MOLECULAR GRAPHICS & MODELLING53   48 - 58   9 2014

Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method Peer-reviewed

Hiroyuki Ando, Yasuteru Shigeta, Takeshi Baba, Chiduru Watanabe, Yoshio Okiyama, Yuji Mochizuki, Masayoshi Nakano

Molecular Physics113 ( 3-4 ) 319 - 326   8 2014

Improved Description of the Orbital Relaxation Effect by Practical Use of the Self-Energy Peer-reviewed

Masaaki Saitow, Tomonori Ida, Yuji Mochizuki

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY114 ( 9 ) 577 - 586   5 2014

Accuracy of the fragment molecular orbital (FMO) calculations for DNA: Total energy, molecular orbital, and inter-fragment interaction energy Peer-reviewed

Kaori Fukuzawa, Chiduru Watanabe, Ikuo Kurisaki, Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka, Yuto Komeiji

COMPUTATIONAL AND THEORETICAL CHEMISTRY1034   7 - 16   4 2014

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 ( 4 ) 17 - 25   2014

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems Peer-reviewed

Shigenori Tanaka, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Kaori Fukuzawa

Phys. Chem. Chem. Phys.16 ( 22 ) 10310 - 10344   2014

Fragment molecular orbital−based molecular dynamics (FMO-MD) simulations on hydrated Cu(II) ion Peer-reviewed

Yuji Kato, Takayuki Fujiwara, Yuto Komeiji, Tatsuya Nakano, Hirotoshi Mori, Yoshio Okiyama, Yuji Mochizuki

Chem-Bio Informatics Journal14 ( 0 ) 1 - 13   2014

Modeling of peptide–silica interaction based on four-body corrected fragment molecular orbital (FMO4) calculations Peer-reviewed

Yoshio Okiyama, Takayuki Tsukamoto, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochizuki

Chemical Physics Letters566   25 - 31   4 2013

Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design Peer-reviewed

Chiduru Watanabe, Kaori Fukuzawa, Yoshio Okiyama, Takayuki Tsukamoto, Akifumi Kato, Shigenori Tanaka, Yuji Mochizuki, Tatsuya Nakano

Journal of Molecular Graphics and Modelling41   31 - 42   4 2013

Importance of spin-orbit coupling effect and solvent effect in electronic transition assignments of Pt-II complexes: In the case of cis/trans-[(PtCl2)-Cl-II(NH3)(2)] Peer-reviewed

Hirotoshi Mori, Ryohei Kojima, Yuji Mochizuki, Waka Uenohara, Izumi Umezawa, Nobuyuki Matsushita

JOURNAL OF MOLECULAR STRUCTURE1035   218 - 223   3 2013

Device, system, method and program for producing fragment model Peer-reviewed

Mochizuki Yuji, Tsukamoto Takayuki, Fukuzawa Kaori

    3 2013

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   42 - 46   2013

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   25 - 31   2013

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31   64 - 72   2013

Analysis of Global Ecosystem Ecology by Fragment Molecular Orbital (FMO) Method--Analyses of the interactions between virus hemagglutinins and their receptors-- Peer-reviewed

Maruyama Tadashi, Shimane Yasuhiro, Ohishi Kazue, Iwasawa Misako, Hatada Yuji, Usui Keiko, Takaki Yoshihiro, Yoshida Takao, Tanaka Shigenori, Anzaki Satoshi, other

Annual Report of the Earth Simulator Center April2014   2013

Dynamic fragmentation with static fragments (DF/SF) algorithm designed for ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) simulations of polypeptides Peer-reviewed

Yuto Komeiji, Takayuki Fujiwara, Yoshio Okiyama, Yuji Mochizuki

Chem-Bio Informatics Journal13 ( 0 ) 45 - 57   2013

Ab initio path integral Monte Carlo simulations for water trimer with electron correlation effects Peer-reviewed

Takatoshi Fujita, Shigenori Tanaka, Takayuki Fujiwara, Masa-Aki Kusa, Yuji Mochizuki, Motoyuki Shiga

COMPUTATIONAL AND THEORETICAL CHEMISTRY997   7 - 13   10 2012

Interaction energy calculation system, method and program Peer-reviewed

Nakano Tatsuya, Mochizuki Yuji, Fukuzawa Kaori

    8 2012

FMO-MD Simulations on the Hydration of Formaldehyde in Water Solution with Constraint Dynamics Peer-reviewed

Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki

CHEMISTRY-A EUROPEAN JOURNAL18 ( 31 ) 9714 - 9721   7 2012

Partial geometry optimization with FMO-MP2 gradient: Application to TrpCage Peer-reviewed

Takayuki Tsukamoto, Yuji Mochizuki, Naoki Watanabe, Kaori Fukuzawa, Tatsuya Nakano

CHEMICAL PHYSICS LETTERS535   157 - 162   5 2012

Differences in hydration between cis- and trans-platin: Quantum insights by ab initio fragment molecular orbital-based molecular dynamics (FMO-MD) Peer-reviewed

Hirotoshi Mori, Natsumi Hirayama, Yuto Komeiji, Yuji Mochizuki

COMPUTATIONAL AND THEORETICAL CHEMISTRY986   30 - 34   4 2012

Excited state calculation for free-base and metalloporphyrins with the partially renormalized polarization propagator approach Peer-reviewed

Masaaki Saitow, Yuji Mochizuki

CHEMICAL PHYSICS LETTERS525-26   144 - 149   2 2012

Efficient Calculation of Fragment Molecular Orbital Method with Continuous Multipole Method

Tatsuya Nakano, Katsumi Yamashita, Katsunori Segawa, Yoshio Okiyama, Chiduru Watanabe, Kaori Fukuzawa, Shigenori Tanaka, Yuji Mochidzuki

Journal of Computer Aided Chemistry13 ( 0 ) 44 - 50   2012

New fragmentation of fragment molecular orbital method applicable to fragment based drug design Peer-reviewed

Watanabe Chiduru, Fukuzawa Kaori, Okiyama Yoshio, Tsukamoto Takayuki, Kato Akifumi, Tanaka Shigenori, Nakano Tatsuya, Mochizuki Yuji

    2012

Development of the four-body corrected fragment molecular orbital (FMO4) method Peer-reviewed

Tatsuya Nakano, Yuji Mochizuki, Katsumi Yamashita, Chiduru Watanabe, Kaori Fukuzawa, Katsunori Segawa, Yoshio Okiyama, Takayuki Tsukamoto, Shigenori Tanaka

Chemical Physics Letters523   128 - 133   1 2012

Ab Initio Path Integral Molecular Dynamics and Monte Carlo Simulations for Water Trimer and Oligopeptide Peer-reviewed

Takatoshi Fujita, Masa-Aki Kusa, Takayuki Fujiwara, Yuji Mochizuki, Shigenori Tanaka

ADVANCES IN QUANTUM MONTE CARLO1094   187 - +   2012

Antigen-antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation Peer-reviewed

Akio Yoshioka, Kazutomo Takematsu, Ikuo Kurisaki, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS130 ( 4-6 ) 1197 - 1202   12 2011

Higher-order correlated calculations based on fragment molecular orbital scheme Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Kaori Fukuzawa, Naoki Taguchi, Shigenori Tanaka

THEORETICAL CHEMISTRY ACCOUNTS130 ( 2-3 ) 515 - 530   10 2011

Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations Peer-reviewed

Akio Yoshioka, Kaori Fukuzawa, Yuji Mochizuki, Katsumi Yamashita, Tatsuya Nakano, Yoshio Okiyama, Eri Nobusawa, Katsuhisa Nakajima, Shigenori Tanaka

Journal of Molecular Graphics and Modelling30   110 - 119   9 2011

4f-in-core model core potentials for trivalent lanthanides Peer-reviewed

Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, You Osanai, Eisaku Miyoshi

CHEMICAL PHYSICS LETTERS510 ( 4-6 ) 261 - 266   7 2011

Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme Peer-reviewed

Yoshio Okiyama, Kaori Fukuzawa, Haruka Yamada, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters509 ( 1-3 ) 67 - 71   6 2011

Fragment molecular orbital-based molecular dynamics (FMO-MD) method with MP2 gradient Peer-reviewed

Yuji Mochizuki, Tatsuya Nakano, Yuto Komeiji, Katsumi Yamashita, Yoshio Okiyama, Hikaru Yoshikawa, Hiroshi Yamataka

Chemical Physics Letters504 ( 1-3 ) 95 - 99   2 2011

Fragment molecular orbital calculations for excitation energies of blue- and yellow-fluorescent proteins Peer-reviewed

Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano

CHEMICAL PHYSICS LETTERS504 ( 1-3 ) 76 - 82   2 2011

Development of QC2AS- A computer algebra system for symbolic quantum chemical computations Peer-reviewed

Takeshi Osoekawa, Yuji Mochizuki, Kazuhiro Kyokoyama

Proceedings - 2011 International Conference on Computational Science and Its Applications, ICCSA 2011   102 - 109   2011

Fragment molecular orbital (FMO) study on stabilization mechanism of neuro-oncological ventral antigen (NOVA)-RNA complex system Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM962 ( 1-3 ) 45 - 55   12 2010

Theoretical study of hydration models of trivalent rare-earth ions using model core potentials Peer-reviewed

Takayuki Fujiwara, Hirotoshi Mori, Yuji Mochizuki, Hiroshi Tatewaki, Eisaku Miyoshi

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM949 ( 1-3 ) 28 - 35   6 2010

Large-scale FMO-MP3 calculations on the surface proteins of influenza virus, hemagglutinin (HA) and neuraminidase (NA) Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Naoki Taguchi, Yoshio Okiyama, Misako Tsuboi, Tatsuya Nakano, Shigenori Tanaka

Chemical Physics Letters493 ( 4-6 ) 346 - 352   6 2010

Flexible ligand recognition of peroxisome proliferator-activated receptor-gamma (PPAR gamma) Peer-reviewed

Kenji Yamagishi, Keiko Yamamoto, Yuji Mochizuki, Tatsuya Nakano, Sachiko Yamada, Hiroaki Tokiwa

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS20 ( 11 ) 3344 - 3347   6 2010

Acceleration of fragment molecular orbital calculations with Cholesky decomposition approach Peer-reviewed

Yoshio Okiyama, Tatsuya Nakano, Katsumi Yamashita, Yuji Mochizuki, Naoki Taguchi, Shigenori Tanaka

Chemical Physics Letters490 ( 1-3 ) 84 - 89   4 2010

Fragment molecular orbital-based molecular dynamics (FMO-MD) simulations on hydrated Zn(II) ion Peer-reviewed

Takayuki Fujiwara, Yuji Mochizuki, Yuto Komeiji, Yoshio Okiyama, Hirotoshi Mori, Tatsuya Nakano, Eisaku Miyoshi

Chemical Physics Letters490 ( 1-3 ) 41 - 45   4 2010

Three-body expansion and generalized dynamic fragmentation improve the fragment molecular orbital-based molecular dynamics (FMO-MD) Peer-reviewed

Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano

CHEMICAL PHYSICS LETTERS484 ( 4-6 ) 380 - 386   1 2010

Theoretical Analysis of the Molecular Mechanism of Stabilization of Nova-RNA Complex System: Fragment Molecular Orbital Method Based Quantum Chemical Calculation For the Effect of the Complex Formation on the Electronic State of Biomacromolecular System Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL JOURNAL98 ( 3 ) 74A - 74A   1 2010

Gröbner Basis Technique for Algebraic Formulas in Electron Correlation Theories Peer-reviewed

Osoekawa Takeshi, Shinohara Naoyuki, Mochizuki Yuji, Yokoyama Kazuhiro

Computational Science and Its Applications (ICCSA), 2010 International Conference on   17   2010

Does Amination of Formaldehyde Proceed Through a Zwitterionic Intermediate in Water? Fragment Molecular Orbital Molecular Dynamics Simulations by Using Constraint Dynamics Peer-reviewed

Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano

CHEMISTRY-A EUROPEAN JOURNAL16 ( 22 ) 6430 - 6433   2010

1P260 Fragment molecular orbital calculation of the absorption maxima of bacteriorhodopsin and pharaonis phoborhodopsin (Photobiology: Vision & Photoreception, The 48th Annual Meeting of the Biophysical Society of Japan) Peer-reviewed

Hayashi Tomohiko, Taguchi Naoki, Mochizuki Yuji, Sakurai Minoru

Seibutsu Butsuri50 ( supplement2 ) S65   2010

Accuracy of fragmentation in ab initio calculations of hydrated sodium cation Peer-reviewed

Takatoshi Fujita, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS478 ( 4-6 ) 295 - 300   8 2009

Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding Peer-reviewed

Kazutomo Takematsu, Kaori Fukuzawa, Katsumi Omagari, Setsuko Nakajima, Katsuhisa Nakajima, Yuji Mochizuki, Tatsuya Nakano, Hirofumi Watanabe, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B113 ( 15 ) 4991 - 4994   4 2009

Application of Dyson-corrected second-order perturbation theories Peer-reviewed

Yuji Mochizuki

CHEMICAL PHYSICS LETTERS472 ( 1-3 ) 143 - 148   4 2009

Ab initio quantum-chemical study on emission spectra of bioluminescent luciferases by fragment molecular orbital method Peer-reviewed

Ayumu Tagami, Nobuhiro Ishibashi, Dai-ichiro Kato, Naoki Taguchi, Yuji Mochizuki, Hirofumi Watanabe, Mika Ito, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS472 ( 1-3 ) 118 - 123   4 2009

Fragment molecular orbital-based molecular dynamics (FMO-MD), a quantum simulation tool for large molecular systems Peer-reviewed

Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Dmitri G. Fedorov

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM898 ( 1-3 ) 2 - 7   3 2009

Fragment Molecular Orbital Calculations on Red Fluorescent Proteins (DsRed and mFruits) Peer-reviewed

Naoki Taguchi, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Kaori Fukuzawa, Takeshi Ishikawa, Minoru Sakurai, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B113 ( 4 ) 1153 - 1161   1 2009

Fragment Molecular Orbital Method-Based Molecular Dynamics (FMO-MD) as a Simulator for Chemical Reactions in Explicit Solvation Peer-reviewed

Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano

JOURNAL OF COMPUTATIONAL CHEMISTRY30 ( 1 ) 40 - 50   1 2009

Developments of FMO methodology and graphical user interface in ABINIT-MP Peer-reviewed

Nakano Tatsuya, Mochizuki Yuji, Kato Akifumi, Fukuzawa Kaori, Ishikawa Takeshi, Amari Shinji, Kurisaki Ikuo, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems   37 - 62   2009

Application of the fragment molecular orbital method for determination of atomic charges on polypeptides. II. Towards an improvement of force fields used for classical molecular dynamics simulations Peer-reviewed

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Kuniyoshi Ebina, Shigenori Tanaka

Chemical Physics Letters467 ( 4-6 ) 417 - 423   1 2009

Analysis of Mutation Mechanisms of Influenza Virus Based on the Fragment Molecular Orbital Method Peer-reviewed

Tanaka Shigenori, Mochizuki Yuji, Fukuzawa Kaori, Yamashita Katsumi, Nakano Tatsuya

Annual Report of the Earth Simulator Center April2010   2009

7 Application of the FMO Method to Specific Molecular Recognition of Biomacromolecules Peer-reviewed

Fukuzawa Kaori, Mochizuki Yuji, Nakano Tatsuya, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems   133 - 169   2009

4 Excited States of Photoactive Proteins by Configuration Interaction Studies Peer-reviewed

Mochizuki Yuji, Nakano Tatsuya, Taguchi Naoki, Tanaka Shigenori

The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems   63 - 89   2009

3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (Protein: Function, 2SP6 Towards Supercomputiong for Electronic Structures of Biological Peer-reviewed

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri49 ( supplement ) S161   2009

2SP6-07 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding (2SP6 Towards Supercomputing for Electronic Structures of Biological Macromolecules, The Peer-reviewed

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri49 ( supplement ) S15   2009

3P-063 Possibility of Mutation Prediction of Influenza Hemagglutinin by Combination of Hemadsorption Experiment and Quantum Chemical Calculation for Antibody Binding(Protein:Function,2SP6 Towards Supercomputiong for Electronic Structures of Biological Macromolecules,Symposia,The 47th Annual Meeting of the Biophysical Society of Japan)

Takematsu Kazutomo, Fukuzawa Kaori, Omagari Katsumi, Nakajima Katsuhisa, Nakajima Setsuko, Mochizuki Yuji, Nakano Tatsuya, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri49   S161   2009

An application of fragment interaction analysis based on local MP2 Peer-reviewed

Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Shigenori Tanaka, Kiyoshi Tanaka

CHEMICAL PHYSICS LETTERS463 ( 1-3 ) 189 - 194   9 2008

Ab initio fragment molecular orbital study of molecular interactions in liganded retinoid X receptor: Specification of residues associated with ligand inducible information transmission Peer-reviewed

Mika Ito, Kaori Fukuzawa, Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B112 ( 38 ) 12081 - 12094   9 2008

COMP 246-Simulation study of RNA-binding protein by fragment molecular orbital (FMO) method Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY236   8 2008

Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method Peer-reviewed

Tatsunori Iwata, Kaori Fukuzawa, Katsuhisa Nakajima, Sachiko Aida-Hyugaji, Yuji Mochizuki, Hirofumi Watanabe, Shigenori Tanaka

COMPUTATIONAL BIOLOGY AND CHEMISTRY32 ( 3 ) 198 - 211   6 2008

Large scale FMO-MP2 calculations on a massively parallel-vector computer Peer-reviewed

Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Tatsuya Nakano, Kaori Fukuzawa, Kazutomo Takematsu, Hirofumi Watanabe, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS457 ( 4-6 ) 396 - 403   5 2008

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 Peer-reviewed

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY A112 ( 10 ) 1986 - 1998   3 2008

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

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY A112 ( 10 ) 1986 - 1998   3 2008

How does an S(N)2 reaction take place in solution? Full ab initio MD simulations for the hydrolysis of the methyl diazonium ion Peer-reviewed

Makoto Sato, Hiroshi Yamataka, Yuto Komeiji, Yuji Mochizuki, Takeshi Ishikawa, Tatsuya Nakano

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY130 ( 8 ) 2396 - 2397   2 2008

A practical use of self-energy shift for the description of orbital relaxation Peer-reviewed

Yuji Mochizuki

CHEMICAL PHYSICS LETTERS453 ( 1-3 ) 109 - 116   2 2008

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

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 Chem9   47 - 54   2008

Research on Innovative Simulation Software Peer-reviewed

Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Mochizuki Yuji, Yamashita Katsumi, Nakano Tatsuya, Yamamoto Takenori, Yamasaki Takahiro, Ohno Takahisa

Annual Report of the Earth Simulator Center April2008   2008

Infantosi, AFC, 5, 273 Ioannidis, JPA, 39 Iwata, T., 198 Ji, Z., 243 Peer-reviewed

Josic K, Kandemir-Cavas C, Kanwar JR, Karabencheva TG, Khaladkar M, Khoshmanesh K, Kim H, Kim JR, Kiran K, Komeiji Y

Computational Biology and Chemistry32   470   2008

Multi-reference calculations of nitric oxide dimer Peer-reviewed

Naoki Taguchi, Yuji Mochizuki, Takeshi Ishikawa, Kiyoshi Tanaka

CHEMICAL PHYSICS LETTERS451 ( 1-3 ) 31 - 36   1 2008

Fragment interaction analysis based on local MP2 Peer-reviewed

Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka

THEORETICAL CHEMISTRY ACCOUNTS118 ( 5-6 ) 937 - 945   12 2007

Fragment interaction analysis based on local MP2

Takeshi Ishikawa, Yuji Mochizuki, Shinji Amari, Tatsuya Nakano, Hiroaki Tokiwa, Shigenori Tanaka, Kiyoshi Tanaka

THEORETICAL CHEMISTRY ACCOUNTS118 ( 5-6 ) 937 - 945   12 2007

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method Peer-reviewed

Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL CHEMISTRY130 ( 1-2 ) 1 - 9   10 2007

Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method

Ikuo Kurisaki, Kaori Fukuzawa, Yuto Komeiji, Yuji Mochizuki, Tatsuya Nakano, Janine Imada, Arleta Chmielewski, Stuart M. Rothstein, Hirofumi Watanabe, Shigenori Tanaka

BIOPHYSICAL CHEMISTRY130 ( 1-2 ) 1 - 9   10 2007

Modification for spin-adapted version of configuration interaction singles with perturbative doubles Peer-reviewed

Yuji Mochizuki, Kiyoshi Tanaka

Chemical Physics Letters443 ( 4-6 ) 389 - 397   6 8 2007

Modification for spin-adapted version of configuration interaction singles with perturbative doubles

Yuji Mochizuki, Kiyoshi Tanaka

CHEMICAL PHYSICS LETTERS443 ( 4-6 ) 389 - 397   8 2007

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme Peer-reviewed

Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai

THEORETICAL CHEMISTRY ACCOUNTS117 ( 4 ) 541 - 553   4 2007

Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism Peer-reviewed

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B111 ( 13 ) 3525 - 3533   4 2007

Ab initio fragment molecular orbital study of molecular interactions between liganded retinoid x receptor and its coactivator: Roles of helix 12 in the coactivator binding mechanism

Mika Ito, Kaori Fukuzawa, Yuji Mochizuki, Tatsuya Nakano, Shigenori Tanaka

JOURNAL OF PHYSICAL CHEMISTRY B111 ( 13 ) 3525 - 3533   4 2007

Parallelized integral-direct CIS(D) calculations with multilayer fragment molecular orbital scheme

Yuji Mochizuki, Kiyoshi Tanaka, Katsumi Yamashita, Takeshi Ishikawa, Tatsuya Nakano, Shinji Amari, Katsunori Segawa, Tadashi Murase, Hiroaki Tokiwa, Minoru Sakurai

THEORETICAL CHEMISTRY ACCOUNTS117 ( 4 ) 541 - 553   4 2007

A fully quantum mechanical simulation study on the lowest n-π* state of hydrated formaldehyde

Yuji Mochizuki, Yuto Komeiji, Takeshi Ishikawa, Tatsuya Nakano, Hiroshi Yamataka

Chemical Physics Letters437 ( 1-3 ) 66 - 72   22 3 2007

A graphical symmetric group approach for a spin adapted full configuration interaction: partitioning of a configuration graph into sets of closed-shell and open-shell graphs Peer-reviewed

Kiyoshi Tanaka, Yuji Mochizuki, Takeshi Ishikawa, Hidemi Terashima, Hiroaki Tokiwa

THEORETICAL CHEMISTRY ACCOUNTS117 ( 3 ) 397 - 405   3 2007

A fully quantum mechanical simulation study on the lowest n-pi(*) state of hydrated formaldehyde Peer-reviewed

Yuji Mochizuki, Yuto Komeiji, Takeshi Ishikawa, Tatsuya Nakano, Hiroshi Yamataka

CHEMICAL PHYSICS LETTERS437 ( 1-3 ) 66 - 72   3 2007

Frontier Simulation Software for Industrial Science

Makoto Tsubokura, Yuji Mochizuki, Katsumi Yamashita, Tadashi Murase, Kenji Yamagishi, Hiroaki Tokiwa, Tatsuya Nakano, Takenori Yamamoto, Takahisa Ohno

Annual Report of the Earth Simulator Center April 2005 - March 200656 ( 4 ) 299 - 304   2007

On Mechanism of Enhanced Fluorescence in Green Fluorescent Protein Peer-reviewed

STARIKOV EVGENI B, Panas Itai, MOCHIZUKI YUJI, TANAKA SHIGENORI, Luo Yi, AA}gren Hans

Biophysical Reviews and Letters2 ( 03n04 ) 221 - 227   2007

Fragment molecular orbital calculations on red fluorescent protein (DsRed) Peer-reviewed

Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS433 ( 4-6 ) 360 - 367   1 2007

Application of the fragment molecular orbital method for determination of atomic charges on polypeptides Peer-reviewed

Yoshio Okiyama, Hirofumi Watanabe, Kaori Fukuzawa, Tatsuya Nakano, Yuji Mochizuki, Takeshi Ishikawa, Shigenori Tanaka, Kuniyoshi Ebina

Chemical Physics Letters449 ( 4-6 ) 329 - 335   2007

Ab initio FMO-MD method reimplemented and applied to pure water Peer-reviewed

Yuto Komeiji, Takeshi Ishikawa, Yuji Mochizuki, Hiroshi Yamataka, Tatsuya Nakano

COMPUTATION IN MODERN SCIENCE AND ENGINEERING VOL 2, PTS A AND B2 ( 2 ) 1261 - +   2007

2P058 Theoretical study on the sequence specific recognition mechanism of Pumilio RNA-binding domain by Fragment Molecular Orbital (FMO) method (Proteins-structure and structure-function relationship, Poster Presentations) Peer-reviewed

Kurisaki Ikuo, Fukuzawa Kaori, Nakano Tatsuya, Mochizuki Yuji, Watanabe Hirofumi, Tanaka Shigenori

Seibutsu Butsuri47 ( supplement ) S127   2007

Fragment molecular orbital calculations on red fluorescent protein (DsRed)

Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Takeshi Ishikawa, Kiyoshi Tanaka, Minoru Sakurai, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS433 ( 4-6 ) 360 - 367   1 2007

Application of Fragment Molecular Orbital (FMO) Method to Nano-Bio Field

NAKANO Tatsuya, MOCHIZUKI Yuji, AMARI Shinji, KOBAYASHI Masato, FUKUZAWA Kaori, TANAKA Shigenori

Journal of Computer Chemistry, Japan6 ( 3 ) 173 - 184   1 1 2007

Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules

FUKUZAWA Kaori, NAKANO Tatsuya, KATO Akifumi, MOCHIZUKI Yuji, TANAKA Shigenori

Journal of Chemical Software6 ( 3 ) 185 - 198   1 1 2007

A graphical symmetric group approach for a spin adapted full configuration interaction

望月 祐志

K. Tanaka, Y. Mochizuki, T. Ishikawa, H. Terashima, and H. Tokiwa, ( 117 ) 397 - 405   1 1 2007

Erratum: Intra- and intermodular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study (Journal of Computational Chemistry (2006) 27 (948)) Peer-reviewed

Fukuzawa, K., Komeiji, Y., Mochizuki, Y., Kato, A., Nakano, T., Tanaka, S.

Journal of Computational Chemistry28 ( 13 )   2007

Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method (vol 110, pg 24276, 2006) Peer-reviewed

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B110 ( 47 ) 24276 - 24276   11 2006

Application of fragment molecular orbital scheme to silicon-containing systems Peer-reviewed

Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS430 ( 4-6 ) 361 - 366   10 2006

Application of fragment molecular orbital scheme to silicon-containing systems

Takeshi Ishikawa, Yuji Mochizuki, Kenji Imamura, Tatsuya Nakano, Hirotoshi Mori, Hiroaki Tokiwa, Kiyoshi Tanaka, Eisaku Miyoshi, Shigenori Tanaka

CHEMICAL PHYSICS LETTERS430 ( 4-6 ) 361 - 366   10 2006

Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method Peer-reviewed

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B110 ( 32 ) 16102 - 16110   8 2006

Fragment molecular orbital calculations on large scale systems containing heavy metal atom Peer-reviewed

Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

CHEMICAL PHYSICS LETTERS427 ( 1-3 ) 159 - 165   8 2006

Fragment molecular orbital calculations on large scale systems containing heavy metal atom

Takeshi Ishikawa, Yuji Mochizuki, Tatsuya Nakano, Shinji Amari, Hirotoshi Mori, Hiroaki Honda, Takatoshi Fujita, Hiroaki Tokiwa, Shigenori Tanaka, Yuto Komeiji, Kaori Fukuzawa, Kiyoshi Tanaka, Eisaku Miyoshi

CHEMICAL PHYSICS LETTERS427 ( 1-3 ) 159 - 165   8 2006

Molecular interactions between estrogen receptor and its ligand studied by the ab initio fragment molecular orbital method

Kaori Fukuzawa, Yuji Mochizuki, Shigenori Tanaka, Kazuo Kitaura, Tatsuya Nakano

JOURNAL OF PHYSICAL CHEMISTRY B110 ( 32 ) 16102 - 16110   8 2006

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study Peer-reviewed

K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

JOURNAL OF COMPUTATIONAL CHEMISTRY27 ( 8 ) 948 - 960   6 2006

Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study

K Fukuzawa, Y Komeiji, Y Mochizuki, A Kato, T Nakano, S Tanaka

JOURNAL OF COMPUTATIONAL CHEMISTRY27 ( 8 ) 948 - 960   6 2006

Dynamic polarizability calculation with fragment molecular orbital scheme Peer-reviewed

Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka

CHEMICAL PHYSICS LETTERS418 ( 4-6 ) 418 - 422   2 2006

Dynamic polarizability calculation with fragment molecular orbital scheme

Y Mochizuki, T Ishikawa, K Tanaka, H Tokiwa, T Nakano, S Tanaka

CHEMICAL PHYSICS LETTERS418 ( 4-6 ) 418 - 422   2 2006

VISCANA: Visualized cluster analysis of protein-ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening Peer-reviewed

S Amari, M Aizawa, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano

JOURNAL OF CHEMICAL INFORMATION AND MODELING46 ( 1 ) 221 - 230   1 2006

Revolutionary Simulation Software for 21st Century Peer-reviewed

Kato Chisachi, Tsubokura Makoto, Yamade Yoshinobu, Arakawa Takamichi, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa, o, h

Annual Report of the Earth Simulator Center April2007   2006

Developments and applications of ABINIT-MP software based on the fragment molecular orbital method Peer-reviewed

Tatsuya Nakano, Yuji Mochizuki, Kaori Fukuzawa, Shinji Amari, Shigenori Tanaka

Modern Methods for Theoretical Physical Chemistry of Biopolymers   39 - 52   2006

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, JW Zhang, K Fukuzawa, Y Mochizuki, Y Iwasawa, K Nakata, H Chuman, T Nakano

JOURNAL OF CHEMICAL INFORMATION AND MODELING46 ( 1 ) 221 - 230   1 2006

A size-extensive modification of super-CI for orbital relaxation Peer-reviewed

Yuji Mochizuki

Chemical Physics Letters410 ( 1-3 ) 165 - 171   10 7 2005

1A configuration analysis for fragment interaction Peer-reviewed

Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS410 ( 4-6 ) 247 - 253   7 2005

A size-extensive modification of super-Cl for orbital relaxation

Y Mochizuki

CHEMICAL PHYSICS LETTERS410 ( 1-3 ) 165 - 171   7 2005

1A configuration analysis for fragment interaction

Y Mochizuki, K Fukuzawa, A Kato, S Tanaka, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS410 ( 4-6 ) 247 - 253   7 2005

Configuration interaction singles method with multilayer fragment molecular orbital scheme Peer-reviewed

Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS406 ( 4-6 ) 283 - 288   5 2005

Configuration interaction singles method with multilayer fragment molecular orbital scheme

Y Mochizuki, S Koikegami, S Amari, K Segawa, K Kitaura, T Nakano

CHEMICAL PHYSICS LETTERS406 ( 4-6 ) 283 - 288   5 2005

Frontier Simulation Software for Industrial Science Peer-reviewed

Kato Chisachi, Tsubokura Makoto, Mochizuki Yuji, Yamashita Katsumi, Murase Tadashi, Yamagishi Kenji, Tokiwa Hiroaki, Nakano Tatsuya, Yamamoto Takenori, Ohno Takahisa

Annual Report of the Earth Simulator Center April2006 ( 4 )   2005

Fragment Molecular Orbital Study on Molecular Interaction between Estrogen Receptor and Their Ligands

FUKUZAWA, MOCHIZUKI, TANAKA, AMARI, KITAURA, AND, Nakano

Proceedings of 7th Congress of the World Association of Theoretically Oriented Chemists (WATOC) (Cape Town, South Africa)ES-P23,   2005

A parallelized integral-direct second-order Moller-Plesset perturbation theory method with a fragment molecular orbital scheme Peer-reviewed

Y Mochizuki, T Nakano, S Koikegami, S Tanimori, Y Abe, U Nagashima, K Kitaura

THEORETICAL CHEMISTRY ACCOUNTS112 ( 5-6 ) 442 - 452   12 2004

A parallelized integral-direct second-order Moller-Plesset perturbation theory method with a fragment molecular orbital scheme

Y Mochizuki, T Nakano, S Koikegami, S Tanimori, Y Abe, U Nagashima, K Kitaura

THEORETICAL CHEMISTRY ACCOUNTS112 ( 5-6 ) 442 - 452   12 2004

Large scale MP2 calculations with fragment molecular orbital scheme Peer-reviewed

Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura

CHEMICAL PHYSICS LETTERS396 ( 4-6 ) 473 - 479   10 2004

Large scale MP2 calculations with fragment molecular orbital scheme

Y Mochizuki, S Koikegami, T Nakano, S Amari, K Kitaura

CHEMICAL PHYSICS LETTERS396 ( 4-6 ) 473 - 479   10 2004

Development of integral transformation modules for correlated calculations

Y. Mochizuki, U. Nagashima

J. Comp. Chem. Jpn.3 ( 1 ) 1 - 12   2004

Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces Peer-reviewed

Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa

CHEMICAL PHYSICS LETTERS377 ( 1-2 ) 236 - 242   8 2003

Comparative study of dehydrogenation at Pt(111)/water and Pt(111)/vacuum of methanol interfaces

Y Okamoto, O Sugino, Y Mochizuki, T Ikeshoji, Y Morikawa

CHEMICAL PHYSICS LETTERS377 ( 1-2 ) 236 - 242   8 2003

Prolapses in four-component relativistic Gaussian basis sets Peer-reviewed

H Tatewaki, T Koga, Y Mochizuki

CHEMICAL PHYSICS LETTERS375 ( 3-4 ) 399 - 405   7 2003

Prolapses in four-component relativistic Gaussian basis sets

H Tatewaki, T Koga, Y Mochizuki

CHEMICAL PHYSICS LETTERS375 ( 3-4 ) 399 - 405   7 2003

Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution Peer-reviewed

S Tsushima, TX Yang, Y Mochizuki, Y Okamoto

CHEMICAL PHYSICS LETTERS375 ( 1-2 ) 204 - 212   6 2003

Ab initio study on the structures of Th(IV) hydrate and its hydrolysis products in aqueous solution

S Tsushima, TX Yang, Y Mochizuki, Y Okamoto

CHEMICAL PHYSICS LETTERS375 ( 1-2 ) 204 - 212   6 2003

Theoretical study of hydrolysis reactions of tetravalent thorium ion Peer-reviewed

Y Okamoto, Y Mochizuki, S Tsushima

CHEMICAL PHYSICS LETTERS373 ( 1-2 ) 213 - 217   5 2003

On the electronic structure of CmFn (n=1-4) by all-electron Dirac-Hartree-Fock calculations Peer-reviewed

Y Mochizuki, H Tatewaki

JOURNAL OF CHEMICAL PHYSICS118 ( 20 ) 9201 - 9207   5 2003

Theoretical study of hydrolysis reactions of tetravalent thorium ion

Y Okamoto, Y Mochizuki, S Tsushima

CHEMICAL PHYSICS LETTERS373 ( 1-2 ) 213 - 217   5 2003

On the electronic structures of Th4+ and Ac3+ hydrate models Peer-reviewed

Yuji Mochizuki, Satoru Tsushima

Chemical Physics Letters372 ( 1-2 ) 114 - 120   22 4 2003

On the electronic structures of Th4+ and Ac3+ hydrate models

Y Mochizuki, S Tsushima

CHEMICAL PHYSICS LETTERS372 ( 1-2 ) 114 - 120   4 2003

Comments on relativistic basis sets Peer-reviewed

H Tatewaki, Y Mochizuki

THEORETICAL CHEMISTRY ACCOUNTS109 ( 1 ) 40 - 42   2 2003

Comments on relativistic basis sets

Hiroshi Tatewaki, Yuji Mochizuki

Theoretical Chemistry Accounts109 ( 1 ) 40 - 42   1 2 2003

Electric structure calculations on heavy element systems using the DIRAC code Peer-reviewed

Mochizuki Yuji

    2003

On the electronic of CmFn(n=1-4) by all-electron Dirac -Hartree-Fock calculations

望月 祐志

（不明） ( 118 ) 9201 - 9207   1 1 2003

Four-component relativistic calculations on the mono-ammine complexes of trivalent f0, f7, and f14 ions

Yuji Mochizuki, Yasuharu Okamoto

Chemical Physics Letters359 ( 3-4 ) 331 - 336   20 6 2002

Four-component relativistic calculations on the mono-ammine complexes of trivalent f(0), f(7), and f(14) ions Peer-reviewed

Y Mochizuki, Y Okamoto

CHEMICAL PHYSICS LETTERS359 ( 3-4 ) 331 - 336   6 2002

On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations Peer-reviewed

Y Mochizuki, H Tatewaki

JOURNAL OF CHEMICAL PHYSICS116 ( 20 ) 8838 - 8842   5 2002

On the electronic structure of Cm(H2O)(n)(3+) (n=1,2,4,6) by all-electron Dirac-Hartree-Fock calculations

Y Mochizuki, H Tatewaki

JOURNAL OF CHEMICAL PHYSICS116 ( 20 ) 8838 - 8842   5 2002

Vectorization of direct Fock matrix construction in DIRAC-DHF calculations Peer-reviewed

Y Mochizuki, M Matsumura, T Yokura, Y Hirahara, T Imamura

JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY39 ( 2 ) 195 - 199   2 2002

Size, order, and dimensional relations for silicon cluster polarizabilities Peer-reviewed

B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren

JOURNAL OF PHYSICAL CHEMISTRY A106 ( 2 ) 395 - 399   1 2002

Ab initio MO studies on the hydration of trivalent curium ion Peer-reviewed

Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto

Journal of Nuclear Science and Technology39 ( sup3 ) 418 - 421   2002

Size, order, and dimensional relations for silicon cluster polarizabilities

B Jansik, B Schimmelpfennig, P Norman, Y Mochizuki, Y Luo, H Agren

JOURNAL OF PHYSICAL CHEMISTRY A106 ( 2 ) 395 - 399   1 2002

Vectorization of direct fock matrix construction in DIRAC-DHF calculations

Yuji Mochizuki, Masayuki Matsumura, Tetsui-Chi Yokura, Yukio Hirahara, Toshiyuki Imamura

Journal of Nuclear Science and Technology39 ( 2 ) 195 - 199   2002

Ab initio MO studies on the hydration of trivalent curium ion

Yuji Mochizuki, Hiroshi Tatewaki, Yasuharu Okamoto

Journal of Nuclear Science and Technology39 ( 3 ) 418 - 421   2002

Modification of nonrelativistic gaussian basis sets for relativistic calculations

Hiroshi Tatewaki, Yuji Mochizuki, Toshikatsu Koga, Jacek Karwowski

Journal of Chemical Physics115 ( 20 ) 9160 - 9164   22 11 2001

Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions

Yuji Mochizuki, Hiroshi Tatewaki

Chemical Physics273 ( 2-3 ) 135 - 148   15 11 2001

Four-component relativistic calculations on the complexes between a water molecule and trivalent lanthanoid and actinoid ions Peer-reviewed

Y Mochizuki, H Tatewaki

CHEMICAL PHYSICS273 ( 2-3 ) 135 - 148   11 2001

Modification of nonrelativistic Gaussian basis sets for relativistic calculations Peer-reviewed

H Tatewaki, Y Mochizuki, T Koga, J Karwowski

JOURNAL OF CHEMICAL PHYSICS115 ( 20 ) 9160 - 9164   11 2001

Vapor-liquid equilibrium data for the four binary systems containing fluorocarbon, hydrofluorocarbon, and fluorinated ethers at 101.3 kPa Peer-reviewed

K. Tochigi, T. Satou, K. Kurihara, K. Ochi, H. Yamamoto, Y. Mochizuki, T. Sako

Journal of Chemical and Engineering Data46 ( 4 ) 913 - 917   7 2001

HF-STEX and RASSCF calculations on nitrogen K-shell X-ray absorption of purine base and its derivative Peer-reviewed

Y Mochizuki, H Koide, T Imamura, H Takemiya

JOURNAL OF SYNCHROTRON RADIATION8 ( 2 ) 1003 - 1005   3 2001

Polarizability of silicon clusters Peer-reviewed

Y Mochizuki, H Agren

CHEMICAL PHYSICS LETTERS336 ( 5-6 ) 451 - 456   3 2001

HF-STEX and RASSCF calculations nitrogen K-shell X-ray absorption of purine base and its derivative

望月 祐志

（不明） ( 8 ) 1003 - 1005   1 1 2001

Polarizability of silicon clusters

望月 祐志

（不明） ( 273 ) 135 - 148   1 1 2001

A theoretical investigation of sulphur K-shell X-ray absorption of cysteine Peer-reviewed

Y Mochizuki, H Agren, LGM Pettersson, Carravetta, V

CHEMICAL PHYSICS LETTERS309 ( 3-4 ) 241 - 248   8 1999

Multireference coupled-pair approximation study of the CuSi molecule Peer-reviewed

M Tomonari, Y Mochizuki, K Tanaka

THEORETICAL CHEMISTRY ACCOUNTS101 ( 5 ) 332 - 335   4 1999

Theoretical investigation of the GaF molecule and its positive ion Peer-reviewed

Y Mochizuki, K Tanaka

THEORETICAL CHEMISTRY ACCOUNTS101 ( 4 ) 257 - 261   3 1999

Theoretical spectroscopic constants of the GaN molecule Peer-reviewed

Y Mochizuki, K Tanaka

THEORETICAL CHEMISTRY ACCOUNTS101 ( 4 ) 292 - 296   3 1999

MULTI-REFERENCE COUPLED PAIR APPROXIMATION: a state-universal approach of a CEPA type variant of MRSDCI Peer-reviewed

Tanaka Kiyoshi, Sakai Takeo, Mochizuki Yuji

Recent Advances in Multireference Methods4   95   1999

Molecular Orbital Study on the Oxidative Decomposition of Hfc-32 Peer-reviewed

Mochizuki Yuji

Data/Code/Japan atomic energy research institute (Tokyo)99   015   1999

Theoretical study of the spectroscopic constants of low-lying states of Ga-2 Peer-reviewed

TK Ghosh, K Tanaka, Y Mochizuki

THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE451 ( 1-2 ) 61 - 71   9 1998

Precise control of pn-junction profiles for GaN-based LD structures using GaN substrates with low dislocation densities Peer-reviewed

N Kuroda, C Sasaoka, A Kimura, A Usui, Y Mochizuki

JOURNAL OF CRYSTAL GROWTH189   551 - 555   6 1998

Theoretical investigation on the GaH molecule and its positive ion Peer-reviewed

Y Mochizuki, K Tanaka

THEORETICAL CHEMISTRY ACCOUNTS99 ( 2 ) 88 - 94   4 1998

Determination of valence band splitting parameters in GaN Peer-reviewed

AA Yamaguchi, Y Mochizuki, H Sunakawa, A Usui

JOURNAL OF APPLIED PHYSICS83 ( 8 ) 4542 - 4544   4 1998

Uniaxial stress effects on valence band structures of GaN Peer-reviewed

AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui

NITRIDE SEMICONDUCTORS482   893 - 898   1998

A CSF-based multi-reference coupled pair approximation III. An application to F2, As2 and As+ 2 Peer-reviewed

Tanaka Kiyoshi, Mochizuki Yuji

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)98 ( 4 ) 165   1998

Program linkage method for using dummy arguments to link program having hierarchical structure Peer-reviewed

Takada Toshikazu, Mochizuki Yuji

    10 1997

Computational study of the spectroscopic constants of the ground state of the As-2 molecule Peer-reviewed

Y Mochizuki, K Tanaka

CHEMICAL PHYSICS LETTERS274 ( 1-3 ) 264 - 268   8 1997

Reflectance spectroscopy on GaN films under uniaxial stress Peer-reviewed

AA Yamaguchi, Y Mochizuki, C Sasaoka, A Kimura, M Nido, A Usui

APPLIED PHYSICS LETTERS71 ( 3 ) 374 - 376   7 1997

Theoretical study of the surface reaction mechanism of GaN with HCl Peer-reviewed

Y Okamoto, T Takada, Y Mochizuki

JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS & EXPRESS LETTERS35 ( 12B ) L1641 - L1643   12 1996

Generalized doubly symbolic formulation for integral-driven direct configuration interaction method Peer-reviewed

Y Mochizuki, N Nishi, Y Hirahara, T Takada

THEORETICA CHIMICA ACTA93 ( 4 ) 211 - 233   4 1996

Epitaxial growth method of semiconductor crystal and molecular beam epitaxy apparatus for the same Peer-reviewed

Mochizuki Yuji, Usui Akira, Takada Toshikazu

    4 1996

Generalized doubly symbolic formulation for integral-driven direct configuration interaction method

Yuji Mochizuki, Naoki Nishi, Yukio Hirahara, Toshikazu Takada

Theoretical Chemistry Accounts93 ( 4 ) 211 - 233   1996

Method for epitaxial growth of semiconductor crystal by using halogenide Peer-reviewed

Mochizuki Yuji, Chiba Yoshie, Takada Toshikazu, Usui Akira

    11 1995

ON THE REACTION SCHEME FOR TI/TIN CHEMICAL-VAPOR-DEPOSITION (CVD) PROCESS USING TICL4 Peer-reviewed

Y MOCHIZUKI, Y OKAMOTO, A ISHITANI, K HIROSE, T TAKADA

JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS34 ( 3A ) L326 - L329   3 1995

THEORETICAL-STUDY ON THE DIRECT REACTION BETWEEN ASH3 AND SURFACE-ADSORBED GACL Peer-reviewed

Y MOCHIZUKI, A USUI, S HANDA, T TAKADA

JOURNAL OF CRYSTAL GROWTH148 ( 1-2 ) 96 - 105   2 1995

THEORETICAL-STUDIES ON THE CHLORIDE ALE PROCESS Peer-reviewed

Y MOCHIZUKI, T TAKADA, A USUI

APPLIED SURFACE SCIENCE82-3   200 - 207   12 1994

THEORETICAL-STUDY OF AS2 DESORPTION FROM THE GA DANGLING-BOND SITE Peer-reviewed

Y MOCHIZUKI, T TAKADA, C SASAOKA, A USUI, E MIYOSHI, Y SAKAI

PHYSICAL REVIEW B49 ( 7 ) 4658 - 4667   2 1994

THEORETICAL-STUDY OF THE CL DESORPTION REACTION INDUCED BY H-2 IN THE CHLORIDE ATOMIC LAYER EPITAXY Peer-reviewed

Y MOCHIZUKI, T TAKADA, T SAKUMA, S HANDA, C SASAOKA, A USUI

JOURNAL OF CRYSTAL GROWTH135 ( 1-2 ) 259 - 268   1 1994

The combination of computational techniques such as computer graphics (CG), molecular dynamics (MD) and quantum chemistry (QC) methods are demonstrated to be effective for investigating the dynamics and formation of ordered metal species in zeolite pores. Peer-reviewed

Mochizuki Y, Takada T, Usui A

Applied Surface Science82 ( 83 ) 543   1994

Theoretical Studies on the Dielectric Breakdown of the SiO_2 Thin Films Peer-reviewed

YOKOZAWA Ayumi, OHTA Noriko, MOCHIZUKI Yuji, ISHITANI Akihiko, TAKADA Toshikazu

Science reports of the Research Institutes, Tohoku University. Ser. A, Physics, chemistry and metallurgy39 ( 1 ) 81 - 84   1994

THEORETICAL-STUDY OF THE GALLIUM CHLORIDE MOLECULE AND ITS INTERACTION WITH ARSENIC DANGLING BONDS Peer-reviewed

Y MOCHIZUKI, T TAKADA, A USUI

PHYSICAL REVIEW B47 ( 20 ) 13420 - 13431   5 1993

NEW CONCERTED MECHANISM OF THE CL-REMOVAL REACTION INDUCED BY H-2 IN CHLORIDE ATOMIC LAYER EPITAXY Peer-reviewed

Y MOCHIZUKI, T TAKADA, A USUI

JAPANESE JOURNAL OF APPLIED PHYSICS PART 2-LETTERS32 ( 2A ) L197 - L199   2 1993

THEORETICAL-STUDIES ON THE ALE PROCESS OF GAAS CRYSTALS Peer-reviewed

Y MOCHIZUKI, T TAKADA

NEC RESEARCH & DEVELOPMENT33 ( 3 ) 518 - 531   7 1992

ELECTRONIC-STRUCTURE OF LOWER SINGLET-STATES OF BINUCLEAR COPPER-ACETATE MONOHYDRATE Peer-reviewed

K OGASAWARA, Y MOCHIZUKI, T NORO, K TANAKA

CANADIAN JOURNAL OF CHEMISTRY-REVUE CANADIENNE DE CHIMIE70 ( 2 ) 393 - 398   2 1992

A THEORETICAL-STUDY OF THE CUOH MOLECULE Peer-reviewed

Y MOCHIZUKI, T TAKADA, A MURAKAMI

CHEMICAL PHYSICS LETTERS185 ( 5-6 ) 535 - 543   10 1991

ELECTRONIC-STRUCTURE OF THE LINEAR FORM OF OCUO Peer-reviewed

Y MOCHIZUKI, K TANAKA, H KASHIWAGI

CHEMICAL PHYSICS151 ( 1 ) 11 - 20   3 1991

A THEORETICAL-STUDY OF THE BENT FORM OF CUO2 Peer-reviewed

Y MOCHIZUKI, U NAGASHIMA, S YAMAMOTO, H KASHIWAGI

CHEMICAL PHYSICS LETTERS164 ( 2-3 ) 225 - 230   12 1989

ELECTRONIC-STRUCTURE OF CO ADSORBED ON SMALL CU CLUSTERS - THEORETICAL-STUDY ON EXCITED-STATES Peer-reviewed

Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI

PHYSICAL REVIEW B39 ( 16 ) 11907 - 11913   6 1989

ABINITIO CAS SCF/MRSDCI STUDY OF THE CUCH2 CLUSTER Peer-reviewed

Y MOCHIZUKI, K TANAKA, K OHNO, H TATEWAKI, S YAMAMOTO

CHEMICAL PHYSICS LETTERS152 ( 6 ) 457 - 463   11 1988

Theoretical Study of the Electronic Structure of CO Adsorbed on Small Cu Clusters Peer-reviewed

Tanaka K, Mochizuki Y, Kawaguchi T, Ohno K, Tatewaki H

Microclusters   82   1987

散逸粒子動力学(DPD)プログラムCAMUSの新規開発と性能評価 Peer-reviewed

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   126 - 128  

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   42 - 46  

AMOSSWEB: ab initio molecular orbital calculation service system in the world-wide web environment Peer-reviewed

Mochizukia Yuji, Yamamotob Akinori, Hiraharab Yukio, Okamotob Naoki, Nishizawab Kaori, Okamotoa Yasuharu, Handab Susumu, Sakumab Toshihiro, Nakadab Hiroshi, Sanoa Tohru, o

Summary of this category Peer-reviewed

Dumitrache A, Frunzulica F, Ionescu TC, c{C } }ekinmez Abdulkerim, Karaosmano{\u{g } }lu Bari{\c{s } }can, Erg{\"u}l, O}zg{\"u}r, Komeiji Yuto, Mochizuki Yuji, Nakano Tatsuya, Mori Hirotoshi