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Researcher Information

last modified:2024/07/21

Associate Professor KAWAGUCHI, Kazutomo

Mail

Faculty, Affiliation

Faculty of Mathematics and Physics, Institute of Science and Engineering

College and School Educational Field

Division of Mathematical and Physical Science, Graduate School of Natural Science and Technology
School of Mathematics and Physics, College of Science and Engineering

Laboratory

Academic Background

【Academic background(Doctoral/Master's Degree)】
Nagoya University Doctor Graduate School, Division of Natural Science 200803 Completed
【Academic background(Bachelor's Degree)】
Nagoya University 200303
【Degree】
Ph. D.

Career

Post Doctral Fellow(2008/04/01-2010/09/30)

Year & Month of Birth

1981/01

Academic Society



Award

Specialities

Biological physics/Chemical physics/Soft matter physics、Biophysics

Speciality Keywords

Research Themes

Formation mechanism of protein complex

Books

Papers

  •  Conformations of Three Types of Ultra-Long-Chain Fatty Acids in Multicomponent Lipid Bilayers Kazutomo Kawaguchi,Hidemi Nagao,Hideo Shindou,Hiroshi Noguchi Journal of Physical Chemistry B 126 45 9316 2022/11/17
  •  A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer Kazutomo Kawaguchi, Satoshi Nakagawa, Isman Kurniawan, Koichi Kodama, Muhammad Saleh Arwansyah, Hidemi Nagao Molecular Physics 5 116 649-657 2018
  •  Molecular dynamics study of lipid bilayer asymmetry induced by ion concentration gradient and electronic polarizability Kazutomo Kawaguchi,Seiichiro Ito,Hiroaki Saito,Hidemi Nagao Molecular Simulation 1 2022/02/02 
  •  A simple coarse-grained model for interacting protein complex Molecular Physics 5 115 587-597 2017
  •  MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms Journal of Chemical Theory and Computation 7 9 3201-3209 2013/07

show all

  •  Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect Satoshi Nakagawa, Isman Kurniawan, Koichi Kodama, Muhammad Saleh Arwansyah, Kazutomo Kawaguchi, Hidemi Nagao Molecular Physics 116 5 666-677 2018
  •  Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics AIP Conference Proceedings 1518 637-640 2013
  •  Molecular dynamics analyses of the dissociation process of ADP from Hsp90 INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 24 112 3791-3795 2012/06
  •  Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation JPS Conf. Proc. 1 012056 2014
  •  Decomposition analysis of free energy profile for Hsp90-ADP association Molecular Simulation 42 896-901 2016
  •  Theoretical prediction of optical absorption maxima for photosensory receptor mutants Kazutomo Kawaguchi,Takahisa Yamato CHEMICAL PHYSICS LETTERS 430 4-6 386 2006/10
  •  A molecular dynamics study of Hras-GTP and GDP complexes: The properties of water molecules around guanine nucleotide T. Miyakawa,R. Morikawa,M. Takasu,K. Sugimori,K. Kawaguchi,H. Saito,H. Nagao AIP Conference Proceedings 1518 594 2013 
  •  Molecular dynamics analyses of the dissociation process of ADP from Hsp90 Kazutomo Kawaguchi,Hiroyuki Takagi,Masashi Iwayama,Megumi Nishimura,Takeshi Miyakawa,Hiroaki Saito,Masako Takasu,Hidemi Nagao INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 24 3791 2012/12 
  •  A theoretical study on redox potential and pKa of [2Fe-2S] cluster model from iron-sulfur proteins Isman Kurniawan,Isman Kurniawan,Kazutomo Kawaguchi,Mitsuo Shoji,Toru Matsui,Yasuteru Shigeta,Hidemi Nagao Bulletin of the Chemical Society of Japan 91 9 1451 2018/01/01 
  •  A simple coarse-grained model for interacting protein complex Kazutomo Kawaguchi,Satoshi Nakagawa,Shogo Kinoshita,Makoto Wada,Hiroaki Saito,Hidemi Nagao MOLECULAR PHYSICS 115 5 587 2017
  •  Decomposition analysis of free energy profile for Hsp90-ADP association Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao MOLECULAR SIMULATION 42 11 896 2016
  •  A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules Masashi Iwayama,Isman Kurniawan,Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao MOLECULAR SIMULATION 41 10-12 936 2015/08
  •  MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program for Large-Scale Systems with Long-Range Forces Calculated by Fast Multipole Method (FMM) and Highly Scalable Fine-Grained New Parallel Processing Algorithms Yoshimichi Andoh,Noriyuki Yoshii,Kazushi Fujimoto,Keisuke Mizutani,Hidekazu Kojima,Atsushi Yamada,Susumu Okazaki,Kazutomo Kawaguchi,Hidemi Nagao,Kensuke Iwahashi,Fumiyasu Mizutani,Kazuo Minami,Shin-ichi Ichikawa,Hidemi Komatsu,Shigeru Ishizuki,Yasuhiro Takeda,Masao Fukushima JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9 7 3201 2013/07
  •  Transition state analysis of azurin via Go-like model M. Rusmerryani,M. T. Pakpahan,M. Nishimura,M. Takasu,K. Kawaguchi,H. Saito,H. Nagao AIP Conference Proceedings 1518 641 2013 
  •  Molecular Dynamics Study on Entrainment Phenomenon in Model Molecular Systems Hidemi Nagao,Shuhei Kawamoto,Micke Rusmerryani,Acep Purqon,Kazutomo Kawaguchi,Hiroaki Saito 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU 1518 729 2013 
  •  Theoretical model for assessing properties of local structures in metalloprotein M. Koyimatu,H. Shimahara,M. Iwayama,K. Sugimori,K. Kawaguchi,H. Saito,H. Nagao AIP Conference Proceedings 1518 626 2013 
  •  Molecular dynamics study of gramicidin a in lipid bilayer: Structure and lateral pressure profile Hiroaki Saito,Masashi Iwayama,Hiroyuki Takagi,Megumi Nishimura,Takeshi Miyakawa,Kazutomo Kawaguchi,Masako Takasu,Taku Mizukami,Hidemi Nagao INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 112 24 3834 2012/12 
  •  Stress tensor analysis of the protein quake of photoactive yellow protein Kana Koike,Kazutomo Kawaguchi,Takahisa Yamato PHYSICAL CHEMISTRY CHEMICAL PHYSICS 10 10 1400 2008/03
  •  Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90 Kazutomo Kawaguchi,Hiroaki Saito,Susumu Okazaki,Hidemi Nagao CHEMICAL PHYSICS LETTERS 588 226 2013/11 
  •  Network of Water Molecules Around Guanine Nucleotide in the Hras–GTP and -GDP Complexes by MD Simulations Takeshi Miyakawa,Ryota Morikawa,Masako Takasu,Kimikazu Sugimori,Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao JPS Conf. Proc. 1 016006 2014/03 
  •  Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics Kazutomo Kawaguchi,Hiroyuki Takagi,Masako Takasu,Hiroaki Saito,Hidemi Nagao 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU 1518 637 2013 
  •  Analysis of Water Molecules in the Hras-GTP and GDP Complexes with Molecular Dynamics Simulations Takeshi Miyakawa,Ryota Morikawa,Masako Takasu,Akira Dobashi,Kimikazu Sugimori,Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao ADVANCES IN QUANTUM METHODS AND APPLICATIONS IN CHEMISTRY, PHYSICS, AND BIOLOGY 27 351 2013
  •  Molecular dynamics study of binary POPC bilayers: molecular condensing effects on membrane structure and dynamics SAITO Hiroaki IOP Conf. Series: Journal of Physics: Conf. Series 1136 1136 012022 2018 
  •  A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer Kazutomo Kawaguchi,Satoshi Nakagawa,Isman Kurniawan,Koichi Kodama,Muhammad Saleh Arwansyah,Hidemi Nagao Molecular Physics 116 5-6 649 2018/03/19
  •  Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex Takeshi Miyakawa,Ryota Morikawa,Masako Takasu,Kimikazu Sugimori,Taku Mizukami,Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao International Journal of Quantum Chemistry 113 21 2333 2013/11/05 
  •  Evaluation of Scoring Functions for Protein-ligand Docking M. T. Pakpahan,M. Rusmerryani,K. Kawaguchi,H. Saito,H. Nagao 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU 1518 645 2013 
  •  Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect Satoshi Nakagawa,Isman Kurniawan,Koichi Kodama,Muhammad Saleh Arwansyah,Kazutomo Kawaguchi,Hidemi Nagao Molecular Physics 116 5-6 666 2018/03/19
  •  Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations Takeshi Miyakawa,Ryota Morikawa,Masako Takasu,Kimikazu Sugimori,Kazutomo Kawaguchi,Hiroaki Saito,Hidemi Nagao MOLECULAR PHYSICS 112 3-4 526 2014/02 
  •  Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A Hiroaki Saito,Megumi Nishimura,Hiroyuki Takagi,Takeshi Miyakawa,Kazutomo Kawaguchi,Hidemi Nagao 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU 1518 633 2013 
  •  Conformational Stability of Met20 Loop of DHFR : A molecular Dynamics Study Megumi Nishimura,Hiroaki Saito,Kazutomo Kawaguchi,Hidemi Nagao 4TH INTERNATIONAL SYMPOSIUM ON SLOW DYNAMICS IN COMPLEX SYSTEMS: KEEP GOING TOHOKU 1518 654 2013 
  •  Quantum Chemical Study of Axial Ligand Effect on the Electronic Properties of Type I Copper Protein Kurniawan Isman,Kawaguchi Kazutomo,Sugimori Kimikazu,Sakurai Takeshi,Nagao Hidemi CHEMISTRY LETTERS 47 9 1172 2018/09
  •  The Study of the Octanol-Water Partition Coefficient by the Computational Chemistry Method Koichi KODAMA,Arwan SYAH,Kazutomo KAWAGUCHI,Toru MATSUI,Hidemi NAGAO,Yasuteru SHIGETA Journal of Computer Chemistry, Japan 18 5 241 2019 
  •  Conformation of ultra-long-chain fatty acid in lipid bilayer: Molecular dynamics study Kazutomo Kawaguchi,Koh M. Nakagawa,Satoshi Nakagawa,Hideo Shindou,Hidemi Nagao,Hiroshi Noguchi The Journal of Chemical Physics 153 16 165101 2020/10/28 
  •  Free energy profiles of lipid translocation across pure POPC and POPC/CHOL bilayer: all-atom molecular dynamics study Hiroaki Saito,Tetsuya Morishita,Taku Mizukami,Ken-ichi Nishiyama,Kazutomo Kawaguchi,Hidemi Nagao IOP Conf. Series: Journal of Physics: Conf. Series 1290 012020 2019/11
  •  Theoretical Study of Dissociation Process of Plastocyanins by PaCS-MD Simulation D Fitrasari,M S Arwansyah,K Kawaguchi,A Purqon,Suprijadi,H Nagao Journal of Physics: Conference Series 2207 1 012021 2022/03/01 
  •  Theoretical Study of Complex Aspirin and Hydroxypropyl-β-cyclodextrin in Solvent Phase H Jayyinunnisya,L S Solihat,K Sugimori,K Kawaguchi,H Nagao Journal of Physics: Conference Series 2207 1 012022 2022/03/01 
  •  Theoretical study of conformational transition of CDK4 by association of cyclin D3 Kawaguchi Kazutomo,Arwansyah Muhammad Saleh,Kataoka Tatsuki,Nagao Hidemi MOLECULAR PHYSICS 117 17 2355 2019/09/02
  •  Theoretical studies on electronic structure and properties of type I copper center in copper proteins KURNIAWAN Isman,Kawaguchi Kazutomo,SUGIMORI Kimikazu,SAKURAI Takeshi,Nagao Hidemi The Science Reports of Kanazawa University = The Science Reports of Kanazawa University 63 1 2019 

Conference Presentations

  • Molecular dynamics study of ultra-long-chain fatty acids in lipid bilayer(conference:9th International Discussion Meeting on Relaxation in Complex Systems)(2023/08/18)
  • Binding free energy calculation for mutated protein complex system(2023/11/14)
  • Development of Coarse-grained model for protein complex(conference:20th IUPAB Congress)(2021/10/04)
  • Coarse-grained model for protein-nucleotide interaction(conference:XXXII IUPAP Conference on Computational Physics)(2021/08/01)
  • Theoretical study of complex formation of Plastocyanin and Cytochrome f(2021/11/25)

show all

  • Theoretical study on a resting membrane potential by using all-atom molecular dynamics simulations(2018/09/15)
  • Theoretical Study of Intermolecular Interaction for Protein Systems (conference:International Workshop on Computational Science 2017)(2017/02/15)
  • Development of a coarse-grained model for charged amino acid residues(2017/09/19)

Others

  •  Conformation of Ultra-Long Chain Fatty Acid in Lipid Bilayer Activity Report 2022 Institute for Solid State Physics, The University of Tokyo  2023/07/01
  •  Molecular Dynamics Study of Ultra-Long Chain Fatty Acid in Lipid Bilayer Activity Report 2022 Supercomputer Center, Institute for Solid State Physics, The University of Tokyo  2023/06/01

Arts and Fieldwork

Patent

Theme to the desired joint research

○Molecular dynamics simulation for biomolecular system

Grant-in-Aid for Scientific Research

○「分子動力学計算によるアミノ酸変異タンパク質複合体の結合自由エネルギーシフトの予測」(2023-2025) 

Competitive research funding,Contribution

Collaborative research,Consignment study

Classes (Bachelors)

○Presentation and Debate (Freshman Seminar II)(2021)
○Freshman Seminar I(2021)
○Exercise in Mechanics 2(2021)
○Academic Skills(2021)
○Presentation and Debate(2021)
○Computer Experiments 2(2021)
○Computer Experiments 2(2020)
○Exercise in Mechanics 2(2020)
○Selected Topics(2020)
○Exercise in Mechanics 2(2019)
○Computer Experiments 2(2019)
○Research Work in Computational Experimental Science(2018)
○Exercise in Mechanics 2(2018)
○Computer Experiments 2(2018)
○Computer Experiments 2(2017)
○Exercise in Mechanics 2(2017)
○Research Work in Computational Experimental Science(2017)
○Computer Experiments 2(2016)
○Exercise in Mechanics 2(2016)
○Research Work in Computational Experimental Science(2016)
○Computer Experiments 2(2010)
○Exercise in Thermodynamics Statistical Mechanics 2(2010)

Classes (Graduate Schools)

○Scientific Presentation B(2021)
○Introduction to Frontiers of Computational Science a(2021)
○Topics in Computational Science b(2021)
○Computational Chemistry and Bioscience B(2021)
○Topics in Computational Science a(2021)
○Computational Chemistry and Bioscience A(2021)
○Introduction to Frontiers of Computational Science b(2021)
○Computational Chemistry and Bioscience a(2021)
○Computational Chemistry and Bioscience b(2021)
○Applied Computational Science a(2021)
○Applied Computational Science b(2021)
○Research Work B(2021)
○Research Work B(2021)
○Scientific Presentation B(2021)
○Scientific Presentation B(2020)
○Scientific Presentation B(2020)
○Computational Chemistry and Bioscience B(2020)
○Computational Chemistry and Bioscience A(2020)
○Computational Chemistry and Bioscience a(2020)
○Introduction to Frontiers of Computational Science a(2020)
○Computational Chemistry and Bioscience b(2020)
○Introduction to Frontiers of Computational Science b(2020)
○Research Work B(2020)
○Special Lectures on Computational Science(2020)
○Research Work B(2020)
○Applied Computational Science a(2020)
○Applied Computational Science b(2020)
○Computational Chemistry and Bioscience b(2019)
○Applied Computational Science b(2019)
○Introduction to Frontiers of Computational Science b(2019)
○Introduction to Frontiers of Computational Science a(2019)
○Research Work B(2019)
○Scientific Presentation B(2019)
○Scientific Presentation B(2019)
○Research Work B(2019)
○Computational Chemistry and Bioscience a(2019)
○Applied Computational Science a(2019)
○Introduction to Frontiers of Computational Science b(2018)
○Introduction to Frontiers of Computational Science a(2018)
○Computational Chemistry and Bioscience a(2018)
○Computational Chemistry and Bioscience b(2018)
○Applied Computational Science a(2018)
○Applied Computational Science b(2018)
○Seminar B(2018)
○Research Work B(2018)
○Exercise B(2018)
○Cooperative Studies with Jaist(2018)
○Topics in Computational Science a(2018)
○Topics in Computational Science b(2018)
○Exercise B(2017)
○Introduction to Frontiers of Computational Science a(2017)
○Research Work B(2017)
○Introduction to Frontiers of Computational Science b(2017)
○Seminar B(2017)
○Topics in Computational Science a(2016)
○Introduction to Frontiers of Computational Science b(2016)
○Introduction to Frontiers of Computational Science a(2016)
○Exercise B(2016)
○Applied Computational Science b(2016)
○Applied Computational Science a(2016)
○Seminar B(2016)
○Computational Chemistry and Bioscience b(2016)
○Topics in Computational Science b(2016)
○Computational Chemistry and Bioscience a(2016)
○Research Work B(2016)
○Exercise B(2012)
○Seminar B(2012)
○Introduction to Frontiers of Computational Science(2012)
○Research Work B(2012)
○Research Work(2011)

International Project

International Students

Lecture themes

Others (Social Activities)

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