Okumura Hisashi 奥村久士

… Alternative Names

OKUMURA HISASHI 奥村久士

奥村久士オクムラヒサシ

奥村久志オクムラヒサシ

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Researcher Number	80360337
External Links
Affiliation (Current)	2025: 大学共同利用機関法人自然科学研究機構(機構直轄研究施設), 生命創成探究センター, 准教授
Affiliation (based on the past Project Information) *help	2023 – 2024: 大学共同利用機関法人自然科学研究機構(機構直轄研究施設), 生命創成探究センター, 准教授 2021 – 2022: 大学共同利用機関法人自然科学研究機構(新分野創成センター、アストロバイオロジーセンター、生命創成探究, 生命創成探究センター, 准教授 2012 – 2017: 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 計算科学研究センター, 准教授 2011: 大学共同利用機関法人自然科学研究機構(共通施設), 計算科学研究センター, 准教授 2007: Nagoya University, 大学院・理学研究科, COE特任講師 … More 2007: 名古屋大学, 大学院・理学研究科, 特任講師 2006: 名古屋大学, 大学院理学研究科, COE特任講師 2006: 名古屋大学, 大学院理学研究科, 特任講師 2005: 自然科学研究機構, 分子科学研究所, 助手 2004 – 2005: 分子科学研究所, 理論分子科学研究系, 助手 2003: 岡崎国立共同研究機構, 分子科学研究所, 助手 Less
Review Section/Research Field	Principal Investigator Basic Section 43040:Biophysics-related / Science and Engineering / Biophysics/Chemical physics / Mathematical physics/Fundamental condensed matter physics Except Principal Investigator Basic Section 52010:General internal medicine-related / Science and Engineering
Keywords	Principal Investigator 分子動力学 / アミロイド線維 / 分子動力学シミュレーション / 界面 / 流れ / タンパク質凝集体 / 水 / ポリアラニン / アミロイドβペプチド / 赤外線レーザー … More / アミロイド / シミュレーション / 分子動力学法 / ペプチド / タンパク質 / 流体力学 / レナード・ジョーンズ流体 / 熱流体 / 液体力学 / シンプレクティック性 / 拡張アンサンブル / 生体分子 / 非平衡統計力学 … More Except Principal Investigator 蛋白質ミスフォールディング病 / 立体構造予測 / 折り畳み / 蛋白質 / 膜タンパク質 / マルチバーリック法 / レプリカ交換法 / モンテカルロ法 / 計算機シミュレーション / マルチカノニカル法 / 拡張アンサンブル法 / 分子動力学法 / 分子シミュレーション / タンパク質の折り畳み Less

脂質膜上の流れによるペプチドの凝集促進機構を分子動力学シミュレーションで解明するPrincipal Investigator
- Principal Investigator
  
  奥村久士
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  National Institutes of Natural Sciences
蛋白質ミスフォールディング病全般に対するペプチドを用いた治療法開発
- Principal Investigator
  
  中村和裕
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 52010:General internal medicine-related
- Research Institution
  Gunma University
Molecular dynamics simulation for the destruction mechanism of amyloid fibrils by laser irradiationPrincipal Investigator
- Principal Investigator
  
  Okumura Hisashi
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 43040:Biophysics-related
- Research Institution
  National Institutes of Natural Sciences
アミロイド線維の動的秩序形成過程の全貌の理論的解明Principal Investigator
- Principal Investigator
  
  奥村久士
- Project Period (FY)
  2016 – 2017
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
親水性/疎水性溶液界面でのアミロイドベータペプチド凝集機構の理論的研究Principal Investigator
- Principal Investigator
  
  奥村久士
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
Development of new molecular dynamics simulation methods and application to protein folding problemPrincipal Investigator
- Principal Investigator
  
  OKUMURA HISASHI
- Project Period (FY)
  2011 – 2014
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biophysics/Chemical physics
- Research Institution
  Okazaki Research Facilities, National Institutes of Natural Sciences
ナノスケールの非定常流を記述する流体力学の統計力学的検証Principal Investigator
- Principal Investigator
  
  奥村久士
- Project Period (FY)
  2005 – 2007
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Mathematical physics/Fundamental condensed matter physics
- Research Institution
  Nagoya University
  Institute for Molecular Science
拡張アンサンブル法による蛋白質折り畳み機構の研究
- Principal Investigator
  
  岡本祐幸
- Project Period (FY)
  2003 – 2007
- Research Category
  
  Grant-in-Aid for Scientific Research on Priority Areas
- Review Section
  
  Science and Engineering
- Research Institution
  Nagoya University
  Institute for Molecular Science
  Okazaki National Research Institutes

[Book] Probing protein misfolding and dissociation with an infrared free-electron laser, Methods in Enzymology, Volume 679 "Integrated Methods in Protein Biochemistry: Part B", Chap. 32023
- Author(s)
  Hisashi Okumura, Takayasu Kawasaki, and Kazuhiro Nakamura
- Total Pages
  32
- Publisher
  Academic Press
- ISBN
  9780323992640
- Data Source
  KAKENHI-PROJECT-21K06118
[Book] 「In Silico 創薬」第4章第1節「高速計算プログラムGEMBによる分子動力学シミュレーションの実際」2018
- Author(s)
  奥村久士
- Publisher
  技術情報協会
- ISBN
  9784861046889
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Book] ベルゲソン生化学の物理的基礎2004
- Author(s)
  谷村吉隆, 佐藤啓, 依田隆夫, 秋山良, 藤原進, 奥村久士共訳(P.R.Bergethon著)
- Total Pages
  603
- Publisher
  シュプリンガー・フェアラーク東京
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] The Double-Layered Structure of Amyloid-β Assemblage on GM1-Containing Membranes Catalytically Promotes Fibrillization2023
- Author(s)
  Yagi-Utsumi Maho、Itoh Satoru G.、Okumura Hisashi、Yanagisawa Katsuhiko、Kato Koichi、Nishimura Katsuyuki
- Journal Title
  
  ACS Chemical Neuroscience
  
  Volume: 14 Issue: 15 Pages: 2648-2657
- DOI
  10.1021/acschemneuro.3c00192
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K06040, KAKENHI-PROJECT-21K06118
[Journal Article] Probing protein misfolding and dissociation with an infrared free-electron laser2023
- Author(s)
  Okumura Hisashi、Kawasaki Takayasu、Nakamura Kazuhiro
- Journal Title
  
  Methods in Enzymology
  
  Volume: 679 Pages: 65-96
- DOI
  10.1016/bs.mie.2022.08.047
- ISBN
  9780323992640
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] Dissociation process of polyalanine aggregates by free electron laser irradiation2023
- Author(s)
  Okumura Hisashi、Itoh Satoru G.、Zen Heishun、Nakamura Kazuhiro
- Journal Title
  
  PLOS ONE
  
  Volume: 18 Issue: 9 Pages: e0291093-e0291093
- DOI
  10.1371/journal.pone.0291093
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] Perspective for Molecular Dynamics Simulation Studies of Amyloid-β Aggregates2023
- Author(s)
  Okumura Hisashi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 127 Issue: 51 Pages: 10931-10940
- DOI
  10.1021/acs.jpcb.3c06051
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] 超音波と赤外線レーザーによるアミロイド線維の破壊を分子動力学シミュレーションで見る2023
- Author(s)
  奥村久士
- Journal Title
  
  高圧力の科学と技術
  
  Volume: 33 Pages: 76-82
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] 赤外自由電子レーザによるアミロイド線維破壊の分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Journal Title
  
  レーザ加工学会誌
  
  Volume: 29 Pages: 160-165
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] Molecular Dynamics Simulation Studies on the Aggregation of Amyloid-β Peptides and Their Disaggregation by Ultrasonic Wave and Infrared Laser Irradiation2022
- Author(s)
  Hisashi Okumura and Satoru G. Itoh
- Journal Title
  
  Molecules
  
  Volume: 27 Issue: 8 Pages: 2483-2483
- DOI
  10.3390/molecules27082483
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K06118
[Journal Article] Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations.2021
- Author(s)
  Okumura H, Itoh SG, Nakamura K, Kawasaki T.
- Journal Title
  
  J. Phys. Chem. B
  
  Volume: in press Issue: 19 Pages: 2361-2368
- DOI
  10.1021/acs.jpcb.0c11491
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K07242, KAKENHI-PROJECT-21K06118, KAKENHI-PROJECT-21K06040
[Journal Article] Theoretical approaches for dynamical ordering of biomolecular systems2018
- Author(s)
  Okumura Hisashi、Higashi Masahiro、Yoshida Yuichiro、Sato Hirofumi、Akiyama Ryo
- Journal Title
  
  Biochimica et Biophysica Acta(BBA) - General Subjects
  
  Volume: 1862 Issue: 2 Pages: 212-228
- DOI
  10.1016/j.bbagen.2017.10.001
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15K05249, KAKENHI-PUBLICLY-16H00774, KAKENHI-PUBLICLY-16H00778, KAKENHI-PUBLICLY-16H00790, KAKENHI-PROJECT-18J14387, KAKENHI-PLANNED-25102002
[Journal Article] Antigen-dependent fluorescence response of anti-c-Myc Quenchbody studied by molecular dynamics simulations2018
- Author(s)
  Yoshiharu Mori, Hisashi Okumura, Takayoshi Watanabe, Takahiro Hohsaka
- Journal Title
  
  Chem. Phys. Lett.
  
  Volume: 698 Pages: 223-226
- DOI
  10.1016/j.cplett.2018.03.011
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H00790, KAKENHI-ORGANIZER-25102001, KAKENHI-PLANNED-25102006, KAKENHI-PROJECT-15K13739, KAKENHI-PROJECT-16K18532
[Journal Article] Classical Molecular Dynamics Simulation to Understand Role of a Zinc Ion for Aggregation of Amyloid-β Peptides2018
- Author(s)
  Hiroaki Nishizawa and Hisashi Okumura
- Journal Title
  
  J. Comput. Chem. Jpn.
  
  Volume: 17 Issue: 1 Pages: 76-79
- DOI
  10.2477/jccj.2018-0005
- NAID
  130006555813
- ISSN
  1347-1767, 1347-3824
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-16H00790, KAKENHI-PROJECT-16J05827, KAKENHI-WRAPUP-18H05203
[Journal Article] Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin2017
- Author(s)
  Yamauchi Masataka、Okumura Hisashi
- Journal Title
  
  The Journal of Chemical Physics
  
  Volume: 147 Issue: 18 Pages: 184107-184107
- DOI
  10.1063/1.4996431
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Journal Article] Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density-functional tight-binding theory and particle mesh Ewald method2016
- Author(s)
  Hiroaki Nishizawa and Hisashi Okumura
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 37 Issue: 31 Pages: 2701-2711
- DOI
  10.1002/jcc.24497
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H00790, KAKENHI-PROJECT-16J05827
[Journal Article] Oligomer formation of amyloid-β(29-42) from its monomers using the Hamiltonian replica-permutation molecular dynamics simulation2016
- Author(s)
  Satoru G. Itoh and Hisashi Okumura
- Journal Title
  
  J. Phys. Chem. B
  
  Volume: 120 Issue: 27 Pages: 6555-6561
- DOI
  10.1021/acs.jpcb.6b03828
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-16H00790, KAKENHI-PROJECT-16K18531
[Journal Article] Structural and fluctuational difference between two ends of Aβ amyloid fibril: MD simulation predicts only one end has open conformations2016
- Author(s)
  Hisashi Okumura and Satoru G. Itoh
- Journal Title
  
  Sci. Rep.
  
  Volume: 6 Issue: 1 Pages: 38422-38422
- DOI
  10.1038/srep38422
- Peer Reviewed / Acknowledgement Compliant / Open Access
- Data Source
  KAKENHI-PUBLICLY-16H00790, KAKENHI-PROJECT-16K18531
[Journal Article] Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms2015
- Author(s)
  Y. MORI and H. OKUMURA
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 36 Issue: 31 Pages: 2344-2349
- DOI
  10.1002/jcc.24213
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-26102550
[Journal Article] Manifold correction method for the Nose-Hoover and Nose-Poincare molecular dynamics simulations2014
- Author(s)
  H. Okumura, S. G. Itoh, A. M. Ito, H. Nakamura, and T. Fukushima
- Journal Title
  
  J. Phys. Soc. Jpn.
  
  Volume: 83 Issue: 2 Pages: 24003-24003
- DOI
  10.7566/jpsj.83.024003
- NAID
  40019984185
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Ｔransformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations2014
- Author(s)
  H.-L. Chiang, C.-J. Chen, H. Okumura, and C.-K. Hu
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 35 Issue: 19 Pages: 1430-1437
- DOI
  10.1002/jcc.23633
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PUBLICLY-26102550
[Journal Article] Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations2014
- Author(s)
  S. G. Itoh and H. Okumura
- Journal Title
  
  J. Phys. Chem. B
  
  Volume: 118 Issue: 39 Pages: 11428-11436
- DOI
  10.1021/jp505984e
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296, KAKENHI-PUBLICLY-26102550
[Journal Article] Amyloid fibril disruption by ultrasonic cavitation: Nonequilibrium molecular dynamics simulations2014
- Author(s)
  H. Okumura and S. G. Itoh
- Journal Title
  
  J. Am. Chem. Soc.
  
  Volume: 136 Issue: 30 Pages: 10549-10552
- DOI
  10.1021/ja502749f
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296, KAKENHI-PUBLICLY-26102550
[Journal Article] Pressure-induced helical structure of a peptide studied by simulated tempering molecular dynamics simulations2013
- Author(s)
  Y. Mori and H. Okumura
- Journal Title
  
  J. Phys. Chem. Lett.
  
  Volume: 4 Issue: 12 Pages: 2079-2083
- DOI
  10.1021/jz400769w
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325
[Journal Article] Cutoff effect in the Nose-Poincare and Nose-Hoover thermostats2013
- Author(s)
  T. Sakaguchi and H. Okumura
- Journal Title
  
  J. Phys. Soc. Jpn
  
  Volume: 82 Issue: 3 Pages: 034001-034001
- DOI
  10.7566/jpsj.82.034001
- NAID
  40019609368
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325
[Journal Article] Transformation of a design peptide between the alpha-helix and beta-hairpin structures by a helix-strand replica-exchange molecular dynamics simulation2013
- Author(s)
  H. Okumura and S. G. Itoh
- Journal Title
  
  Phys. Chem. Chem. Phys.
  
  Volume: 15 Issue: 33 Pages: 13852-13861
- DOI
  10.1039/c3cp44443k
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules2013
- Author(s)
  S. G. Itoh and H. Okumura
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 34 Issue: 8 Pages: 622-639
- DOI
  10.1002/jcc.23167
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Replica-permutation method with the Suwa-Todo algorithm beyond the replica-exchange method2013
- Author(s)
  S. G. Itoh and H. Okumura
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 9 Issue: 1 Pages: 570-581
- DOI
  10.1021/ct3007919
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-beta (29-42) peptides2013
- Author(s)
  S. G. Itoh and H. Okumura
- Journal Title
  
  J. Comput. Chem.
  
  Volume: 34 Issue: 29 Pages: 2493-2497
- DOI
  10.1002/jcc.23402
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Decomposition-order effects of time-integrator on ensemble averages for the Nose-Hoover thermostat2013
- Author(s)
  S. G. Itoh, T. Morishita, and H. Okumura
- Journal Title
  
  J. Chem. Phys.
  
  Volume: 139 Issue: 6 Pages: 64103-64103
- DOI
  10.1063/1.4817194
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325, KAKENHI-PROJECT-24740296
[Journal Article] Temperature and pressure denaturation of chignolin: Folding and unfolding simulation by multibaric-multithermal molecular dynamics method2012
- Author(s)
  H. Okumura
- Journal Title
  
  Proteins
  
  Volume: 80 Issue: 10 Pages: 2397-2416
- DOI
  10.1002/prot.24125
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325
[Journal Article] Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water2011
- Author(s)
  H. Okumura
- Journal Title
  
  Phys. Chem. Chem. Phys.
  
  Volume: 13 Issue: 1 Pages: 114-126
- DOI
  10.1039/c0cp00371a
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325
[Journal Article] Length dependence of polyglycine conformations in vacuum2011
- Author(s)
  S. G. Itoh and H. Okumura
- Journal Title
  
  J. Phys. Soc. Jpn
  
  Volume: 80 Issue: 9 Pages: 094801-094801
- DOI
  10.1143/jpsj.80.094801
- NAID
  40018996934
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23740325
[Journal Article] Multibaric-multithermal molecular dynamics simulation: Generalized Nose-Poincare-Andersen method2007
- Author(s)
  H. Okumura and Y. Okamoto
- Journal Title
  
  Mol. Sim. 33
  
  Pages: 91-96
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles2007
- Author(s)
  H.Okumura, S.G.Itoh, Y.Okamoto
- Journal Title
  
  Journal of Chemical Physics 126
- NAID
  120006545076
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal molecular dynamics simulation of alanine dipe ptide in explicit water2007
- Author(s)
  H. Okumura & Y. Okamoto
- Journal Title
  
  Bulletin of the Chemical Society of Japan 80
  
  Pages: 1114-1123
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles2007
- Author(s)
  H.Okumura, S.G.Itoh, Y.Okamoto
- Journal Title
  
  J. Chem. Phys. 126
  
  Pages: 84103-84103
- NAID
  120006545076
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Multibaric-multithermal molecular dynamics simulation : generalized Nose-Poincare-Andersen method2007
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 91-96
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Hydrodynamics in a Nanoscale Liquid : Comparisons with Molecular Dynamics in Non-stationary Processes2007
- Author(s)
  H.Okumura
- Journal Title
  
  Mol. Phys. 104
  
  Pages: 3751-3756
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Multibaric-multithermal molecular dynamics simulation of alanine dipep tide in explicit water2007
- Author(s)
  H. Okumura and Y. Okamoto
- Journal Title
  
  Bull. Chem. Soc. Jpn. 80
  
  Pages: 1114-1123
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Generalized-ensemble algorithms for molecular dynamics simulations2007
- Author(s)
  S.G.Itoh, H.Okumura, Y.Okamoto
- Journal Title
  
  Molecular Simulation 33
  
  Pages: 47-56
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Generalized-ensemble algorithms for molecular dynamics simulations2007
- Author(s)
  S. G. Itoh, and H. Okumura and Y. Okamoto
- Journal Title
  
  Mol. Sim. 33
  
  Pages: 47-56
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Equation of state and structural properties of the Weeks-Chandler-Andersen fluid2006
- Author(s)
  D.M.Heyes, H.Okumura
- Journal Title
  
  J. Chem. Phys. 124
  
  Pages: 164507-164507
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Multibaric-multithermal ensemble molecular dynamics simulations2006
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  J.Comput.Chem. 27
  
  Pages: 379-395
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] First derivative of the hard-sphere radial distribution function at contact2006
- Author(s)
  D.M.Heyes, M.Cass, A.C.Branka, H.Okumura
- Journal Title
  
  J. Phys. : Condens. Matter 18
  
  Pages: 7553-7558
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Stationary temperature profiles in a liquiad nano-channel : comparisons between molecular dynamics simulation and classical hydrostatics2006
- Author(s)
  H.Okumura, D.M.Heyes
- Journal Title
  
  Phys. Rev. E 74
  
  Pages: 61201-61201
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Multibaric-multithermal ensemble molecular dynamics simulations2006
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Journal of Computational Chemistry 27
  
  Pages: 379-395
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Some physical properties of the Weeks-Chandler -Andersen fluid2006
- Author(s)
  D.M.Heyes, H.Okumura
- Journal Title
  
  Mol. Sim. 32
  
  Pages: 45-50
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Molecular simulations in the multibaric-multithermal Ensembles2005
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Comput.Phys.Commun. 169
  
  Pages: 317-321
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] マルチバーリック・マルチサーマルアンサンブルにおけるレナード・ジョーンズ流体のシミュレーション2005
- Author(s)
  奥村久士, 岡本祐幸
- Journal Title
  
  物性研究 85
  
  Pages: 341-346
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal ensemble simulations for fluid systems2005
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Physica A 350
  
  Pages: 150-158
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Liquid-gas phase transitions studied by multibaric-multithermal Monte Carlo simulations2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  J.Phys.Soc.Jpn. 73
  
  Pages: 3304-3311
- NAID
  110001979299
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Monte Carlo simulations in new generalized isobaric-isothermal ensemble2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Trans.MRS-J. 29
  
  Pages: 3783-3786
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Molecular dynamics simulations in multibaric-multithermal ensemble2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Chem.Phys.Lett. 383
  
  Pages: 403-408
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Monte Carlo simulations in generalized isobaric-isothermal ensembles2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Phys.Rev.E 70
  
  Pages: 26702-26702
- NAID
  120006545921
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Multibaric-multithermal ensemble simulation for simple liquids2004
- Author(s)
  H.Okumura, Y.Okamoto
- Journal Title
  
  Mol.Sim. 30
  
  Pages: 847-852
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Comparisons between a molecular dynamics and hydrodynamics treatment of non-stationary thermal processes in a liquid2004
- Author(s)
  H.Okumura, D.M.Heyes
- Journal Title
  
  Phys.Rev.E 70
  
  Pages: 61206-61206
- Data Source
  KAKENHI-PROJECT-15076213
[Journal Article] Some physical properties of the Weeks-Chandler-Andersen Fluid
- Author(s)
  D.M.Heyes, H.Okumura
- Journal Title
  
  Mol.Phys. (印刷中)
- Data Source
  KAKENHI-PROJECT-17740260
[Journal Article] Equation of state and structural properties of the Weeks-Chandler-Andersen Fluid
- Author(s)
  D.M.Heyes, H.Okumura
- Journal Title
  
  J.Chem.Phys. (印刷中)
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Disease-related proteins studied by molecular dynamics simulations2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  ACS Global Innovation Imperatives - 7th International Conference on Computation for Science and Technology
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 中赤外レーザーによるアミロイドβ凝集体の選択的破壊2023
- Author(s)
  奥村久士
- Organizer
  多元技術融合光プロセス研究会
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Molecular dynamics simulation for the causative substance of Alzheimer's disease2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  5th International Conference on Materials Research and Innovation
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Aggregation and disaggregation of amyloid-β peptides observed by all-atom molecular dynamics simulations2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  The 26th International Annual Symposium on Computational Science and Engineering
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] コンピュータシミュレーョンで見るアルツハイマー病原因物質の分子動画2023
- Author(s)
  奥村久士
- Organizer
  第32回高速分子動画オンラインセミナー
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] All-atom molecular dynamics simulations for the formation and dissociation of amyloid-β aggregates / アミロイドβ凝集体の形成と解離の全原子分子動力学シミュレーション2023
- Author(s)
  奥村久士
- Organizer
  第61回日本生物物理学会年会シンポジウム「Liquid-liquid phase separation and amyloid formation driven by dynamic solution environments / 動的溶液環境が駆動する生体内液液相分離とアミロイド線維化」
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 病気の原因となるタンパク質の分子動力学シミュレーション2023
- Author(s)
  奥村久士
- Organizer
  企業研究会第36期CAMMフォーラム
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Replica-permutation and nonequilibrium molecular dynamics simulations for protein aggregates2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  Biomolecules and Nanostructures 8
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Amyloid-fibril dissociation observed by nonequilibrium molecular dynamics simulation2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  The 16th Eurasia Conference on Chemical Sciences
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Generalized-ensemble and nonequilibrium molecular dynamics simulations of protein aggregates2023
- Author(s)
  Hisashi Okumura
- Organizer
  Asia and Pacific Conference of Theoretical and Computational Chemistry
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Key factors for aggregation and disaggregation of amyloid-β peptides revealed by molecular dynamics simulations2023
- Author(s)
  Hisashi OKUMURA
- Organizer
  19th International Conference of Computational Methods in Sciences and Engineering
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Protein aggregation and disaggregation by generalized-ensemble and nonequilibrium molecular dynamics simulations2022
- Author(s)
  Hisashi Okumura
- Organizer
  4th International Conference on Materials Research and Innovation
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 生体機能に重要な分子の全原子分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  Biothermology Workshop 2022
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 非平衡分子動力学シミュレーションで見る極限環境下におけるアミロイド線維破壊2022
- Author(s)
  奥村久士
- Organizer
  第63回高圧討論会
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 分子動力学シミュレーションで見る赤外自由電子レーザーによるアミロイド線維の破壊2022
- Author(s)
  奥村久士
- Organizer
  第35回日本放射光学会年会・放射光科学合同シンポジウム　企画講演：赤外自由電子レーザーによる物質研究の現状と未来展望
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] アミロイドβペプチドの凝集と解離の分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  第59回日本生物物理学会年会シンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] アミロイドβペプチド凝集体の非平衡分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  Mie Meeting of Quantum Science
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 新型コロナウイルスの増殖とアルツハイマー病の発症に関するタンパク質の分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  スーパーコンピュータワークショップ2021
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Disaggregation of amyloid-β aggregates observed by nonequilibrium molecular dynamics simulations2022
- Author(s)
  Hisashi Okumura
- Organizer
  18th International Conference of Computational Methods in Sciences and Engineering
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 病気に関係する生体分子の分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  生理学研究所ネットワーク型研究加速事業報告会
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] アミロイド線維の非平衡分子動力学シミュレーション2022
- Author(s)
  奥村久士
- Organizer
  山形大学理学部　離散数理セミナー
- Invited
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] 分子動力学法で調べた赤外自由電子レーザーによるアミロイド線維の破壊とヘリックス構造の安定化2021
- Author(s)
  奥村久士，伊藤暁, 中村和裕, 川崎平康
- Organizer
  第35回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Molecular dynamics simulation of disease-related biomolecules2021
- Author(s)
  Hisashi Okumura
- Organizer
  2nd International Conference on Materials Research and Innovation
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Role of water molecules and helix-structure stabilization in the laser-induced disruption of amyloid fibrils observed by nonequilibrium molecular dynamics simulations2021
- Author(s)
  Hisashi Okumura
- Organizer
  Skype seminar
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] Nonequilibrium molecular dynamics simulation to reveal a role of water molecules in laser-induced disruption of amyloid brils2021
- Author(s)
  Hisashi Okumura, Satoru G. Itoh, Kazuhiro Nakamura, Takayasu Kawasaki
- Organizer
  XXXI I IUPAP Conference on Computational Physics (CCP2021)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06118
[Presentation] アミロイド線維の生体分子動力学シミュレーション2018
- Author(s)
  奥村久士
- Organizer
  企業研究会第31期CAMMフォーラム本例会
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 気液界面でのアミロイドβフラグメントの凝集シミュレーション2018
- Author(s)
  奥村久士
- Organizer
  日本物理学会　第73回年次大会
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 分子動力学シミュレーションによる親水性/疎水性界面でのアミロイドβフラグメントの凝集2017
- Author(s)
  奥村久士
- Organizer
  第11回分子科学討論会
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations for aggregation and disaggregation of amyloid-β peptides2017
- Author(s)
  Hisashi Okumura
- Organizer
  EMN Meeting on Computation and Theory 2017
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 分子動力学シミュレーションによるアミロイド線維の形成過程と破壊過程2017
- Author(s)
  奥村久士
- Organizer
  近畿化学協会コンピュータ化学部会例会
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 親水性/疎水性界面におけるアミロイドβフラグメントの凝集の分子動力学シミュレーション2017
- Author(s)
  奥村久士
- Organizer
  日本生物物理学会　第55回年会
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations for creation and disruption of amyloid fibrils2017
- Author(s)
  Hisashi Okumura
- Organizer
  International Symposium on Molecular Science - Physical Chemistry/Theoretical Chemistry, Chemoinformatics, Computational Chemistry
- Place of Presentation
  Keio University, Yokohama, Kanagawa, Japan
- Year and Date
  2017-03-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] アミロイド線維の分子動力学シミュレーション2017
- Author(s)
  奥村久士
- Organizer
  慶應義塾大学理工学部物理学科談話会
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] All-Atom Molecular Dynamics Simulations of Amyloid-β Fragment Aggregation2017
- Author(s)
  Hisashi Okumura, Satoru G. Itoh
- Organizer
  The 5th International Symposium on Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
- Place of Presentation
  The University of Tokyo, Meguro, Tokyo, Japan
- Year and Date
  2017-01-21
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 気液界面でのアミロイドβ(16-22)の凝集シミュレーション2017
- Author(s)
  奥村久士
- Organizer
  第31回分子シミュレーション討論会
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Amyloid fibril formation by molecular dynamics simulations2017
- Author(s)
  Hisashi Okumura
- Organizer
  NCTS December Workshop on Critical Phenomena and Complex Systems
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Equilibrium and nonequilibrium molecular dynamics simulations of Aβ amyloid fibrils2017
- Author(s)
  Hisashi Okumura
- Organizer
  10th International Conference on Computational Physics
- Place of Presentation
  Holiday Inn, Sands Cotai Central, Macau, China
- Year and Date
  2017-01-16
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations of Aβ amyloid fibrils in equilibrium and nonequilibrium systems2017
- Author(s)
  Hisashi Okumura
- Organizer
  3rd Japan-Thai workshop on Theoretical and Computational Chemistry 2017
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations for fluctuation and disruption of amyloid fibril2017
- Author(s)
  Hisashi Okumura
- Organizer
  NCTS March Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  National Tsing Hua University, Hsinchu, Taiwan
- Year and Date
  2017-03-30
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 分子動力学シミュレーションで調べたアミロイド線維の揺らぎと破壊2017
- Author(s)
  奥村久士
- Organizer
  第2回計算分子科学の若手研究会
- Place of Presentation
  金沢工業大学，石川県金沢市
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] All-atom molecular dynamics simulations to reveal dynamical ordering of amyloid fibril2017
- Author(s)
  Hisashi Okumura
- Organizer
  International Conference of Computational Methods in Sciences and Engineering 2017
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] アミロイド線維のシミュレーション‐構造サンプリングと非平衡分子動力学‐2017
- Author(s)
  奥村久士
- Organizer
  第11回革新的量子化学シンポジウム～量子的自然の叡智と美～
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Simulational studies of Aβ amyloid fibrils by equilibrium and nonequilibrium molecular dynamics method2017
- Author(s)
  Hisashi Okumura
- Organizer
  Annual Symposium on Computational Science and Engineering
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] All-atom molecular dynamics simulations of Aβ amyloid fibrils2017
- Author(s)
  Hisashi Okumura
- Organizer
  Institute for Protein Research (IPR) Seminar
- Place of Presentation
  Osaka University, Suita, Osaka, Japan
- Year and Date
  2017-01-26
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] アミロイドベータペプチドの分子動力学シミュレーション2017
- Author(s)
  奥村久士，伊藤暁
- Organizer
  スーパーコンピュータワークショップ2016
- Place of Presentation
  岡崎コンファレンスセンター，愛知県岡崎市
- Year and Date
  2017-02-01
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations of amyloid fibrils2016
- Author(s)
  奥村久士
- Organizer
  2016 NCTS March Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  National Tsing Hua University, Hsinchu, Taiwan
- Year and Date
  2016-03-28
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Pressure induced structural change of proteins by molecular dynamics simulations2016
- Author(s)
  奥村久士
- Organizer
  Eighth Japan-Korea Seminars on Biomolecular Sciences
- Place of Presentation
  Institute for Molecular Science, Okazaki, Aichi, Japan
- Year and Date
  2016-02-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] 分子動力学シミュレーションによるアミロイドβペプチドの集合と離散2016
- Author(s)
  奥村久士
- Organizer
  第四回CUTEシンポジウム：コンピュータ化学
- Place of Presentation
  三重大学，三重県津市
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Dynamical ordering of amyloid fibril studied by molecular dynamics simulations2016
- Author(s)
  Hisashi Okumura
- Organizer
  Thai-Japan Symposium in Chemistry
- Place of Presentation
  Chiang Mai University, Chiang Mai, Thailand
- Year and Date
  2016-11-14
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations for assembly and disassembly of Aβ amyloid fibrils2016
- Author(s)
  Hisashi Okumura
- Organizer
  8th IKUSTAR
- Place of Presentation
  Kasetsart University, Bangkok, Thailand
- Year and Date
  2016-06-02
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] All-atom molecular dynamics simulations of amyloid-beta fibril in explicit water2016
- Author(s)
  Hisashi Okumura, Satoru G. Itoh
- Organizer
  STATPHYS26
- Place of Presentation
  Palais des congres, Lyon, France
- Year and Date
  2016-07-18
- Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Suwa-Todo algorithm in generalized-ensemble algorithms: Replica-permutation and simulated tempering methods2016
- Author(s)
  Hisashi Okumura
- Organizer
  Free Energy Landscape of Protein Folding and Dynamics by Simulations based on Enhanced Conformational Sampling Algorithms
- Place of Presentation
  Nagoya University, Nagoya, Aichi, Japan
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations to study dynamical ordering of amyloid fibril2016
- Author(s)
  Hisashi Okumura
- Organizer
  NCTS October Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  National Taiwan University, Hsinchu, Taiwan
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] Molecular dynamics simulations of proteins under high pressure2016
- Author(s)
  奥村久士
- Organizer
  Pure and Applied Chemistry International Conference 2016
- Place of Presentation
  Bangkok International Trade & Exhibition Centre, Bangkok, Thailand
- Year and Date
  2016-01-09
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] 分子動力学シミュレーションの基礎と生体分子の動的秩序形成研究への応用2016
- Author(s)
  奥村久士
- Organizer
  第3回新学術領域研究「動的秩序と機能」若手研究会
- Place of Presentation
  加賀観光ホテル，石川県加賀市
- Year and Date
  2016-10-11
- Invited
- Data Source
  KAKENHI-PUBLICLY-16H00790
[Presentation] 分子動力学シミュレーションによるアミロイド線維の離合集散2016
- Author(s)
  奥村久士
- Organizer
  日本化学会第96春季年会
- Place of Presentation
  同志社大学京田辺キャンパス　京都府京田辺市
- Year and Date
  2016-03-24
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Molecular dynamics simulations for aggregation and disaggregation of amyloid-β peptides2015
- Author(s)
  奥村久士
- Organizer
  2015 Taiwan International Workshop on Biological Physics and Complex Systems
- Place of Presentation
  National Taiwan University, Taipei, Taiwan
- Year and Date
  2015-06-24
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Molecular dynamics simulations for oligomerization and disruption of amyloid-β fibril2015
- Author(s)
  奥村久士
- Organizer
  The International Chemical Congress of Pacific Basin Societies 2015 (Pacifichem 2015)
- Place of Presentation
  Hawaii Convention Center, Honolulu, Hawaii, USA
- Year and Date
  2015-12-15
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Nonequilibrium molecular dynamics simulation of amyloid-fibril disassembly by supersonic cavitation2015
- Author(s)
  奥村久士
- Organizer
  International workshop on complex phenomena from molecule to society
- Place of Presentation
  University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Year and Date
  2015-11-24
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Replica-permutation method for protein simulation and amyloid disruption by cavitation in non-equilibrium molecular dynamics simulation2014
- Author(s)
  Hisashi Okumura
- Organizer
  Joint IMS-KU workshop on molecular sciences towards green sustainability
- Place of Presentation
  Kasetsart University, Bangkok, Thailand
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] All-atom molecular dynamics simulations of amyloid-fibril disruption and peptide oligomerization2014
- Author(s)
  Hisashi Okumura
- Organizer
  Mini Symposium
- Place of Presentation
  Institute for Molecular Science, Okazaki, Aichi, Japan
- Year and Date
  2014-12-17
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] All-atom molecular dynamics simulations of amyloid-fibril disruption and peptide oligomerization2014
- Author(s)
  Hisashi Okumura
- Organizer
  Mini Symposium
- Place of Presentation
  Institute for Molecular Science, Okazaki, Aichi, Japan
- Year and Date
  2014-12-17
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] キャビテーションによるアミロイド破壊の非平衡分子動力学シミュレーション2014
- Author(s)
  奥村久士
- Organizer
  山手イブニングセミナー
- Place of Presentation
  岡崎統合バイオサイエンスセンター（愛知県岡崎市）
- Year and Date
  2014-06-06
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] キャビテーションによるアミロイド破壊の非平衡分子動力学シミュレーション2014
- Author(s)
  奥村久士
- Organizer
  山手イブニングセミナー
- Place of Presentation
  岡崎統合バイオサイエンスセンター（愛知県岡崎市）
- Year and Date
  2014-06-06
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Replica-permutation molecular dynamics simulation of biomolecules2014
- Author(s)
  Hisashi Okumura
- Organizer
  Pure and Applied Chemistry International Conference 2014
- Place of Presentation
  Centara Hotel, Khon Kaen, Thailand
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Introduction to molecular dynamics simulation and its application2013
- Author(s)
  Hisashi Okumura
- Organizer
  Sokendai Asian Winter School, National Institute for Fusion Science
- Place of Presentation
  National Institute for Fusion Science, Toki, Japan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Replica-permutation method for protein simulations and pressure-induced denaturation2013
- Author(s)
  Hisashi Okumura
- Organizer
  Sixth Japan-Korea Seminars on Biomolecular Sciences
- Place of Presentation
  Institute for Molecular Science, Okazaki, Japan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Molecular dynamics simulations for amyloid disruption by supersonic wave2013
- Author(s)
  Hisashi Okumura
- Organizer
  2013 NCTS November Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] New Type of the Hamiltonian Replica-Exchange Molecular Dynamics Method2012
- Author(s)
  H. Okumura
- Organizer
  2012 NCTS Spring Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] All-Atom Generalized-Ensemble Molecular Dynamics Simulations of Proteins2012
- Author(s)
  H. Okumura
- Organizer
  5th Japan-Russia International Workshop “Molecular Simulation Studies in Material and Biological Sciences”
- Place of Presentation
  Joint Institute for Nuclear Research, Moscow, Russia
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Generalized-ensemble Molecular Dynamics Simulations for Temperature and Pressure Denaturation of a Protein2012
- Author(s)
  H. Okumura
- Organizer
  Indo-Japan Workshop on Recent Advances in Spectroscopy and Microscopy: Fundamentals and Applications to Materials and Biology
- Place of Presentation
  Hyderabad University, Hyderabad, India
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Multibaric-multithermal molecular dynamics simulations for temperature and pressure denaturation of a protein2012
- Author(s)
  H. Okumura
- Organizer
  The 17th Biophysics Conference of Biophysical Society of Republic of China
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Helix-strand replica-exchange molecular dynamics method and its application2012
- Author(s)
  H. Okumura
- Organizer
  2012 NCTS November Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] マルチバーリック・マルチサーマル分子動力学法によるアラニンジペプチドの力場依存性2007
- Author(s)
  奥村久士、岡本祐幸
- Organizer
  日本物理学会第62回年次大会
- Place of Presentation
  札幌
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Symplectic molecular dynamics integrator for rigid-body molecules in the canonical ensemble2007
- Author(s)
  Hisashi Okumura
- Organizer
  2007 NCTS May Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Chinese Culture University, Taipei
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] 拡張アンサンブル分子動力学法によるペプチドの研究2007
- Author(s)
  奥村久士、岡本祐幸
- Organizer
  第21回分子シミュレーション討論会
- Place of Presentation
  金沢
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Temperature and pressure dependence of a peptide studied by multibaric-multithermal moleculal dynamics simulations2007
- Author(s)
  Hisashi Okumura
- Organizer
  2007 NCTS May Workshop on Critical Phenomena and Complex Systems
- Place of Presentation
  Chinese Culture University, Taipei
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] シンプレクティック拡張アンサンブル法による水中の生体分子の温度・圧力依存性2007
- Author(s)
  奥村久士、岡本祐幸
- Organizer
  第1回分子科学討論会
- Place of Presentation
  仙台
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Multibaric-multithermal molecular dynamics simulations of alanine dipeptide2007
- Author(s)
  Hisashi Okumura
- Organizer
  Conference on Computational Physics 2007
- Place of Presentation
  Brussels, Belgium
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Multibaric-multithermal molecular dynamics simulations of alanine dipeptide2007
- Author(s)
  Hisashi Okumura
- Organizer
  2007 Taiwan International Workshop on Biological Physics and Complex Systems
- Place of Presentation
  Academia Sinica, Taipei
- Data Source
  KAKENHI-PROJECT-17740260
[Presentation] Molecular dynamics simulations for amyloid fibril disruption and dimerization of amyloid-beta peptides
- Author(s)
  Hisashi Okumura
- Organizer
  2nd International Conference on Computational Science and Engineering
- Place of Presentation
  Ho Chi Minh City, Vietnam
- Year and Date
  2014-08-21 – 2014-08-23
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] アミロイド線維の形成初期過程と破壊の分子動力学シミュレーション
- Author(s)
  奥村久士
- Organizer
  スーパーコンピュータワークショップ2015
- Place of Presentation
  分子科学研究所（愛知県岡崎市）
- Year and Date
  2015-01-29 – 2015-01-30
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril
- Author(s)
  Hisashi Okumura
- Organizer
  11th International Conference of Computational Methods in Sciences and Engineering
- Place of Presentation
  Athens, Greece
- Year and Date
  2015-03-20 – 2015-03-23
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Generalized-ensemble algorithms to determine free-energy landscape of proteins
- Author(s)
  Hisashi Okumura
- Organizer
  10th International Conference of Computational Methods in Sciences and Engineering
- Place of Presentation
  Athens, Greece
- Year and Date
  2014-04-04 – 2014-04-07
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Multibaric-multithermal molecular dynamics simulations of alanine dipeptide and chignolin
- Author(s)
  奥村久士
- Organizer
  2011 NCTS June Workshop on Critical Phenomena and Complex Systems(招待講演)
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Generalized-ensemble molecular dynamics simulations
- Author(s)
  Hisashi Okumura
- Organizer
  UST-Sokendai Joint Seminar on Computational Sciences
- Place of Presentation
  Daejeon, Korea
- Year and Date
  2014-07-29 – 2014-08-01
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] 拡張アンサンブル分子動力学法によるタンパク質の温度・圧力変性
- Author(s)
  奥村久士
- Organizer
  「自然科学における階層と全体」シンポジウム(招待講演)
- Place of Presentation
  安保ホール（愛知県）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] アミロイド線維の破壊と形成初期過程の分子動力学シミュレーション
- Author(s)
  奥村久士
- Organizer
  第二回CUTEシンポジウム
- Place of Presentation
  三重大学（三重）
- Year and Date
  2014-10-30 – 2014-10-31
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] タンパク質シミュレーションのための新しい拡張アンサンブル分子動力学法
- Author(s)
  奥村久士
- Organizer
  「非平衡を制御する科学」第２回研究会(招待講演)
- Place of Presentation
  鳥取大学（鳥取県）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] 親水性/疎水性溶液界面でのアミロイドベータペプチド凝集機構の理論的研究
- Author(s)
  奥村久士
- Organizer
  新学術領域「動的秩序と機能」全体班会議
- Place of Presentation
  粟津温泉おびし荘（石川県小松市）
- Year and Date
  2014-08-04 – 2014-08-07
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Nonequilibrium and generalized-ensemble molecular dynamics simulations for amyloid fibril
- Author(s)
  Hisashi Okumura
- Organizer
  11th International Conference of Computational Methods in Sciences and Engineering
- Place of Presentation
  Athens, Greece
- Year and Date
  2015-03-20 – 2015-03-23
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Temperature and pressure denaturation of a protein and peptide by multibaric-multithermal molecular dynamics simulations
- Author(s)
  奥村久士
- Organizer
  Forth Japan-Korea Seminar on Biomolecular Sciences - Experiments and Simulations(招待講演)
- Place of Presentation
  Cultural Center of Todaiji-Temple, Nara, Japan
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] アミロイド線維の破壊と形成初期過程の分子動力学シミュレーション
- Author(s)
  奥村久士
- Organizer
  第二回CUTEシンポジウム
- Place of Presentation
  三重大学（三重県津市）
- Year and Date
  2014-10-30 – 2014-10-31
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] 拡張アンサンブル分子動力学法の開発とタンパク質への応用
- Author(s)
  奥村久士
- Organizer
  「非平衡を制御する科学」第１回研究会(招待講演)
- Place of Presentation
  核融合科学研究所（岐阜県）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Molecular dynamics simulations for amyloid fibril disruption and dimerization of amyloid-beta peptides
- Author(s)
  Hisashi Okumura
- Organizer
  2nd International Conference on Computational Science and Engineering
- Place of Presentation
  Ho Chi Minh City, Vietnam
- Year and Date
  2014-08-21 – 2014-08-23
- Invited
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] マルチバーリック・マルチサーマル分子動力学シミュレーションによるシニョリンの温度・圧力変性の研究
- Author(s)
  奥村久士
- Organizer
  第11回日本蛋白質科学会年会
- Place of Presentation
  ホテル阪急エキスポパーク（大阪）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Temperature and pressure denaturation of a protein by all-atom generalized-ensemble molecular dynamics simulations
- Author(s)
  奥村久士
- Organizer
  2011 Taiwan International Workshop on Biological Physics and Complex Systems(招待講演)
- Place of Presentation
  Academia Sinica, Taipei, Taiwan
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] アミロイド線維の形成初期過程と破壊の分子動力学シミュレーション
- Author(s)
  奥村久士
- Organizer
  スーパーコンピュータワークショップ2015
- Place of Presentation
  分子科学研究所（愛知県岡崎市）
- Year and Date
  2015-01-29 – 2015-01-30
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] マルチバーリック・マルチサーマル分子動力学法によるシニョリンの温度・圧力変性
- Author(s)
  奥村久士
- Organizer
  日本生物物理学会　第49回年会
- Place of Presentation
  兵庫県立大学（兵庫県）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] Generalized-ensemble molecular dynamics simulations
- Author(s)
  Hisashi Okumura
- Organizer
  UST-Sokendai Joint Seminar on Computational Sciences
- Place of Presentation
  Daejeon, Korea
- Year and Date
  2014-07-29 – 2014-08-01
- Invited
- Data Source
  KAKENHI-PUBLICLY-26102550
[Presentation] Protein simulations by new generalized-ensemble molecular dynamics algorithms
- Author(s)
  奥村久士
- Organizer
  The 5th Mini-Symposium on Liquids(招待講演)
- Place of Presentation
  Okayama University, Okayama, Japan
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] マルチバーリック・マルチサーマル分子動力学シミュレーションによるシニョリンの温度・圧力変性
- Author(s)
  奥村久士
- Organizer
  第25回分子シミュレーション討論会
- Place of Presentation
  東京工業大学（東京都）
- Data Source
  KAKENHI-PROJECT-23740325
[Presentation] シニョリンのマルチバーリック・マルチサーマル分子動力学シミュレーション
- Author(s)
  奥村久士
- Organizer
  日本物理学会　2011年秋季大会
- Place of Presentation
  富山大学（富山県）
- Data Source
  KAKENHI-PROJECT-23740325

1. 岡本祐幸 (70185487)

# of Collaborated Projects: 1 results

# of Collaborated Products: 12 results
2. 中村和裕 (10327835)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
3. 川崎平康

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
4. 秋山良

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
5. 伊藤暁

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Okumura Hisashi 奥村 久士

OKUMURA HISASHI 奥村 久士

奥村 久士 オクムラ ヒサシ

奥村 久志 オクムラ ヒサシ

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脂質膜上の流れによるペプチドの凝集促進機構を分子動力学シミュレーションで解明するPrincipal Investigator

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蛋白質ミスフォールディング病全般に対するペプチドを用いた治療法開発

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Molecular dynamics simulation for the destruction mechanism of amyloid fibrils by laser irradiationPrincipal Investigator

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アミロイド線維の動的秩序形成過程の全貌の理論的解明Principal Investigator

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親水性/疎水性溶液界面でのアミロイドベータペプチド凝集機構の理論的研究Principal Investigator

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Development of new molecular dynamics simulation methods and application to protein folding problemPrincipal Investigator

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ナノスケールの非定常流を記述する流体力学の統計力学的検証Principal Investigator

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拡張アンサンブル法による蛋白質折り畳み機構の研究

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[Book] Probing protein misfolding and dissociation with an infrared free-electron laser, Methods in Enzymology, Volume 679 "Integrated Methods in Protein Biochemistry: Part B", Chap. 32023

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[Book] 「In Silico 創薬」第4章第1節「高速計算プログラムGEMBによる分子動力学シミュレーションの実際」2018

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[Book] ベルゲソン 生化学の物理的基礎2004

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[Journal Article] The Double-Layered Structure of Amyloid-β Assemblage on GM1-Containing Membranes Catalytically Promotes Fibrillization2023

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[Journal Article] Probing protein misfolding and dissociation with an infrared free-electron laser2023

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Okumura Hisashi 奥村久士

OKUMURA HISASHI 奥村久士

奥村久士オクムラヒサシ

奥村久志オクムラヒサシ

[Book] ベルゲソン生化学の物理的基礎2004