Publication

Software

• “DCDFTBMD: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum Mechanical Molecular Dynamics Simulations”
  Y. Nishimura, H. Nakai, J. Comput. Chem., 40 (15),1538-1549 (2019).

Theory and Implementation

• “Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density functional tight-binding, and massively parallel computation”
  H. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, H. Nakai, J. Comput. Chem., 37 (21), 1983-1992 (2016).
• “Parallel implementation of efficient charge–charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations”
  Y. Nishimura, H. Nakai, J. Comput. Chem., 39 (2), 105-116 (2018).
• “A perspective on density-functional tight-binding parameterization towards transition metals”
  C.-P. Chou, H. Nakai, 分子シミュレーション研究会会誌“アンサンブル”, 20 (1), 8-17 (2018).
• “Development of Large-Scale Excited-State Calculations Based on the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method”
  N. Komoto, T. Yoshikawa, J. Ono, Y. Nishimura, H. Nakai, J. Chem. Theory Comput., 15 (3), 1719-1727 (2019).
• “GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-DependentDensity-functional Tight-binding”
  T. Yoshikawa, N. Komoto, Y. Nishimura, H. Nakai, J. Comuput. Chem., 40 (31), 2778-2786 (2019).
• “Large-Scale Molecular Dynamics Simulation for Ground and Excited States based on Divide-and-Conquer Long-Range Corrected Density Functional Tight-Binding Method”
  N. Komoto, T. Yoshikawa, Y. Nishimura, H. Nakai, J. Chem. Theory Comput., 16 (4), 2369-2378 (2020).
• “Spin-flip approach within time-dependent density functional tight-binding method: Theory and applications”
  M. Inanori, T. Yoshikawa, Y. Ikabata, Y. Nishimura, H. Nakai, J. Comput. Chem., 41 (16), 1538-1548 (2020).
• “Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations”
  Y. Nishimura, H. Nakai, J. Comput. Chem., 41 (19), 1759-1772 (2020).
• “Non-adiabatic molecular dynamics with divide-and-conquer type large-scale excited-state calculations”
  H. Uratani, H. Nakai, J. Chem. Phys., 152 (22), 224109-1-14 (2020).
• “Fast nonadiabatic molecular dynamics via spin-flip time-dependent density-functional tight-binding approach: Application to nonradiative relaxation of tetraphenylethylene with locked aromatic rings”
  H. Uratani, T. Morioka, T. Yoshikawa, H. Nakai, J. Chem. Theory Comput., 16 (12), 7299-7313 (2020).
• “Trajectory surface hopping approach to condensed-phase nonradiative relaxation dynamics using divide-and-conquer spin-flip time-dependent density-functional tight-binding”
  H. Uratani, T. Yoshikawa, H. Nakai, J. Chem. Theory Comput., 17 (3), 1290-1300 (2021).
• “Quantum chemical calculations for up to one hundred million atoms using DCDFTBMD code on supercomputer Fugaku”
  Y. Nishimura, H. Nakai, Chem. Lett., 50 (8), 1546-1550 (2021).
• “Scalable Ehrenfest molecular dynamics exploiting the locality of density-functional tight-binding Hamiltonian”
  H. Uratani, H. Nakai, J. Chem. Theory Comput., 17 (12), 7384-7396 (2021).
• “Species-selective nanoreactor molecular dynamics simulations based on linear-scaling tight-binding quantum chemical calculations”
  Y. Nishimura, H. Nakai, J. Chem. Phys., 158 (5), 054106-1-10 (2023).
• “Enabling large-scale quantum path integral molecular dynamics simulations through the integration of DCDFTBMD and i-PI codes”
  Y. Nishimura, H. Nakai, J. Chem. Phys., 158 (16), 164101-1-8 (2023).
• “Implementation of Nonadiabatic Molecular Dynamics for Intersystem Crossing Based on a Time-Dependent Density-Functional Tight-Binding Method”
  S. Ohno, H. Uratani, H. Nakai, J. Phys. Chem. A, 128 (29), 5999-6009 (2024).

Application

• “Divide-and-conquer-type density-functional tight-binding simulations of proton diffusion in a bulk water system”
  H. Nakai, A. W. Sakti, Y. Nishimura, J. Phys. Chem. B, 120 (1), 217-221 (2016).
• “Divide-and-conquer-type density-functional tight-binding simulations of hydroxide ion diffusion in bulk water”
  A. W. Sakti, Y. Nishimura, H. Nakai, J. Phys. Chem. B, 121 (6), 1362-1371 (2017).
• “Density-functional tight-binding molecular dynamics simulations of excess proton diffusion in ice I_h, Ice I_c, Ice III, and melted ice VI phases”
  A. W. Sakti, Y. Nishimura, C.-P. Chou, H. Nakai, J. Phys. Chem. A, 122 (1), 33-40 (2018).
• “Contrasting mechanisms for CO₂ absorption and regeneration processes in aqueous amine solutions: Insights from density-functional tight-binding molecular dynamics simulations”
  H. Nakai, Y. Nishimura, T. Kaiho, T. Kubota, H. Sato, Chem. Phys. Lett., 647, 127-131 (2016).
• “Divide-and-conquer density-functional tight-binding molecular dynamics study on the formation of carbamate ions during CO₂ chemical absorption in amine solutions”
  A. W. Sakti, Y. Nishimura, H. Sato, H. Nakai, Bull. Chem. Soc. Jpn., 90 (11), 1230-1235 (2017).
• “Rigorous pKa estimation of amine species using density-functional tight-binding-based metadynamics simulations”
  A. W. Sakti, Y. Nishimura, H. Nakai, J. Chem. Theory Comput., 14 (1), 351-356 (2018).
• “Theoretical analysis of carrier ion diffusion in superconcentrated electrolyte solutions for sodium-ion batteries”
  M. Okoshi, C.-P. Chou, H. Nakai, J. Phys. Chem. B, 122 (9), 2600-2609 (2018).
• “Simulations of synthesis of the boron-nitride nanostructures in a hot, high pressure gas volume”
  P. S. Krstic, L. Han, S. Irle, H. Nakai, Chem. Sci., 9 (15), 3803-3819 (2018).
• “Reversible sodium metal electrodes: Is fluorine an essential interphasial component?”
  K. Doi, Y. Yamada, M. Okoshi, J. Ono, C.-P. Chou, H. Nakai, A. Yamada, Angew. Chem. Int. Ed., 58 (24), 8024-8028 (2019).
• “Sodium- and potassium-hydrate melts containing asymmetric imide anions for high-voltage aqueous batteries”
  Q. Zheng, S. Miura, S. Ko, K. Miyazaki, E. Watanabe, M. Okoshi, C.-P. Chou, Y. Nishimura, H. Nakai, T. Kamiya, T. Honda, J. Akikusa, Y. Yamada, A. Yamada, Angew. Chem. Int. Ed., 58 (40), 14202-14207 (2019).
• “Quantum mechanical molecular dynamics simulations of polaron formation in methylammonium lead iodide perovskite”
  H. Uratani, C.-P. Chou, H. Nakai, Phys. Chem. Chem. Phys., 22 (1), 97-106 (2020).
• “Confined water-mediated high proton conduction in hydrophobic channel of a synthetic nanotube”
  K. Otake, K. Otsubo, T. Komatsu, S. Dekura, J. M. Taylor, R. Ikeda, K. Sugimoto, A. Fujiwara, C.-P. Chou, A. W. Sakti, Y. Nishimura, H. Nakai, H. Kitagawa, Nat. Commun., 11, 843-1-7 (2020).
• “Density-functional tight-binding study of carbonaceous species diffusion on the (100)-γ-Al2O3 Surface”
  A. W. Sakti, C.-P. Chou, H. Nakai, ACS Omega, 5 (12), 6862-6871 (2020).
• “Weighted histogram analysis method for multiple short-time metadynamics simulations”
  J. Ono, H. Nakai, Chem. Phys. Lett, 751, 137384-1-7 (2020).
• “Simulating the coupled structural–electronic dynamics of photoexcited lead iodide perovskites”
  H. Uratani, H. Nakai, J. Phys. Chem. Lett., 11 (11), 4448-4455 (2020).
• “Hydroxide ion carrier for proton pumps in bacteriorhodopsin: Primary proton transfer”
  J. Ono, M. Imai, Y. Nishimura, H. Nakai, J. Phys. Chem. B, 124 (39), 8524-8539 (2020).
• “Is oxygen diffusion faster in bulk CeO2 or on a (111)-CeO2 surface? A theoretical study”
  A. W. Sakti, C.-P. Chou, Y. Nishimura, H. Nakai, Chem. Lett., 50 (4), 568-571 (2021).
• “Quantum-mechanical molecular dynamics simulations on secondary proton transfer in bacteriorhodopsin using realistic models”
  H. Nakai, T. Takemura, J. Ono, Y. Nishimura, J. Phys. Chem. B, 125 (39), 10947-10963 (2021).
• “Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations”
  J. Ono, U. Koshimizu, Y. Fukunishi, H. Nakai, Chem. Phys. Lett., 794, 139489-1-8 (2022).
• “Hydroxide ion mechanism for long-range proton pumping in the third proton transfer of bacteriorhodopsin”
  J. Ono, C. Okada, H. Nakai, ChemPhysChem, 23, e202200109-1-11 (2022).
• “Nanoscale and Real-Time Nuclear–Electronic Dynamics Simulation Study of Charge Transfer at the Donor–Acceptor Interface in Organic Photovoltaics”
  H. Uratani, H. Nakai, J. Phys. Chem. Lett., 14 (9), 2292-2300 (2023).
• “Neutral-to-ionic photoinduced phase transition of tetrathiafulvalene-p-chloranil by electronic and vibrational excitation: A real-time nuclear–electronic dynamics simulation study”
  T. Hanada, H. Uratani, H. Nakai, J. Chem. Phys., 159 (5), 054101-1-7 (2023).
• “Quantum mechanical assessment on the optical properties of capsanthin conformers”
  P. A. Putro, A. W. Sakti, F. Ahmad, H. Nakai, H. Alatas, J. Comput. Chem., 44 (30), 2319-2331 (2023).
• “Born–Oppenheimer molecular dynamics study on collective protein dynamics invoked by ultrafast photoisomerization of retinal chromophore in bacteriorhodopsin”
  H. Nakai, H. Uratani, T. Morioka, J. Ono, Chem. Phys. Lett., 830, 140818-1-5 (2023).
• “Fabrication of solid polymer electrolyte based on carboxymethyl cellulose complexed with lithium acetate salt as Lithium-ion battery separator”
  D. A. Darmawan, E. Yulianti, Q. Sabrina, K. Ishida, A. W. Sakti, H. Nakai, E. Pramono, S. T. C. L. Ndruru, Polym. Compos., 45 (3), 2032-2049 (2024).
• “Density-functional tight-binding molecular dynamics study on fixation reaction of CO2 to styrene oxide catalyzed by Mg-MOF-74 metal-organic framework”
  C.-P. Chou, A. W. Sakti, Y. Tsuchiya, Y. Sekine, H. Nakai, Chem. Lett., 53 (1), upae004-1-5 (2024).

Reviews/Japanese

• “分割統治型密度汎関数強束縛分子動力学 (DC-DFTB-MD) 法の最近の展開” (Recent advances in divide-and-conquer density-functional tight-binding molecular dynamics simulations (DC-DFTB-MD))
  西村 好史, 海寳 丈彰, 中井 浩巳, J. Comput. Chem. Jpn., 14 (3), 43-46 (2015).
• “分割統治型密度汎関数強束縛分子動力学（DC-DFTB-MD）法によるナノスケール系化学反応シミュレーション”
  西村 好史, 中井 浩巳, 分子シミュレーション研究会会誌“アンサンブル”, 18 (2), 95-101 (2016).
• “分割統治型密度汎関数強束縛（DC-DFTB）法に対する最近の開発と応用”
  西村 好史, 中井 浩巳, 分子シミュレーション研究会会誌“アンサンブル”, 20 (1), 18-23 (2018).
• “光受容タンパク質の機構解明に向けた分割統治型時間依存密度汎関数強束縛法の開発” (Development of the divide-and-conquer time-dependent density functional tight-binding method for photoreceptor protein)
  河本 奈々, 吉川 武司, 小野 純一,中井 浩巳, J. Comput. Chem. Jpn., 17 (3), 127-129 (2018).
• “DCDFTBMDプログラムの公開”（Release of DCDFTBMD Program）
  西村 好史, 吉川 武司, 中井 浩巳, J. Comput. Chem. Jpn., 17 (5), A21-A27 (2018).
• “分割統治型密度汎関数強束縛分子動力学(DC-DFTB-MD)法による表面反応シミュレーション：Pt(111)表面上のプロトン拡散”(Surface Reaction Simulation based on Divide-and-Conquer Type Density Functional Tight-Binding Molecular Dynamics (DC-DFTB-MD) Method : Case for Proton Diffusion on Pt(111))
  中井 浩巳, 西村 好史, Aditya Wibawa Sakti, Tanabat Mudchimo, 周 建斌, 表面と真空, 62 (5), 486-491 (2019). (2018年日本表面真空学会学術講演会特集号III)
• “大規模量子分子動力学法によるNaイオン二次電池用超濃厚電解液の溶液構造とキャリアイオンダイナミクスの理論的解析”
  大越 昌樹, 周 建斌, 中井 浩巳, 電気化学, 87, 233-238 (2019). (特集:革新的二次電池に向けた電解液/電解質研究の最新動向)
• “ペロブスカイト太陽電池材料におけるポーラロン形成の量子的分子動力学シミュレーション” (Quantum mechanical molecular dynamics simulations of polaron formation in a perovskite solar cell material)
  浦谷 浩輝, 周 建斌, 中井 浩巳, J. Comput. Chem. Jpn., 18 (3), 142-144 (2019).
• “Development of divide-and-conquer density-functional tight-binding method for theoretical research on Li-ion battery”
  C.-P. Chou, A. W. Sakti, Y. Nishimura, H. Nakai, Chem. Rec., 19 (4), 746-757 (2019).
• “Recent Advances in Quantum-Mechanical Molecular Dynamics Simulations of Proton Transfer Mechanism in Various Water-Based Environments”
  A. W. Sakti, Y. Nishimura, H. Nakai, WIREs Comput. Mol. Sci., 10 (1), e1419-1-20 (2020).
• “バクテリオロドプシンの分子動画に基づく大規模量子分子動力学法によるプロトン移動反応の解析”
  小野 純一, 今井 みの莉, 西村 好史, 中井 浩巳, 分子シミュレーション学会誌“アンサンブル”, 23 (3), 171-175 (2021).
• “COVID-19の経口治療薬開発に向けたハイブリッド型in Silico創薬” (Hybrid in Silico drug discovery study toward the development of oral antivirals for COVID-19)
  小清水 初花, 小野 純一, 福西 快文, 中井 浩巳, J. Comput. Chem. Jpn., 21 (2), 48-51 (2022).
• “光活性イエロータンパク質の光反応サイクルにおけるtrans-cis光異性化過程の量子的分子動力学シミュレーション解析” (Quantum Molecular Dynamics Simulation for trans-cis Photoisomerization Process in Photocycle of Photoactive Yellow Protein)
  石田 賢亮, 西村 好史, 中井 浩巳, J. Comput. Chem. Jpn., 22 (2), 9-11 (2023).