{"id":47,"date":"2026-03-29T17:34:14","date_gmt":"2026-03-29T08:34:14","guid":{"rendered":"http:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/?page_id=47"},"modified":"2026-03-29T17:34:14","modified_gmt":"2026-03-29T08:34:14","slug":"%e8%ab%96%e6%96%87%e4%b8%80%e8%a6%a7","status":"publish","type":"page","link":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/?page_id=47&lang=en","title":{"rendered":"Publication"},"content":{"rendered":"<h2 class=\"block-editor-rich-text__editable editor-rich-text__editable\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" data-is-placeholder-visible=\"false\" aria-label=\"\u898b\u51fa\u3057\u3092\u5165\u529b...\" aria-autocomplete=\"list\">Software<\/h2>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.25804\">&#8220;DCDFTBMD: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum Mechanical Molecular Dynamics Simulations&#8221; <\/a><br \/>\nY. Nishimura, H. Nakai, <em>J. Comput<\/em>. <em>Chem.<\/em>, <strong>40<\/strong> (15),1538-1549 (2019).<\/li>\n<\/ul>\n<h2 class=\"block-editor-rich-text__editable editor-rich-text__editable\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" data-is-placeholder-visible=\"false\" aria-label=\"\u898b\u51fa\u3057\u3092\u5165\u529b...\" aria-autocomplete=\"list\"><span style=\"font-size: x-large;\" data-rich-text-format-boundary=\"true\">Theory and Implementation<\/span><\/h2>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.24419\">&#8220;Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density functional tight-binding, and massively parallel computation&#8221;<\/a><br \/>\nH. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, H. Nakai,\u00a0<em>J. Comput. Chem.<\/em>,\u00a0<strong>37<\/strong>\u00a0(21), 1983-1992 (2016).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.25086\">&#8220;Parallel implementation of efficient charge\u2013charge interaction evaluation scheme in periodic divide-and-conquer density-functional tight-binding calculations&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai,\u00a0<em>J. Comput. Chem.<\/em>,\u00a0<strong>39<\/strong> (2), 105-116 (2018).<\/li>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/mssj\/20\/1\/20_8\/_article\/-char\/ja\">&#8220;A perspective on density-functional tight-binding parameterization towards transition metals&#8221;<\/a><br \/>\nC.-P. Chou, H. Nakai, \u5206\u5b50\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u7814\u7a76\u4f1a\u4f1a\u8a8c\u201c\u30a2\u30f3\u30b5\u30f3\u30d6\u30eb\u201d,\u00a0<strong>20<\/strong> (1), 8-17 (2018).<\/li>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jctc.8b01214\">&#8220;Development of Large-Scale Excited-State Calculations Based on the Divide-and-Conquer Time-Dependent Density Functional Tight-Binding Method&#8221;<\/a><br \/>\nN. Komoto, T. Yoshikawa, J. Ono, Y. Nishimura, H. Nakai,\u00a0<em>J. Chem. Theory Comput.<\/em>, <strong>15<\/strong> (3), 1719-1727 (2019).<\/li>\n<li><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jcc.26053\">&#8220;GPU-Accelerated Large-Scale Excited-State Simulation Based on Divide-and-Conquer Time-DependentDensity-functional Tight-binding&#8221;<\/a><br \/>\nT. Yoshikawa, N. Komoto, Y. Nishimura, H. Nakai, <em>J. Comuput. Chem.<\/em>, <strong>40<\/strong> (31), 2778-2786 (2019).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.9b01268\">&#8220;Large-Scale Molecular Dynamics Simulation for Ground and Excited States based on Divide-and-Conquer Long-Range Corrected Density Functional Tight-Binding Method&#8221;<\/a><br \/>\nN. Komoto, T. Yoshikawa, Y. Nishimura, H. Nakai, <em>J. Chem. Theory Comput.<\/em>, <strong>16<\/strong> (4), 2369-2378 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.26197\">&#8220;Spin-flip approach within time-dependent density functional tight-binding method: Theory and applications&#8221;<\/a><br \/>\nM. Inanori, T. Yoshikawa, Y. Ikabata, Y. Nishimura, H. Nakai, <em>J. Comput. Chem.<\/em>,\u00a0<strong>41<\/strong> (16), 1538-1548 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.26217\">&#8220;Hierarchical parallelization of divide-and-conquer density functional tight-binding molecular dynamics and metadynamics simulations&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai, <em>J. Comput. Chem.<\/em>,\u00a0<strong>41<\/strong> (19), 1759-1772 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1063\/5.0006831\">&#8220;Non-adiabatic molecular dynamics with divide-and-conquer type large-scale excited-state calculations&#8221;<\/a><br \/>\nH. Uratani, H. Nakai, <em>J. Chem. Phys.<\/em>, <strong>152<\/strong> (22), 224109-1-14 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.0c00936\">&#8220;Fast nonadiabatic molecular dynamics via spin-flip time-dependent density-functional tight-binding approach: Application to nonradiative relaxation of tetraphenylethylene with locked aromatic rings&#8221;<\/a><br \/>\nH. Uratani, T. Morioka, T. Yoshikawa, H. Nakai, <em>J. Chem. Theory Comput.<\/em>, <strong>16<\/strong> (12), 7299-7313 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.0c01155\">&#8220;Trajectory surface hopping approach to condensed-phase nonradiative relaxation dynamics using divide-and-conquer spin-flip time-dependent density-functional tight-binding&#8221;<\/a><br \/>\nH. Uratani, T. Yoshikawa, H. Nakai, <em>J. Chem. Theory Comput.<\/em>, <strong>17<\/strong> (3), 1290-1300 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1246\/cl.210263\">&#8220;Quantum chemical calculations for up to one hundred million atoms using DCDFTBMD code on supercomputer Fugaku&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai, <em>Chem. Lett.<\/em>, <strong>50<\/strong> (8), 1546-1550 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.1c00950\">&#8220;Scalable Ehrenfest molecular dynamics exploiting the locality of density-functional tight-binding Hamiltonian&#8221;<\/a><br \/>\nH. Uratani, H. Nakai, <em>J. Chem. Theory Comput.<\/em>, <strong>17<\/strong> (12), 7384-7396 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1063\/5.0132573\">&#8220;Species-selective nanoreactor molecular dynamics simulations based on linear-scaling tight-binding quantum chemical calculations&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai, <em>J. Chem. Phys.<\/em>, <strong>158<\/strong> (5), 054106-1-10 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1063\/5.0147535\">&#8220;Enabling large-scale quantum path integral molecular dynamics simulations through the integration of DCDFTBMD and i-PI codes&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai, <em>J. Chem. Phys.<\/em>, <strong>158<\/strong> (16), 164101-1-8 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpca.4c02422\">&#8220;Implementation of Nonadiabatic Molecular Dynamics for Intersystem Crossing Based on a Time-Dependent Density-Functional Tight-Binding Method&#8221;<\/a><br \/>\nS. Ohno, H. Uratani, H. Nakai, <em>J. Phys. Chem. A<\/em>, <strong>128<\/strong> (29), 5999-6009 (2024).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1016\/j.cplett.2025.142474\">&#8220;Extension of quantum-chemistry-based accelerated molecular dynamics by decomposing total energy into constituent atoms: A case study for density functional tight-binding simulations of condensed phase systems&#8221;<\/a><br \/>\nY. Nishimura, H. Nakai, <em>Chem. Phys. Lett.<\/em>, <strong>882<\/strong>, 142474-1-9 (2026).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpclett.6c00047\">&#8220;Development of a Fluctuation-Assisted Molecular Dynamics Method for the Efficient Exploration of Chemical Reactions&#8221;<\/a><br \/>\nS. Tsukamura, Y. Nishimura, H. Nakai, <em>J. Phys. Chem. Lett.<\/em>, <strong>17<\/strong> (11), 3102-3107 (2026).<\/li>\n<\/ul>\n<h2 class=\"block-editor-rich-text__editable editor-rich-text__editable\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" data-is-placeholder-visible=\"false\" aria-label=\"\u898b\u51fa\u3057\u3092\u5165\u529b...\" aria-autocomplete=\"list\">Application<\/h2>\n<ul>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.5b12439\">&#8220;Divide-and-conquer-type density-functional tight-binding simulations of proton diffusion in a bulk water system&#8221;<\/a><br \/>\nH. Nakai, A. W. Sakti, Y. Nishimura,\u00a0<em>J. Phys. Chem. B<\/em>,\u00a0<strong>120<\/strong>\u00a0(1), 217-221 (2016).<\/li>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.6b10659\">&#8220;Divide-and-conquer-type density-functional tight-binding simulations of hydroxide ion diffusion in bulk water&#8221;<\/a><br \/>\nA. W. Sakti, Y. Nishimura, H. Nakai,\u00a0<em>J. Phys. Chem. B<\/em>,\u00a0<strong>121<\/strong>\u00a0(6), 1362-1371 (2017).<\/li>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpca.7b10664\">&#8220;Density-functional tight-binding molecular dynamics simulations of excess proton diffusion in ice I<sub>h<\/sub>, Ice I<sub>c<\/sub>, Ice III, and melted ice VI phases&#8221;<\/a><br \/>\nA. W. Sakti, Y. Nishimura, C.-P. Chou, H. Nakai, <em>J. Phys. Chem. A<\/em>,\u00a0<strong>122<\/strong>\u00a0(1), 33-40 (2018).<\/li>\n<li><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S000926141600083X\">&#8220;Contrasting mechanisms for CO<sub>2<\/sub>\u00a0absorption and regeneration processes in aqueous amine solutions: Insights from density-functional tight-binding molecular dynamics simulations&#8221;<\/a><br \/>\nH. Nakai, Y. Nishimura, T. Kaiho, T. Kubota, H. Sato,\u00a0<em>Chem. Phys. Lett.<\/em>,\u00a0<strong>647<\/strong>, 127-131 (2016).<\/li>\n<li><a href=\"https:\/\/www.journal.csj.jp\/doi\/10.1246\/bcsj.20170142\">&#8220;Divide-and-conquer density-functional tight-binding molecular dynamics study on the formation of carbamate ions during CO<sub>2<\/sub>\u00a0chemical absorption in amine solutions&#8221;<\/a><br \/>\nA. W. Sakti, Y. Nishimura, H. Sato, H. Nakai, <em>Bull. Chem. Soc. Jpn.<\/em>,\u00a0<strong>90<\/strong>\u00a0(11), 1230-1235 (2017).<\/li>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jctc.7b00855\">&#8220;Rigorous p<em>K<\/em><span style=\"font-size: 12px;\">a<\/span> estimation of amine species using density-functional tight-binding-based metadynamics simulations&#8221;<\/a><br \/>\nA. W. Sakti, Y. Nishimura, H. Nakai, <em>J. Chem. Theory Comput.<\/em>,\u00a0<strong>14<\/strong>\u00a0(1), 351-356 (2018).<\/li>\n<li><a href=\"https:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.7b10589\">&#8220;Theoretical analysis of carrier ion diffusion in superconcentrated electrolyte solutions for sodium-ion batteries&#8221;<\/a><br \/>\nM. Okoshi, C.-P. Chou, H. Nakai,\u00a0<em>J. Phys. Chem. B<\/em>,\u00a0<strong>122<\/strong>\u00a0(9), 2600-2609 (2018).<\/li>\n<li><a href=\"https:\/\/pubs.rsc.org\/en\/content\/articlelanding\/2018\/sc\/c8sc00667a\">&#8220;Simulations of synthesis of the boron-nitride nanostructures in a hot, high pressure gas volume&#8221;<\/a><br \/>\nP. S. Krstic, L. Han, S. Irle, H. Nakai,\u00a0<em>Chem. Sci.<\/em>,\u00a0<strong>9<\/strong>\u00a0(15), 3803-3819 (2018).<\/li>\n<li value=\"251\"><a href=\"https:\/\/doi.org\/10.1002\/anie.201901573\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Reversible sodium metal electrodes: Is fluorine an essential interphasial component?&#8221;<\/a><br \/>\nK. Doi, Y. Yamada, M. Okoshi, J. Ono, C.-P. Chou, H. Nakai, A. Yamada, <i>Angew. Chem. Int. Ed.,<\/i> <strong>58<\/strong> (24), 8024-8028 (2019).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/anie.201908830\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Sodium- and potassium-hydrate melts containing asymmetric imide anions for high-voltage aqueous batteries&#8221;<\/a><br \/>\nQ. 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, <em>Angew. Chem. Int. Ed.,<\/em> <strong>58<\/strong> (40), 14202-14207 (2019).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1039\/C9CP04739E\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Quantum mechanical molecular dynamics simulations of polaron formation in methylammonium lead iodide perovskite&#8221;<\/a><br \/>\nH. Uratani, C.-P. Chou, H. Nakai<em>, Phys. Chem. Chem. Phys.,<\/em> <strong>22<\/strong> (1), 97-106 (2020).<\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41467-020-14627-z\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Confined water-mediated high proton conduction in hydrophobic channel of a synthetic nanotube&#8221;<\/a><br \/>\nK. 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,<em> Nat. Commun.,<\/em> <strong>11<\/strong>, 843-1-7 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acsomega.0c00203\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Density-functional tight-binding study of carbonaceous species diffusion on the (100)-<em>\u03b3<\/em>-Al<span style=\"font-size: 12px;\">2<\/span>O<span style=\"font-size: 12px;\">3<\/span> Surface&#8221;<\/a><br \/>\nA. W. Sakti, C.-P. Chou, H. Nakai,<em> ACS Omega,<\/em> <strong>5 <\/strong>(12), 6862-6871 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1016\/j.cplett.2020.137384\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Weighted histogram analysis method for multiple short-time metadynamics simulations&#8221;<\/a><br \/>\nJ. Ono, H. Nakai,<em> Chem. Phys. Lett,<\/em> <strong>751<\/strong>, 137384-1-7 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpclett.0c01028\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Simulating the coupled structural\u2013electronic dynamics of photoexcited lead iodide perovskites&#8221;<\/a><br \/>\nH. Uratani, H. Nakai,<em> J. Phys. Chem. Lett.,<\/em> <strong>11 <\/strong>(11), 4448-4455 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpcb.0c05507\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Hydroxide ion carrier for proton pumps in bacteriorhodopsin: Primary proton transfer&#8221;<\/a><br \/>\nJ. Ono, M. Imai, Y. Nishimura, H. Nakai,<em> J. Phys. Chem. B,<\/em> <strong>124 <\/strong>(39), 8524-8539 (2020).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1246\/cl.200895\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Is oxygen diffusion faster in bulk CeO<span style=\"font-size: 12px;\">2<\/span> or on a (111)-CeO<span style=\"font-size: 12px;\">2<\/span> surface? A theoretical study&#8221;<\/a><br \/>\nA. W. Sakti, C.-P. Chou, Y. Nishimura, H. Nakai,<em> Chem. Lett.,<\/em> <strong>50 <\/strong>(4), 568-571 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpcb.1c06231\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Quantum-mechanical molecular dynamics simulations on secondary proton transfer in bacteriorhodopsin using realistic models&#8221;<\/a><br \/>\nH. Nakai, T. Takemura, J. Ono, Y. Nishimura,<em> J. Phys. Chem. B,<\/em> <strong>125 <\/strong>(39), 10947-10963 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1016\/j.cplett.2022.139489\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations&#8221;<\/a><br \/>\nJ. Ono, U. Koshimizu, Y. Fukunishi, H. Nakai,<em> Chem. Phys. Lett.,<\/em> <strong>794<\/strong>, 139489-1-8 (2022).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/cphc.202200109\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Hydroxide ion mechanism for long-range proton pumping in the third proton transfer of bacteriorhodopsin&#8221;<\/a><br \/>\nJ. Ono, C. Okada, H. Nakai,<em> ChemPhysChem,<\/em> <strong>23<\/strong>, e202200109-1-11 (2022).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpclett.2c03808\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Nanoscale and Real-Time Nuclear\u2013Electronic Dynamics Simulation Study of Charge Transfer at the Donor\u2013Acceptor Interface in Organic Photovoltaics&#8221;<\/a><br \/>\nH. Uratani, H. Nakai,<em> J. Phys. Chem. Lett.,<\/em> <strong>14 <\/strong>(9), 2292-2300 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1063\/5.0159424\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Neutral-to-ionic photoinduced phase transition of tetrathiafulvalene-<em>p<\/em>-chloranil by electronic and vibrational excitation: A real-time nuclear\u2013electronic dynamics simulation study&#8221;<\/a><br \/>\nT. Hanada, H. Uratani, H. Nakai,<em> J. Chem. Phys.,<\/em> <strong>159 <\/strong>(5), 054101-1-7 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/jcc.27199\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Quantum mechanical assessment on the optical properties of capsanthin conformers&#8221;<\/a><br \/>\nP. A. Putro, A. W. Sakti, F. Ahmad, H. Nakai, H. Alatas,<em> J. Comput. Chem.,<\/em> <strong>44 <\/strong>(30), 2319-2331 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1016\/j.cplett.2023.140818\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Born\u2013Oppenheimer molecular dynamics study on collective protein dynamics invoked by ultrafast photoisomerization of retinal chromophore in bacteriorhodopsin&#8221;<\/a><br \/>\nH. Nakai, H. Uratani, T. Morioka, J. Ono, <em>Chem. Phys. Lett.,<\/em> <strong>830<\/strong>, 140818-1-5 (2023).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/pc.27902\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Fabrication of solid polymer electrolyte based on carboxymethyl cellulose complexed with lithium acetate salt as Lithium-ion battery separator&#8221;<\/a><br \/>\nD. A. Darmawan, E. Yulianti, Q. Sabrina, K. Ishida, A. W. Sakti, H. Nakai, E. Pramono, S. T. C. L. Ndruru,<em> Polym. Compos.,<\/em> <strong>45 <\/strong>(3), 2032-2049 (2024).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1093\/chemle\/upae004\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Density-functional tight-binding molecular dynamics study on fixation reaction of CO2 to styrene oxide catalyzed by Mg-MOF-74 metal-organic framework&#8221;<\/a><br \/>\nC.-P. Chou, A. W. Sakti, Y. Tsuchiya, Y. Sekine, H. Nakai,<em> Chem. Lett.,<\/em> <strong>53 <\/strong>(1), upae004-1-5 (2024).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1038\/s42004-025-01790-x\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Insights into proton transfer dynamics in histidine tautomers of amyloid-\u03b2 (1-40)&#8221;<\/a><br \/>\nY. Tang, Y. Nishimura, N. Li, H. Li, A. Salimi, K. Ishida, A. W. Sakti, H. Nakai, R. Parida, J. Y. Lee,<em> Commun. Chem.,<\/em> <strong>8<\/strong>, 408-1-10 (2025).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1021\/acs.jpcc.5c07064\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;Density-Functional Tight-Binding Molecular Dynamics Simulation of Graphene Oxide-Ionic Liquid Electrolyte Interface in Sodium-Ion Batteries&#8221;<\/a><br \/>\nM. F. Maahury, A. W. Sakti, H. Nakai,<em> J. Phys. Chem. C,<\/em> <strong>130 <\/strong>(12), 4524-4537 (2023).<\/li>\n<\/ul>\n<h2 class=\"block-editor-rich-text__editable editor-rich-text__editable\" role=\"textbox\" contenteditable=\"true\" aria-multiline=\"true\" data-is-placeholder-visible=\"false\" aria-label=\"\u898b\u51fa\u3057\u3092\u5165\u529b...\" aria-autocomplete=\"list\">Reviews\/Japanese<\/h2>\n<ul>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/jccj\/14\/3\/14_2015-0031\/_article\/-char\/ja\/\">&#8220;\u5206\u5272\u7d71\u6cbb\u578b\u5bc6\u5ea6\u6c4e\u95a2\u6570\u5f37\u675f\u7e1b\u5206\u5b50\u52d5\u529b\u5b66 (DC-DFTB-MD) \u6cd5\u306e\u6700\u8fd1\u306e\u5c55\u958b&#8221; (Recent advances in divide-and-conquer density-functional tight-binding molecular dynamics simulations (DC-DFTB-MD))<\/a><br \/>\n\u897f\u6751 \u597d\u53f2, \u6d77\u5bf3 \u4e08\u5f70, \u4e2d\u4e95 \u6d69\u5df3,\u00a0<em>J. Comput. Chem. Jpn.<\/em>,\u00a0<strong>14<\/strong>\u00a0(3), 43-46 (2015).<\/li>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/mssj\/18\/2\/18_95\/_article\/-char\/ja\/\">&#8220;\u5206\u5272\u7d71\u6cbb\u578b\u5bc6\u5ea6\u6c4e\u95a2\u6570\u5f37\u675f\u7e1b\u5206\u5b50\u52d5\u529b\u5b66\uff08DC-DFTB-MD\uff09\u6cd5\u306b\u3088\u308b\u30ca\u30ce\u30b9\u30b1\u30fc\u30eb\u7cfb\u5316\u5b66\u53cd\u5fdc\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3&#8221;<\/a><br \/>\n\u897f\u6751 \u597d\u53f2, \u4e2d\u4e95 \u6d69\u5df3, \u5206\u5b50\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u7814\u7a76\u4f1a\u4f1a\u8a8c\u201c\u30a2\u30f3\u30b5\u30f3\u30d6\u30eb\u201d,\u00a0<strong>18<\/strong>\u00a0(2), 95-101 (2016).<\/li>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/mssj\/20\/1\/20_18\/_article\/-char\/ja\">&#8220;\u5206\u5272\u7d71\u6cbb\u578b\u5bc6\u5ea6\u6c4e\u95a2\u6570\u5f37\u675f\u7e1b\uff08DC-DFTB\uff09\u6cd5\u306b\u5bfe\u3059\u308b\u6700\u8fd1\u306e\u958b\u767a\u3068\u5fdc\u7528&#8221;<\/a><br \/>\n\u897f\u6751 \u597d\u53f2, \u4e2d\u4e95 \u6d69\u5df3, \u5206\u5b50\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u7814\u7a76\u4f1a\u4f1a\u8a8c\u201c\u30a2\u30f3\u30b5\u30f3\u30d6\u30eb\u201d,\u00a0<strong>20<\/strong> (1), 18-23 (2018).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.2477\/jccj.2018-0032\">&#8220;\u5149\u53d7\u5bb9\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u6a5f\u69cb\u89e3\u660e\u306b\u5411\u3051\u305f\u5206\u5272\u7d71\u6cbb\u578b\u6642\u9593\u4f9d\u5b58\u5bc6\u5ea6\u6c4e\u95a2\u6570\u5f37\u675f\u7e1b\u6cd5\u306e\u958b\u767a&#8221; (Development of the divide-and-conquer time-dependent density functional tight-binding method for photoreceptor protein)<\/a><br \/>\n\u6cb3\u672c \u5948\u3005, \u5409\u5ddd \u6b66\u53f8, \u5c0f\u91ce \u7d14\u4e00,\u4e2d\u4e95 \u6d69\u5df3,\u00a0<em>J. Comput. Chem. Jpn.<\/em>,\u00a0<strong>17<\/strong>\u00a0(3), 127-129 (2018).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.2477\/jccj.2018-0052\" target=\"_blank\" rel=\"noopener noreferrer\">&#8220;DCDFTBMD\u30d7\u30ed\u30b0\u30e9\u30e0\u306e\u516c\u958b&#8221;\uff08Release of DCDFTBMD Program\uff09<\/a><br \/>\n\u897f\u6751 \u597d\u53f2, \u5409\u5ddd \u6b66\u53f8, \u4e2d\u4e95 \u6d69\u5df3,\u00a0<em>J. Comput. Chem. Jpn.,\u00a0<\/em><strong>17<\/strong> (5), A21-A27 (2018).<\/li>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/vss\/62\/8\/62_20180399\/_article\/-char\/ja\/\">&#8220;\u5206\u5272\u7d71\u6cbb\u578b\u5bc6\u5ea6\u6c4e\u95a2\u6570\u5f37\u675f\u7e1b\u5206\u5b50\u52d5\u529b\u5b66(DC-DFTB-MD)\u6cd5\u306b\u3088\u308b\u8868\u9762\u53cd\u5fdc\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\uff1aPt(111)\u8868\u9762\u4e0a\u306e\u30d7\u30ed\u30c8\u30f3\u62e1\u6563&#8221;(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))<\/a><br \/>\n\u4e2d\u4e95 \u6d69\u5df3, \u897f\u6751 \u597d\u53f2, Aditya Wibawa Sakti, Tanabat Mudchimo, \u5468 \u5efa\u658c,\u00a0<i>\u8868\u9762\u3068\u771f\u7a7a<\/i>,\u00a0<b>62<\/b>\u00a0(5), 486-491 (2019). (2018\u5e74\u65e5\u672c\u8868\u9762\u771f\u7a7a\u5b66\u4f1a\u5b66\u8853\u8b1b\u6f14\u4f1a\u7279\u96c6\u53f7III)<\/li>\n<li><a href=\"https:\/\/doi.org\/10.5796\/denkikagaku.19-FE0024\">&#8220;\u5927\u898f\u6a21\u91cf\u5b50\u5206\u5b50\u52d5\u529b\u5b66\u6cd5\u306b\u3088\u308bNa\u30a4\u30aa\u30f3\u4e8c\u6b21\u96fb\u6c60\u7528\u8d85\u6fc3\u539a\u96fb\u89e3\u6db2\u306e\u6eb6\u6db2\u69cb\u9020\u3068\u30ad\u30e3\u30ea\u30a2\u30a4\u30aa\u30f3\u30c0\u30a4\u30ca\u30df\u30af\u30b9\u306e\u7406\u8ad6\u7684\u89e3\u6790&#8221;<\/a><br \/>\n\u5927\u8d8a \u660c\u6a39, \u5468 \u5efa\u658c, \u4e2d\u4e95 \u6d69\u5df3, <em>\u96fb\u6c17\u5316\u5b66<\/em>, <strong>87<\/strong>, 233-238 (2019).\u00a0(\u7279\u96c6:\u9769\u65b0\u7684\u4e8c\u6b21\u96fb\u6c60\u306b\u5411\u3051\u305f\u96fb\u89e3\u6db2\/\u96fb\u89e3\u8cea\u7814\u7a76\u306e\u6700\u65b0\u52d5\u5411)<\/li>\n<li><a href=\"https:\/\/doi.org\/10.2477\/jccj.2019-0025\">&#8220;\u30da\u30ed\u30d6\u30b9\u30ab\u30a4\u30c8\u592a\u967d\u96fb\u6c60\u6750\u6599\u306b\u304a\u3051\u308b\u30dd\u30fc\u30e9\u30ed\u30f3\u5f62\u6210\u306e\u91cf\u5b50\u7684\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u201d (Quantum mechanical molecular dynamics simulations of polaron formation in a perovskite solar cell material)<\/a><br \/>\n\u6d66\u8c37 \u6d69\u8f1d, \u5468 \u5efa\u658c, \u4e2d\u4e95 \u6d69\u5df3,\u00a0<i>J. Comput. Chem. Jpn.<\/i>, <strong>18<\/strong> (3), 142-144 (2019).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.1002\/tcr.201800141\">&#8220;Development of divide-and-conquer density-functional tight-binding method for theoretical research on Li-ion battery&#8221;<\/a><br \/>\nC.-P. Chou, A. W. Sakti, Y. Nishimura, H. Nakai, <i>Chem. Rec.<\/i>, <b>19<\/b> (4), 746-757 (2019).<\/li>\n<li><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/wcms.1419\">&#8220;Recent Advances in Quantum-Mechanical Molecular Dynamics Simulations of Proton Transfer Mechanism in Various Water-Based Environments&#8221;<\/a><br \/>\nA. W. Sakti, Y. Nishimura, H. Nakai, <i>WIREs Comput. Mol. Sci.<\/i>, <b>10<\/b> (1), e1419-1-20 (2020).<\/li>\n<li><a href=\"https:\/\/www.jstage.jst.go.jp\/article\/mssj\/23\/3\/23_171\/_article\/-char\/ja\">&#8220;\u30d0\u30af\u30c6\u30ea\u30aa\u30ed\u30c9\u30d7\u30b7\u30f3\u306e\u5206\u5b50\u52d5\u753b\u306b\u57fa\u3065\u304f\u5927\u898f\u6a21\u91cf\u5b50\u5206\u5b50\u52d5\u529b\u5b66\u6cd5\u306b\u3088\u308b\u30d7\u30ed\u30c8\u30f3\u79fb\u52d5\u53cd\u5fdc\u306e\u89e3\u6790&#8221;<\/a><br \/>\n\u5c0f\u91ce \u7d14\u4e00, \u4eca\u4e95 \u307f\u306e\u8389, \u897f\u6751 \u597d\u53f2, \u4e2d\u4e95 \u6d69\u5df3, \u5206\u5b50\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u5b66\u4f1a\u8a8c\u201c\u30a2\u30f3\u30b5\u30f3\u30d6\u30eb\u201d, <strong>23<\/strong> (3), 171-175 (2021).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.2477\/jccj.2022-0029\">&#8220;COVID-19\u306e\u7d4c\u53e3\u6cbb\u7642\u85ac\u958b\u767a\u306b\u5411\u3051\u305f\u30cf\u30a4\u30d6\u30ea\u30c3\u30c9\u578b<em>in Silico<\/em>\u5275\u85ac\u201d (Hybrid <em>in Silico<\/em> drug discovery study toward the development of oral antivirals for COVID-19)<\/a><br \/>\n\u5c0f\u6e05\u6c34 \u521d\u82b1, \u5c0f\u91ce \u7d14\u4e00, \u798f\u897f \u5feb\u6587, \u4e2d\u4e95 \u6d69\u5df3, <i>J. Comput. Chem. Jpn.<\/i>, <strong>21<\/strong> (2), 48-51 (2022).<\/li>\n<li><a href=\"https:\/\/doi.org\/10.2477\/jccj.2023-0033\">&#8220;\u5149\u6d3b\u6027\u30a4\u30a8\u30ed\u30fc\u30bf\u30f3\u30d1\u30af\u8cea\u306e\u5149\u53cd\u5fdc\u30b5\u30a4\u30af\u30eb\u306b\u304a\u3051\u308b<em>trans-cis<\/em>\u5149\u7570\u6027\u5316\u904e\u7a0b\u306e\u91cf\u5b50\u7684\u5206\u5b50\u52d5\u529b\u5b66\u30b7\u30df\u30e5\u30ec\u30fc\u30b7\u30e7\u30f3\u89e3\u6790\u201d (Quantum Molecular Dynamics Simulation for <em>trans-cis<\/em> Photoisomerization Process in Photocycle of Photoactive Yellow Protein)<\/a><br \/>\n\u77f3\u7530 \u8ce2\u4eae, \u897f\u6751 \u597d\u53f2, \u4e2d\u4e95 \u6d69\u5df3, <i>J. Comput. Chem. Jpn.<\/i>, <strong>22<\/strong> (2), 9-11 (2023).<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Software &#8220;DCDFTBMD: Divide-and-Conquer Density Functional Tight-Binding Program for Huge-System Quantum  &hellip; <a href=\"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/?page_id=47&#038;lang=en\" class=\"more-link\"><span class=\"screen-reader-text\">&#8220;Publication&#8221; \u306e<\/span>\u7d9a\u304d\u3092\u8aad\u3080<\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_locale":"en_US","_original_post":"http:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/?page_id=45","footnotes":""},"class_list":["post-47","page","type-page","status-publish","hentry","en-US"],"_links":{"self":[{"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/pages\/47","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=47"}],"version-history":[{"count":1,"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/pages\/47\/revisions"}],"predecessor-version":[{"id":48,"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=\/wp\/v2\/pages\/47\/revisions\/48"}],"wp:attachment":[{"href":"https:\/\/www.chem.waseda.ac.jp\/dcdftbmd\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=47"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}