Hierarchical structures of amorphous solids characterized by persistent homology Y Hiraoka, T Nakamura, A Hirata, EG Escolar, K Matsue, Y Nishiura Proceedings of the National Academy of Sciences 113 (26), 7035-7040, 2016 | 395 | 2016 |

Persistent homology and many-body atomic structure for medium-range order in the glass T Nakamura, Y Hiraoka, A Hirata, EG Escolar, Y Nishiura Nanotechnology 26 (30), 304001, 2015 | 143 | 2015 |

Structure and properties of densified silica glass: characterizing the order within disorder Y Onodera, S Kohara, PS Salmon, A Hirata, N Nishiyama, S Kitani, ... NPG Asia Materials 12 (1), 85, 2020 | 75 | 2020 |

Experimental test of a new equality: Measuring heat dissipation in an optically driven colloidal system S Toyabe, HR Jiang, T Nakamura, Y Murayama, M Sano Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 75 (1 …, 2007 | 62 | 2007 |

Effect of the cation on the stability of cation–glyme complexes and their interactions with the [TFSA]− anion S Tsuzuki, T Mandai, S Suzuki, W Shinoda, T Nakamura, T Morishita, ... Physical Chemistry Chemical Physics 19 (28), 18262-18272, 2017 | 57 | 2017 |

Persistent homology analysis for materials research and persistent homology software: HomCloud I Obayashi, T Nakamura, Y Hiraoka journal of the physical society of japan 91 (9), 091013, 2022 | 55 | 2022 |

Free energy analysis of vesicle-to-bicelle transformation W Shinoda, T Nakamura, SO Nielsen Soft Matter 7 (19), 9012-9020, 2011 | 48 | 2011 |

Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems T Nakamura, W Shinoda, T Ikeshoji The Journal of chemical physics 135 (9), 2011 | 39 | 2011 |

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS T Nakamura, S Kawamoto, W Shinoda Computer Physics Communications 190, 120-128, 2015 | 36 | 2015 |

A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation S Kawamoto, T Nakamura, SO Nielsen, W Shinoda The Journal of chemical physics 139 (3), 2013 | 29 | 2013 |

Derivation of the nonlinear fluctuating hydrodynamic equation from the underdamped Langevin equation T Nakamura, A Yoshimori Journal of Physics A: Mathematical and Theoretical 42 (6), 065001, 2009 | 21 | 2009 |

Persistence homology of entangled rings F Landuzzi, T Nakamura, D Michieletto, T Sakaue Physical Review Research 2 (3), 033529, 2020 | 18 | 2020 |

Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory T Nakamura, W Shinoda The Journal of Chemical Physics 138 (12), 2013 | 18 | 2013 |

Fluctuation-response relation of many Brownian particles under nonequilibrium conditions T Nakamura, S Sasa Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 77 (2 …, 2008 | 14 | 2008 |

Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction T Morishita, T Nakamura, W Shinoda, AM Ito Chemical Physics Letters 706, 633-640, 2018 | 9 | 2018 |

Effects of anion on liquid structures of ionic liquids at graphene electrode interface analyzed by molecular dynamics simulations S Tsuzuki, T Nakamura, T Morishita, W Shinoda, S Seki, Y Umebayashi, ... Batteries & Supercaps 3 (7), 658-667, 2020 | 7 | 2020 |

Microscopic description of yielding in glass based on persistent homology T Shirai, T Nakamura journal of the physical society of japan 88 (7), 074801, 2019 | 7 | 2019 |

Characterizing reaction route map of realistic molecular reactions based on weight rank clique filtration of persistent homology B Murayama, M Kobayashi, M Aoki, S Ishibashi, T Saito, T Nakamura, ... Journal of Chemical Theory and Computation 19 (15), 5007-5023, 2023 | 6 | 2023 |

Systematic derivation of coarse-grained fluctuating hydrodynamic equations for many Brownian particles under nonequilibrium conditions T Nakamura, S Sasa Physical Review E—Statistical, Nonlinear, and Soft Matter Physics 74 (3 …, 2006 | 5 | 2006 |

Cooperative Reaction of Hydrogen-Networked Water Molecules at the SiC–H_{2}O_{2} Solution Interface: Microscopic Insights from *Ab Initio* Molecular DynamicsT Morishita, M Kayanuma, T Nakamura, T Kato The Journal of Physical Chemistry C 126 (30), 12441-12449, 2022 | 4 | 2022 |