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Journal of Chemical Theory and Computation|August 18, 2020
Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurements with Biomolecular SimulationsSotaro Fuchigami, Toru Niina, Shoji TakadaJournal of Chemical Theory and Computation|January 8, 2020
Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular SimulationsToru Niina, Sotaro Fuchigami, Shoji TakadaFrontiers in Molecular Biosciences|March 29, 2021
Case Report: Bayesian Statistical Inference of Experimental Parameters via Biomolecular Simulations: Atomic Force MicroscopySotaro Fuchigami, Toru Niina, Shoji TakadaFrontiers in Molecular Biosciences|May 16, 2022
Inferring Conformational State of Myosin Motor in an Atomic Force Microscopy Image via Flexible Fitting Molecular SimulationsSotaro Fuchigami, Shoji TakadaJournal of Chemical Theory and Computation|April 25, 2023
Particle Smoother to Assimilate Asynchronous Movie Data of High-Speed AFM with MD SimulationsSuguru Kato, Shoji Takada, Sotaro FuchigamiScientific Reports|January 4, 2023
End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy imagesYasuhiro Matsunaga, Sotaro Fuchigami, Tomonori Ogane, et al.Biophysical Journal|July 14, 2025
OpenCafeMol: A coarse-grained biomolecular simulator on GPU with its application to vesicle fusionYutaka Murata, Toru Niina, Shoji TakadaScientific Reports|May 20, 2020
Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motorShintaroh Kubo, Toru Niina, Shoji TakadaBiophysical Journal|October 6, 2022
The stoichiometric interaction model for mesoscopic MD simulations of liquid-liquid phase separationYutaka Murata, Toru Niina, Shoji TakadaBiophysical Journal|September 29, 2022
FO-F1 coupling and symmetry mismatch in ATP synthase resolved in every FO rotation stepShintaroh Kubo, Toru Niina, Shoji TakadaPageof 14