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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 TakadaJournal 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 TakadaBiophysical Journal|September 29, 2022
FO-F1 coupling and symmetry mismatch in ATP synthase resolved in every FO rotation stepShintaroh Kubo, Toru Niina, Shoji TakadaPlos Computational Biology|July 20, 2021
Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structureToru Niina, Yasuhiro Matsunaga, 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 TakadaJournal of Computational Chemistry|July 8, 2026
OpenCafeMol With 3SPN.2 DNA Model: GPU Acceleration for Long-Time Coarse-Grained Chromatin SimulationsMasataka Yamauchi, Yutaka Murata, Toru Niina, et al.Plos Computational Biology|December 2, 2017
Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulationsToru Niina, Giovanni B Brandani, Cheng Tan, et al.Pageof 2