Publications

Research Articles

 : Open Access.

•  The Particle Filter Method to Integrate High-Speed Atomic Force Microscopy Measurement with Biomolecular Simulations
  • Sotaro Fuchigami, Toru Niina, and Shoji Takada. JCTC (2020).
  •  bioRxiv: https://doi.org/10.1101/2020.03.12.988485
•  Molecular dynamics simulation of proton-transfer coupled rotations in ATP synthase FO motor
  • Shintaroh Kubo†, Toru Niina†, and Shoji Takada († equal contribution). Scientific Reports (2020).
  •  bioRxiv: https://doi.org/10.1101/618504
•  Flexible Fitting of Biomolecular Structures to Atomic Force Microscopy Images via Biased Molecular Simulations
  • Toru Niina, Sotaro Fuchigami, and Shoji Takada. JCTC (2020).
  •  bioRxiv: https://doi.org/10.1101/793901
•  DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations
  • Giovanni B. Brandani, Toru Niina, Cheng Tan, and Shoji Takada. Nucleic Acids Research (2018).
•  Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations
  • Toru Niina†, Giovanni B. Brandani†, Cheng Tan, and Shoji Takada († equal contribution). PLoS Computational Biology (2017).

Research Software

See Projects also.

• E-Cell4. An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
  • Kaizu Kazunari, Nishida Kozo, Sakamoto Yuki, Kato Suguru, Niina Toru, Nishida Naoki, Aota Naohiro, Koizumi Moriyoshi, Takahashi Koichi
  • Zenodo: https://doi.org/10.5281/zenodo.1119017
• Mjolnir. general purpose coarse-grained molecular dynamics simulation package
  • Toru Niina, Yutaka Murata.
  • Zenodo: https://doi.org/10.5281/zenodo.3727649
• afmize
  • Toru Niina, Suguru Kato.
  • Zenodo: https://doi.org/10.5281/zenodo.2556444
• libasd
  • Toru Niina
  • Zenodo: https://doi.org/10.5281/zenodo.1209118