RIKEN Center for Computational Science Life and Medical Science Application Interface Platform Development Unit

Unit Leader: Yasuhiro Matsunaga (D.Sc.)

Japanese Page

Research Summary

The structure and dynamics of biomacromolecules are not only crucial for maintaining life activities but are also related to diseases, making their detailed observation important. We are developing AI-based technologies to combine image data obtained from advanced experimental methods such as High-Speed AFM, Cryo-EM/ET, and state-of-the-art microscopy techniques with the three-dimensional structures of biomacromolecules. Additionally, we are developing application interfaces and workflow technologies to integrate measurement data with molecular structures and dynamics. Furthermore, we are developing an application interface platform to connect software developed for scientific research using high-performance computing with AI.

Main Research Fields

Biological Sciences

Related Research Fields

Chemistry
Complex Systems

Keywords

Integrated Modeling
Data Assimilation
Molecular Dynamics Simulation

Selected Publications

1. J. Jung, K. Yagi, C. Tan, H. Oshima, T. Mori, I.Yu, Y. Matsunaga,C. Kobayashi, S. Ito, D. Ugarte La Torre, Y. Sugita*
"GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and QM/MM models",
J. Phys. Chem. B. 128, 6028-6048 (2024).
2. *T. Ishizone*, Y. Matsunaga, S. Fuchigami, and K. Nakamura
"Representation of Protein Dynamics Disentangled by Time-Structure-Based Prior",
J. Chem. Theory Comput. 20, 436-450 (2023).
3. *Y. Matsunaga*, S. Fuchigami, T. Ogane, and S. Takada
"End-to-End Differentiable Blind Tip Reconstruction for Noisy Atomic Force Microscopy Images",
Sci. Rep. 13, 129 (2023)
4. Y. Matsunaga, M. Kamiya, H. Oshima, J. Jung, S. Ito, and Y. Sugia*
"Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation*,
Biophys. Rev. 14, 1503-1512 (2022).
5. T. Ogane, D. Noshiro, T. Ando, A. Yamashita, Y. Sugita, and Y. Matsunaga*
"Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images*,
PLoS Comput. Biol. 18, e1010384 (23 pages) (2022).
6. Y. Matsunaga, and Y. Sugita*
"Use of single-molecule time-series data for refining conformational dynamics in molecular simulations*,
Curr. Opin. Struct. Biol. 61, 153-159 (2020).
7. Y. Matsunaga, and Y. Sugita*,
"Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning*,
eLife 7, e32668 (2018).
8. Y. Matsunaga, and Y. Sugita*,
"Refining Markov State Models for conformational dynamics using ensemble-averaged data and time-series trajectories*,
J. Chem. Phys. 148, 241731 (2018).

Lab Members

Principal investigator

Yasuhiro Matsunaga: Unit Leader

Contact Information

Integrated Innovation Building (IIB)
6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo
650-0047, Japan
Email: ymatsunaga@riken.jp