D.Sc. (Information and Media Science) Kobe University, Japan
2003
M.A. (Earth and Planetary Sciences) Kobe University, Japan
2001
B.S. (Earth and Planetary Sciences) Kobe University, Japan
RESEARCH AND TEACHING EXPERIENCES
2017
Leading Initiative for Excellent Young Researchers candidate
2016-Present
Research Fellow of the Japan Science and Technology Agency (PRESTO)
2014-present
Research Scientist, RIKEN, Japan
2011-2014
Special Postdoctoral Researcher, RIKEN Advanced Institute for Computational Science (AICS), Japan
2008-2011
Postdoctoral Researcher, RIKEN, Japan
2007-2008
Researcher, Yokohama City University, Japan
2007
Researcher, Kobe University, Japan
2004
Research Fellow of JSPS, Kobe University, Japan
PROFESSIONAL AFFILIATIONS
The Biophysical Society of Japan, Protein Science Society of Japan, BioSuperComputing Research Community
RESEARCH PROJECTS
MD simulations of large conformational changes in proteins
Path-sampling methods for exploring reaction coordinates of complex systems
PUBLICATIONS
Y. Matsunaga and Y. Sugita, "Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning." eLife, 7, e32668 (2018)
Y. Matsunaga and Y. Sugita, "Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories." J. Chem. Phys. 148, 41731 (2018)
Y. Matsunaga, T. Yamane, T. Terada, K. Moritsugu, H. Fujisaki, S. Murakami, M. Ikeguchi, A. Kidera, "Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB" eLife 7:e31715 (2018)
C. Kobayashi*, J. Jung*, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, Y. Sugita., "GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms" J. Comput. Chem. 38, 2193-2206 (2017) (*equally contributed)
Y. Matsunaga, Yasuaki Komuro, Chigusa Kobayashi, Jaewoon Jung,
Takaharu Mori, and Y. Sugita, “Dimensionality of Collective Variables
for Describing Conformational Changes of a Multi-Domain Protein”
Journal of Physical Chemistry Letters 7, 1446–1451 (2016)
C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, Y. Sugita, “Domain
Motion Enhanced (DoME) Model for Efficient Conformational Sampling of
Multidomain Proteins” Journal of Physical Chemistry B 119, 14584-14593
(2015)
H. Fujisaki, K. Moritsugu, Y. Matsunaga, T. Morishita, and L.
Maragliano, "Extended phase-space methods for enhanced sampling in
molecular simulations: a review.", Front. Bioeng. Biotechnol. Volume
3, Article 125 (2015) doi:10.3389/fbioe.2015.00125
Y. Matsunaga, A. Kidera, and Y. Sugita, "Sequential data
assimilation for single-molecule FRET photon-counting data" Journal of
Chemical Physics 142, 214115 (12 pages) (2015).
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and
Y. Sugita, "GENESIS: a hybrid‐parallel and multi‐scale molecular
dynamics simulator with enhanced sampling algorithms for biomolecular
and cellular simulations, WIREs Comput. Mol. Sci." DOI:
10.1002/wcms.1220 (2015).
Y. Matsunaga, A. Baba, C. B. Li, J. E. Straub, M. Toda, T. Komatsuzaki, and R. S. Berry "Spatio-temporal hierarchy in the dynamics of a minimalist protein model" J. Chem. Phys, 139, 215101-1 - 215101-13 (2013).
Y. Matsunaga, R. Koike, M. Ota, J.H. Tame, and A. Kidera "Influence of Structural Symmetry on Protein Dynamics" PLoS One 7, e50011 (2012).
Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera “Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase” PLoS Comput. Biol. 8, e1002555 (2012).
S. Fuchigami, H. Fujisaki, Y. Matsunaga, and A. Kidera "Protein Functional Motions: Basic Concepts and Computational Methodologies" Adv. Chem. Phys. 145, 35-82 (2011).
D.M. Leitner, Y. Matsunaga, C.B. Li, T. Komatsuzaki, A. Shojiguchi, and M. Toda, "Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics" Adv. Chem. Phys. 145, 83 (2011).
Y. Matsunaga, C.B. Li, and T. Komatsuzaki "Cooperativity at different space and time scales in multiscale protein dynamics" Phys. Rev. E 82, 016213-1 - 016213-12 (2010).
Y. Matsunaga, S. Fuchigami, and A. Kidera "Multivariate Frequency Domain Analysis of Protein Dynamics" J. Chem. Phys. 130, 124104-1 - 124104-8 (2009).
A. Kidera, K. Moristugu, Y. Matsunaga, and H. Fujisaki, "Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics", Proteins: Energy, Heat and Signal Flow, Chapter 5, p107-127 (2009), CRC Press.
Y. Matsunaga, C.B. Li, and T. Komatsuzaki "Anomalous Diffusion in Folding Dynamics of Minimalist Protein Landscape" Phys. Rev. Lett. 99, 238103-1 - 238103-4 (2007).
G.J. Rylance, R.L. Johnston, Y. Matsunaga, C.B. Li, A. Baba, and T. Komatsuzaki "Topographical complexity of multidimensional energy landscapes" Proc. Nat. Acad. Sci. U.S.A. 103, 18551-18555 (2006).
C.B. Li, Y. Matsunaga, M. Toda, and T. Komatsuzaki "Phase Space Reaction Network on a Multisaddle Energy Landscape: HCN isomerization" J Chem. Phys. 123, 184301-1 - 184301-13 (2005).
T. Komatsuzaki, K. Hoshino, Y. Matsunaga, G.J. Rylance, R.L. Johnston, and D.J. Wales "How Many Dimensions are Required to Approximate the Potential Energy Landscape of a Model Protein?" J. Chem. Phys. 122, 084714-1 - 084714-9 (2005).
T. Komatsuzaki, K. Hoshino, and Y. Matsunaga "Regularity in Chaotic Transitions on Multibasin Landscapes" Adv. Chem. Phys. 130B, 257-313 (2005).
K. Hoshino, Y. Matsunaga, M. Miller, D.J. Wales, and T. Komatsuzaki "A Coarse-Graining of Energy Landscapes of Proteins -Structural Stability of the Most Stable States-" AIP conference series for Slow Dynamics in Complex Systems 708, 344-345 (2004).
Y. Matsunaga and T. Komatsuzaki "Protein Folding Dynamics: Ergodic Behavior in Principal Component Space" AIP conference series for Slow Dynamics in Complex Systems 708, 342-343 (2004).
Y. Matsunaga, K.S. Kostov, and T. Komatsuzaki, "Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes" AIP conference series for Slow Dynamics in Complex Systems 708, 302-305 (2004).
Y. Matsunaga, K.S. Kostov, and T. Komatsuzaki "Multibasin Dynamics in Off-Lattice Minimalist Protein Landscapes" J. Phys. Chem. A 106, 10898-10907 (2002).
