Yasuhiro Matsunaga

J-GLOBAL         Last updated: Apr 22, 2019 at 13:26
 
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Name
Yasuhiro Matsunaga
Nickname
ymatsunaga
Affiliation
Saitama University
Job title
Researcher
Degree
D. Sci.(Kobe University)
Research funding number
60464525
ORCID ID
0000-0003-2872-3908

Research Areas

 
 

Academic & Professional Experience

 
Apr 2018
 - 
Mar 2019
Research Scientist, Center for Computational Science, RIKEN
 
Oct 2016
 - 
Today
JST PRESTO
 
Apr 2014
 - 
Mar 2018
Research Scientist, Advanced Institute for Computational Science, RIKEN
 
Apr 2011
 - 
Mar 2014
Special Postdoctoral Researcher, RIKEN Advanced Institute for Computational Science
 
Apr 2008
 - 
Mar 2011
Researcher, RIKEN
 
Jul 2007
 - 
Mar 2008
Researcher, Yokohama City University
 
Apr 2007
 - 
Jun 2007
Researcher, Kobe University
 
Apr 2004
 - 
Mar 2006
Research Fellow, Japan Society for the Promotion of Science (JSPS)
 

Published Papers

 
H. Fujisaki, K. Moritsugu, and Y. Matsunaga
International Journal of Molecular Sciences   19 3177 (19 pages)   Oct 2018   [Refereed][Invited]
Y. Matsunaga, and Y. Sugita
eLife   7 e32668 (19 pages)   May 2018   [Refereed]
Y. Matsunaga, and Y. Sugita
148 241731 (7 pages)   Apr 2018   [Refereed][Invited]
Y. Matsunaga, T. Yamane, T. Terada, K. Moritsugu, H. Fujisaki, S. Murakami, M. Ikeguchi, and A. Kidera
eLife   7 e31715 (19 pages)   Mar 2018   [Refereed]
C. Kobayashi, J. Jung, Y. Matsunaga, T. Mori, T. Ando, K. Tamura, M. Kamiya, and Y. Sugita
Journal of Computational Chemistry   38 2193-2206   Jul 2017   [Refereed]
Y. Matsunaga, Y. Komuro, C. Kobayashi, J. Jung, T. Mori, and Y. Sugita
The Journal of Physical Chemistry Letters   7 1446-1451   Apr 2016   [Refereed]
C. Kobayashi, Y. Matsunaga, R. Koike, M. Ota, and Y. Sugita
The Journal of Physical Chemistry B   119 14584-14593   Nov 2015   [Refereed]
Y. Matsunaga, A. Kidera, and Y. Sugita
The Journal of Chemical Physics   142(21) 214115   Jun 2015   [Refereed]
J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Yoda, M. Feig, and Y. Sugita
WIREs Comput. Mol. Sci.      May 2015   [Refereed]
H. Fujisaki, K. Moritsugu, Y. Matsunaga, T. Morishita, and L. Maragliano
Frontiers in Bioengineering and Biotechnology   3 125   Sep 2015   [Refereed]
Y. Matsunaga, A. Baba, C.-B. Li, J. E. Straub, M. Toda, T. Komatsuzaki, and R. S. Berry
The Journal of Chemical Physics   139 215101   Dec 2013   [Refereed]
Y. Matsunaga, R. Koike, M. Ota, J.H. Tame, A. Kidera
PLoS ONE   7(11) e50011   Nov 2012   [Refereed]
Y. Matsunaga, H. Fujisaki, T. Terada, T. Furuta, K. Moritsugu, and A. Kidera
PLoS computational biology   8 e1002555   Jun 2012   [Refereed]
Y. Matsunaga, C.B. Li, and T. Komatsuzaki
Physical review. E, Statistical, nonlinear, and soft matter physics   82(1,Pt.2) 016213   Jul 2010   [Refereed]
Y. Matsunaga, S. Fuchigami, and A. Kidera
The Journal of chemical physics   130(12) 124104   Mar 2009   [Refereed]
Y. Matsunaga, C.B. Li, T. Komatsuzaki
Physical Review Letters   99 238103   Dec 2007   [Refereed]
G.J. Rylance, R.L. Johnston, Y. Matsunaga, C.B. Li, A. Baba, T. Komatsuzaki
Proceedings of the National Academy of Sciences of the United States of America   103(49) 18551-18555   Dec 2006   [Refereed]
C.B. Li, Y. Matsunaga, M. Toda, T. Komatsuzaki
The Journal of Chemical Physics   123 184301   Nov 2005   [Refereed]
T. Komatsuzaki, K. Hoshino, Y. Matsunaga, G.J. Rylance, R.L. Johnston, D.J. Wales
The Journal of Chemical Physics   122 84714   Feb 2005   [Refereed]
T. Komatsuzaki, K. Hoshino and Y. Matsunaga
Advances in Chemical Physics   130B 257-313   2005   [Refereed]
Y. Matsunaga, K.S. Kostov and T. Komatsuzaki
Journal of Physical Chemistry A   106(45) 10898-10907   2002   [Refereed]

Misc

 
Yasuhiro Matsunaga
Ensemble   16 29-35   Jan 2014   [Refereed][Invited]
Yasuhiro Matsunaga
統計数理      2014   [Refereed][Invited]
MATSUNAGA Yasuhiro, KOMATSUZAKI Tamiki
Kobunshi   57(2) 58-61   Feb 2008   [Invited]
K. Hoshino, Y. Matsunaga, M. Miller, D. J. Wales, and T. Komatsuzaki
AIP conference series for Slow Dynamics in Complex Systems   708 344-345   2004   [Refereed]
Y. Matsunaga and T. Komatsuzaki
AIP conference series for Slow Dynamics in Complex Systems   708 342-343   2004   [Refereed]
Y. Matsunaga, K.S. Kostov and T. Komatsuzaki
AIP conference series for Slow Dynamics in Complex Systems   708 302-305   2004   [Refereed]
KOMATSUZAKI Tamiki, MATSUNAGA Yasuhiro
Biophysics   42(6) 285-289   Nov 2002   [Refereed][Invited]

Books etc

 
Protein Functional Motions: Basic Concepts and Computational Methodologies
S. Fuchigami, H. Fujisaki, Y. Matsunaga, and A. Kidera
Advances in Chemical Physics Vol. 145, page 35-82 (2011)   2011   
Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics
D. M. Leitner, Y. Matsunaga, C.-B. Li, T. Komatsuzaki, A. Shojiguchi, and M. Toda
Advances in Chemical Physics Vol. 145 page 83-122 (2011)   2011   
Molecular Dynamics Simulation of Proteins: Two Models of Anharmonic Dynamics
A. Kidera, K. Moristugu, Y. Matsunaga, and H. Fujisaki
Proteins: Energy, Heat and Signal Flow, Chapter 5, p107-127 (2009), CRC Press.   2009   

Conference Activities & Talks

 
Energetics and conformational pathways of functional rotation in the multidrug transporter AcrB [Invited]
Yasuhiro Matsunaga
15 Sep 2018   
Integrative modeling of protein folding dynamics from experiments and simulation [Invited]
Yasuhiro Matsunaga
Telluride Workshop on “The Complexity of Dynamics and Kinetics from Single Molecules to Cells” Telluride, Colorado USA   22 Jun 2017   
Functional dynamics of multidrug transporter AcrB studied by string method [Invited]
Yasuhiro Matsunaga
22 Mar 2017   
Drug extrusion mechanism of the multidrug transporter AcrB studied by molecular dynamics simulation [Invited]
Yasuhiro Matsunaga
18 Mar 2017   
Markov state modeling of protein folding dynamics by combining single-molecule experiments and simulations [Invited]
Yasuhiro Matsunaga
Simulations Encounter with Data Science, Institute of Statistical Mathematics, Tokyo, Japan   10 Mar 2017   
Drug extrusion mechanism of multidrug transporter AcrB studied by molecular dynamics simulations [Invited]
Yasuhiro Matsunaga
Rare Event Sampling and Related Topics II, Institute of Statistical Mathematics, Tokyo, Japan   28 Mar 2015   
Finding Conformational Transition Pathways in Biomolecules with the String Method and Sequential Data Assimilation [Invited]
Yasuhiro Matsunaga
Rare Event Sampling and Related Topics I, Institute of Statistical Mathematics, Tokyo, Japan   4 Mar 2014   
Sequential data assimilation of single-molecule FRET photon-counting data by using molecular dynamics simulations [Invited]
Yasuhiro Matsunaga
Workshop on Molecular Simulations of Biophysics and Biochemistry, RIKEN AICS, Kobe, Japan   21 Nov 2013   

Works

 
Yasuhiro Matsunaga   Software   2018 - Today
MDToolbox: A Julia package for statistical analysis of molecular dynamics trajectories
Yasuhiro Matsunaga   Software   2012 - Today
MDToolbox: A MATLAB/Octave toolbox for statistical analysis of molecular dynamics trajectories
Y. Sugita, J. Jung, T. Mori, C. Kobayashi, Y. Matsunaga, T. Imai, T. Yoda   Software   2015 - Today

Research Grants & Projects

 
Project Year: Oct 2016 - Mar 2020    Investigator(s): Yasuhiro Matsunaga