Komatsuzaki Group, Hokkaido University
Last updated : 2024/05/24

HOME | sitemap | Japanese

Yutaka NAGAHATA

ynagahata Research fellow
E-mail: Please rewrite (AT SIGN) and (DOT) as @ and .
TEL:
(011)706-9458
FAX:
(011)706-9437
Office:
Research Institute for Electronic Science, 5th floor, room 105
Mailing address:
Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan

Research Interests

To illuminate physical phenomena considered as stochastic process from molecular dynamics

The equilibrium statistical mechanics is based on hypotheses —statistical property of observed physical phenomena has “uniform in space” and “uniform in time (stationary): mostly due to its observation time scale cannot capture dynamics behind” —. However non-uniform system such as bio-system both hypotheses are suspicious. In the case, bases of analysis should be based on dynamics of molecules but our knowledge has not reached there yet (even for some small molecules, we still cannot capture clear picture of chemical reactions from dynamical point of view). My focus of subjects is from reactivity of molecules to allosteric change in protein and diffusion in non-uniform space (for example in cell). And my aim is to bridge several time- and space-scales. I want to explore these physical phenomena (that had considered as stochastic process) based on molecular dynamics and want to understand how (“looking like”) stochastic processes emerge from molecular dynamics with developing methods to analyze and with creating theory to construct those methods.

Awards

  • 2015.10.26 Best Poster Award at The 9th Annual Meeting of Japan Society for Molecular Science [URL]
  • 2015.06.04 Best Poster Prize at 31st Symposium on Chemical Kinetics and Dynamics.
  • 2014.12.17 Poster Award at The 15th Ries-Hokudai International Symposium 響[hibiki].
  • 2014.03.11 Presentation Award at the Meeting of Hokkaido Branch of the Biophysical Society of Japan.
  • 2012.8.31 Best Question award at Summer School for the Organization of Young Biophysicists.
  • 2010.3.10. An excellent award in a Sakigake mathematical workshop on “cooperation between applied mathematics and physics- let’s make and move your mathematical model.

Published Papers

2024

[7]Yutaka Nagahata, Masato Kobayashi, Mikito Toda, Satoshi Maeda, Tetsuya Taketsugu, Tamiki Komatsuzaki
An encompassed representation of timescale hierarchies in first-order reaction network
Proceedings of the National Academy of Sciences 121(21), pp.e2317781121, (2024)
DOI: 10.1073/pnas.2317781121

2021

[6]Yutaka Nagahata, Rigoberto Hernandez, Tamiki Komatsuzaki
Phase space geometry of isolated to condensed chemical reactions
J. Chem. Phys. 155, pp.210901-1-210901-17 (2021)
DOI: 10.1063/5.0059618
File Selected by cover art

[5]Yuta Mizuno, Mikoto Takigawa, Saki Miyashita, Yutaka Nagahata, Hiroshi Teramoto, Tamiki Komatsuzaki
An algorithm for computing phase space structures in chemical reaction dynamics using Voronoi tessellation
Physica D: Nonlinear Phenomena 428, (2021)
DOI: 10.1016/j.physd.2021.133047

2015

[4]Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
Deciphering Time Scale Hierarchy in Reaction Networks
The Journal of Physical Chemistry B 120(8), pp.1961-1971 (2015)
DOI: 10.1021/acs.jpcb.5b09941

[3]Yosuke Sumiya, Yutaka Nagahata, Tamiki Komatsuzaki, Tetsuya Taketsugu, Satoshi Maeda
Kinetic Analysis for the Multistep Profiles of Organic Reactions: Significance of the Conformational Entropy on the Rate Constants of the Claisen Rearrangement
The Journal of Physical Chemistry A 119(48), pp.11641-11649 (2015)
DOI: 10.1021/acs.jpca.5b09447

2013

[2]Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
Reactivity boundaries for chemical reactions associated with higher index and multiple saddles
Physical Review E 88(4), pp.42923-42923-11 (2013)
DOI: 10.1103/PhysRevE.88.042923
(Figure 6d from this paper was selected to be displayed on PRE journal web site as part of "Kaleidoscope")

[1]Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
Reactivity Boundaries to Separate the Fate of a Chemical Reaction Associated with an Index-two saddle
Physical Review E 87(6), pp.62817 , (2013)
DOI: 10.1103/PhysRevE.87.062817

Presentations

2023

[10]Yutaka Nagahata, David J. Wales, Tamiki Komatsuzaki
Challenges for finding bottleneck of energy landscape
The 5th conference of Theory and Applications of Computational Chemistry (TACC)(9.4-9.9 ,2023), Hokkaido University, Sapporo 9, 5 (Poster)

2022

[9]Yuta Mizuno, Mikoto Takigawa, Saki Miyashita, Yutaka Nagahata, Hiroshi Teramoto, Tamiki Komatsuzaki
An algorithm for computing phase space structures in chemical reaction dynamics using Voronoi tessellation
37th Symposium on Chemical Kinetics and Dynamics(6.1-6.3 ,2022), Online, Sendai, Japan 6, 3 (Oral)

2015

[8]Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Tetsuya Taketsugu, Tamiki Komatsuzaki
Developing high precision algorithm to predict observation timescale hierarchy of an isomerization reaction network
The 16th RIES-Hokudai International Symposium(11.10-11.11 ,2015), Chateraise Gateaux Kingdom Sapporo, Sapporo, Japan 11, 10 (Poster)

[7]Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
Deciphering timescale hierarchy encoded in complex reaction networks
31st Symposium on Chemical Kinetics and Dynamics(6.3-6.5 ,2015), Frontier Research in Applied Sciences Bldg., Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 6, 3 (poster)

[6]Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
Timescale hierarchies of complex reaction network
Workshop on dynamical systems and computation 2015‎(3.3-3.6 ,2015), Hokkaido University, Sapporo, Hokkaido 3, 4 (oral)

2014

[5]Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
An extraction of embedded timescale hierarchies buried in complex reaction network
The 15th Ries-Hokudai International Symposium 響[hibiki](12.16-12.17 ,2014), CHÂTERAISÉ Gateaux Kingdom SAPPORO, Sapporo, Hokkaido 12, 16 (poster)

2013

[4]Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun Biu Li, Tamiki Komatsuzaki
Toward understanding hierarchical structure of complex reaction networks extracted from single molecule time series
The 14th RIES-HOKUDAI International Symposium 網[mou](12. 11-12. 12 ,2013), CHÂTERAISÉ Gateaux Kingdom SAPPORO, Sapporo, Japan 12, 11 (poster)

[3]Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
Identifying states in Markov chain steady state network extracted from time series by finding minimum transition probability
The Complexity of Dynamics and Kinetics in Many Dimensions(6.18 ,2013), Telluride Intermediate School, Telluride, CO., US (Oral)

[2]Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
Reactivity Boundaries to Separate the Fate of a Chemical Reaction Associated with Multiple Saddles
Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases ,Telluride Intermediate School(6.13 ,2013), Telluride, CO., US (Oral)

2011

[1]Yutaka Nagahata, Shinnosuke Kawai, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
Deterministic properties of a saddle with two reactive degrees-of-freedoms
12th RIES-Hokudai International Symposium (11.21-11.22 ,2011), Chateraise Gateaux Kingdom Sapporo (poster)

所属学会

  • 日本物理学会
  • 分子科学会
  • 日本化学会

他