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1

How does a choice of Markov partition affect the resultant symbolic dynamics?

Teramoto, Hiroshi, Komatsuzaki, Tamiki

Journal:

Chaos An Interdisciplinary Journal of Nonlinear Science

Year:

2010

Language:

english

File:

PDF, 392 KB

english, 2010

2

A new method to improve validity range of Lie canonical perturbation theory: with a central focus on a concept of non-blow-up region

Teramoto, Hiroshi, Toda, Mikito, Komatsuzaki, Tamiki

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2014

Language:

english

File:

PDF, 2.00 MB

english, 2014

3

A bad arm existence checking problem: How to utilize asymmetric problem structure?

Tabata, Koji, Nakamura, Atsuyoshi, Honda, Junya, Komatsuzaki, Tamiki

Journal:

Machine Learning

Year:

2019

Language:

english

File:

PDF, 622 KB

english, 2019

4

Erratum: “Classification of Hamiltonians in neighborhoods of band crossings in terms of the theory of singularities” [J. Math. Phys. 58, 073502 (2017)]

Teramoto, Hiroshi, Kondo, Kenji, Izumiya, Shyūichi, Toda, Mikito, Komatsuzaki, Tamiki

Journal:

Journal of Mathematical Physics

Year:

2019

Language:

english

File:

PDF, 3.82 MB

english, 2019

5

Erratum: “Classification of Hamiltonians in neighborhoods of band crossings in terms of the theory of singularities” [J. Math. Phys. 58, 073502 (2017)]

Teramoto, Hiroshi, Kondo, Kenji, Izumiya, Shyūichi, Toda, Mikito, Komatsuzaki, Tamiki

Journal:

Journal of Mathematical Physics

Year:

2019

File:

PDF, 3.82 MB

2019

6

A new steric substituent constant Ωs based on molecular mechanics calculations

Minoru Hirota, Kazuhisa Sakakibara, Tamiki Komatsuzaki, Ikuo Akai

Journal:

Computers & Chemistry

Year:

1991

Language:

english

File:

PDF, 713 KB

english, 1991

7

Energetics of proton transfer in liquid water. I. Ab initio study for origin of many-body interaction and potential energy surfaces

Tamiki Komatsuzaki, Iwao Ohmine

Journal:

Chemical Physics

Year:

1994

Language:

english

File:

PDF, 2.51 MB

english, 1994

8

A dividing surface free from a barrier recrossing motion in many-body systems

Tamiki Komatsuzaki, Masataka Nagaoka

Journal:

Chemical Physics Letters

Year:

1997

Language:

english

File:

PDF, 525 KB

english, 1997

9

A new steric subtituent constant Ωs. Characteristic feature and comparison with some other steric constants

Tamiki Komatsuzaki, Ikuo Akai, Kazuhisa Sakakibara, Minoru Hirota

Journal:

Year:

1992

Language:

english

File:

PDF, 1.13 MB

english, 1992

10

A new method for evaluating the steric hindrance by substituent

Tamiki Komatsuzaki, Kazuhisa Sakakibara, Minoru Hirota

Journal:

Tetrahedron Letters

Year:

1989

Language:

english

File:

PDF, 265 KB

english, 1989

11

Dynamical foundation and limitations of statistical reaction theory

Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda

Journal:

Communications in Nonlinear Science and Numerical Simulation

Year:

2008

Language:

english

File:

PDF, 326 KB

english, 2008

12

How many dimensions are required to approximate the potential energy landscape of a model protein?

Komatsuzaki, Tamiki, Hoshino, Kyoko, Matsunaga, Yasuhiro, Rylance, Gareth J., Johnston, Roy L., Wales, David J.

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 441 KB

english, 2005

13

Long-Term Observation of Fluorescence of Free Single Molecules To Explore Protein-Folding Energy Landscapes

Kamagata, Kiyoto, Kawaguchi, Toshifumi, Iwahashi, Yoshitomo, Baba, Akinori, Fujimoto, Kazuya, Komatsuzaki, Tamiki, Sambongi, Yoshihiro, Goto, Yuji, Takahashi, Satoshi

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 479 KB

english, 2012

14

Extracting Complex Network and Effective Free Energy Landscape of Protein Fluctuation from Single-Molecule Time Series

Komatsuzaki, Tamiki, Li, Chun-Biu, Baba, Akinori

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

15

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Multidimensional Energy Landscapes in Single-Molecule Biophysics

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 1.75 MB

english, 2011

16

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Single-Molecule FRET of Protein-Folding Dynamics

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 2.13 MB

english, 2011

17

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Author Index

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 140 KB

english, 2011

18

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Staring at a Protein: Ensemble and Single-Molecule Investigations on Protein-Folding Dynamics

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 2.00 MB

english, 2011

19

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Subject Index

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 110 KB

english, 2011

20

Dynamic Disorder in Single-Enzyme Experiments: Facts and Artifacts

Terentyeva, Tatyana G., Engelkamp, Hans, Rowan, Alan E., Komatsuzaki, Tamiki, Hofkens, Johan, Li, Chun-Biu, Blank, Kerstin

Journal:

Year:

2012

Language:

english

File:

PDF, 1.95 MB

english, 2012

21

[Advances in Chemical Physics] Single-Molecule Biophysics (Experiment and Theory) || Free Energy Landscapes of Proteins: Insights from Mechanical Probes

Komatsuzaki, Tamiki, Kawakami, Masaru, Takahashi, Satoshi, Yang, Haw, Silbey, Robert J.

Year:

2011

Language:

english

File:

PDF, 396 KB

english, 2011

22

Numerical Construction of Estimators for Single-Molecule Fluorescence Measurements

Kawai, Shinnosuke, Cooper, David, Landes, Christy, Mootz, Henning D., Yang, Haw, Komatsuzaki, Tamiki

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.64 MB

english, 2013

23

Effect of timescale on energy landscape: Distinction between free-energy landscape and potential of mean force

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Review E

Year:

2013

Language:

english

File:

PDF, 838 KB

english, 2013

24

Aggregated Markov Model Using Time Series of Single Molecule Dwell Times with Minimum Excessive Information

Li, Chun-Biu, Komatsuzaki, Tamiki

Journal:

Physical Review Letters

Year:

2013

Language:

english

File:

PDF, 519 KB

english, 2013

25

Quantum reaction boundary to mediate reactions in laser fields

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 881 KB

english, 2011

26

[Advances in Chemical Physics] Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems: Clusters and Proteins (Advances in Chemical Physics) || Protein Functional Motions: Basic Concepts and Computational Methodologies

Komatsuzaki, Tamiki, Berry, R. Stephen, Leitner, David M.

Year:

2011

Language:

english

File:

PDF, 614 KB

english, 2011

27

[Advances in Chemical Physics] Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems: Clusters and Proteins (Advances in Chemical Physics) || Ergodic Problems for Real Complex Systems in Chemical Physics

Komatsuzaki, Tamiki, Berry, R. Stephen, Leitner, David M.

Year:

2011

Language:

english

File:

PDF, 3.48 MB

english, 2011

28

Flow and Stop Protocol for the Long-Time Observation of Fluorescence from Free Single Molecules: Application to the Time-Series Analysis of Protein Folding

Kamagata, Kiyoto, Baba, Akinori, Komatsuzaki, Tamiki, Takahashi, Satoshi

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 121 KB

english, 2011

29

Time-Resolved Single Molecule Fluorescence Spectroscopy of an α-Chymotrypsin Catalyzed Reaction

Terentyeva, Tatyana G., Hofkens, Johan, Komatsuzaki, Tamiki, Blank, Kerstin, Li, Chun-Biu

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.90 MB

english, 2013

30

Non-Markovian properties and multiscale hidden Markovian network buried in single molecule time series

Sultana, Tahmina, Takagi, Hiroaki, Morimatsu, Miki, Teramoto, Hiroshi, Li, Chun-Biu, Sako, Yasushi, Komatsuzaki, Tamiki

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 834 KB

english, 2013

31

Cooperativity at different space and time scales in multiscale protein dynamics

Matsunaga, Yasuhiro, Li, Chun-Biu, Komatsuzaki, Tamiki

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 807 KB

english, 2010

32

New Quantification of Local Transition Heterogeneity of Multiscale Complex Networks Constructed from Single-Molecule Time Series

Li, Chun-Biu, Yang, Haw, Komatsuzaki, Tamiki

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.31 MB

english, 2009

33

Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis

Shuang, Bo, Cooper, David, Taylor, J. Nick, Kisley, Lydia, Chen, Jixin, Wang, Wenxiao, Li, Chun Biu, Komatsuzaki, Tamiki, Landes, Christy F.

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 1.72 MB

english, 2014

34

A Dynamical Propensity Rule for Transitions in Chemical Reactions †

Komatsuzaki, Tamiki, Berry, R. Stephen

Journal:

Journal of Physical Chemistry A

Year:

2002

Language:

english

File:

PDF, 115 KB

english, 2002

35

Multibasin Dynamics in Off-Lattice Minimalist Protein Landscapes †

Matsunaga, Yasuhiro, Kostov, Konstantin S., Komatsuzaki, Tamiki

Journal:

Journal of Physical Chemistry A

Year:

2002

Language:

english

File:

PDF, 310 KB

english, 2002

36

Regularity in chaotic reaction paths II: Ar6. Energy dependence and visualization of the reaction bottleneck

Komatsuzaki, Tamiki, Stephen Berry, R

Journal:

Physical Chemistry Chemical Physics

Year:

1999

Language:

english

File:

PDF, 352 KB

english, 1999

37

Electronic spectra of ion pairs of picrate ion with alkali-metal polyether complexes in non-aqueous solvents

Sawada, Kiyoshi, Chigira, Fumie, Satoh, Keiichi, Komatsuzaki, Tamiki

Journal:

Journal of the Chemical Society Faraday Transactions

Year:

1997

Language:

english

File:

PDF, 523 KB

english, 1997

38

Dynamic reaction coordinate in thermally fluctuating environment in the framework of the multidimensional generalized Langevin equations

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.47 MB

english, 2010

39

Hierarchy of reaction dynamics in a thermally fluctuating environment

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 2.01 MB

english, 2010

40

Why and how do systems react in thermally fluctuating environments?

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Chemistry Chemical Physics

Year:

2011

Language:

english

File:

PDF, 2.06 MB

english, 2011

41

Nonlinear dynamical effects on reaction rates in thermally fluctuating environments

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Chemistry Chemical Physics

Year:

2010

Language:

english

File:

PDF, 1.61 MB

english, 2010

42

Phase-space reaction network on a multisaddle energy landscape: HCN isomerization

Li, Chun-Biu, Matsunaga, Yasuhiro, Toda, Mikito, Komatsuzaki, Tamiki

Journal:

The Journal of Chemical Physics

Year:

2005

Language:

english

File:

PDF, 1.53 MB

english, 2005

43

Definability of No-Return Transition States in the High-Energy Regime above the Reaction Threshold

Li, Chun-Biu, Shoujiguchi, Akira, Toda, Mikito, Komatsuzaki, Tamiki

Journal:

Physical Review Letters

Year:

2006

Language:

english

File:

PDF, 569 KB

english, 2006

44

Fractional behavior in multidimensional Hamiltonian systems describing reactions

Shojiguchi, Akira, Li, Chun-Biu, Komatsuzaki, Tamiki, Toda, Mikito

Journal:

Physical Review E

Year:

2007

Language:

english

File:

PDF, 1.30 MB

english, 2007

45

Fractional behavior in nonergodic reaction processes of isomerization

Shojiguchi, Akira, Li, Chun-Biu, Komatsuzaki, Tamiki, Toda, Mikito

Journal:

Physical Review E

Year:

2007

Language:

english

File:

PDF, 208 KB

english, 2007

46

Erratum: Fractional behavior in multidimensional Hamiltonian systems describing reactions [Phys. Rev. E 76 , 056205 (2007)]

Shojiguchi, Akira, Li, Chun-Biu, Komatsuzaki, Tamiki, Toda, Mikito

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 28 KB

english, 2008

47

Study on ‘‘regularity’’ of barrier recrossing motion

Komatsuzaki, Tamiki, Nagaoka, Masataka

Journal:

The Journal of Chemical Physics

Year:

1996

Language:

english

File:

PDF, 531 KB

english, 1996

48

Regularity in chaotic reaction paths. I. Ar[sub 6]

Komatsuzaki, Tamiki, Berry, R. Stephen

Journal:

The Journal of Chemical Physics

Year:

1999

Language:

english

File:

PDF, 579 KB

english, 1999

49

Robust Existence of a Reaction Boundary to Separate the Fate of a Chemical Reaction

Kawai, Shinnosuke, Komatsuzaki, Tamiki

Journal:

Physical Review Letters

Year:

2010

Language:

english

File:

PDF, 847 KB

english, 2010

50

Regularity in chaotic reaction paths III: Ar[sub 6] local invariances at the reaction bottleneck

Komatsuzaki, Tamiki, Berry, R. Stephen

Journal:

The Journal of Chemical Physics

Year:

2001

Language:

english

File:

PDF, 550 KB

english, 2001

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