Komatsuzaki Group

Publications

Paper

2017|2016 |2015 |2014 |2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 | 1996 | 1995 | 1994

1994

[126]Tamiki Komatsuzaki, Iwao Ohmine
Energetics of Proton Transfer in Liquid Water I; Ab initio Study for Origin of Many-Body Interaction and Potential Energy Surfaces
Chemical Physics, Special Issue 'dissipative dynamics' 180, pp.239-269 (1994)

1996

[125]Tamiki Komatsuzaki, Masataka Nagaoka
Study on "Regularity" of the Barrier Recrossing Motion
Journal of Chemical Physics 105, pp.10838-10848 (1996)

[124]Tamiki Komatsuzaki, Iwao Ohmine
Proton Transfer in Liquid Water II; A Semiempirical Method to Describe Chemical Reactions
Molecular Simulation 16, pp.321-344 (1996)

[123]Tamiki Komatsuzaki, Masataka Nagaoka, Peter Hanggi
A Study on Near-Integrability of Recrossing Motions in Many-Body Chemical Reaction Systems
Bussei Kenkyu (Kyoto) 66, pp.1039-1049 (1996)

1997

[122]Kiyoshi Sawada, Fumie Chigira, Keiichi Satoh, Tamiki Komatsuzaki
Electronic Spectra of Ion-Pairs of Picrate Ion with Alkali Metal Polyether Complexes in Non-aqueous Solvents
Journal of the Chemical Society, Faraday Transactions 2. 93(10), pp.1903-1908 (1997)

[121]Tamiki Komatsuzaki, Masataka Nagaoka
A Dividing Surface Free From a Barrier Recrossing Motion in Many-Body Systems
Chemical Physics Letters 265, pp.91-98 (1997)

1999

[120]Tamiki Komatsuzaki, R. Stephen Berry
Regularity in Chaotic Reaction Path II: Ar6 -Energy Dependence and Visualization of the Reaction Bottleneck-
Physical Chemistry Chemical Physics 1, pp.1387-1397 (1999)

[119]Tamiki Komatsuzaki, R. Stephen Berry
Regularity in Chaotic Reaction Path I: Ar6
Journal of Chemical Physics 110(18), pp.9160-9173 (1999)

2000

[118]Tamiki Komatsuzaki, R. Stephen Berry
Local Regularity and Non-recrossing Path in Transition States -A New Strategy in Chemical Reaction Theories
Journal of Molecular Structure 506, pp.55-70 (2000)

2001

[117]Tamiki Komatsuzaki, R. Stephen Berry
Regularity in Chaotic Reaction Path III:Ar6 -Local Invariances at the Reaction Bottleneck-
Journal of Chemical Physics 130, pp.4105-4117 (2001)

[116]Tamiki Komatsuzaki, R. Stephen Berry
'Dynamical Hierarchy in Transition States: Why and How Does a System Climb over the Mountain?
Proceedings of National Academy of Sciences USA 98, pp.7666-7671 (2001)

[115]Tamiki Komatsuzaki, Mikito Toda
Proceeding Reports on 'Dynamical Problems on Lugged Energy Landscapes I -Survey of Intermediate Regime between Selectivity and Stochasticity'
Bussei Kenkyu (Kyoto) 76(1), pp.45-143 (2001)

[114]Tamiki Komatsuzaki
Deterministic Property of Chemical Reactions in the (Thermally) Fluctuating World -Solution of Recrossing Problem from 1930s-
Bussei Kenkyu (Kyoto) 76(1), pp.1-44 (2001)

2002

[113]Yasuhiro Matsunaga, Konstantin S. Kostov, Tamiki Komatsuzaki
Multi-Basin Dynamics in Off-Lattice Minimalist Protein Landscapes
Journal of Physical Chemistry A 106, pp.10898-10907 (2002)

[112]Tamiki Komatsuzaki, R. Stephen Berry
A Dynamical Propensity Rule of Transitions in Chemical Reactions
Journal of Physical Chemistry A 106, pp.10945-10950 (2002)
(invited)

[111]Tamiki Komatsuzaki, R. Stephen Berry
Erratum: "Regularity in chaotic reaction paths. I. Ar6" [J. Chem. Phys. 110, 9160 (1999)]'
Journal of Chemical Physics 116, pp.862-862 (2002)

[110]Tamiki Komatsuzaki, R. Stephen Berry
Chemical Reaction Dynamics: Many-Body Chaos and Regularity
Advances in Chemical Physics 123, pp.79-152 (2002)
ed. by I. Prigogine and S. A. Rice, John-Wiley & Sons, Inc. (invited) (2002): advertisement, Book Review by Mark E. Tuckerman Journal of American Chemical Society, 125,6596-6597 (2003)

[109]Masaki Sasai, Tamiki Komatsuzaki, Mikito Toda
Tales about Funnel -Why can Natural Proteins Fold into the Native State Uniquely and Efficiently?-
Bussei Kenkyu (Kyoto) 78, pp.475-509 (2002)

[108]Yasuhiro Matsunaga
Hierarchical Regularity of Protein Folding Dynamics
Bussei Kenkyu (Kyoto) 78, pp.457-462 (2002)

[107]Tamiki Komatsuzaki
Deterministic Property in the (Thermally) Fluctuating World -Why does a Reacting System pass through the Saddle?
Bussei Kenkyu (Kyoto) 78, pp.354-364 (2002)

[106]Mikito Toda, Tamiki Komatsuzaki
Proceeding Reports on 'Dynamical Problems on Lugged Energy Landscapes II -Survey of Intermediate Regime between Selectivity and Stochasticity'
Bussei Kenkyu (Kyoto) 78, pp.349-474 (2002)

[105]Tamiki Komatsuzaki, Yasuhiro Matsunaga
Dynamics of Protein Folding -Abnormal Diffusion and Hierarchical Regularity
Seibutsu Butsuri (Journal of Biophysical Society of Japan) 42, pp.285-289 (2002)

2004

[104]K. Hoshino, Y. Matsunaga, M. Miller, D.J. Wales, Tamiki 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, pp.344-345 (2004)

[103]Y. Matsunaga, Tamiki Komatsuzaki
Protein Folding Dynamics: Ergodic Behavior in Principal Component Space
AIP conference series for Slow Dynamics in Complex Systems 708, pp.342-343 (2004)

[102]Y. Matsunaga, K.S. Kostov, Tamiki Komatsuzaki
Hierarchical Regularity in Multi-Basin Dynamics on Protein Landscapes
AIP conference series for Slow Dynamics in Complex Systems 708, pp.302-305 (2004)

[101]Mikito Toda, Tamiki Komatsuzaki, Tetsuro Konishi, R.Stephen Berry, Stuart A. Rice
Report of YIYP international Symposium on Geometrical Structures of Phase Space in Multi-Dimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems
Bussei Kenkyu (Kyoto) 83, pp.176-188 (2004)

[100]Yasuhiro Matsunaga
Protein Folding Dynamics -Anomalous diffusion and dynamical correlation-
Bussei Kenkyu (Kyoto) (Selected Master Thesis in Japan) 81, pp.571-592 (2004)

2005

[99]Chun Biu Li, Yasuhiro Matsunaga, Mikito Toda, Tamiki Komatsuzaki
Phase Space Reaction Network on a Multisaddle Energy Landscape: HCN isomerization
Journal of Chemical Physics 123, pp.184301(1)-184301(13) (2005)

[98]Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga, Gareth J. Rylance, Roy L. Johnston, David J. Wales
How Many Dimension is Required to Approximate Potential Energy Landscape of A Model Protein?
Journal of Chemical Physics 122, pp.084714(1)-084714(9) (2005)
This paper was selected in "Virtual Journal of Biological Physics Research "Protein Conformational Dynamics/Folding " 9(5)(2005)".

[97]
(Edition)"Geometric Structures of Phase Space in Multi-Dimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems"
Advances in Chemical Physics 130A, 130B, (2005)
ed. by M. Toda, T. Komatsuzaki, T. Konishi, R. S. Berry and S. A. Rice, John-Wiley & Sons, Inc. 1224 pages

[96]Tamiki Komatsuzaki, Kyoko Hoshino, Y. Matsunaga
Regularity in Chaotic Transitions on Multi-Basin Landscapes
Advances in Chemical Physics 130(B), pp.257-313 (2005)

[95]Tamiki Komatsuzaki, R. Stephen Berry
Regularity in Chaotic Transitions on Two-Basin Landscapes
Advances in Chemical Physics 130(A), pp.143-170 (2005)

[94]Chun Biu Li, M. Toda, T. Komatsuzaki
Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction
Bussei Kenkyu (Kyoto) 84(3), pp.481-482 (2005)

2006

[93]Gareth J. Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun Biu Li, Akinori Baba, Tamiki Komatsuzaki
Topographical complexity of multidimensional energy landscapes
Proceedings of National Academy of Sciences USA 103, pp.18551, (2006)
This paper was selected in "Virtual Journal of Biological Physics Research "Protein Conformational Dynamics/Folding " 12(12) (2006)".

[92]Chun Biu Li, Akira Shojiguchi, Mikito Toda, Tamiki Komatsuzaki
Erratum: Dynamical Hierarchy in Transition States of Reactions
Few-Body Systems 40, pp.129-129 (2006)

[91]Chun Biu Li, Akira Shojiguchi, Mikito Toda, Tamiki Komatsuzaki
Erratum: Definability of No-Return Transition States in the High-Energy Regime above the Reaction Threshold [Phys. Rev. Lett. 97, 028302 (2006)]
Physical Review Letters 97, pp.129901, (2006)

[90]Akira Shojiguchi, Akinori Baba, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
Wavelet Analysis and Arnold Web Picture for Detecting Energy Transfer in Hamiltonian Dynamical System
Laser Physics 16(7), pp.1097-1106 (2006)

[89]Chun Biu Li, Akira Shojiguchi, Mikito Toda, Tamiki Komatsuzaki
Definability of No-return Transition States in High Energy Regime Above Threshold
Physical Review Letters 97, pp.028302-028305 (2006)

[88]Chun Biu Li, Akira Shojiguchi, Mikito Toda, Tamiki Komatsuzaki
Dynamical Hierarchy in Transition States of Reactions
Few-Body Systems 38, pp.173-179 (2006)

[87]Satoshi Noda, Akinori Baba, Tamiki Komatsuzaki
Collective Motion of Water Field and Structural Transition Dynamics of Biomolecules
Bussei Kenkyu (Kyoto) 86(1), pp.123-129 (2006)

[86]Kyoko Hoshino, Y. Matusnaga, Gareth J. Rylance, Roy L. Johnston, David J. Wales, Tamiki Komatsuzaki
Structural Diversity of Protein Energy Landscape and New Visualization of Multidimensional Energy Landscapes
Bussei Kenkyu (Kyoto) 86(1), pp.117-122 (2006)

[85]Chun Biu Li, M. Toda, T. Komatsuzaki
Geometrical Structure buried in the Phase Space of Stochastic Structural Transition
Bussei Kenkyu (Kyoto) 86(1), pp.77-81 (2006)

[84]Sotaro Fuchigami, Tamiki Komatsuzaki, Mikito Toda
Proceeding Reports on 'Dynamical Problems on Lugged Energy Landscapes I -Proteins and the surroundings'
Bussei Kenkyu (Kyoto) 86(1), pp.37-154 (2006)

2007

[83]Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
Fractional Behavior in Multi-Dimensional Hamiltonian Systems Describing Reactions
Physical Review E 76, pp.056205(1)-056205(14) (2007)

[82]Akinori Baba, Tamiki Komatsuzaki
Construction of effective free energy landscape from single molecule time series
Proceedings of National Academy of Sciences USA 104(49), pp.19297-19302 (2007)
This paper was selected in "Virtual Journal of Biological Physics Research "Single Molecule Dynamics", 14(12)(2007)".

[81]Yasuhiro Matsunaga, Chun Biu Li, Tamiki Komatsuzaki
Anomalous Diffusion in Folding Dynamics on Minimalist Protein Landscape
Physical Review Letters 99, pp.238103, (2007)
This paper was selected in "Virtual Journal of Biological Physics Research "Protein Conformational Dynamics/Folding " 14(12)(2007)".

[80]Masahito Kinoshita, Kiyoto Kamagata, Akio Maeda, Yuji Goto, Tamiki Komatsuzaki, Satoshi Takahashi
Development of a technique for the investigation of folding dynamics of single proteins for extended time periods
Proceedings of National Academy of Sciences USA 104, pp.10453, (2007)
This paper was selected in "Virtual Journal of Biological Physics Research "Protein Conformational Dynamics/Folding " 14(2)(2007)".

[79]Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
'Fractional behavior in nonergodic reaction processes of isomerization
Physical Review E (rapid communication) 75, pp.035204(R), (2007)

[78]Shinnosuke Kawai, Yo Fujimura, Okitsugu Kajimoto, Takefumi Yamashita, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
Dimension reduction for extracting geometrical structure of multidimensional phase space: Application to fast energy exchange in the reaction O(1D)+N2O →NO+NO
Physical Review A 75, pp.022714, (2007)

[77]Tomohiro Shirakawa, Yukio-Pegio Gunji, T. Komatsuzaki
Cross Talk between Planetary Science and Nonlinear Science:from Chemical Reaction to Biocomputing
YUSEIJIN (Japanese society of planetary science) 16(4), pp.322-329 (2007)

[76]Kazuto Sei, Tamiki Komatsuzaki
Complex Network extracted from Single-Molecule Time Series -Dynamic Structure on Kantorovich Metric Space
Bussei Kenkyu (Kyoto) , (2007)

2008

[75]Hiroshi Teramoto, Tamiki Komatsuzaki
Exploring Remnant of Invariants Buried in a Deep Potential Well in Chemical Reactions
Journal of Chemical Physics 129, pp.094302, (2008)

[74]Hiroshi Teramoto, Tamiki Komatsuzaki
Probing Remnants of Invariants to Mediate Energy Exchange in Highly-Chaotic Many-dimensional Systems
Physical Review E 78, pp.017202, (2008)

[73]Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
Erratum: Fractional Behavior in Multi-Dimensional Hamiltonian Systems Describing Reactions
Physical Review E 77, pp.019902, (2008)

[72]Chun Biu Li, Haw Yang, Tamiki Komatsuzaki
Multiscale Complex Network of Protein Conformational Fluctuation Buried in Single Molecule Time Series
Proceedings of National Academy of Sciences USA 105, pp.536-541 (2008)
This paper was selected in "Virtual Journal of Biological Physics Research "Single Molecule Dynamics", 15(3) (2008)"

[71]Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda
Dynamical Foundation and Limitations of Statistical Reaction Theory
Communications in Nonlinear Science and Numerical Simulation 13, pp.857-657 (2008)

[70]Tamiki Komatsuzaki
What can we learn from Single-Molecule Time Series?
Bussei Kenkyu (Kyoto) 91, pp.121-130 (2008)

[69]Motoi Miyazu
Letter from Local Branch: Hokkaido Branch of the Biophysical Society of Japan (contribute article to introduction of laboratories)
The Biophysical Society of Japan, SEIBUTSU BUTSURI 48(4), pp.258-259 (2008)

[68]Tamiki Komatsuzaki
State Transition Network Extracted from Single-Molecule Time Series
Seibutsu Butsuri (Journal of Biophysical Society of Japan) 48(5), pp.282-283 (2008)

[67]Yasuhiro Matsunaga, Tamiki Komatsuzaki
Polymer and Chaos: Anomalous Diffusion and Hierarchical Regularity
KOUBUNSHI (Japanese society of polymer science) 57(2), pp.58-61 (2008)

2009

[66]Shinnosuke Kawai, Tamiki Komatsuzaki
Dynamic pathways to mediate reactions buried in thermal fluctuations. I. Time-dependent normal form theory for multidimensional Langevin equation
Journal of Chemical Physics 131, pp.224505 (1)-224505(11) (2009)
This article was selected as the December 2009 issue of JCP: BioChemical Physics, 3 (12), (2009)

[65]Shinnosuke Kawai, Tamiki Komatsuzaki
Dynamic pathways to mediate reactions buried in thermal fluctuations II: numerical illustrations using a model system
Journal of Chemical Physics 131, pp.224506(1)-224506(9) (2009)
This article was selected as the December 2009 issue of JCP: BioChemical Physics, 3 (12), (2009).

[64]Chun Biu Li, Mikito Toda, Tamiki Komatsuzaki
Bifurcation of no-return transition states in many-body chemical reactions
Journal of Chemical Physics 130, pp.124116, (2009)

[63]Chun Biu Li, Haw Yang, Tamiki Komatsuzaki
New Quantification of Local Transition Heterogeneity of Multiscale Complex Networks Constructed from Single-Molecule Time Series
Journal of Physical Chemistry B 113(44), pp.14732-14741 (2009)

2010

[62]Tamiki Komatsuzaki, Chun Biu Li, Shinnosuke Kawai
Robustness and Diversity of Transitions in a Sea of Chaos and Stochastic Fluctuation
AIP Conference Proceedings "International Conference of Numerical Analysis and Applied Mathematics 2010" 1281(1), pp.1582-1584 (2010)

[61]Shinnosuke Kawai, Tamiki Komatsuzaki
Dynamical Reaction Coordinate in Thermally Fluctuating Environments in the Framework of Multidimensional Generalized Langevin Equations
Physical Chemistry Chemical Physics 12, pp.15382-15391 (2010)

[60]Hiroshi Teramoto, Tamiki Komatsuzaki
How does a choice of Markov partition affect the resultant symbolic dynamics?
Chaos 20, pp.037113, (2010)
URL Focus Issue on "Intrinsic and Designed Computation: Information processing in dynamical Systems" selected as Top 20 Most Read Articles 2010

[59]Shinnosuke Kawai, Tamiki Komatsuzaki
Robust existence of a reaction boundary to separate the fate of a chemical reaction
Physical Review Letters 105, pp.048304, (2010)

[58]Yasuhiro Matsunaga, Chun Biu Li, Tamiki Komatsuzaki
Collectivity at Different Space and Time Scales in Multiscale Protein Dynamics
Physical Review E 82, pp.016213, (2010)
This paper was selected in "Virtual Journal of Biological Physics Research "Protein Conformational Dynamics/Folding " 20(3) (2010)".

[57]Shinnosuke Kawai, Tamiki Komatsuzaki
Nonlinear Dynamical Effects on Reaction Rates in Thermally Fluctuating Environments
Physical Chemistry Chemical Physics 12, pp.7636-7647 (2010)

[56]Shinnosuke Kawai, Tamiki Komatsuzaki
Hierarchy of Reaction Dynamics in a Thermally Fluctuating Environment
Physical Chemistry Chemical Physics 12, pp.7626-7635 (2010)

[55]Hiroshi Teramoto, Tamiki Komatsuzaki
Possible Folding Patterns of Stable/Unstable Manifolds in Many Degrees of Freedom Hamiltonian Systems and Their Relationship with Properties of Dynamical Systems
From Hyperbolic Systems to Many-Degrees of Freedom Dynamical Systems, RIMS Kokyuroku, Research Institute for Mathematical Sciences (RIMS) 1688, pp.26-38 (2010)

2011

[54]Tamiki Komatsuzaki
My memory of Prof. Shuichi Tasaki
Bussei Kenkyuu (Kyoto) 97, pp.286-290 (2011)

[53]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
Advanced Understanding of Transport Phenomena in High-dimensional Dynamical systems: Normally Hyperbolic Invariant Manifold, its Stable/Unstable Invariant Manifolds and their Breakdown
Bussei Kenkyu(Kyoto) 97, pp.547-559 (2011)

[52]Shinnosuke Kawai, Tamiki Komatsuzaki
Why and how do systems react in thermally fluctuating environments?
Physical Chemistry Chemical Physics (Perspective) 13, pp.21217-21229 (2011)
This paper was selected in "Virtual Journal of Biological Physics Research "STATISTICAL AND NONLINEAR PHYSICS", 22(11) (2011)

[51]Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
Decomposability of Multivariate Interactions
Complex Systems 20, pp.165-179 (2011)

[50]Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
Spatial Heterogeneity of Multivariate Dependence
AIP Conference Proceedings ''International Conference of Numerical Analysis and Applied Mathematics 2011'' 1389, pp.991-991 (2011)

[49]Shinnosuke Kawai, Tamiki Komatsuzaki
Derivation of the Generalized Langevin Equation in Non-stationary environments
Journal of Chemical Physics 134, pp.114523, (2011)
This article was selected as the March 2011 issue of JCP: BioChemical Physics, 5 (3), (2011)

[48]Shinnosuke Kawai, Tamiki Komatsuzaki
Phase Space Geometry of Dynamics Passing through Saddle Coupled with Spatial Rotation
Journal of Chemical Physics 134, pp.084304, (2011)

[47]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
A Dynamical Switching of a Reaction Coordinate to Carry the System Through to a Different Product State at High Energies
Physical Review Letters 106, pp.054101, (2011)

[46]Shinnosuke Kawai, Tamiki Komatsuzaki
Quantum Reaction Boundary to Mediate Reactions in Laser Fields
Journal of Chemical Physics 134, pp.024317, (2011)

[45]Akinori Baba, Tamiki Komatsuzaki
Extracting the Underlying Effective Free Energy Landscape From Single-Molecule Time Series --- Local Equilibrium States and their Network
Physical Chemistry Chemical Physics 13(4), pp.1395-1406 (2011)
This paper was selected in "Virtual Journal of Biological Physics Research "Single Molecule Dynamics", 21(2) (2011)".

[44]David M. Leitner, Yasuhiro Matsunaga, Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics
Advances in Chemical Physics 145, pp.83-122 (2011)

[43]Shinnosuke Kawai, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
Dynamical Reaction Theory based on Geometric Structures of Phase Space
Advances in Chemical Physics 145, pp.123-170 (2011)

[42]Tamiki Komatsuzaki, Akinori Baba, Shinnosuke Kawai, Mikito Toda, John E. Straub, R. Stephen Berry
Ergodic Problems for Real Complex Systems in Chemical Physics
Advances in Chemical Physics 145, pp.171-220 (2011)

[41]T. Komatsuzaki, R. S. Berry, D.M. Leitner
(Edition)"Advancing Theory for Kinetics and Dynamics of Complex, Many-Dimensional Systems: Clusters and Proteins"
Advances in Chemical Physics 145, (2011)
ed. by T. Komatsuzaki, R. S. Berry, D.M. Leitner John-Wiley & Sons, Inc. ISBN: 978-0-470-64371-6 (2011).

2012

[40]Mikito Toda, Tamiki Komatsuzaki
Proceeding Reports on 'Dynamical Problems on Lugged Energy Landscapes IV -Survey of Intermediate Regime between Selectivity and Stochasticity'
BUSSEI KENKYUU 1(3), pp.013502【6pages】, (2012)

[39]Kiyoto Kamagata, Toshifumi Kawaguchi, Yoshitomo Iwahashi, Akinori Baba, Kazuya Fujimoto, Tamiki Komatsuzaki, Yoshihiro Sambongi, Yuji Goto, Satoshi Takahashi
Long-term observation of fluorescence of free single molecules to explore protein-folding energy landscapes
Journal of American Chemical Society 134(28), pp.11525-11532 (2012)
DOI: 10.1021/ja3020555

[38]Shinnosuke Kawai, Tamiki Komatsuzaki
Laser Control of Chemical Reactions by Phase Space Structures
Bulletin of the Chemical Society of Japan 85, pp.854-861 (2012)
(Awarded as the BCSJ award and chosen as the cover art of the volume)

[37]Tatyana Terentyeva, Hans Engelkamp, Alan Rowan, Tamiki Komatsuzaki, Johan Hofkens, Chun Biu Li, Kerstin Blank
Dynamic Disorder in Single Enzyme Experiments: Facts and Artifacts
ACS Nano 6(1), pp.346-354 (2012)
DOI: 10.1021/nn203669r
(Chosen as a highlighted article In Nano, Volume 6, issue 1(2012))

[36]Akinori Baba, Tamiki Komatsuzaki
Multidimensional Energy Landscapes in Single Molecule Biophysics
Advances in Chemical Physics 146, pp.299-328 (2012)
DOI: 10.1002/9781118131374.ch11

[35]T. Komatsuzaki, S. Takahashi, M. Kawakami, Haw Yang, Robert Silbey
(Edition)Single Molecule Biophysics: Experiment and Theory
Advances in Chemical Physics 146, (2012)
DOI: 10.1002/9781118131374
John-Wiley& Sons, Inc. ISBN: 978-1-1-180-5780-3.

2013

[34]Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
Non-Markovian properties and multiscale Hidden Markovian Network Buried in Single Molecule Time Series
The Journal of Chemical Physics 139, pp.245101-245101-12 (2013)
DOI: 10.1063/1.4848719
This paper was chosen as one of the most-accessed articles in Biological Molecules and Networks from The Journal of Chemical Physics.

[33]Yasuhiro Matsunaga, Akinori Baba, Chun Biu Li, John Straub, Mikito Toda, Tamiki Komatsuzaki, R. Stephen Berry
Spatio-temporal hierarchy in the dynamics of a minimalist protein model
The Journal of Chemical Physics 139, pp.215101-215101-13 (2013)
DOI: 10.1063/1.4834415

[32]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")

[31]Hiroshi Teramoto, George Haller, Tamiki Komatsuzaki
Detecting invariant manifolds as stationary Lagrangian coherent structures in autonomous dynamical systems
Chaos 23, pp.043107 -43107-12 (2013)
DOI: 10.1063/1.4824314

[30]Chun-Biu Li, Tamiki Komatsuzaki
Aggregated Markov Model Using Time Series of Single Molecule Dwell Times with Minimum Excessive Information
Physical Review Letters 111, pp.58301-58301-5 (2013)
DOI: 10.1103/PhysRevLett.111.058301

[29]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

[28]Shinnosuke Kawai, David Cooper, Christy F. Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
Numerical Construction of Estimators for single-molecule fluorescence measurements
The Journal of Physical Chemistry B 117(27), pp.8061 , (2013)
DOI: 10.1021/jp402328m

[27]Shinnosuke Kawai, Tamiki Komatsuzaki
Effect of Timescale on Energy Landscape: Distinction between Free Energy Landscape and Potential of Mean Force
Physical Review E (Rapid Communication) 87(3), pp.30803 , (2013)
DOI: 10.1103/PhysRevE.87.030803

[26]Tamiki Komatsuzaki
Wish to listen to the individuality of molecules existing on biological dynamics system
IMS Letters 67, pp.17, (2013)

[25]Tatyana Terentyeva, Johan Hofkens, Tamiki Komatsuzaki, Kerstin Blank, Chun-Biu Li
Time-Resolved Single Molecule Fluorescence Spectroscopy of an α-Chymotrypsin Catalyzed Reaction
Journal of Physical Chemistry B 117 (5), pp.1252-1260 (2013)
DOI: 10.1021/jp310663v

2014

[24]Tamiki Komatsuzaki
Bridge the Differences between Top-down and Bottom-up
Seitai no Kagaku 65(5), pp.444-445 (2014)

[23]Hideyuki Yaginuma, Shinnosuke Kawai, Kazuhito V. Tabata, Keisuke Tomiyama, Akira Kakizuka, Tamiki Komatsuzaki, Hiroyuki Noji, Hiromi Imamura
Diversity in ATP concentrations in a single bacterial cell population revealed by quantitative single-cell imaging
Scientific Reports 4(6522), pp.1-7 (2014)
DOI: 10.1038/srep06522

[22]Chun-Biu Li, Tamiki Komatsuzaki
Handling Noisy Data from Single Molecule Experiments
SEIBUTSU BUTSURI 54(5), pp.257-258 (2014)
DOI: 10.2142/biophys.54.257

[21]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
A New Method to Improve Validity Range of Lie Canonical Perturbation Theory: With a Central Focus on a Concept of Non Blow-Up Region
Theoretical Chemistry Accounts 133, pp.1571, (2014)
DOI: 10.1007/s00214-014-1571-9

[20]Preetom Nag, Hiroshi Teramoto, Chun-Biu Li, Joseph Z. Terdik, Norbert F. Scherer, Tamiki Komatsuzaki
Local-heterogeneous responses and transient dynamics of cage breaking
The Journal of Chemical Physics 141, pp.104907-1-104907-12 (2014)
DOI: 10.1063/1.4894866

[19]B. Shuang, D. Cooper, J. N. Taylor, L. Kisley, J. Chen, W. Wang, C.-B. Li, T. Komatsuzaki, C. F. Landes
Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis
The Journal of Physical Chemistry Letters 5, pp.3157-3161 (2014)
DOI: 10.1021/jz501435p

2015

[18]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
Understandings of chemical reaction dynamics in terms of dynamical systems theory
AIP Conference Proceedings 1702(90042), (2015)
DOI: 10.1063/1.4938850

[17]C.B. Li, H. Ueno, R. Watanabe, H. Noji, T. Komatsuzaki
ATP hydrolysis assists phosphate release and promotes reaction ordering in F1-ATPase
Nature Communications 6(10223), (2015)
DOI: 10.1038/ncomms10223

[16]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

[15]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

[14]Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
Mechanism and Experimental Observability of Global Switching Between Reactive and Nonreactive Coordinates at High Total Energies
PHYSICAL REVIEW LETTERS 115(093003), (2015)
DOI: 10.1103/PhysRevLett.115.093003

[13]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
Breakdown Mechanism of Normally Hyperbolic Invariant Manifold in terms of unstable periodic orbits and homoclinic/heteroclinic orbits in Hamiltonian Systems
Nonlinearity 28, pp.2677-2698 (2015)
DOI: 10.1088/0951-7715/28/8/2677

[12]J. N. Taylor, C.-B. Li, D. Cooper, C. F. Landes, T. Komatsuzaki
Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series
Scientific Reports 5, pp.9174-1-9174-9 (2015)
DOI: 10.1038/srep09174

[11]Y. Tamiya, S. Shinkai, Y. Aizawa
Log-Weibull Law in Fermi-Pasta-Ulam Oscillator Chain : Induction Time as Nekhoroshev Stability Time
ASTE; Advances in Science, Technology and Environmentology, Special issue on New Challenges in Complex Systems Science B11, pp.181-184 (2015)

[10]Chun Biu Li
Challenges in Constructing State-Space Network Models for Complex Systems at the Single Molecule Level
ASTE; Advances in Science, Technology and Environmentology, Special issue on New Challenges in Complex Systems Science B11, pp.51-54 (2015)

[9]Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
A coarse graining method to extract cooperative modes of water molecules
ASTE; Advances in Science, Technology and Environmentology, Special issue on New Challenges in Complex Systems Science B11, pp.7-12 (2015)

[8]Satoru Tsugawa, Yoji Aizawa
Statistical Laws of the Ensemble Average Associated with Allan Variance
ASTE; Advances in Science, Technology and Environmentology, Special issue on New Challenges in Complex Systems Science B11, pp.197-199 (2015)

2016

[7]Laurent Wiesenfeld, Wing-Fai Thi, Paola Caselli, Alexandre Faure, Luca Bizzocchi, João Brandão, Denis Duflot, Eric Herbst, Stephen J. Klippenstein, Tamiki Komatsuzaki, Cristina Puzzarini, Octavio oncero, Hiroshi Teramoto, Mikito Toda, Ad van der Avoird, Holger Waalkens
Theory of Gas Phase Scattering and Reactivity for Astrochemistry
Report from the Workshop on Theory of Gas Phase Scattering and Reactivity for Astrochemistry Nov 23 – Dec 4, 2015 , (2016)

[6]Tamiki Komatsuzaki
データ科学雑感
生物物理 56(4), pp.197-197 (2016)
DOI: 10.2142/biophys.56.197

[5]L. Hong, M. Dumond, S. Tsugawa, A. Sapala, A.-L. Routier-Kierzkowska, Y. Zhou, C. Chen, A. Kiss, M. Zhu, O. Hamant, R. S. Smith, T. Komatsuzaki, C.-B. Li, A. Boudaoud & A. H. K. Roeder
Variable cell growth yields reproducible organ development through spatiotemporal averaging
Developmental Cell 38(1), pp.15-32 (2016)
DOI: 10.1016/j.devcel.2016.06.016

[4]Satoru Tsugawa, Nathan Hervieux, Olivier Hamant, Arezki Boudaoud, Richard S. Smith, Chun-Biu Li, Tamiki Komatsuzaki
Extracting subcellular fibrillar alignment with error estimation: Application to microtubules
Biophysical Journal 110(8), pp.1836-1844 (2016)
DOI: 10.1016/j.bpj.2016.03.011

2017

[3]伊藤 創祐, 沙川 貴大
ネットワーク上の情報熱力学とその生体情報処理への応用
日本物理学会誌 72(9), pp.658-658 (2017)

[2]Jonas Alfermann, Xun Sun, Florian Mayerthaler, Thomas E. Morrell, Eva Dehling, Gerrit Volkmann, Tamiki Komatsuzaki, Haw Yang, Henning D. Mootz
FRET monitoring of a nonribosomal peptide synthetase
Nature Chemical Biology 13, pp.1009-1015 (2017)
DOI: 10.1038/nchembio.2435

[1]Hiroshi Teramoto, Kenji Kondo, Shyuichi Izumiya, Mikito Toda, Tamiki Komatsuzaki
Classification of Hamiltonians in neighborhoods of band crossings in terms of the theory of singularities
Journal of Mathematical Physics 58, pp.073502-1-073502-39 (2017)
DOI: 10.1063/1.4991662

Books

1994

[12]Tamiki Komatsuzaki
Molecular Dynamics Methods including Quantum Chemical Effect in The 6th extension lecture of Division of Chemical Information and Computer Science, The Chemical Society of Japan , pp.19-30

2002

[11] Tamiki Komatsuzaki, R.Stephen Berry
A New Propensity Rule of Transitions in Chemical Reactions: Why and How Does a Reacting System Climb over the Saddle? edited by Okamoto, M, Terashima, M. Toda, Tamiki Komatsuzaki, R.Stephen Berry, pp.163-167

2003

[10]Tamiki Komatsuzaki
Dynamics of Chemical Reactions and Chaos -Revisit of Transition State Concept, Lecture Note Series in the 43rd Summer School of Molecular Science , pp.1-56

2011

[9]Chun Biu Li, Tamiki Komatsuzaki
Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series in Cell Signaling Reactions: Single-Molecular Kinetic Analysis (Springer) , ISBN: 978-90-481-9863-4
(invited)

2012

[8]Tamiki Komatsuzaki
Anthology for celebrating 50th year of Molecular Science Summer school for Young Scientists in To 50th year of Molecular Science Summer school for Young Scientists

[7]Tamiki Komatsuzaki
Toward establishing new practical molecular theory to unveil single molecule experiments in the second advanced watching survey on developing a novel transdisciplinary research field "Molecular Science for Higher order Molecular Systems: challenges of experiments and theories" , pp.31-34

[6]Tamiki Komatsuzaki
On the Occasion of Publication of Festschrift in Honour of 50th Anniversary of Summer School of Young Molecular Scientists’ Association in Festschrift in honour of 50th Anniversary of Summer School of Young Molecular Scientists’ 58

2013

[5]Shinnosuke Kawai, Tamiki Komatsuzaki
Dynamics of Chemical Reaction around a Saddle Point - What divides reacting and non-reacting trajectories? in Reaction Rate Constant Computations; Theories and Applications edited by Keli Han and Tianshu Chu (RSC) , ISBN: 978-1-84973-650-3

[4]Thomas Peacock, George Haller
in Lagrangian coherent structures : the hidden skeleton of fluid flows translated translated by Tamiki Komatsuzaki (Parity)

2016

[3]寺本 央, 戸田 幹人, 河野 裕彦, 高橋 正彦, 小松崎 民樹
化学反応の行き先を変える“スイッチ”─エネルギーの上昇で反応経路が切り替わる新現象 (月刊「化学」71(5))

2017

[2]Meysam Tavakoli, J. Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé
Advances in Chemical Physics: "Single Molecule Data Analysis: An Introduction" Edited by Stuart A. Rice, Aaron R. Dinner (Wiley)

[1]小松崎民樹
少数性生物学:第5章「少数の個性~分子にも個性?~」 永井健治(編), 冨樫祐一(編) (株式会社 日本評論社)