Researcher Database

KOMATSUZAKI TAMIKI
Research Institute for Electronic Science Research Center of Mathematics for Social Creativity
Professor

Researcher Profile and Settings

Affiliation

  • Research Institute for Electronic Science Research Center of Mathematics for Social Creativity

Job Title

  • Professor

URL

Research funding number

  • 30270549

J-Global ID

Research Interests

  • 時系列解析 データマイニング 生体情報 非平衡・非線形物理学 統計物理学 化学物理 生物物理 化学反応 分子動力学 タンパク質・核酸の構造・動態・機能 フォールディング 1分子計測・操作 非平衡・複雑系   Functions Folding Single Molecule Measurement Complex Systems   Dynamics   Nolinear Physics Statistical Physics Chemical Physics Biological Physics Chemical Reaction Molecular Dynamics Protein Structure   Time Series Analysis Data Mining Biological Information Nonequilibrium   

Research Areas

  • Life sciences / Biophysics
  • Nanotechnology/Materials / Basic physical chemistry
  • Natural sciences / Bio-, chemical, and soft-matter physics
  • Natural sciences / Mathematical physics and basic theory

Academic & Professional Experience

  • 2019/07 - Today 北海道大学人間知・脳・AI研究教育センター 兼務教員
  • 2018/10 - Today Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University PI
  • 2018/04 - Today Hokkaido University Graduate School of Chemical Sciences and Engineering
  • 2017/04 - Today 北海道大学共同プロジェクト拠点「知識メディアラボラトリ」 運営委員
  • 2015/04 - Today Hokkaido University Research Institute for Electronic Science
  • 2007/10 - Today Hokkaido University Graduate School of Life Science
  • 2019/05 - 2019/05 リヨン高等師範学校(Ecole normale supérieure de Lyon) 客員教授
  • 2015/04 - 2019/03 Hokkaido University Research Institute for Electronic Science
  • 2018/11 - 2018/12 リヨン高等師範学校(Ecole normale supérieure de Lyon) 客員教授
  • 2016/06 - 2016/07 ブルゴーニュ大学 CNRS-Université de Bourgogne 客員教授
  • 2015/04 - 2016/03 Chuo University Faculty of Science and Engineering, Department of Physics
  • 2008/04 - 2015/03 数学連携研究センター 教授 兼任
  • 2007/10 - 2015/03 Hokkaido University Research Institute for Electronic Science
  • 2003/07 - 2007/09 21世紀COEプログラム「惑星系の起源と進化」兼任
  • 1999/07 - 2007/09 Kobe University Graduate School of Science and Technology, Department of Information and Media Science
  • 1999/07 - 2007/09 Kobe University Faculty of Science, Department of Earth and Planetary Sciences
  • 2006/04 - 2007/03 Hiroshima University Faculty of Science, Department of Chemistry
  • 2005/04 - 2006/03 Institute for Molecular Science
  • 2004/04 - 2005/03 Ibaraki University Graduate School of Science and Engineering
  • 2003/04 - 2004/03 The University of Tokyo
  • 2001/04 - 2002/03 Shiga University Faculty of Education
  • 1998/04 - 1999/06 シカゴ大学化学科 research associate(医療保険、退職金完備)
  • 1997/03 - 1998/03 シカゴ大学化学科 日本学術振興会 特別研究員(PD)
  • 1994/04 - 1997/02 基礎化学研究所(現、京都大学福井謙一記念研究センター) 研究員/日本学術振興会 特別研究員(PD)

Association Memberships

  • American Association for the Advancement of Science   SAIM(Society for Industrial and Applied Mathematics)   JAPAN SOCIETY FOR MOLECULAR SCIENCE   WATOC(World Association of Theoretically Oriented Chemists)   アメリカ化学会   日本蛋白質科学会   日本物理学会   日本生物物理学会   日本化学会   

Research Activities

Published Papers

  • Yuya Sugie, Yuki Yoshida, Normann Mertig, Takashi Takemoto, Hiroshi Teramoto, Atsuyoshi Nakamura, Ichigaku Takigawa, Shin-ichi Minato, Masanao Yamaoka, Tamiki Komatsuzaki
    CoRR abs/2004.03819 2020 [Refereed][Not invited]
  • Tabata, Koji, Nakamura, Atsuyoshi, Honda, Junya, Komatsuzaki, Tamiki
    MACHINE LEARNING 0885-6125 2019/10 [Refereed][Not invited]
     
    We study a bad arm existence checking problem in a stochastic K-armed bandit setting, in which a player's task is to judge whether a positive arm exists or all the arms are negative among given K arms by drawing as small number of arms as possible. Here, an arm is positive if its expected loss suffered by drawing the arm is at least a given threshold theta(U), and it is negative if that is less than another given threshold theta(L) (<= theta(U)). This problem is a formalization of diagnosis of disease or machine failure. An interesting structure of this problem is the asymmetry of positive and negative arms' roles; finding one positive arm is enough to judge positive existence while all the arms must be discriminated as negative to judge whole negativity. In the case with Delta = theta(U) - theta(L) > 0, we propose elimination algorithms with arm selection policy (policy to determine the next arm to draw) and decision condition (condition to conclude positive arm's existence or the drawn arm's negativity) utilizing this asymmetric problem structure and prove its effectiveness theoretically and empirically.
  • Helal KM, Taylor JN, Cahyadi H, Okajima A, Tabata K, Itoh Y, Tanaka H, Fujita K, Harada Y, Komatsuzaki T
    FEBS letters 593 (18) 2535 - 2544 0014-5793 2019/09 [Refereed][Not invited]
  • Komatsuzaki T, Pressé S, Senet P
    The journal of physical chemistry. B 123 (30) 6387 - 6388 1520-6106 2019/08/01 [Refereed][Not invited]
  • Taylor JN, Mochizuki K, Hashimoto K, Kumamoto Y, Harada Y, Fujita K, Komatsuzaki T
    The journal of physical chemistry. B American Chemical Society ({ACS}) 123 (20) 4358 - 4372 1520-6106 2019/05 [Refereed][Not invited]
  • Koji Tabata, Atsuyoshi Nakamura, Junya Honda, Tamiki Komatsuzaki
    CoRR abs/1901.11200 2019 [Refereed][Not invited]
  • J. Nicholas Taylor, Menahem Pirchi, Gilad Haran, Tamiki Komatsuzaki
    Journal of Chemical Physics 148 (12) 123325  0021-9606 2018/03/28 [Refereed][Not invited]
     
    Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.
  • Yuji Tamiya, Rikiya Watanabe, Hiroyuki Noji, Chun-Biu Li, Tamiki Komatsuzaki
    Physical Chemistry Chemical Physics 20 (3) 1872 - 1880 1463-9076 2018 [Refereed][Not invited]
     
    F1-ATPase (F1) is an efficient rotary protein motor, whose reactivity is modulated by the rotary angle to utilize thermal fluctuation. In order to elucidate how its kinetics are affected by the change in the fluctuation, we have extended the reaction-diffusion formalism [R. Watanabe et al., Biophys. J., 2013, 105, 2385] applicable to a wider range of temperatures based on experimental data analysis of F1 derived from thermophilic Bacillus under high ATP concentration conditions. Our simulation shows that the rotary angle distribution manifests a stronger non-equilibrium feature as the temperature increases, because ATP hydrolysis and Pi release are more accelerated compared with the timescale of rotary angle relaxation. This effect causes the rate coefficient obtained from dwell time fitting to deviate from the Arrhenius relation in Pi release, which has been assumed in the previous activation thermodynamic quantities estimation using linear Arrhenius fitting. Larger negative correlation is also found between hydrolysis and Pi release waiting time in a catalytic dwell with the increase in temperature. This loss of independence between the two successive reactions at the catalytic dwell sheds doubt on the conventional dwell time fitting to obtain rate coefficients with a double exponential function at temperatures higher than 65 °C, which is close to the physiological temperature of the thermophilic Bacillus.
  • Yuji Tamiya, Rikiya Watanabe, Hiroyuki Noji, Chun-Biu Li, Tamiki Komatsuzaki
    Physical Chemistry Chemical Physics 20 (3) 1872 - 1880 1463-9076 2018 [Refereed][Not invited]
     
    F1-ATPase (F1) is an efficient rotary protein motor, whose reactivity is modulated by the rotary angle to utilize thermal fluctuation. In order to elucidate how its kinetics are affected by the change in the fluctuation, we have extended the reaction-diffusion formalism [R. Watanabe et al., Biophys. J., 2013, 105, 2385] applicable to a wider range of temperatures based on experimental data analysis of F1 derived from thermophilic Bacillus under high ATP concentration conditions. Our simulation shows that the rotary angle distribution manifests a stronger non-equilibrium feature as the temperature increases, because ATP hydrolysis and Pi release are more accelerated compared with the timescale of rotary angle relaxation. This effect causes the rate coefficient obtained from dwell time fitting to deviate from the Arrhenius relation in Pi release, which has been assumed in the previous activation thermodynamic quantities estimation using linear Arrhenius fitting. Larger negative correlation is also found between hydrolysis and Pi release waiting time in a catalytic dwell with the increase in temperature. This loss of independence between the two successive reactions at the catalytic dwell sheds doubt on the conventional dwell time fitting to obtain rate coefficients with a double exponential function at temperatures higher than 65 °C, which is close to the physiological temperature of the thermophilic Bacillus.
  • Yuya Sugie, Array,Array,Array, Hiroshi Teramoto, Array,Array, Shin-ichi Minato, Masanao Yamaoka,Array
    Theory and Practice of Natural Computing - 7th International Conference, TPNC 2018, Dublin, Ireland, December 12-14, 2018, Proceedings Springer 111 - 123 2018 [Refereed][Not invited]
  • Takashi Takemoto, Array, Masato Hayashi, Saki Susa-Tanaka, Hiroshi Teramoto, Atsuyoshi Nakamura, Ichigaku Takigawa, Shin-ichi Minato, Tamiki Komatsuzaki, Masanao Yamaoka
    2018 International Conference on ReConFigurable Computing and FPGAs, ReConFig 2018, Cancun, Mexico, December 3-5, 2018 IEEE 1 - 8 2018 [Refereed][Not invited]
  • Nathan Hervieux, Satoru Tsugawa, Antoine Fruleux, Mathilde Dumond, Anne-Lise Routier-Kierzkowska, Tamiki Komatsuzaki, Arezki Boudaoud, John C. Larkin, Richard S. Smith, Chun-Biu Li, Olivier Hamant
    CURRENT BIOLOGY 27 (22) 3468 - + 0960-9822 2017/11 [Refereed][Not invited]
     
    A landmark of developmental biology is the production of reproducible shapes, through stereotyped morphogenetic events. At the cell level, growth is often highly heterogeneous, allowing shape diversity to arise. Yet, how can reproducible shapes emerge from such growth heterogeneity? Is growth heterogeneity filtered out? Here, we focus on rapidly growing trichome cells in the Arabidopsis sepal, a reproducible floral organ. We show via computational modeling that rapidly growing cells may distort organ shape. However, the cortical microtubule alignment along growth-derived maximal tensile stress in adjacent cells would mechanically isolate rapidly growing cells and limit their impact on organ shape. In vivo, we observed such microtubule response to stress and consistently found no significant effect of trichome number on sepal shape in wild-type and lines with trichome number defects. Conversely, modulating the microtubule response to stress in katanin and spiral2 mutant made sepal shape dependent on trichome number, suggesting that, while mechanical signals are propagated around rapidly growing cells, the resistance to stress in adjacent cells mechanically isolates rapidly growing cells, thus contributing to organ shape reproducibility.
  • Jonas Alfermann, Xun Sun, Florian Mayerthaler, Thomas E. Morrell, Eva Dehling, Gerrit Volkmann, Tamiki Komatsuzaki, Haw Yang, Henning D. Mootz
    NATURE CHEMICAL BIOLOGY 13 (9) 1009 - + 1552-4450 2017/09 [Refereed][Not invited]
     
    Nonribosomal peptide synthetases (NRPSs) are multidomain enzyme templates for the synthesis of bioactive peptides. Large-scale conformational changes during peptide assembly are obvious from crystal structures, yet their dynamics and coupling to catalysis are poorly understood. We have designed an NRPS FRET sensor to monitor, in solution and in real time, the adoption of the productive transfer conformation between phenylalanine-binding adenylation (A) and peptidyl-carrier-protein domains of gramicidin synthetase I from Aneurinibacillus migulanus. The presence of ligands, substrates or intermediates induced a distinct fluorescence resonance energy transfer (FRET) readout, which was pinpointed to the population of specific conformations or, in two cases, mixtures of conformations. A pyrophosphate switch and lysine charge sensors control the domain alternation of the A domain. The phenylalanine-thioester and phenylalanine-AMP products constitute a mechanism of product inhibition and release that is involved in ordered assembly-line peptide biosynthesis. Our results represent insights from solution measurements into the conformational dynamics of the catalytic cycle of NRPSs.
  • SINGLE MOLECULE DATA ANALYSIS: AN INTRODUCTION
    Tavakoli Meysam, Taylor J. Nicholas, Li Chun-Biu, Komatsuzaki Tamiki, Presse Steve
    ADVANCES IN CHEMICAL PHYSICS, VOL 162 162 205 - 305 0065-2385 2017 [Refereed][Not invited]
  • Lilan Hong, Mathilde Dumond, Satoru Tsugawa, Aleksandra Sapala, Anne-Lise Routier-Kierzkowska, Yong Zhou, Catherine Chen, Annamaria Kiss, Mingyuan Zhu, Olivier Hamant, Richard S. Smith, Tamiki Komatsuzaki, Chun-Biu Li, Arezki Boudaoud, Adrienne H. K. Roeder
    DEVELOPMENTAL CELL 38 (1) 15 - 32 1534-5807 2016/07 [Refereed][Not invited]
     
    Organ sizes and shapes are strikingly reproducible, despite the variable growth and division of individual cells within them. To reveal which mechanisms enable this precision, we designed a screen for disrupted sepal size and shape uniformity in Arabidopsis and identified mutations in the mitochondrial i-AAA protease FtsH4. Counterintuitively, through live imaging we observed that variability of neighboring cell growth was reduced in ftsh4 sepals. We found that regular organ shape results from spatiotemporal averaging of the cellular variability in wild-type sepals, which is disrupted in the less-variable cells of ftsh4 mutants. We also found that abnormal, increased accumulation of reactive oxygen species (ROS) in ftsh4 mutants disrupts organ size consistency. In wild-type sepals, ROS accumulate in maturing cells and limit organ growth, suggesting that ROS are endogenous signals promoting termination of growth. Our results demonstrate that spatiotemporal averaging of cellular variability is required for precision in organ size.
  • Satoru Tsugawa, Nathan Hervieux, Oliver Hamant, Arezki Boudaoud, Richard S. Smith, Chun-Biu Li, Tamiki Komatsuzaki
    BIOPHYSICAL JOURNAL 110 (8) 1836 - 1844 0006-3495 2016/04 [Refereed][Not invited]
     
    The order and orientation of cortical microtubule (CMT) arrays and their dynamics play an essential role in plant morphogenesis. To extract detailed CMT alignment structures in an objective, local, and accurate way, we propose an error-based extraction method that applies to general fluorescence intensity data on three-dimensional cell surfaces. Building on previous techniques to quantify alignments, our method can determine the statistical error for specific local regions, or the minimal scales of local regions for a desired accuracy goal. After validating our method with synthetic images with known alignments, we demonstrate the ability of our method to quantify subcellular CMT alignments on images with microtubules marked with green fluorescent protein in various cell types. Our method could also be applied to detect alignment structures in other fibrillar elements, such as actin filaments, cellulose, and collagen.
  • Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    JOURNAL OF PHYSICAL CHEMISTRY B 120 (8) 1961 - 1971 1520-6106 2016/03 [Refereed][Not invited]
     
    Markovian dynamics on complex reaction networks are one of the most intriguing subjects in a wide range of research fields including chemical reactions, biological physics, and ecology. To represent the global kinetics from one node (corresponding to a basin on an energy landscape) to another requires information on multiple pathways that directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discrete time Markov chain derived from first-order rate equations. The TSs can naturally take into account the multiple pathways connecting any pair of nodes. We also propose a new type of disconnectivity graph (DG) to capture the hierarchical organization of different time scales of reactions that can capture changes in the network due to changes in the observation. The crux is the introduction of the minimum conductance cut (MCC) in graph clustering, corresponding to the dividing surface across the network having the "smallest" transition probability between two disjoint subnetworks (superbasins on the energy landscape) in the network. We present a new combinatorial search algorithm for finding this MCC. We apply our method to a reaction network of Claisen rearrangement of allyl vinyl ether that consists of 23 nodes and 66 links (saddles on the energy landscape) connecting them. We compare the kinetic properties of our DG to those of the transition matrix of the rate equations and show that our graph can properly reveal the hierarchical, organization of time scales in a network.
  • Yosuke Sumiya, Yutaka Nagahata, Tamiki Komatsuzaki, Tetsuya Taketsugu, Satoshi Maeda
    JOURNAL OF PHYSICAL CHEMISTRY A 119 (48) 11641 - 11649 1089-5639 2015/12 [Refereed][Not invited]
     
    The significance of kinetic analysis as a tool for understanding the reactivity and selectivity of organic reactions has recently been recognized. However, conventional simulation approaches that solve rate equations numerically are not amenable to multistep reaction profiles consisting of fast and slow elementary steps. Herein, we present an efficient and robust approach for evaluating the overall rate constants of multistep reactions via the recursive contraction of the rate equations to give the overall rate constants for the products and byproducts. This new method was applied to the Claisen rearrangement of allyl vinyl ether, as well as a substituted allyl vinyl ether. Notably, the profiles of these reactions contained 23 and 84 local minima, and 66 and 278 transition states, respectively. The overall rate constant for the Claisen rearrangement of allyl vinyl ether was consistent with the experimental value. The selectivity of the Claisen rearrangement reaction has also been assessed using a substituted allyl vinyl ether. The results of this study showed that the conformational entropy in these flexible chain molecules had a substantial impact on the overall rate constants. This new method could therefore be used to estimate the overall rate constants of various other organic reactions involving flexible molecules.
  • Chun-Biu Li, Hiroshi Ueno, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    NATURE COMMUNICATIONS 6 10223  2041-1723 2015/12 [Refereed][Not invited]
     
    F-1-ATPase (F-1) is a rotary motor protein that can efficiently convert chemical energy to mechanical work of rotation via fine coordination of its conformational motions and reaction sequences. Compared with reactant binding and product release, the ATP hydrolysis has relatively little contributions to the torque and chemical energy generation. To scrutinize possible roles of ATP hydrolysis, we investigate the detailed statistics of the catalytic dwells from high-speed single wild-type F-1 observations. Here we report a small rotation during the catalytic dwell triggered by the ATP hydrolysis that is indiscernible in previous studies. Moreover, we find in freely rotating F-1 that ATP hydrolysis is followed by the release of inorganic phosphate with low synthesis rates. Finally, we propose functional roles of the ATP hydrolysis as a key to kinetically unlock the subsequent phosphate release and promote the correct reaction ordering.
  • Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
    PHYSICAL REVIEW LETTERS 115 (9) 093003  0031-9007 2015/08 [Refereed][Not invited]
     
    We present a mechanism of global reaction coordinate switching, namely, a phenomenon in which the reaction coordinate dynamically switches to another coordinate as the total energy of the system increases. The mechanism is based on global changes in the underlying phase space geometry caused by a switching of dominant unstable modes from the original reactive mode to another nonreactive mode in systems with more than 2 degrees of freedom. We demonstrate an experimental observability to detect a reaction coordinate switching in an ionization reaction of a hydrogen atom in crossed electric and magnetic fields. For this reaction, the reaction coordinate is a coordinate along which electrons escape and its switching changes the escaping direction from the direction of the electric field to that of the magnetic field and, thus, the switching can be detected experimentally by measuring the angle-resolved momentum distribution of escaping electrons.
  • J. Nicholas Taylor, Chun-Biu Li, David R. Cooper, Christy F. Landes, Tamiki Komatsuzaki
    SCIENTIFIC REPORTS 5 9174  2045-2322 2015/03 [Refereed][Not invited]
     
    Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.
  • Hideyuki Yaginuma, Shinnosuke Kawai, Kazuhito V. Tabata, Keisuke Tomiyama, Akira Kakizuka, Tamiki Komatsuzaki, Hiroyuki Noji, Hiromi Imamura
    SCIENTIFIC REPORTS 4 6522  2045-2322 2014/10 [Refereed][Not invited]
     
    Recent advances in quantitative single-cell analysis revealed large diversity in gene expression levels between individual cells, which could affect the physiology and/or fate of each cell. In contrast, for most metabolites, the concentrations were only measureable as ensemble averages of many cells. In living cells, adenosine triphosphate (ATP) is a critically important metabolite that powers many intracellular reactions. Quantitative measurement of the absolute ATP concentration in individual cells has not been achieved because of the lack of reliable methods. In this study, we developed a new genetically-encoded ratiometric fluorescent ATP indicator 'QUEEN'', which is composed of a single circularly-permuted fluorescent protein and a bacterial ATP binding protein. Unlike previous FRET-based indicators, QUEEN was apparently insensitive to bacteria growth rate changes. Importantly, intracellular ATP concentrations of numbers of bacterial cells calculated from QUEEN fluorescence were almost equal to those from firefly luciferase assay. Thus, QUEEN is suitable for quantifying the absolute ATP concentration inside bacteria cells. Finally, we found that, even for a genetically-identical Escherichia coli cell population, absolute concentrations of intracellular ATP were significantly diverse between individual cells from the same culture, by imaging QUEEN signals from single cells.
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    THEORETICAL CHEMISTRY ACCOUNTS 133 (11) 1571 (15 pages)  1432-881X 2014/09 [Refereed][Not invited]
     
    Validity ranges of Lie canonical perturbation theory (LCPT) are investigated in terms of non-blow-up regions. We investigate how the validity ranges depend on the perturbation order in two systems, one of which is a simple Hamiltonian system with one degree of freedom and the other is a HCN molecule. Our analysis of the former system indicates that non-blow-up regions become reduced in size as the perturbation order increases. In case of LCPT by Dragt and Finn and that by Deprit, the non-blow-up regions enclose the region inside the separatrix of the Hamiltonian, but it may not be the case for LCPT by Hori. We also analyze how well the actions constructed by these LCPTs approximate the true action of the Hamiltonian in the non-blow-up regions and find that the conventional truncated LCPT does not work over the whole region inside the separatrix, whereas LCPT by Dragt and Finn without truncation does. Our analysis of the latter system indicates that non-blow-up regions do not necessarily cover the whole regions inside the HCN well. We propose a new perturbation method to improve non-blow-up regions and validity ranges inside them. Our method is free from blowing up and retains the same normal form as the conventional LCPT. We demonstrate our method in the two systems and show that the actions constructed by our method have larger validity ranges than those by the conventional and our previous methods proposed in Teramoto and Komatsuzaki (J Chem Phys 129:094302, 2008; Phys Rev E 78:017202, 2008).
  • Preetom Nag, Hiroshi Teramoto, Chun-Biu Li, Joseph Z. Terdik, Norbert F. Scherer, Tamiki Komatsuzaki
    JOURNAL OF CHEMICAL PHYSICS 141 (10) 104907  0021-9606 2014/09 [Refereed][Not invited]
     
    Quantifying the interactions in dense colloidal fluids requires a properly designed order parameter. We present a modified bond-orientational order parameter, (psi) over bar (6), to avoid problems of the original definition of bond-orientational order parameter. The original bond-orientational order parameter can change discontinuously in time but our modified order parameter is free from the discontinuity and, thus, it is a suitable measure to quantify the dynamics of the bond-orientational ordering of the local surroundings. Here we analyze (psi) over bar (6) in a dense driven monodisperse quasi-two-dimensional colloidal fluids where a single particle is optically trapped at the center. The perturbation by the trapped and driven particle alters the structure and dynamics of the neighboring particles. This perturbation disturbs the flow and causes spatial and temporal distortion of the bond-orientational configuration surrounding each particle. We investigate spatio-temporal behavior of (psi) over bar (6) by a Wavelet transform that provides a time-frequency representation of the time series of (psi) over bar (6). It is found that particles that have high power in frequencies corresponding to the inverse of the timescale of perturbation undergo distortions of their packing configurations that result in cage breaking and formation dynamics. To gain insight into the dynamic structure of cage breaking and formation of bond-orientational ordering, we compare the cage breaking and formation dynamics with the underlying dynamical structure identified by Lagrangian Coherent Structures (LCSs) estimated from the finite-time Lyapunov exponent (FTLE) field. The LCSs are moving separatrices that effectively divide the flow into distinct regions with different dynamical behavior. It is shown that the spatial distribution of the FTLE field and the power of particles in the wavelet transform have positive correlation, implying that LCSs provide a dynamic structure that dominates the dynamics of cage breaking and formation of the colloidal fluids. (C) 2014 AIP Publishing LLC.
  • Bo Shuang, David Cooper, J. Nick Taylor, Lydia Kisley, Jixin Chen, Wenxiao Wang, Chun Biu Li, Tamiki Komatsuzaki, Christy F. Landes
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS 5 (18) 3157 - 3161 1948-7185 2014/09 [Refereed][Not invited]
     
    We introduce a step transition and state identification (STaSI) method for piecewise constant single-molecule data with a newly derived minimum description length equation as the objective function. We detect the step transitions using the Student's t test and group the segments into states by hierarchical clustering. The optimum number of states is determined based on the minimum description length equation. This method provides comprehensive, objective analysis of multiple traces requiring few user inputs about the underlying physical models and is faster and more precise in determining the number of states than established and cutting-edge methods for single-molecule data analysis. Perhaps most importantly, the method does not require either time-tagged photon counting or photon counting in general and thus can be applied to a broad range of experimental setups and analytes.
  • Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    JOURNAL OF CHEMICAL PHYSICS 139 (24) 245101 - 245101-12 0021-9606 2013/12 [Refereed][Not invited]
     
    We present a novel scheme to extract a multiscale state space network (SSN) from single-molecule time series. The multiscale SSN is a type of hidden Markov model that takes into account both multiple states buried in the measurement and memory effects in the process of the observable whenever they exist. Most biological systems function in a nonstationary manner across multiple timescales. Combined with a recently established nonlinear time series analysis based on information theory, a simple scheme is proposed to deal with the properties of multiscale and nonstationarity for a discrete time series. We derived an explicit analytical expression of the autocorrelation function in terms of the SSN. To demonstrate the potential of our scheme, we investigated single-molecule time series of dissociation and association kinetics between epidermal growth factor receptor (EGFR) on the plasma membrane and its adaptor protein Ash/Grb2 (Grb2) in an in vitro reconstituted system. We found that our formula successfully reproduces their autocorrelation function for a wide range of timescales (up to 3 s), and the underlying SSNs change their topographical structure as a function of the timescale; while the corresponding SSN is simple at the short timescale (0.033-0.1 s), the SSN at the longer timescales (0.1 s to similar to 3 s) becomes rather complex in order to capture multiscale nonstationary kinetics emerging at longer timescales. It is also found that visiting the unbound form of the EGFR-Grb2 system approximately resets all information of history or memory of the process. (C) 2013 AIP Publishing LLC.
  • Yasuhiro Matsunaga, Akinori Baba, Chun-Biu Li, John E. Straub, Mikito Toda, Tamiki Komatsuzaki, R. Stephen Berry
    JOURNAL OF CHEMICAL PHYSICS 139 (21) 215101 - 215101-13 0021-9606 2013/12 [Refereed][Not invited]
     
    A method for time series analysis of molecular dynamics simulation of a protein is presented. In this approach, wavelet analysis and principal component analysis are combined to decompose the spatio-temporal protein dynamics into contributions from a hierarchy of different time and space scales. Unlike the conventional Fourier-based approaches, the time-localized wavelet basis captures the vibrational energy transfers among the collective motions of proteins. As an illustrative vehicle, we have applied our method to a coarse-grained minimalist protein model. During the folding and unfolding transitions of the protein, vibrational energy transfers between the fast and slow time scales were observed among the large-amplitude collective coordinates while the other small-amplitude motions are regarded as thermal noise. Analysis employing a Gaussian-based measure revealed that the time scales of the energy redistribution in the subspace spanned by such large-amplitude collective coordinates are slow compared to the other small-amplitude coordinates. Future prospects of the method are discussed in detail. (C) 2013 AIP Publishing LLC.
  • Hiroshi Teramoto, George Haller, Tamiki Komatsuzaki
    CHAOS 23 (4) 043107 - 043107-12 1054-1500 2013/12 [Refereed][Not invited]
     
    Normally hyperbolic invariant manifolds (NHIMs) are well-known organizing centers of the dynamics in the phase space of a nonlinear system. Locating such manifolds in systems far from symmetric or integrable, however, has been an outstanding challenge. Here, we develop an automated detection method for codimension-one NHIMs in autonomous dynamical systems. Our method utilizes Stationary Lagrangian Coherent Structures (SLCSs), which are hypersurfaces satisfying one of the necessary conditions of a hyperbolic LCS, and are also quasi-invariant in a well-defined sense. Computing SLCSs provides a quick way to uncover NHIMs with high accuracy. As an illustration, we use SLCSs to locate two-dimensional stable and unstable manifolds of hyperbolic periodic orbits in the classic ABC flow, a three-dimensional solution of the steady Euler equations. (C) 2013 AIP Publishing LLC.
  • Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 88 (4) 42923 - 42923-11 1539-3755 2013/10/29 [Refereed][Not invited]
     
    Reactivity boundaries that divide the origin and destination of trajectories are of crucial importance to reveal the mechanism of reactions, which was recently found to exist robustly even at high energies for index 1 saddles. Here we revisit the concept of the reactivity boundary and propose a more general definition that can involve a single reaction associated with a bottleneck composed of higher-index saddles and/or several saddle points with different indices, where the normal form theory, based on expansion around a single stationary point, does not work. We numerically demonstrate the reactivity boundary by using a reduced model system of the H5 + cation where the proton exchange reaction takes place through a bottleneck composed of two index 2 saddle points and two index 1 saddle points. The cross section of the reactivity boundary in the reactant region of the phase space reveals which initial conditions are effective in making the reaction happen and thus sheds light on the reaction mechanism. © 2013 American Physical Society.
  • Chun-Biu Li, Tamiki Komatsuzaki
    PHYSICAL REVIEW LETTERS 111 (5) 058301 - 058301-5 0031-9007 2013/08 [Refereed][Not invited]
     
    Statistics of the dwell times, the stationary state distributions (SSDs), are often studied to infer the underlying kinetics from a single molecule finite-level time series. However, it is well known that the underlying kinetic scheme, a hidden Markov model (HMM), cannot be identified uniquely from the SSDs because some features of the underlying HMM are hidden by finite-level measurements. Here, we quantify the amount of excessive information in a given HMM that is not warranted by the measured SSDs and extract the HMM with minimum excessive information as the most objective representation of the data. The method is applied to a single molecule enzymatic turnover experiment, and the origin of dynamic disorder is discussed in terms of the network properties of the HMM.
  • Shinnosuke Kawai, David Cooper, Christy Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
    JOURNAL OF PHYSICAL CHEMISTRY B 117 (27) 8061 - 8074 1520-6106 2013/07 [Refereed][Not invited]
     
    A novel scheme to estimate the values of the underlying physical quantity and those of any functions of the quantity from measured observable(s) contaminated with stochastic noise is presented for any arbitrary probability distribution. The constructed estimators can either maximize the unbiasedness (i.e., minimize the amount of the deviation of the expectation value from the true value buried in the measurement) or minimize the risk (the average,deviation from the true value) depending on the relative priority of unbiasedness and risk in the data analysis. The performance of the constructed estimators is demonstrated with computer simulations of Forster-type resonance energy transfer (FRET), measurements and also with FRET experimental data of the agonist-binding domain of the GluA2 subunit of AMPA receptors with agonists chloro- and iodo-willardiines and with adenylate kinase both in the apo form and with substrates AMP-PNP and AMP. It is shown that the estimators constructed by the present method can quantify faithfully not only the physical quantity to be monitored but also the functions of that quantity for a wide range of values.
  • Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    PHYSICAL REVIEW E 87 (6) 062817 - 062817-4 1539-3755 2013/06 [Refereed][Not invited]
     
    Reactivity boundaries that divide the destination and the origin of trajectories are of crucial importance to reveal the mechanism of reactions. We investigate whether such reactivity boundaries can be extracted for higher index saddles in terms of a nonlinear canonical transformation successful for index-one saddles by using a model system with an index-two saddle. It is found that the true reactivity boundaries do not coincide with those extracted by the transformation taking into account a nonlinearity in the region of the saddle even for small perturbations, and the discrepancy is more pronounced for the less repulsive direction of the index-two saddle system. The present result indicates an importance of the global properties of the phase space to identify the reactivity boundaries, relevant to the question of what reactant and product are in phase space, for saddles with index more than one.
  • Shinnosuke Kawai, Tamiki Komatsuzaki
    PHYSICAL REVIEW E 87 (3) 030803 - 030803-4 1539-3755 2013/03 [Refereed][Not invited]
     
    We investigate the effects of the timescale of motion on the shape of energy landscapes. The distinction between the free-energy landscape and the potential of mean force is clarified. The former is related to a thermal equilibrium distribution for chosen coordinates, whereas the latter is determined by the mean force exerted on the coordinates in the equilibrium. It is found that the condition for these two energy landscapes to be the same is the constancy of the mean square velocity with respect to the position coordinate. However, even when the condition holds for the chosen coordinates, as the timescale of observation increases, the averaging effect causes a decrease in the mean square velocity nonuniformly in the configuration space, resulting in a larger distinction between the free-energy landscape and the potential of mean force. The results are expected to provide an important basis for the study of long time scale phenomena in large systems. DOI: 10.1103/PhysRevE.87.030803
  • Tatyana G. Terentyeva, Johan Hofkens, Tamiki Komatsuzaki, Kerstin Blank, Chun-Biu Li
    JOURNAL OF PHYSICAL CHEMISTRY B 117 (5) 1252 - 1260 1520-6106 2013/02 [Refereed][Not invited]
     
    Single molecule fluorescence spectroscopy offers great potential for studying enzyme kinetics. A number of fluorescence reporter systems allow for monitoring the sequence of individual reaction events with a confocal microscope. When using a time-correlated single photon counting (TCSPC) detection scheme, additional information about the fluorescence lifetimes of the fluorophores can be obtained. We have applied a TCSPC detection scheme for studying the kinetics of alpha-chymotrypsin hydrolyzing a double-substituted rhodamine 110-based fluorogenic substrate in a two-step reaction. On the basis of the lifetime information, it was possible to discriminate the intermediate and the final product. At the high substrate concentration used, only the formation of the intermediate was observed. No rebinding of the intermediate followed by rhodamine 110 formation occurred at these high concentrations. We have further found no alterations in the fluorescence lifetime of this intermediate that would indicate changes in the local environment of the fluorophore originating from strong interactions with the enzyme. Our results clearly show the power of using lifetime-resolved measurements for investigating enzymatic reactions at the single molecule level.
  • 力学的決定性と統計性の中間領域を探る IV
    小松崎民樹, 戸田幹人
    物性研究 1 (3) 2012/11 [Refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 85 (8) 854 - 861 0009-2673 2012/08 [Refereed][Not invited]
     
    The question of what initial conditions or what kinds of laser fields can effectively carry a system to the desired products is one of the most intriguing subjects in chemistry. In this paper, a scheme for designing a laser field to guide a chemical reaction system into the product is presented on the basis of the phase space structure of the reaction with an illustrative simple example. The method exploits recent findings [Kawai et al., J. Chem. Phys. 2011, 134, 024317] that have revealed the existence of a rigorous reactivity boundary separating the reactive and nonreactive trajectories in the phase space (more precisely, the semiclassical phase space representation of the quantum system). Referring to the time propagation of the system, the method designs an electric field that actively shifts this reactivity boundary so that it catches more the system in the reactant and releases the system in the product. The success of this scheme for designing of the field gives a further support to the interpretation for the laser control of chemical reactions.
  • Kiyoto Kamagata, Toshifumi Kawaguchi, Yoshitomo Iwahashi, Akinori Baba, Kazuya Fujimoto, Tamiki Komatsuzaki, Yoshihiro Sambongi, Yuji Goto, Satoshi Takahashi
    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134 (28) 11525 - 11532 0002-7863 2012/07 [Refereed][Not invited]
     
    A method was developed to detect fluorescence intensity signals from single molecules diffusing freely in a capillary cell. A unique optical system based on a spherical mirror was designed to enable quantitative detection of the fluorescence intensity. Furthermore, "flow-and-stop" control of the sample can extend the observation time of single molecules to several seconds, which is more than 1000 times longer than the observation time available using a typical confocal method. We used this method to scrutinize the fluorescence time series of the labeled cytochrome c in the unfolded state. Time series analyses of the trajectories based on local equilibrium state analysis revealed dynamically differing substates on a millisecond avenue for experimental characterization of the protein-folding energy landscape. time scale. This system presents a new avenue for experimental characterization of the protein-folding energy landscape.
  • Hiroaki Takagi, Miki Morimatsu, Yasushi Sako
    SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146 146 195 - 215 0065-2385 2012 [Refereed][Not invited]
  • Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    Complex Systems 20 (2) 2011 [Refereed][Not invited]
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
    COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION 13 (5) 857 - 867 1007-5704 2008/07 [Refereed][Not invited]
     
    We study the foundation and limitations of the statistical reaction theory. In particular, we focus our attention to the question of whether the rate constant can be defined for nonergodic systems. Based on the analysis of the Arnold web in the reactant well, we show that the survival probability exhibits two types of behavior: one where it depends on the residential time as the power-law decay and the other where it decays exponentially. The power-law decay casts a doubt on definability of the rate constant for nonergodic systems. We indicate that existence of the two types of behavior comes from sub-diffusive motions in remote regions from resonance overlap. Moreover, based on analysis of nonstationary features of trajectories, we can understand how the normally hyperbolic invariant manifold (NHIM) is connected with the Arnold web. We propose that the following two features play a key role in understanding the reactions where ergodicity is broken, i.e., whether the Arnold web is nonuniform and how the NHIM is connected with the Arnold web. (C) 2006 Elsevier B.V. All rights reserved.
  • Akinori Baba, Tamiki Komatsuzaki
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (49) 19297 - 19302 0027-8424 2007/12 [Refereed][Not invited]
     
    A scheme for extracting an effective free energy landscape from single-molecule time series is presented. This procedure uniquely identifies a non-Gaussian distribution of the observable associated with each local equilibrium state (LES). Both the number of LESS and the shape of the non-Gaussian distributions depend on the time scale of observation. By assessing how often the system visits and resides in a chosen LES and escapes from one LES to another (with checking whether the local detailed balance is satisfied), our scheme naturally leads to an effective free energy landscape whose topography depends on in which time scale the system experiences the underlying landscape. For example, two metastable states are unified as one if the time scale of observation is longer than the escape time scale for which the system can visit mutually these two states. As an illustrative example, we present the application of extracting the effective free energy landscapes from time series of the end-to-end distance of a three-color, 46-bead model protein. It indicates that the time scales to attain the local equilibrium tend to be longer in the unfolded state than those in the compact collapsed state.
  • Masahito Kinoshita, Kiyoto Kamagata, Akio Maeda, Yuji Goto, Tamiki Komatsuzaki, Satoshi Takahashi
    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104 (25) 10453 - 10458 0027-8424 2007/06 [Refereed][Not invited]
     
    A technique was developed for the detection of fluorescence signals from free single molecules for extended time periods and was applied to the characterization of the unfolded states of iso-1-cytochrome c (cyt c). Protein molecules labeled with fluorescent dye were slowly injected into a capillary at concentrations that allow for the observation of one molecule at a time. A laser was introduced into the capillary coaxially, and the fluorescence was imaged as traces by using a lens with a large focal depth and wide field of view. Thus, the traces reflect the time-dependent changes in the fluorescence signals from single proteins. Cyt c was labeled with Alexa Fluor 532 at the C-terminal cysteine (cyt c-Alexa). in bulk experiments, cyt c-Alexa was shown to possess different fluorescence intensity for the native state, the unfolded state (U), and the intermediate state. Single-molecule traces of cyt c-Alexa were recorded by using the device. Intensity histograms of the traces revealed two distributions with broad and narrow widths, which were interpreted to correspond to the U and intermediate state, respectively, observed in the bulk measurements. The broad width of the U suggested the existence of a relatively slow conformational dynamics, which might be consistent with the correlation time (approximate to 15 ms) estimated from the traces assignable to the U. The technique was expected to reveal dynamics of proteins along the folding processes without artifacts caused by immobilization.
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
    PHYSICAL REVIEW E 75 (3) 1539-3755 2007/03 [Refereed][Not invited]
     
    We present numerical evidence of fractional behavior in reactions for a prototype model of three-degree-of-freedom isomerization. The survival probability in the well exhibits two distinct ranges of time scales: one where it decreases with a power law, and the other where it decreases exponentially. Trajectories corresponding to power law decays exhibit 1/f spectra and subdiffusion in action space, and those with exponential decays exhibit Lorentzian spectra and normal diffusion. The existence of these two types of behavior is explained on the basis of nonergodicity in the network of nonlinear resonances (Arnold web) in the well, and connection between the saddle and the Arnold web. Implications of the fractional dynamics are discussed in terms of Maxwell's demon in molecules.
  • Tamiki Komatsuzaki, R. Stephen Berry
    GEOMETRIC STRUCTURES OF PHASE SPACE IN MULTIDIMENSIONAL CHAOS: APPLICATIONS TO CHEMICAL REACTION DYNAMICS IN COMPLEX SYSTEMS, PT A 130 143 - 170 0065-2385 2005 [Refereed][Not invited]
  • Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga
    GEOMETRIC STRUCTURES OF PHASE SPACE IN MULTIDIMENSIONAL CHAOS: APPLICATIONS TO CHEMICAL REACTION DYNAMICS IN COMPLEX SYSTEMS, PT B 130 257 - 313 0065-2385 2005 [Refereed][Not invited]
  • A NEW STERIC SUBSTITUENT CONSTANT OMEGA-S. CHARACTERISTIC FEATURE AND COMPARISON WITH SOME OTHER STERIC CONSTANTS
    T KOMATSUZAKI, AKAI, I, K SAKAKIBARA, M HIROTA
    TETRAHEDRON 48 (9) 1539 - 1556 0040-4020 1992/02 [Refereed][Not invited]
     
    A new steric substituent constant, OMEGA-s, was proposed in order to evaluate the kinetic steric effect. OMEGA-s is isotropic and dependent most significantly on the number of beta-carbon atoms. The rates of several reactions were shown to be correlated with OMEGA-s better than with Es.
  • M HIROTA, K SAKAKIBARA, T KOMATSUZAKI, AKAI, I
    COMPUTERS & CHEMISTRY 15 (3) 241 - 248 0097-8485 1991 [Refereed][Not invited]
     
    A new steric substituent constant OMEGA-s was defined and the procedure for its calculation is given. It was calculated from the geometries and the relative free energies of the conformers of substituents from MM2.
  • A NEW STERIC SUBSTITUENT PARAMETER OMEGA-S - SOPHISTICATION OF CALCULATION AND CORRELATION WITH THE KINETIC DATA OF SEVERAL REACTIONS
    T KOMATSUZAKI, K SAKAKIBARA, M HIROTA
    CHEMISTRY LETTERS (10) 1913 - 1916 0366-7022 1990/10 [Refereed][Not invited]

Books etc

  • Minorities and Small Numbers from Molecules to Organisms in Biology-Toward a New Understanding of Biological Phenomena
    KOMATSUZAKI TAMIKI (Single workChapter 5 "The Personality of Small Numbers: Do Molecules Have Personality?")
    Springer 2018/11
  • 化学反応理論の普遍性:GRRMに期するもの
    小松崎 民樹 (Single work)
    IQCE NEWS (量子化学探索研究所) 2018
  • 少数性生物学
    小松崎 民樹 (Joint work第5章「少数の個性~分子にも個性?~」)
    株式会社 日本評論社 2017
  • Advances in Chemical Physics
    Meysam Tavakoli, J. Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé (Joint workSingle Molecule Data Analysis: An Introduction)
    Wiley 2017
  • 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
    寺本 央, 戸田 幹人, 河野 裕彦, 高橋 正彦, 小松崎 民樹 (Joint work)
    月刊「化学」71(5) 2016
  • Dynamics of Chemical Reaction around a Saddle Point - What divides reacting and non-reacting trajectories?
    Shinnosuke Kawai, Tamiki Komatsuzaki (Joint workReaction Rate Constant Computations; Theories and Applications, CHAPTER 7)
    RSC Publishing 2013/11
  • ラグランジュ協同構造―流体の流れに隠れた骨格
    小松崎 民樹 (Single translation)
    2013
  • Reaction Rate Constant Computations; Theories and Applications
    Shinnosuke Kawai, Tamiki Komatsuzaki (Joint workDynamics of Chemical Reaction around a Saddle Point - What divides reacting and non-reacting trajectories?)
    RSC 2013
  • Advances in Chemical Physics 146
    Akinori Baba, Tamiki Komatsuzaki (Joint workMultidimensional Energy Landscapes in Single Molecule Biophysics)
    John-Wiley& Sons, Inc. 2012
  • Advances in Chemical Physics 145
    David M. Leitner, Yasuhiro Matsunaga, Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda (Joint workNon-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics)
    2011
  • Cell Signaling Reactions: Single-Molecular Kinetic Analysis
    Chun Biu Li, Tamiki Komatsuzaki (Joint workExtracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series)
    Springer 2011
  • Advances in Chemical Physics 130(A)
    Tamiki Komatsuzaki, R. Stephen Berry (Joint workRegularity in Chaotic Transitions on Two-Basin Landscapes)
    2005
  • Advances in Chemical Physics 130(B)
    Tamiki Komatsuzaki, Kyoko Hoshino, Y. Matsunaga (Joint workRegularity in Chaotic Transitions on Multi-Basin Landscapes)
    2005
  • Advances in Chemical Physics 130A, 130B
    M. Toda, T. Komatsuzaki, T. Konishi, R. S. Berry, S. A. Rice (Joint editorGeometric Structures of Phase Space in Multi-Dimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems)
    John-Wiley & Sons, Inc. 2005
  • Advances in Chemical Physics 123
    Tamiki Komatsuzaki, R. Stephen Berry (Joint workChemical Reaction Dynamics: Many-Body Chaos and Regularity)
    John-Wiley & Sons, Inc. 2002

Conference Activities & Talks

  • Causal inference in Leader-follower relationship  [Not invited]
    KOMATSUZAKI TAMIKI
    ICSB 2019: Singularity Biology: small elements change the function of the whole systems  2019/10
  • A leadership-based phase transition in a flocking model with activated and un-activated agents  [Not invited]
    Sulimon Sattari, Tamiki Komatusaki, Mikito Toda, Sky Nicholson, Jason Green, Udoy Basak
    第57回日本生物物理学会年会  2019/09
  • An Information-theoretic approach toward identifying the leader(s) and aggregation place in Dictyostelium Discoideum colony  [Not invited]
    Basak Udoy Sankar, Sattari Sulimon, Horikawa Kazuki, Komatsuzaki Tamiki
    第57回日本生物物理学会年会  2019/09
  • 一細胞ラマン計測と情報科学の融合による細胞診断の迅速解析技術の開発  [Not invited]
    小松崎 民樹
    CREST・さきがけ複合領域「計測技術と高度情報処理の融合によるインテリジェント計測・解析手法の開発と応用」第4回CREST 領域会議  2019/08
  • Raman pathology and its phenotypic landscape for Non-alcoholic fatty liver diseases  [Invited]
    KOMATSUZAKI TAMIKI
    The Complexity of Dynamics and Kinetics from Single Molecules to Cells  2019/06
  • アデニレートキナーゼの一分子観察データから再構成するエネルギー地形の階層性  [Not invited]
    James Nicholas Taylor, Menahem Pirchi, Gilad Haran, 小松崎 民樹
    第22回理論化学討論会  2019/05
  • Deciphering hierarchical features in reaction network and energy landscape  [Invited]
    KOMATSUZAKI TAMIKI
    Network analysis to elucidate natural system dynamics, diversity and performance  2019/05
  • Identification of Leader(s) in a Dictyostelium Discoideum colony: An Information-theoretic Approach  [Not invited]
    Udoy Sankar Basak, Sulimon Sattari, Sosuke Ito, Kazuki Horikawa, Tamiki Komatsuzaki
    生物物理・回折構造生物学 合同研究会  2019/03
  • A sandbox model system for understanding leadership in collective motion  [Not invited]
    Sulimon Sattari, Udoy Basak, Schuyler Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    生物物理・回折構造生物学 合同研究会  2019/03
  • Analysis of Raman Microscopic Images of Liver Tissu to Predict Non-alcholic Fatty Liver Disease  [Not invited]
    Helal Khalifa Mohammad, Cahyadi Harsono, Taylor J. Nicholas, Okajima Akira, Kumamoto Yasuaki, Tanaka Hideo, Harada Yoshinori, Komatsuzaki Tamiki
    生物物理・回折構造生物学 合同研究会  2019/03
  • Mathematical information measurement science: acceleration of Raman spectroscopy by bridging information science  [Not invited]
    小松崎 民樹
    バイオ情報計測技術研究会  2019/03
  • 1分子時系列情報からどのように背後の反応ネットワーク を抽出できるのか?  [Invited]
    小松崎 民樹
    「生命動態の理解と制御のための基盤技術の創出」研究領域 第 7 回領域会議・第 11 回数理デザイン道場  2019/01
  • How can one bridge information science and measurement science to accelerate the measurements?  [Invited]
    KOMATSUZAKI TAMIKI
    The 22nd SANKEN International Symposium The 17th SANKEN Nanotechnology International Symposium "Next Generation Science and Technology for Super Smart Society"  2019/01
  • 病理診断迅速化に向けたバンディットアルゴリズムの応用  [Not invited]
    田畑公次, 中村篤祥, 小松崎民樹
    北海道大学電子科研究所平成 30年度 研究交流会  2019/01
  • Application of Singularity Theory to Material Science  [Not invited]
    Hiroshi Teramoto, Asahi Tsuchida, Yutaro Kabata, Kenji Kondo, Katsusuke Nabeshima, Shyūichi Izumiya, Mikito Toda, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • Data-Driven Analysis of Raman Microscopic Images of Human Follicular Thyroid Cells  [Not invited]
    J. Nicholas Taylor, Kentaro Mochizuki, Katsumasa Fujita, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • The origin of why and how reactions take place: Reaction cylinders by Voronoi tessellation  [Not invited]
    Mikoto Takigawa, Sulimon Sattari, Sosuke Ito, Hiroshi Teramoto, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • Bad Arm Existence Checking Algorithms with Bandit Feedback  [Not invited]
    Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • A sandbox model system for analyzing leadership in collective motion  [Not invited]
    Sulimon Sattari, Udoy Basak, Sky Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • Information-theoretical Approaches to Raman Microscopic Images to Predict Non-alcoholic Fatty Liver Disease  [Not invited]
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • Information theoretic approach to identify the leader(s) in Dictyostelium Discoideum colony  [Not invited]
    Udoy S. Basak, Sulimon Sattari, Sosuke Ito, Kazuki Horikawa, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium  2018/12
  • 非対称性を利用した悪腕存在チェックアルゴリズム  [Not invited]
    田畑 公次, 中村 篤祥, 小松崎 民樹
    第21回情報論的学習理論ワークショップ  2018/11
  • Revisit transition state theory: Past, Present, Future  [Invited]
    KOMATSUZAKI TAMIKI
    Workshop “Trends in Computational Molecular Biophysics”  2018/11
  • ラマン計測と情報科学:情報科学は計測を迅速化できるか  [Invited]
    小松崎 民樹
    第1回 計測インフォマティクス 計測インフォマティクス 研究会、人工知能学会 第2種研究会  2018/09
  • Multivariate Data-driven Approaches to Raman Hyper-spectral Images to Diagnose Non-alcoholic Fatty Liver Disease (NAFLD)  [Not invited]
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    Annual Conference on Biophysical Society of Japan  2018/09
  • Information theoretic approach to reveal singularity in biology  [Invited]
    KOMATSUZAKI TAMIKI
    Annual Conference on Biophysical Society of Japan  2018/09
  • Normal Forms in Singularity Theory for Geometric Classifications of Band Structures  [Not invited]
    Hiroshi Teramoto, Asahi Tsuchida, Yutaro Kabata, Kenji Kondo, KatsusukeNabeshima, ShyūichiIzumiya, Mikito Toda, Tamiki Komatsuzaki
    Dynamics Days Europe 2018  2018/09
  • 一細胞ラマン計測と情報科学の融合による 細胞診断の迅速解析技術の開発  [Not invited]
    小松崎 民樹
    CRESTさきがけ複合領域「情報計測」CREST第3回領域会議  2018/08
  • Phase Space geometry and Chemical Reaction Dynamics in Driven Systems  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride Workshop "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases"  2018/07
  • Open questions in Higher rank saddles and related  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride Workshop "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases"  2018/07
  • How One can Extract Energy Landscape from Single -Molecule Time Series under the Existence of Noise?  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride Workshop "Biophysical Dynamics"  2018/07
  • How One can Extract Energy Landscape from Single-Molecule Time Series under the Existence of Noise?  [Invited]
    KOMATSUZAKI TAMIKI
    Department Seminar, Johns Hopkins University, Department of Chemistry  2018/07
  • 新概念コンピューティングとは?  [Invited]
    小松崎 民樹
    平成30年度北海道大学公開講座「去る時代、来る時代を考える」  2018/07
  • 1細胞ラマン分光イメージングに基づく細胞場の分子データ科学  [Not invited]
    小松崎 民樹
    新学術領域研究「分子夾雑化学」 分子夾雑の生命化学 第二回領域会議  2018/05
  • 1細胞ラマン分光イメージングと情報科学の高度融合を目指して  [Invited]
    小松崎 民樹
    ImPACT合田プログラム Serendipityセミナー  2018/04
  • Understanding cell colony dynamics from images using velocity extraction and analysis  [Not invited]
    Sulimon Sattari, Tamiki Komatsuzaki, Schuyler B. Nicholson, Jason R. Green
    理研シンポジウム「細胞システムの動態と論理X」  2018/04
  • 一細胞ラマン計測と情報科学の高度融合による情報計測技術  [Invited]
    小松崎 民樹
    2017年度第2回バイオ単分子研究会  2018/03
  • Understanding cell colony dynamics from images using velocity extraction and analysis  [Not invited]
    Sulimon Sattari, Tamiki Komatsuzaki
    2017年度日本生物物理学会北海道支部例会  2018/03
  • Mulitivariate Data-driven approach to Raman Hyper-spectral Images to Diagnose Non-alcoholic Fatty Liver Disease(NAFLD)  [Not invited]
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    2017年度日本生物物理学会北海道支部例会  2018/03
  • 1細胞ラマン分光イメージングと情報科学のinterdependentな融合を目指して  [Invited]
    小松崎 民樹
    第65回応用物理学会春季学術講演会  2018/03
  • 試行回数の少ない悪腕存在チェックアルゴリズム  [Not invited]
    田畑 公次, 中村 篤祥, 本多 淳也, 小松崎 民樹
    人工知能学会第106回人工知能基本問題研究会  2018/03
  • 多階層システム生物学におけるデータ駆動科学の展開  [Not invited]
    田畑公次, 中村篤祥, 小松崎民樹
    北海道大学電子科学研究所 平成29年度 研究交流会  2018/01
  • 北大と日立基礎研センタ連携による新概念コンピューティングの理論と応用  [Invited]
    小松崎 民樹
    AIMaP 異分野連携のノウハウの共有と水平展開を目指すワークショップ  2017/12
  • 一細胞ラマン計測と情報科学の融合による少数性の生命科学  [Invited]
    小松崎 民樹
    2017年度生命科学系学会合同年次大会  2017/12
  • ラマン分光イメージング計測と情報科学との高度融合  [Not invited]
    小松崎民樹, 中村篤祥, 藤田克昌, 原田義規
    2017年度 人・環境と物質をつなぐイノベーション創出 ダイナミックアライアンスG3分科会ー異分野融合とイノベーション創出を目指してー  2017/11
  • ラマン分光イメージングにおける情報計測技術の展開  [Not invited]
    小松崎 民樹
    基盤(S) 離散構造処理系プロジェクト 「2017年度 秋のワークショップ」  2017/11
  • グレイゾーン幅を利用した悪腕存在チェックアルゴリズム  [Not invited]
    田畑 公次, 中村 篤祥, 本多 淳也, 小松崎 民樹
    第20回情報論的学習理論ワークショップ  2017/11
  • How one can extract energy landscape from single molecule time series under the existence of noise?  [Invited]
    KOMATSUZAKI TAMIKI
    The 2nd Korea-Japan Joint Symposium on Single-Molecule Biophysics  2017/11
  • ラマンスペクトルで細胞の病態を分ける-PCAとランダムフォレストを用いて-  [Not invited]
    山田 寛子, 田畑公次, Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, 伊藤創祐, 熊本康昭, 田中秀央, 原田義規, 小松崎民樹
    研究会「理論と実験」2017  2017/10
  • 断熱エネルギー面交差近傍でのハミルトニアンの特異点論による分類  [Not invited]
    寺本央, 泉屋周一, 小松崎民樹
    日本物理学会2017年秋季大会  2017/09
  • How can one quantify singularity in cells from Single Cell Raman Imaging?  [Invited]
    KOMATSUZAKI TAMIKI
    第55回日本生物物理学会年会  2017/09
  • Information-theoretical data analysis approaches to Raman micro-spectroscopic images  [Not invited]
    Helal Khalifa mohammad,Cahyadi Harsono, Taylor, J. nicholas, Okajima Akira, Kumamoto Yasuaki, Tanaka Hideo, Harada Yoshinori, Komatsuzaki Tamiki
    第11回分子科学討論会  2017/09
  • Energy landscapes learned from single molecule FRET time series: Role of Photobleaching  [Invited]
    KOMATSUZAKI TAMIKI
    Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments  2017/09
  • Global Transition States in Reaction Network  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride Workshop on Chemistry & Dynamics in Complex Environments  2017/06
  • Data-driven mathematics in single cell Raman imaging  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride Workshop on The Complexity of Dynamics and Kinetics from Single Molecules to Cells  2017/06
  • 多階層システム生物学におけるデータ駆動科学の展開  [Not invited]
    小松崎 民樹
    「新学術領域研究」スパースモデリングの深化と高次元データ駆動科学の創成 2017年度第1回公開シンポジウム  2017/06
  • 一細胞ラマン計測と情報科学の融合による細胞診断  [Invited]
    小松崎 民樹
    2017年度人工知能学会全国大会  2017/05
  • 1細胞ラマンスペクトル画像から抽出する細胞状態タキソノミ―  [Not invited]
    小松崎 民樹
    平成28年度新分野創成センターイメージングサイエンス研究分野プロジェクト成果発表会  2017/03
  • 1細胞ラマン分光イメージング画像から読み解く情報計測科学  [Not invited]
    小松崎 民樹
    バイオ計測解析技術研究会  2017/03
  • Data-Driven Analysis of Raman Microscopic Images  [Not invited]
    J.N. Taylor, C.-B. Li, K. Fujita, T. Komatsuzaki
    電子科学研究所 研究交流会  2017/01
  • 分子から細胞の個性に関するデータ駆動型数理科学  [Invited]
    小松崎 民樹
    第1117回生物科学セミナー  2016/12
  • The Non-equilibrium Effects on Reaction Kinetics of F1-ATPase  [Not invited]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium  2016/12
  • Data-Driven Approaches to Raman Microscopic Image Analysis  [Not invited]
    J.N. Taylor, Chun-Biu Li, Katsumasa Fujita, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium  2016/12
  • Dynamical Heterogeneity During Collective Migration of MDCK Epithelial Monolayer  [Not invited]
    Preetom Nag, Khalifa Mohammad Helal, Hiroshi Teramoto, Chun-Biu Li, Hisashi Haga, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium  2016/12
  • Collective Cell Migration: Underlying Dynamics and Emergent Structures of Heterogeneity  [Not invited]
    Khalifa Mohammad Helal, Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Hisashi Haga, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium  2016/12
  • マイノリティ細胞を彫りだすデータ科学  [Invited]
    小松崎 民樹
    第39回日本分子生物学会年会  2016/12
  • Predicting Biological Cell Aggregation Using Scalable Random Forest Decision Trees  [Not invited]
    SATTARI, Sulimon, KOMATSUZAKI, Tamiki
    The 18th RIES-Hokudai International Symposium  2016/11
  • Apparent Nonequilibrium Behavior in Single-Molecule FRET Time-Series Induced by Photophysics  [Not invited]
    J. Nicholas Taylor, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium  2016/11
  • Bad Arm Existence Checking Algorithm  [Not invited]
    Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium  2016/11
  • Raman Microscopic Image Analysis based on Information-theoretic Approach  [Not invited]
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium  2016/11
  • Toward Molecular Propagation through Degenerated Electron Energy Level Crossings  [Not invited]
    Hiroshi Teramoto, Shyūichi Izumiya, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium  2016/11
  • Spatial heterogeneous and transient dynamics during collective cell migration in a monolayer of MDCK epithelial cells  [Not invited]
    Nag Preetom, Khalifa Helal, Teramoto Hiroshi, Yamaguchi Naoya, Li Chun-Biu, Haga Hisashi, Komatsuzaki Tamiki
    第54回日本生物物理学会年会  2016/11
  • 1細胞ラマン分光イメージングから如何にして細胞の個性を定量化するか?  [Invited]
    小松崎 民樹
    第54回日本生物物理学会年会  2016/11
  • Data Driven Approaches to Raman Microscopic Analysis  [Not invited]
    J. N. Taylor, K. Fujita, T. Komatsuzaki
    第54回日本生物物理学会年会  2016/11
  • 一細胞ラマン計測とスパース学習、バンディット手法などの情報科学の融合による細胞診断の迅速解析  [Not invited]
    小松崎 民樹
    基盤(S)離散構造処理系プロジェクト「2016年度 秋のワークショップ」  2016/11
  • 一細胞ラマン計測と情報科学の融合による細胞診断の迅速解析技術の開発  [Invited]
    小松崎 民樹
    CREST・さきがけ複合領域 「計測技術と高度情報処理の融合によるインテリジェント計測・解析手法の開発と応用」, キックオフ会議  2016/11
  • 少数系から複雑反応ネットワークを含む遷移状態概念の深化と制御  [Invited]
    小松崎 民樹
    特設分野研究「遷移状態制御」研究代表者交流会  2016/10
  • Data-Driven Approaches to Raman Microscopic Image Analysis  [Not invited]
    J. N. Taylor, K. Fujita, T. Komatsuzaki
    「理論と実験」研究会2016  2016/10
  • Molecular Functions and Energy Landscapes Extracted from Single Molecule Time Series Data  [Invited]
    KOMATSUZAKI TAMIKI
    HOKUDAI-NCTU Joint Symposium on Nano, Photo and Bio Sciences in 2016  2016/10
  • 時間解像度に依存した反応ネットワークの階層的変化とその予測手法の開発  [Not invited]
    永幡 裕, 前田 理, 寺本 央, 武次 徹也, 小松崎 民樹
    分子科学討論会2016  2016/09
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [Invited]
    KOMATSUZAKI TAMIKI
    Energy Landscapes: Theory and Applications  2016/06
  • Phase Space geometry and Chemical Reaction Dynamics: Past, Present, and Future  [Invited]
    KOMATSUZAKI TAMIKI
    Seminar of the ICB/Nanosciences department  2016/06
  • Single Molecule Biophysics: How can One extract the Underlying Markovian/non-Markovian Network from Noisy and Short Time Series?  [Invited]
    KOMATSUZAKI TAMIKI
    IXXI-ENS Lyon seminar  2016/06
  • Defining Global Transition State over an Entire Markov Network  [Invited]
    KOMATSUZAKI TAMIKI
    Seminar of the ICB/Nanosciences department  2016/06
  • Single Molecule Biophysics: How can One Dig the Underlying Network from Noisy and Short Time Series?  [Invited]
    KOMATSUZAKI TAMIKI
    Seminar of the ICB/Nanosciences department  2016/06
  • Defining Global Transition State over an Entire Markov Network  [Invited]
    KOMATSUZAKI TAMIKI
    Seminar at Beijing Computational Science Research Center  2016/05
  • 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奇現象  [Not invited]
    小松崎民樹, 寺本央, 戸田幹人, 河野裕彦, 高橋正彦
    附置研究所間アライアンスによるナノとマクロをつなぐ物質・デバイス・システム創製戦略プロジェクト 平成27年度成果報告会  2016/05
  • シロイヌナズナの萼片組織に見る植物細胞集団の振動現象  [Not invited]
    小松崎 民樹
    理研シンポジウム: 細胞システムの動態と論理VIII  2016/04
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    第89回現象数理セミナー  2016/04
  • Molecular Data Science Perspectives for Individuality Covering from Molecules to Cells  [Invited]
    KOMATSUZAKI TAMIKI
    統合生命医科学研究センター疾患生物学セミナー  2016/03
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [Invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Computational Chemistry (CC) Symposium in ICCMSE  2016/03
  • The key and unlock mechanisms in F1-ATPase unveiled by single molecule time series analysis  [Not invited]
    Chun-Biu Li, Hiroshi Ueno, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    新学術領域「少数性生物学」 研究成果報告会  2016/03
  • 少数性生物学の新展開:分子個性から細胞個性へ  [Not invited]
    小松崎 民樹
    新学術領域「少数性生物学」 研究成果報告会  2016/03
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    偏微分方程式姫路研究会  2016/03
  • Data-driven quantification of heterogeneous microenvironments in live-cell Raman microscopic images  [Not invited]
    J. Nick Taylor, Almar F. Palonpon, Chun Biu Li, Katsumasa Fujita, Tamiki Komatsuzaki
    The Biophysical Society 2016 BPS Annual Meeting  2016/02
  • On the Relationship between Local Microtubule and Cell Growth in Plants  [Not invited]
    津川 暁, Chun Biu Li, 小松崎 民樹
    Mathematical Sciences Evening Seminar  2016/02
  • 生物個性学:分子から細胞へ  [Not invited]
    小松崎 民樹
    少数性生物学研究会2016~少数性生物学の未来を語る~  2016/02
  • Correlated Oscillation in Microtubule Fluctuation and Cell Growth in Arabidopsis Sepal  [Not invited]
    津川 暁, Chun Biu Li, 小松崎 民樹
    第132回植物科学セミナー  2016/01
  • Toward deciphering cell individuality in systems biology  [Invited]
    KOMATSUZAKI TAMIKI
    Symposium #137 Life at Small Copy Numbers (The 2015 International Chemical Congress of Pacific Basin Societies)  2015/12
  • Data-driven quantification of heterogeneous microenvironments in live-cell Raman microscopic images  [Not invited]
    J. Nick Taylor, Almar F. Palonpon, Chun Biu Li, Katsumasa Fujita, Tamiki Komatsuzaki
    Symposium #121 Deciphering molecular complexity from protein functions to cellular network (The 2015 International Chemical Congress of Pacific Basin Societies)  2015/12
  • Energy landscapes and conformation network learned from single molecule time series  [Invited]
    KOMATSUZAKI TAMIKI
    Symposium #121 Deciphering molecular complexity from protein functions to cellular network (The 2015 International Chemical Congress of Pacific Basin Societies)  2015/12
  • 特異点論によるバンド間交差の分類  [Not invited]
    寺本 央, 戸田 幹人, 近藤 憲治, 小松崎 民樹
    第1回「トポロジーが紡ぐ物質科学のフロンティア」領域研究会  2015/12
  • Dynamical Reaction Theory: Beyond the conventional perturbation theory  [Invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Colloquium on kinetics and scattering theory for astrophysics (Nov 26-27) (in a part of the extended workshop “Theory of Gas Phase Scattering and Reactivity for Astrophysics(Nov 23-Dec 8)” along COST ‘Our chemical History’Action CM1401)  2015/11
  • Phase Space geometry and Chemical Reaction Dynamics: Past, Present, and Future  [Invited]
    KOMATSUZAKI TAMIKI
    Colloquium on kinetics and scattering theory for astrophysics (Nov 26-27) (in a part of the extended workshop “Theory of Gas Phase Scattering and Reactivity for Astrophysics(Nov 23-Dec 8)” along COST ‘Our chemical History’Action CM1401)  2015/11
  • Developing high precision algorithm to predict observation timescale hierarchy of an isomerization reaction network  [Not invited]
    Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Tetsuya Taketsugu, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium  2015/11
  • Classification and Control of electron energy level crossings in terms of the theory of singularity  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium  2015/11
  • Kinetics of Multiple conductance levels of Mechanosensitive Ion Channel  [Not invited]
    Genming Wang, Chun-Biu Li, Hitoshi Tatsumi, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium  2015/11
  • The Onset of Non-equilibrium Effects at High Temperature in the Reaction Kinetics of F1-ATPase  [Not invited]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium  2015/11
  • マルコフ連鎖の時間階層的クラスタリング  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    ERATO湊離散構造処理系プロジェクト 「2015年度 秋のワークショップ」  2015/11
  • Single Molecule Biophysics: How can One Dig the Underlying Network from Noisy and Short Time Series?  [Invited]
    KOMATSUZAKI TAMIKI
    International Conference on “Challenges in Data Science: a Complex Systems Perspective  2015/10
  • 細胞内レベルでの微小管配向の抽出  [Not invited]
    津川 暁, Chun Biu Li, 小松崎 民樹
    「理論と実験」研究会2015  2015/10
  • The temperature dependence and non-equilibrium properties of the single F1-ATPase kinetics  [Not invited]
    田宮 裕治, Chun Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    「理論と実験」研究会2015  2015/10
  • Identifying Different Reaction Processes in terms of Graph Laplacian  [Invited]
    Hiroshi Teramoto, Alireza Hadjighasem, Daniel Karrasch, George Haller, Tamiki Komatsuzaki
    ランダム力学系理論とその応用  2015/09
  • 1分子時系列データから解読するエネルギー地形とネットワーク  [Invited]
    小松崎 民樹
    「データ駆動科学の新展開」ミニ研究会  2015/09
  • 非平衡効果が引き起こすF1分子モーターの非アレニウス型温度依存性  [Not invited]
    田宮 裕治, Chun-Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    第9回分子化学討論会  2015/09
  • 複雑分子系の異性化反応ネットワークに埋め込まれた時間階層構造の解読  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    第9回分子化学討論会  2015/09
  • 特異点論を用いた非断熱交差の安定性と分岐の解析  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    日本物理学会2015年秋季大会  2015/09
  • 複合化学反応系の分子シミュレーション-第一原理シミュレーションから分子技術へ-  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    化学反応経路探索のニューフロンティア  2015/09
  • 少数系から複雑反応ネットワークを含む遷移状態概念の深化と制御  [Invited]
    小松崎 民樹
    特設分野「遷移状態制御」研究代表者交流会  2015/09
  • 複雑反応ネットワークに埋め込まれた時間階層構造の解読  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    第53回日本生物物理学会  2015/09
  • 植物の中の局所微小管と細胞成長の関係について  [Not invited]
    Satoru Tsugawa, Chun-Biu Li, Tamiki Komatsuzaki
    第53回日本生物物理学会  2015/09
  • 非平衡効果が引き起こすF1分子モーターの非アレニウス型温度依存性  [Not invited]
    田宮 裕治, Chun-Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    第53回日本生物物理学会  2015/09
  • Single Molecule Time Series Analysis of F1-ATPase to Unravel the Role of Bound-ATP Hydrolysis  [Not invited]
    Chun-Biu Li, Tamiki Komatsuzaki
    第53回日本生物物理学会  2015/09
  • Classification and control of electron energy level crossings  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    北大理論化学ワークショッ プ  2015/09
  • 審査員の経験からみたポイント  [Invited]
    小松崎 民樹
    平成27年度 北海道大学科研費申請セミナー  2015/09
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [Invited]
    Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kohno, Tamiki Komatsuzaki
    Telluride summer workshop “Geometry of Chemical Reaction Dynamics”  2015/08
  • Transition States from Gas Phase, Condensed Phase to Complex Networks  [Invited]
    KOMATSUZAKI TAMIKI
    Telluride summer workshop “Geometry of Chemical Reaction Dynamics”  2015/08
  • 複雑な異性化反応ネットワークに埋め込まれた時間階層構造の解読法の開発  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    日本化学会北海道支部 2015年 夏季研究発表会  2015/07
  • Sumi-Marcus 型ポテンシャルモデルを用いた F1分子モーターの反応速度定数の解析  [Not invited]
    田宮 裕治, Chun-Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    日本化学会北海道支部 2015年 夏季研究発表会  2015/07
  • グラフラプラシアンによる異なる反応プロセスの同定  [Not invited]
    寺本 央, Alireza Hadjighasem, Daniel Karrasch, George Haller, 小松崎 民樹
    RIMS 研究集会『力学系とその諸分野への応用』  2015/07
  • 一細胞計測で見えてきたバクテリア細胞内ATP濃度の多様性  [Not invited]
    柳沼秀幸, 河合信之輔, 田端和仁, 冨山佳祐, 垣塚彰, 小松崎民樹, 岡田康志, 野地博行, 今村博臣
    第67回日本細胞生物学会大会  2015/06
  • How can we define a transition state over a network?  [Invited]
    KOMATSUZAKI TAMIKI
    R. Stephen Berry Tribune Symposium  2015/06
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [Invited]
    KOMATSUZAKI TAMIKI
    Chemistry and Dynamics in Complex Environments  2015/06
  • Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series  [Not invited]
    Nick Taylor, Chun Biu Li, David R. Cooper, Christy F. Landes, Tamiki Komatsuzaki
    The Complexity of Dynamics and Kinetics from Single Molecules to Cells  2015/06
  • Energy Landscapes learned from Single-Molecule Time-Series: Dimensionality and Disconnectivity Graph  [Not invited]
    KOMATSUZAKI TAMIKI
    The Complexity of Dynamics and Kinetics from Single Molecules to Cells  2015/06
  • マルコフ連鎖の時間階層的クラスタリング  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 武次 徹也, 小松崎 民樹
    ERATO湊離散構造処理系プロジェクト 「2015年度 初夏のワークショップ」  2015/06
  • 「モデル先行の科学」から「データから彫りだす科学」へ  [Not invited]
    小松崎 民樹
    「俺が考える少数性生物学の次」討論会 新学術領域「少数性生物学」第9回領域会議  2015/06
  • 少数分子反応ネットワーク理論の構築 (7)  [Not invited]
    冨樫 祐一, 小松崎 民樹, 李 振風, 寺本 央, 新海 創也, Holger Flechsig, James Nick Taylor, 中川 正基
    新学術領域「少数性生物学」第9回領域会議  2015/06
  • Deciphering timescale hierarchy encoded in complex reaction networks  [Not invited]
    NAGAHATA Yutaka, MAEDA Satoshi, TERAMOTO Hiroshi, LI Chun-Biu, HORIYAMA Takashi, TAKETSUGU Tetsuya, KOMATSUZAKI Tamiki
    31st Symposium on Chemical Kinetics and Dynamics  2015/06
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
    31st Symposium on Chemical Kinetics and Dynamics  2015/06
  • A Dynamical Switching of Reactive and Nonreactive Modes at High Energies  [Not invited]
    Tamiki Komatsuzaki, Mikito Toda, Hiroshi Teramoto
    2015 SIAM Conference on Dynamical Systems  2015/05
  • A Dynamical Switching of Reactive and Nonreactive Modes at High Energies epartment of Chemistry and Chemical Biology  [Invited]
    KOMATSUZAKI TAMIKI
    Department Seminar in Department of Chemistry and Chemical Biology  2015/05
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [Invited]
    KOMATSUZAKI TAMIKI
    Department Seminar in Department of Chemistry  2015/05
  • Identifying different reaction processes in terms of graph laplacian  [Invited]
    Hiroshi Teramoto, Tamiki Komatsuzaki
    IlLuminyating 2015  2015/05
  • 蛍光画像から微小管配向構造の抽出  [Not invited]
    津川 暁, Chun Biu Li, 小松崎 民樹
    早稲田大学相澤研究室研究会  2015/04
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [Not invited]
    小松崎民樹, 戸田幹人, 寺本央, 河野裕彦, 高橋正彦
    平成26年度アライアンス成果報告会  2015/04
  • 蛍光画像から微小管配向構造を抽出する方法について  [Not invited]
    津川 暁, Chun Biu Li, 小松崎 民樹
    理研シンポジウム「細胞システムの動態と論理 Ⅶ」  2015/04
  • F1 分子モーターの温度依存性  [Not invited]
    田宮 裕治, Chun Biu Li, 渡邉 力也, 野地 博行, 小松崎 民樹
    理研シンポジウム「細胞システムの動態と論理 Ⅶ」  2015/04
  • Energy landscapes derived from single molecule spectroscopy and complex networks  [Invited]
    KOMATSUZAKI TAMIKI
    Architecture, dynamics, and functionality of molecular biosystems  2015/03
  • Understandings of Chemical Reaction Dynamics in terms of Dynamical System Theory  [Invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Computational Chemistry (CC) Symposium in ICCMSE  2015/03
  • 単一バクテリア細胞内ATP濃度の多様性  [Not invited]
    柳沼秀幸, 河合信之輔, 田端和仁, 冨山佳祐, 垣塚彰, 小松崎民樹, 岡田康志, 野地博行, 今村博臣
    生命動態の分子メカニズムと数理 生命動態システム科学四拠点・CREST・PRESTO合同シンポジウム  2015/03
  • Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis  [Not invited]
    B. Shuang, D. Cooper, J. N. Taylor, L. Kisley, J. Chen, W. Wang, C.-B. Li, T. Komatsuzaki, C. F. Landes
    2015 Oil & Gas High Performance Computing Workshop  2015/03
  • Timescale hierarchies of complex reaction network  [Not invited]
    永幡 裕, 寺本 央, 堀山 貴史, Chun-Biu Li, 小松崎 民樹
    Workshop on dynamical systems and computation 2015  2015/03
  • Hierarchical structure of no-return transition states  [Invited]
    KOMATSUZAKI TAMIKI
    Spectroscopy and Dynamics of Molecules and Clusters 2015  2015/02
  • Chance and necessity in reactions under thermal fluctuation & chaos Department of Chemistry  [Invited]
    KOMATSUZAKI TAMIKI
    Indian Institute of Technology Kanpur seminar  2015/02
  • 少数分子反応ネットワーク理論の構築 (4)  [Not invited]
    冨樫 祐一, 小松崎 民樹, 李 振風, 寺本 央, 新海 創也
    新学術領域研究「少数性生物学」第8回領域会議  2015/01
  • Data Scientific Approaches to the Quantification and Interpretation of Raman Microscopic Images of Living Cells  [Not invited]
    J. Nick Taylor, Chun-Biu Li, Tamiki Komatsuzaki
    新学術領域研究「少数性生物学」第8回領域会議  2015/01
  • Survey and study on effects of discreteness and fewness in chemical reaction dynamics  [Not invited]
    Hiroshi Teramoto, Tamiki Komatsuzaki
    新学術領域研究「少数性生物学」第8回領域会議  2015/01
  • Developing “hierarchical” spectral clustering decoded by the mathematical nature of a Markov chain: - timescale hierarchical nature of isomerization reaction network of C5H8O -  [Not invited]
    永幡 裕, 寺本 央, Chun-Biu Li, 小松崎 民樹
    河原林/湊プロジェクト合同WS予餞会Winter2015  2015/01
  • Markov連鎖の持つ時間階層構造について:複雑分子系の異性化反応ネットワークを例に  [Invited]
    永幡 裕, 寺本 央, 堀山 貴史, Chun-Biu Li, 小松崎 民樹
    非平衡ダイナミクスセミナー  2015/01
  • 力学系理論による化学反応動力学の解明  [Not invited]
    小松崎 民樹
    電子科学研究所・研究交流会  2015/01
  • Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis  [Not invited]
    Bo Shuang, David Cooper, J. Nick Taylor, Lydia Kisley, Jixin Chen, Wenxiao Wang, Chun Biu Li, Tamiki Komatsuzaki, Chrisy Landes
    The 2015 Quantitative BioImaging Conference  2015/01
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [Not invited]
    KOMATSUZAKI TAMIKI
    The 8th biennial workshop on Single Molecule Biophysics (SMB)  2015/01
  • ボトムアップとトップダウンの橋渡し:少数性⽣物学のおける分⼦個性  [Not invited]
    小松崎 民樹
    第3 回 少数性⽣物学討論会  2014/12
  • An extraction method of local microtubule alignments in Arabidopsis sepal  [Not invited]
    Satoru Tsugawa, Chun-Biu Li, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki]  2014/12
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [Not invited]
    J.N. Taylor, Chun Biu Li, David R. Cooper, Christy F. Landes, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki]  2014/12
  • Temperature Dependence of Molecular Motor  [Not invited]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki]  2014/12
  • An extraction of embedded timescale hierarchies buried in complex reaction network  [Not invited]
    Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki]  2014/12
  • Local-heterogeneous responses and transient dynamics in colloidal fluids  [Not invited]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Joseph Z. Terdik, Norbert F. Scherer, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki]  2014/12
  • Dynamic Disorder in Single Enzyme Experiments: Facts and Artifacts  [Not invited]
    KOMATSUZAKI TAMIKI
    附置研究所間アライアンスによるナノとマクロをつなぐ物質・デバイス・システム創製戦略プロジェクト(ナノマクロ物質・デバイス・システム創製アライアンス), 医療材料・デバイス・システムグループ G3 分科会, G3 Meeting  2014/11
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [Invited]
    KOMATSUZAKI TAMIKI
    XIXth International Workshop on Quantum Systems in Chemistry, Physics and Biology  2014/11
  • Data Driven Approach to Dynamics of Protein Motor  [Not invited]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    New Challenges in Complex Systems Science  2014/10
  • Chemical Reaction Dynamics and Chaos  [Invited]
    KOMATSUZAKI TAMIKI
    New Challenges in Complex Systems Science  2014/10
  • ボトムアップとトップダウンの橋渡し:少数性生物学のおける分子個性  [Not invited]
    小松崎 民樹
    第2回少数性生物学討論会  2014/10
  • 複雑分子系の構造異性化反応ネットワークに埋め込まれた時間階層構造の抽出  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    研究会「理論と実験」2014  2014/10
  • 熱揺らぎに埋もれた力学的な反応経路  [Invited]
    小松崎 民樹
    研究会「理論と実験」2014  2014/10
  • A Dynamical Switching of Reactive Mode ⇔ Nonreactive Mode at High Energies for a Hydrogen Atom in Crossed Electric and Magnetic Fields  [Invited]
    KOMATSUZAKI TAMIKI
    11th Asian International Seminar on Atomic and Molecular Physics  2014/10
  • 複雑分子系の異性化反応ネットワークに埋め込まれた時間階層構造の抽出  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    第52回日本生物物理学会年会  2014/09
  • 分子個性と少数性  [Not invited]
    小松崎 民樹
    第52回日本生物物理学会年会  2014/09
  • Dynamical heterogeneity and dynamics of cage breaking and formation in colloidal fluids  [Not invited]
    Nag Preetom, Teramoto Hiroshi, Li Chun-Biu, Komatsuzaki Tamiki
    第52回日本生物物理学会年会  2014/09
  • 複雑分子系の異性化反応ネットワークに埋め込まれた時間階層構造の抽出  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    第8回分子科学討論会  2014/09
  • 少数性の生物学において顕在化する分子個性  [Invited]
    小松崎 民樹
    日本物理学会2014年秋季大会  2014/09
  • 正準変換摂動理論の有効領域の拡張法とそれによる振動子間の非線系共鳴によるエネルギー移動の解明  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    日本物理学会2014年秋季大会  2014/09
  • 複雑分子系に埋め込まれた時間階層構造が映す化学分野の“非常識”  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    ERATO湊離散構造処理系プロジェクト 「2014年度 秋のワークショップ」  2014/09
  • 非線形時系列解析による分子の振動エネル ギー移動の解析  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    北大理論化学合同Workshop  2014/09
  • F1 分子モーターにおける温度依存性の高い反応段階について  [Not invited]
    田宮 裕治, Chun-Biu Li, 渡邉力也, 野地博行, 小松崎民樹
    北大理論化学合同Workshop  2014/09
  • Energy landscapes learned from time series and networks  [Invited]
    KOMATSUZAKI TAMIKI
    Energy Landscapes : From Single Molecules to Soft Matter  2014/08
  • 数学の力で読み解く一分子時系列〜F1分子モーターを題材として〜  [Not invited]
    田宮 裕治, Chun-Biu Li, 渡邉力也, 野地博行, 小松崎民樹
    第54回 生物物理若手の会 夏の学校  2014/08
  • Reaction Coordinate Switching Mechanism, on the Possibility of Its Experimental Verification and Its Quantum Manifestation  [Invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications  2014/07
  • Chance and Necessity in Reactions Under Chaos and Stochastic Fluctuation  [Invited]
    KOMATSUZAKI TAMIKI
    The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications  2014/07
  • Extracting Cooperative modes between a biological molecule and water molecules  [Invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    International Workshop "Over the Barriers of Transition Paths: Dynamical Processes in Proteins and Complex Molecular Systems"  2014/06
  • Energy Landscapes Constructed From Single-molecule Time Series And Reaction Networks  [Invited]
    KOMATSUZAKI TAMIKI
    Macromolecular dynamics: structure, function and diseases  2014/06
  • Theories Should Meet Experiments: What Can We Extract From Time Series Data?  [Invited]
    KOMATSUZAKI TAMIKI
    Beijing Computational Science Research Center (CSRC) Seminar  2014/06
  • 複雑分子系における構造異性化反応ネットワークの理解に向けて  [Not invited]
    永幡 裕, 前田 理, 寺本 央, Chun-Biu Li, 堀山 貴史, 武次 徹也, 小松崎 民樹
    第17回理論化学討論会  2014/05
  • 生体分子と水の過渡的な集団運動の抽出  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    第17回理論化学討論会  2014/05
  • Energy Landscapes Constructed From Single-Molecule Time Series and Reaction Networks  [Invited]
    KOMATSUZAKI TAMIKI
    The 2014 Les Houches - TSRC Protein Dynamics Workshop  2014/05
  • ノイジーなFRETデータから多重経路を考慮に入れた自由エネルギー地形を抽出する  [Not invited]
    小松崎 民樹
    理研シンポジウム:細胞システムの動態と論理Ⅵ  2014/04
  • タンパク質一分子計測から得られたマルコフ連鎖がもつ時間階層構造の理解に向けて  [Not invited]
    永幡裕, 寺本央, Chun-Biu Li, 小松崎民樹
    日本物理学会 第69回年次大会  2014/03
  • パターン形成における本質的な高次相関情報量の抽出  [Not invited]
    宮川尚紀, 寺本央, 河合信之輔, 李振風, 小松崎民樹
    日本物理学会 第69回年次大会  2014/03
  • Dynamical heterogeneity and cage breaking dynamics in colloidal fluids in terms of Lagrangian Coherent structures (LCSs)  [Not invited]
    寺本央, Preetom Nag、Chun Biu Li, 小松崎民樹
    2013 年度日本生物物理学会北海道支部例会  2014/03
  • タンパク質の時系列から得られたMarkov連鎖の解析に向けて:グラフの分割とクラスタリングで定義する複雑な化学反応における状態とその時間階層構造  [Not invited]
    永幡 裕, 堀山 貴史, 前田 理, 寺本 央, Chun-Biu Li, 小松崎 民樹
    2013 年度日本生物物理学会北海道支部例会  2014/03
  • Extracting coherent dynamics in colloidal fluids in terms of Lagrangian Coherent structures (LCSs)  [Not invited]
    Teramoto Hiroshi, Nag Preetom, Li Chun-Biu, Komatsuzaki Tamiki
    International Life-Science Symposium  2014/03
  • 少数分子反応ネットワーク理論の構築  [Not invited]
    冨樫 祐一, 小松崎 民樹, 李 振風, 寺本 央, 新海 創也小松崎
    新学術領域研究「少数性生物学」第6回領域会議  2014/02
  • 生体分子と水の過渡的な協同運動の抽出  [Not invited]
    寺本 央, 戸田幹人, 小松崎民樹
    新学術領域研究「少数性生物学」第6回領域会議  2014/02
  • Constructing Kinetic Scheme Objectively from Dwell-Time Time Series with Exact Information Content  [Not invited]
    Chun-Biu Li, Tamiki Komatsuzaki
    新学術領域研究「少数性生物学」第6回領域会議  2014/02
  • Extracting the Underlying Free Energy Landscape Buried in Photon-by- Photon based Single-Molecule Measurements  [Not invited]
    J. Nick Taylor, Chun-Biu Li, Tamiki Komatsuzaki
    新学術領域研究「少数性生物学」第6回領域会議  2014/02
  • コロイド流体の動的協同運動のLagrangian Coherent Structureによる抽出  [Not invited]
    寺本央, Preetom Nag、Chun Biu Li, 小松崎民樹
    北海道大学電子科学研究所平成25年度研究交流会  2014/01
  • Relation between dynamics of individual trajectories and that of their ensemble distributions -Spectral Analysis of Individual Trajectories-  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • An Information-Theoretical Approach to Local Equilibrium State Analysis for Single-Molecule Time-Series  [Not invited]
    J. N. Taylor, C.B. Li, S. Kawai, T. Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Scrutiny of Heterogeneity in Memory by Extracting Reaction Network Buried in Single Molecule Time Series of EGFR and Grb2  [Not invited]
    Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Toward understanding hierarchical structure of complex reaction networks extracted from single molecule time series  [Not invited]
    Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Coherent dynamics in colloidal fluids in terms of Lagrangian Coherent Structures (LCSs)  [Not invited]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Information of multi-order correlation in pattern formation  [Not invited]
    Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Extracting the Protein-folding Dynamics from Single Molecule Time Series  [Not invited]
    Kunihiko Ibe, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou]  2013/12
  • Essential Coordinates to Describe the Dynamics of Many-atom Systems  [Invited]
    Shinnosuke Kawai, Hiroshi Teramoto, Tamiki Komatsuzaki
    5th JCS International Symposium on Theoretical Chemistry  2013/12
  • タンパク質一分子の計測から得られた定常マルコフ連鎖がもつ時間階層構造の理解に向けて  [Not invited]
    永幡 裕, 寺本 央, Li Chun-Biu, 小松崎 民樹
    ERATO湊離散構造処理系プロジェクト 「2013年度 秋のワークショップ」  2013/11
  • スペクトル解析による生体分子の構造転移モードの解析  [Invited]
    寺本央, 戸田幹人, 小松崎民樹
    第1回アライアンス若手研究交流会~計算・計測・合成の融合~  2013/11
  • タンパク質一分子の計測から得られた定常マルコフ連鎖がもつ時間階層構造の理解に向けて  [Not invited]
    永幡 裕, 寺本 央, 堀山 貴史, Chun-Biu Li, 小松崎 民樹
    ERATO湊離散構造処理系プロジェクト 「2013年度 秋のワークショップ」  2013/11
  • 分子個性(Dynamic disorder):一分子生物学から産まれた新しい概念?  [Invited]
    小松崎 民樹
    第2回バイオ単分子研究会  2013/11
  • 力学系をみる二つの視点:軌道と分布の描像、の関係  [Invited]
    寺本央, 戸田幹人, 小松崎民樹
    関東力学系セミナー  2013/11
  • An Information-Theoretical approach to Local Equilibrium State Analysis for Single-Molecule Time-Series  [Not invited]
    J. Nick Taylor, Li Chun-Biu, Kawai Shinnosuke, Komatsuzaki Tamiki
    第51回日本生物物理学会年会  2013/10
  • Quantifying the absolute ATP concentration inside single bacteria cells  [Not invited]
    Hideyuki Yaginuma, Shinnosuke Kawai, Keisuke Tomiyama, Kazuhito V. Tabata, Tamiki Komatsuzaki, Hiromi Imamura, Hiroyuki Noji
    第51回日本生物物理学会年会  2013/10
  • Coherent dynamics in colloidal fluids in terms of Lagrangian coherent structures (LCS)  [Not invited]
    Nag Preetom, Teramoto Hiroshi, Li Chun-Biu, Komatsuzaki Tamiki
    第51回日本生物物理学会年会  2013/10
  • 分子イメージングから要素間の高次相互作用の定量化に向けて  [Invited]
    小松崎 民樹
    第51回日本生物物理学会年会  2013/10
  • 一分子時系列から抽出されたマルコフ連鎖 定常ネットワーク における遷移確率が“最小”となる分子の“状態”の同定  [Not invited]
    永幡 裕, 寺本 央, Li Chun-Biu, 小松崎 民樹
    第51回日本生物物理学会年会  2013/10
  • A Multiscale Kinetic Scheme Extracted from EGFR-Grb2 Single Molecule Reaction  [Not invited]
    Sultana Tahmina, Takagi Hiroaki, Morimatsu Miki, Teramoto Hiroshi, Li Chun-Biu, Sako Yasushi, Komatsuzaki Tamiki
    第51回日本生物物理学会年会  2013/10
  • Toward the Decoding of Single Nucleotides Tunneling Current by Change Point Analysis  [Not invited]
    Chun-Biu Li, Tamiki Komatsuzaki
    Technologies for Medical Diagnosis and Therapy Symposium  2013/10
  • Let Systems Tell for themselves: Energy Landscape and Complex Network  [Not invited]
    James N. Taylor, Shinnosuke Kawai, Chun Biu Li, Tamiki
    Technologies for Medical Diagnosis and Therapy Symposium  2013/10
  • Dynamic Disorder 再考:解析の虚実  [Invited]
    小松崎 民樹
    研究会「理論と実験」2013  2013/10
  • 天文学から生まれたカオスと化学動力学の出会い  [Not invited]
    小松崎 民樹
    Symposium on Cross-Talk between Chemistry and Planetary Sciences  2013/10
  • 個々の軌道の振舞いとその集団分布の振舞いの関係~一軌道レベルでのスペクトル解析法とそれによる溶質分子と水の協同運動の抽出~  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    第36回溶液化学シンポジウム プレシンポジウム  2013/10
  • 定常マルコフ連鎖から階層構造を抽出する際に生じる組み合わせ爆発  [Not invited]
    永幡 裕, 寺本 央, 堀山 貴史, Chun-Biu Li, 小松崎 民樹
    湊離散構造処理系プロジェクト ERATO セミナー  2013/10
  • 反応座標切替機構の量子的兆候  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    第7回分子科学討論会2013京都  2013/09
  • 時間スケールに依存して変化する実効自由度とエネルギー地形  [Not invited]
    河合 信之輔, 寺本 央, 小松崎 民樹
    第7回分子科学討論会2013京都  2013/09
  • 反応の運命を分ける反応性境界: 定義の一般化とH5+プロトン移動反応における反応性境界の抽出  [Not invited]
    永幡 裕, 寺本 央, Chun-Biu Li, 河合 信之輔, 小松崎 民樹
    第7回分子科学討論会2013京都  2013/09
  • Identifying the most distinct disjoint sets to extract hierarchical structure in Markov chain steady state network extracted from time series by finding “minimum” transition probability  [Not invited]
    Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry  2013/08
  • Information of multi-order correlation in pattern formation  [Not invited]
    Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry  2013/08
  • Co-operative motion in colloidal fluids in terms of Lagrangian Coherent Structures(LCS)  [Not invited]
    Nag Preetom, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry  2013/08
  • Toward System Molecular Biology & Data Science  [Not invited]
    KOMATSUZAKI TAMIKI
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry  2013/08
  • 確率の起源:偶然と必然の原理  [Invited]
    小松崎 民樹
    第1回少数性生物学トレーニングコース  2013/08
  • 実験データからノイズを取り除き背後の物理量を評価する方法  [Not invited]
    河合信之輔, David Cooper, Christy Landes・Henning, D. Mootz, Haw Yang, 小松崎民
    日本化学会北海道支部2013年夏季研究発表会  2013/07
  • 2つの反応方向を持つサドルにおける化学反応:行先・起源を分ける反応性境界の抽出  [Not invited]
    永幡 裕, 寺本 央, Chun-Biu Li, 河合 信之輔, 小松崎 民樹
    日本化学会北海道支部2013年夏季研究発表会  2013/07
  • Dynamical Conformation Coordinations in Non-Ribosomal Peptide Synthetases  [Not invited]
    Mootz, H.D, Komatsuzaki, T, Yang, H, Sun, X, Morrell, T.E, Rafalska-Metcalf, I.U, Alfermann, J, Volkmann, G, Dehling, E, Li, C.-B, Kawai, S, Taylor, N. J
    HFSP 2013 Awardees Meeting  2013/07
  • Revisiting Energy Landscape, Timescale, Coarse-Graining  [Invited]
    KOMATSUZAKI TAMIKI
    Chemistry and Dynamics in Complex Environments  2013/06
  • Identifying states in Markov chain steady state network extracted from time series by finding minimum transition probability  [Not invited]
    Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The Complexity of Dynamics and Kinetics in Many Dimensions  2013/06
  • Revisiting Energy Landscape & Extracting it from FRET measurement  [Not invited]
    KOMATSUZAKI TAMIKI
    The Complexity of Dynamics and Kinetics in Many Dimensions  2013/06
  • Phase Space Geometrical Aspects in Condensed Phase Reactions  [Not invited]
    KOMATSUZAKI TAMIKI
    Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases  2013/06
  • Reactivity Boundaries to Separate the Fate of a Chemical Reaction Associated with Multiple Saddles  [Not invited]
    Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases  2013/06
  • Unbiased estimation of physical properties in noisy experimental data  [Not invited]
    Shinnosuke Kawai, David Cooper, Christy Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
    IMS Workshop on "Hierarchical Molecular Dynamics: From Ultrafast Spectroscopy to Single Molecule Measurements"  2013/05
  • データ駆動型モデリングと一分子動態解析における虚実  [Invited]
    小松崎 民樹
    日本顕微鏡学会第69回学術講演会  2013/05
  • Energy Landscapes Constructed From Single-Molecule Time Series and Reaction Networks  [Invited]
    KOMATSUZAKI TAMIKI
    The 2014 Les Houches - TSRC Protein Dynamics Workshop  2013/05
  • A microscopic ruler tells us the underlying networks in single molecule measurements  [Invited]
    KOMATSUZAKI TAMIKI
    Nanoscale Science Seminars 2013:A Microscopic ruler tells us the underlying networks in single molecule measurements  2013/05
  • 階層性と多様性を内包する生命動態システムの解析基盤創成  [Not invited]
    小松崎 民樹, Chun Biu Li, 寺本央, 河合信之輔, James N. Taylor
    平成24年度アライアンス成果報告会  2013/04
  • 生体分子と水の過渡的な協同運動の抽出  [Not invited]
    寺本央, 戸田幹人, 小松崎民樹
    日本物理学会 第69回年次大会  2013/03
  • Capturing Full Information Contents from Single Molecule Dwell-time Time Series with Minimum Excessive Information  [Not invited]
    Chun Biu Li, Tamiki Komatsuzaki
    The Physical Society of Japan (JPS) 2013 (68th) Annual Meeting  2013/03
  • 任意の確率分布に対する推定量の数値的構成  [Not invited]
    河合 信之輔, David Cooper, Christy landes、Henning, D. Mootz, Haw Yang, 小松崎 民樹
    日本物理学会第68回年次大会  2013/03
  • 法双曲的不変多様体崩壊の量子的兆候  [Not invited]
    寺本 央, 戸田 幹人, 小松崎 民樹
    日本物理学会第68回年次大会  2013/03
  • Stationary Lagrangian Coherent Structureによる化学反応動力学の理解  [Not invited]
    寺本 央, 戸田 幹人, 小松崎 民樹
    日本化学会第93春季年会(2013)  2013/03
  • Multiscale Hidden Markovian Network Buried in Recognition Reaction of EGFR and Grb2.  [Not invited]
    Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    2012年度 日本生物物理学会北海道支部例会  2013/03
  • 1分子データをどれだけ正しく読み取れるか?  [Not invited]
    小松崎 民樹
    「物質・デバイス領域共同研究拠点」[B-1]公開シンポジウム  2013/02
  • Toward Deciphering Molecular Individuality in sSystems Biology  [Invited]
    KOMATSUZAKI TAMIKI
    French-Japanese Seminar on "Bioinspired Methods and Applications"  2013/02
  • 多自由度化学反応系の本質部分を記述する少数自由度の抽出  [Not invited]
    河合信之輔, 寺本央, 小松崎民樹
    化学系学協会北海道支部2013年冬季研究発表会  2013/01
  • 2つの反応方向をもつサドルにおける化学反応:反応の運命を分ける反応性境界の抽出  [Not invited]
    永幡裕, 寺本央, 李振風, 河合信之輔, 小松崎民樹
    化学系学協会北海道支部2013年冬季研究発表会  2013/01
  • 一分子時系列から掘り起こす多次元自由エネルギー地形の情報理論的構成法の開発  [Not invited]
    千葉勇太, 河合信之輔, 馬場昭典, 寺本央, 李振風, 小松崎民樹
    化学系学協会北海道支部2013年冬季研究発表会  2013/01
  • 蛋白質機能に対するデータ駆動的モデリング  [Invited]
    小松崎 民樹
    東北大学 原子分子材料科学高等研究機構 Half-day workshop  2013/01
  • Toward deciphering molecular individuality in systems biology  [Not invited]
    Chun Biu Li, Tamiki Komatsuzaki
    Gordon Research Conferences, Stochastic Physics in Biology  2013/01
  • Let Single Molecule Time Series Tell for Itself: Energy Landscape and Complex Network  [Invited]
    KOMATSUZAKI TAMIKI
    4th France-Japan Joint Seminar "Imaging of spatiotemporal hierarchies in living cells – an overview of dynamics from molecules to cells -"  2013/01
  • 一分子酵素反応実験におけるDynamic disorderの起源  [Not invited]
    小松崎 民樹
    第85回日本生化学会大会  2012/12
  • Extracting Quasi Normally Repelling Material Surface by Re-formulating Variational Lagrangian Coherent Structure (LCS) Theory  [Not invited]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Tamiki Komatsuzak
    The 13th RIES-Hokudai International Symposium  2012/12
  • Effect of Time Scales on the Essential Dimensionality of a Dynamical System  [Not invited]
    Shinnosuke Kawai, Hiroshi Teramoto, Tamiki Komatsuzaki
    The 13th RIES-Hokudai International Symposium  2012/12
  • .Extracting cooperative mode of water and peptide in terms of a local Green function  [Not invited]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 13th RIES-Hokudai International Symposium  2012/12
  • Deciphering complex hierarchical living systems in single molecule biology  [Invited]
    KOMATSUZAKI TAMIKI
    2nd Discussion Symposium on Artificial Life and Biomimetic Functional Materials  2012/12
  • Modeling Single Molecule Kinetics Objectively from Dwell-time time series  [Invited]
    Chun-Biu Li, Tamiki Komatsuzaki
    International Workshop on Quantitative Biology 2012  2012/11
  • 1分子時系列情報から読み解く反応ネットワーク:分子動態を多階層な複雑ネット ワークのなかでどう議論できるか?  [Invited]
    小松崎 民樹
    文部科学省「物質・デバイス領域共同研究拠点」第2回複雑系数理とその応用に関するシンポジウム  2012/11
  • Toward deciphering reality of molecular dynamics in systems biology  [Not invited]
    KOMATSUZAKI TAMIKI
    RIES - CIS Joint Symposium  2012/10
  • Exploring the Operating Principles and Cooperative Motions from Single F1-ATPase Time Series  [Not invited]
    Chun Biu LI, Tamiki Komatsuzaki
    Paradigm Innovation in Biology: novel strategy and thinking  2012/10
  • Construction of "Optimal" Estimators for Arbitrary Probability Distributions  [Not invited]
    Shinnosuke Kawai, Tamiki Komatsuzaki
    Paradigm Innovation in Biology: novel strategy and thinking  2012/10
  • Theories should meet measurements: What Can We Extract from Time Data?  [Invited]
    KOMATSUZAKI TAMIKI
    Paradigm Innovation in Biology: novel strategy and thinking  2012/10
  • 過剰情報量を最小にする反応スキーム  [Not invited]
    小松崎 民樹
    研究会「理論と実験」2012  2012/10
  • 一分子酵素反応実験におけるDynamic disorder解釈の虚実:我々は何を観ているのか?  [Not invited]
    小松崎 民樹
    生理学研究所研究会「超階層シグナル伝達研究の新展開」  2012/10
  • 遷移状態とは何か-鞍点の周辺で起こる運動とその制御  [Not invited]
    河合 信之輔, 小松崎 民樹
    シンポジウム「化学反応経路探索のニューフロンティア2012」  2012/09
  • 複雑分子系を読み解くための新しい1分子理論  [Not invited]
    Chun Biu Li, 小松崎 民樹
    第6回分子科学討論会  2012/09
  • 高次ランクサドルを含めた化学反応ダイナミクスにおける反応の境界  [Not invited]
    永幡 裕, 河合 信之輔, 寺本 央, Chun-Biu Li, 小松崎 民樹
    第6回分子科学討論会  2012/09
  • A novel computational procedure for locating Lagrangian coherent structure(LCS) from Variational LCS theory.  [Not invited]
    Preetom Nag, Hiroshi Teramoto,Chun Biu Li, Tamiki Komatsuzaki
    The Physical Society of Japan (JPS) 2012 Fall Meeting  2012/09
  • 反変Lyapunovベクトルを用いた法反発的不変面の構成法  [Not invited]
    寺本央, George Haller, 小松崎民樹
    日本物理学会 2012年秋季大会  2012/09
  • 凝縮相ダイナミクスにおける時間スケールのエネルギー地形への影響  [Not invited]
    河合 信之輔, 小松崎 民樹
    第6回分子科学討論会  2012/09
  • Constructing unbiased estimators for arbitrary probability distribution  [Invited]
    Kawai, S, Mootz, H.D, Yang, H, Komatsuzaki, T
    HFSP 12th Annual Awardees Meeting  2012/07
  • Transition States and Reaction Coordinates in Complex Systems  [Invited]
    KOMATSUZAKI TAMIKI
    Searching for Reaction Coordinates and Order Parameters  2012/06
  • Theories Should Meet Experiments: What Can We Extract from Time Series Data?  [Invited]
    KOMATSUZAKI TAMIKI
    Characterizing Landscapes: From Biomolecules to Cellukar Networks  2012/06
  • Extracting Boundary of Reaction Associated with an Index-two-saddle from a Two Degree-of-Freedom System  [Not invited]
    NAGAHATA Yutaka, TERAMOTO Hiroshi, LI, Chun-Biu, KAWAI Shinnosuke, KOMATSUZAKI Tamiki
    28th Symposium on Chemical Kinetics and Dynamics  2012/06
  • 一分子酵素反応の動態解析における虚実:我々は何を観ているのか?  [Not invited]
    小松崎 民樹
    細胞システムの動態と論理IV  2012/04
  • 一分子反応の動態解析における虚実:我々は何を観ているのか?  [Invited]
    小松崎 民樹
    最先端研究開発支援プログラム「1分子解析技術を基盤とした革新ナノバイオデバイスの開発研究-超高速単分子DNAシークエンシング、超低濃度ウイルス検知、極限生体分子モニタリングの実現-」講演会  2012/04

MISC

  • Takashi Takemoto, Normann Mertig, Masato Hayashi, Saki Susa-Tanaka, Hiroshi Teramoto, Atsuyoshi Nakamura, Ichigaku Takigawa, Shin Ichi Minato, Tamiki Komatsuzaki, Masanao Yamaoka  2018 International Conference on Reconfigurable Computing and FPGAs, ReConFig 2018  2019/02/13  [Not refereed][Not invited]
     
    © 2018 IEEE. QBoost is a recently proposed machine learning algorithm, designed to exploit the benefits of emerging annealing processors which solve NP hard problems in combinatorial optimization a hundred times faster than conventional CPUs. In this paper, we present the first FPGA-based implementation of QBoost, incorporating a large-scale annealing processor with 2704 spins. In contrast to previous implementations, based on quantum annealers, we utilize the flexibility of FPGAs for implementing a fast, integrated QBoost engine which combines the annealing processor and the modules of the hyperparameter search on a single FPGA. As opposed to quantum annealers, this accelerates the time required for scanning the hyperparameter space from the order of hours to a single second.
  • 中村篤祥, ペリシエ オレリアン, 田畑公次, 小松崎民樹  日本細胞生物学会大会(Web)  71st-  ROMBUNNO.1SEp‐07 (WEB ONLY)  2019  [Not refereed][Not invited]
  • 田畑公次, 中村篤祥, 小松崎民樹  電子情報通信学会技術研究報告  118-  (284(IBISML2018 44-104)(Web))  353‐360 (WEB ONLY)  2018/10/29  [Not refereed][Not invited]
  • 原田義規, CAHYADI Harsono, HELAL Khalifa, 岡嶋亮, 田畑公次, TAYLOR Nick, 熊本康昭, 高松哲郎, 小松崎民樹, 田中秀央  日本病理学会会誌  107-  (1)  368  -368  2018/04/26  [Not refereed][Not invited]
  • 機械学習による非アルコール性脂肪性肝疾患モデルのラマン分光分析
    原田 義規, Cahyadi Harsono, Helal Khalifa, 岡嶋 亮, 田畑 公次, Taylor Nick, 熊本 康昭, 高松 哲郎, 小松崎 民樹, 田中 秀央  日本病理学会会誌  107-  (1)  368  -368  2018/04  [Not refereed][Not invited]
  • 田畑公次, 中村篤祥, 本多淳也, 本多淳也, 小松崎民樹  人工知能学会人工知能基本問題研究会資料  106th-  94‐99  2018/03/07  [Not refereed][Not invited]
  • 小松崎民樹, 小松崎民樹  応用物理学会春季学術講演会講演予稿集(CD-ROM)  65th-  ROMBUNNO.19p‐D102‐5  2018/03/05  [Not refereed][Not invited]
  • 【少数性生物学ってなんだ?少数の因子が生命システムを制御する】 少数と個性 分子の数と生命らしさ
    冨樫 祐一, 新海 創也, 小松崎 民樹  実験医学  35-  (19)  3190  -3196  2017/12  [Not refereed][Not invited]
     
    従来の生化学における反応の考え方は、酵素など、反応にかかわる物質の濃度に基づいている。この「濃度」の概念は、各成分が莫大な数の無個性な分子の集まりであることを前提としている。ところが、生体分子のなかには、細胞あたり1〜数個しかないものや、個々の分子が「個性」をもつとされるものもある。われわれは、数理モデルに基づく予言や、計測データの詳細な解析により、少数分子とその個性が反応にもたらす効果を明らかにしようとしてきた。その一端を紹介する。(著者抄録)
  • 少数性の生命科学:Minor要素の振舞いがシステム全体に影響を及ぼす思わぬ仕掛け 一細胞ラマン計測と情報科学の融合による少数性の生命科学
    小松崎 民樹  生命科学系学会合同年次大会  2017年度-  [2PS14  -1]  2017/12  [Not refereed][Not invited]
  • 冨樫祐一, 新海創也, 小松崎民樹  実験医学  35-  (19)  3190‐3196  2017/12/01  [Not refereed][Not invited]
  • 少数性の生命科学:Minor要素の振舞いがシステム全体に影響を及ぼす思わぬ仕掛け 一細胞ラマン計測と情報科学の融合による少数性の生命科学
    小松崎 民樹  生命科学系学会合同年次大会  2017年度-  [2PS14  -1]  2017/12  [Not refereed][Not invited]
  • 寺本央, 泉屋周一, 小松崎民樹  日本物理学会講演概要集(CD-ROM)  72-  (2)  ROMBUNNO.24aPS‐29  2017/09/25  [Not refereed][Not invited]
  • Hiroshi Teramoto, Kenji Kondo, Shyuichi Izumiya, Mikito Toda, Tamiki Komatsuzaki  JOURNAL OF MATHEMATICAL PHYSICS  58-  (7)  2017/07  [Not refereed][Not invited]
     
    We classify two-by-two traceless Hamiltonians depending smoothly on a threedimensional Bloch wavenumber and having a band crossing at the origin of the wavenumber space. Recently these Hamiltonians attract much interest among researchers in the condensed matter field since they are found to be effective Hamiltonians describing the band structure of the exotic materials such as Weyl semimetals. In this classification, we regard two such Hamiltonians as equivalent if there are appropriate special unitary transformation of degree 2 and diffeomorphism in the wavenumber space fixing the origin such that one of the Hamiltonians transforms to the other. Based on the equivalence relation, we obtain a complete list of classes up to codimension 7. For each Hamiltonian in the list, we calculate multiplicity and Chern number [D. J. Thouless et al., Phys. Rev. Lett. 49, 405 (1982); M.V. Berry, Proc. R. Soc. A 392, 45 (1983); and B. Simon, Phys. Rev. Lett. 51, 2167 (1983)], which are invariant under an arbitrary smooth deformation of the Hamiltonian. We also construct a universal unfolding for each Hamiltonian and demonstrate how they can be used for bifurcation analysis of band crossings. Published by AIP Publishing.
  • 小松崎民樹  日本生化学会大会(Web)  90th-  ROMBUNNO.2PS14‐1 (WEB ONLY)  2017  [Not refereed][Not invited]
  • 小松崎民樹  人工知能学会全国大会論文集(CD-ROM)  31st-  ROMBUNNO.2I4‐OS‐10b‐5  2017  [Not refereed][Not invited]
  • 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 Roncero, Hiroshi Teramoto, Mikito Toda, Ad van der Avoird, Holger Waalkens  2016/10/03  [Not refereed][Not invited]
     
    Because of the very peculiar conditions of chemistry in many astrophysical
    gases (low densities, mostly low temperatures, kinetics-dominated chemical
    evolution), great efforts have been devoted to study molecular signatures and
    chemical evolution. While experiments are being performed in many laboratories,
    it appears that the efforts directed towards theoretical works are not as
    strong.
    This report deals with the present status of chemical physics/physical
    chemistry theory, for the qualitative and quantitative understanding of
    kinetics of molecular scattering, being it reactive or inelastic. By gathering
    several types of expertise, from applied mathematics to physical chemistry,
    dialog is made possible, as a step towards new and more adapted theoretical
    frameworks, capable of meeting the theoretical, methodological and numerical
    challenges of kinetics-dominated gas phase chemistry in astrophysical
    environments.
    A state of the art panorama is presented, alongside present-day strengths and
    shortcomings. However, coverage is not complete, being limited in this report
    to actual attendance of the workshop. Some paths towards relevant progress are
    proposed.
  • Meysam Tavakoli, J. Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé  2016/06/02  [Not refereed][Not invited]
     
    We review methods of data analysis for biophysical data with a special
    emphasis on single molecule applications. Our review is intended for anyone,
    from student to established researcher. For someone just getting started, we
    focus on exposing the logic, strength and limitations of each method and cite,
    as appropriate, the relevant literature for implementation details. We review
    traditional frequentist and Bayesian parametric approaches to data analysis and
    subsequently extend our discussion to recent non-parametric and information
    theoretic methods.
  • 寺本央, 戸田幹人, 河野裕彦, 高橋正彦, 小松崎民樹  化学  71-  (5)  25‐30  2016/05/01  [Not refereed][Not invited]
  • 小松崎 民樹  生物物理  56-  (4)  197  -197  2016  [Not refereed][Not invited]
  • 小松崎民樹  日本分子生物学会年会プログラム・要旨集(Web)  39th-  ROMBUNNO.2PS1‐3 (WEB ONLY)  2016  [Not refereed][Not invited]
  • 永幡裕, 前田理, 寺本央, 武次徹也, 小松崎民樹  分子科学討論会講演プログラム&要旨(Web)  10th-  ROMBUNNO.3P151 (WEB ONLY)  2016  [Not refereed][Not invited]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki  AIP Conference Proceedings  1702-  2015/12/31  [Not refereed][Not invited]
     
    Dynamical systems theory has been providing firm understandings of chemical reaction dynamics since the beginning of the twentieth century. Dynamical systems theory provides two ways to understand the system: One is a geometric view based on invariant manifolds and the other is a statistical view based on Ergodic theory. In this paper, we mainly focus on the geometric view and list three phenomena in which the geometric view plays an important role.
  • 寺本央, 戸田幹人, 小松崎民樹  日本物理学会講演概要集(CD-ROM)  70-  (2)  ROMBUNNO.16PCQ-2  2015/09/24  [Not refereed][Not invited]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki  NONLINEARITY  28-  (8)  2677  -2698  2015/08  [Not refereed][Not invited]
     
    We analyze the mechanism of breakdown of normally hyperbolic invariant manifolds (NHIMs) based on unstable periodic orbits, homoclinic and heteroclinic orbits in NHIMs for Hamiltonian systems. First, we classify the breakdown mechanism in terms of the characteristic multipliers (the eigenvalues of the phase space Jacobian matrix) of unstable periodic orbits in the NHIM and elucidate the classification for systems of three degrees of freedom. Second, we also present an index that provides a sufficient condition under which the NHIM ceases to exist in more global regions along the homoclinic and heteroclinic orbits in the NHIM. We demonstrate local and global features of the breakdown of the NHIM for a hydrogen atom in crossed electric and magnetic fields. Our analysis of unstable periodic orbits of shorter periods indicates that local features of the breakdown are highly inhomogeneous, depending on each periodic orbit. This manifests an inherent dynamical feature for systems of more than two degrees of freedom. Contrastingly, our analysis of homoclinic orbits indicates that the energy at which the NHIM breaks down does not depend on each homoclinic orbit. This result suggests the existence of a global breakdown of the NHIM behind these homoclinic orbits since these homoclinic orbits run through broader phase space regions.
  • 柳沼秀幸, 柳沼秀幸, 柳沼秀幸, 河合信之輔, 河合信之輔, 田端和仁, 冨山佳祐, 垣塚彰, 小松崎民樹, 岡田康志, 野地博行, 野地博行, 今村博臣, 今村博臣  日本細胞生物学会大会要旨集  67回-  162  -162  2015/06  [Not refereed][Not invited]
  • A coarse graining method to extract cooperative modes of water molecules
    TODA Mikito, Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki  Advances in Science, Technology and Environmentology  2015  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  70-  (0)  2015  [Not refereed][Not invited]
  • 田宮裕治, 田宮裕治, LI Chun‐Biu, LI Chun‐Biu, 渡邉力也, 野地博行, 小松崎民樹  分子科学討論会講演プログラム&要旨(Web)  9th-  ROMBUNNO.2P097 (WEB ONLY)  2015  [Not refereed][Not invited]
  • 永幡裕, 前田理, 寺本央, 寺本央, LI Chun‐Biu, 堀山貴史, 武次徹也, 小松崎民樹, 小松崎民樹  分子科学討論会講演プログラム&要旨(Web)  9th-  ROMBUNNO.1P088 (WEB ONLY)  2015  [Not refereed][Not invited]
  • 柳沼秀幸, 河合信之輔, 田端和仁, 冨山佳祐, 垣塚彰, 小松崎民樹, 野地博行, 今村博臣  日本生体エネルギー研究会討論会講演要旨集  40th-  38  -39  2014/12/11  [Not refereed][Not invited]
  • 小松崎民樹  生体の科学  65-  (5)  444  -445  2014/10/15  [Not refereed][Not invited]
  • 小松崎民樹  日本物理学会講演概要集  69-  (2)  221  2014/08/22  [Not refereed][Not invited]
  • 寺本央, 戸田幹人, 小松崎民樹  日本物理学会講演概要集  69-  (2)  170  2014/08/22  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  RSC Theoretical and Computational Chemistry Series  154  -179  2014/03/27  [Not refereed][Not invited]
  • 寺本央, 戸田幹人, 小松崎民樹  日本物理学会講演概要集  69-  (1)  437  2014/03/05  [Not refereed][Not invited]
  • 宮川尚紀, 寺本央, 河合信之輔, LI C‐B, LI C‐B, 小松崎民樹  日本物理学会講演概要集  69-  (1)  334  2014/03/05  [Not refereed][Not invited]
  • 永幡裕, 寺本央, LI Chun‐Biu, 小松崎民樹  日本物理学会講演概要集  69-  (1)  359  2014/03/05  [Not refereed][Not invited]
  • Miyagawa N, Teramoto H, Kawai S, Li C-B, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  69-  (0)  2014  [Not refereed][Not invited]
  • Yaginuma Hideyuki, Kawai Shinnosuke, Tabata Kazuhito, Tomiyama Keisuke, Kakizuka Akira, Komatsuzaki Tamiki, Okada Yasushi, Noji Hiroyuki, Imamura Hiromi  Seibutsu Butsuri  54-  (1)  S130  2014  [Not refereed][Not invited]
  • 永幡裕, 前田理, 寺本央, 寺本央, LI Chun‐Biu, 堀山貴史, 武次徹也, 小松崎民樹, 小松崎民樹  分子科学討論会講演プログラム&要旨(Web)  8th-  ROMBUNNO.1E15 (WEB ONLY)  2014  [Not refereed][Not invited]
  • Nagahata Yutaka, Teramoto Hiroshi, Li Chun-Biu, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  69-  (0)  2014  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  69-  (0)  2014  [Not refereed][Not invited]
  • Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  69-  (0)  2014  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  69-  (0)  2014  [Not refereed][Not invited]
  • ピーコック トーマス, ハラー ジョージ, 小松崎 民樹  パリティ  28-  (11)  4  -12  2013/11  [Not refereed][Not invited]
  • 少数個分子の協同が生み出す生命機能のメカニズム 分子イメージングから要素間の高次相互作用の定量化に向けて(Biological functions derived from cooperation of a small number of molecules Toward quantifying higher-order interactions among elements from molecular imaging)
    小松崎 民樹  生物物理  53-  (Suppl.1-2)  S95  -S95  2013/09  [Not refereed][Not invited]
  • 寺本 央, 戸田 幹人, 小松崎 民樹  数理解析研究所講究録  1827-  (1827)  154  -170  2013/03  [Not refereed][Not invited]
  • 寺本 央, 戸田 幹人, 小松崎 民樹  数理解析研究所講究録  1827-  (1827)  154  -170  2013/03  [Not refereed][Not invited]
  • 生命動態システムのなかに生き残る分子の個性を聴きたい
    小松崎 民樹  分子研レターズ  67-  17  -18  2013/03  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  68-  (0)  2013  [Not refereed][Not invited]
  • Nagahata Yutaka, Teramoto Hrosi, Li Chun-Biu, Kawai Shinnosuke, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  68-  (0)  2013  [Not refereed][Not invited]
  • Kawai Shinnosuke, Cooper David, Landes Christy, Mootz Henning D, Yang Haw, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  68-  (0)  2013  [Not refereed][Not invited]
  • 分子科学若手の会夏の学校50周年記念文集に寄せて
    小松崎 民樹  分子科学若手の会夏の学校50周年記念文集  2012/03  [Not refereed][Not invited]
  • Kikuchi M, Kawai S, Teramoto H, Li CB, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Akinori Baba, Tamiki Komatsuzaki  SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146  146-  299  -327  2012  [Not refereed][Not invited]
  • T. Komatsuzaki, M. Kawakami, S. Takahashi, H. Yang, R. J. Silbey  SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146  146-  XIII  -XV  2012  [Not refereed][Not invited]
     
    © 2012 by John Wiley & Sons, Inc. All rights reserved. Discover the experimental and theoretical developments in optical single-molecule spectroscopy that are changing the ways we think about molecules and atoms. The Advances in Chemical Physics series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. This latest volume explores the advent of optical single-molecule spectroscopy, and how atomic force microscopy has empowered novel experiments on individual biomolecules, opening up new frontiers in molecular and cell biology and leading to new theoretical approaches and insights. Organized into two parts-one experimental, the other theoretical-this volume explores advances across the field of single-molecule biophysics, presenting new perspectives on the theoretical properties of atoms and molecules. Single-molecule experiments have provided fresh perspectives on questions such as how proteins fold to specific conformations from highly heterogeneous structures, how signal transductions take place on the molecular level, and how proteins behave in membranes and living cells.This volume is designed to further contribute to the rapid development of single-molecule biophysics research. Filled with cutting-edge research reported in a cohesive manner not found elsewhere in the literature, each volume of the Advances in Chemical Physics series serves as the perfect supplement to any advanced graduate class devoted to the study of chemical physics.
  • Akinori Baba, Tamiki Komatsuzaki  SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146  146-  299  -327  2012  [Not refereed][Not invited]
  • Tatyana G. Terentyeva, Hans Engelkamp, Alan E. Rowan, Tamiki Komatsuzaki, Johan Hofkens, Chun-Biu Li, Kerstin Blank  ACS NANO  6-  (1)  346  -354  2012/01  [Not refereed][Not invited]
     
    Using a single-molecule fluorescence approach, the time series of catalytic events of an enzymatic reaction can be monitored, yielding a sequence of fluorescent "on"- and "off"-states. An accurate on/off-assignment Is complicated by the intrinsic and extrinsic noise in every single-molecule fluorescence experiment. Using simulated data, the performance of the most widely employed binning and thresholding approach was systematically compared to change point analysis. It is shown that the underlying on- and off-histograms as well as the off-autocorrelation are not necessarily extracted from the "signal" buried in noise. The shapes of the on- and off-histograms are affected by artifacts Introduced by the analysis procedure and depend on the signal-to-noise ratio and the overall fluorescence intensity. For experimental data where the background Intensity is not constant over time we consider change point analysis to be more accurate. When using change point analysis for data of the enzyme a-chymotrypsin, no characteristics of dynamic disorder was found. In light of these results, dynamic disorder might not be a general sign of enzymatic reactions.
  • Chiba Y, Kawai S, Baba A, Teramoto H, Li CB, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Miyagawa N, Teramoto H, Li Chun Biu, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Nagahata Yutaka, Kawai Shinnosuke, Teramoto Hirosi, Li Chun-Bin, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Kawai Shinnosuke, Teramoto Hiroshi, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • Teramoto Hiroshi, Haller George, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  67-  (0)  2012  [Not refereed][Not invited]
  • 1分子実験を読み解くための新しい実践型分子理論を目指して
    小松崎 民樹  第二次先端ウオッチング調査:融合領域の創生「高次分子システムのための分子  31  -34  2012  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  物性研究  97-  (3)  547  -559  2011/12  [Not refereed][Not invited]
     
    In this paper, we discuss our recent development for the understandings of transport phenomena in dynamical systems in terms of normally hyperbolic invariant manifolds (NHIMs) and their stable/unstable manifolds, following a discussion with Professor Shuichi Tasaki by one of the authors, Komatsuzaki, while they chatted with drinking coffee or tea at the institute for fundamental chemistry in Kyoto. In dynamical systems, a NHIM is a representative invariant structure that is structually stable. In addition, the stable/unstable manifolds emanating from the NHIM, especially those that have codimension one, play an important role for transports in phase space. The importance of the NHIM and its stable/unstable manifolds, to turn the other way, indicates that the breakdown of these structures can have a big consequence for the transports. For example, a phenomena recently found by the authors, a switching of the reaction coordinate with the other nonreactive coordinate, is one of the consequences for the breakdown of the NHIM. In order to investigate the breakdowm mechanism of the NHIM, we focus on unstable periodic orbits embedded in the NHIM. We classify the breakdown patterns at these periodic orbits into six patterns. In the last section, we discuss more global features of the breakdown mechanism and its dependency on the system dimensions.
  • Tamiki Komatsuzaki, Tamiki Komatsuzaki, Masaru Kawakami, Masaru Kawakami, Satoshi Takahashi, Satoshi Takahashi, Haw Yang, Robert J. Silbey  Single Molecule Biophysics: Experiment and Theory  146-  2011/11/23  [Not refereed][Not invited]
  • Tamiki Komatsuzaki, R. Stephen Berry, David M. Leitner  Advances in Chemical Physics  145-  2011/07/01  [Not refereed][Not invited]
  • 寺本 央, 小松崎 民樹  数理解析研究所講究録  1742-  (1742)  127  -136  2011/05  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  134-  (11)  2011/03  [Not refereed][Not invited]
     
    The generalized Langevin equation (GLE) is extended to the case of nonstationary bath. The derivation starts with the Hamiltonian equation of motion of the total system including the bath, without any assumption on the form of Hamiltonian or the distribution of the initial condition. Then the projection operator formulation is utilized to obtain a low-dimensional description of the system dynamics surrounded by the nonstationary bath modes. In contrast to the ordinary GLE, the mean force becomes a time-dependent function of the position and the velocity of the system. The friction kernel is found to depend on both the past and the current times, in contrast to the stationary case where it only depends on their difference. The fluctuation-dissipation theorem, which relates the statistical property of the random force to the friction kernel, is also derived for general nonstationary cases. The resulting equation of motion is as simple as the ordinary GLE, and is expected to give a powerful framework to analyze the dynamics of the system surrounded by a nonstationary bath. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3561065]
  • Flow and Stop Protocol for the Long-Time Observation of Fluorescence from Free Single Molecules: Application to the Time-Series Analysis of Protein Folding
    Kiyoto Kamagata, Akinori Baba, Tamiki Komatsuzaki, Satoshi Takahashi  BIOPHYSICAL JOURNAL  100-  (3)  212  -213  2011/02  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  134-  (8)  2011/02  [Not refereed][Not invited]
     
    Nonlinear reaction dynamics through a rank-one saddle is investigated for many-particle system with spatial rotation. Based on the recently developed theories of the phase space geometry in the saddle region, we present a theoretical framework to incorporate the spatial rotation which is dynamically coupled with the internal vibrational motions through centrifugal and Coriolis interactions. As an illustrative simple example, we apply it to isomerization reaction of HCN with some nonzero total angular momenta. It is found that no-return transition state (TS) and a set of impenetrable reaction boundaries to separate the "past" and "future" of trajectories can be identified analytically under rovibrational couplings. The three components of the angular momentum are found to have distinct effects on the migration of the "anchor" of the TS and the reaction boundaries through rovibrational couplings and anharmonicities in vibrational degrees of freedom. This method provides new insights in understanding the origin of a wide class of reactions with nonzero angular momentum. (C) 2011 American Institute of Physics. [doi:10.1063/1.3554906]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  134-  (2)  2011/01  [Not refereed][Not invited]
     
    Dynamics of passage over a saddle is investigated for a quantum system under the effect of time-dependent external field (laser pulse). We utilize the recently developed theories of nonlinear dynamics in the saddle region, and extend them to incorporate both time-dependence of the external field and quantum mechanical effects of the system. Anharmonic couplings and laser fields with any functional form of time dependence are explicitly taken into account. As the theory is based on the Weyl expression of quantum mechanics, interpretation is facilitated by the classical phase space picture, while no "classical approximation" is involved. We introduce a quantum reactivity operator to extract the reactive part of the system. In a model system with an optimally controlled laser field for the reaction, it is found that the boundary of the reaction in the phase space, extracted by the reactivity operator, is modulated with time by the effect of the laser field, to "catch" the system excited in the reactant region, and then to "release" it into the product region. This method provides new insights in understanding the origin of optimal control of chemical reactions by laser fields. (C) 2011 American Institute of Physics. [doi:10.1063/1.3528937]
  • Akinori Baba, Tamiki Komatsuzaki  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  13-  (4)  1395  -1406  2011  [Not refereed][Not invited]
     
    We present a new self-consistent procedure to construct a multidimensional effective free energy landscape from a scalar single molecule time series, when single molecules experience the landscape within a given timescale of "observation." The theory is based on a framework we recently developed to extract a set of local equilibrium states (LESs) and their network from a scalar time series, such as distance between dye molecules tagged in a biomolecule. We scrutinize the appropriateness of the assumptions of local equilibration and local detailed balance among LESs at the single molecule level within the given timescale, rather than postulating them a priori. The self-consistent procedure in this article incorporates the effect of local correlation of the system dynamics inside potential basins, and the effect of finiteness of the sampled data points in assigning the boundary between different LESs. We propose a new simple scheme to assign the dimensionality of the energy landscape from a single molecule time series. We also address the question of what the molecules actually "feel" from the underlying landscape at the single
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  106-  (5)  2011/01  [Not refereed][Not invited]
     
    Questions of how the nature of a reaction coordinate that dominates the reaction ceases to exist and whether some new features emerge as an increase of total energy of systems are investigated for many degrees of freedom Hamiltonian systems. As a model system, a hydrogen atom in crossed electric and magnetic fields is scrutinized. It is shown that, when the total energy increases, the reaction coordinate no longer dominates the reaction as did at the lower energies. In turn, a new reaction coordinate emerges, connecting totally different reactant and product states. Furthermore, depending on which parts of the phase space the system traverses through the saddle, the system nonuniformly experiences the switching of the reaction coordinate leading to the different product state. The universal mechanism of the cessation and the switching of the reaction coordinate at high energy regimes above the saddle is investigated.
  • Shinnosuke Kawai, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda  ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS: ADVANCES IN CHEMICAL PHYSICS, VOL 145  145-  123  -169  2011  [Not refereed][Not invited]
  • David M. Leitner, Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki, Akira Shojiguchi, Mikito Toda  ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS: ADVANCES IN CHEMICAL PHYSICS, VOL 145  145-  83  -122  2011  [Not refereed][Not invited]
  • Tamiki Komatsuzaki, Akinori Baba, Shinnosuke Kawai, Mikito Toda, John E. Straub, R. Stephen Berry  ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS: ADVANCES IN CHEMICAL PHYSICS, VOL 145  145-  171  -220  2011  [Not refereed][Not invited]
  • Tamiki Komatsuzaki, R. Stephen Berry, David M. Leitner  ADVANCING THEORY FOR KINETICS AND DYNAMICS OF COMPLEX, MANY-DIMENSIONAL SYSTEMS: CLUSTERS AND PROTEINS: ADVANCES IN CHEMICAL PHYSICS, VOL 145  145-  XI  -XII  2011  [Not refereed][Not invited]
     
    © 2011 by John Wiley & Sons, Inc. All rights reserved. This series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. Volume 145 in the series continues to report recent advances with significant, up-to-date chapters by internationally recognized researchers.
  • Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki  NUMERICAL ANALYSIS AND APPLIED MATHEMATICS ICNAAM 2011: INTERNATIONAL CONFERENCE ON NUMERICAL ANALYSIS AND APPLIED MATHEMATICS, VOLS A-C  1389-  991  -994  2011  [Not refereed][Not invited]
     
    How do global patterns emerge in complex systems from the underlying interactions or correlation among their composite elements? To what extent do higher order correlations play a significant role in the development of global patterns? In this article, we employ and generalize the recently developed information-theoretic quantity, connected information (Schneidman et al., Phys. Rev. Lett., 91, 238701 (2003)), to quantify the hierarchical multivariate dependence hidden in complex systems. By using as an illustrative example the nonlinear voter model on a two dimensional lattice which shows distinctive spatial patterns in different parameter regions of the system, we demonstrate how different features of the underlying correlations among the elements, such as their orders and strengths, depend on the types of the global patterns, and also how the "microscopic" origin of spatial dynamical heterogeneities can be unveiled in terms of the local decomposition of the connected information. The correspondence of the connected information with various geometrical concepts in the space of probability distribution is also discussed.
  • Chun Biu Li, Tamiki Komatsuzaki  Cell Signaling Reactions: Single-Molecular Kinetic Analysis  221  -263  2011  [Not refereed][Not invited]
     
    Single molecule spectroscopy provides us with a new means to look deeply into the question of how an individual molecule behaves when performing biological functions in a thermally fluctuating environment. However, what information one can extract from the observed data is still an open question. We overview our new method which extracts the underlying reaction scheme, a state-space network (SSN), from the time series data of an experimental measurement. We demand that a time series analysis should provide not only an interpretation of the dynamical behavior but also provide new insights into biological functions buried in ensemble-based measurements. Our method is based on the combination of information theory and Wavelet multiresolution decomposition analysis. The resultant reaction scheme does not rely on an a priori ansatz like local equilibrium and detailed balance. It is mathematically assured as unique, minimally complex and stochastic, but best predictive. We demonstrate the potential of this method by applying it to the analysis of an anomalous conformation in Flavin oxidoreductase dependent on the timescale of observation. We also discuss future perspectives concerning its use as a new means for the exploration of single molecule biophysics. © Springer Science+Business Media B.V. 2011.
  • T. Komatsuzaki, M. Kawakami, S. Takahashi, H. Yang, R. J. Silbey  APPLIED MICROBIOLOGY AND MOLECULAR BIOLOGY IN OILFIELD SYSTEMS  146-  V  -VI  2011  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  13-  (48)  21217  -21229  2011  [Not refereed][Not invited]
     
    Many chemical reactions, including those of biological importance, take place in thermally fluctuating environments. Compared to isolated systems, there arise markedly different features due to the effects of energy dissipation through friction and stochastic driving by random forces reflecting the fluctuation of the environment. Investigation of how robustly the system reacts under the influence of thermal fluctuation, and elucidating the role of thermal fluctuation in the reaction are significant subjects in the study of chemical reactions. In this article, we start with overviewing the generalized Langevin equation (GLE), which has long been used and continues to be a powerful tool to describe a system surrounded by a thermal environment. It has been also generalized further to treat a nonstationary environment, in which the conventional fluctuation-dissipation theorem no longer holds. Then, within the framework of the Langevin equation we present a method recently developed to extract a new reaction coordinate that is decoupled from all the other coordinates in the region of a rank-one saddle linking the reactant and the product. The reaction coordinate is buried in nonlinear couplings among the original coordinates under the influence of stochastic random force. It was ensured that the sign of this new reaction coordinate (= a nonlinear functional of the original coordinates, velocities, friction, and random force) at any instant is sufficient to determine in which region, the reactant or the product, the system finally arrives. We also discuss how one can extend the method to extract such a coordinate from the GLE framework in stationary and nonstationary environments, where memory effects exist in dynamics of the reaction.
  • Miyagawa N, Teramoto H, Li C.B, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  66-  (0)  2011  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  66-  (0)  2011  [Not refereed][Not invited]
  • Kawai Shinnosuke, Teramoto Hiroshi, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  66-  (0)  2011  [Not refereed][Not invited]
  • Itoh Masahiro, Baba Akinori, Li Chun Biu, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  66-  (0)  2011  [Not refereed][Not invited]
  • Teramoto Hiroshi, Toda Mikito, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  66-  (0)  2011  [Not refereed][Not invited]
  • Tamiki Komatsuzaki, Tamiki Komatsuzaki, Chun Biu Li, Shinnosuke Kawai  AIP Conference Proceedings  1281-  1582  -1584  2010/12/01  [Not refereed][Not invited]
     
    The origin of chance and necessity in change of the states of the system is discussed under the existence of chaos and stochastic fluctuation. The mathematical framework lies on the application of normal form theory to a wide class of many-degrees of freedom (dof) Hamiltonian systems and (generalized) Langevin systems in the region of rank-one saddle on the potential. The well-known resonance condition can never be met in the region of rank-one saddle, which results in a deterministic reaction path even in a sea of chaos in many-dof Hamiltonian systems. However, as the total energy increases further, the corresponding invariant manifolds such as normally hyperbolic invariant manifolds (NHIM) start to ruin and/or bifurcate. The correspondence for systems under thermal fluctuation in the Langevin thermostat is also discussed, which is expected to shed light on the principle of robust functions in biological systems. © 2010 American Institute of Physics.
  • Shinnosuke Kawai, Tamiki Komatsuzaki  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  12-  (47)  15382  -15391  2010/12  [Not refereed][Not invited]
     
    A framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in a multidimensional Langevin equation is extended to the generalized Langevin equations without a priori assumption of the forms of the potential (in general, nonlinearly coupled systems) and the friction kernel. The equation of motion with memory effect can be transformed into an equation without memory at the cost of an increase in the dimensionality of the system, and hence the theoretical framework developed for the (nonlinear) Langevin formulation can be generalized to the non-Markovian process with colored noise. It is found that the increased dimension can be physically interpreted as effective modes of the fluctuating environment. As an illustrative example, we apply this theory to a multidimensional generalized Langevin equation for motion on the Muller-Brown potential surface with an exponential friction kernel. Numerical simulations find a boundary between the highly reactive region and the less reactive region in the space of initial conditions. The location of the boundary is found to depend significantly on both the memory kernel and the nonlinear couplings. The theory extracts a reaction coordinate whose sign determines the fate of the reaction taking into account thermally fluctuating environments, memory effect, and nonlinearities. It is found that the location of the boundary of reactivity is satisfactorily reproduced as the zero of the statistical average of the new reaction coordinate, which is an analytical functional of both the original position coordinates and velocities of the system, and of the properties of the environment.
  • Hiroshi Teramoto, Tamiki Komatsuzaki  CHAOS  20-  (3)  2010/09  [Not refereed][Not invited]
     
    The mutual relationship among Markov partitions is investigated for one-dimensional piecewise monotonic map. It is shown that if a Markov partition is regarded as a map-refinement of the other Markov partition, that is, a concept we newly introduce in this article, one can uniquely translate a set of symbolic sequences by one Markov partition to those by the other or vice versa. However, the set of symbolic sequences constructed using Markov partitions is not necessarily translated with each other if there exists no map-refinement relation among them. By using a roof map we demonstrate how the resultant symbolic sequences depend on the choice of Markov partitions. (C) 2010 American Institute of Physics. [doi:10.1063/1.3491097]
  • Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki  PHYSICAL REVIEW E  82-  (1)  2010/07  [Not refereed][Not invited]
     
    A method proposed by Matsunaga et al. (Phys. Rev. Lett. 99, 238103 (2007) ] is applied to simple stochastic models and two model proteins composed of 46 amino beads with three different kinds of residues. The method, which is based on the combination of the principal component analysis and the finite size Lyapunov exponent, characterize the coarse-grained dynamics in different spatiotemporal hierarchies in protein dynamics. The application of the method to model proteins reveals that the low-indexed (large-variance) principal components carry less-divergent, regularized dynamics at the coarse-grained scales on a less-frustrated energy landscape, whereas this less-divergent nature is less pronounced for a protein model with a more frustrated energy landscape. It is also revealed that our technique can differentiate the collective motions on the projected principal component space inherent to the system and the apparent collective behavior which can appear even in high-dimensional stochastic systems.
  • Shinnosuke Kawai, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  105-  (4)  2010/07  [Not refereed][Not invited]
     
    Nonlinear dynamics around a rank-one saddle is investigated in a high energy regime above the reaction threshold. The transition state (TS) is considered as a surface of a "point of no return'' through which all reactive trajectories pass only once in the process of climbing over the saddle before being captured in the product state. A no-return TS ceases to exist above a certain high energy regime. However, even at high energies where the no-return TS can no longer exist, it is shown that "an impenetrable barrier'' in the phase space robustly persists, which acts as a boundary between reactive and nonreactive trajectories. This implies that we can yet predict the fate of reactions even when the no-return TS may not exist. As an example, we show the analysis of dynamical systems theory for a hydrogen atom in crossed electric and magnetic fields.
  • 寺本 央, 小松崎 民樹  数理解析研究所講究録  1688-  (1688)  26  -38  2010/05  [Not refereed][Not invited]
  • Extracting Complex Network and Effective Free Energy Landscape of Protein Fluctuation from Single-Molecule Time Series
    Tamiki Komatsuzaki, Chun-Biu Li, Akinori Baba  BIOPHYSICAL JOURNAL  98-  (3)  184A  -184A  2010/01  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  12-  (27)  7636  -7647  2010  [Not refereed][Not invited]
     
    A framework to calculate the rate constants of condensed phase chemical reactions of manybody systems is presented without relying on the concept of transition state. The theory is based on a framework we developed recently adopting a multidimensional underdamped Langevin equation in the region of a rank-one saddle. The theory provides a reaction coordinate expressed as an analytical nonlinear functional of the position coordinates and velocities of the system (solute), the friction constants, and the random force of the environment (solvent). Up to moderately high temperature, the sign of the reaction coordinate can determine the final destination of the reaction in a thermally fluctuating media, irrespective of what values the other (nonreactive) coordinates may take. In this paper, it is shown that the reaction probability is analytically derived as the probability of the reaction coordinate being positive, and that the integration with the Boltzmann distribution of the initial conditions leads to the exact reaction rate constant when the local equilibrium holds and the quantum effect is negligible. Because of analytical nature of the theory taking into account all nonlinear effects and their combination with fluctuation and dissipation, the theory naturally provides us with the firm mathematical foundation of the origin of the reactivity of the reaction in a fluctuating media.
  • Shinnosuke Kawai, Tamiki Komatsuzaki  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  12-  (27)  7626  -7635  2010  [Not refereed][Not invited]
     
    Nonlinear dynamics in the passage over a rank-one saddle is investigated as a function of temperature in the presence of stochastic, thermal fluctuation. The analyses are based on a framework we developed recently adopting a multidimensional underdamped Langevin equation (without any assumption for the form of the potential of mean force). The framework can in principle provide a single coordinate to enable us to predict the final destination of the reaction in a thermally fluctuating media. At each temperature, the preciseness or the error of the reaction coordinate is evaluated in capturing the true reaction dynamics at different levels of approximations. By using the Muller-Brown potential as an illustrative example, it is found that a hierarchy of dynamical structure exists in the region of a rank-one saddle, in which the crossing dynamics qualitatively changes as the temperature increases. We discuss the mechanism of how the reaction coordinate persists, which provides a boundary of the reaction to divide the phase space into the reactive and the nonreactive regions, even in the presence of thermal fluctuation.
  • Nagahata Y, Teramoto H, Li C. -B, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Sakurai Daisuke, Komatsuzaki Tamiki, Teramoto Hiroshi, Li Chun Biu  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Teramoto Hiroshi  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Miyagawa N, Teramoto H, Li C. -B, Komatsuzaki T  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Itoh Masahiro, Baba Akinori, Li Chun Biu, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Kawai Shinnosuke, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  65-  (0)  2010  [Not refereed][Not invited]
  • Shinnosuke Kawai, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  131-  (22)  2009/12  [Not refereed][Not invited]
     
    The framework recently developed for the extraction of a dynamic reaction coordinate to mediate reactions buried in thermal fluctuation is examined with a model system. Numerical simulations are carried out for an underdamped Langevin equation with the Muumlller-Brown potential surface, which contains three wells and two saddles, and are compared to the prediction by the theory. Reaction probabilities for specific initial conditions of the system as well as their average over the Boltzmann distribution are investigated in the position space and in a space spanned by the position coordinates and the velocities of the system. The nonlinear couplings between the reactive and the nonreactive modes are shown to have significant effects on the reactivity in the model system. The magnitude and the direction of the nonlinear effect are different for the two saddles, which is found to be correctly reproduced by our theory. The whole position-velocity space of the model system is found to be divided into the two distinct regions: One is of mainly reactive (with reaction probability more than half) initial conditions and the other, the mainly nonreactive (with reaction probability less than half) ones. Our theory can actually assign their boundaries as the zero of the statistical average of the new reaction coordinate as an analytical functional of both the original position coordinates and velocities of the system (solute), as well as of the random force and the friction constants from the environment (solvent). The result validates the statement in the previous paper that the sign of the reaction coordinate thus extracted determines the fate of the reaction. Physical interpretation of the reactivity under thermal fluctuation that is naturally derived, thanks to the analyticity of the theoretical framework, is also exemplified for the model system.
  • Shinnosuke Kawai, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  131-  (22)  2009/12  [Not refereed][Not invited]
     
    We present a novel theory which enables us to explore the mechanism of reaction selectivity and robust functions in complex systems persisting under thermal fluctuation. The theory constructs a nonlinear coordinate transformation so that the equation of motion for the new reaction coordinate is independent of the other nonreactive coordinates in the presence of thermal fluctuation. In this article we suppose that reacting systems subject to thermal noise are described by a multidimensional Langevin equation without a priori assumption for the form of potential. The reaction coordinate is composed not only of all the coordinates and velocities associated with the system (solute) but also of the random force exerted by the environment (solvent) with friction constants. The sign of the reaction coordinate at any instantaneous moment in the region of a saddle determines the fate of the reaction, i.e., whether the reaction will proceed through to the products or go back to the reactants. By assuming the statistical properties of the random force, one can know a priori a well-defined boundary of the reaction which separates the full position-velocity space in the saddle region into mainly reactive and mainly nonreactive regions even under thermal fluctuation. The analytical expression of the reaction coordinate provides the firm foundation on the mechanism of how and why reaction proceeds in thermal fluctuating environments.
  • Chun-Biu Li, Haw Yang, Tamiki Komatsuzaki  JOURNAL OF PHYSICAL CHEMISTRY B  113-  (44)  14732  -14741  2009/11  [Not refereed][Not invited]
     
    A new measure is presented to quantify the local topographical feature, i.e., diversity in transitions from a state to the others, on complex networks. This measure is composed of two contributions: one is related to the number of outgoing links from a state (known as degree) and the other is related to heterogeneity in transition probabilities from a state to the others associated with the links. To illustrate the potential of the new measure, we apply it to the multiscale state space networks (SSNs) extracted directly from the single-molecule time series of protein fluctuation of the NADH:flavin oxidoreductase complex by using a recently developed technique [Li, C. B.; Yang, H.; Komatsuzaki, T. Proc. Natl. Acad, Sci. U.S.A. 2008, 105, 536]. We find that the multiscale SSN network structures dependent on the time scale of observation are not differentiated significantly in the topological feature of the SSNs where the connectivity pattern among the nodes is solely taken into account, but instead in the weighted properties of the network including the heterogeneous strengths of transitions and the resident probabilities of the nodes. The relationship of the transition heterogeneity with the anomalous diffusion observed in the single-molecule measurement is also discussed.
  • Chun-Biu Li, Mikito Toda, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  130-  (12)  2009/03  [Not refereed][Not invited]
     
    A new method is presented to study bifurcation of no-return transition states (TSs) at potential saddles for systems of many degrees of freedom (dof). The method enables us to investigate analytically when and how the no-return TS bifurcates. Our method reveals a new aspect of bifurcation for systems of many dof, i.e., the action variables of the bath dof play a role of control parameters as long as they remain approximately conserved. As an illustrative example, we demonstrate our new method by using a three atomic exchange reaction. The bifurcation of no-return TSs gives rise to a short-lived intermediate state at the saddle, which results in the overestimation of the reaction rate. Hence, the understanding of the bifurcation of the no-return TS is crucial to capture the complexity in kinetics and dynamics of the reactions. The definability of no-return TSs in many-body chemical reactions is also addressed under the occurrence of bifurcation above the reaction threshold.
  • Sei Kazuto, Li Chun Biu, Komatsuzaki Tamiki  Seibutsu Butsuri  49-  (0)  2009  [Not refereed][Not invited]
  • 小松崎 民樹  物性研究  91-  (2)  121  -130  2008/11  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • KOMATSUZAKI Tamiki  Seibutsu Butsuri  48-  (5)  282  -283  2008/09/25  [Not refereed][Not invited]
  • Hiroshi Teramoto, Tamiki Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  129-  (9)  2008/09  [Not refereed][Not invited]
     
    We revisit the concept of "remnant of invariant manifolds" originally discussed by Shirts and Reinhardt in a two degrees of freedom Henon-Heiles system [J. Chem. Phys. 77, 5204 (1982)]. This is regarded as the remnants of a destroyed invariant manifold that can dominate the transport in phase space even at high energy regions where most of all tori vanish. We present a novel technique to extract such remnants of invariants from a sea of chaos in highly nonlinear coupled molecular systems in terms of the canonical perturbation theory based on Lie transforms. As an illustrative example we demonstrate in HCN isomerization reaction that the conventional procedure based on a finite order truncation of the coordinate transformation prevent us from detecting remnants of invariants. However, our technique correctly captures the underlying remnants of invariants that shed light on the energetics of chemical reaction, that is, how the reactive mode acquires (releases) energy from (to) the other vibrational mode in order to overcome the potential barrier (to be trapped in the potential well). We also found the qualitative difference between the two potential wells, HCN and CNH, which coincides with the nearest neighbor level spacing distribution of the vibrational quantum states within the wells. (C) 2008 American Institute of Physics.
  • Hiroshi Teramoto, Tamiki Komatsuzaki  PHYSICAL REVIEW E  78-  (1)  2008/07  [Not refereed][Not invited]
     
    A technique is presented to scrutinize a piece of remnants of invariants [R. B. Shirts and W. P. Reinhardt, J. Chem. Phys. 77, 15 (1982)] buried in chaos in many degrees of freedom (DOF) dynamical systems in terms of canonical perturbation theory based on Lie transforms. The transformed canonical variables are often evaluated by the truncation of the coordinate transformation at a finite order in the original Hamiltonian system. However, the truncation of canonical variables gives rise to a loss of the symplectic property of the system. This results in apparent abrupt fluctuation of the action integrals, which yields a misinterpretation. We demonstrate, in a three-DOF Hamiltonian system of HCN isomerization reaction, that our technique can detect remnants of invariants buried in the potential well even at energies higher than the potential barrier, although the conventional truncation scheme fails to do so. This technique makes it possible to shed light on the physical insight into how the reactive mode exchanges its energy with the other modes and through which resonance the energy exchange takes place in reacting systems.
  • Akira Shojiguchi, Chun Biu Li, Tamiki Komatsuzaki, Mikito Toda  Physical Review E - Statistical, Nonlinear, and Soft Matter Physics  77-  2008/01/15  [Not refereed][Not invited]
  • Chun-Biu Li, Haw Yang, Tamiki Kornatsuzaki  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA  105-  (2)  536  -541  2008/01  [Not refereed][Not invited]
     
    Conformational dynamics of proteins can be interpreted as itinerant motions as the protein traverses from one state to another on a complex network in conformational space or, more generally, in state space. Here we present a scheme to extract a multiscale state space network (SSN) from a single-molecule time series. Analysis by this method enables us to lift degeneracy-different physical states having the same value for a measured observable-as much as possible. A state or node in the network is defined not by the value of the observable at each time but by a set of subsequences of the observable overtime. The length of the subsequence can tell us the extent to which the memory of the system is able to predict the next state. As an illustration, we investigate the conformational fluctutation dynamics probed by single-molecule electron transfer (ET), detected on a photon-by-photon basis. We show that the topographical features of the SSNs depend on the time scale of observation; the longer the time scale, the simpler the underlying SSN becomes, leading to a transition of the dynamics from anomalous diffusion to normal Brownian diffusion.
  • Sei Kazuto, Baba Akinori, Li Chun-Biu, Komatsuzaki Tamiki  Seibutsu Butsuri  48-  (0)  2008  [Not refereed][Not invited]
  • Yasuhiro Matsunaga, Tamiki Komatsuzaki  Kobunshi  57-  (2)  58  -61  2008  [Not refereed][Not invited]
     
    A novel method is proposed which quantifies collectivity emerging at coarse-grained space and time scales in multi-scale protein dynamics. This is based on the combination of the principal component (PC) and the finite size Lyapunov exponent (FSLE). This method can systematically assess the coarse-grained dynamics at different scales in the reduced PC space. As an illustrative vehicle, we apply the method to a model protein composed of 46 amino beads with three different types of residues. We show how the motion of the model protein changes depending on the space scales and the choice of degrees of freedom. In particular, anomalous superdiffusion is revealed along the first PC in the unfolded state. The implication of the existence of superdiffusion in the folding dynamics is discussed. © 2008, The Society of Polymer Science, Japan. All rights reserved.
  • SHIRAKAWA Tomohiro, GUNJI Yukio-Pegio, KOMATSUZAKI Tamiki  Planetary people  16-  (4)  322  -329  2007/12/25  [Not refereed][Not invited]
     
    惑星科学と非線形科学にはどのような接点があるのであろうか?カオスの源流は恒星力学の三体問題に端を発していることは周知の通りであるが両者の関係はそれだけではない.天文学者堀源一郎氏が開発したリー正準変換摂動理論は,カオスの発展の素地をつくっただけではなく,化学反応や蛋白質の構造変化における「偶然と必然」の原理を解き明かそうとしている.しかしながら,この問題が宇宙船の安価な惑星間航路を如何に,惑星系の重力場が存在する宇宙空間から,抽出するかという問題と等価であることは殆ど知られていない.また,NASAはDNA,粘菌といった生物計算の構築原理を2002年から10年間3千万ドルという巨額の予算を投じて研究し,次世代の宇宙探査開発に活かそうとしている.本稿ではこうした惑星科学と非線形科学との間の新しいクロストークに関連した我々の最近の研究成果を紹介する.
  • Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  99-  (23)  2007/12  [Not refereed][Not invited]
     
    A novel method is proposed to quantify collectivity at different space and time scales in multiscale dynamics of proteins. This is based on the combination of the principal component (PC) and the concept recently developed for multiscale dynamical systems called the finite size Lyapunov exponent. The method can differentiate the well-known apparent correlation along the low-indexed PCs in multidimensional Brownian systems from the correlated motion inherent to the system. As an illustration, we apply the method to a model protein of 46 amino beads with three different types of residues. We show how the motion of the model protein changes depending on the space scales and the choices of degrees of freedom. In particular, anomalous superdiffusion is revealed along the low-indexed PC in the unfolded state. The implication of superdiffusion in the process of folding is also discussed.
  • 生体系時系列データから動力学諸量を抽出する方法論(From time series of biological systems to their dynamical)
    寺本 央, 小松崎 民樹  生物物理  47-  (Suppl.1)  S41  -S41  2007/11  [Not refereed][Not invited]
  • 蛋白質の折り畳み運動を観測するための一分子測定手法の開発(Development of a technique for the investigation of folding dynamics of single proteins for extended time periods)
    木下 雅仁, 鎌形 清人, 前田 晃央, 後藤 祐児, 小松崎 民樹, 高橋 聡  生物物理  47-  (Suppl.1)  S139  -S139  2007/11  [Not refereed][Not invited]
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda  PHYSICAL REVIEW E  76-  (5)  2007/11  [Not refereed][Not invited]
     
    The fractional behavior is presented for a minimal Hamiltonian system of three degrees of freedom which describes reaction processes. The model has a double-well potential where the Arnold web within the well is nonuniform. The survival probability within the well exhibits power law decay in addition to exponential decay. Moreover, the trajectories of the power law decay exhibit 1/f spectra and subdiffusion in the action space, while the trajectories of the exponential decay show Lorentzian spectra and normal diffusion. Transient features of these statistical properties reveal the dynamical connection, i.e., how trajectories approach to (depart from) the Arnold web from (to) the region around the potential saddle. In particular, a wavelet analysis enables us to extract transient features of the resonances. Based on these results, we suggest that resonance junctions including higher-order resonances are important for understanding the dynamical origins of the fractional behavior in reaction processes.
  • PHYS 583-Capturing the multiple-time-scale dynamical state-network buried in the time series of single molecule experiments
    Chun Biu Li, Tamiki Komatsuzaki  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  234-  2007/08  [Not refereed][Not invited]
  • Shinnosuke Kawai, Yo Fujimura, Okitsugu Kajimoto  PHYSICAL REVIEW A  75-  (2)  2007/02  [Not refereed][Not invited]
     
    One of the most fundamental problems in studying general Hamiltonian systems with many degrees of freedom is to extract a low-dimensional subsystem including the essential dynamics. In this paper, a new partial normal form (PNF) method is developed to reduce the number of coupling terms in the Hamiltonian and to simplify the dynamics analyses. The PNF method allows one to decouple many unimportant bath modes as well as the reactive mode from the system by assessing the significance of the coupling terms. The method is applied to the chemical reaction O(D-1)+N2O -> NO+NO, which was found to exhibit efficient energy exchange between the two NO stretching modes despite the short lifetime of the reaction intermediate [S. Kawai , J. Chem. Phys. 124, 184315 (2006)]. Through the analysis of the two-dimensional PNF Hamiltonian subsystem, it is found that the motion of the subsystem preserves the "normal mode picture" of the symmetric and antisymmetric NO stretching modes despite its high energy. Then the vibrational energy, initially localized in the newly formed NO bond, is transferred to the reactants' NO bond through the beating between the symmetric and antisymmetric stretching modes. The preservation of the normal mode picture and the short period of the beating explain the fast energy exchange between the two NO bonds. This successful application proves that the PNF method can extract the essential small subspace from many-degrees-of-freedom Hamiltonian systems.
  • Teramoto Hiroshi, Komatsuzaki Tamiki  Seibutsu Butsuri  47-  (0)  2007  [Not refereed][Not invited]
  • Kinoshita Masahito, Kamagata Kiyoto, Maeda Akio, Goto Yuji, Komatsuzaki Tamiki, Takahashi Satoshi  Seibutsu Butsuri  47-  (0)  2007  [Not refereed][Not invited]
  • Sei Kazuto, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Shojiguchi A, Li Chun Biu, Komatsuzaki T, Toda M  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Sei Kazuto, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Demirplak Mustafa, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Noda Satoshi, Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Matsunaga Yasuhiro, Li Chun-Biu, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  62-  (0)  2007  [Not refereed][Not invited]
  • Gareth J. Rylance, Roy L. Johnston, Yasuhiro Matsunaga, Chun-Biu Li, Akinori Baba, Tamiki Komatsuzaki  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA  103-  (49)  18551  -18555  2006/12  [Not refereed][Not invited]
     
    A scheme for visualizing and quantifying the complexity of multidimensional energy landscapes and multiple pathways is presented employing principal component-based disconnectivity graphs and the Shannon entropy of relative "sizes" of superbasins. The principal component-based disconnectivity graphs incorporate a metric relationship between the stationary points of the system, which enable us to capture not only the actual assignment of the superbasins but also the size of each superbasin in the multidimensional configuration space. The landscape complexity measure quantifies the degree of topographical complexity of a multidimensional energy landscape and tells us at which energy regime branching of the main path becomes significant, making the system more likely to be kinetically trapped in local minima. The path complexity measure quantifies the difficulty encountered by the system to reach a connected local minimum by the path in question, implying that the more significant the branching points along the path the more difficult it is to end up in the desired local minimum. As an illustrative example, we apply this analysis to two kinds of small model protein systems exhibiting a highly frustrated and an ideal funnel-like energy landscape.
  • C. B. Li, A. Shojiguchi, M. Toda, T. Komatsuzaki  Few-Body Systems  40-  (1-2)  129  2006/12  [Not refereed][Not invited]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (12)  2006/09  [Not refereed][Not invited]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (12)  2006/09  [Not refereed][Not invited]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (2)  2006/07  [Not refereed][Not invited]
     
    No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above the reaction threshold, even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom starts to lose locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in the high-energy regime above the reaction threshold.
  • A. Shojiguchi, A. Baba, C. B. Li, T. Komatsuzaki, M. Toda  LASER PHYSICS  16-  (7)  1097  -1106  2006/07  [Not refereed][Not invited]
     
    Our motivation is to understand how, in chemical reactions, the reaction coordinate effectively gains dynamical energy from the other degrees of freedom (i.e., bath coordinates) avoiding thermalization of the redistributed energy. In such a system, the phase space structure should be not homogeneous; i.e., the system is never ergodic. In this study, we introduce a way to capture the inhomogeneity of the phase space and to monitor energy transfers among their partial degrees of freedom in nonergodic systems using wavelet analysis and a picture of the Arnold web. First, we examine several simple energy transfer processes, i.e., a motion on a resonance line, between resonance lines, and around a resonance junction in a simple three-degree-of-freedom (DOF) system and show how the elemental processes of the intramolecular vibrational energy redistribution (IVR) are detected by our tools. We especially note that the structure of the higher order resonance of the system can be detected by wavelet analysis and motion in the action space. Next, we analyze a reaction process in a simple Hamiltonian system of 3 DOF with a double-well potential, i.e., a system with a transition state of the center-saddle-center type, and detect energy transfers in the reactive process. The aim of the study is to propose a way to characterize the inhomogeneity of the phase space, e.g., the reactive doorway, which leads to controllability of the chemical reaction by light, i.e., control of the reaction by selectively preparing an initial state in the reactive doorway by optical excitation.
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (2)  2006/07  [Not refereed][Not invited]
     
    No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above the reaction threshold, even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom starts to lose locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in the high-energy regime above the reaction threshold.
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (2)  2006/07  [Not refereed][Not invited]
     
    No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above the reaction threshold, even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom starts to lose locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in the high-energy regime above the reaction threshold.
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki  PHYSICAL REVIEW LETTERS  97-  (2)  2006/07  [Not refereed][Not invited]
     
    No-return transition states (TSs) defined in multidimensional phase space, where recrossing trajectories through the commonly used "configuration" TS pass only once, robustly exist up to a moderately high-energy regime above the reaction threshold, even when nonlinear resonances among the bath degrees of freedom perpendicular to the reaction coordinate result in local chaos. However, at much higher energy when global chaos appears in the bath space, the separability of the reaction coordinate from the bath degrees of freedom starts to lose locally. In the phase space near the saddles, it is found that the slower the system passes the TS, the more recrossing trajectories reappear. Their implications and mechanisms are discussed concerning to what extent one can define no-return TSs in the high-energy regime above the reaction threshold.
  • CB Li, A Shojiguchi, M Toda, T Komatsuzaki  FEW-BODY SYSTEMS  38-  (2-4)  173  -179  2006/06  [Not refereed][Not invited]
     
    We present a partial normalization procedure of Lie canonical perturbation theory to elucidate the phase space geometry of the transition state in the multidimensional phase space for a wide range of energy above the threshold. State selectivity and dynamical correlation along the evolution of reactions will also be discussed.
  • Li Chun Biu, Toda Mikito, Komatsuzaki Tamiki  物性研究  86-  (1)  77  -81  2006/04  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • 渕上 壮太郎, 小松崎 民樹, 戸田 幹人  物性研究  86-  (1)  37  -42  2006/04  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。研究会報告
  • 星野 恭子, 松永 康佑, Lylance Gareth J, Johnston Roy L, Wales David J, 小松崎 民樹  物性研究  86-  (1)  117  -122  2006/04  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • 納多 哲史, 馬場 昭典, 小松崎 民樹  物性研究  86-  (1)  123  -129  2006/04  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • 生体分子の一分子時系列解析: 測定値の分布関数による状態推定法
    2006  [Not refereed][Not invited]
  • 1分子時系列解析と分子科学
    2006  [Not refereed][Not invited]
  • 一分子時系列情報に潜む状態遷移ネットワークの構成論と可視化技術の開発
    2006  [Not refereed][Not invited]
  • Causal structures ofε-machine constructed from time series: Analogy with dynamical systems theory
    2006  [Not refereed][Not invited]
  • 測定値の分布形状に基づく一分子時系列解析法:局所エルゴード状態の推定と自由エネルギー面の再構築
    2006  [Not refereed][Not invited]
  • 1分子時系列情報に基づく反応ネットワーク構造の構成論とその複雑さ解析
    2006  [Not refereed][Not invited]
  • 測定値の分布形状に基づく一分子時系列解析法:局所エルゴード状態の推定と自由エネルギー面の再構築
    2006  [Not refereed][Not invited]
  • 1分子時系列情報から解読される生体分子系の動態構造
    2006  [Not refereed][Not invited]
  • 1分子計測時系列情報から読み取るたんぱく質系の動的構造
    2006  [Not refereed][Not invited]
  • 時系列情報から再構成する状態空間構造と化学反応動力学
    2006  [Not refereed][Not invited]
  • 分子異性化反応のモデルにおける異常拡散
    2006  [Not refereed][Not invited]
  • Randomness and Memory in Single Molecule Time Series
    2006  [Not refereed][Not invited]
  • Extracting Dynamics from Time Series Data of single Molecule Experiments on a photon-by-photon Basis
    2006  [Not refereed][Not invited]
  • A discrete wavelet time series analysis;the hierarchy of dynamics of biomolecules
    2006  [Not refereed][Not invited]
  • A construction of the underlying free energy landscape from single molecule time series
    2006  [Not refereed][Not invited]
  • Extracting Protein Conformational Dynamics on a Photon-by-Photon Basis in Single Molecule Electron Transfer
    2006  [Not refereed][Not invited]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006  [Not refereed][Not invited]
  • A Local ergodic state analysis of single molecule time series
    2006  [Not refereed][Not invited]
  • Construction of Effective Free Energy Landscape from Single Molecule Time Series of Biomolecules
    2006  [Not refereed][Not invited]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006  [Not refereed][Not invited]
  • A Local ergodic state analysis of single molecule time series
    2006  [Not refereed][Not invited]
  • What can one learn about the underlying free energy landscape or dynamical structure from single molecule time series?
    2006  [Not refereed][Not invited]
  • Dynamical Hierarchy of Transitions in Chemical Reactions
    2006  [Not refereed][Not invited]
  • Water Field Dynamics in the Vicinity of Proteins
    2006  [Not refereed][Not invited]
  • Mechanism of fast energy exchange between two NO vibrations in a short lifetime path of O(1D)+N2O -> NO+NO
    Physical Review A  in press-  2006  [Not refereed][Not invited]
  • Geometrical Structure buried in the Phase Space of Stochastic Structural Transition
    物性研究  86-1,77-81-  2006  [Not refereed][Not invited]
  • Dynamical Foundation and Limitations of Statistical Reaction Theory
    Communications in Nonlinear Science and Numerical Simulation  in press-  2006  [Not refereed][Not invited]
  • 複雑な多谷ポテンシャルエネルギー面上で生起する動力学諸問題III─タンパク質とその周辺─(研究会報告)
    物性研究  86-  2006  [Not refereed][Not invited]
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    物性研究  86-1,123-129-  2006  [Not refereed][Not invited]
  • タンパク質エネルギー地形における構造多様性と多次元エネルギー地形の新しい可視化手法」
    物性研究  86-1,117-122-  2006  [Not refereed][Not invited]
  • 「複雑な多谷ポテンシャルエネルギー面上で生起する動力学諸問題III─タンパク質とその周辺─(研究会報告)」
    物性研究  86-1,37-154-  2006  [Not refereed][Not invited]
  • Randomness and Memory in Single Molecule Time Series
    2006  [Not refereed][Not invited]
  • Extracting Dynamics from Time Series Data of single Molecule Experiments on a photon-by-photon Basis
    2006  [Not refereed][Not invited]
  • A discrete wavelet time series analysis;the hierarchy of dynamics of biomolecules
    2006  [Not refereed][Not invited]
  • A construction of the underlying free energy landscape from single molecule time series
    2006  [Not refereed][Not invited]
  • Extracting Protein Conformational Dynamics on a Photon-by-Photon Basis in Single Molecule Electron Transfer
    2006  [Not refereed][Not invited]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006  [Not refereed][Not invited]
  • A Local ergodic state analysis of single molecule time series
    2006  [Not refereed][Not invited]
  • Construction of Effective Free Energy Landscape from Single Molecule Time Series of Biomolecules
    2006  [Not refereed][Not invited]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006  [Not refereed][Not invited]
  • A Local ergodic state analysis of single molecule time series
    2006  [Not refereed][Not invited]
  • What can one learn about the underlying free energy landscape or dynamical structure from single molecule time series?
    2006  [Not refereed][Not invited]
  • Dynamical Hierarchy of Transitions in Chemical Reactions
    2006  [Not refereed][Not invited]
  • Water Field Dynamics in the Vicinity of Proteins
    2006  [Not refereed][Not invited]
  • Mechanism of fast energy exchange between two NO vibrations in a short lifetime path of O(1D)+N2O -> NO+NO
    Physical Review A  in press-  2006  [Not refereed][Not invited]
  • Dynamical Foundation and Limitations of Statistical Reaction Theory
    Communications in Nonlinear Science and Numerical Simulation  in press-  2006  [Not refereed][Not invited]
  • Sei Kazuto, Baba Akinori, Li Chun Biu, Komatsuzaki Tamiki  Seibutsu Butsuri  46-  (2)  2006  [Not refereed][Not invited]
  • Noda Satoshi, Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • Li Chun Biu, Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • Shojiguchi A, Li Chun Biu, Komatsuzaki T, Toda M  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • Shojiguchi A, Li Chun Biu, Komatsuzaki T, Toda M  Meeting Abstracts of the Physical Society of Japan  61-  (0)  2006  [Not refereed][Not invited]
  • CB Li, Y Matsunaga, M Toda, T Komatsuzaki  JOURNAL OF CHEMICAL PHYSICS  123-  (18)  2005/11  [Not refereed][Not invited]
     
    By using the HCN/CNH isomerization reaction as an illustrative vehicle of chemical reactions on multisaddle energy landscapes, we give explicit visualizations of molecular motions associated with a straight-through reaction tube in the phase space inside which all reactive trajectories pass from one basin to another, with eliminating recrossing trajectories in the configuration space. This visualization provides us with a chemical intuition of how chemical species "walk along" the reaction-rate slope in the multidimensional phase space compared with the intrinsic reaction path in the configuration space. The distinct nonergodic features in the two different HCN and CNH wells can be easily demonstrated by a section of Poincare surface of section in those potential minima, which predicts in a priori the pattern of trajectories residing in the potential well. We elucidate the global phase-space structure which gives rise to the non-Markovian dynamics or the dynamical correlation of sequential multisaddle chemical reactions. The phase-space structure relevant to the controllability of the product state in chemical reactions is also discussed. (c) 2005 American Institute of Physics.
  • Mikito Toda, Tamiki Komatsuzaki, Tetsuro Konishi, R. Stephen Berry, Stuart A. Rice, Stuart A. Rice  Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems  130-  2005/05/12  [Not refereed][Not invited]
  • Mikito Toda, Tamiki Komatsuzaki, Tetsuro Konishi, R. Stephen Berry, Stuart A. Rice  Geometric Structures of Phase Space in Multidimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems  130-  1  -542  2005/05/12  [Not refereed][Not invited]
     
    This series provides the chemical physics field with a forum for critical, authoritative evaluations of advances in every area of the discipline. Volume 130 in the series continues to report recent advances with significant, up-to-date chapters by internationally recognized researchers.
  • T Komatsuzaki, K Hoshino, Y Matsunaga, GJ Rylance, RL Johnston, DJ Wales  JOURNAL OF CHEMICAL PHYSICS  122-  (8)  2005/02  [Not refereed][Not invited]
     
    A scheme to approximate the multidimensional potential energy landscape in terms of a minimal number of degrees of freedom is proposed using a linear transformation of the original atomic Cartesian coordinates. For one particular off-lattice model protein the inherent frustration can only be reproduced satisfactorily when a relatively large number of coordinates are employed. However, when this frustration is removed in a G (o) over bar -type model, the number of coordinates required is significantly lower, especially around the global potential energy minimum. To aid our interpretation of the results we consider modified disconnectivity graphs where a measure of the structural diversity and a metric relation between the stationary points are incorporated. (C) 2005 American Institute of Physics.
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    2005  [Not refereed][Not invited]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005  [Not refereed][Not invited]
  • 1分子時系列の背後に潜む自由エネルギー曲面を如何に再構成するか?
    2005  [Not refereed][Not invited]
  • 離散ウェーブレット変換を用いた一分子時系列における動力学の階層性の解析(The dynamical hierarchy of single molecule time series using a discrete wavelet transform analysis)
    2005  [Not refereed][Not invited]
  • 生体分子の構造転移に伴う近傍の「水の場」の協同的運動(Collective motion of water field in the vicinity of the structural transition of biomolecule)
    2005  [Not refereed][Not invited]
  • 多次元エネルギー地形の状態空間構造に基づく生体分子系の構造転移ダイナミクスの原理的理解(Understanding of the Origin of Transitions in Biological Molecules from the State Space Structures on Multi-dimensional Energy Landscapes)
    2005  [Not refereed][Not invited]
  • 一分子時系列からの多次元自由エネルギー地形の再構築と分子記憶
    2005  [Not refereed][Not invited]
  • タンパク質系の協調的運動に対するカオス時系列解析 (Chaotic time series analysis of collective motions in proteins)
    2005  [Not refereed][Not invited]
  • 粗視化された「水の場」を用いたポリアラニンの構造転移に伴う水の集団運動の解析
    2005  [Not refereed][Not invited]
  • 生体分子の一分子時系列情報に基づく遷移配列解析: 自由エネルギー面の再構成と分子記憶
    2005  [Not refereed][Not invited]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005  [Not refereed][Not invited]
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    2005  [Not refereed][Not invited]
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    2005  [Not refereed][Not invited]
  • 生体分子の構造変化における周囲の水の動態場に観測される流体力学的構造
    2005  [Not refereed][Not invited]
  • 生体分子と粗視化した水の動的相互作用の抽出
    2005  [Not refereed][Not invited]
  • HCNの異性化反応の非エルゴード性
    2005  [Not refereed][Not invited]
  • 1分子時系列情報から構成される状態空間構造:反応遷移ネットワーク構造
    2005  [Not refereed][Not invited]
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    2005  [Not refereed][Not invited]
  • 化学反応はなぜ生起するのか?:遷移状態概念再考
    2005  [Not refereed][Not invited]
  • 生体分子と粗視化した水の動的相互作用の抽出
    2005  [Not refereed][Not invited]
  • 高次元相空間における法双曲的不変多様体・安定(不安定)不変多様体が織り成す化学反応ネットワーク描像:蛋白質フォールディングのおける一方向性の力学的原理
    2005  [Not refereed][Not invited]
  • なぜ、如何にして反応は生起するのか?:化学反応における選択性と統計性
    2005  [Not refereed][Not invited]
  • 一分子時系列に基づく多次元自由エネルギーランドスケープと分子記憶
    2005  [Not refereed][Not invited]
  • 1分子時系列情報から構成される状態空間構造:反応遷移ネットワーク構造
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy in Transitions of ChemicalReactions:Definability of No-return Transition State
    2005  [Not refereed][Not invited]
  • How does single molecule time series tell us about the underlying multidimensional free energy and state space landscapes?
    2005  [Not refereed][Not invited]
  • Complexity of Dynamics on Multidimensional Energy Landscapes in Chemical reactions & Proteins
    2005  [Not refereed][Not invited]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005  [Not refereed][Not invited]
  • A construction of multidimensional free energy landscape from an ensemble of single molecule time series of biomolecules
    2005  [Not refereed][Not invited]
  • Vibrational energy redistribution via geometrical structures in the multi-dimensional phase space of chemical reaction
    2005  [Not refereed][Not invited]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005  [Not refereed][Not invited]
  • Geometrical structure of the multidimensional phase space transport in chemical reactions
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy in Transitions of Chemical Reactions
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy of Transitions in Chemical Reactions and Protein Dynamics
    2005  [Not refereed][Not invited]
  • Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction
    物性研究  84-3、481-482-  2005  [Not refereed][Not invited]
  • Regularity in Chaotic Transitions on Two-Basin Landscapes' eds. by M.Toda, T.Komatsuzaki, T.Konishi, R.S. Berry and S.A. Rice,John-Wiley & Sons, Inc.
    Advances in Chemical Physics  130-Part A 143-170-  2005  [Not refereed][Not invited]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005  [Not refereed][Not invited]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy in Transitions of ChemicalReactions:Definability of No-return Transition State
    2005  [Not refereed][Not invited]
  • How does single molecule time series tell us about the underlying multidimensional free energy and state space landscapes?
    2005  [Not refereed][Not invited]
  • Complexity of Dynamics on Multidimensional Energy Landscapes in Chemical reactions & Proteins
    2005  [Not refereed][Not invited]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005  [Not refereed][Not invited]
  • A construction of multidimensional free energy landscape from an ensemble of single molecule time series of biomolecules
    2005  [Not refereed][Not invited]
  • Vibrational energy redistribution via geometrical structures in the multi-dimensional phase space of chemical reaction
    2005  [Not refereed][Not invited]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005  [Not refereed][Not invited]
  • Geometrical structure of the multidimensional phase space transport in chemical reactions
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy in Transitions of Chemical Reactions
    2005  [Not refereed][Not invited]
  • Dynamical Hierarchy of Transitions in Chemical Reactions and Protein Dynamics
    2005  [Not refereed][Not invited]
  • Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction
    2005  [Not refereed][Not invited]
  • Regularity in Chaotic Transitions on Two-Basin Landscapes' eds. by M.Toda, T.Komatsuzaki, T.Konishi, R.S. Berry and S.A. Rice,John-Wiley & Sons, Inc.
    130-Part A 143-170-  2005  [Not refereed][Not invited]
  • Toda M, Komatsuzaki T  Seibutsu Butsuri  45-  (0)  2005  [Not refereed][Not invited]
  • Matsunaga Y, Biu Li Chun, Komatsuzaki T  Seibutsu Butsuri  45-  (0)  2005  [Not refereed][Not invited]
  • Noda S, Baba A, Komatsuzaki T  Seibutsu Butsuri  45-  (0)  2005  [Not refereed][Not invited]
  • Sato S, Baba A, Komatsuzaki T  Seibutsu Butsuri  45-  (0)  2005  [Not refereed][Not invited]
  • Baba A, Komatsuzaki T  Seibutsu Butsuri  45-  (0)  2005  [Not refereed][Not invited]
  • Noda Satoshi, Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  60-  (0)  2005  [Not refereed][Not invited]
  • Baba Akinori, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  60-  (0)  2005  [Not refereed][Not invited]
  • 生体高分子の構造転移キネテックスにおけるRuggednessによる加速現象
    2004  [Not refereed][Not invited]
  • 生体分子系の構造転移ダイナミックスにおける複雑時系列解析
    2004  [Not refereed][Not invited]
  • 生体分子ダイナミクスの状態空間幾何学:1分子時系列情報からわかること
    2004  [Not refereed][Not invited]
  • 化学反応の動力学とカオスー現状と将来
    2004  [Not refereed][Not invited]
  • タンパク質エネルギー地形における自由度の縮約化と時系列解析
    2004  [Not refereed][Not invited]
  • タンパク質エネルギー地形における構造多様性と多次元エネルギー地形の新しい可視化手法
    2004  [Not refereed][Not invited]
  • 「相空間構造に基づく多遷移反応動力学とメソスケールで発現する新規なダイナミックス」特定領域「強光子場」
    2004  [Not refereed][Not invited]
  • What can a Single Molecule Time Series Data Tell Us? -Regularity in Structural Transitions on MultiBasin Energy Landscapes of Proteins-
    2004  [Not refereed][Not invited]
  • Regularity in Chaotic Tramsitions on Multi-Basin Energy Landscapes
    2004  [Not refereed][Not invited]
  • How can We Extract Dynamical Information from Time Series Data?
    2004  [Not refereed][Not invited]
  • Geometrical Structure of Phase Space for Chemical Reaction Dynamics: What Kinds of Molecular Motions are Associated with Phase Space Modes in Chaos?
    2004  [Not refereed][Not invited]
  • Geometrical Structure Buried in the Phase space of Stochastic Structural Transition: Perspectives from Time Series Analysis
    2004  [Not refereed][Not invited]
  • Y Matsunaga, T Komatsuzaki  SLOW DYNAMICS IN COMPLEX SYSTEMS  708-  342  -343  2004  [Not refereed][Not invited]
     
    Using a novel method for determining the time scale for the self-averaging of properties of many body systems, the effective ergodic behavior of a coarse-grained protein model was investigated in terms of both the chemical characters and the principal components. The ergodic behavior was examined in detail with a focus on the time scale needed to obtain effective ergodicity.
  • Y Matsunaga, KS Kostov, T Komatsuzaki  SLOW DYNAMICS IN COMPLEX SYSTEMS  708-  302  -305  2004  [Not refereed][Not invited]
     
    We analyze time series of potential energy fluctuations and principal components at several temperatures for two kinds of off-lattice 46-bead models that have two distinctive energy landscapes. The less-frustrated "funnel" energy landscape brings about stronger nonstationary behavior of the potential energy fluctuations at the folding temperature than the other, rather frustrated energy landscape at the collapse temperature. By combining principal component analysis with an embedding nonlinear time-series analysis, it is shown that the fast fluctuations with small amplitudes of 70-80% of the principal components cause the time series to become almost "random" in only 100 simulation steps. However, the stochastic feature of the principal components tends to be suppressed through a wide range of degrees of freedom at the transition temperature.
  • A coarse-graining of energy landscape of proteins - Structural stability of the most stable states
    K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki  SLOW DYNAMICS IN COMPLEX SYSTEMS  708-  344  -345  2004  [Not refereed][Not invited]
     
    The minimal sets of degrees of freedom, to persist the multidimensional topographical feature are investigated for the funnel, and frustrated energy landscapes of proteins. The robustness of local energy topographies near the global energy minimum structures against a perturbation is also discussed.
  • What can a Single Molecule Time Series Data Tell Us? -Regularity in Structural Transitions on MultiBasin Energy Landscapes of Proteins-
    2004  [Not refereed][Not invited]
  • Regularity in Chaotic Tramsitions on Multi-Basin Energy Landscapes
    2004  [Not refereed][Not invited]
  • How can We Extract Dynamical Information from Time Series Data?
    2004  [Not refereed][Not invited]
  • Geometrical Structure of Phase Space for Chemical Reaction Dynamics: What Kinds of Molecular Motions are Associated with Phase Space Modes in Chaos?
    2004  [Not refereed][Not invited]
  • Geometrical Structure Buried in the Phase space of Stochastic Structural Transition: Perspectives from Time Series Analysis
    2004  [Not refereed][Not invited]
  • A coarse-graining of energy landscape of proteins - Structural stability of the most stable states
    K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki  SLOW DYNAMICS IN COMPLEX SYSTEMS  708-  344  -345  2004  [Not refereed][Not invited]
     
    The minimal sets of degrees of freedom, to persist the multidimensional topographical feature are investigated for the funnel, and frustrated energy landscapes of proteins. The robustness of local energy topographies near the global energy minimum structures against a perturbation is also discussed.
  • K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki  SLOW DYNAMICS IN COMPLEX SYSTEMS  708-  344  -345  2004  [Not refereed][Not invited]
     
    The minimal sets of degrees of freedom, to persist the multidimensional topographical feature are investigated for the funnel, and frustrated energy landscapes of proteins. The robustness of local energy topographies near the global energy minimum structures against a perturbation is also discussed.
  • Shimono M, Komatsuzaki T  Seibutsu Butsuri  44-  (0)  2004  [Not refereed][Not invited]
  • Extracting dynamical information about protein folding from time series analysis.
    K Kostov, M Toda, Y Matsunaga, T Komatsuzaki  ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY  226-  U427  -U427  2003/09  [Not refereed][Not invited]
  • 祖視化されたスケールで現れる隠れたコヒーレンス:46ビーズ蛋白質おもちゃの場合・Steven Chuらのリボザイムのdocked-undocked state間転移の研究の紹介
    2003  [Not refereed][Not invited]
  • 1分子時系列情報に基づく生体分子の構造転移パスウェイの多重性・多型性解析
    2003  [Not refereed][Not invited]
  • タンパク質フォールディングのダイナミックス:主成分空間のエルゴード性
    2003  [Not refereed][Not invited]
  • タンパク質エネルギー地形における自由度の縮約化
    2003  [Not refereed][Not invited]
  • タンパク質フォールディングのダイナミックス:主成分空間のエルゴード性
    2003  [Not refereed][Not invited]
  • 1分子時系列情報に基づく生体分子の構造転移パスウェイの多重性・多型性解析
    2003  [Not refereed][Not invited]
  • 水の場としての集団運動と生体分子の構造転移ダイナミックス
    2003  [Not refereed][Not invited]
  • 生体分子時系列情報からの状態空間の再構成と主成分解析
    2003  [Not refereed][Not invited]
  • 1分子時系列の背後に潜む自由エネルギー曲面を如何に再構成するか?
    2003  [Not refereed][Not invited]
  • Matsunaga Y, Komatsuzaki T  Seibutsu Butsuri  43-  (0)  2003  [Not refereed][Not invited]
  • Hoshino Kyoko, Matsunaga Ysuhiro, Koga Nobuyasu, Takada Shoji, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  58-  (0)  2003  [Not refereed][Not invited]
  • Matsunaga Yasuhiro, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  58-  (0)  2003  [Not refereed][Not invited]
  • Komatsuzaki Tamiki, Matsunaga Yasuhiro, Toda Mikito  Meeting Abstracts of the Physical Society of Japan  58-  (0)  2003  [Not refereed][Not invited]
  • KOMATSUZAKI Tamiki, MATSUNAGA Yasuhiro  Seibutsu Butsuri  42-  (6)  285  -289  2002/11/25  [Not refereed][Not invited]
     
    The observed kinetics of protein folding is a consequence of averaging over an ensemble of many activated barrier crossings with multiple time scales. The future of the recent remarkable experimental developments in single molecule spectroscopy holds great promise to reveal the complexity of protein folding dynamics. A few theoretical possible means to address and clarify the dynamical complexity such as abnormal diffusion of a protein are presented.<br>
  • T Komatsuzaki, RS Berry  JOURNAL OF PHYSICAL CHEMISTRY A  106-  (45)  10945  -10950  2002/11  [Not refereed][Not invited]
     
    A new dynamical propensity rule for transitions of a system crossing the barrier from one potential minimum to one another is derived from dynamical system theory. The rule is based on the existence of a no-return dividing hypersurface in the system's phase space in the vicinity of saddles of the multidimensional potential surface of a strongly coupled, chaotic system. We present numerical evidence of the rule's validity by applying it to the rearrangements of a cluster of six argon atoms.
  • Y Matsunaga, KS Kostov, T Komatsuzaki  JOURNAL OF PHYSICAL CHEMISTRY A  106-  (45)  10898  -10907  2002/11  [Not refereed][Not invited]
     
    We analyze time series of potential energy fluctuations and principal components at several temperatures for two kinds of off-lattice 46-bead models that have two distinctive energy landscapes. The less-frustrated "funnel" energy landscape brings about stronger nonstationary behavior of the potential energy fluctuations at the folding temperature than the other, rather frustrated energy landscape at the collapse temperature with a significant 1/f(alpha)(alpha approximate to 1.5) noise structure and a significant deviation of the Allan variance from the law of large numbers. The principal components are analyzed by an embedding nonlinear time-series analysis. The fast fluctuations with small amplitudes of similar to70-80% of the principal components cause the time series to become almost "random" in only 100 simulation steps. However, the stochastic feature of the principal components tends to be suppressed through a wide range of degrees of freedom at the transition temperature.
  • 小松崎 民樹  物性研究  78-  (4)  354  -364  2002/07  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • 笹井 理生, 小松崎 民樹, 戸田 幹人  物性研究  78-  (4)  475  -509  2002/07  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • Tamiki Komatsuzaki, R. Stephen Berry  Journal of Chemical Physics  116-  (2)  862  2002/01/08  [Not refereed][Not invited]
  • T Komatsuzaki, RS Berry  ADVANCES IN CHEMICAL PHYSICS, VOL 123  123-  79  -152  2002  [Not refereed][Not invited]
  • Matsunaga Y, Komatsuzaki T  Seibutsu Butsuri  42-  (2)  2002  [Not refereed][Not invited]
  • T Komatsuzaki, RS Berry  JOURNAL OF CHEMICAL PHYSICS  115-  (9)  4105  -4117  2001/09  [Not refereed][Not invited]
     
    We recently developed a new method to extract a many-body phase-space dividing surface, across which the transmission coefficient for the classical reaction path is unity. The example of isomerization of a 6-atom Lennard-Jones cluster showed that the action associated with the reaction coordinate is an approximate invariant of motion through the saddle regions, even at moderately high energies, at which most or all the other modes are chaotic [J. Chem. Phys. 105, 10838 (1999); Phys. Chem. Chem. Phys. 1, 1387 (1999)]. In the present article, we propose a new algorithm to analyze local invariances about the transition state of N-particle Hamiltonian systems. The approximate invariants of motion associated with a reaction coordinate in phase space densely distribute in the sea of chaotic modes in the region of the transition state. Using projections of distributions in only two principal coordinates, one can grasp and visualize the stable and unstable invariant manifolds to and from a hyperbolic point of a many-body nonlinear system, like those of the one-dimensional, integrable pendulum. This, in turn, reveals a new type of phase space bottleneck in the region of a transition state that emerges as the total energy increases, which may trap a reacting system in that region. (C) 2001 American Institute of Physics.
  • T Komatsuzaki, RS Berry  PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA  98-  (14)  7666  -7671  2001/07  [Not refereed][Not invited]
     
    How a reacting system climbs through a transition state during the course of a reaction has been an intriguing subject for decades. Here we present and quantify a technique to identify and characterize local invariances about the transition state of an IV-particle Hamiltonian system, using Lie canonical perturbation theory combined with microcanonical molecular dynamics simulation. We show that at least three distinct energy regimes of dynamical behavior occur in the region of the transition state, distinguished by the extent of their local dynamical invariance and regularity. Isomerization of a six-atom Lennard-Jones cluster illustrates this: up to energies high enough to make the system manifestly chaotic, approximate invariants of motion associated with a reaction coordinate in phase space imply a many-body dividing hypersurface in phase space that is free of recrossings even in a sea of chaos. The method makes it possible to visualize the stable and unstable invariant manifolds leading to and from the transition state, i.e., the reaction path in phase space, and how this regularity turns to chaos with increasing total energy of the system. This, in turn, illuminates a new type of phase space bottleneck in the region of a transition state that emerges as the total energy and mode coupling increase, which keeps a reacting system increasingly trapped in that region.
  • 小松崎 民樹  物性研究  76-  (1)  1  -44  2001/04  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。
  • Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  56-  (0)  2001  [Not refereed][Not invited]
  • Matsunaga Yasuhiro, Komatsuzaki Tamiki  Meeting Abstracts of the Physical Society of Japan  56-  (0)  2001  [Not refereed][Not invited]
  • T Komatsuzaki, RS Berry  JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM  506-  55  -70  2000/07  [Not refereed][Not invited]
     
    We analyze local regularities in the regions of transition states of a 6-atom Lennard-Jones cluster to demonstrate how one can choose a non-recrossing reaction path in phase space along which the transmission coefficient for the classical reaction path is unity from threshold up to a moderately high energy, above which the transition state is chaotic, and how one can picture the nonlinear, full-phase-space character of the dividing hypersurface by projecting it into spaces of only a few dimensions. These overcome one of the long-standing ambiguities in chemical reaction theories, the recrossing problem, up to moderately high energies, and make transition state theory more generalized, applicable even in cases in which apparent recrossings spoil the conventional theory. (C) 2000 Elsevier Science B.V. All rights reserved.
  • T Komatsuzaki, RS Berry  JOURNAL OF CHEMICAL PHYSICS  110-  (18)  9160  -9173  1999/05  [Not refereed][Not invited]
     
    We scrutinize the saddle crossings of a simple cluster of six atoms to show (a) that it is possible to choose a coordinate system in which the transmission coefficient for the classical reaction path is unity at all energies up to a moderately high energy, above which the transition state is chaotic; (b) that at energies just more than sufficient to allow passage across the saddle, all or almost all the degrees of freedom of the system are essentially regular in the region of the transition state; and (c) that the degree of freedom associated with the reaction coordinate remains essentially regular through the region of the transition state, even to moderately high energies. Microcanonical molecular dynamics simulation of Ar-6 bound by pairwise Lennard-Jones potentials reveals the mechanics of passage. We use Lie canonical perturbation theory to construct the nonlinear transformation to a hyperbolic coordinate system which reveals these regularities. This transform "rotates away'' the recrossings and nonregular behavior, especially of the motion along the reaction coordinate, leaving a coordinate and a corresponding dividing surface in phase space which minimize recrossings and mode-mode mixing in the transition state region. The action associated with the reactive mode tends to be an approximate invariant of motion through the saddle crossings throughout a relatively wide range of energy. Only at very low energies just above the saddle could any other approximate invariants of motion be found for the other, nonreactive modes. No such local invariants appeared at energies at which the modes are all chaotic and coupled to one another. (C) 1999 American Institute of Physics. [S0021-9606(99)50918-5].
  • T Komatsuzaki, RS Berry  PHYSICAL CHEMISTRY CHEMICAL PHYSICS  1-  (6)  1387  -1397  1999/03  [Not refereed][Not invited]
     
    Reaction trajectories reveal regular behavior in the reactive degree of freedom and unit transmission coefficients as the system crosses the saddle region separating reactants and products. The regularity persists up to moderately high energies, even when all other degrees of freedom are chaotic. This behavior is apparent in a representation obtained by transformation with Lie canonical perturbation theory. The dividing surface in this representation is analogous to the conventional dividing surface in the sense that it is the point set for which the reaction coordinate has the constant value it has at the saddle-point singularity. However the nonlinear, full phase-space character of the transformation makes the new crossing surface a complicated, abstract object whose interpretation and visualization, the objective of this paper, can be realized by cataloging the recrossings as they disappear in successively higher orders of perturbation, and by projection into spaces of only a few dimensions. The result is a conceptual interpretation of how regular behavior persists in a reactive degree of freedom.
  • KOMATSUZAKI Tamiki, BERRY Stephen  Meeting Abstracts of the Physical Society of Japan  53-  (0)  1998  [Not refereed][Not invited]
  • K Sawada, F Chigira, K Satoh, T Komatsuzaki  JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS  93-  (10)  1903  -1908  1997/05  [Not refereed][Not invited]
     
    Absorption spectra of ion pairs of picrate ion with the alkali-metal ion complexes of poly(oxyethylene)monododecyl ethers [C12H25(OC2H4)(n)OH, DEOn; (n = 4, 6 and 8)] and tetraalkylammonium ions, have been measured in water-saturated non-polar solvents, 1,2-dichloroethane (1,2-DCE) and xylene (Xy). The wavenumber of absorption maxima (nu(max)) of the ion pairs in 1,2-DCE was evaluated by taking into consideration the dissociation of the ion pairs. Those values show a good correlation with the reciprocal of the interionic distance of the ion pair except for the hydrated lithium complexes and with the nu(max) in Xy. The values of the nu(max) in various non-polar solvents were determined for the ion pair of the DEO6-potassium ion complex. These values were inversely correlated with the E-T, value, which is the parameter of solvent polarity. The electronic structures and ion pair structures of picrate ion forming the ion pair with alkali-metal ion complexes were scrutinized by using ab initio calculations. The results obtained experimentally and theoretically revealed: (i) that the change in the electronic excitation energy depends on the interionic distance between the picrate ion and the counter cation in the ion pair and (ii) that the interaction between the picrate ion and the counter cation is predominantly electrostatic.
  • T Komatsuzaki, M Nagaoka  CHEMICAL PHYSICS LETTERS  265-  (1-2)  91  -98  1997/01  [Not refereed][Not invited]
     
    A dividing surface is newly proposed in a many-body phase space, over which the system trajectories do not recross if the saddle crossing motions are regarded as quasiperiodic, As an example, the recrossing dynamics of a four-degrees of freedom Hamiltonian, a model of proton transfer reaction of malonaldehyde, is investigated. It is shown that the apparent barrier recrossing motions observed over a naive dividing surface in the configurational space are 'rotated away', by a nonlinear canonical transformation, to no-return single crossing motions over the new dividing surface defined in the phase space.
  • 小松崎 民樹, 長岡 正隆, Hanggi Peter  物性研究  66-  (5)  1039  -1049  1996/08  [Not refereed][Not invited]
     
    この論文は国立情報学研究所の電子図書館事業により電子化されました。ポスター
  • Tamiki Komatsuzaki, Masataka Nagaoka  Journal of Chemical Physics  105-  (24)  10838  -10848  1996  [Not refereed][Not invited]
     
    A method to scrutinize "regularity© of barrier recrossing dynamics of chemical reactions in the vicinity of the transition state is developed by using Lie canonical perturbation theory (LCPT). As an example, the recrossing dynamics of a four-degrees of freedom Hamiltonian regarded as a model of proton transfer reaction of malonaldehyde is investigated. It is shown that the second order LCPT is essential to describe frequent saddle recrossings whose total number of crossings is greater than three, and reproduces the time-dependent transmission coefficient. It is found that the local recrossing dynamics can be regarded as quasiperiodic and a well-defined reaction coordinate along which no barrier recrossings occur, can be extracted in the phase space by using the second order LCPT Hamiltonian. We also formulate a new transition state theory which allows us to estimate the reaction rate constant taking account of the barrier recrossing effect if the recrossings are near-integrable in the short time but long enough to determine the final state of the recrossing dynamics. © 1996 American Institute of Physics.
  • T Komatsuzaki, Ohmine, I  MOLECULAR SIMULATION  16-  (4-6)  321  -344  1996  [Not refereed][Not invited]
     
    A new semiempirical method is developed to deal with the proton transfer in liquid water. In the previous work, we have shown that two- and three-body charge transfer interactions and electrostatic interactions are the most important factors to describe the potential energy surfaces (PES) of the proton transfer in liquid water [Chemical Physics 180, 239-269, 1994]. In order to take account of these factors, we develop a semiempirical method imposing the principle of electronegativity equalization to the Atoms in Molecule (AIM) method. The method is free from the well-known discrepancy of the traditional AIM methods, that is, the fractional molecular charges at large molecular separation, and thus can be applied to the. charge transfer reactions. Intra- and intermolecular physical quantities, such as total energies, force vectors, dipole moment vectors and intermolecular charge transfer, obtained by the present method are found to be in good agreement with those by ab initio calculation.
  • T KOMATSUZAKI, OHMINE, I  CHEMICAL PHYSICS  180-  (2-3)  239  -269  1994/03  [Not refereed][Not invited]
     
    The energetics of proton transfer in liquid water is investigated by using ab initio calculation. The molecular electronic interaction of hydrated proton clusters is classified into many-body interaction elements by a new energy decomposition method. It is found that up to three-body molecular interaction is essential to describe the potential energy surface. The three-body effect mainly arises from the (non-classical) charge transfer and strongly depends on their configuration. Higher than three-body effects are small enough to be neglected. To simulate the liquid state reactions, two cluster models including all water molecules up to the second shell in the proton transfer reactions are employed. It is shown that these proton transfer reactions only involve small potential energy barriers of a few kcal/mol or less when structural rearrangement of the solvent is induced along the proton movement.

Awards & Honors

  • 2014 科研費審査員表彰
     
    受賞者: 小松崎 民樹
  • 2012 Bulletin of the Chemical Society of Japan (BCSJ) Award
     
    受賞者: KOMATSUZAKI TAMIKI
  • 2010 Human Frontier Science Program (HFSP) Grant Award
     
    受賞者: KOMATSUZAKI TAMIKI

Research Grants & Projects

  • Development of Data-driven Mathematical Analysis for Single Cells and Singularity Cells
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    Date (from‐to) : 2018/06 -2023/03 
    Author : 小松崎 民樹, 中村 篤祥, 小野 峻佑
  • 一細胞ラマン計測と情報科学の融合による細胞診断の迅速解析技術の開発
    JST:CREST
    Date (from‐to) : 2016/10 -2022/03 
    Author : KOMATSUZAKI TAMIKI
  • データサイエンスと非線形科学の融合による新たな非平衡現象の探求
    二国間交流事業共同研究・セミナー
    Date (from‐to) : 2018/04 -2020/03 
    Author : 小松崎 民樹
  • 生命動態システムに対する分子データ科学の構築
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2017/04 -2020/03 
    Author : 小松崎 民樹
     
    ラマン分光イメージングは非侵襲、非標識でサンプルに含有される(小分子も含めた)分子全体を網羅的に反映し、細胞や組織中の細胞、細胞核の形態だけでは検出・分類できない分子情報を包含している。今年度は、微弱なラマン信号から空間情報をできるだけ保持したままS/N比を向上させるsuperpixel分割法を導入し、光子統計によるポアソンノイズを考慮にいれたラマン組織学の情報解析技術を開発した。速度歪み理論に立脚したクラスター分類、状態識別に重要な波数(ラマンシフト)をアンサンブル学習(ランダムフォレスト)に基づいて同定する手法、ならびに各クラスターの密度分布関数を細胞、組織状態を識別する記述子として考案した。具体的に、細胞、細胞核の形態情報では診断が困難な甲状腺濾胞がんのがん診断、非アルコール性脂肪肝疾患(NAFL)の線維症へ応用した。前者においては、一細胞に跨がって平均化されたラマンスペクトルを用いたクラスター分類予測(精度78%)に比べて、その記述子を用いた予測(精度90%)のほうが顕著に優位であること、すなわち、識別にはsubcellularスケールの空間解像度が最低限必要であること、後者においては組織学的には非アルコール性脂肪性肝炎(NASH)同定に必要な繊維化などの形態異常は見られないものの、NAFL群のなかでは、ラマン分光的には正常肝細胞、NASHにそれぞれほぼ等しいクラスに大別されること、すなわち、まだ病理が組織学的には観察されていない極めて初期段階でも組織状態を見分けられる可能性が高いことを新規に見いだした。
  • 1細胞ラマン分光イメージングに基づく細胞場の分子データ科学
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    Date (from‐to) : 2018/04 -2019/03 
    Author : 小松崎 民樹
     
    1細胞ラマン分光イメージングは、非破壊かつ非侵襲に、小分子からタンパク質の分子情報を網羅的に評価し、細胞場の環境変動を反映するビックデータを提供する。しかしながら、「膨大なスペクトルデータから、如何にして細胞場の環境の化学的多様性、変動度を定量できるか」は未開拓状態である。本研究課題では、1細胞ラマン分光イメージングに基づいて、膨大なスペクトルデータから背後の細胞場の化学多様性および環境変動を定量する分子データ解析技術を開発し、細胞場の物理化学的理解を目指し、細胞場の環境変動が細胞の状態や機能に及ぼす影響を体系的に明らかにすることを目的として研究を遂行した。
    我々はC型、B型肝炎とともに三大肝疾患のひとつである非アルコール性脂肪性肝疾患(NAFLD)の線維症を予測するラットモデルを対象に、ラマンスペクトル画像が張る高次元空間を次元削減することでデータ構造を可視化するアルゴリズムならびにアンサンブル機械学習のひとつであるランダムフォレストに基づく病理診断に重要なラマンシフト群の同定を行う方法論を各々開発し、まだ組織学的な病理が観察されていない初期段階でも組織状態を見分ける情報解析技術を考案した。この方法は、細胞や組織のミクロ場の差異をラマン分光イメージングで定量することで、まだ組織学的な変化がみられない初期段階においても、細胞診断が可能であることを示すものであり、今後、その動態の定量などを可能とする方法論の開拓が望まれる。
  • Systems Biology of Minority and Majority of Cells
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2016/04 -2019/03 
    Author : 小松崎 民樹
     
    細胞の集団運動は、癌の成長、創傷治癒、器官発生といった多くの生物学的過程において重要である。例えば、アメーバDictyostelium discoideum(Dicty)は飢餓状態になると化学物質cAMPを周囲に放出することを通して近隣の他の細胞と相互作用する。その結果、反応拡散系で有名なベロウソフ・ジャボチンスキー反応のような、細胞群を通るらせん波のパターンを生み出すことが知られている。本研究課題では、最初にcAMPを放出する少数のリーダー細胞とそのcAMPに呼応して自身もcAMPを放出するフォロワー細胞から生じる細胞集団運動の間の因果関係を画像情報だけから抽出・推定することを目的として研究を進めてきた。 当該年度は、鳥などの集団運動を扱うVicsekモデルを変形し、異なる相互作用関係を陽に入れたシミュレーションモデルを考案し、その相互作用関係を移動エントロピー、固有情報量(intrinsic information)、共有情報量(shared information)、シナジー情報量(synergistic information)から同定可能であるかを検討した。移動エントロピーは、ある確率変数X(n)のみを知ったときに次の時刻で生じるX(n+1)のもつ不確かさ度が、別の確率変数Y(n)も知ることで、どれくらい減少するかを評価することで、YからXへの因果律を推定するものであり因果推論において最もよく用いられている。近年、移動イントロピーのなかにはX(n)からX(n+1)への情報伝搬も含まれているため、純粋にYからXへの固有情報量だけを取り扱っていないことが示唆されている。我々は、モデル系に加える摂動(ノイズ)の大きさに依存して、それらの割合が顕著に変化することを見いだし、移動エントロピーによる因果推論を正しく行うために注意を要することを明らかにした。
  • 多階層システム生物学におけるデータ駆動科学の展開
    新学術領域研究
    Date (from‐to) : 2017/04 -2018/03 
    Author : 小松崎 民樹
  • Deepening transition state concept and control of reaction kinetics from a few body systems to complex reaction networks
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2015/07 -2018/03 
    Author : Komatsuzaki Tamiki
     
    We uncovered a novel phenomenon which switches a path of reactions from a coordinate that used to describe the progress of reactions to another one that used not to do along with the total energy of the system increases by using the concept of Chaos theory called breakdown of normally hyperbolic invariant manifold. Due to this progress, we also successfully proposed how to verify this new phenomenon experimentally by taking dissociation reaction of an electron from a hydrogen-atom as an example which was under crossed homogeneous electric and magnetic fields. In addition, we newly proposed a global transition state over many underlying basins/states that governs the complex kinetics over reaction networks. This is defined as the slowest dividing surface over the network among all possible dividing surfaces and can extract complex hierarchical structure of reaction timescales. We proposed a new guideline for reaction controls applicable for both theoretically and experimentally.
  • 多階層システム生物学におけるデータ駆動科学の展開
    新学術領域研究
    Date (from‐to) : 2016/04 -2017/03 
    Author : 小松崎 民樹
  • Exploration of Systems Biology of Molecular Individuality
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research
    Date (from‐to) : 2013/04 -2016/03 
    Author : Komatsuzaki Tamiki, LI Chun-Biu, KAWAI Shinnosuke
     
    From single molecule finite time series that changes discretely such as opened or closed, (substrate) bound or unbound, we developed a novel analysis method that objectively elucidates the state of molecules in terms of network representation and enables us to predict the future output of the molecular data in time. In addition, by developing a novel data analysis method that does not assume a form of function of likelihood, we revealed the molecular mechanism of efficient energy conversion in F1-ATPase that synthesizes “energy money”inside cell, ATP, and ATP hydrolysis designs the order of reactions.
  • Development of analysis theories on life dynamical systems with hierarchy and robustness
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2013/04 -2016/03 
    Author : Komatsuzaki Tamiki, LI Chun-Biu, TERAMOTO Hiroshi
     
    By applying chaos theory developed in the field of celestial mechanics into microscopic chemical reactions, we predicted theoretically that a discrete switching between the reaction/non-reaction coordinate emerges as the total energy increases, and provided an experimental means to prove this unknown phenomenon. From experimentally observed, single molecule time series whose signal-to-noise ratio is low, we developed data-driven mathematical science to reconstruct the underlying information such as network structures and energy landscapes with properly elucidating the measurement errors and errors arising from finiteness of the data, and confirmed their versatility experimentally.
  • Constructing a theoretical framework to study reaction networks involving a small number of molecules: modeling with consideration of minority and hierarchy
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
    Date (from‐to) : 2011/04 -2016/03 
    Author : TOGASHI Yuichi, KOMATSUZAKI Tamiki, LI Chun-Biu, TERAMOTO Hiroshi, SHINKAI Soya, FLECHSIG Holger, TAYLOR James N., TSUGAWA Satoru, NAKAGAWA Masaki
     
    We developed multiple theories to explain chemo-mechanical complex networks involving a small number of elements, such as a general theory to predict small-number effects in catalytic reaction networks and a dynamic simulation approach to evaluate mechanical communication pathways between molecules or subunits. We also devised methods to analyze noisy data, including model-free change point analysis, error-based extraction of free-energy landscapes, and modeling with minimum excessive information that is not warranted by the data, to provide a basis to explain the individuality of molecules and cells using data science. We demonstrated the validity and applicability of these theoretical results for actual experiments in the field of “minority biology”.
  • Geometric Structure of Multi-dimensional Chaos and Its Application to Reactions in Non-equilibrium
    Japan Society for the Promotion of Science:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
    Date (from‐to) : 2004 -2006 
    Author : TODA Mikito, KOMATSUAZKI Tamiki
     
    We have formulated the dynamical theory of reactions based on the concept of normally hyperbolic invariant manifolds (NHIMs). This enables us to obtain a mathematically firm foundation of the concept of "transition states" in reaction processes. Moreover, it offers a possibility of going over the conventional ideas of reactions. The first is the possibility of breakdown of the normal hyperbolicity caused by chaos on the NHIM. Note that normal hyperbilicity means that instability along the normal directions is larger than that along the tangential directions. However, when chaos on the NHIM becomes comparable to the instability along the normal directions, the normal hyperbolicity is at the edge of breaking down. We have constructed a model system where this phenomenon can be analyzed using the Lie transformation and Pade summation. The breakdown means, in the context of reactions, that a new set of degrees of freedom start to contribute collective degrees of freedom describing reactions. This opens a new horizon in studying the reaction processes. The second achievement is to indicate that a power-law behavior is observed when the dynamics in the potential well is non-ergodic. We have constructed a model where the Arnold web in the well is sparse and non-uniform. The distribution of residence times exhibit a power-law properties and the dynamics in the well show anomalous diffusion. These phenomena indicate that the traditional concept of the reaction rate constat does not exists any more. The above two aspects of the reaction processes indicate that the dynamical theory of reactions offer a new possibility of understanding reactions.
  • 蛋白質折り畳みにおける分子遷移のカオスと複雑性
  • 1分子時系列情報に基づく反応ネットワーク構造の構成論とその複雑さ解析
  • 生体分子機能および化学反応網における選択性と統計性のダイナミックス基盤の創生
  • 蛋白質の折り畳み運動解明を目指した一分子観測法の確立-一分子観察実験のための新しいデータ解析手法の開発
  • Nonequilibrium Reaction Dynamics Theory Based on the Geometrical Structure of Phase Space
  • Chaos and complexity in the dynamics of molecular transitions during protein folding
  • A Constructive Theory of Reaction Network and Complexity Analysis from Single Molecule Time Series
  • An Establishment of Dynamical Foundations of Selectivity and Stochasticity in Biomolecule Functions
  • New Single Molecule Measurement toward full understanding of the complexity of Protein Folding

Educational Activities

Teaching Experience

  • On-the-fly Raman image microscopy by reinforcement machine learningOn-the-fly Raman image microscopy by reinforcement machine learning The University of Tokyo
  • Supramolecular Chemistry
    開講年度 : 2018
    課程区分 : 学士課程
    開講学部 : 理学部
    キーワード : 超伝導、ナノ空間、磁性体、薄膜、電子スピン、化学反応、選択性と統計性、数理科学、力学系

Campus Position History

  • 2015年4月1日 
    2017年3月31日 
    電子科学研究所附属社会創造数学研究センター長
  • 2017年4月1日 
    2019年3月31日 
    電子科学研究所附属社会創造数学研究センター長

Position History

  • 2015年4月1日 
    2017年3月31日 
    電子科学研究所附属社会創造数学研究センター長
  • 2017年4月1日 
    2019年3月31日 
    電子科学研究所附属社会創造数学研究センター長

Committee Membership

  • 2019/12 - Today   Biophysical Reviews, Springer Nature IUPAB   Special Issue Editor


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