研究者データベース

小松﨑 民樹(コマツザキ タミキ)
電子科学研究所 附属社会創造数学研究センター
教授

基本情報

所属

  • 電子科学研究所 附属社会創造数学研究センター

職名

  • 教授

学位

  • 博士(理学)(総合研究大学院大学(分子科学研究所))

ホームページURL

科研費研究者番号

  • 30270549

J-Global ID

研究キーワード

  • 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   

研究分野

  • ライフサイエンス / 生物物理学
  • ナノテク・材料 / 基礎物理化学
  • 自然科学一般 / 生物物理、化学物理、ソフトマターの物理
  • 自然科学一般 / 数理物理、物性基礎

職歴

  • 2019年07月 - 現在 北海道大学人間知・脳・AI研究教育センター 兼務教員
  • 2018年10月 - 現在 北海道大学化学反応創成研究拠点 (WPI-ICReDD) PI
  • 2018年04月 - 現在 北海道大学 大学院総合化学院物質化学コース 兼任 教授
  • 2017年04月 - 現在 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年04月 - 現在 北海道大学 電子科学研究所附属社会創造数学研究センター データ数理 研究分野(改組) 教授
  • 2007年10月 - 現在 北海道大学 大学院生命科学院生命融合科学コース 教授 兼任
  • 2019年05月 - 2019年05月 リヨン高等師範学校(Ecole normale supérieure de Lyon) 客員教授
  • 2015年04月 - 2019年03月 北海道大学 電子科学研究所附属社会創造数学研究センター センター長
  • 2018年11月 - 2018年12月 リヨン高等師範学校(Ecole normale supérieure de Lyon) 客員教授
  • 2016年06月 - 2016年07月 ブルゴーニュ大学 CNRS-Université de Bourgogne 客員教授
  • 2015年04月 - 2016年03月 中央大学 理工学部物理学科 非常勤講師
  • 2008年04月 - 2015年03月 数学連携研究センター 教授 兼任
  • 2007年10月 - 2015年03月 北海道大学 電子科学研究所分子生命数理研究分野 教授
  • 2003年07月 - 2007年09月 21世紀COEプログラム「惑星系の起源と進化」兼任
  • 1999年07月 - 2007年09月 神戸大学 大学院自然科学研究科情報メディア科学専攻 助教授併任
  • 1999年07月 - 2007年09月 神戸大学 理学部地球惑星科学科非線形科学研究室 助教授
  • 2006年04月 - 2007年03月 広島大学 理学部化学科 非常勤講師
  • 2005年04月 - 2006年03月 分子科学研究所理論研究系 分子基礎理論第四研究部門 客員助教授
  • 2004年04月 - 2005年03月 茨城大学大学院理工学研究科 非常勤講師
  • 2003年04月 - 2004年03月 東京大学 教養部・大学院総合文化研究科 非常勤講師
  • 2001年04月 - 2002年03月 滋賀大学教育学部 非常勤講師
  • 1998年04月 - 1999年06月 シカゴ大学化学科 research associate(医療保険、退職金完備)
  • 1997年03月 - 1998年03月 シカゴ大学化学科 日本学術振興会 特別研究員(PD)
  • 1994年04月 - 1997年02月 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)

所属学協会

  • American Association for the Advancement of Science   SIAM(Society for Industrial and Applied Mathematics)   分子科学会   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   

研究活動情報

論文

  • Nobuo Shimamoto, Mikito Toda, Shigetoshi Nara, Tamiki Komatsuzaki, Kiyoto Kamagata, Takashi Kinebuchi, Jun-Ichi Tomizawa
    Scientific reports 10 1 15624 - 15624 2020年09月24日 [査読有り][通常論文]
     
    We scrutinize the length dependency of the binding affinity of bacterial repressor TrpR protein to trpO (specific site) on DNA. A footprinting experiment shows that the longer the DNA length, the larger the affinity of TrpR to the specific site on DNA. This effect termed "antenna effect" might be interpreted as follows: longer DNA provides higher probability for TrpR to access to the specific site aided by one-dimensional diffusion along the nonspecific sites of DNA. We show that, however, the antenna effect cannot be explained while detailed balance holds among three kinetic states, that is, free protein/DNA, nonspecific complexes, and specific complex. We propose a working hypothesis that slow degree(s) of freedom in the system switch(es) different potentials of mean force causing transitions among the three states. This results in a deviation from detailed balance on the switching timescale. We then derive a simple reaction diffusion/binding model that describes the antenna effect on TrpR binding to its target operator. Possible scenarios for such slow degree(s) of freedom in TrpR-DNA complex are addressed.
  • Udoy S. Basak, Sulimon Sattari, Kazuki Horikawa, Tamiki Komatsuzaki
    PHYSICAL REVIEW E 102 1 2020年07月 [査読有り][通常論文]
     
    An information-theoretic scheme is proposed to estimate the underlying domain of interactions and the timescale of the interactions for many-particle systems. The crux is the application of transfer entropy which measures the amount of information transferred from one variable to another, and the introduction of a "cutoff distance variable" which specifies the distance within which pairs of particles are taken into account in the estimation of transfer entropy. The Vicsek model often studied as a metaphor of collectively moving animals is employed with introducing asymmetric interactions and an interaction timescale. Based on ensemble data of trajectories of the model system, it is shown that using the interaction domain significantly improves the performance of classification of leaders and followers compared to the approach without utilizing knowledge of the domain. Given an interaction timescale estimated from an ensemble of trajectories, the first derivative of transfer entropy averaged over the ensemble with respect to the cutoff distance is presented to serve as an indicator to infer the interaction domain. It is shown that transfer entropy is superior for inferring the interaction radius compared to cross correlation, hence resulting in a higher performance for inferring the leader-follower relationship. The effects of noise size exerted from environment and the ratio of the numbers of leader and follower on the classification performance are also discussed.
  • Udoy S. Basak, Sulimon Sattari, Kazuki Horikawa, Tamiki Komatsuzaki
    Physical Review E 102 1 012404 - 012404 2020年07月 [査読有り][通常論文]
     
    © 2020 American Physical Society. An information-theoretic scheme is proposed to estimate the underlying domain of interactions and the timescale of the interactions for many-particle systems. The crux is the application of transfer entropy which measures the amount of information transferred from one variable to another, and the introduction of a "cutoff distance variable"which specifies the distance within which pairs of particles are taken into account in the estimation of transfer entropy. The Vicsek model often studied as a metaphor of collectively moving animals is employed with introducing asymmetric interactions and an interaction timescale. Based on ensemble data of trajectories of the model system, it is shown that using the interaction domain significantly improves the performance of classification of leaders and followers compared to the approach without utilizing knowledge of the domain. Given an interaction timescale estimated from an ensemble of trajectories, the first derivative of transfer entropy averaged over the ensemble with respect to the cutoff distance is presented to serve as an indicator to infer the interaction domain. It is shown that transfer entropy is superior for inferring the interaction radius compared to cross correlation, hence resulting in a higher performance for inferring the leader-follower relationship. The effects of noise size exerted from environment and the ratio of the numbers of leader and follower on the classification performance are also discussed.
  • 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年04月08日 [査読無し][通常論文]
     
    Minor embedding heuristics have become an indispensable tool for compiling problems in quadratically unconstrained binary optimization (QUBO) into the hardware graphs of quantum and CMOS annealing processors. While recent embedding heuristics have been developed for annealers of moderate size (about 2000 nodes) the size of the latest CMOS annealing processor (with 102,400 nodes) poses entirely new demands on the embedding heuristic. This raises the question, if recent embedding heuristics can maintain meaningful embedding performance on hardware graphs of increasing size. Here, we develop an improved version of the probabilistic-swap-shift-annealing (PSSA) embedding heuristic [which has recently been demonstrated to outperform the standard embedding heuristic by D-Wave Systems (Cai et al., 2014)] and evaluate its embedding performance on hardware graphs of increasing size. For random-cubic and Barabasi-Albert graphs we find the embedding performance of improved PSSA to consistently exceed the threshold of the best known complete graph embedding by a factor of 3.2 and 2.8, respectively, up to hardware graphs with 102,400 nodes. On the other hand, for random graphs with constant edge density not even improved PSSA can overcome the deterministic threshold guaranteed by the existence of the best known complete graph embedding. Finally, we prove a new upper bound on the maximal embeddable size of complete graphs into hardware graphs of CMOS annealers and show that the embedding performance of its currently best known complete graph embedding has optimal order for hardware graphs with fixed coordination number.
  • Tamiki Komatsuzaki, Haruki Nakamura, Jeremy Tame, Saeko Yanaka, Takeharu Nagai, Kuniaki Nagayama
    Biophysical Reviews 12 2 183 - 185 2020年04月 [査読有り][通常論文]
  • Tomoyasu Aizawa, Makoto Demura, Kazutoshi Gohara, Hisashi Haga, Koichiro Ishimori, Masataka Kinjo, Tamiki Komatsuzaki, Katsumi Maenaka, Min Yao
    Biophysical Reviews 12 2 233 - 236 2020年04月 [査読無し][通常論文]
  • Koji Tabata, Atsuyoshi Nakamura, Junya Honda, Tamiki Komatsuzaki
    Machine Learning 109 2 327 - 372 2020年02月01日 [査読有り][通常論文]
     
    © 2019, The Author(s), under exclusive licence to Springer Science+Business Media LLC, part of Springer Nature. 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 θU, and it is negative if that is less than another given threshold θL(≤ θU). 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 Δ= θU- θL> 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.
  • Hiroshi Teramoto, Kenji Kondo, Shyuichi Izumiya, Mikito Toda, Tamiki Komatsuzaki
    JOURNAL OF MATHEMATICAL PHYSICS 60 12 2019年12月 [査読有り][通常論文]
  • Khalifa Mohammad Helal, James Nicholas Taylor, Harsono Cahyadi, Akira Okajima, Koji Tabata, Yoshito Itoh, Hideo Tanaka, Katsumasa Fujita, Yoshinori Harada, Tamiki Komatsuzaki
    FEBS Letters 593 18 2535 - 2544 2019年09月01日 [査読有り][通常論文]
     
    © 2019 Federation of European Biochemical Societies Histopathology requires the expertise of specialists to diagnose morphological features of cells and tissues. Raman imaging can provide additional biochemical information to benefit histological disease diagnosis. Using a dietary model of nonalcoholic fatty liver disease in rats, we combine Raman imaging with machine learning and information theory to evaluate cellular-level information in liver tissue samples. After increasing signal-to-noise ratio in the Raman images through superpixel segmentation, we extract biochemically distinct regions within liver tissues, allowing for quantification of characteristic biochemical components such as vitamin A and lipids. Armed with microscopic information about the biochemical composition of the liver tissues, we group tissues having similar composition, providing a descriptor enabling inference of tissue states, contributing valuable information to histological inspection.
  • Tamiki Komatsuzaki, Steve Presse, Patrick Senet
    JOURNAL OF PHYSICAL CHEMISTRY B 123 30 6387 - 6388 2019年08月 [査読有り][通常論文]
  • J. Nicholas Taylor, Kentaro Mochizuki, Kosuke Hashimoto, Yasuaki Kumamoto, Yoshinori Harada, Katsumasa Fujita, Tamiki Komatsuzaki
    Journal of Physical Chemistry B 123 20 4358 - 4372 2019年05月23日 [査読有り][通常論文]
     
    © 2019 American Chemical Society. We use Raman microscopic images with high spatial and spectral resolution to investigate differences between human follicular thyroid (Nthy-ori 3-1) and follicular thyroid carcinoma (FTC-133) cells, a well-differentiated thyroid cancer. Through comparison to classification of single-cell Raman spectra, the importance of subcellular information in the Raman images is emphasized. Subcellular information is extracted through a coarse-graining of the spectra at high spatial resolution (∼1.7 μm2), producing a set of characteristic spectral groups representing locations having similar biochemical compositions. We develop a cell classifier based on the frequencies at which the characteristic spectra appear within each of the single cells. Using this classifier, we obtain a more accurate (89.8%) distinction of FTC-133 and Nthy-ori 3-1, in comparison to single-cell spectra (77.6%). We also infer which subcellular components are important to cellular distinction; we find that cancerous FTC-133 cells contain increased populations of lipid-containing components and decreased populations of cytochrome-containing components relative to Nthy-ori 3-1, and that the regions containing these contributions are largely outside the cell nuclei. In addition to increased classification accuracy, this approach provides rich subcellular information about biochemical differences and cellular locations associated with the distinction of the normal and cancerous follicular thyroid cells.
  • Koji Tabata, Atsuyoshi Nakamura, Junya Honda, Tamiki Komatsuzaki
    CoRR abs/1901.11200 2019年01月31日 [査読無し][通常論文]
     
    We study a bad arm existing checking problem in which a player's task is to judge whether a positive arm exists or not 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. 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 (non-positive) arms' roles; finding one positive arm is enough to judge existence while all the arms must be discriminated as negative to judge non-existence. We propose an algorithms with arm selection policy (policy to determine the next arm to draw) and stopping condition (condition to stop drawing arms) utilizing this asymmetric problem structure and prove its effectiveness theoretically and empirically.
  • Tamiki Komatsuzaki
    Minorities and Small Numbers from Molecules to Organisms in Biology: Toward a New Understanding of Biological Phenomena 31 - 37 2018年11月03日 [査読有り][通常論文]
  • J. Nicholas Taylor, Menahem Pirchi, Gilad Haran, Tamiki Komatsuzaki
    JOURNAL OF CHEMICAL PHYSICS 148 12 123325 - 123325 2018年03月 [査読有り][通常論文]
     
    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. Published by AIP Publishing.
  • Yuji Tamiya, Rikiya Watanabe, Hiroyuki Noji, Chun-Biu Li, Tamiki Komatsuzaki
    Physical chemistry chemical physics : PCCP 20 3 1872 - 1880 2018年01月17日 [査読有り][通常論文]
     
    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 2018年 [査読有り][通常論文]
     
    © 2017 Owner Societies. 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, Yuki Yoshida, Normann Mertig, Takashi Takemoto, Hiroshi Teramoto, Atsuyoshi Nakamura, Ichigaku Takigawa, Shin-ichi Minato, Masanao Yamaoka, Tamiki Komatsuzaki
    Theory and Practice of Natural Computing - 7th International Conference, TPNC 2018, Dublin, Ireland, December 12-14, 2018, Proceedings 111 - 123 2018年 [査読有り][通常論文]
  • 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) 1 - 8 2018年 [査読有り][通常論文]
     
    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.
  • 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 - + 2017年11月 [査読有り][通常論文]
     
    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 - + 2017年09月 [査読有り][通常論文]
     
    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.
  • Meysam Tavakoli, J. Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Presse
    ADVANCES IN CHEMICAL PHYSICS, VOL 162 162 205 - 305 2017年 [査読有り][通常論文]
  • 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 2016年07月 [査読有り][通常論文]
     
    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 2016年04月 [査読有り][通常論文]
     
    © 2016 Biophysical Society. 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 2016年03月03日 [査読有り][通常論文]
     
    © 2015 American Chemical Society. 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 time scale of 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.
  • Chun Biu Li, Hiroshi Ueno, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    Nature Communications 6 10223 - 10223 2015年12月17日 [査読有り][通常論文]
     
    F1 -ATPase (F1) 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 F1 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 F1 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.
  • Yosuke Sumiya, Yutaka Nagahata, Tamiki Komatsuzaki, Tetsuya Taketsugu, Satoshi Maeda
    JOURNAL OF PHYSICAL CHEMISTRY A 119 48 11641 - 11649 2015年12月 [査読有り][通常論文]
     
    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.
  • Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
    PHYSICAL REVIEW LETTERS 115 9 093003 - 093003 2015年08月 [査読有り][通常論文]
     
    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 - 9174 2015年03月17日 [査読有り][通常論文]
     
    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 - 6522 2014年10月 [査読有り][通常論文]
     
    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.
  • 戸田 幹人, Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Theoretical Chemistry Accounts 133 11 1571 (15 pages)  2014年09月 [査読有り][通常論文]
     
    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 - 104907 2014年09月 [査読有り][通常論文]
     
    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 2014年09月 [査読有り][通常論文]
     
    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 2013年12月28日 [査読有り][通常論文]
     
    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 ∼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. © 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 2013年12月07日 [査読有り][通常論文]
     
    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. © 2013 AIP Publishing LLC.
  • Hiroshi Teramoto, George Haller, Tamiki Komatsuzaki
    CHAOS 23 4 043107 - 043107 2013年12月 [査読有り][通常論文]
     
    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 042923 - 042923 2013年10月29日 [査読有り][通常論文]
     
    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 2013年08月01日 [査読有り][通常論文]
     
    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. © 2013 American Physical Society.
  • Shinnosuke Kawai, David Cooper, Christy Landes, Henning D. Mootz, Haw Yang, Tamiki Komatsuzaki
    Journal of Physical Chemistry B 117 27 8061 - 8074 2013年07月11日 [査読有り][通常論文]
     
    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 Förster-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. © 2013 American Chemical Society.
  • Yutaka Nagahata, Hiroshi Teramoto, Chun Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 87 6 062817 - 062817 2013年06月25日 [査読有り][通常論文]
     
    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. © 2013 American Physical Society.
  • Shinnosuke Kawai, Tamiki Komatsuzaki
    PHYSICAL REVIEW E 87 3 030803 - 030803-4 2013年03月 [査読有り][通常論文]
     
    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 Terentyeva, Johan Hofkens, Tamiki Komatsuzaki, Kerstin Blank, Chun-Biu Li
    Journal of Physical Chemistry B 117 5 1252 - 1260 2013年02月 [査読有り][通常論文]
     
    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年11月 [査読有り][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki
    BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 85 8 854 - 861 2012年08月 [査読有り][通常論文]
     
    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 2012年07月 [査読有り][通常論文]
     
    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 2012年 [査読有り][通常論文]
  • Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    Complex Syst. 20 2 2011年 [査読有り][通常論文]
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda
    COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION 13 5 857 - 867 2008年07月 [査読有り][通常論文]
     
    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 2007年12月04日 [査読有り][通常論文]
     
    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. © 2007 by The National Academy of Sciences of the USA.
  • 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 2007年06月 [査読有り][通常論文]
     
    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 035204 - 035204 2007年03月 [査読有り][通常論文]
     
    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 2005年 [査読有り][通常論文]
  • 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 2005年 [査読有り][通常論文]
  • T KOMATSUZAKI, AKAI, I, K SAKAKIBARA, M HIROTA
    TETRAHEDRON 48 9 1539 - 1556 1992年02月 [査読有り][通常論文]
     
    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.
  • Minoru Hirota, Kazuhisa Sakakibara, Tamiki Komatsuzaki, Ikuo Akai
    Comput. Chem. 15 3 241 - 248 1991年 [査読有り][通常論文]
     
    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.
  • T KOMATSUZAKI, K SAKAKIBARA, M HIROTA
    CHEMISTRY LETTERS 10 1913 - 1916 1990年10月 [査読有り][通常論文]
  • T KOMATSUZAKI, K SAKAKIBARA, M HIROTA
    TETRAHEDRON LETTERS 30 25 3309 - 3312 1989年 [査読有り][通常論文]

書籍

  • Minorities and Small Numbers from Molecules to Organisms in Biology-Toward a New Understanding of Biological Phenomena
    小松崎 民樹 (担当:単著範囲:Chapter 5 "The Personality of Small Numbers: Do Molecules Have Personality?")
    Springer 2018年11月
  • 化学反応理論の普遍性:GRRMに期するもの
    小松崎 民樹 (担当:単著)
    IQCE NEWS (量子化学探索研究所) 2018年
  • 少数性生物学
    小松崎 民樹 (担当:共著範囲:第5章「少数の個性~分子にも個性?~」)
    株式会社 日本評論社 2017年
  • Advances in Chemical Physics
    Meysam Tavakoli, J. Nicholas Taylor, Chun-Biu Li, Tamiki Komatsuzaki, Steve Pressé (担当:共著範囲:Single Molecule Data Analysis: An Introduction)
    Wiley 2017年
  • 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 (担当:共著)
    月刊「化学」71(5) 2016年
  • Dynamics of Chemical Reaction around a Saddle Point - What divides reacting and non-reacting trajectories?
    Shinnosuke Kawai, Tamiki Komatsuzaki (担当:共著範囲:Reaction Rate Constant Computations; Theories and Applications, CHAPTER 7)
    RSC Publishing 2013年11月
  • 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 (担当:単訳)
    2013年
  • Reaction Rate Constant Computations; Theories and Applications
    Shinnosuke Kawai, Tamiki Komatsuzaki (担当:共著範囲:Dynamics of Chemical Reaction around a Saddle Point - What divides reacting and non-reacting trajectories?)
    RSC 2013年
  • Advances in Chemical Physics 146
    Akinori Baba, Tamiki Komatsuzaki (担当:共著範囲:Multidimensional Energy Landscapes in Single Molecule Biophysics)
    John-Wiley& Sons, Inc. 2012年
  • Advances in Chemical Physics 145
    David M. Leitner, Yasuhiro Matsunaga, Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda (担当:共著範囲:Non-Brownian Phase Space Dynamics of Molecules, the Nature of their Vibrational States, and non-RRKM Kinetics)
    2011年
  • Cell Signaling Reactions: Single-Molecular Kinetic Analysis
    Chun Biu Li, Tamiki Komatsuzaki (担当:共著範囲:Extracting the Underlying Unique Reaction Scheme from a Single-Molecule Time Series)
    Springer 2011年
  • Advances in Chemical Physics 130(A)
    Tamiki Komatsuzaki, R. Stephen Berry (担当:共著範囲:Regularity in Chaotic Transitions on Two-Basin Landscapes)
    2005年
  • Advances in Chemical Physics 130(B)
    Tamiki Komatsuzaki, Kyoko Hoshino, Y. Matsunaga (担当:共著範囲:Regularity in Chaotic Transitions on Multi-Basin Landscapes)
    2005年
  • Advances in Chemical Physics 130A, 130B
    M. Toda, T. Komatsuzaki, T. Konishi, R. S. Berry, S. A. Rice (担当:共編者(共編著者)範囲:Geometric Structures of Phase Space in Multi-Dimensional Chaos: Applications to Chemical Reaction Dynamics in Complex Systems)
    John-Wiley & Sons, Inc. 2005年
  • Advances in Chemical Physics 123
    Tamiki Komatsuzaki, R. Stephen Berry (担当:共著範囲:Chemical Reaction Dynamics: Many-Body Chaos and Regularity)
    John-Wiley & Sons, Inc. 2002年

講演・口頭発表等

  • On-the-fly Raman image microscopy by reinforcement machine learning: How to accelerate the measurement?  [招待講演]
    Tamiki Komatsuzaki
    SCIX2020 2020年10月 口頭発表(招待・特別)
  • 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
    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 5 回 CREST 領域会議 2020年10月 口頭発表(一般)
  • Raman imaging for cancer diagnosis
    Jean-Emmanuel Clement, Kenntaro Mochizuki, Katsumasa Fujita, Tamiki Komatsuzaki
    第58回日本生物物理学会年会 2020年09月 ポスター発表
  • Vector analysis of amoeba motion with respect to the propagation of chemoattractant cyclic-AMP
    Hossain Md. Motaleb, Sattari Sulimon, Basak Udoy S, Horikawa Kazuki, Komatsuzaki Tamiki
    第58回日本生物物理学会年会 2020年09月 ポスター発表
  • Inferring domain of Interactions among Dictyostelium discoideum colony from the Ensemble of Trajectories of cells
    Basak Udoy S, Sattari Sulimon, Hossain Md. Motaleb, Horikawa Kazuki, Komatsuzaki Tamiki
    第58回日本生物物理学会年会 2020年09月 ポスター発表
  • Quantifying the length- and time-scales of influence of cells in collective motion
    Sattari Sulimon, Basak Udoy, Motaleb Md. Hossain, 堀川 一樹, 小松崎 民樹
    第58回日本生物物理学会年会 2020年09月 ポスター発表
  • Geometrical aspect of chemical reaction dynamics in thermally fluctuating environments and Future Directions  [招待講演]
    Tamiki Komatsuzaki
    Chaos Indicators, Phase Space and Chemical Reaction Dynamics 2020年05月 口頭発表(招待・特別)
  • 古典的軌道計算とボロノイ分割を用いた反応チューブの計算方法
    宮下彩季, 滝川皇, 水野雄太, 寺本央, 小松崎民樹
    化学系学協会北海道支部2020年冬季研究発表会 2020年01月 ポスター発表
  • シンギュラリティ生物学における情報✕計測
    小松崎 民樹
    シンギュラリティ生物学×細胞ダイバース合同ワークショップ 2020年01月 口頭発表(一般)
  • A computational method for reaction tubes based on trajectory calculation and Voronoi tessellation
    滝川 皇, 宮下 彩季, 水野 雄太, 寺本 央, 小松崎 民樹
    北海道大学電子科学研究所 2019年度 研究交流会 2020年01月 口頭発表(一般)
  • An Information-theoretic approach to identify the interaction radius of a group of collectively moving animals
    Udoy. S Basak, Sulimon Sattari, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • A sandbox model system for analyzing leadership in collective motion
    Sulimon Sattari, Udoy Basak, Sky Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • Bad Arm Existence Checking Algorithm with Bandit Feeedback
    Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • Raman Microscopic Histology using Ensemble Learning for Non-alcoholic Fatty Liver Disease
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • High Resolution Raman Microscopic Detection of Follicular Thyroid Cancer Cells with Unsupervised Machine Learning  [通常講演]
    J. Nicholas Taylor, Kentaro Mochizuki, Kosuke Hashimoto, Yasuaki Kumamoto, Yoshinori Harada, Katsumasa Fujita, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • Raman Imaging for Exploring Cancer Metabolism  [通常講演]
    Jean-Emmanuel Clément, Mochizuki Kentaro, Katsumasa Fujita, Tamiki Komatsuzaki
    The 20th RIES-HOKUDAI International Symposium 2019年12月 ポスター発表
  • On-the-fly Raman image microscopy by reinforcement machine learning  [招待講演]
    小松崎 民樹
    Biomedical Raman Imaging 2019 2019年11月 口頭発表(招待・特別)
  • Accelerated Raman hyperspectral imaging for cancer diagnosis
    Jean-Emmanuel Clement, Shunsuke Ono, Kentaro Mochizuki, Katsumasa Fujita, Tamiki Komatsuzaki
    Biomedical Raman Imaging 2019 2019年11月 口頭発表(一般)
  • Raman Hyperspectral Image Analysis Using Ensemble Learning for Non-alcoholic Fatty Liver Disease
    Khalifa Mohammad Helal, Harsono Cahyadi, J. Nicholas Taylor, Akira Okajima, Yasuaki Kumamoto, Hideo Tanaka, Yoshinori Harada, Tamiki Komatsuzaki
    Biomedical Raman Imaging 2019 2019年11月 口頭発表(一般)
  • Causal inference in Leader-follower relationship  [通常講演]
    小松崎 民樹
    ICSB 2019: Singularity Biology: small elements change the function of the whole systems 2019年10月 口頭発表(一般)
  • A leadership-based phase transition in a flocking model with activated and un-activated agents  [通常講演]
    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年09月 ポスター発表
  • An Information-theoretic approach toward identifying the leader(s) and aggregation place in Dictyostelium Discoideum colony  [通常講演]
    Basak Udoy Sankar, Sattari Sulimon, Horikawa Kazuki, Komatsuzaki Tamiki
    第57回日本生物物理学会年会 2019年09月 ポスター発表
  • 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  [通常講演]
    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年08月 口頭発表(一般)
  • Raman pathology and its phenotypic landscape for Non-alcoholic fatty liver diseases  [招待講演]
    小松崎 民樹
    The Complexity of Dynamics and Kinetics from Single Molecules to Cells 2019年06月 口頭発表(招待・特別)
  • 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  [通常講演]
    James Nicholas Taylor, Menahem Pirchi, Gilad Haran, 小松崎 民樹
    第22回理論化学討論会 2019年05月 口頭発表(一般)
  • Deciphering hierarchical features in reaction network and energy landscape  [招待講演]
    小松崎 民樹
    Network analysis to elucidate natural system dynamics, diversity and performance 2019年05月 口頭発表(招待・特別)
  • Identification of Leader(s) in a Dictyostelium Discoideum colony: An Information-theoretic Approach  [通常講演]
    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年03月 口頭発表(一般)
  • A sandbox model system for understanding leadership in collective motion  [通常講演]
    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年03月 口頭発表(一般)
  • Analysis of Raman Microscopic Images of Liver Tissu to Predict Non-alcholic Fatty Liver Disease  [通常講演]
    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年03月 口頭発表(一般)
  • Mathematical information measurement science: acceleration of Raman spectroscopy by bridging information science  [通常講演]
    小松崎 民樹
    バイオ情報計測技術研究会 2019年03月 口頭発表(一般)
  • 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?  [招待講演]
    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年01月 口頭発表(招待・特別)
  • How can one bridge information science and measurement science to accelerate the measurements?  [招待講演]
    小松崎 民樹
    The 22nd SANKEN International Symposium The 17th SANKEN Nanotechnology International Symposium "Next Generation Science and Technology for Super Smart Society" 2019年01月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年01月 口頭発表(一般)
  • Application of Singularity Theory to Material Science  [通常講演]
    Hiroshi Teramoto, Asahi Tsuchida, Yutaro Kabata, Kenji Kondo, Katsusuke Nabeshima, Shyūichi Izumiya, Mikito Toda, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • Data-Driven Analysis of Raman Microscopic Images of Human Follicular Thyroid Cells  [通常講演]
    J. Nicholas Taylor, Kentaro Mochizuki, Katsumasa Fujita, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • The origin of why and how reactions take place: Reaction cylinders by Voronoi tessellation  [通常講演]
    Mikoto Takigawa, Sulimon Sattari, Sosuke Ito, Hiroshi Teramoto, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • Bad Arm Existence Checking Algorithms with Bandit Feedback  [通常講演]
    Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • A sandbox model system for analyzing leadership in collective motion  [通常講演]
    Sulimon Sattari, Udoy Basak, Sky Nicholson, Jason Green, Mikito Toda, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • Information-theoretical Approaches to Raman Microscopic Images to Predict Non-alcoholic Fatty Liver Disease  [通常講演]
    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年12月 ポスター発表
  • Information theoretic approach to identify the leader(s) in Dictyostelium Discoideum colony  [通常講演]
    Udoy S. Basak, Sulimon Sattari, Sosuke Ito, Kazuki Horikawa, Tamiki Komatsuzaki
    The 19th RIES-HOKUDAI International Symposium 2018年12月 ポスター発表
  • 非対称性を利用した悪腕存在チェックアルゴリズム  [通常講演]
    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年11月 口頭発表(一般)
  • Revisit transition state theory: Past, Present, Future  [招待講演]
    小松崎 民樹
    Workshop “Trends in Computational Molecular Biophysics” 2018年11月 口頭発表(招待・特別)
  • 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  [招待講演]
    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年09月 口頭発表(招待・特別)
  • Multivariate Data-driven Approaches to Raman Hyper-spectral Images to Diagnose Non-alcoholic Fatty Liver Disease (NAFLD)  [通常講演]
    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年09月 ポスター発表
  • Information theoretic approach to reveal singularity in biology  [招待講演]
    小松崎 民樹
    Annual Conference on Biophysical Society of Japan 2018年09月 口頭発表(招待・特別)
  • Normal Forms in Singularity Theory for Geometric Classifications of Band Structures  [通常講演]
    Hiroshi Teramoto, Asahi Tsuchida, Yutaro Kabata, Kenji Kondo, KatsusukeNabeshima, ShyūichiIzumiya, Mikito Toda, Tamiki Komatsuzaki
    Dynamics Days Europe 2018 2018年09月 口頭発表(一般)
  • 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  [通常講演]
    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年08月
  • Phase Space geometry and Chemical Reaction Dynamics in Driven Systems  [招待講演]
    小松崎 民樹
    Telluride Workshop "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases" 2018年07月 口頭発表(招待・特別)
  • Open questions in Higher rank saddles and related  [招待講演]
    小松崎 民樹
    Telluride Workshop "Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases" 2018年07月 口頭発表(招待・特別)
  • How One can Extract Energy Landscape from Single -Molecule Time Series under the Existence of Noise?  [招待講演]
    小松崎 民樹
    Telluride Workshop "Biophysical Dynamics" 2018年07月
  • How One can Extract Energy Landscape from Single-Molecule Time Series under the Existence of Noise?  [招待講演]
    小松崎 民樹
    Department Seminar, Johns Hopkins University, Department of Chemistry 2018年07月 公開講演,セミナー,チュートリアル,講習,講義等
  • 新概念コンピューティングとは?  [招待講演]
    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年07月
  • 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  [通常講演]
    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年05月
  • 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  [招待講演]
    小松崎 民樹
    ImPACT合田プログラム Serendipityセミナー 2018年04月
  • Understanding cell colony dynamics from images using velocity extraction and analysis  [通常講演]
    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年04月
  • 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  [招待講演]
    小松崎 民樹
    2017年度第2回バイオ単分子研究会 2018年03月
  • Understanding cell colony dynamics from images using velocity extraction and analysis  [通常講演]
    Sulimon Sattari, Tamiki Komatsuzaki
    2017年度日本生物物理学会北海道支部例会 2018年03月
  • Mulitivariate Data-driven approach to Raman Hyper-spectral Images to Diagnose Non-alcoholic Fatty Liver Disease(NAFLD)  [通常講演]
    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年03月
  • 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  [招待講演]
    小松崎 民樹
    第65回応用物理学会春季学術講演会 2018年03月
  • 試行回数の少ない悪腕存在チェックアルゴリズム  [通常講演]
    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年03月
  • 多階層システム生物学におけるデータ駆動科学の展開  [通常講演]
    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年01月
  • 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  [招待講演]
    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年12月
  • 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  [招待講演]
    小松崎 民樹
    2017年度生命科学系学会合同年次大会 2017年12月
  • ラマン分光イメージング計測と情報科学との高度融合  [通常講演]
    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年11月
  • ラマン分光イメージングにおける情報計測技術の展開  [通常講演]
    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年11月
  • 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  [通常講演]
    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年11月
  • How one can extract energy landscape from single molecule time series under the existence of noise?  [招待講演]
    小松崎 民樹
    The 2nd Korea-Japan Joint Symposium on Single-Molecule Biophysics 2017年11月
  • 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-  [通常講演]
    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年10月
  • 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  [通常講演]
    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年09月
  • How can one quantify singularity in cells from Single Cell Raman Imaging?  [招待講演]
    小松崎 民樹
    第55回日本生物物理学会年会 2017年09月
  • Information-theoretical data analysis approaches to Raman micro-spectroscopic images  [通常講演]
    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年09月
  • Energy landscapes learned from single molecule FRET time series: Role of Photobleaching  [招待講演]
    小松崎 民樹
    Deciphering complex energy landscape and kinetic network from single molecules to cells: a new challenge to make theories meet experiments 2017年09月
  • Global Transition States in Reaction Network  [招待講演]
    小松崎 民樹
    Telluride Workshop on Chemistry & Dynamics in Complex Environments 2017年06月
  • Data-driven mathematics in single cell Raman imaging  [招待講演]
    小松崎 民樹
    Telluride Workshop on The Complexity of Dynamics and Kinetics from Single Molecules to Cells 2017年06月
  • 多階層システム生物学におけるデータ駆動科学の展開  [通常講演]
    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年06月
  • 一細胞ラマン計測と情報科学の融合による細胞診断  [招待講演]
    小松崎 民樹
    2017年度人工知能学会全国大会 2017年05月
  • 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―  [通常講演]
    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年03月
  • 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  [通常講演]
    小松崎 民樹
    バイオ計測解析技術研究会 2017年03月
  • Data-Driven Analysis of Raman Microscopic Images  [通常講演]
    J.N. Taylor, C.-B. Li, K. Fujita, T. Komatsuzaki
    電子科学研究所 研究交流会 2017年01月
  • 分子から細胞の個性に関するデータ駆動型数理科学  [招待講演]
    小松崎 民樹
    第1117回生物科学セミナー 2016年12月
  • The Non-equilibrium Effects on Reaction Kinetics of F1-ATPase  [通常講演]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium 2016年12月
  • Data-Driven Approaches to Raman Microscopic Image Analysis  [通常講演]
    J.N. Taylor, Chun-Biu Li, Katsumasa Fujita, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium 2016年12月
  • Dynamical Heterogeneity During Collective Migration of MDCK Epithelial Monolayer  [通常講演]
    Preetom Nag, Khalifa Mohammad Helal, Hiroshi Teramoto, Chun-Biu Li, Hisashi Haga, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium 2016年12月
  • Collective Cell Migration: Underlying Dynamics and Emergent Structures of Heterogeneity  [通常講演]
    Khalifa Mohammad Helal, Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Hisashi Haga, Tamiki Komatsuzaki
    The 17th RIES-Hokudai International Symposium 2016年12月
  • マイノリティ細胞を彫りだすデータ科学  [招待講演]
    小松崎 民樹
    第39回日本分子生物学会年会 2016年12月
  • Predicting Biological Cell Aggregation Using Scalable Random Forest Decision Trees  [通常講演]
    SATTARI, Sulimon, KOMATSUZAKI, Tamiki
    The 18th RIES-Hokudai International Symposium 2016年11月
  • Apparent Nonequilibrium Behavior in Single-Molecule FRET Time-Series Induced by Photophysics  [通常講演]
    J. Nicholas Taylor, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium 2016年11月
  • Bad Arm Existence Checking Algorithm  [通常講演]
    Koji Tabata, Atsuyoshi Nakamura, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium 2016年11月
  • Raman Microscopic Image Analysis based on Information-theoretic Approach  [通常講演]
    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年11月
  • Toward Molecular Propagation through Degenerated Electron Energy Level Crossings  [通常講演]
    Hiroshi Teramoto, Shyūichi Izumiya, Tamiki Komatsuzaki
    The 18th RIES-Hokudai International Symposium 2016年11月
  • Spatial heterogeneous and transient dynamics during collective cell migration in a monolayer of MDCK epithelial cells  [通常講演]
    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年11月
  • 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?  [招待講演]
    小松崎 民樹
    第54回日本生物物理学会年会 2016年11月
  • Data Driven Approaches to Raman Microscopic Analysis  [通常講演]
    J. N. Taylor, K. Fujita, T. Komatsuzaki
    第54回日本生物物理学会年会 2016年11月
  • 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  [通常講演]
    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年11月
  • 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  [招待講演]
    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年11月
  • 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  [招待講演]
    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年10月
  • Data-Driven Approaches to Raman Microscopic Image Analysis  [通常講演]
    J. N. Taylor, K. Fujita, T. Komatsuzaki
    「理論と実験」研究会2016 2016年10月
  • Molecular Functions and Energy Landscapes Extracted from Single Molecule Time Series Data  [招待講演]
    小松崎 民樹
    HOKUDAI-NCTU Joint Symposium on Nano, Photo and Bio Sciences in 2016 2016年10月
  • 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  [通常講演]
    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年09月
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [招待講演]
    小松崎 民樹
    Energy Landscapes: Theory and Applications 2016年06月
  • Phase Space geometry and Chemical Reaction Dynamics: Past, Present, and Future  [招待講演]
    小松崎 民樹
    Seminar of the ICB/Nanosciences department 2016年06月
  • Single Molecule Biophysics: How can One extract the Underlying Markovian/non-Markovian Network from Noisy and Short Time Series?  [招待講演]
    小松崎 民樹
    IXXI-ENS Lyon seminar 2016年06月
  • Defining Global Transition State over an Entire Markov Network  [招待講演]
    小松崎 民樹
    Seminar of the ICB/Nanosciences department 2016年06月
  • Single Molecule Biophysics: How can One Dig the Underlying Network from Noisy and Short Time Series?  [招待講演]
    小松崎 民樹
    Seminar of the ICB/Nanosciences department 2016年06月
  • Defining Global Transition State over an Entire Markov Network  [招待講演]
    小松崎 民樹
    Seminar at Beijing Computational Science Research Center 2016年05月
  • 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  [通常講演]
    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年05月
  • 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  [通常講演]
    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年04月
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [通常講演]
    寺本央, 戸田幹人, 小松崎民樹
    第89回現象数理セミナー 2016年04月
  • Molecular Data Science Perspectives for Individuality Covering from Molecules to Cells  [招待講演]
    小松崎 民樹
    統合生命医科学研究センター疾患生物学セミナー 2016年03月
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [招待講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Computational Chemistry (CC) Symposium in ICCMSE 2016年03月
  • The key and unlock mechanisms in F1-ATPase unveiled by single molecule time series analysis  [通常講演]
    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年03月
  • 少数性生物学の新展開:分子個性から細胞個性へ  [通常講演]
    小松崎 民樹
    新学術領域「少数性生物学」 研究成果報告会 2016年03月
  • Classification of Electron Energy Level Crossings in terms of the Theory of Singularities and Analysis of Non-Adiabatic Transitions around the Crossings  [通常講演]
    寺本央, 戸田幹人, 小松崎民樹
    偏微分方程式姫路研究会 2016年03月
  • Data-driven quantification of heterogeneous microenvironments in live-cell Raman microscopic images  [通常講演]
    J. Nick Taylor, Almar F. Palonpon, Chun Biu Li, Katsumasa Fujita, Tamiki Komatsuzaki
    The Biophysical Society 2016 BPS Annual Meeting 2016年02月
  • On the Relationship between Local Microtubule and Cell Growth in Plants  [通常講演]
    津川 暁, Chun Biu Li, 小松崎 民樹
    Mathematical Sciences Evening Seminar 2016年02月
  • 生物個性学:分子から細胞へ  [通常講演]
    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年02月
  • Correlated Oscillation in Microtubule Fluctuation and Cell Growth in Arabidopsis Sepal  [通常講演]
    津川 暁, Chun Biu Li, 小松崎 民樹
    第132回植物科学セミナー 2016年01月
  • Toward deciphering cell individuality in systems biology  [招待講演]
    小松崎 民樹
    Symposium #137 Life at Small Copy Numbers (The 2015 International Chemical Congress of Pacific Basin Societies) 2015年12月
  • Data-driven quantification of heterogeneous microenvironments in live-cell Raman microscopic images  [通常講演]
    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年12月
  • Energy landscapes and conformation network learned from single molecule time series  [招待講演]
    小松崎 民樹
    Symposium #121 Deciphering molecular complexity from protein functions to cellular network (The 2015 International Chemical Congress of Pacific Basin Societies) 2015年12月
  • 特異点論によるバンド間交差の分類  [通常講演]
    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年12月
  • Dynamical Reaction Theory: Beyond the conventional perturbation theory  [招待講演]
    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年11月
  • Phase Space geometry and Chemical Reaction Dynamics: Past, Present, and Future  [招待講演]
    小松崎 民樹
    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年11月
  • Developing high precision algorithm to predict observation timescale hierarchy of an isomerization reaction network  [通常講演]
    Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Tetsuya Taketsugu, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium 2015年11月
  • Classification and Control of electron energy level crossings in terms of the theory of singularity  [通常講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium 2015年11月
  • Kinetics of Multiple conductance levels of Mechanosensitive Ion Channel  [通常講演]
    Genming Wang, Chun-Biu Li, Hitoshi Tatsumi, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium 2015年11月
  • The Onset of Non-equilibrium Effects at High Temperature in the Reaction Kinetics of F1-ATPase  [通常講演]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 16th RIES-Hokudai International Symposium 2015年11月
  • マルコフ連鎖の時間階層的クラスタリング  [通常講演]
    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年11月
  • Single Molecule Biophysics: How can One Dig the Underlying Network from Noisy and Short Time Series?  [招待講演]
    小松崎 民樹
    International Conference on “Challenges in Data Science: a Complex Systems Perspective 2015年10月
  • 細胞内レベルでの微小管配向の抽出  [通常講演]
    津川 暁, Chun Biu Li, 小松崎 民樹
    「理論と実験」研究会2015 2015年10月
  • The temperature dependence and non-equilibrium properties of the single F1-ATPase kinetics  [通常講演]
    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年10月
  • Identifying Different Reaction Processes in terms of Graph Laplacian  [招待講演]
    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年09月
  • 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  [招待講演]
    小松崎 民樹
    「データ駆動科学の新展開」ミニ研究会 2015年09月
  • 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  [通常講演]
    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年09月
  • 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  [通常講演]
    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年09月
  • 特異点論を用いた非断熱交差の安定性と分岐の解析  [通常講演]
    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年09月
  • 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-  [通常講演]
    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年09月
  • 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  [招待講演]
    小松崎 民樹
    特設分野「遷移状態制御」研究代表者交流会 2015年09月
  • 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  [通常講演]
    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年09月
  • 植物の中の局所微小管と細胞成長の関係について  [通常講演]
    Satoru Tsugawa, Chun-Biu Li, Tamiki Komatsuzaki
    第53回日本生物物理学会 2015年09月
  • 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  [通常講演]
    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年09月
  • Single Molecule Time Series Analysis of F1-ATPase to Unravel the Role of Bound-ATP Hydrolysis  [通常講演]
    Chun-Biu Li, Tamiki Komatsuzaki
    第53回日本生物物理学会 2015年09月
  • Classification and control of electron energy level crossings  [通常講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    北大理論化学ワークショッ プ 2015年09月
  • 審査員の経験からみたポイント  [招待講演]
    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年09月
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [招待講演]
    Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kohno, Tamiki Komatsuzaki
    Telluride summer workshop “Geometry of Chemical Reaction Dynamics” 2015年08月
  • Transition States from Gas Phase, Condensed Phase to Complex Networks  [招待講演]
    小松崎 民樹
    Telluride summer workshop “Geometry of Chemical Reaction Dynamics” 2015年08月
  • 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  [通常講演]
    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年07月
  • 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  [通常講演]
    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年07月
  • グラフラプラシアンによる異なる反応プロセスの同定  [通常講演]
    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年07月
  • 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  [通常講演]
    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年06月
  • How can we define a transition state over a network?  [招待講演]
    小松崎 民樹
    R. Stephen Berry Tribune Symposium 2015年06月
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [招待講演]
    小松崎 民樹
    Chemistry and Dynamics in Complex Environments 2015年06月
  • Error-based Extraction of States and Energy Landscapes from Experimental Single-Molecule Time-Series  [通常講演]
    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年06月
  • Energy Landscapes learned from Single-Molecule Time-Series: Dimensionality and Disconnectivity Graph  [通常講演]
    小松崎 民樹
    The Complexity of Dynamics and Kinetics from Single Molecules to Cells 2015年06月
  • マルコフ連鎖の時間階層的クラスタリング  [通常講演]
    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年06月
  • 「モデル先行の科学」から「データから彫りだす科学」へ  [通常講演]
    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年06月
  • 少数分子反応ネットワーク理論の構築 (7)  [通常講演]
    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年06月
  • Deciphering timescale hierarchy encoded in complex reaction networks  [通常講演]
    NAGAHATA Yutaka, MAEDA Satoshi, TERAMOTO Hiroshi, LI Chun-Biu, HORIYAMA Takashi, TAKETSUGU Tetsuya, KOMATSUZAKI Tamiki
    31st Symposium on Chemical Kinetics and Dynamics 2015年06月
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [通常講演]
    Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
    31st Symposium on Chemical Kinetics and Dynamics 2015年06月
  • A Dynamical Switching of Reactive and Nonreactive Modes at High Energies  [通常講演]
    Tamiki Komatsuzaki, Mikito Toda, Hiroshi Teramoto
    2015 SIAM Conference on Dynamical Systems 2015年05月
  • A Dynamical Switching of Reactive and Nonreactive Modes at High Energies epartment of Chemistry and Chemical Biology  [招待講演]
    小松崎 民樹
    Department Seminar in Department of Chemistry and Chemical Biology 2015年05月
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [招待講演]
    小松崎 民樹
    Department Seminar in Department of Chemistry 2015年05月
  • Identifying different reaction processes in terms of graph laplacian  [招待講演]
    Hiroshi Teramoto, Tamiki Komatsuzaki
    IlLuminyating 2015 2015年05月
  • 蛍光画像から微小管配向構造の抽出  [通常講演]
    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年04月
  • A Global Dynamical Switching of a Reaction Coordinate and its Experimental Observability  [通常講演]
    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年04月
  • 蛍光画像から微小管配向構造を抽出する方法について  [通常講演]
    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年04月
  • F1 分子モーターの温度依存性  [通常講演]
    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年04月
  • Energy landscapes derived from single molecule spectroscopy and complex networks  [招待講演]
    小松崎 民樹
    Architecture, dynamics, and functionality of molecular biosystems 2015年03月
  • Understandings of Chemical Reaction Dynamics in terms of Dynamical System Theory  [招待講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    Computational Chemistry (CC) Symposium in ICCMSE 2015年03月
  • 単一バクテリア細胞内ATP濃度の多様性  [通常講演]
    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年03月
  • Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis  [通常講演]
    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年03月
  • Timescale hierarchies of complex reaction network  [通常講演]
    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年03月
  • Hierarchical structure of no-return transition states  [招待講演]
    小松崎 民樹
    Spectroscopy and Dynamics of Molecules and Clusters 2015 2015年02月
  • Chance and necessity in reactions under thermal fluctuation & chaos Department of Chemistry  [招待講演]
    小松崎 民樹
    Indian Institute of Technology Kanpur seminar 2015年02月
  • 少数分子反応ネットワーク理論の構築 (4)  [通常講演]
    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年01月
  • Data Scientific Approaches to the Quantification and Interpretation of Raman Microscopic Images of Living Cells  [通常講演]
    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年01月
  • Survey and study on effects of discreteness and fewness in chemical reaction dynamics  [通常講演]
    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年01月
  • Developing “hierarchical” spectral clustering decoded by the mathematical nature of a Markov chain: - timescale hierarchical nature of isomerization reaction network of C5H8O -  [通常講演]
    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年01月
  • 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  [招待講演]
    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年01月
  • 力学系理論による化学反応動力学の解明  [通常講演]
    小松崎 民樹
    電子科学研究所・研究交流会 2015年01月
  • Fast Step Transition and State Identification (STaSI) for Discrete Single-Molecule Data Analysis  [通常講演]
    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年01月
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [通常講演]
    小松崎 民樹
    The 8th biennial workshop on Single Molecule Biophysics (SMB) 2015年01月
  • 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  [通常講演]
    小松崎 民樹
    第3 回 少数性⽣物学討論会 2014年12月
  • An extraction method of local microtubule alignments in Arabidopsis sepal  [通常講演]
    Satoru Tsugawa, Chun-Biu Li, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki] 2014年12月
  • Error-based Extraction of Effective Free Energy Landscapes from Experimental Single-Molecule Time-Series  [通常講演]
    J.N. Taylor, Chun Biu Li, David R. Cooper, Christy F. Landes, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki] 2014年12月
  • Temperature Dependence of Molecular Motor  [通常講演]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki] 2014年12月
  • An extraction of embedded timescale hierarchies buried in complex reaction network  [通常講演]
    Yutaka Nagahata, Satoshi Maeda, Hiroshi Teramoto, Chun-Biu Li, Takashi Horiyama, Tetsuya Taketsugu, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki] 2014年12月
  • Local-heterogeneous responses and transient dynamics in colloidal fluids  [通常講演]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Joseph Z. Terdik, Norbert F. Scherer, Tamiki Komatsuzaki
    The 15th Ries-Hokudai International Symposium 響[hibiki] 2014年12月
  • Dynamic Disorder in Single Enzyme Experiments: Facts and Artifacts  [通常講演]
    小松崎 民樹
    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年11月
  • A kinetic disconnectivity graph to decode timescale hierarchy buried in reaction networks  [招待講演]
    小松崎 民樹
    XIXth International Workshop on Quantum Systems in Chemistry, Physics and Biology 2014年11月
  • Data Driven Approach to Dynamics of Protein Motor  [通常講演]
    Yuji Tamiya, Chun-Biu Li, Rikiya Watanabe, Hiroyuki Noji, Tamiki Komatsuzaki
    New Challenges in Complex Systems Science 2014年10月
  • Chemical Reaction Dynamics and Chaos  [招待講演]
    小松崎 民樹
    New Challenges in Complex Systems Science 2014年10月
  • 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  [通常講演]
    小松崎 民樹
    第2回少数性生物学討論会 2014年10月
  • 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  [通常講演]
    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年10月
  • 熱揺らぎに埋もれた力学的な反応経路  [招待講演]
    小松崎 民樹
    研究会「理論と実験」2014 2014年10月
  • A Dynamical Switching of Reactive Mode ⇔ Nonreactive Mode at High Energies for a Hydrogen Atom in Crossed Electric and Magnetic Fields  [招待講演]
    小松崎 民樹
    11th Asian International Seminar on Atomic and Molecular Physics 2014年10月
  • 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  [通常講演]
    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年09月 ポスター発表
  • 分子個性と少数性  [通常講演]
    小松崎 民樹
    第52回日本生物物理学会年会 2014年09月 口頭発表(一般)
  • Dynamical heterogeneity and dynamics of cage breaking and formation in colloidal fluids  [通常講演]
    Nag Preetom, Teramoto Hiroshi, Li Chun-Biu, Komatsuzaki Tamiki
    第52回日本生物物理学会年会 2014年09月 ポスター発表
  • 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  [通常講演]
    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年09月 口頭発表(一般)
  • 少数性の生物学において顕在化する分子個性  [招待講演]
    小松崎 民樹
    日本物理学会2014年秋季大会 2014年09月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年09月 口頭発表(一般)
  • 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”  [通常講演]
    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年09月 ポスター発表
  • 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  [通常講演]
    寺本央, 戸田幹人, 小松崎民樹
    北大理論化学合同Workshop 2014年09月 口頭発表(一般)
  • 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  [通常講演]
    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年09月 口頭発表(一般)
  • Energy landscapes learned from time series and networks  [招待講演]
    小松崎 民樹
    Energy Landscapes : From Single Molecules to Soft Matter 2014年08月
  • 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〜  [通常講演]
    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年08月 ポスター発表
  • Reaction Coordinate Switching Mechanism, on the Possibility of Its Experimental Verification and Its Quantum Manifestation  [招待講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications 2014年07月
  • Chance and Necessity in Reactions Under Chaos and Stochastic Fluctuation  [招待講演]
    小松崎 民樹
    The 10th AIMS Conference on Dynamical Systems, Differential Equations and Applications 2014年07月
  • Extracting Cooperative modes between a biological molecule and water molecules  [招待講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    International Workshop "Over the Barriers of Transition Paths: Dynamical Processes in Proteins and Complex Molecular Systems" 2014年06月
  • Energy Landscapes Constructed From Single-molecule Time Series And Reaction Networks  [招待講演]
    小松崎 民樹
    Macromolecular dynamics: structure, function and diseases 2014年06月
  • Theories Should Meet Experiments: What Can We Extract From Time Series Data?  [招待講演]
    小松崎 民樹
    Beijing Computational Science Research Center (CSRC) Seminar 2014年06月
  • 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  [通常講演]
    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年05月 口頭発表(一般)
  • 生体分子と水の過渡的な集団運動の抽出  [通常講演]
    寺本央, 戸田幹人, 小松崎民樹
    第17回理論化学討論会 2014年05月 口頭発表(一般)
  • Energy Landscapes Constructed From Single-Molecule Time Series and Reaction Networks  [招待講演]
    小松崎 民樹
    The 2014 Les Houches - TSRC Protein Dynamics Workshop 2014年05月
  • 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  [通常講演]
    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年04月 口頭発表(一般)
  • 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  [通常講演]
    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年03月 口頭発表(一般)
  • パターン形成における本質的な高次相関情報量の抽出  [通常講演]
    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年03月 口頭発表(一般)
  • Dynamical heterogeneity and cage breaking dynamics in colloidal fluids in terms of Lagrangian Coherent structures (LCSs)  [通常講演]
    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年03月 口頭発表(一般)
  • 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  [通常講演]
    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年03月 口頭発表(一般)
  • Extracting coherent dynamics in colloidal fluids in terms of Lagrangian Coherent structures (LCSs)  [通常講演]
    Teramoto Hiroshi, Nag Preetom, Li Chun-Biu, Komatsuzaki Tamiki
    International Life-Science Symposium 2014年03月 口頭発表(一般)
  • 少数分子反応ネットワーク理論の構築  [通常講演]
    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年02月 口頭発表(一般)
  • 生体分子と水の過渡的な協同運動の抽出  [通常講演]
    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年02月 ポスター発表
  • Constructing Kinetic Scheme Objectively from Dwell-Time Time Series with Exact Information Content  [通常講演]
    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年02月 ポスター発表
  • Extracting the Underlying Free Energy Landscape Buried in Photon-by- Photon based Single-Molecule Measurements  [通常講演]
    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年02月 ポスター発表
  • コロイド流体の動的協同運動のLagrangian Coherent Structureによる抽出  [通常講演]
    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年01月 ポスター発表
  • Relation between dynamics of individual trajectories and that of their ensemble distributions -Spectral Analysis of Individual Trajectories-  [通常講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • An Information-Theoretical Approach to Local Equilibrium State Analysis for Single-Molecule Time-Series  [通常講演]
    J. N. Taylor, C.B. Li, S. Kawai, T. Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Scrutiny of Heterogeneity in Memory by Extracting Reaction Network Buried in Single Molecule Time Series of EGFR and Grb2  [通常講演]
    Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Toward understanding hierarchical structure of complex reaction networks extracted from single molecule time series  [通常講演]
    Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Coherent dynamics in colloidal fluids in terms of Lagrangian Coherent Structures (LCSs)  [通常講演]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Information of multi-order correlation in pattern formation  [通常講演]
    Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Extracting the Protein-folding Dynamics from Single Molecule Time Series  [通常講演]
    Kunihiko Ibe, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The 14th RIES-HOKUDAI International Symposium 網[mou] 2013年12月 ポスター発表
  • Essential Coordinates to Describe the Dynamics of Many-atom Systems  [招待講演]
    Shinnosuke Kawai, Hiroshi Teramoto, Tamiki Komatsuzaki
    5th JCS International Symposium on Theoretical Chemistry 2013年12月 ポスター発表
  • 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  [通常講演]
    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年11月 口頭発表(一般)
  • 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  [招待講演]
    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年11月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年11月 ポスター発表
  • 分子個性(Dynamic disorder):一分子生物学から産まれた新しい概念?  [招待講演]
    小松崎 民樹
    第2回バイオ単分子研究会 2013年11月 口頭発表(招待・特別)
  • 力学系をみる二つの視点:軌道と分布の描像、の関係  [招待講演]
    寺本央, 戸田幹人, 小松崎民樹
    関東力学系セミナー 2013年11月 口頭発表(招待・特別)
  • An Information-Theoretical approach to Local Equilibrium State Analysis for Single-Molecule Time-Series  [通常講演]
    J. Nick Taylor, Li Chun-Biu, Kawai Shinnosuke, Komatsuzaki Tamiki
    第51回日本生物物理学会年会 2013年10月 ポスター発表
  • Quantifying the absolute ATP concentration inside single bacteria cells  [通常講演]
    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年10月 ポスター発表
  • Coherent dynamics in colloidal fluids in terms of Lagrangian coherent structures (LCS)  [通常講演]
    Nag Preetom, Teramoto Hiroshi, Li Chun-Biu, Komatsuzaki Tamiki
    第51回日本生物物理学会年会 2013年10月 ポスター発表
  • 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  [招待講演]
    小松崎 民樹
    第51回日本生物物理学会年会 2013年10月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年10月 ポスター発表
  • A Multiscale Kinetic Scheme Extracted from EGFR-Grb2 Single Molecule Reaction  [通常講演]
    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年10月 ポスター発表
  • Toward the Decoding of Single Nucleotides Tunneling Current by Change Point Analysis  [通常講演]
    Chun-Biu Li, Tamiki Komatsuzaki
    Technologies for Medical Diagnosis and Therapy Symposium 2013年10月 ポスター発表
  • Let Systems Tell for themselves: Energy Landscape and Complex Network  [通常講演]
    James N. Taylor, Shinnosuke Kawai, Chun Biu Li, Tamiki
    Technologies for Medical Diagnosis and Therapy Symposium 2013年10月 ポスター発表
  • Dynamic Disorder 再考:解析の虚実  [招待講演]
    小松崎 民樹
    研究会「理論と実験」2013 2013年10月 口頭発表(招待・特別)
  • 天文学から生まれたカオスと化学動力学の出会い  [通常講演]
    小松崎 民樹
    Symposium on Cross-Talk between Chemistry and Planetary Sciences 2013年10月 口頭発表(一般)
  • 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~  [通常講演]
    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年10月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年10月 公開講演,セミナー,チュートリアル,講習,講義等
  • 反応座標切替機構の量子的兆候  [通常講演]
    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年09月 口頭発表(一般)
  • 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  [通常講演]
    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年09月 口頭発表(一般)
  • 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  [通常講演]
    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年09月 口頭発表(一般)
  • 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  [通常講演]
    Yutaka Nagahata, Hiroshi Teramoto, Takashi Horiyama, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry 2013年08月 口頭発表(一般)
  • Information of multi-order correlation in pattern formation  [通常講演]
    Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry 2013年08月 口頭発表(一般)
  • Co-operative motion in colloidal fluids in terms of Lagrangian Coherent Structures(LCS)  [通常講演]
    Nag Preetom, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry 2013年08月 口頭発表(一般)
  • Toward System Molecular Biology & Data Science  [通常講演]
    小松崎 民樹
    A Symposium on Single Molecule Biophysics and Cyt c Biochemistry 2013年08月 口頭発表(一般)
  • 確率の起源:偶然と必然の原理  [招待講演]
    小松崎 民樹
    第1回少数性生物学トレーニングコース 2013年08月 公開講演,セミナー,チュートリアル,講習,講義等
  • 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  [通常講演]
    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年07月 口頭発表(一般)
  • 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  [通常講演]
    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年07月 口頭発表(一般)
  • Dynamical Conformation Coordinations in Non-Ribosomal Peptide Synthetases  [通常講演]
    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年07月 ポスター発表
  • Revisiting Energy Landscape, Timescale, Coarse-Graining  [招待講演]
    KOMATSUZAKI TAMIKI
    Chemistry and Dynamics in Complex Environments 2013年06月 口頭発表(招待・特別)
  • Identifying states in Markov chain steady state network extracted from time series by finding minimum transition probability  [通常講演]
    Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    The Complexity of Dynamics and Kinetics in Many Dimensions 2013年06月 口頭発表(一般)
  • Revisiting Energy Landscape & Extracting it from FRET measurement  [通常講演]
    KOMATSUZAKI TAMIKI
    The Complexity of Dynamics and Kinetics in Many Dimensions 2013年06月 口頭発表(招待・特別)
  • Phase Space Geometrical Aspects in Condensed Phase Reactions  [通常講演]
    KOMATSUZAKI TAMIKI
    Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases 2013年06月 口頭発表(招待・特別)
  • Reactivity Boundaries to Separate the Fate of a Chemical Reaction Associated with Multiple Saddles  [通常講演]
    Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    Geometry of Chemical Reaction Dynamics in Gas and Condensed Phases 2013年06月 口頭発表(一般)
  • Unbiased estimation of physical properties in noisy experimental data  [通常講演]
    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年05月 ポスター発表
  • 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  [招待講演]
    小松崎 民樹
    日本顕微鏡学会第69回学術講演会 2013年05月 口頭発表(招待・特別)
  • Energy Landscapes Constructed From Single-Molecule Time Series and Reaction Networks  [招待講演]
    KOMATSUZAKI TAMIKI
    The 2014 Les Houches - TSRC Protein Dynamics Workshop 2013年05月 口頭発表(招待・特別)
  • A microscopic ruler tells us the underlying networks in single molecule measurements  [招待講演]
    KOMATSUZAKI TAMIKI
    Nanoscale Science Seminars 2013:A Microscopic ruler tells us the underlying networks in single molecule measurements 2013年05月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年04月 ポスター発表
  • 生体分子と水の過渡的な協同運動の抽出  [通常講演]
    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年03月 口頭発表(一般)
  • Capturing Full Information Contents from Single Molecule Dwell-time Time Series with Minimum Excessive Information  [通常講演]
    Chun Biu Li, Tamiki Komatsuzaki
    The Physical Society of Japan (JPS) 2013 (68th) Annual Meeting 2013年03月 口頭発表(一般)
  • 任意の確率分布に対する推定量の数値的構成  [通常講演]
    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年03月 口頭発表(一般)
  • 法双曲的不変多様体崩壊の量子的兆候  [通常講演]
    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年03月 口頭発表(一般)
  • Stationary Lagrangian Coherent Structureによる化学反応動力学の理解  [通常講演]
    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年03月 口頭発表(一般)
  • Multiscale Hidden Markovian Network Buried in Recognition Reaction of EGFR and Grb2.  [通常講演]
    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年03月 公開講演,セミナー,チュートリアル,講習,講義等
  • 1分子データをどれだけ正しく読み取れるか?  [通常講演]
    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年02月 口頭発表(一般)
  • Toward Deciphering Molecular Individuality in sSystems Biology  [招待講演]
    小松崎 民樹
    French-Japanese Seminar on "Bioinspired Methods and Applications" 2013年02月 口頭発表(招待・特別)
  • 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  [通常講演]
    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年01月 口頭発表(一般)
  • 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  [通常講演]
    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年01月 口頭発表(一般)
  • 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  [通常講演]
    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年01月 口頭発表(一般)
  • 蛋白質機能に対するデータ駆動的モデリング  [招待講演]
    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年01月 公開講演,セミナー,チュートリアル,講習,講義等
  • Toward deciphering molecular individuality in systems biology  [通常講演]
    Chun Biu Li, Tamiki Komatsuzaki
    Gordon Research Conferences, Stochastic Physics in Biology 2013年01月 ポスター発表
  • Let Single Molecule Time Series Tell for Itself: Energy Landscape and Complex Network  [招待講演]
    小松崎 民樹
    4th France-Japan Joint Seminar "Imaging of spatiotemporal hierarchies in living cells – an overview of dynamics from molecules to cells -" 2013年01月 口頭発表(招待・特別)
  • 一分子酵素反応実験におけるDynamic disorderの起源  [通常講演]
    小松崎 民樹
    第85回日本生化学会大会 2012年12月 口頭発表(一般)
  • Extracting Quasi Normally Repelling Material Surface by Re-formulating Variational Lagrangian Coherent Structure (LCS) Theory  [通常講演]
    Preetom Nag, Hiroshi Teramoto, Chun Biu Li, Tamiki Komatsuzak
    The 13th RIES-Hokudai International Symposium 2012年12月 ポスター発表
  • Effect of Time Scales on the Essential Dimensionality of a Dynamical System  [通常講演]
    Shinnosuke Kawai, Hiroshi Teramoto, Tamiki Komatsuzaki
    The 13th RIES-Hokudai International Symposium 2012年12月 ポスター発表
  • .Extracting cooperative mode of water and peptide in terms of a local Green function  [通常講演]
    Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    The 13th RIES-Hokudai International Symposium 2012年12月 ポスター発表
  • Deciphering complex hierarchical living systems in single molecule biology  [招待講演]
    小松崎 民樹
    2nd Discussion Symposium on Artificial Life and Biomimetic Functional Materials 2012年12月 口頭発表(招待・特別)
  • Modeling Single Molecule Kinetics Objectively from Dwell-time time series  [招待講演]
    Chun-Biu Li, Tamiki Komatsuzaki
    International Workshop on Quantitative Biology 2012 2012年11月 口頭発表(招待・特別)
  • 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?  [招待講演]
    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年11月 口頭発表(招待・特別)
  • Toward deciphering reality of molecular dynamics in systems biology  [通常講演]
    小松崎 民樹
    RIES - CIS Joint Symposium 2012年10月 口頭発表(招待・特別)
  • Exploring the Operating Principles and Cooperative Motions from Single F1-ATPase Time Series  [通常講演]
    Chun Biu LI, Tamiki Komatsuzaki
    Paradigm Innovation in Biology: novel strategy and thinking 2012年10月 ポスター発表
  • Construction of "Optimal" Estimators for Arbitrary Probability Distributions  [通常講演]
    Shinnosuke Kawai, Tamiki Komatsuzaki
    Paradigm Innovation in Biology: novel strategy and thinking 2012年10月 ポスター発表
  • Theories should meet measurements: What Can We Extract from Time Data?  [招待講演]
    小松崎 民樹
    Paradigm Innovation in Biology: novel strategy and thinking 2012年10月 口頭発表(招待・特別)
  • 過剰情報量を最小にする反応スキーム  [通常講演]
    小松崎 民樹
    研究会「理論と実験」2012 2012年10月 公開講演,セミナー,チュートリアル,講習,講義等
  • 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?  [通常講演]
    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年10月 公開講演,セミナー,チュートリアル,講習,講義等
  • 遷移状態とは何か-鞍点の周辺で起こる運動とその制御  [通常講演]
    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年09月 口頭発表(一般)
  • 複雑分子系を読み解くための新しい1分子理論  [通常講演]
    Chun Biu Li, 小松崎 民樹
    第6回分子科学討論会 2012年09月 口頭発表(一般)
  • 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  [通常講演]
    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年09月 ポスター発表
  • A novel computational procedure for locating Lagrangian coherent structure(LCS) from Variational LCS theory.  [通常講演]
    Preetom Nag, Hiroshi Teramoto,Chun Biu Li, Tamiki Komatsuzaki
    The Physical Society of Japan (JPS) 2012 Fall Meeting 2012年09月 ポスター発表
  • 反変Lyapunovベクトルを用いた法反発的不変面の構成法  [通常講演]
    寺本央, George Haller, 小松崎民樹
    日本物理学会 2012年秋季大会 2012年09月 ポスター発表
  • 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  [通常講演]
    河合 信之輔, 小松崎 民樹
    第6回分子科学討論会 2012年09月 口頭発表(一般)
  • Constructing unbiased estimators for arbitrary probability distribution  [招待講演]
    Kawai, S, Mootz, H.D, Yang, H, Komatsuzaki, T
    HFSP 12th Annual Awardees Meeting 2012年07月 ポスター発表
  • Transition States and Reaction Coordinates in Complex Systems  [招待講演]
    小松崎 民樹
    Searching for Reaction Coordinates and Order Parameters 2012年06月 口頭発表(招待・特別)
  • Theories Should Meet Experiments: What Can We Extract from Time Series Data?  [招待講演]
    小松崎 民樹
    Characterizing Landscapes: From Biomolecules to Cellukar Networks 2012年06月 口頭発表(招待・特別)
  • Extracting Boundary of Reaction Associated with an Index-two-saddle from a Two Degree-of-Freedom System  [通常講演]
    NAGAHATA Yutaka, TERAMOTO Hiroshi, LI, Chun-Biu, KAWAI Shinnosuke, KOMATSUZAKI Tamiki
    28th Symposium on Chemical Kinetics and Dynamics 2012年06月 口頭発表(一般)
  • 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?  [通常講演]
    小松崎 民樹
    細胞システムの動態と論理IV 2012年04月 公開講演,セミナー,チュートリアル,講習,講義等
  • 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?  [招待講演]
    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年04月 公開講演,セミナー,チュートリアル,講習,講義等

その他活動・業績

  • Udoy S. Basak, Sulimon Sattari, Hossain M. Motaleb, Kazuki Horikawa, Tamiki Komatsuzaki 2020年09月18日 [査読無し][通常論文]
     
    Transfer entropy in information theory was recently shown [Phys. Rev. E 102, 012404 (2020)] to enable us to elucidate the interaction domain among interacting particles solely from an ensemble of trajectories. There, only pairs of particles whose distances are shorter than some distance variable, termed cutoff distance, are taken into account in the computation of transfer entropies. The prediction performance in capturing the underlying interaction domain is subject to noise level exerted on the particles and the sufficiency of statistics of the interaction events. In this paper, the dependence of the prediction performance is scrutinized systematically on noise level and the length of trajectories by using a modified Vicsek model. The larger the noise level and the shorter the time length of trajectories, the more the derivative of average transfer entropy fluctuates, which makes it difficult to identify the interaction domain in terms of the position of global minimum of the derivative of average transfer entropy. A measure to quantify the degree of strong convexity at coarse-grained level is proposed. It is shown that the convexity score scheme can identify the interaction distance fairly well even while the position of global minimum of the derivative of average transfer entropy does not.
  • 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年02月13日 [査読無し][通常論文]
     
    © 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年 [査読無し][通常論文]
  • 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年10月29日 [査読無し][通常論文]
  • 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年04月26日 [査読無し][通常論文]
  • 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年04月 [査読無し][通常論文]
  • 田畑 公次, 中村 篤祥, 本多 淳也, 小松崎 民樹 人工知能基本問題研究会 106 94 -99 2018年03月16日 [査読無し][通常論文]
  • 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年03月05日 [査読無し][通常論文]
  • 冨樫 祐一, 新海 創也, 小松崎 民樹 実験医学 35 (19) 3190 -3196 2017年12月 [査読無し][通常論文]
     
    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年12月 [査読無し][通常論文]
  • 冨樫祐一, 新海創也, 小松崎民樹 実験医学 35 (19) 3190‐3196 2017年12月01日 [査読無し][通常論文]
  • 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年12月 [査読無し][通常論文]
  • Hiroshi Teramoto, Kenji Kondo, Shyuichi Izumiya, Mikito Toda, Tamiki Komatsuzaki JOURNAL OF MATHEMATICAL PHYSICS 58 (7) 2017年07月 [査読有り][通常論文]
     
    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年 [査読無し][通常論文]
  • 小松崎 民樹 人工知能学会全国大会論文集 2017 (0) 2I4OS10b5 -2I4OS10b5 2017年 [査読無し][通常論文]
     

    近年、圧縮センシング等の発展に加えて、生きた細胞のラマン分光画像がつくる高次元空間のうち、少数次元で細胞状態を分類できることなどが明らかとなってきた。本講演では、低いシグナル/ノイズ比を考慮に入れたファジクラスタリングによる細胞状態分別に関する研究成果を紹介しつつ、情報科学と計測科学の融合が如何に生命科学において重要であるかを論じる

  • 寺本 央, 泉屋 周一, 小松崎 民樹 日本物理学会講演概要集 72 (0) 2624 -2624 2017年 [査読無し][通常論文]
  • 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年10月03日 [査読無し][通常論文]
     
    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年06月01日 [査読無し][通常論文]
     
    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, 髙橋 正彦, 小松﨑 民樹 化学 = Chemistry 71 (5) 25 -30 2016年05月 [査読無し][通常論文]
  • 小松崎 民樹 生物物理 56 (4) 197 -197 2016年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年09月24日 [査読無し][通常論文]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki NONLINEARITY 28 (8) 2677 -2698 2015年08月 [査読有り][通常論文]
     
    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, 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 日本細胞生物学会大会講演要旨集 67回 162 -162 2015年06月 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2015 (ICCMSE 2015) 1702 2015年 [査読有り][通常論文]
     
    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 70 (0) 2568 -2568 2015年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年12月11日 [査読無し][通常論文]
  • 小松崎民樹 生体の科学 65 (5) 444 -445 2014年10月15日 [査読無し][通常論文]
  • 小松崎民樹 日本物理学会講演概要集 69 (2) 221 2014年08月22日 [査読無し][通常論文]
  • 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年08月22日 [査読無し][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki RSC Theoretical and Computational Chemistry Series 154 -179 2014年03月27日 [査読無し][通常論文]
  • 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年03月05日 [査読無し][通常論文]
  • 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年03月05日 [査読無し][通常論文]
  • 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年03月05日 [査読無し][通常論文]
  • 宮川 尚紀, 寺本 央, 河合 信之輔, 李 振風, 小松崎 民樹 日本物理学会講演概要集 69 (0) 334 -334 2014年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 寺本 央, 戸田 幹人, 小松崎 民樹 日本物理学会講演概要集 69 (0) 437 -437 2014年 [査読無し][通常論文]
  • 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年11月 [査読無し][通常論文]
  • 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年03月 [査読無し][通常論文]
  • 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年03月 [査読無し][通常論文]
  • 寺本 央, 戸田 幹人, 小松崎 民樹 日本物理学会講演概要集 68 (0) 318 -318 2013年 [査読無し][通常論文]
  • 永幡 裕, 寺本 央, 李 振飆, 河合 信之輔, 小松崎 民樹 日本物理学会講演概要集 68 (0) 337 -337 2013年 [査読無し][通常論文]
  • 河合 信之輔, Cooper David, Landes Christy, Mootz Henning D., Yang Haw, 小松崎 民樹 日本物理学会講演概要集 68 (0) 462 -462 2013年 [査読無し][通常論文]
  • 小松崎 民樹, 戸田 幹人 日本物理學會誌 67 (7) 521 -521 2012年07月05日 [査読無し][通常論文]
  • 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年03月 [査読無し][通常論文]
  • Tatyana G. Terentyeva, Hans Engelkamp, Alan E. Rowan, Tamiki Komatsuzaki, Johan Hofkens, Chun Biu Li, Kerstin Blank ACS Nano 6 (1) 346 -354 2012年01月24日 [査読有り][通常論文]
     
    Figure Persented: 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 α-chymotrypsin, no characteristics of dynamic disorder was found. In light of these results, dynamic disorder might not be a general sign of enzymatic reactions. © 2011 American Chemical Society.
  • 菊地 正浩, 河合 信之輔, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 67 (0) 431 -431 2012年 [査読無し][通常論文]
  • Akinori Baba, Tamiki Komatsuzaki SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146 146 299 -327 2012年 [査読有り][通常論文]
  • T. Komatsuzaki, M. Kawakami, S. Takahashi, H. Yang, R. J. Silbey SINGLE-MOLECULE BIOPHYSICS: EXPERIMENT AND THEORY, VOL 146 146 XIII -XV 2012年 [査読無し][通常論文]
     
    © 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年 [査読無し][通常論文]
  • 千葉 勇太, 河合 信之輔, 馬場 昭典, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 67 (0) 430 -430 2012年 [査読無し][通常論文]
  • 宮川 尚紀, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 67 (0) 363 -363 2012年 [査読無し][通常論文]
  • 永幡 裕, 河合 信之輔, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 67 (0) 300 -300 2012年 [査読無し][通常論文]
  • 寺本 央, 戸田 幹人, 小松崎 民樹 日本物理学会講演概要集 67 (0) 300 -300 2012年 [査読無し][通常論文]
  • 河合 信之輔, 寺本 央, 小松崎 民樹 日本物理学会講演概要集 67 (0) 397 -397 2012年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 寺本 央, 戸田 幹人, 小松崎 民樹 物性研究 97 (3) 547 -559 2011年12月 [査読無し][通常論文]
     
    本稿では、小松崎と田崎秀一氏との17年前の(財)基礎化学研究所でのお茶のみ場での議論等から、はじまった一連の研究が、法双曲不変多様体、安定/不安定多様体の研究を経て、どのような展開をむかえ、どのように広がっているかを、高次元系への展開を中心にして、それらの研究の一翼を担った著者たちの視点から論ずる。力学系において、法双曲不変多様体は構造安定な不変多様体を代表するものであり、そこから伸びる安定/不安定多様体は、特にそれらの力学系の余次元が低いものは、相空間中の輸送現象を理解するために重要な役割を果たす。そのことは裏を返せば、法双曲不変多様体の崩壊も、輸送現象に重要な影響を与えうるということを示唆する。例えば、我々が近年発見した「反応座標のスイッチング」と呼ばれる現象も法双曲不変多様体の崩壊により引き起こされるものである。法双曲不変多様体の崩壊メカニズムを論ずるために、我々は、その法双曲不変多様体に埋め込まれている不安定周期軌道に着目する。我々の分類によると、一般力学系に対しては、法双曲不変多様体の不安定周期軌道周りの崩壊パターンは6種類に分類できることがわかる。最後に、より大域的な崩壊メカニズムとそのメカニズムの次元依存性に関して述べる。
  • 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年11月23日 [査読無し][通常論文]
  • Tamiki Komatsuzaki, R. Stephen Berry, David M. Leitner Advances in Chemical Physics 145 2011年07月01日 [査読無し][通常論文]
  • 寺本 央, 小松崎 民樹 数理解析研究所講究録 1742 (1742) 127 -136 2011年05月 [査読無し][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 134 (11) 114523 -114523 2011年03月 [査読有り][通常論文]
     
    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]
  • Kiyoto Kamagata, Akinori Baba, Tamiki Komatsuzaki, Satoshi Takahashi BIOPHYSICAL JOURNAL 100 (3) 212 -213 2011年02月 [査読有り][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 134 (8) 084304 -084304 2011年02月 [査読有り][通常論文]
     
    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]
  • Akinori Baba, Tamiki Komatsuzaki Physical Chemistry Chemical Physics 13 (4) 1395 -1406 2011年01月28日 [査読有り][通常論文]
     
    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 molecule level. © 2011 the Owner Societies.
  • Shinnosuke Kawai, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 134 (2) 024317 -024317 2011年01月 [査読有り][通常論文]
     
    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]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki PHYSICAL REVIEW LETTERS 106 (5) 054101 -054101 2011年01月 [査読有り][通常論文]
     
    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年 [査読有り][通常論文]
  • 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年 [査読有り][通常論文]
  • 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年 [査読有り][通常論文]
  • 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年 [査読有り][通常論文]
     
    © 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年 [査読有り][通常論文]
     
    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年 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13 (48) 21217 -21229 2011年 [査読有り][通常論文]
     
    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.
  • 寺本 央, 戸田 幹人, 小松崎 民樹 日本物理学会講演概要集 66 (0) 340 -340 2011年 [査読無し][通常論文]
  • 伊藤 正寛, 馬場 昭典, 李 振風, 小松崎 民樹 日本物理学会講演概要集 66 (0) 408 -408 2011年 [査読無し][通常論文]
  • 寺本 央, 戸田 幹人, 小松崎 民樹 日本物理学会講演概要集 66 (0) 236 -236 2011年 [査読無し][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (47) 15382 -15391 2010年12月 [査読有り][通常論文]
     
    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) 037113 -037113 2010年07月13日 [査読有り][通常論文]
     
    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. © 2010 American Institute of Physics.
  • Yasuhiro Matsunaga, Chun-Biu Li, Tamiki Komatsuzaki PHYSICAL REVIEW E 82 (1) 016213 -016213 2010年07月 [査読有り][通常論文]
     
    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) 048304 -048304 2010年07月 [査読有り][通常論文]
     
    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.
  • Tamiki Komatsuzaki, Chun-Biu Li, Akinori Baba BIOPHYSICAL JOURNAL 98 (3) 184A -184A 2010年01月 [査読有り][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12 (27) 7636 -7647 2010年 [査読有り][通常論文]
     
    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年 [査読有り][通常論文]
     
    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.
  • Tamiki Komatsuzaki, Chun Biu Li, Shinnosuke Kawai NUMERICAL ANALYSIS AND APPLIED MATHEMATICS, VOLS I-III 1281 1582 -1584 2010年 [査読有り][通常論文]
     
    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 (dot) 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.
  • 永幡 裕, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 65 (0) 327 -327 2010年 [査読無し][通常論文]
  • 桜井 大督, 小松崎 民樹, 寺本 央, 李 振風 日本物理学会講演概要集 65 (0) 330 -330 2010年 [査読無し][通常論文]
  • 寺本 央, 小松崎 民樹 日本物理学会講演概要集 65 (0) 391 -391 2010年 [査読無し][通常論文]
  • 宮川 尚紀, 寺本 央, 李 振風, 小松崎 民樹 日本物理学会講演概要集 65 (0) 399 -399 2010年 [査読無し][通常論文]
  • 河合 信之輔, 小松崎 民樹 日本物理学会講演概要集 65 (0) 410 -410 2010年 [査読無し][通常論文]
  • Shinnosuke Kawai, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 131 (22) 224506 -224506 2009年12月 [査読有り][通常論文]
     
    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) 224505 -224505 2009年12月 [査読有り][通常論文]
     
    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年05月11日 [査読有り][通常論文]
     
    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 singlemolecule 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. © 2009 American Chemical Society.
  • Chun-Biu Li, Mikito Toda, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 130 (12) 124116 -124116 2009年03月 [査読有り][通常論文]
     
    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 生物物理 49 (0) S165 2009年 [査読無し][通常論文]
  • 小松崎 民樹 物性研究 91 (2) 121 -130 2008年11月 [査読無し][通常論文]
     
    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。
  • 小松崎 民樹 生物物理 48 (5) 282 -283 2008年09月25日 [査読無し][通常論文]
  • Hiroshi Teramoto, Tamiki Komatsuzaki JOURNAL OF CHEMICAL PHYSICS 129 (9) 094302 -094302 2008年09月 [査読有り][通常論文]
     
    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) 017202 -017202 2008年07月 [査読有り][通常論文]
     
    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.
  • Chun Biu Li, Haw Yang, Tamiki Komatsuzaki Proceedings of the National Academy of Sciences of the United States of America 105 (2) 536 -541 2008年01月15日 [査読有り][通常論文]
     
    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 over time. 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. © 2008 by The National Academy of Sciences of the USA.
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda PHYSICAL REVIEW E 77 (1) 2008年01月 [査読有り][通常論文]
  • Sei Kazuto, Baba Akinori, Li Chun-Biu, Komatsuzaki Tamiki 生物物理 48 (0) S137 2008年 [査読無し][通常論文]
  • 松永 康佑, 小松崎 民樹 高分子 57 (2) 58 -61 2008年 [査読有り][通常論文]
     
    複数の階層的時間スケールにまたがるタンパク質の"複雑"なダイナミックスを特徴づけるために,従来のリヤプノフ指数を有限サイズ領域に拡張した有限サイズリヤプノフ指数という解析手法を導入する。粗視化タンパク質モデルの折れたたみダイナミックスに対して,この手法を応用するとともに,観測された異常拡散現象について議論する。
  • 白川 智弘, 郡司 ペギオ幸夫, 小松崎 民樹 遊・星・人 : 日本惑星科学会誌 16 (4) 322 -329 2007年12月25日 [査読無し][通常論文]
     
    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) 238103 -238103 2007年12月 [査読有り][通常論文]
     
    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.
  • 寺本 央, 小松崎 民樹 生物物理 47 (Suppl.1) S41 -S41 2007年11月 [査読無し][通常論文]
  • 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年11月 [査読無し][通常論文]
  • Akira Shojiguchi, Chun-Biu Li, Tamiki Komatsuzaki, Mikito Toda PHYSICAL REVIEW E 76 (5) 056205 -056205 2007年11月 [査読有り][通常論文]
     
    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.
  • Tamiki Komatsuzaki, Akinori Baba ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 2007年08月 [査読有り][通常論文]
  • Chun Biu Li, Tamiki Komatsuzaki ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 234 2007年08月 [査読有り][通常論文]
  • Shinnosuke Kawai, Yo Fujimura, Okitsugu Kajimoto, Takefumi Yamashita, Chun Biu Li, Tamiki Komatsuzaki, Tamiki Komatsuzaki, Mikito Toda Physical Review A 75 (2) 2007年02月 [査読無し][通常論文]
     
    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 (D1) + N2 O→NO+NO, which was found to exhibit efficient energy exchange between the two NO stretching modes despite the short lifetime of the reaction intermediate. 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. © 2007 The American Physical Society.
  • 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 (0) S139 2007年 [査読無し][通常論文]
  • 清 一人, 小松崎 民樹 日本物理学会講演概要集 62 (0) 335 -335 2007年 [査読無し][通常論文]
  • デミールプラーク ムスタファ, 小松崎 民樹 日本物理学会講演概要集 62 (0) 297 -297 2007年 [査読無し][通常論文]
  • 納多 哲史, 馬場 昭典, 小松崎 民樹 日本物理学会講演概要集 62 (0) 342 -342 2007年 [査読無し][通常論文]
  • 松永 康佑, 李 振風, 小松崎 民樹 日本物理学会講演概要集 62 (0) 337 -337 2007年 [査読無し][通常論文]
  • 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年12月05日 [査読有り][通常論文]
     
    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. © 2006 by The National Academy of Sciences of the USA.
  • C. B. Li, A. Shojiguchi, M. Toda, T. Komatsuzaki Few-Body Systems 40 (1-2) 129 2006年12月 [査読有り][通常論文]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki PHYSICAL REVIEW LETTERS 97 (12) 2006年09月 [査読無し][通常論文]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki PHYSICAL REVIEW LETTERS 97 (12) 2006年09月 [査読有り][通常論文]
  • Chun-Biu Li, Akira Shoujiguchi, Mikito Toda, Tamiki Komatsuzaki Physical review letters 97 (2) 028302 -028302 2006年07月14日 [査読有り][通常論文]
     
    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年07月 [査読無し][通常論文]
     
    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年07月 [査読無し][通常論文]
     
    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年07月 [査読無し][通常論文]
     
    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年07月 [査読有り][通常論文]
     
    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.
  • C. B. Li, A. Shojiguchi, M. Toda, T. Komatsuzaki Few-Body Systems 38 (2-4) 173 -179 2006年06月 [査読有り][通常論文]
     
    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年04月 [査読無し][通常論文]
     
    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年04月 [査読無し][通常論文]
     
    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年04月 [査読無し][通常論文]
     
    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年04月 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
  • 1分子時系列解析と分子科学
    2006年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Causal structures ofε-machine constructed from time series: Analogy with dynamical systems theory
    2006年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 分子異性化反応のモデルにおける異常拡散
    2006年 [査読無し][通常論文]
  • Randomness and Memory in Single Molecule Time Series
    2006年 [査読無し][通常論文]
  • Extracting Dynamics from Time Series Data of single Molecule Experiments on a photon-by-photon Basis
    2006年 [査読無し][通常論文]
  • A discrete wavelet time series analysis;the hierarchy of dynamics of biomolecules
    2006年 [査読無し][通常論文]
  • A construction of the underlying free energy landscape from single molecule time series
    2006年 [査読無し][通常論文]
  • Extracting Protein Conformational Dynamics on a Photon-by-Photon Basis in Single Molecule Electron Transfer
    2006年 [査読無し][通常論文]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006年 [査読無し][通常論文]
  • A Local ergodic state analysis of single molecule time series
    2006年 [査読無し][通常論文]
  • Construction of Effective Free Energy Landscape from Single Molecule Time Series of Biomolecules
    2006年 [査読無し][通常論文]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006年 [査読無し][通常論文]
  • A Local ergodic state analysis of single molecule time series
    2006年 [査読無し][通常論文]
  • Dynamical Hierarchy of Transitions in Chemical Reactions
    2006年 [査読無し][通常論文]
  • Water Field Dynamics in the Vicinity of Proteins
    2006年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Geometrical Structure buried in the Phase Space of Stochastic Structural Transition
    物性研究 86-1,77-81 2006年 [査読無し][通常論文]
  • Dynamical Foundation and Limitations of Statistical Reaction Theory
    Communications in Nonlinear Science and Numerical Simulation in press 2006年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 「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年 [査読無し][通常論文]
  • Randomness and Memory in Single Molecule Time Series
    2006年 [査読無し][通常論文]
  • Extracting Dynamics from Time Series Data of single Molecule Experiments on a photon-by-photon Basis
    2006年 [査読無し][通常論文]
  • A discrete wavelet time series analysis;the hierarchy of dynamics of biomolecules
    2006年 [査読無し][通常論文]
  • A construction of the underlying free energy landscape from single molecule time series
    2006年 [査読無し][通常論文]
  • Extracting Protein Conformational Dynamics on a Photon-by-Photon Basis in Single Molecule Electron Transfer
    2006年 [査読無し][通常論文]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006年 [査読無し][通常論文]
  • A Local ergodic state analysis of single molecule time series
    2006年 [査読無し][通常論文]
  • Construction of Effective Free Energy Landscape from Single Molecule Time Series of Biomolecules
    2006年 [査読無し][通常論文]
  • A Persistence of Long-Time Memory in Coarse-Grained Site-Velocity Field of Liquid Water
    2006年 [査読無し][通常論文]
  • A Local ergodic state analysis of single molecule time series
    2006年 [査読無し][通常論文]
  • What can one learn about the underlying free energy landscape or dynamical structure from single molecule time series?
    2006年 [査読無し][通常論文]
  • Dynamical Hierarchy of Transitions in Chemical Reactions
    2006年 [査読無し][通常論文]
  • Water Field Dynamics in the Vicinity of Proteins
    2006年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Dynamical Foundation and Limitations of Statistical Reaction Theory
    Communications in Nonlinear Science and Numerical Simulation in press 2006年 [査読無し][通常論文]
  • Sei Kazuto, Baba Akinori, Li Chun Biu, Komatsuzaki Tamiki 生物物理 46 (2) S281 2006年 [査読無し][通常論文]
  • 納多 哲史, 馬場 昭典, 小松崎 民樹 日本物理学会講演概要集 61 (0) 348 -348 2006年 [査読無し][通常論文]
  • Li Chun Biu, 馬場 昭典, 小松崎 民樹 日本物理学会講演概要集 61 (0) 347 -347 2006年 [査読無し][通常論文]
  • 小路口 暁, Li Chun Biu, 小松崎 民樹, 戸田 幹人 日本物理学会講演概要集 61 (0) 267 -267 2006年 [査読無し][通常論文]
  • 小路口 暁, Li Chun Biu, 小松崎 民樹, 戸田 幹人, リー チュンビュー 日本物理学会講演概要集 61 (0) 217 -217 2006年 [査読無し][通常論文]
  • Chun-Biu Li, Yasuhiro Matsunaga, Mikito Toda, Tamiki Komatsuzaki The Journal of chemical physics 123 (18) 184301 -184301 2005年11月08日 [査読有り][通常論文]
     
    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.
  • 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年05月12日 [査読無し][通常論文]
  • 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年05月12日 [査読無し][通常論文]
     
    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.
  • Tamiki Komatsuzaki, Kyoko Hoshino, Yasuhiro Matsunaga, Gareth J Rylance, Roy L Johnston, David J Wales The Journal of chemical physics 122 (8) 84714 -84714 2005年02月22日 [査読有り][通常論文]
     
    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 Go-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.
  • 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年 [査読無し][通常論文]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 生体分子と粗視化した水の動的相互作用の抽出
    2005年 [査読無し][通常論文]
  • HCNの異性化反応の非エルゴード性
    2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 化学反応はなぜ生起するのか?:遷移状態概念再考
    2005年 [査読無し][通常論文]
  • 生体分子と粗視化した水の動的相互作用の抽出
    2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Dynamical Hierarchy in Transitions of ChemicalReactions:Definability of No-return Transition State
    2005年 [査読無し][通常論文]
  • How does single molecule time series tell us about the underlying multidimensional free energy and state space landscapes?
    2005年 [査読無し][通常論文]
  • Complexity of Dynamics on Multidimensional Energy Landscapes in Chemical reactions & Proteins
    2005年 [査読無し][通常論文]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005年 [査読無し][通常論文]
  • A construction of multidimensional free energy landscape from an ensemble of single molecule time series of biomolecules
    2005年 [査読無し][通常論文]
  • Vibrational energy redistribution via geometrical structures in the multi-dimensional phase space of chemical reaction
    2005年 [査読無し][通常論文]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005年 [査読無し][通常論文]
  • Geometrical structure of the multidimensional phase space transport in chemical reactions
    2005年 [査読無し][通常論文]
  • Dynamical Hierarchy in Transitions of Chemical Reactions
    2005年 [査読無し][通常論文]
  • Dynamical Hierarchy of Transitions in Chemical Reactions and Protein Dynamics
    2005年 [査読無し][通常論文]
  • Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction
    物性研究 84-3、481-482 2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005年 [査読無し][通常論文]
  • Dynamical Reaction Conduit in Chaotic Multi-dimensional Phase Space: Molecular Motions and the Origin of Stochastic Transitions
    2005年 [査読無し][通常論文]
  • Dynamical Hierarchy in Transitions of ChemicalReactions:Definability of No-return Transition State
    2005年 [査読無し][通常論文]
  • How does single molecule time series tell us about the underlying multidimensional free energy and state space landscapes?
    2005年 [査読無し][通常論文]
  • Complexity of Dynamics on Multidimensional Energy Landscapes in Chemical reactions & Proteins
    2005年 [査読無し][通常論文]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005年 [査読無し][通常論文]
  • A construction of multidimensional free energy landscape from an ensemble of single molecule time series of biomolecules
    2005年 [査読無し][通常論文]
  • Vibrational energy redistribution via geometrical structures in the multi-dimensional phase space of chemical reaction
    2005年 [査読無し][通常論文]
  • How does a polypeptide give rise to the helix-coil transition with interacting the surrounding water field?
    2005年 [査読無し][通常論文]
  • Geometrical structure of the multidimensional phase space transport in chemical reactions
    2005年 [査読無し][通常論文]
  • Dynamical Hierarchy in Transitions of Chemical Reactions
    2005年 [査読無し][通常論文]
  • Dynamical Hierarchy of Transitions in Chemical Reactions and Protein Dynamics
    2005年 [査読無し][通常論文]
  • Chaotic Reaction Dynamics and the Phase Space Geometry of Multidimensional Chemical Reaction
    2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 松永 康佑, Biu Li Chun, 小松崎 民樹 生物物理 45 (0) S46 2005年 [査読無し][通常論文]
  • 納多 哲史, 馬場 昭典, 小松崎 民樹 生物物理 45 (0) S48 2005年 [査読無し][通常論文]
  • 佐藤 祥子, 馬場 昭典, 小松崎 民樹 生物物理 45 (0) S210 2005年 [査読無し][通常論文]
  • 納多 哲史, 馬場 昭典, 小松崎 民樹 日本物理学会講演概要集 60 (0) 243 -243 2005年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 化学反応の動力学とカオスー現状と将来
    2004年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 「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年 [査読無し][通常論文]
  • What can a Single Molecule Time Series Data Tell Us? -Regularity in Structural Transitions on MultiBasin Energy Landscapes of Proteins-
    2004年 [査読無し][通常論文]
  • Regularity in Chaotic Tramsitions on Multi-Basin Energy Landscapes
    2004年 [査読無し][通常論文]
  • How can We Extract Dynamical Information from Time Series Data?
    2004年 [査読無し][通常論文]
  • Geometrical Structure of Phase Space for Chemical Reaction Dynamics: What Kinds of Molecular Motions are Associated with Phase Space Modes in Chaos?
    2004年 [査読無し][通常論文]
  • Geometrical Structure Buried in the Phase space of Stochastic Structural Transition: Perspectives from Time Series Analysis
    2004年 [査読無し][通常論文]
  • Y Matsunaga, T Komatsuzaki SLOW DYNAMICS IN COMPLEX SYSTEMS 708 342 -343 2004年 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
     
    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.
  • K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki SLOW DYNAMICS IN COMPLEX SYSTEMS 708 344 -345 2004年 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
  • Regularity in Chaotic Tramsitions on Multi-Basin Energy Landscapes
    2004年 [査読無し][通常論文]
  • How can We Extract Dynamical Information from Time Series Data?
    2004年 [査読無し][通常論文]
  • Geometrical Structure of Phase Space for Chemical Reaction Dynamics: What Kinds of Molecular Motions are Associated with Phase Space Modes in Chaos?
    2004年 [査読無し][通常論文]
  • Geometrical Structure Buried in the Phase space of Stochastic Structural Transition: Perspectives from Time Series Analysis
    2004年 [査読無し][通常論文]
  • K Hoshino, Y Matsunaga, M Miller, DJ Wales, T Komatsuzaki SLOW DYNAMICS IN COMPLEX SYSTEMS 708 344 -345 2004年 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
     
    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 Kostov, M Toda, Y Matsunaga, T Komatsuzaki ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY 226 U427 -U427 2003年09月 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • タンパク質エネルギー地形における自由度の縮約化
    2003年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 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年 [査読無し][通常論文]
  • 松永 康佑, 小松崎 民樹 生物物理 43 (0) S92 2003年 [査読無し][通常論文]
  • 星野 恭子, 松永 康佑, 古賀 信康, 高田 彰二, 小松崎 民樹 日本物理学会講演概要集 58 (0) 334 -334 2003年 [査読無し][通常論文]
  • 松永 康佑, 小松崎 民樹 日本物理学会講演概要集 58 (0) 356 -356 2003年 [査読無し][通常論文]
  • 小松崎 民樹, 松永 康佑, 戸田 幹人 日本物理学会講演概要集 58 (0) 356 -356 2003年 [査読無し][通常論文]
  • 小松崎 民樹, 松永 康佑 生物物理 42 (6) 285 -289 2002年11月25日 [査読無し][通常論文]
     
    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.
  • Tamiki Komatsuzaki, R. Stephen Berry Journal of Physical Chemistry A 106 (45) 10945 -10950 2002年11月14日 [査読有り][通常論文]
     
    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.
  • Yasuhiro Matsunaga, Konstantin S. Kostov, Tamiki Komatsuzaki Journal of Physical Chemistry A 106 (45) 10898 -10907 2002年11月14日 [査読有り][通常論文]
     
    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/fα(α ≈ 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 ∼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.
  • 小松崎 民樹 物性研究 78 (4) 354 -364 2002年07月 [査読無し][通常論文]
     
    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年07月 [査読無し][通常論文]
     
    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年01月08日 [査読無し][通常論文]
  • T Komatsuzaki, RS Berry ADVANCES IN CHEMICAL PHYSICS, VOL 123 123 79 -152 2002年 [査読無し][通常論文]
  • T Komatsuzaki, RS Berry JOURNAL OF CHEMICAL PHYSICS 115 (9) 4105 -4117 2001年09月 [査読無し][通常論文]
     
    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年07月 [査読無し][通常論文]
     
    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年04月 [査読無し][通常論文]
     
    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。
  • 小松崎 民樹 日本物理学会講演概要集 56 (0) 211 -211 2001年 [査読無し][通常論文]
  • 松永 康佑, 小松崎 民樹 日本物理学会講演概要集 56 (0) 272 -272 2001年 [査読無し][通常論文]
  • T Komatsuzaki, RS Berry JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM 506 55 -70 2000年07月 [査読無し][通常論文]
     
    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年05月 [査読無し][通常論文]
     
    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年03月 [査読無し][通常論文]
     
    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.
  • 小松崎 民樹, BERRY Stephen 日本物理学会講演概要集 53 (0) 702 -702 1998年 [査読無し][通常論文]
  • K Sawada, F Chigira, K Satoh, T Komatsuzaki JOURNAL OF THE CHEMICAL SOCIETY-FARADAY TRANSACTIONS 93 (10) 1903 -1908 1997年05月 [査読無し][通常論文]
     
    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年01月 [査読無し][通常論文]
     
    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年08月 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
     
    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年 [査読無し][通常論文]
     
    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年03月 [査読無し][通常論文]
     
    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.

受賞

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

共同研究・競争的資金等の研究課題

  • 細胞集団とシンギュラリティ細胞のデータ駆動型数理解析技術の開発
    日本学術振興会:科学研究費助成事業 新学術領域研究(研究領域提案型)
    研究期間 : 2018年06月 -2023年03月 
    代表者 : 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
    科学技術振興機構:CREST
    研究期間 : 2016年10月 -2022年03月 
    代表者 : 小松崎 民樹
  • 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
    研究期間 : 2018年04月 -2020年03月 
    代表者 : 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
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2017年04月 -2020年03月 
    代表者 : 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
    日本学術振興会:科学研究費助成事業 新学術領域研究(研究領域提案型)
    研究期間 : 2018年04月 -2019年03月 
    代表者 : 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。
  • 細胞の集団と少数性のシステム生物学
    日本学術振興会:科学研究費助成事業 挑戦的萌芽研究
    研究期間 : 2016年04月 -2019年03月 
    代表者 : 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
    研究期間 : 2017年04月 -2018年03月 
    代表者 : 小松崎 民樹
  • 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
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2015年07月 -2018年03月 
    代表者 : 小松崎 民樹, 寺本 央
     
    法双曲的不変多様体の崩壊と呼ばれるカオス理論の概念を用い,系全体のエネルギーの増大とともに反応の経路が反応座標から非反応座標へと切り替わる新奇な分岐現象を見出すとともに、一様な電場と磁場を直交させた状況下で水素原子から電子が解離する反応を例にその実験的な検証方法を提案した。この他、反応ネットワーク上に定義された任意の分断面のなかでその往来の時間スケールが最も遅いものを「反応を支配する遷移状態」として定義し、複雑な反応時間の階層構造を抽出する方法などを新たに開発した。理論、実験において反応制御に対する新しい指針を提出することに成功した。
  • 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
    研究期間 : 2016年04月 -2017年03月 
    代表者 : 小松崎 民樹
  • 分子個性を彫り出すシステム生物学の探求
    日本学術振興会:科学研究費助成事業 挑戦的萌芽研究
    研究期間 : 2013年04月 -2016年03月 
    代表者 : 小松崎 民樹, 李 振風, 河合 信之輔
     
    開いているか/閉じているか,結合しているか/離れているか,といった有限個で連続的でない飛び飛びの値をもつ分子の時系列データから,分子の状態をネットワークという表現を用いて客観的に評価し,分子が将来取り得るデータ出力を予想する新しい解析手法を開発することなどに成功した。また、背後のモデルをあらかじめ想定しない汎用なデータ解析手法を開発し、細胞内“エネルギー通貨”であるアデノシン三リン酸(ATP)を合成するタンパク質F1-ATPaseにおける高効率なエネルギー変換の重要な仕組みを解明した。ATPの加水分解反応が反応順序を制御する“鍵”の役割をすることを新規に発見した。
  • 階層性と頑健性をもつ生命動態システムの解析基盤構築
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2013年04月 -2016年03月 
    代表者 : 小松崎 民樹, 李 振風, 寺本 央
     
    宇宙科学分野で進展してきたカオス理論をミクロな化学反応の動きに適用し、エネルギーが高くなると化学反応の行き先を切り替えるスイッチが広範囲に出現する新奇現象を理論的に予言し、その実験的な検証方法を提案するなど化学反応における基礎理論の構築に成功した。また、実験で計測されるシグナル/ノイズ比が低い1分子時系列データから、計測誤差・有限サンプリングによる誤差を正しく評価し、背後に存在する生体分子に関する情報(ネットワーク構造、エネルギー地形)を再構成するデータ駆動型数理科学の手法を開発し、その有用性を実証した。
  • 少数分子反応ネットワーク理論の構築-少数性と階層性の観点からのモデリング-
    日本学術振興会:科学研究費助成事業 新学術領域研究(研究領域提案型)
    研究期間 : 2011年04月 -2016年03月 
    代表者 : 冨樫 祐一, 小松崎 民樹, 李 振風, 寺本 央, 新海 創也, 津川 暁, 中川 正基
     
    触媒反応ネットワークにおける少数分子効果を予言する一般的理論、分子・サブユニット間の力学的な情報伝達の経路を評価する手法などを開発し、少数要素が関与する化学・力学複合的なネットワークへの理論的枠組みを整備した。尤度関数を必要としない変化点解析法、誤差を考慮に入れた自由エネルギー地形抽出法、データが保証していない過剰情報量を最小にするモデリング手法など、少数性生物学に関する計測に不可避のノイズを克服する解析手法を開発し、分子個性・細胞個性のデータ科学への基盤を構築した。これらを応用し、領域内の実験対象に即した理論を構築・実証した。
  • 多自由度カオスの相空間構造に基付く非平衡反応動力学の構築
    日本学術振興会:科学研究費助成事業 基盤研究(B)
    研究期間 : 2004年 -2006年 
    代表者 : 戸田 幹人, 小松崎 民樹
     
    (1)動力学的反応論の立場から、「遷移状態」概念の適用限界を明らかにした。この限界は次の二つの場合がある。第一は法双曲的不変多様体の分岐である。第二は法双曲的不変多様体上のカオスが強くなることに起因する「遷移状態」の消失である。第一は2自由度系でも起こりうるが、第二の場合は3自由度系以上でのみ見られる現象であり、これまで考えられてこなかった可能性である。法双曲的不変多様体近傍における標準形理論に基付いて従来の「遷移状態」概念が、このような二つの場合に適用できなくなること示すとともに、これを越える新たな理論的方向性を示唆した。 (2)非エルゴード適なポテンシャル井戸を持つ3自由度系以上の反応過程において、べき的な挙動が存在することを明らかにした。このようなべき的挙動の存在は、従来の現象論的な反応論で用いられてきたレート方程式の適用限界を示している。特に分子レベルの情報処理の問題と関連して、「マックスウエルの悪魔」の観点から見ても重要である。ウエーブレットを用いた共鳴解析に基付き、このべき的挙動が共鳴交差の階層性に起因する可能性を指摘した。 (3)ウエーブレットを用いた時系列解析をたんぱく質モデルの分子動力学に応用し、ゆっくりした集団運動の抽出に有用であることを示した。また非定常な分子動力学計算の時系列解析においても、多項式フィッティングと組み合わせることで、非定常な集団運動の抽出に有効であることを明らかにした。さらに時間スケールの異なる運動の間の相関関数を用いて、異なるスケール間の運動の伝達を解析した。
  • 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

教育活動情報

主要な担当授業

  • ナノ物性化学
    開講年度 : 2018年
    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

大学運営

学内役職歴

  • 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

委員歴

  • 2019年12月 - 現在   日本生物物理学会   Biophysics Physicobiology 副編集委員長
  • 2019年12月 - 現在   Biophysical Reviews, Springer Nature IUPAB   Special Issue Editor
  • 2019年06月 - 現在   科学技術振興機構・さきがけ「革新的な量子情報処理技術基盤の創出」   アドバイザー
  • 2019年06月 - 現在   日本生物物理学会   副会長
  • 2018年01月 - 現在   人工知能学会第2種研究会 計測インフォマティクス研究会 (Special Interest Group on Measurement Informatics: SIG-MEI)   幹事
  • 2017年04月 - 現在   生物物理学会北海道支部   幹事
  • 2017年02月 - 現在   “Scientific Reports” Division of Chemical Physics   Editorial Board
  • 2013年01月 - 現在   “Biophysics and Physicobiology”   Editorial Board
  • 2009年04月 - 現在   (財)新世代研究所「バイオ単分子研究会」   研究会委員
  • 2019年04月 - 2019年09月   JST/ERATO   選考パネルメンバー
  • 2018年04月 - 2018年09月   JST/ERATO   選考パネルメンバー
  • 2017年04月 - 2018年03月   日本化学会北海道支部   学会賞推薦委員・学術賞等推薦委員
  • 2015年06月 - 2017年06月   生物物理学会   理事・代議員
  • 2015年04月 - 2016年03月   科学技術調査資料作成委託事業「数学・数理科学を活用した異分野融合研究の動向調査(代表者:国立大学法人東北大学知の創出センター)」   協力機関責任者
  • 2014年03月 - 2016年02月   日本化学会北海道支部支部   役員(幹事)
  • 2014年01月 - 2015年06月   生物物理学会   代議員
  • 2009年04月 - 2012年03月   (財)国際高等研究所「諸科学の共通言語としての数学の発掘と数理科学への展開(高橋陽一郎<京都大学数理解析研究所教授>委員長)」   研究会委員
  • 2007年01月 - 2008年12月   生物物理学会   学会誌編集委員
  • 2006年01月 - 2008年12月   The Telluride science research center   Board of directors


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