研究者データベース

寺本 央(テラモト ヒロシ)
電子科学研究所 附属社会創造数学研究センター
准教授

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

  • 准教授

学位

  • 博士(学術)(東京大学)

ホームページURL

科研費研究者番号

  • 90463728

J-Global ID

研究キーワード

  • 集団運動   タンパク質   協同運動   Koopman演算子   Lagrange協同構造   Lagrangian Coherent Structure   エネルギー論   ペプチド   水   動力学   粗視化   連続の方程式   DNA   化学反応ダイナミックス   生物物理   化学物理   非平衡定常状態   エネルギー地形   ネットワーク   法双曲的不変多様体   遷移状態   一分子計測   カオス力学系   化学反応ダイナミクス   1分子計測(SMD)   生体分子   複雑ネットワーク   

研究分野

  • 自然科学一般 / 生物物理、化学物理、ソフトマターの物理

職歴

  • 2017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 准教授
  • 2016年10月 - 現在 科学技術振興機構 さきがけ研究者
  • 2016年06月 - 2017年03月 日立基礎研センタ 客員主任研究員
  • 2009年 - 2011年 北海道大学 電子科学研究所 助教

研究活動情報

論文

  • 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 Springer 2018年 [査読有り][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.
  • Alireza Hadjighasem, Daniel Karrasch, Hiroshi Teramoto, George Haller
    PHYSICAL REVIEW E 93 6 063107  2016年06月 [査読有り][通常論文]
     
    One of the ubiquitous features of real-life turbulent flows is the existence and persistence of coherent vortices. Here we show that such coherent vortices can be extracted as clusters of Lagrangian trajectories. We carry out the clustering on a weighted graph, with the weights measuring pairwise distances of fluid trajectories in the extended phase space of positions and time. We then extract coherent vortices from the graph using tools from spectral graph theory. Our method locates all coherent vortices in the flow simultaneously, thereby showing high potential for automated vortex tracking. We illustrate the performance of this technique by identifying coherent Lagrangian vortices in several two-and three-dimensional flows.
  • 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 [査読有り][通常論文]
     
    Markovian dynamics on complex reaction networks are one of the most intriguing subjects in a wide range of research fields including chemical reactions, biological physics, and ecology. To represent the global kinetics from one node (corresponding to a basin on an energy landscape) to another requires information on multiple pathways that directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discrete time Markov chain derived from first-order rate equations. The TSs can naturally take into account the multiple pathways connecting any pair of nodes. We also propose a new type of disconnectivity graph (DG) to capture the hierarchical organization of different time scales of reactions that can capture changes in the network due to changes in the observation. The crux is the introduction of the minimum conductance cut (MCC) in graph clustering, corresponding to the dividing surface across the network having the "smallest" transition probability between two disjoint subnetworks (superbasins on the energy landscape) in the network. We present a new combinatorial search algorithm for finding this MCC. We apply our method to a reaction network of Claisen rearrangement of allyl vinyl ether that consists of 23 nodes and 66 links (saddles on the energy landscape) connecting them. We compare the kinetic properties of our DG to those of the transition matrix of the rate equations and show that our graph can properly reveal the hierarchical, organization of time scales in a network.
  • 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.
  • Hiroshi Teramoto, Mikito Toda, Masahiko Takahashi, Hirohiko Kono, Tamiki Komatsuzaki
    PHYSICAL REVIEW LETTERS 115 9 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.
  • 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.
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    THEORETICAL CHEMISTRY ACCOUNTS 133 11 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  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.
  • Tahmina Sultana, Hiroaki Takagi, Miki Morimatsu, Hiroshi Teramoto, Chun-Biu Li, Yasushi Sako, Tamiki Komatsuzaki
    JOURNAL OF CHEMICAL PHYSICS 139 24 245101  2013年12月 [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 similar to 3 s) becomes rather complex in order to capture multiscale nonstationary kinetics emerging at longer timescales. It is also found that visiting the unbound form of the EGFR-Grb2 system approximately resets all information of history or memory of the process. (C) 2013 AIP Publishing LLC.
  • Hiroshi Teramoto, George Haller, Tamiki Komatsuzaki
    CHAOS 23 4 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  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.
  • Keiro Watanabe, Hiroshi Teramoto, Nobuaki Suzuki, Masayuki Inui, Hideaki Yukawa
    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 97 11 4917 - 4926 2013年06月 [査読有り][通常論文]
     
    The non-essential Corynebacterium glutamicum sigma factor, sigB, modulates global gene expression during the transition from exponential growth to the stationary phase. Utilizing a signal peptide derived from C. glutamicum R CgR_0949, a sigB disruption mutant able to secrete 3- to 5-fold more green fluorescence protein (GFP) and alpha-amylase than the wild type strain was isolated. The signal peptide selectively enabled the mutant to produce greater amounts of both proteins, which were in turn secreted in culture medium in greater quantities than previously acknowledged. A peak GFP productivity of 2.8 g/l was attained, representing the highest GFP productivity reported in C. glutamicum to date. CgR_0949 signal sequence length (30 residues), type (Tat) or the target protein identity (GFP or alpha-amylase) had no measurable effect on the magnitude of the protein accumulation and consequent secretion. It therefore follows that actual experimentation remains the fastest way to identify suitable signal sequences in C. glutamicum. More secretion studies may reveal even greater secretion productivity by C. glutamicum and consequently present an attractive avenue to further enhance the utility of C. glutamicum as an industrial workhorse.
  • Yutaka Nagahata, Hiroshi Teramoto, Chun-Biu Li, Shinnosuke Kawai, Tamiki Komatsuzaki
    PHYSICAL REVIEW E 87 6 062817  2013年06月 [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.
  • Hiroshi Teramoto, Keiro Watanabe, Nobuaki Suzuki, Masayuki Inui, Hideaki Yukawa
    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 91 3 677 - 687 2011年08月 [査読有り][通常論文]
     
    Efficient protein secretion, the basis of large-scale production of many compounds central to the biotechnology industry, is achieved by signal peptide and propeptide optimization in addition to optimizing host factors affecting heterologous protein production. Here, we fused green fluorescent protein (GFP) to the recently identified Tat-type secretory signal peptide of CgR0949 to demonstrate a high-yield protein secretion system of Corynebacterium glutamicum. The resultant secretion vector facilitated effective secretion of active-form GFP (20 mg l(-1)) into C. glutamicum culture medium. The expression of GFP was enhanced 2.9-fold using the Shine-Dalgarno sequence of triosephosphate isomerase in the secretion vector. Moreover, GFP drastically accumulated in the culture supernatant upon addition of calcium chloride even though Ca2+ addition did neither enhanced the transcription of gfp nor resulted in the accumulation of cytosolic GFP. Active-form GFP concentration reached 1.8 g l(-1) after 48-h incubation in a jar fermentor. Likewise, alpha-amylase accumulation in C. glutamicum cultures was also enhanced by Ca2+ addition, suggesting that Ca2+ may affect general protein secretion in C. glutamicum.
  • Masatomo Ito, Tatsuya Suzuki, Naoki Wakiyama, Hiroshi Teramoto, Etsuo Yonemochi, Katsuhide Terada
    CHEMICAL & PHARMACEUTICAL BULLETIN 59 7 868 - 873 2011年07月 [査読有り][通常論文]
     
    A nondestructive transmittance near-infrared (NIR) method for detecting off-centered cores in dry-coated (DC) tablets was developed as a monitoring system in the DC tableting process. Caffeine anhydrate was used as a core active pharmaceutical ingredient (API), and DC tablets were made by the direct compression method. NIR spectra were obtained from these intact DC tablets using the transmittance method. The reference assay was performed with H PLC. Calibration models were generated by partial least squares (PLS) regression and principal component regression (PCR) utilizing external validations. Hierarchical cluster analysis (HCA) of the results confirmed that NIR spectroscopy correctly detected off-centered cores in DC tablets. We formulated and used the Centering Index (CI) to evaluate the precision of core alignment and generated an NIR calibration model that could correctly predict this index. The principal component (PC) 1 loading vector of the final calibration model indicated that it could specifically detect the misalignment of tablet cores. The model also had good linearity and accuracy. The CIs of unknown sample tablets predicted by the final calibration model and those calculated through the HPLC analysis were closely parallel with each other. These results demonstrate the validity of the final calibration model and the utility of the transmittance NIR spectroscopic method developed in this study as a monitoring system in DC tableting process.
  • 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 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.
  • 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]
  • Hiroshi Teramoto, Mikito Toda, Tamiki Komatsuzaki
    PHYSICAL REVIEW LETTERS 106 5 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.
  • Naoki Miyagawa, Hiroshi Teramoto, Chun-Biu Li, Tamiki Komatsuzaki
    Complex Systems 20 2 2011年 [査読有り][通常論文]
  • Masatomo Ito, Tatsuya Suzuki, Shuichi Yada, Hiroaki Nakagami, Hiroshi Teramoto, Etsuo Yonemochi, Katsuhide Terada
    JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS 53 3 396 - 402 2010年11月 [査読有り][通常論文]
     
    Calibration models for nondestructive NIR analysis of API (active pharmaceutical ingredient) contents in two separate layers of intact bilayer tablets were established. These models will enable the use of NIR transmittance spectroscopy in bilayer tableting processes for the control of API contents in separate layers Acetaminophen and caffeine anhydrate were used as APIs, and tablets were made by the direct compression method Their NIR spectra were measured in the transmittance mode The reference assay was performed by HPLC. Calibration models were generated by the partial least-squares (PLS) regression The initial calibration generated models with insufficient linearity and accuracy because the fluctuation range of tablet thickness was excessively large and irrelevant information on the thickness fluctuation was included in the models. By narrowing the fluctuation range to determine the proper range for acceptable prediction accuracy, it was confirmed that calibration models with less irrelevant information can be generated when the range was 4 30 +/- 0 06 mm or narrower. Furthermore, the fluctuation range of 4 30 +/- 0.06 mm was considered to be empirically valid in covering the fluctuation actually observed in ordinary tableting processes Thus, the sample tablets within this range were used to generate the final calibration models, and calibration models sufficient in linearity and accuracy were established In addition, It was proven that controlling the irradiated side was unnecessary. Namely, It is not necessary to keep the same side of sampled tablets for the online NIR analysis during bilayer tableting It is useful, in order to obtain adequate calibration models, to evaluate the variable factors that affect the linearity and accuracy of the generated models and restrict the range of models or use a subset of prepared samples Loading vectors, explained variances, and correlation coefficients between components and scores are important for the evaluation of variable factors. (C) 2010 Elsevier B.V All rights reserved.
  • Hiroshi Teramoto, Tamiki Komatsuzaki
    CHAOS 20 3 037113  2010年09月 [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. (C) 2010 American Institute of Physics. [doi:10.1063/1.3491097]
  • Nomathemba Loice Chigu, Sinji Hirosue, Chie Nakamura, Hiroshi Teramoto, Hirofumi Ichinose, Hiroyuki Wariishi
    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 87 5 1907 - 1916 2010年08月 [査読有り][通常論文]
     
    Cytochrome P450 monooxygenases (P450s) involved in anthracene metabolism by the white-rot basidiomycete Phanerochaete chrysosporium were identified by comprehensive screening of both catalytic potentials and transcriptomic profiling. Functional screening of P. chrysosporium P450s (PcCYPs) revealed that 14 PcCYP species catalyze stepwise conversion of anthracene to anthraquinone via intermediate formation of anthrone. Moreover, transcriptomic profiling explored using a complementary DNA microarray system demonstrated that 12 PcCYPs are up-regulated in response to exogenous addition of anthracene. Among the up-regulated PcCYPs, five species showed catalytic activity against anthracene. Based upon both catalytic and transcriptional properties, these five species are most likely to play major roles in anthracene metabolic processes in vivo. Thus, the combination of functional screening and a microarray system may provide a novel strategy for obtaining a thorough understanding of the catalytic functions and biological impacts of PcCYPs.
  • Hiroshi Teramoto, Tamiki Komatsuzaki
    JOURNAL OF CHEMICAL PHYSICS 129 9 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  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.
  • Hiroshi Teramoto, Kazuo Takatsuka
    JOURNAL OF CHEMICAL PHYSICS 126 12 124110  2007年03月 [査読有り][通常論文]
     
    We develop a method to extract local integrals, that is, integrals defined locally in the linear regime of an arbitrary point in phase space. The individual integral represents a vibrational mode. We also propose an index that quantifies the extent of connection between neighboring local integrals. Those pieces that are smoothly connected over a wide range represent a global structure of phase space. With a six-atomic Lennard-Jones cluster, we show that it is possible to identify which vibrational mode in the potential basin correlates smoothly to that in the area of transition state, which is nothing but a reactive mode. As an application of the method, we attempt to enhance the structural transition by exciting the reactive mode thus found. This method works successfully as shown in numerical calculations. (c) 2007 American Institute of Physics.
  • Tatsuro Oda, Kuniaki Tsuchiya, Tetsuaki Arai, Takashi Togo, Hirotake Uchikado, Rohan de Silva, Andrew Lees, Haruhiko Akiyama, Chie Haga, Kenji Ikeda, Motoichiro Kato, Yuji Kato, Tsunekatsu Hara, Mitsumoto Onaya, Koji Hori, Hiroshi Teramoto, Itaru Tominaga
    NEUROPATHOLOGY 27 1 81 - 89 2007年02月 [査読有り][通常論文]
     
    We report a 51-year-old female with Pick's disease with Pick bodies (PDPB) showing a brainweight of 530 g. This case was considered to be a very rare case of PDPB, in which the lesion developed in the temporal and frontal lobes and later spread to the parietal lobe, occipital lobe, brainstem, cerebellum and spinal cord. This case showed very atypical clinicopathological findings. Clinically, bulging eyes and myoclonus were observed. Neuropathologically, Pick bodies were widely distributed beyond the usual distribution areas to the parietal cortices, occipital cortices, dentate nuclei, motor neuron nuclei in the brain stem, and spinal cord. The atypical clinical symptoms and the widespread neuropathological abnormalities observed in this case seem to represent an extremely extended form of PDPB.
  • Yoshimitsu Ishikawa, Hiroshi Teramoto, Yasuhiro Morii, Tomio Kawato, Kunifumi Nakanishi, Akio Nakayama, Tetsuyuki Kurata, Shigeru Yachi, Kazuhiro Kobayashi, Tomoya Teragaki, Takahiro Nishioka
    2007 SID INTERNATIONAL SYMPOSIUM, DIGEST OF TECHNICAL PAPERS, VOL XXXVIII, BOOKS I AND II 38 1393 - + 2007年 [査読有り][通常論文]
     
    We have developed the new transflective technology that is named as TF-SWAN. TF-SWAN is based on ECB mode, which uses a new optical design with a combination lambda/4 plate. TF-SWAN have realized a high transmittance and wide viewing angle characteristics. We have applied the technology to 8.4 '' transflective TFT-LCD. We have confirmed the excellent performances with a wide viewing angle of +/- 80 degrees in the horizontal direction, high brightness of 300 nits, high contrast ratio of more than 300 and a wide operating temperature range (from -40 to 85 degrees centigrade). Our new technology is suitable for automobile application.
  • Hiroshi Teramoto, Kazuo Takatsuka
    JOURNAL OF CHEMICAL PHYSICS 125 19 194301  2006年11月 [査読有り][通常論文]
     
    The nonseparability of vibrational and rotational motions of a nonrigid molecule placed in the rotationally isotropic space induces several important effects on the dynamics of intramolecular energy flow and chemical reaction. However, most of these studies have been performed within the framework of classical mechanics. We present a semiclassical theory for the motions of such nonrigid molecules and apply to the energy quantization of three body atomic cluster. It is shown numerically that the semiclassical spectum given without the correct account of the rotational symmetry suffers from unnecessary broadening of the resultant spectral lines and moreover from spurious peaks. (c) 2006 American Institute of Physics.
  • H Teramoto, S Sasa
    PHYSICAL REVIEW E 72 6 060102  2005年12月 [査読有り][通常論文]
     
    In systems far from equilibrium, the fluctuation-dissipation relation is violated due to the lack of detailed balance. Recently, for a class of Langevin equations, it has been proved that this violation is related to energy dissipation as an equality [Phys. Rev. Lett. 95, 130602 (2005)]. We provide a microscopic description of this equality by studying a nonequilibrium colloidal system on the basis of classical mechanics with some physical assumptions.
  • H Teramoto, K Takatsuka
    JOURNAL OF CHEMICAL PHYSICS 122 7 074101  2005年02月 [査読有り][通常論文]
     
    The Hamilton dynamics of a molecule in a translationally and/or rotationally symmetric field is kept rigorously constrained in its phase space. The relevant dynamical laws should therefore be extracted from these constrained motions. An internal space that is induced by a projection of such a limited phase space onto configuration space is an intrinsically curved space even for a system of zero total angular momentum. In this paper we discuss the general effects of this curvedness on dynamics and structures of molecules in such a manner that is invariant with respect to the selection of coordinates. It is shown that the regular coordinate originally defined by Riemann is particularly useful to expose the curvature correction to the dynamics and statisitcal properties of molecules. These effects are significant both qualitatively and quantitatively and are studied in two aspects. One is the direct effect on dynamics: A trajectory receives a Lorentz-like force from the curved space as though it was placed in a magnetic field. The well-known problem of the trapping phenomenon at the transition state is analyzed from this point of view. By showing that the trapping force is explicitly described in terms of the curvature of the internal space, we clarify that the physical origin of the trapped motion is indeed originated from the curvature of the internal space and hence is not dependent of the selection of coordinate system. The other aspect is the effect of phase space volume arising from the curvedness: We formulate a general expression of the curvature correction of the classical density of states and extract its physical significance in the molecular geometry along with reaction rate in terms of the scalar curvature and volume loss (gain) due to the curvature. The transition state theory is reformulated from this point of view and it is applied to the structural transition of linear chain molecules in the so-called dihedral angle model. It is shown that the curvature effect becomes large roughly linearly with the size of molecule. (C) 2005 American Institute of Physics.
  • H Teramoto, H Tanaka, H Wariishi
    APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 66 3 312 - 317 2004年12月 [査読有り][通常論文]
     
    The fungal metabolism of 4-nitrophenol (4-NP) was investigated using the lignin-degrading basidiomycete, Phanerochaete chrysosporium. Despite its phenolic feature, 4-NP was not oxidized by extracellular ligninolytic peroxidases. However, 4-NP was converted to 1,2-dimethoxy-4-nitrobenzene via intermediate formation of 4-nitroanisole by the fungus only under ligninolytic conditions. The metabolism proceeded via hydroxylation of the aromatic ring and methylation of phenolic hydroxyl groups. Although the involvement of nitroreductase in the metabolism of 2,4-dinitrotoluene by many aerobic and anaerobic microorganisms including P. chrysosporium has been reported, no formation of 4-aminophenol was observed during 4-NP metabolism. The formation of 1,2-dimethoxy-4-nitrobenzene was effectively inhibited by exogenously added piperonyl butoxide, a cytochrome P450 inhibitor, suggesting that cytochrome P450 is involved in the hydroxylation reaction. Thus, P. chrysosporium seems to utilize hydroxylation and methylation reactions to produce a more susceptible structure for an oxidative metabolic system.
  • H Teramoto, H Tanaka, H Wariishi
    FEMS MICROBIOLOGY LETTERS 234 2 255 - 260 2004年05月 [査読有り][通常論文]
     
    The degradation of a series of nitroaromatic compounds by the lignin-degrading fungus Phanerochaete chrysosporium was examined. From 4-nitrotoluene (4-NT), several metabolic intermediates were identified. Initially, 4-NT was converted to 4-nitrobenzyl alcohol (4-NBA), followed by the oxidation reactions to form 4-nitrobenzaldehyde and 4-nitrobenzoic acid, albeit slowly. Exogenously added 4-nitrobenzaldehyde and 4-nitrobenzoic acid were predominantly reduced to 4-NBA. The fungal formation of 4-NBA was inhibited by piperonyl butoxide, a cytochrome P450 inhibitor, Suggesting the involvement of cytochrome P450 in the hydroxylation of the methyl group. Similarly, 2-, and 3-nitrotoluenes and 4-chlorotoluene were converted to the corresponding arylalcohols by P. chrysosporium. On the other hand, toluene and 4-methoxytoluene were not converted. Thus, P. chrysosporium possesses an alkyl hydroxylation activity against aromatic compounds substituted with a strong electron-withdrawing group. (C) 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.
  • K Hori, Tominaga, I, T Inada, T Oda, S Hirai, Hori, I, M Onaya, H Teramoto
    PSYCHIATRY AND CLINICAL NEUROSCIENCES 57 6 603 - 604 2003年12月 [査読有り][通常論文]

書籍

  • 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

その他活動・業績

共同研究・競争的資金等の研究課題

  • 特異点論の物質科学への応用
    科学技術振興機構:さきがけ
    研究期間 : 2016年10月 -2020年03月 
    代表者 : 寺本央

教育活動情報

主要な担当授業

  • 数学概論
    開講年度 : 2018年
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 組み合わせ最適化、グラフ理論、専用ハードウェア、イジング型計算機、量子アニーリング
  • 入門線形代数学
    開講年度 : 2018年
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 連立1次方程式, 逆行列, 固有値, 固有ベクトル
  • 微分積分学Ⅱ
    開講年度 : 2018年
    課程区分 : 学士課程
    開講学部 : 全学教育
    キーワード : 原始関数, 積分, 重積分, リ-マン和, 変数変換


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