National Institute of Technology, Tsuruoka College

www.tsuruoka-nct.ac.jp/
Tsuruoka, Japan
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Iwaoka N.,National Institute of Technology, Tsuruoka College | Takano H.,Keio University
Journal of the Physical Society of Japan | Year: 2017

The conformational fluctuations of a glassy short polymer melt are studied by coarse-grained molecular dynamics simulations and principal component analysis (PCA). The distribution of PCA eigenvalues, which measure static fluctuations of the polymers, shows a clear difference between above and below the conventional glass transition temperature Tg. The approximate conformational entropy of the polymers also indicates a transition near Tg. This is evidence that the static properties of polymers in the melt signal the glass transition. ©2017 The Physical Society of Japan.


Kobayashi Y.,National Institute of Technology, Tsuruoka College | Kanda K.,National Institute of Technology, Tsuruoka College
AIP Conference Proceedings | Year: 2017

In recent years, record and analysis of environmental information have become easier by using ICT. However, Grasp of the growing conditions of crops have been left to the decision of a skilled farmers. We need new sensing technology that new farmers and young farmers can find the condition of the crops. Skilled farmers decide growing conditions from the color of leaves. This study aims to develop a new sensor using the method. For that, we did the basic research on the leaf color and the growing of crops. The absorption spectrum of the leaves is analyzed by spectrometer. In addition, the amount of chlorophyll is measured by chlorophyll meter. It compare with absorption spectrum of the leaf. From the measurement results, The wavelength(676.791nm) which is most affected by chlorophyll in the leaf was ascertained. In addition, the relation between the absorption spectrum at the characteristic wavelength and the change in the chlorophyll amount was obtained. These results suggest that this measurement can be used for comprehension of the growth condition of crops. © 2017 Author(s).


Eighteen tripeptides that fit into the thermally vibrating active site of cathepsin K were discovered by alternating artificial intelligence and molecular simulation. The 18 tripeptides fit the active site better than the cysteine protease inhibitor E64, and a better inhibitor of cathepsin K could be designed considering these tripeptides. Among the 18 tripeptides, Phe–Arg–Asp and Tyr–Arg–Asp fit the active site the best and their structural similarity should be considered in the design process. Interesting factors emerged from the structure of the decision tree, and its structural information will guide exploration of potential inhibitor molecules for proteases. © 2017


Nishiyama K.,National Institute of Technology, Tsuruoka College
Chemical Physics Letters | Year: 2016

The behavior of 15 dipeptides on thermally fluctuating cathepsin K was investigated by molecular dynamics and docking simulations. Four dipeptides were distributed on sites near the active center, and the variations were small. Eleven dipeptides were distributed on sites far from the active center, and the variations were large for nine dipeptides and very large for the other two. The decision tree was constructed using genetic programming, and it accurately classified the 15 dipeptides. The decision tree would accurately estimate the behavior of various peptides, and should significantly contribute to the design of useful peptides. © 2016 Elsevier B.V. All rights reserved.


Nishiyama K.,National Institute of Technology, Tsuruoka College
Applied Physics Letters | Year: 2013

The binding of peptides of 2-10 glycine residues (2-10Gly) to papain on nanofabricated hydrophobic Si surfaces was investigated by molecular dynamics and docking simulations. 5Gly, 7Gly, 9Gly, and 10Gly were distributed on sites near the active center of papain on the Si surface, while 6-10Gly were distributed on sites near the active center of free papain. The Si surface changed the substrate specificity of papain, and modification of this surface should allow full control of substrate specificity. Molecular surgery of proteins in cells may be realized using papain on specially designed surfaces. © 2013 AIP Publishing LLC.


Motohashi H.,National Institute of Technology, Tsuruoka College
Nihon Kikai Gakkai Ronbunshu, B Hen/Transactions of the Japan Society of Mechanical Engineers, Part B | Year: 2010

Influence of sectional shape on power characteristics of open cross flow type micro water turbine was investigated by model experiments. An increase of number of blades caused improvement of turbine efficiency. Ratio of inner diameter to outer diameter of a turbine hardly influences on turbine power characteristics. Efficiency of large turbines was higher than small ones. Following two effects were confirmed by field tests. ( 1 ) Scale effect : Efficiency obtained by field tests using a turbine with a diameter of 1.2m was higher than model tests. (2) Suppress effect of overload: Maximum generated power showed a tendency to be suppressed for a condition supposing over discharge.


Nishiyama K.,National Institute of Technology, Tsuruoka College
Chemical Physics Letters | Year: 2011

We investigated the specific bindings of peptides of 1-10 glycine residues (1-10GLY) on dynamic papain surfaces via molecular dynamics and docking simulations. Although the binding specificities of 1-5GLY on papain fluctuated little with time, the binding specificities of 6-10GLY on papain considerably fluctuated with time. Some residues had a significant impact on bindings of 6-10GLY to sites near active center of papain, and some of their residues were specific for each 6GLY, 8GLY, and 10GLY. Modification of these specific residues should allow for control of binding specificity of 6GLY, 8GLY, and 10GLY to the active center. © 2011 Elsevier B.V. All rights reserved.


Nishiyama K.,National Institute of Technology, Tsuruoka College
Journal of Applied Physics | Year: 2010

The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural changes in the highly flexible residues in papain were larger. Binding stability and sites would be significantly influenced by the highly flexible residues. Analysis of such residues would provide an important guideline for clarification of enzymatic activities and modification of structural dynamics of such residues would allow us to control enzymatic activities. © 2010 American Institute of Physics.


Nishiyama K.,National Institute of Technology, Tsuruoka College
Chemical Physics Letters | Year: 2011

We investigated the substrate specificity of papain dynamic structures for peptides of 8-10 glycine residues (8-10GLY) via molecular dynamics and docking simulations. The substrate specificity of papain for 8-10GLY fluctuated considerably with time. There were several residues that were different among those that had a significant impact on binding (RESIDUES-IMPACT) with 10GLY, 9GLY, and 8GLY. Modification of these different residues should allow for control of substrate specificity, providing a framework for modifying substrate specificity in papain and other enzymes. © 2010 Elsevier B.V. All rights reserved.


Nishiyama K.,National Institute of Technology, Tsuruoka College
Chemical Physics Letters | Year: 2015

The binding behavior of 2-10Gly (peptides with between 2 and 10 glycine residues) to cathepsin K was investigated by molecular dynamics and docking simulations. 3Gly, 6-7Gly, and 9-10Gly was distributed on sites near the active center, although 2Gly, 4-5Gly, and 8Gly were not. The percentage of highly flexible residues was relatively lower in the distribution area of 2-10Gly, although the percentage of rigid residues was larger. Furthermore, the percentages varied significantly among the distribution areas. Delicate modification of the thermal fluctuations in proteins would enable regulation of peptide binding, and, in turn, the ability to control their functions. © 2015 Elsevier B.V. All rights reserved.

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