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Inverse problem of persistent homology: A new method for structural analysis of proteins.

Research Project

Project/Area Number 26610042
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Foundations of mathematics/Applied mathematics
Research InstitutionTohoku University (2015-2016)
Kyushu University (2014)

Principal Investigator

Hiraoka Yasuaki  東北大学, 原子分子材料科学高等研究機構, 教授 (10432709)

Co-Investigator(Kenkyū-buntansha) 泉 俊輔  広島大学, 理学研究科, 教授 (90203116)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Keywordsパーシステント写像 / 特異点
Outline of Final Research Achievements

In this research, we have formulated mathematical framework of inverse problems about persistent homology, and have developed a software which is applicable to real data. First, in direct problems, we studied the correspondence from point cloud data to persistence diagrams as differentiable maps. Then, we developed an algorithm to solve inverse solutions by using Newton method based on implicit function theorem. The developed software was applied to practical structural analysis of proteins and materials science.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (11 results)

All 2016 2015 Other

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 7 results,  Acknowledgement Compliant: 2 results) Presentation (1 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Remarks (1 results)

  • [Journal Article] Membrane Protein Analyses Using Alkylated Trihydroxyacetophenone (ATHAP) as a MALDI Matrix2016

    • Author(s)
      Fukuyama, Yuko; Nakajima, Chihiro; Izumi, Shunsuke; Tanaka, Koichi
    • Journal Title

      Analytical Chemistry

      Volume: 88(3) Issue: 3 Pages: 1688-1695

    • DOI

      10.1021/acs.analchem.5b03700

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Relative interleavings and applications to sensor networks2016

    • Author(s)
      Yasuaki Hiraoka and Genki Kusano
    • Journal Title

      Japan J.Indust. Appl. Math.

      Volume: 33 Issue: 1 Pages: 99-120

    • DOI

      10.1007/s13160-016-0208-x

    • NAID

      210000174986

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Persistent homology and many-body atomic structure for medium-range order in the glass2015

    • Author(s)
      Takenobu Nakamura, Yasuaki Hiraoka, Akihiko Hirata,Emerson G Escolar, Yasumasa Nishiura
    • Journal Title

      Nanotechnology

      Volume: 26 Issue: 30 Pages: 304001-304001

    • DOI

      10.1088/0957-4484/26/30/304001

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A topological measurement of protein compressibility2015

    • Author(s)
      M. Gameiro, Y. Hiraoka, S. Izumi, M. Kramar, K. Mischaikov, V. Nanda
    • Journal Title

      Japan Journal of Industrial and Applied Mathematics

      Volume: 32 Issue: 1 Pages: 1-17

    • DOI

      10.1007/s13160-014-0153-5

    • NAID

      210000186738

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dual selective nitration in Arabidopsis: Almost exclusive nitration of PsbO and PsbP, and highly susceptible nitration of four non-PSII proteins, including peroxiredoxin II E2015

    • Author(s)
      M. Takahashi, J. Shigeto, A. Sakamoto, S. Izumi, K. Asada,d H. Morikawa
    • Journal Title

      Electrophoresis

      Volume: 36 Issue: 20 Pages: 2569-2578

    • DOI

      10.1002/elps.201500145

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] A unique mechanism of successful fertilization in a domestic bird.2015

    • Author(s)
      T. Sasanami, S. Izumi, N. Sakurai, T. Hirata, S. Mizushima, M. Matsuzaki, G. Hiyama, E. Yorinaga, T. Yoshimura, K. Ukena and K. Tsutsui
    • Journal Title

      Sci. Rep.

      Volume: 5 Issue: 1 Pages: 7700-7700

    • DOI

      10.1038/srep07700

    • NAID

      120005527162

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] In vitro and in vivo evidence for oxalate oxidase activity of a germin-like protein from azalea2015

    • Author(s)
      Atsushi SAKAMOTO, Takashi NISHIMURA, Yoh-ichi MIYAKI, Shunsuke WATANABE, Hiroshi TAKAGI, Shunsuke IZUMI, Hiroshi SHIMADA
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 458 Issue: 3 Pages: 536-542

    • DOI

      10.1016/j.bbrc.2015.02.002

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Differential regulation of epidermal growth factor receptor by hydrogen peroxide and flagellin in cultured lung alveolar epithelial cells2015

    • Author(s)
      Hiroyuki Nishi, Noriko Maeda,Shunsuke Izumi, Sayomi Higa-Nakamine, Seikichi Toku, Manabu Kakinohana, Kazuhiro Sugahara and Hideyuki Yamamoto
    • Journal Title

      European Journal of Pharmacology

      Volume: 748 Pages: 133-142

    • DOI

      10.1016/j.ejphar.2014.12.016

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Marangoni flow around a camphor disk regenerated by the interaction between camphor and sodium dodecyl sulfate molecules2015

    • Author(s)
      S. Nakata, R. Tenno, A. Deguchi, H. Yamamoto, Y. Hiraga, S. Izumi
    • Journal Title

      Colloids and Surfaces A: Physicochemical and Engineering Aspects

      Volume: 466 Pages: 40-44

    • DOI

      10.1016/j.colsurfa.2014.10.041

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Topological Data Analysis on Materials Science: Statistical Characterization of Glass Transition2016

    • Author(s)
      Yasuaki Hiraoka
    • Organizer
      SoCG 2016
    • Place of Presentation
      Boston(USA)
    • Year and Date
      2016-06-15
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Remarks] 平岡研究室ホームページ

    • URL

      http://www.wpi-aimr.tohoku.ac.jp/hiraoka_labo/

    • Related Report
      2016 Annual Research Report 2015 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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