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Application of 3-dimensional force mapping method to the measurement of biomolecule fluctuations

Research Project

Project/Area Number 26600101
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Thin film/Surface and interfacial physical properties
Research InstitutionKyoto University

Principal Investigator

YAMADA Hirofumi  京都大学, 工学(系)研究科(研究院), 教授 (40283626)

Co-Investigator(Renkei-kenkyūsha) KOBAYASHI Kei  京都大学, 白眉センター, 特定准教授 (40335211)
HIRATA Yoshiki  産業技術総合研究所, 健康工学研究部門, 主任研究員 (10357858)
Project Period (FY) 2014-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywords走査プローブ顕微鏡 / 3次元フォースマッピング技術 / 3次元フォースマッピング技術
Outline of Final Research Achievements

Direct measurements of interaction force field in close proximity to biomolecules, having soft structures, and the spatial distribution of their molecular fluctuations have been realized by the 3-dimensional force mapping method based on frequency modulation atomic force microscopy, which has a molecular-scale imaging capability. The force sensitivity and the detection response time were particularly improved. The measurement time for the dissipation energy directly reflecting the sample fluctuation was also improved. Furthermore, the present method allows us to conduct the quantitative force measurement. The relationship between the dissipation signal and the damping coefficient at a solid-liquid interface was clearly analyzed. Finally 3D map of the hydration structure and the dissipation energy, in connection to the molecular fluctuation, near biomoleules was successfully obtained. The relaxation time of a molecular assembly was estimated from the dissipation measurement.

Report

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

    (46 results)

All 2016 2015 2014 Other

All Int'l Joint Research (1 results) Journal Article (7 results) (of which Peer Reviewed: 7 results,  Acknowledgement Compliant: 3 results,  Open Access: 2 results) Presentation (37 results) (of which Int'l Joint Research: 8 results,  Invited: 6 results) Remarks (1 results)

  • [Int'l Joint Research] Aalto University(フィンランド)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Visualization of trapped charges being ejected from organic thin-film transistor channels by Kelvin-probe force microscopy during gate voltage sweeps2016

    • Author(s)
      Y. Yamagishi, K. Kobayashi, K. Noda, H. Yamada
    • Journal Title

      Applied Physics Letters

      Volume: 108 Issue: 9 Pages: 093302-093302

    • DOI

      10.1063/1.4943140

    • NAID

      120005844268

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular-scale quantitative charge density measurement of biological molecule by frequency modulation atomic force microscopy in aqueous solutions2015

    • Author(s)
      Kenichi Umeda, Kei Kobayashi, Noriaki Oyabu, Kazumi Matsushige, and Hirofumi Yamada
    • Journal Title

      Nanotechnology

      Volume: 26 Issue: 28 Pages: 285103-285103

    • DOI

      10.1088/0957-4484/26/28/285103

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Local impedance measurement of an electrode/single-pentacene-grain interface by frequency-modulation scanning impedance microscopy2015

    • Author(s)
      T. Kimura, K. Kobayashi, and H. Yamada
    • Journal Title

      Journal of Applied Physics

      Volume: 118 Issue: 5 Pages: 055501-055501

    • DOI

      10.1063/1.4927921

    • NAID

      120005844267

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Atom-Resolved Analysis of an Ionic KBr(001) Crystal Surface Covered with a Thin Water Layer by Frequency Modulation Atomic Force Microscopy2015

    • Author(s)
      T. Arai, M.i Koshioka, K. Abe, M. Tomitori , R. Kokawa, M. Ohta, H. Yamada, K. Kobayashi, and N. Oyabu
    • Journal Title

      Langmuir

      Volume: 31 Issue: 13 Pages: 3876-3883

    • DOI

      10.1021/acs.langmuir.5b00087

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Practical aspects of Kelvin-probe force microscopy at solid/liquid interfaces in various liquid media2014

    • Author(s)
      K. Umeda, K. Kobayashi, N. Oyabu, Y. Hirata, K. Matsushige, and H. Yamada
    • Journal Title

      Journal of Applied Physics

      Volume: 116 Issue: 13 Pages: 134307-134307

    • DOI

      10.1063/1.4896881

    • NAID

      120005496652

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Direct Observation of the Influence of Additives on Calcite Hydration by Frequency Modulation Atomic Force Microscopy2014

    • Author(s)
      Y. Araki, K. Tsukamoto, R. Takagi, T. Miyashita, N. Oyabu, K. Kobayashi, and H. Yamada
    • Journal Title

      Crystal growth & design

      Volume: 14 Issue: 12 Pages: 6254-6260

    • DOI

      10.1021/cg500891j

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Accurate formula for dissipative interaction in frequency modulation atomic force microscopy2014

    • Author(s)
      K. Suzuki, K. Kobayashi, A. Labuda, K. Matsushige and H. Yamada
    • Journal Title

      Applied Physics Letters

      Volume: 105 Issue: 23 Pages: 233105-233105

    • DOI

      10.1063/1.4903484

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 液中 FM-AFMによる plasmid DNA のナノスケール水和構造計測2016

    • Author(s)
      木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第63回応用物理学会春季学術講演会
    • Place of Presentation
      東京
    • Year and Date
      2016-03-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] 液中FM-AFMによるDNAオリガミにおけるcrossover構造評価 (2)2016

    • Author(s)
      黄 雲飛, 馬 志鵬, 木南 裕陽, 小林 圭, 山田 啓文, 田畑 修
    • Organizer
      第63回応用物理学会春季学術講演会
    • Place of Presentation
      東京
    • Year and Date
      2016-03-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] 3D-FM-AFMを用いた固液界面における局所水和構造と表面原子構造との相関に関する研究2016

    • Author(s)
      梅田 健一, 小林 圭, 山田 啓文
    • Organizer
      第63回応用物理学会春季学術講演会
    • Place of Presentation
      東京
    • Year and Date
      2016-03-19
    • Related Report
      2015 Annual Research Report
  • [Presentation] 生体分子近傍の水和構造・電荷分布の可視化 ーFM-AFMフォースマッピング法の新たな展開ー2015

    • Author(s)
      山田 啓文, 小林 圭
    • Organizer
      日本顕微鏡学会走査型プローブ顕微鏡分科会「SPMによる高速走査の可能性と応用」
    • Place of Presentation
      越後湯沢
    • Year and Date
      2015-12-06
    • Related Report
      2015 Annual Research Report
  • [Presentation] Molecular-Scale Investigations of Solid-Liquid Interfaces by Frequency Modulation Atomic Force Microscopy2015

    • Author(s)
      H. Yamada
    • Organizer
      10th International Symposium on Atomic Level Characterizations for New Materials and Devices’ 15 (ALC’ 15)(
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2015-10-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 3次元フォースマッピングによるSteptavidin 2次元結晶の水和構造観察2015

    • Author(s)
      宮本 眞之, 木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第76回応用物理学会秋季学術講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] B-Z 転移を含む DNA の液中 FM-AFM 高分解能観察2015

    • Author(s)
      木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第76回応用物理学会秋季学術講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] 液中 FM-AFM による DNA オリガミにおける crossover 構造評価2015

    • Author(s)
      黄 雲飛, 馬 志鵬, 木南 裕陽, 小林 圭, 山田 啓文, 田畑 修
    • Organizer
      第76回応用物理学会秋季学術講演会
    • Place of Presentation
      名古屋
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] Molecular-scale analysis of hydration structures on heterogeneous surfaces by three-dimensional force mapping2015

    • Author(s)
      K. Umeda, K. Kobayashi, H. Yamada
    • Organizer
      The 18th International Conference on Non-Contact Atomic Force Microscopy
    • Place of Presentation
      Cassis, France
    • Year and Date
      2015-09-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Intramolecular structure imaging and orientation manipulation ofendohedral metallofullerenes using room-temperature FM-AFM2015

    • Author(s)
      K. Kobayashi, A. Noda, T. Yamashita, and H. Yamada
    • Organizer
      The 18th International Conference on Non-Contact Atomic Force Microscopy
    • Place of Presentation
      Cassis, France
    • Year and Date
      2015-09-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular-scale visualization of different DNA conformations by using FM-AFM2015

    • Author(s)
      H. Kominami, K. Kobayashi, H. Yamada
    • Organizer
      The 18th International Conference on Non-Contact Atomic Force Microscopy
    • Place of Presentation
      Cassis, France
    • Year and Date
      2015-09-07
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Molecular-scale visualization of hydration structures at solid-liquid interfaces by frequency modulation atomic force microscopy2015

    • Author(s)
      H. Yamada
    • Organizer
      3rd International Symposium on Application of Nano-Geosciences in Petroleum Engineering
    • Place of Presentation
      Kyoto, Japan
    • Year and Date
      2015-09-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Molecular-scale Visualization of Solid-Liquid Interfaces by Frequency Modulation Atomic Force Microscopy2015

    • Author(s)
      H. Yamada
    • Organizer
      NIMS Conference 2015
    • Place of Presentation
      Tsukuba, Japan
    • Year and Date
      2015-07-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Relationship between surface structures/charges and local hydration structures studied by 3D liquid- FM-AFM2015

    • Author(s)
      K. Umeda, K. Kobayashi and H. Yamada
    • Organizer
      International Scanning Probe Microscopy Conference (ISPM2015)
    • Place of Presentation
      Rio De Janeiro, Brazil
    • Year and Date
      2015-06-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Visualization of biomolecules-solution interfaces by frequency modulation AFM and 3D force mapping2015

    • Author(s)
      H. Kominami, K. Kobayashi and H. Yamada
    • Organizer
      International Scanning Probe Microscopy Conference (ISPM2015)
    • Place of Presentation
      Rio De Janeiro, Brazil
    • Year and Date
      2015-06-21
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マイカ基板上に形成されるStreptavidin 2次元結晶の液中FM-AFM高分解能構造観察2015

    • Author(s)
      崔 子鵬、宮本 眞之、木南 裕陽、小林 圭、平田 芳樹、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Research-status Report
  • [Presentation] FM-AFMによる界面活性剤分子集合体構造の形成過程評価 (3)2015

    • Author(s)
      鈴木 一博、小林 圭、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中動作FM-AFMを用いたイオン液体の局所溶媒和構造と表面構造/電荷との相関に関する研究2015

    • Author(s)
      梅田 健一、小林 圭、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-14
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中FM-AFMによる免疫グロブリンM(IgM)の抗原結合評価2015

    • Author(s)
      黄 雲飛、木南 裕陽、小林 圭、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-13
    • Related Report
      2014 Research-status Report
  • [Presentation] FM-AFMおよび3次元フォースマッピング法による生体分子-溶液界面構造の可視化2015

    • Author(s)
      山田 啓文、小林 圭
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-12
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中FM-AFMによる左巻きDNAの高分解能観察2015

    • Author(s)
      木南 裕陽、小林 圭、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-11
    • Related Report
      2014 Research-status Report
  • [Presentation] FM-AFMによるStreptavidin 2次元結晶の液中高分解能観察2015

    • Author(s)
      宮本 眞之、木南 裕陽、崔 子鵬、小林 圭、山田 啓文
    • Organizer
      第62回応用物理学関係連合講演会
    • Place of Presentation
      東海大学, 神奈川
    • Year and Date
      2015-03-11
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular-scale visualization of self-assembly of biomolecules by frequency modulation atomic force microscopy in liquids2015

    • Author(s)
      H. Yamada
    • Organizer
      The XVII Linz Winter Workshop 2015
    • Place of Presentation
      Linz, Austria
    • Year and Date
      2015-01-31 – 2015-02-02
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Molecular-scale visualization of DNA strands with non-B DNA conformations using FM-AFM in liquids2014

    • Author(s)
      H. Kominami, K. Kobayashi, H. Yamada
    • Organizer
      22nd International Colloquium on Scanning Probe Microscopy
    • Place of Presentation
      Atagawa, Japan
    • Year and Date
      2014-12-11 – 2014-12-13
    • Related Report
      2014 Research-status Report
  • [Presentation] High-resolution Imaging of IgM Antibody Molecules by FM-AFM in Aqueous Solutions2014

    • Author(s)
      Y. Huang, H. Kominami, K. Kobayashi and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular-scale Visualization of Self-Assembled Structures of Biomolecules Using FM-AFM in Liquids2014

    • Author(s)
      H. Kominami, K. Kobayashi and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Research-status Report
  • [Presentation] Relationship between surface structures/charges and local hydration structures studied by FM-AFM in liquids2014

    • Author(s)
      K. Umeda, K. Kobayashi and H. Yamada
    • Organizer
      The 7th International Symposium on Surface Science
    • Place of Presentation
      Matsue, Japan
    • Year and Date
      2014-11-03 – 2014-11-07
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中動作 FM-AFM による真核生物 DNA 複製の初期過程イメージング2014

    • Author(s)
      木南 裕陽, 日詰 光治, 荒木 弘之, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-20
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中動作 FM-AFM による IgG 抗体分子 6 量体形成の抗体種依存性2014

    • Author(s)
      木南 裕陽, 井戸 慎一郎, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中FM-AFMによる免疫グロブリンM(IgM)構造評価2014

    • Author(s)
      黄 雲飛, 木南 裕陽, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Research-status Report
  • [Presentation] Avidin-biotin 相互作用のFM-AFM フォースマップ評価2014

    • Author(s)
      李 文尭, 鈴木 一博, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Research-status Report
  • [Presentation] 液中動作FM-AFMを用いた局所水和構造と表面構造/電荷の相関に関する研究(2)2014

    • Author(s)
      梅田 健一, 小林 圭, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-19
    • Related Report
      2014 Research-status Report
  • [Presentation] バイオセンシングに向けた機能性タンパク質のFM-AFM構造観察2014

    • Author(s)
      崔 子鵬, 木南 裕陽, 小林 圭, 平田 芳樹, 山田 啓文
    • Organizer
      第75回応用物理学関係連合講演会
    • Place of Presentation
      北海道大学, 札幌
    • Year and Date
      2014-09-18
    • Related Report
      2014 Research-status Report
  • [Presentation] Relationship between local hydration structures and surface structures/charges studied by liquid-FM-AFM2014

    • Author(s)
      K. Umeda, K. Kobayashi, H. Yamada
    • Organizer
      The 17th International Conference on Non-Contact Atomic Force Microscopy
    • Place of Presentation
      Tsukuba, Japan
    • Year and Date
      2014-08-04 – 2014-08-08
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular-scale Investigation of Antigen Binding to IgG Antibody Self-Assembly Using Frequency-Modulation AFM in Liquids2014

    • Author(s)
      H. Kominami, S. Ido, K. Kobayashi, H. Yamada
    • Organizer
      International Conference on Nanoscience and Technology
    • Place of Presentation
      Colorado, USA
    • Year and Date
      2014-07-20 – 2014-07-25
    • Related Report
      2014 Research-status Report
  • [Presentation] Molecular-scale Investigations of Solid-Liquid Interfaces by both FM-AFM and 3-Dimensional Force Mapping Method2014

    • Author(s)
      H. Yamada
    • Organizer
      XXI International Summer School “Nicolas Cabrera”
    • Place of Presentation
      Madrid, Spain
    • Year and Date
      2014-07-14 – 2014-07-18
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Molecular-scale visualization of biomolecules and their biochemical functions by frequency modulation atomic force microscopy2014

    • Author(s)
      H. Yamada, H. Kominami, K. Umeda, H. Suzuki, K. Kobayashi
    • Organizer
      5th Multifrequency AFM Conference
    • Place of Presentation
      Madrid, Spain
    • Year and Date
      2014-06-16 – 2014-06-18
    • Related Report
      2014 Research-status Report
    • Invited
  • [Remarks] 京都大学工学研究科電子材料物性研究室

    • URL

      http://piezo.kuee.kyoto-u.ac.jp/d/jp

    • Related Report
      2015 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2017-05-10  

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