• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Real-World Modeling on the Hierarchical Dynamics of Living System

Research Project

Project/Area Number 23240044
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionDoshisha University

Principal Investigator

Yoshikawa Kenichi  同志社大学, 生命医科学部, 教授 (80110823)

Co-Investigator(Kenkyū-buntansha) TSUMOTO Kanta  三重大学, 工学研究科, 講師 (80362359)
MOTOIKE Ikuko  東北大学, 情報学研究科, 准教授 (70347178)
ICHIKAWA Masatoshi  京都大学, 理学研究科, 講師 (40403919)
Project Period (FY) 2011-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥43,550,000 (Direct Cost: ¥33,500,000、Indirect Cost: ¥10,050,000)
Fiscal Year 2014: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2013: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2012: ¥7,410,000 (Direct Cost: ¥5,700,000、Indirect Cost: ¥1,710,000)
Fiscal Year 2011: ¥21,320,000 (Direct Cost: ¥16,400,000、Indirect Cost: ¥4,920,000)
Keywords時空間秩序 / 生命物理学 / ゲノムDNA / 人工細胞モデル / 形態形成のモデル / DNA二本鎖損傷 / DNA高次構造 / 細胞サイズ小胞 / 細胞のモデリング / モデル細胞 / ゲノムDNA / DNAの高次構造相転移 / チューリングモデル / 遺伝子のスイッチング / リン脂質小胞 / 空間離散場
Outline of Final Research Achievements

We studied the dynamical aspects of life accompanied by the development of physical consideration, by considering the hierarchical structure: 1) On-off switching of large number of genes embedded in genomic DNA. Biological significance of the discrete nature of the conformational transition was theoretically discussed in relation to robust on/off switching of large number of genes on the process of cell-differentiation. 2) Field hypothesis on living cell. It was shown that unique physic-chemical properties emerge in micro systems, which may concern with the life activity of living cells. 3)Novel non-Turing scenario of body-organization during development was proposed and simple theoretical modeling was successfully achieved.

Report

(5 results)
  • 2015 Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (52 results)

All 2015 2014 2013 2012 2011 Other

All Int'l Joint Research (3 results) Journal Article (23 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 23 results,  Open Access: 6 results,  Acknowledgement Compliant: 6 results) Presentation (16 results) (of which Int'l Joint Research: 2 results,  Invited: 16 results) Book (1 results) Remarks (4 results) Patent(Industrial Property Rights) (5 results)

  • [Int'l Joint Research] Nesmeyanov Institute/Moscow(ロシア連邦)

    • Related Report
      2014 Annual Research Report
  • [Int'l Joint Research] College of Staten Island/City University of New York/NY(米国)

    • Related Report
      2014 Annual Research Report
  • [Int'l Joint Research] Shaoxing University/Shaoxing(China)

    • Related Report
      2014 Annual Research Report
  • [Journal Article] The evolution of spatial ordering of oil drops fast spreading on a water surface2015

    • Author(s)
      Daigo Yamamoto, Chika Nakajima, Akihisa Shioi, Marie Pierre Krafft and Kenichi Yoshikawa
    • Journal Title

      Nature Communications

      Volume: 6 Issue: 1 Pages: 7189-7189

    • DOI

      10.1038/ncomms8189

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Mode bifurcation of a bouncing dumbbell with chirality2015

    • Author(s)
      Yoshitsugu Kubo, Shio Inagaki, Masatoshi Ichikawa, and Kenichi Yoshikawa
    • Journal Title

      Physical Review E

      Volume: 91 Issue: 5 Pages: 052905-052905

    • DOI

      10.1103/physreve.91.052905

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Marked difference in conformational fluctuation between giant DNA molecules in circular and linear forms2015

    • Author(s)
      Takafumi Iwaki, Tomomi Ishido, Ken Hirano, Alexei Lazutin, Valentina V. Vasilevskaya, Takahiro Kenmotsu and Kenichi Yoshikawa
    • Journal Title

      Journal of Chemical Physics

      Volume: 142 Issue: 14 Pages: 145101-145101

    • DOI

      10.1063/1.4916309

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Roughening Dynamics of Radial Imbibition in a Porous Medium2015

    • Author(s)
      Yongjun Chen, Shun N. Watanabe and Kenichi Yoshikawa
    • Journal Title

      J. Phys. Chem.

      Volume: 119 Issue: 22 Pages: 12508-12513

    • DOI

      10.1021/acs.jpcc.5b03157

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Does DNA Exert an Active Role in Generating Cell-Sized Spheres in an Aqueous Solution with a Crowding Binary Polymer?2015

    • Author(s)
      Kanta Tsumoto, Masafumi Arai, Naoki Nakatani, Shun N. Watanabe and Kenichi Yoshikawa
    • Journal Title

      Life

      Volume: 5 Issue: 1 Pages: 459-466

    • DOI

      10.3390/life5010459

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] A toy model for nucleus-sized crowding confinement2015

    • Author(s)
      Chwen-Yang Shew and Kenichi Yoshikawa
    • Journal Title

      J. Phys. Cond. Matt.

      Volume: 27 Issue: 6 Pages: 064118-064118

    • DOI

      10.1088/0953-8984/27/6/064118

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Steadily oscillating axial bands of binary granules in a nearly filled coaxial cylinder2015

    • Author(s)
      Shio Inagaki, Hiroyuki Ebata, and Kenichi Yoshikawa
    • Journal Title

      Physical Review E

      Volume: 91 Issue: 1 Pages: 010201-010201

    • DOI

      10.1103/physreve.91.010201

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Compaction of Double-Stranded DNA by Negatively Charged Proteins and Colloids2015

    • Author(s)
      Anatoly A. Zinchenko and Kenichi Yoshikawa
    • Journal Title

      Current Opinion in Colloid and Interface Science

      Volume: 20 Issue: 1 Pages: 60-65

    • DOI

      10.1016/j.cocis.2014.12.005

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface2013

    • Author(s)
      H. Ito, T. Yamanaka, S. Kato, T . Hamada, M. Takagi, M. Ichikawa, and K. Yoshikawa
    • Journal Title

      Soft Matter

      Volume: 9 Issue: 40 Pages: 9539-9547

    • DOI

      10.1039/c3sm51766g

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effect of low-frequency ultrasound on double-strand breaks in giant DNA molecules2013

    • Author(s)
      Kenji Yoshida, Naoki Ogawa, Kagawa Yukihiro, Hiraku Tabata, Yoshiaki Watanabe, Takahiro Kenmotsu, Yuko Yoshikawa and Kenichi Yoshikawa
    • Journal Title

      Applied Physics Letters

      Volume: 103 Issue: 6 Pages: 63705-63705

    • DOI

      10.1063/1.4818125

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Back-and-forth micromotion of aqueous droplets in a dc electric field2013

    • Author(s)
      Tomo Kurimura, Masatoshi Ichikawa, Masahiro Takinoue and Kenichi Yoshikawa
    • Journal Title

      Physical Reviews E

      Volume: 88 Issue: 4

    • DOI

      10.1103/physreve.88.042918

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural change of DNA induced by nucleoid proteins: Growth phase-specific Fis and stationary phase-specific Dps2013

    • Author(s)
      Yuko T. Sato, Shun N. Watanabe, Takahiro Kenmotsu, Masatoshi Ichikawa, Yuko Yoshikawa, Jun Teramoto, Tadayuki Imanaka, Akira Ishihama and Kenichi Yoshikawa
    • Journal Title

      Biophysical Journal

      Volume: 105 Issue: 4 Pages: 1037-1044

    • DOI

      10.1016/j.bpj.2013.07.025

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Controlling negative and positive photothermal migration of centimeter-sized droplets2013

    • Author(s)
      M. Ichikawa, T. Iwaki, F. Takabatake, K. Miura, N. Magome, K. Yoshikawa
    • Journal Title

      Physical Review E

      Volume: 88 Issue: 1 Pages: 12403-12403

    • DOI

      10.1103/physreve.88.012403

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Probability of double-strand breaks in genome-sized DNA by γ-ray decreases markedly as the DNA concentration increases2013

    • Author(s)
      Shunsuke F Shimobayashi, Takafumi Iwaki, Toshiaki Mori and Kenichi Yoshikawa
    • Journal Title

      Journal of Chemical Physics

      Volume: 138 Issue: 17

    • DOI

      10.1063/1.4802993

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Self-organized Archimedean spiral pattern: Regular bundling of fullerene through solvent evaporation2013

    • Author(s)
      Y.-J., Chen, K. Suzuki, H. Mahara, K. Yoshikawa, T. Yamaguchi
    • Journal Title

      Applied Physics Letters

      Volume: 102 Issue: 4 Pages: 41911-41915

    • DOI

      10.1063/1.4789906

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cell-Sized Liposomes and Droplets: Real-World Modeling of Living Cells2012

    • Author(s)
      Tsutomu Hamada and Kenichi Yoshikawa
    • Journal Title

      Materials

      Volume: 5(11) Issue: 11 Pages: 2292-2305

    • DOI

      10.3390/ma5112292

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Controlling activation site density by low-energy far-field stimulation in cardiac tissue2012

    • Author(s)
      Marcel Hörning, Seiji Takagi and Kenichi Yoshikawa
    • Journal Title

      Physical Review E

      Volume: 85(6) Issue: 6

    • DOI

      10.1103/physreve.85.061906

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rigidity Matching between Cells and the Extracellular Matrix Leads to the Stabilization of Cardiac Conduction2012

    • Author(s)
      Marcel Hörning, Satoru Kidoaki, Takahito Kawano and Kenichi Yoshikawa
    • Journal Title

      Biophysical Journal

      Volume: 102(3) Issue: 3 Pages: 379-387

    • DOI

      10.1016/j.bpj.2011.12.018

    • NAID

      120003988292

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] How environmental solution condistion determine the compaction velocity of single DNA moleules2012

    • Author(s)
      Ken Hirano, Masatoshi Ichikawa, Tomomi Ishido, Mitsuru Ishikawa, Yoshinobu Baba, Kenichi Yoshikawa
    • Journal Title

      Nucleic Acids Research

      Volume: 40 Issue: 1 Pages: 284-289

    • DOI

      10.1093/nar/gkr712

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Critical behavior of megabase-size DNA toward the transition into a compact state2011

    • Author(s)
      Yuko Yoshikawa, Yuki Suzuki, Kozo Yamada, Wakao Fukuda, Kenichi Yoshikawa, Kunio Takeyasu, Tadayuki Imanaka
    • Journal Title

      Journal of Chemical Physics

      Volume: 135 Issue: 22 Pages: 225101-225107

    • DOI

      10.1063/1.3666845

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Highly efficient DNA compaction mediated by an in vivo antitumor-active tetrazolato-bridged dinuclear platinum(II) complex2011

    • Author(s)
      Yuko Yoshikawa
    • Journal Title

      Inorg.Chem.

      Volume: Vol.50 Issue: 22 Pages: 11729-11735

    • DOI

      10.1021/ic2017165

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transformation of acto HMM assembly confined in cell-sized liposome2011

    • Author(s)
      K. Takiguchi, M. Negishi, Y. T.-Takiguchi, M. Homma, and K. Yoshikawa
    • Journal Title

      Langmuir

      Volume: 27(18) Issue: 18 Pages: 11528-11535

    • DOI

      10.1021/la2016287

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness2011

    • Author(s)
      Yuji Higuchi, Takafumi Iwaki and Kenichi Yoshikawa
    • Journal Title

      Physical Review E

      Volume: 84(2) Issue: 2

    • DOI

      10.1103/physreve.84.021924

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] ゲノムDNAの二本鎖切断-超音波・ガンマ線・光励起の比較-2015

    • Author(s)
      吉川研一
    • Organizer
      電子情報通信学会、超音波・応用音響研究会
    • Place of Presentation
      同志社大学(京都府京田辺市)
    • Year and Date
      2015-01-29
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] A working hypothesis on the self-control of whole genome2014

    • Author(s)
      K. Yoshikawa
    • Organizer
      Stem Cells and Devices International SPIRITS Symposium
    • Place of Presentation
      京都府京都市
    • Year and Date
      2014-10-02
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Phase-transition of genomic DNA2014

    • Author(s)
      K.Yoshikawa
    • Organizer
      Graduate School of Biostudies & iCeMS Joint Symposium
    • Place of Presentation
      京都大学(京都府京都市)
    • Year and Date
      2014-09-22
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Real-world Modeling of Living System with Surfactant:Self-organized Structure and Dynamic Function2014

    • Author(s)
      K. Yoshikawa
    • Organizer
      20th Internaional Symposium on Surfactants in Solution
    • Place of Presentation
      Coimbra, Spain
    • Year and Date
      2014-06-22
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 混雑するミクロ環境下で働くゲノムDNA2014

    • Author(s)
      吉川研一
    • Organizer
      細胞生物学会
    • Place of Presentation
      京都大学(京都府京都市)
    • Year and Date
      2014-06-11
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] How to Bridge Life and Matter Through Nonlinear Dynamics2012

    • Author(s)
      吉川研一
    • Organizer
      Oscillations & Dynamic Instabilities in Chemical Systems
    • Place of Presentation
      アメリカ合衆国
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] How to protect fatal damage on genomic DNA: Quantitative ev aluation of double-strand break and application to medicinal chemistry2012

    • Author(s)
      吉川研一
    • Organizer
      22nd International Symposium on Medicinal Chemistry2012(ISMC2012)
    • Place of Presentation
      ドイツ
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Structure and Function of Biological Soft Matters through Hierarchical Dynamics2012

    • Author(s)
      吉川研一
    • Organizer
      2012 Summer School of the HeKKSaGOn Consortium
    • Place of Presentation
      ドイツ
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Phase transition of a single giant DNA: Physics and its biological signflcance2011

    • Author(s)
      吉川研一
    • Organizer
      KITPCのワークショップ「International Conference on Hierarchical Structures in Complex Fluids」
    • Place of Presentation
      中国
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Phase-transition of genomic DNA2011

    • Author(s)
      吉川研一
    • Organizer
      international conference at Strasbourg
    • Place of Presentation
      フランス
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] Non-Turing Scenario on Spatio-Temporal Strucutre Formation2011

    • Author(s)
      吉川研一
    • Organizer
      7th International Conference on Biological Physics, ICBP-2011
    • Place of Presentation
      アメリカ合衆国
    • Related Report
      2011 Annual Research Report
    • Invited
  • [Presentation] How does the higher-order structure of DNA concern with genetic functions?

    • Author(s)
      Kenichi Yoshikawa
    • Organizer
      The International Conference on Medical Physics
    • Place of Presentation
      Brighton, UK
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Specificity of cell-sized confinement

    • Author(s)
      Kenichi Yoshikawa
    • Organizer
      International Workshop “From Soft Matter to Protocell”
    • Place of Presentation
      宮城県仙台市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Phase Transition on Genomic DNA: Its Physics & Biological Significance

    • Author(s)
      Kenichi Yoshikawa
    • Organizer
      German Science Days "Research for Sustainable Development"
    • Place of Presentation
      京都府京都市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Unveiling Intrinsic Characteristics of Genomic DNA

    • Author(s)
      Kenichi Yoshikawa
    • Organizer
      International SPIRITS Symposium
    • Place of Presentation
      京都府京都市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Real-World Modeling on Exotic Aspects of Living Cell

    • Author(s)
      Kenichi Yoshikawa
    • Organizer
      Symposium: Three Domains of Life
    • Place of Presentation
      京都府京都市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Book] パリティ: 細胞の自己組織化"に物理の視点から迫る2011

    • Author(s)
      吉川 研一, 岩城 貴史
    • Publisher
      丸善出版
    • Related Report
      2011 Annual Research Report
  • [Remarks] 同志社大学生命医科学部生命物理学研究室

    • URL

      http://dmpl.doshisha.ac.jp/

    • Related Report
      2014 Annual Research Report
  • [Remarks] 同志社大学生命医科学部生命物理科学研究室

    • URL

      http://dmpl.doshisha.ac.jp/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 研究紹介(同志社大学生命医科学部生命物理学研究室)

    • URL

      http://dmpl.doshisha.ac.jp/

    • Related Report
      2012 Annual Research Report
  • [Remarks] 研究紹介(同志社大学生命医科学部生命物理学研究室)

    • URL

      http://dmpl.doshisha.ac.jp/

    • Related Report
      2011 Annual Research Report
  • [Patent(Industrial Property Rights)] 上皮間葉転換阻害剤及び癌転移治療剤2015

    • Inventor(s)
      吉川研一
    • Industrial Property Rights Holder
      吉川研一
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2015-053282
    • Filing Date
      2015-03-17
    • Related Report
      2014 Annual Research Report
  • [Patent(Industrial Property Rights)] 固体物体を運動させる方法、及び、送液ポンプ2014

    • Inventor(s)
      吉川研一
    • Industrial Property Rights Holder
      吉川研一
    • Industrial Property Rights Type
      特許
    • Filing Date
      2014-04-23
    • Related Report
      2014 Annual Research Report
  • [Patent(Industrial Property Rights)] レーザーを用いて細胞を配列方法2014

    • Inventor(s)
      吉川研一
    • Industrial Property Rights Holder
      吉川研一
    • Industrial Property Rights Type
      特許
    • Filing Date
      2014-09-10
    • Related Report
      2014 Annual Research Report
  • [Patent(Industrial Property Rights)] 内包物質に耐熱性を与えたリポソーム及びその製造法2012

    • Inventor(s)
      市川正敏、吉川研一、石崎昭彦、中部屋恵造
    • Industrial Property Rights Holder
      市川正敏、吉川研一、石崎昭彦、中部屋恵造
    • Industrial Property Rights Type
      特許
    • Filing Date
      2012-09-18
    • Acquisition Date
      2012-10-10
    • Related Report
      2012 Annual Research Report
  • [Patent(Industrial Property Rights)] 複数の被内包リポソームを内包するリポソーム及びその製造方法2012

    • Inventor(s)
      市川正敏、吉川研一、石崎昭彦、中部屋恵造
    • Industrial Property Rights Holder
      市川正敏、吉川研一、石崎昭彦、中部屋恵造
    • Industrial Property Rights Type
      特許
    • Filing Date
      2012-09-18
    • Acquisition Date
      2012-10-10
    • Related Report
      2012 Annual Research Report

URL: 

Published: 2011-04-06   Modified: 2022-02-16  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi