Chromatin loop structure prediction via fatgraph

• Project/Area Number: 24651225
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: System genome science
• Research Institution: The University of Tokyo
• Principal Investigator: KODAMA Hiroki 東京大学, 数理(科)学研究科(研究院), 特任准教授 (40466826)
• Co-Investigator(Kenkyū-buntansha): IHARA Shigeo 東京大学, 先端科学技術研究センター, 教授 (30345136)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2014: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: トポロジー / SO(3)-接続 / ファットグラフ / 生命生体情報学 / 国際研究者交流(オーストリア) / 国際研究者交流(デンマーク) / タンパク質 / カントール集合 / 蛋白質 / 核酸 / 国際情報交換（デンマーク） / 国際研究者交流（オーストリア） / 国際研究者交流（デンマーク）

Outline of Final Research Achievements

SO(3)-connection model of protein is a graph that each vertex is a peptide unit and on each edge rotation matrix of peptide units is given. We used this model to construct a system that visualize the difference of 3D structures of proteins. We contrived a model via Cantor set that explicates the loop structure of Chromatin. We also described pH-induced protein denaturation via grid model of protein.

Research Products

• [Journal Article] Minimal C^1 diffeomorphisms of the circle which admit measurable fundamental domains (2013)
  • Author(s): Hiroki KODAMA and Shigenori MATSUMOTO
  • Journal Title: Proceedings of the American Mathematical Society Volume: 141 Issue: 6 Pages: 2061-2067
  • DOI: 10.1090/s0002-9939-2013-11472-3
  • Peer Reviewed
• [Presentation] Minimal C^1-diffeomorphisms of the circle which admit measurable fundamental domains (2014)
  • Author(s): Hiroki KODAMA
  • Organizer: ICM 2014
  • Place of Presentation: Coex, Seoul, Korea
  • Year and Date: 2014-08-13 – 2014-08-21
• [Presentation] Minimal C^1-diffeomorphisms of the circle which admit measurable fundamental domains (2013)
  • Author(s): Hiroki KODAMA
  • Organizer: Geometry and topology of macromolecule folding
  • Place of Presentation: オーフス大、オーフス、デンマーク