Massive Parallel Evolutionary Computation Theory based on a Molecular Realization of WetGA

• Project/Area Number: 23300084
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Sensitivity informatics/Soft computing
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: YAMAMURA Masayuki 東京工業大学, 総合理工学研究科(研究院), 教授 (00220442)
• Co-Investigator(Renkei-kenkyūsha): SAKAMOTO Kensaku 独立行政法人理化学研究所, チームリーダー (50240685) ; SOMEYA Hiroshi 東海大学, 情報理工学部, 講師 (00333518) ; KOMIYA Ken 東京工業大学, 大学院・総合理工学研究科, 助教 (20396790)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥20,410,000 (Direct Cost: ¥15,700,000、Indirect Cost: ¥4,710,000); Fiscal Year 2013: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2012: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2011: ¥10,920,000 (Direct Cost: ¥8,400,000、Indirect Cost: ¥2,520,000)
• Keywords: ウェットGA / 進化計算 / タンパク質工学 / 最適化 / 高度並列GA / ウェットＧＡ / 高度並列ＧＡ

Research Abstract

We proposed WetGA implemented on biomoleculer experiments based on the knowledge obtained in the applications of evolutionary computation inspired from real life. We achieved the ideal population distribution transition through twelve generations in the application testbed which engineers tyrRS protein to recognize new substrate. We modeled the difficulty of the fitness landscape then actually evolved a new protein by new generation alternation model which can start with one local minima. We analyzed the mutation accumulation distribution in each generation by reading the sequences of all samples. We also proposed a new evolutionary computation scheme assuming massive parallel computer architectures.

Research Products

• [Journal Article] Striking a Mean- and Parent-centric Balance in Real-valued Crossover Operators (2013)
  • Author(s): 染谷博司
  • Journal Title: IEEE Transactions on Evolutionary Computation Volume: 17 Issue: 6 Pages: 737-754
  • DOI: 10.1109/tevc.2012.2200255
  • Peer Reviewed
• [Journal Article] General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming (2013)
  • Author(s): K. Ishimatsu
  • Journal Title: ACS Synthetic Biology Volume: - Issue: 9 Pages: 638-644
  • DOI: 10.1021/sb400102w
  • Peer Reviewed / Open Access
• [Journal Article] Design and Control of Synthetic Biological Systems (2013)
  • Author(s): Ryoji Sekine
  • Journal Title: Natural Computing and Beyond Volume: 6 Pages: 104-114
  • DOI: 10.1007/978-4-431-54394-7_9
  • ISBN: 9784431543930, 9784431543947
  • Peer Reviewed
• [Journal Article] 周波数特性を用いた振動する人工遺伝子回路の自動設計 (2013)
  • Author(s): 林孝文
  • Journal Title: 計測自動制御学会第４０回知能システムシンポジウム資料集 Volume: - Pages: 211-216
• [Journal Article] 人為的なコドン再定義から考える遺伝暗号の進化 (2013)
  • Author(s): 坂本 健作
  • Journal Title: 第15回日本RNA学会 講演論文集 Volume: S-8
• [Journal Article] T unability of the ratio of cell states after the synthetic diversification by the diversity generator (2012)
  • Author(s): 関根 亮二, 山村 雅幸, 萩谷 昌巳, 木賀 大介
  • Journal Title: Communicative and Integrative Biology Volume: 5巻 Issue: 4 Pages: 393-394
  • DOI: 10.4161/cib.20310
  • Peer Reviewed
• [Journal Article] Design strategy for an initial state-independent diversity generator (2012)
  • Author(s): 関根 亮二, 木賀 大介, 山村 雅幸
  • Journal Title: Chem-Bio Informatics Journal Volume: 12 Issue: 0 Pages: 39-49
  • DOI: 10.1273/cbij.12.39
  • NAID: 130004138125
  • ISSN: 1347-0442, 1347-6297
  • Peer Reviewed
• [Journal Article] Design strategy for an initial state-independent diversity generator (2012)
  • Author(s): Ryoji Sekine
  • Journal Title: Chem-Bio Informatics Journal Volume: vol. 12 Pages: 39-49
  • Peer Reviewed
• [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling (2011)
  • Author(s): Sekine, R., Yamamura, M., Ayukawa, S., Ishimatsu, K., Akama, S., Takinoue, M., Hagiya, M., Kiga, D.
  • Journal Title: Proc.Natl.Acad.Sci.U.S.A. Volume: 108 Issue: 44 Pages: 17969-17973
  • DOI: 10.1073/pnas.1105901108
  • Peer Reviewed
• [Presentation] 人為的なコドン再定義から考える遺伝暗号の進化 (2013)
  • Author(s): 坂本 健作, 向井 崇人, 大竹 和正, 染谷 博司
  • Organizer: 第15回日本RNA学会
  • Place of Presentation: 愛媛県・県民文化会館・ひめぎんホール
  • Year and Date: 2013-07-25
• [Presentation] 周波数特性を用いた振動する人工遺伝子回路の自動設計 (2013)
  • Author(s): 林 孝文, 山村 雅幸
  • Organizer: 計測自動制御学会 第40回知能システムシンポジウム
  • Place of Presentation: 京都工芸繊維大学 松ヶ崎キャンパス
  • Year and Date: 2013-03-15