"Semantics of Computational Languages for Biochemical Networks -Elucidating Local- ity and Causality-"

• Project/Area Number: 25400195
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Foundations of mathematics/Applied mathematics
• Research Institution: The University of Tokyo
• Principal Investigator: Hamano Masahiro 東京大学, 情報理工学(系)研究科, 研究員 (50313705)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,510,000 (Direct Cost: ¥2,700,000、Indirect Cost: ¥810,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: 確率プロセス計算 / rule based modelling / chemical master equation / stochastic modelling / steady state dynamics / Brownian ratchet / Michaelis-Menten / Boltzmann distribution / RNA polymerase / master equation / equilibrium kinetics / free energy / kappa 計算 / 化学マスター方程式 / 定常状態 / stochastic petri net / 化学反応ネットワーク

Outline of Final Research Achievements

We investigated the mechano-chemical pathway of RNA Transcription Elongation in terms of computational description of stochastic process calculus. As a semantical counterpart of this, model abstraction was investigated in comparison with quasi-steady-state (QSS) approximation for chemical master equations. Thermodynamical meaning was also given on the stochastic models in terms of free energy distribution for the variously congured agents and of the traditional Michaelis-Menten enzyme kinetics.

Research Products

• [Journal Article] Stochastic Transcription Elongation via Rule Based Modelling (2016)
  • Author(s): Masahiro Hamano
  • Journal Title: Electronic Notes in Theoretical Computer Science, Elsevier. Volume: To appear
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Stochastic Transcription Elongation via Rule Based Modelling (2015)
  • Author(s): Masahiro Hamano
  • Organizer: The Sixth International Workshop on Static Analysis and Systems Biology (SASB 2015)
  • Place of Presentation: Saint-Malo, FRANCE
  • Year and Date: 2015-09-08
  • Int'l Joint Research