title: Hierarchical coarse-graining model for photosystem II including electron and excitation-energy transfer processes.
abstract: We propose a hierarchical reduction scheme to cope with coupled rate equations that describe the dynamics of multi-time-scale photosynthetic reactions. To numerically solve nonlinear dynamical equations containing a wide temporal range of rate constants, we first study a prototypical three-variable model. Using a separation of the time scale of rate constants combined with identified slow variables as (quasi-)conserved quantities in the fast process, we achieve a coarse-graining of the dynamical equations reduced to those at a slower time scale. By iteratively employing this reduction method, the coarse-graining of broadly multi-scale dynamical equations can be performed in a hierarchical manner. We then apply this scheme to the reaction dynamics analysis of a simplified model for an illuminated photosystem II, which involves many processes of electron and excitation-energy transfers with a wide range of rate constants. We thus confirm a good agreement between the coarse-grained and fully (finely) integrated results for the population dynamics.
authors.affiliation: Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan. Electronic address: matsuoka@eniac.scitec.kobe-u.ac.jp.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Matsuoka
authors.affiliation: Graduate School of System Informatics, Department of Computational Science, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan. Electronic address: tanaka2@kobe-u.ac.jp.
authors.forename: Shigenori
authors.initials: S
authors.lastname: Tanaka
authors.affiliation: Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe 657-8501, Japan. Electronic address: ebina@kobe-u.ac.jp.
authors.forename: Kuniyoshi
authors.initials: K
authors.lastname: Ebina
mesh_terms: D003198:Computer Simulation; D004579:Electron Transport / Q000502:physiology / Q000528:radiation effects; D004735:Energy Transfer / Q000502:physiology* / Q000528:radiation effects; D008027:Light; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry* / Q000502:physiology* / Q000528:radiation effects; D008954:Models, Biological; D008956:Models, Chemical; D045332:Photosystem II Protein Complex / Q000737:chemistry* / Q000502:physiology* / Q000528:radiation effects
chemical_list: D045342:Light-Harvesting Protein Complexes; D045332:Photosystem II Protein Complex
keywords: Coarse graining; Electron transfer; Excitation-energy transfer; Multi-scale simulation; Photosynthesis