臺灣博碩士論文加值系統

為了理解在光合系統中複雜激子的能量傳輸行為，建立一個粗粒化模型是必要的。在本次工作中，我們開發了一個系統化的方法。藉由最小分割法來建構光合系統的粗粒化模型。我們使用這個方法處理三種不同的光合作用網路並且這些粗粒化模型可以很好的還原激子能量傳輸的動態演變。這些粗粒化模型可以給我們對這些光合作用系統有新的見解，也可以有效的讓我們理解複雜的動力學反應。

To understand complex excitation energy transfer (EET) networks in photosynthetic systems, building a coarse-grained model is necessary to obtain a simplified representation. Here, we developed a systematic approach to produce coarse-grained models for photosynthetic systems by combining a minimum-cut method and a top-down clustering algorithm. The new approach was applied to investigate EET networks of three photosynthetic systems, and we demonstrate that our approach not only reproduces the population dynamics very well but also provides novel insights into the spatial-temporal EET dynamics in complex photosynthetic systems. The new approach could be a very powerful tool towards the elucidation of complex kinetic networks that is commonly encountered in Chemistry.

口試委員會審定書 iii
誌謝 v
摘要 vii
Abstract ix
1 Introduction 1
2 Excitation Energy Transfer 3
2.1 Model Hamiltonian 3
2.2 Quantum master equation 4
2.3 Excitation energy transfer network 7
3 Network analysis 9
3.1 Minimum-cut binary tree 9
3.2 Coarse-grained model 11
3.2.1 MBT normalized 11
3.2.2 Simple cut-off method 12
3.2.3 Simple ratio cut-off method 13
3.2.4 Ascending cut-off method 13
3.3 Reduced dynamics 14
3.3.1 MBT rearrangement 15
4 Fenna-Mattews-Olson complex 17
4.1 Effective Hamiltonian 17
4.2 Rate constant matrix 18
4.3 MRT population dynamics 18
4.4 Network analysis 20
5 Light Harvesting Complex II 25
5.1 Effective Hamiltonian 25
5.2 Rate constant matrix 26
5.3 MRT population dynamics 26
5.4 Network analysis 26
5.5 Coarsed-grained model 31
6 Photosystem I 39
6.1 Effective Hamiltonian 39
6.2 Rate constant matrix 39
6.3 Network analysis 39
7 Conclusions 45
Bibliography 47

[1] T. R. Calhoun, N. S. Ginsberg, G. S. Schlau-Cohen, Y.-C. Cheng, M. Ballottari, R. Bassi, and G. R. Fleming. Quantum Coherence Enabled Determination of the Energy Landscape in Light-Harvesting Complex II. J. Phys. Chem. B, 113(51):16291–16295, dec 2009.
[2] A. Damjanović, H. M. Vaswani, P. Fromme, and G. R. Fleming. Chlorophyll excitations in photosystem I of Synechococcus elongatus. J. Phys. Chem. B, 106(39):10251–10262, 2002.
[3] L. R. Ford and D. R. Fulkerson. Maximal flow through a network. J. Can. mathématiques, 8:399–404, 1956.
[4] R. Görke, T. Hartmann, and D. Wagner. Dynamic Graph Clustering Using Minimum-Cut Trees. J. Graph Algorithms Appl., 16(2):411–446, 2012.
[5] Y. H. Hwang-Fu, W. Chen, and Y. C. Cheng. A coherent modified Redfield theory for excitation energy transfer in molecular aggregates. Chem. Phys., 447:46–53, 2015.
[6] C. Kreisbeck, T. Kramer, and A. Aspuru-Guzik. Scalable high-performance algorithm for the simulation of exciton dynamics. Application to the light-harvesting complex II in the presence of resonant vibrational modes. J. Chem. Theory Comput., 10(9):4045–4054, 2014.
[7] Z. Liu, H. Yan, K. Wang, T. Kuang, J. Zhang, L. Gui, X. An, and W. Chang. Crystal structure of spinach major light-harvesting complex at 2.72 A resolution. Nature, 428(6980):287–292, 2004.
[8] V. Novoderezhkin, A. Marin, and R. van Grondelle. Intra- and inter-monomeric transfers in the light harvesting LHCII complex: the Redfield–Förster picture. Phys. Chem. Chem. Phys., 13(38):17093, 2011.
[9] V. I. Novoderezhkin, M. A. Palacios, H. Van Amerongen, and R. Van Grondelle. Excitation dynamics in the LHCII complex of higher plants: Modeling based on the 2.72 a crystal structure. J. Phys. Chem. B, 109(20):10493–10504, 2005.
[10] T. Renger, M. E. Madjet, A. Knorr, and F. Müh. How the molecular structure determines the flow of excitation energy in plant light-harvesting complex II. J. Plant Physiol., 168(12):1497–1509, 2011.
[11] G. S. Schlau-Cohen, T. R. Calhoun, N. S. Ginsberg, E. L. Read, M. Ballottari, R. Bassi, R. Van Grondelle, and G. R. Fleming. Pathways of energy flow in LHCII from two-dimensional electronic spectroscopy. J. Phys. Chem. B, 113(46):15352–15363, 2009.
[12] M. Schmidt Am Busch, F. Müh, M. El-Amine Madjet, and T. Renger. The eighth bacteriochlorophyll completes the excitation energy funnel in the FMO protein. J. Phys. Chem. Lett., 2(2):93–98, 2011.
[13] D. E. Tronrud, J. Wen, L. Gay, and R. E. Blankenship. The structural basis for the difference in absorbance spectra for the FMO antenna protein from various green sulfur bacteria. Photosynth. Res., 100(2):79–87, may 2009.
[14] L. Valkunas, G. Trinkunas, J. Chmeliov, and A. V. Ruban. Modeling of exciton quenching in photosystem II. Phys. Chem. Chem. Phys., 11(35):7576–7584, 2009.
[15] R. van Grondelle and V. I. Novoderezhkin. Energy transfer in photosynthesis: experimental insights and quantitative models. Phys Chem Chem Phys, 8(7):793–807, 2006.
[16] J. Wu, Z. Tang, Z. Gong, J. Cao, and S. Mukamel. Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex. J. Phys. Chem. Lett., pages 1240–1245, 2015.