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Title: | 利用網絡分析和粗粒度模型闡明光系統II中捕光動力學 Elucidating Dynamics of Light Harvesting in Photosystem II Using Network Analysis and Coarse-Grained Models |
Authors: | 楊允中 Yun-Chung Yang |
Advisor: | 鄭原忠 Yuan-Chung Cheng |
Keyword: | 光捕獲,網路分析,聚類, Light harvesting,Network analysis,Clustering, |
Publication Year : | 2023 |
Degree: | 碩士 |
Abstract: | 光系統II利用約300個葉綠素來捕獲陽光能量並將其從其天線傳遞至反應中心。這個光收穫過程通過複雜的激發能量轉網絡實現了卓越的效率。我們建立了一個有效的耗散性 Frenkel 激子模型來描述光系統II中的激發能傳遞網絡並應用網絡分析方法來研究激發能傳遞動力學的特性。具體而言,度分佈和小世界性顯示量子離域增強了激發能傳遞網絡的韌性並促進了能量傳遞至反應中心。儘管我們能夠闡明整個光系統II激發能傳遞網絡的特性,然而完整的激發能傳遞網絡過於複雜,無法對光系統II中實現光收集的高量子效率的因素產生有用的見解。為了闡明光系統II激發能傳遞動力學,我們分別採用了分層聚類、最小割、k-均值和譜聚類等方法構建了光系統II激發能傳遞動力學的粗顆粒模型。發現最小割方法能夠產生最佳的粗顆粒模型,準確地描述光系統II激發能傳遞動力學並提供亞單位之間能量流的瓶頸。我們的研究表明,光系統II激發能傳遞網絡中的能量流瓶頸並不總是在子單位的邊界處。簇間的能量傳輸速率較慢約束了光系統II中激子的隨機行走,促進了激發能傳遞至反應中心的發生。此外,負責激發能傳遞的激子態並不總是簇內的最低能量態。這種設計在每一步傳輸中最大程度地減少了能量浪費,從而實現了高效的光收穫。 The photosystem II supercomplex (PSII) utilizes ∼300 chlorophylls to capture sunlight energy and transfer it from its antennas to the reaction center. This light harvesting process exhibits remarkable efficiency achieved by a complex excitation energy transfer (EET) network. We have constructed an effective dissipative Frenkel exciton model to describe the EET network in the PSII and applied the network analysis methods to investigate the characteristics of the EET dynamics. Specifically, the degree distribution and small-worldness show that the quantum delocalization enhances the robustness of the EET network and facilitates the EET to the reaction center. Although we can elucidate the characteristics of the entire PSII EET network, the full EET network is too complex to yield useful insights on factors enabling the high quantum efficiency of light harvesting in PSII. To elucidate the PSII EET dynamics, we constructed coarse-grained models of PSII EET dynamics using hierarchical clustering, minimum-cut, k-means, and spectral clustering methods, respectively. The minimum-cut approach was found to yield the best coarse-grained model to accurately describe the PSII EET dynamics and provide the bottlenecks of energy flow between subunits. Our study shows that the bottlenecks of energy flow in the PSII EET network are not always at the boundaries of subunits. The slow energy transfer rate between clusters constrains the random walk of the excitons in PSII, facilitating the EET to RC. In addition, the exciton states responsible for EET are not always the lowest-energy states within a cluster. This design minimizes energy waste during each transfer step, resulting in high efficiency of light harvesting. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/88409 |
DOI: | 10.6342/NTU202301671 |
Fulltext Rights: | 同意授權(限校園內公開) |
Appears in Collections: | 化學系 |
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ntu-111-2.pdf Access limited in NTU ip range | 20.5 MB | Adobe PDF | View/Open |
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