臺灣博碩士論文加值系統

光合作用系統 II (PSII)仰賴一個巨大的天線複合體用以蒐集充足的光能，這些光能能夠驅動光合作用系統II中的反應中心 (RCs)。在這個光捕捉的過程中，太陽光會激發天線複合體中的色素分子，將光能轉換成激發能。然而，在激發能從天線複合體轉移到RCs的過程中，蛋白質結構的振動會擾動各個色素分子的激發能，從而在PSII上形成一個波動的能量曲面。此外，巨大的天線複合體中的色素分子數目遠遠超過RC中的數目，這樣的差異使得巨大的天線複合體具有更高的自由度，同時也產生了相對應的熵效應。即便在這些限制下，PSII仍能在光捕捉的過程中保持高量子效率。因此，我們需要瞭解大自然使用了哪些策略。了解這些策略對於我們理解PSII如何在限制條件下實現高效能光捕捉至關重要。為此，我們建立了一個光合作用系統II激發能轉移的簡化群集模型，我們能夠建立有效的內能能量曲面。從這個能量曲面上，我們發現在群集中有一些特殊的時標分離(timescale separation)的性質，降低了激發能在天線複合體中的自由度並促進激發能進入反應中心。另外，光合作用系統II在其主要的能量轉移路徑上設計了精巧的能量梯度，這些優化能量曲面的設計是用來達成高效地光捕捉。同時，PSII還利用熱能來克服激發能擾動所產生的障礙。透過研究PSII能量曲面的優化設計，我們可以為未來設計大型高效光捕捉系統提供一些有價值的指引。

Photosystem II (PSII) relies on a large antenna complex to collect sufficient light energy to power its reaction centers (RCs). In this light harvesting process, molecular excitation must pass through the fluctuating energy surface where the static disorder perturb site energies, and overcome unfavorable entropic effects to be transferred from the large antenna to the much smaller RC with low energy loss. It is thus of significant importance to uncover the strategies that the nature applied to achieve the remarkably high quantum efficiency of PSII under the constrains. To this end, we constructed a coarse-grained model for exciton energy transfer in PSII, which allows us to establish an effective internal energy surface for excitation energy transfer in the PSII. We found that the energy landscape exhibits timescale separation characteristics among the clusters, which suppresses the entropic effect and facilitates the energy transfer to the RC. Further investigation revealed that the energy surface is optimized for efficient light harvesting and tolerating static disorder of site energy by using a specifically designed energy gradient along the main energy-transfer pathways and utilization of thermal energy to overcome the barriers. The optimal energy landscape for EET in the PSII provides important insight towards how to achieve highly efficient energy harvesting in a large and fluctuating system.

Verification Letter from the Oral Examination Committee i
Acknowledgements iii
摘要v
Abstract vii
Contents ix
List of Figures xiii
List of Tables xix
Denotation xxi
Chapter 1 Introduction 1
1.1 Light harvesting process in PSII . . . . . . . . . . . . . . . . . . . . 1
1.2 The constraints for light harvesting in PSIIsc. . . . . . . . . . . . . 4
1.3 The EET dynamics in PSIIsc. . . . . . . . . . . . . . . . . . . . . 7
1.4 Theorical Simulation of EET dynamics in PSII . . . . . . . . . . . . 8
1.5 The outline of this work . . . . . . . . . . . . . . . . . . . . . . . . 9
Chapter 2 Theoritical description of EET dynamics in photosynthetic system 13
2.1 Model Hamiltonian . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
2.2 Construction of effecitve Hamiltonian . . . . . . . . . . . . . . . . . 18
2.3 Conbined Generalized Föster and modified Redfield method . . . . . 19
2.4 Simulation of absorption spectrum . . . . . . . . . . . . . . . . . . . 22
2.5 Simulation of migration time . . . . . . . . . . . . . . . . . . . . . . 23
2.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Chapter 3 Construction of effective model and model validation 27
3.1 Construction of effective Hamiltonian . . . . . . . . . . . . . . . . . 28
3.2 Spectral density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
3.3 Fitted site energies . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3.3.1 Slow EET dynamics in LHCII . . . . . . . . . . . . . . . . . . . . 35
3.4 Model validation for EET dynamics in PSIIsc. . . . . . . . . . . . 40
3.4.1 Migration time . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
3.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Chapter 4 The effective internal energy surface in PSIIsc 43
4.1 Static disorder effect in light harvesting . . . . . . . . . . . . . . . . 44
4.2 Effective internal energy surface of PSIIsc. . . . . . . . . . . . . . 47
4.2.1 Construction of effective internal energy surface . . . . . . . . . . . 49
4.2.2 High barriers in effective internal energy surface . . . . . . . . . . . 53
4.3 Timescale separation on EET dynamics in PSIIsc . . . . . . . . . . 56
4.3.1 EET dynamics in upper side of PSIIsc . . . . . . . . . . . . . . . . 57
4.3.2 Energy transfer trajectories to RC . . . . . . . . . . . . . . . . . . . 60
4.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Chapter 5 Inter PSIIsc EET on the thylakoid membrane 65
5.1 The crystal parameters of PSIIscs on the thylakoid membrane . . . . 65
5.2 Migration time between two adjacent PSIIscs . . . . . . . . . . . . 67
5.2.1 Low light adaptive condition . . . . . . . . . . . . . . . . . . . . . 69
5.2.2 High light adaptive condition . . . . . . . . . . . . . . . . . . . . . 72
5.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Chapter 6 The factors govering the QY of light harvesting 79
6.1 Site energies effect on QY . . . . . . . . . . . . . . . . . . . . . . . 80
6.2 The level of static effect on QY . . . . . . . . . . . . . . . . . . . . 85
6.3 Excitonic coupling effect on QY . . . . . . . . . . . . . . . . . . . . 86
6.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Chapter 7 Conclusion 93
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