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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 鄭原忠 | zh_TW |
| dc.contributor.advisor | Yuan-Chung Cheng | en |
| dc.contributor.author | 洪巧爰 | zh_TW |
| dc.contributor.author | Chiao-Yuan Hung | en |
| dc.date.accessioned | 2026-03-05T16:31:34Z | - |
| dc.date.available | 2026-03-06 | - |
| dc.date.copyright | 2026-03-05 | - |
| dc.date.issued | 2026 | - |
| dc.date.submitted | 2026-02-06 | - |
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| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/101892 | - |
| dc.description.abstract | 光系統 I–光捕捉複合體 I（Photosystem I-light-harvesting complex I，PSI-LHCI）儘管具有龐大的系統尺寸與顯著的結構異質性，仍可達到近乎單位的量子產率。雖然 PSI 核心天線中的激發能量傳遞（excitation energy transfer, EET）動力學已受到廣泛研究，但整個 PSI-LHCI 超級複合體中的能量傳遞動力學行為仍未被充分釐清。本研究以豌豆（Pisum sativum）之 PSI-LHCI 為對象，在靜態無序條件下探討其主導性的激發能量傳遞動力學特徵。
本研究首先對一個依量子產率分布之中位數選取的代表性無序實現，應用圖論中的最小割（minimum-cut）方法，建構一個最佳化的 14 群集粗粒化動力學模型，該模型可忠實重現完整系統的佔據數動力學。相同的粗粒化分析亦進一步套用於涵蓋不同量子產率百分位的其他無序實現，以及透過對整體無序系綜進行共識分群（consensus clustering）所獲得的無序平均模型。 在所有情況下，所得的粗粒化描述皆一致揭示：由外圍 LHCI 天線向 PSI 核心的激發能量傳遞呈現穩健的雙分支（two-branch）機制。此動力學架構具有三項關鍵特徵：分支內能量轉移迅速、兩分支之間的直接交換極少，以及一個反覆出現的中心橋接叢集，其扮演控制激發能否進入反應中心（reaction center, RC）的關鍵閘門。這套一致的雙分支動力學圖像顯示，PSI-LHCI 的激發能量傳遞主要受整體傳遞路徑的全域組織所支配，並在靜態無序下仍維持高度魯棒性：能量能在各分支內高效率地被傳遞，而通往反應中心的有效捕獲則由該特徵性的動力學橋樑所導引與匯聚。 | zh_TW |
| dc.description.abstract | Photosystem I–light-harvesting complex I (PSI-LHCI) achieves a near-unity quantum yield despite its large size and pronounced structural heterogeneity. While excitation energy transfer (EET) in the PSI core is well characterized, the transfer dynamics of the full PSI-LHCI supercomplex remain unclear. Here, we investigate the dominant EET dynamics of the PSI-LHCI supercomplex from Pisum sativum under static disorder.
A minimum-cut method from graph theory is applied to a representative disorder realization selected at the median of the quantum yield distribution to construct a 14-cluster coarse-grained kinetic model that faithfully reproduces the population dynamics of the full system. The same coarse-graining analysis is further carried out for additional disorder realizations spanning different quantum-yield percentiles, as well as for a disorder-averaged model obtained via consensus clustering over the full ensemble. In all cases, the resulting coarse-grained descriptions consistently reveal a robust two-branch excitation energy transfer scheme from the peripheral LHCI antenna to the PSI core. This architecture is characterized by fast intra-branch transfer, minimal direct exchange between branches, and a recurrent central bridge cluster that governs access to the reaction center (RC). This consistent two-branch kinetic picture indicates that excitation energy transfer in PSI-LHCI is governed by the global organization of transfer pathways and remains robust under static disorder, with efficient energy transfer occurring within each branch and access to the reaction center funneled through the characteristic kinetic bridge. | en |
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| dc.description.tableofcontents | Contents
Verification Letter from the Oral Examination Committee i Acknowledgements iii 摘要 v Abstract vii Contents ix List of Figures xv List of Tables xxix Denotation xxxi Chapter 1 Introduction 1 1.1 Structure and Function of PSI–LHCI in Higher Plant . . . . . . . . . 1 1.2 Unresolved Issues on Light Harvesting of the PSI–LHCI . . . . . . . 4 1.3 Critical Excitation Energy Transfer Pathways . . . . . . . . . . . . . 6 1.4 Static Disorder and Robustness of Excitation Energy Transfer . . . . 8 1.5 The Outline of This Work . . . . . . . . . . . . . . . . . . . . . . . 9 Chapter 2 Theoretical Background 13 2.1 Effective Hamiltonian for Molecular Aggregates . . . . . . . . . . . 13 2.1.1 System Hamiltonian: Frenkel exciton model . . . . . . . . . . . . . 14 2.1.2 Bath Hamiltonian and system-bath interactions . . . . . . . . . . . 15 2.1.3 Exciton basis and optical properties . . . . . . . . . . . . . . . . . 17 2.2 Theoretical Simulation of Excitation Energy Transfer Dynamics . . . 19 2.2.1 Quantum master equation . . . . . . . . . . . . . . . . . . . . . . . 19 2.2.2 Combined modified Redfield and generalized Förster theory . . . . . 20 2.3 Simulation of Linear Optical Spectra . . . . . . . . . . . . . . . . . 24 2.3.1 Static disorder effect . . . . . . . . . . . . . . . . . . . . . . . . . . 25 2.3.2 Absorption spectrum . . . . . . . . . . . . . . . . . . . . . . . . . 25 2.3.3 Linear dichroism spectrum . . . . . . . . . . . . . . . . . . . . . . 26 Chapter 3 Effective Model for PSI-LHCI Supercomplex 29 3.1 Parameterization of Hamiltonian . . . . . . . . . . . . . . . . . . . . 31 3.1.1 Site energies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 3.1.2 Excitonic couplings . . . . . . . . . . . . . . . . . . . . . . . . . . 32 3.1.3 Spectral density for system-bath interactions . . . . . . . . . . . . . 34 3.2 Determination of the Effective Model Based on Experimental Data . 36 3.2.1 Site energies from fitting to optical spectra of PSI-LHCI . . . . . . . 37 3.2.2 Quantum efficiency of light harvesting . . . . . . . . . . . . . . . . 46 Chapter 4 Network Analysis of EET Dynamics in the PSI-LHCI 49 4.1 Definition of the EET Network . . . . . . . . . . . . . . . . . . . . . 50 4.2 Effects of Static Disorder on the PSI-LHCI EET Network . . . . . . . 50 4.3 Network Analysis Metrics and Methodology . . . . . . . . . . . . . 51 4.3.1 Exciton state alignment across disorder realizations . . . . . . . . . 53 4.3.2 Spatial mapping of exciton states . . . . . . . . . . . . . . . . . . . 54 4.3.3 Node degree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 4.3.4 Edge persistence . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 4.4 Analysis of Network Connectivity in a Representative Realization . . 56 4.5 Statistical Characterization of the EET Network under Static Disorder 58 4.5.1 Spatial maps of average degree of exciton states under static disorder 63 4.5.2 Edge persistence analysis . . . . . . . . . . . . . . . . . . . . . . . 63 4.5.3 Statistical comparison of transfer mechanisms . . . . . . . . . . . . 64 4.5.4 Analysis of degree distributions and decomposition by physical mechanism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 4.6 Impact of Exciton Delocalization on Network Connectivity . . . . . . 75 4.6.1 Rate constant distribution analysis . . . . . . . . . . . . . . . . . . 75 4.6.2 Comparative analysis of degree distributions . . . . . . . . . . . . . 76 4.7 Concluding Remarks and the Need for Coarse-Graining . . . . . . . . 77 Chapter 5 Elucidation of PSI-LHCI EET Network via Coarse-graining 81 5.1 Minimum-Cut Method . . . . . . . . . . . . . . . . . . . . . . . . . 82 5.1.1 Defining the source and sink . . . . . . . . . . . . . . . . . . . . . 83 5.1.2 Dinic’s algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 5.2 Top-Down Clustering Based on the Minimum-Cut Tree . . . . . . . . 86 5.2.1 Definition of inter-cluster effective rate . . . . . . . . . . . . . . . . 87 5.2.2 Number-constrained divisive clustering on a minimum-cut tree . . . 88 5.3 Cluster Model Verification . . . . . . . . . . . . . . . . . . . . . . . 90 5.3.1 Mean absolute error . . . . . . . . . . . . . . . . . . . . . . . . . . 90 5.4 Representative 14-Cluster Model . . . . . . . . . . . . . . . . . . . . 92 5.4.1 Selection of optimal cluster number from MAE . . . . . . . . . . . 93 5.4.2 Analysis of coarse-grained EET dynamics . . . . . . . . . . . . . . 93 5.4.2.1 Two-branch EET pathway architecture in light harvesting of PSI-LHCI . . . . . . . . . . . . . . . . . . . . . 96 5.4.2.2 Efficient intra-branch funneling . . . . . . . . . . . . . 96 5.4.2.3 Kinetics of antenna-to-core transfer . . . . . . . . . . . 98 5.4.2.4 Asymmetric entry to the reaction center . . . . . . . . 98 5.4.2.5 Ultrafast inter-cluster transfer . . . . . . . . . . . . . . 99 5.5 Generalization of the Two-Branch Architecture . . . . . . . . . . . . 100 5.5.1 The central cluster as a kinetic bridge . . . . . . . . . . . . . . . . . 102 Chapter 6 Unified Coarse-Grained Model under Static Disorder 105 6.1 Consensus Clustering . . . . . . . . . . . . . . . . . . . . . . . . . . 106 6.2 Definition of the Disorder-Averaged Inter-Cluster Effective Rate . . . 107 6.3 Unified 14-Cluster Model under Static Disorder . . . . . . . . . . . . 109 6.3.1 Validation of the cluster number selection . . . . . . . . . . . . . . 109 6.3.2 The unified 14-cluster kinetic model . . . . . . . . . . . . . . . . . 111 6.3.2.1 Preservation of the two-branch architecture . . . . . . . 113 6.3.2.2 Symmetry and variations in Lhca-to-Core transfer . . . 116 6.3.2.3 Funneling of excitation energy through a bridge cluster 116 6.3.2.4 Kinetic accessibility of the reaction center . . . . . . . 117 6.4 Robust Kinetic Features Revealed by the Unified Model . . . . . . . 117 Chapter 7 Conclusion 119 References 123 Appendix A — Fitted Site Energies and Model Validation 135 A.1 Site Energies of Lhca Subunits Based on Structural Homology . . . . 135 A.2 Validation of PSI Core Parameters . . . . . . . . . . . . . . . . . . . 136 A.3 Parameters for the PSI-LHCI Effective Model . . . . . . . . . . . . . 141 A.3.1 Tables of fitted site energies . . . . . . . . . . . . . . . . . . . . . . 141 A.4 Additional Details of Lhca1 Spectral Fitting . . . . . . . . . . . . . . 144 Appendix B — Spatial Map of Exciton-State Degree 147 Appendix C — Extended Validation of the 14-Cluster Model 151 C.1 Universality of the Two-Branch Architecture . . . . . . . . . . . . . 151 | - |
| dc.language.iso | en | - |
| dc.subject | PSI–LHCI 超級複合體 | - |
| dc.subject | 激發能量傳遞 | - |
| dc.subject | 靜態無序 | - |
| dc.subject | 粗粒化動力學 | - |
| dc.subject | 最小割分析 | - |
| dc.subject | 激發能量傳遞網路 | - |
| dc.subject | PSI-LHCI supercomplex | - |
| dc.subject | excitation energy transfer | - |
| dc.subject | static disorder | - |
| dc.subject | coarse-grained kinetics | - |
| dc.subject | minimum-cut analysis | - |
| dc.subject | EET network | - |
| dc.title | PSI–LHCI 超級複合體之光捕捉動力學的理論研究 | zh_TW |
| dc.title | A Theoretical Study on the Light-Harvesting Dynamics in the PSI–LHCI Supercomplex | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 114-1 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 金必耀;李祐慈 | zh_TW |
| dc.contributor.oralexamcommittee | Bih-Yaw Jin;Elise Yu-Tzu Li | en |
| dc.subject.keyword | PSI–LHCI 超級複合體,激發能量傳遞靜態無序粗粒化動力學最小割分析激發能量傳遞網路 | zh_TW |
| dc.subject.keyword | PSI-LHCI supercomplex,excitation energy transferstatic disordercoarse-grained kineticsminimum-cut analysisEET network | en |
| dc.relation.page | 155 | - |
| dc.identifier.doi | 10.6342/NTU202600674 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2026-02-09 | - |
| dc.contributor.author-college | 理學院 | - |
| dc.contributor.author-dept | 化學系 | - |
| dc.date.embargo-lift | 2026-03-31 | - |
| 顯示於系所單位： | 化學系 | |
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