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研究生: 李奕璟
Lee, Yi Chin
論文名稱: 在光合作用下生物網路的能量傳遞
Energy Propagation in Biological System for Photosynthesis
指導教授: 林秀豪
Lin, Hsiu Hau
口試委員: 吳國安
陳宣毅
陳岳男
學位類別: 碩士
Master
系所名稱: 理學院 - 物理學系
Department of Physics
論文出版年: 2016
畢業學年度: 104
語文別: 英文
論文頁數: 56
中文關鍵詞: 光合作用林布拉德方程式量子開放系統量子生物
外文關鍵詞: Photosynthesis, Lindblad Equation, Open Quantum System, Quantum Biology
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  • 一直以來,一般的生物系統因為生存環境潮濕且溫暖的關係,所以除了化學結構以外,生物體內並不被認為會存在量子效應。然而,最近的實驗結果發現在光合作用的能量傳遞過程中存在著尚未被清楚解釋的量子同調現象。本篇論文我們將探討由七個FMO複合物蛋白質組成的生物網路是如何藉由量子動力學的方式在光合作用下傳遞能量。透過林布拉德方程式描述約化之後的七維哈密頓量,我們可以將環境對系統的交互作用包含進量子動力學的描述之中。我們藉由數值模擬呈現系統中的能量是如何以非嚴格遞減的方式流到反應中心,同時我們也發現到在能量流動過程中,有些中間態會有能量機率累積的現象。我們的結果顯示量子力學可能遠比預期的還要豐富,同時也說明這些效應無法用半古典理論解釋。根據本篇論文的理論基礎,未來希望能夠完全了解能量與信息在生物系統中傳遞時產生的量子同調現象。


    Biological systems are wet and warm, excluding explicit quantum phenomena except chemical structures and interactions. However, recent experiments reveal strong evidence that energy propagation in photosynthesis remains quantum coherent without full explanation at this point. Here we investigate the quantum dynamics of energy propagation in photosynthesis through the biological network composed of seven primary FMO complex proteins. The effects from the biological environment are included implicitly through the Lindblad equation for the reduced seven-site Hamiltonian. Numerical simulations reveal non-monotonic energy flows to the reaction center and some reoccurrence of probability accumulation in the transient states. Our results show that the quantum dynamics is much richer and cannot be captured by the semi-classical stochastic processes. Further investigation is in order to achieve full understanding of the quantum coherence for energy and information propagations in biological systems.

    1 Introduction 3 2 Lindblad equation 5 2.1 DensityMatrix ............................. 6 2.1.1 BasicProperties......................... 6 2.1.2 System Classification...................... 7 2.2 Semigroup................................ 7 2.2.1 TimeEvolution Operator ................... 7 2.2.2 Semigroup Properties...................... 9 2.3 Dynamical Mapping .......................... 9 2.3.1 Derivation............................ 9 2.3.2 two-spin case .......................... 14 2.3.3 Complete Positivity....................... 16 2.3.4 Kraus Operator......................... 21 2.4 NMR Example ............................. 24 2.5 Multi-level system............................ 26 2.5.1 IncoherenceDecay ....................... 26 2.5.2 Coherence Decay ........................ 27 3 Modeling the FMO complex 30 3.1 Photosynthesis ............................. 30 3.1.1 ExperimentResults....................... 31 3.2 FMOComplex ............................. 32 3.2.1 UnitaryTransformation .................... 35 3.2.2 Decaying rate .......................... 36 4 Numerical Simulations for Exciton Propagation 38 4.1 Concept ................................. 39 4.1.1 Model .............................. 39 4.1.2 Lindblad Dynamic Simulation................. 40 4.2 SimulationIntepretion ......................... 41 4.2.1 Define State and Operator................... 41 4.2.2 Time Evolution MainProgram ................ 42 4.3 Result Discussion............................ 44 4.4 Rotating BasisMethod......................... 48

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