簡易檢索 / 詳目顯示

研究生: 王振倫
Wang, Jhen-Lun
論文名稱: Fenna-Matthews-Olson複合體中激發轉移的量子過程能力之研究
Quantum Process Capabilities of Excitation Transfer in the Fenna-Matthews-Olson Complex
指導教授: 李哲明
Li, Che-Ming
學位類別: 碩士
Master
系所名稱: 工學院 - 工程科學系
Department of Engineering Science
論文出版年: 2019
畢業學年度: 107
語文別: 英文
論文頁數: 87
中文關鍵詞: Fenna-Matthews-Olson複合體量子同調量子糾纏量子過程能力量子過程
外文關鍵詞: Fenna-Matthews-Olson complex, Quantum coherence, Quantum entanglement, Quantum process capability, Quantum process
相關次數: 點閱:177下載:0
分享至:
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報
  • Fenna-Matthews-Olson(FMO)複合體是一個八體結構,被某些類型的細菌用於將激發從光捕獲接收端轉移到行光合作用的反應中心;在本篇論文,我們以定量精確的方式表徵FMO複合體中激發轉移的量子力學特徵,並引入兩種不同的量度來量化糾纏生成、同調性產生和保存、疊加產生的能力、以及量子態在室溫下能量轉移的動態過程的疊加。由於這些能力的度量不依賴被處理狀態的任何細節,因此我們提供了一種全面的方法,用以研究不同量子過程能力和生物功能之間的關係,包含激發能量的轉移在演化進程中,量子力學特徵之變化;激發能量轉移的穩健性,和突變、局部缺陷等異常情況的關聯。

    The Fenna-Matthews-Olson (FMO) complex is an eight-site structure used by certain types of bacteria to transfer excitations from a light-harvesting antenna to a reaction center. Here, we characterize several prescribed quantum-mechanical features of the excitation transfer in the FMO complex in a quantitatively precise manner. Two different measures are introduced to quantify the capabilities of entanglement generation, coherence creation and preservation, and superposition creation of quantum states for the dynamical process of energy transfer at room temperature. Since these capability measures do not depend on any specifics of the states being processed, our method provides a comprehensive way to investigate the relationship between different quantum process capabilities and biological function, including the change of mechanical characteristics of the excitation transfer in the FMO complex which evolves as time goes on, and the robustness of excitation energy transfer under mutations, local defects, and other abnormal situations.

    摘要 i Abstract ii 誌謝iii Table of Contents iv List of Tables viii List of Figures ix Nomenclature xi Chapter 1.Introduction 1 1.1.Background ............1 1.2.Motivation .............1 1.3.Purpose ............3 1.4.Outline .............3 Chapter 2.Fundamentals of Quantum Mechanics 5 2.1.The postulates of quantum mechanics ........5 2.1.1.Postulate 1 – State space .........5 2.1.2.Postulate 2 – Quantum evolution .......6 2.1.3.Postulate 3 – Quantum measurement .......7 2.1.4.Postulate 4 – Composite systems .......9 2.2.General properties of the density operator ......10 2.3.Quantum operations formalism ........11 2.4.Master equation ............11 2.5.Quantum process tomography ........13 Chapter 3.Quantum Process Capability 17 3.1.Properties of capability measure .........18 3.2.Quantum composition and quantum robustness .....18 3.2.1.Quantum composition .........18 3.2.2.Quantum robustness ........19 3.3.Quantum process capability ..........20 3.3.1.Coherence creation and coherence preservation .....21 3.3.2.Superposition creation ........22 3.3.3.Entanglement generation .........23 Chapter 4.Quantum Qrocess Capabilities of Excitation Transfer in the FMO Complex: the Study on the Evolution of the FMO Complex 25 4.1.The background of the FMO complex ........25 4.1.1.Recent research of quantum characteristics of the FMO complex: the study on the evolution of the FMO complex .....27 4.1.2.Hamiltonian ..........27 4.1.3.Lindblad master equation .........28 4.2.The evolution of the FMO complex ........29 4.3.Quantum process capabilities of the FMO: the ancestral VS.current structure 30 4.3.1.Coherence creation and coherence preservation .....30 4.3.2.Superposition creation ........43 4.3.3.Entanglement generation .........46 4.4.Conclusion ............57 Chapter 5.Quantum Qrocess Capabilities of Excitation Transfer in the FMO Complex in the Presence of Defects 59 5.1.The background ............59 5.1.1.The background of the study on the FMO Complex in the presence of defects ...........59 5.1.2.Hamiltonian ..........60 5.2.Quantum process capabilities of the FMO: the unmodified condition VS.the presence of defects ..........62 5.2.1.Coherence creation and coherence preservation .....62 5.2.2.Superposition creation ........67 5.2.3.Entanglement generation .........69 5.3.Conclusion ............72 Chapter 6.Summary and Outlook 73 6.1.Summary .............73 6.2.Outlook ............74 References 75 Appendix A.Quantum Qrocess Capabilities of Excitation Transfer in the Sevensite FMO Complex in the Presence of Defects 79

    [1] J Thomas Beatty, Jörg Overmann, Michael T Lince, Ann K Manske, Andrew S Lang,
    Robert E Blankenship, Cindy L Van Dover, Tracey A Martinson, and F Gerald Plumley.
    An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent.
    Proceedings of the National Academy of Sciences, 102(26):9306–9310, 2005.
    [2] Masoud Mohseni, Yasser Omar, Gregory S Engel, and Martin B Plenio. Quantum effects
    in biology. Cambridge University Press, 2014.
    [3] Gregory D Scholes, Graham R Fleming, Alexandra Olaya-Castro, and Rienk Van Grondelle.
    Lessons from nature about solar light harvesting. Nature chemistry, 3(10):763,
    2011.
    [4] Neill Lambert, Yueh-Nan Chen, Yuan-Chung Cheng, Che-Ming Li, Guang-Yin Chen,
    and Franco Nori. Quantum biology. Nature Physics, 9(1):10, 2013.
    [5] Stéphanie Valleau, Romain A Studer, Florian Häse, Christoph Kreisbeck, Rafael G Saer,
    Robert E Blankenship, Eugene I Shakhnovich, and Alán Aspuru-Guzik. Absence of
    selection for quantum coherence in the fenna–matthews–olson complex: a combined
    evolutionary and excitonic study. ACS central science, 3(10):1086–1095, 2017.
    [6] Carsten Olbrich, Thomas LC Jansen, Jörg Liebers, Mortaza Aghtar, Johan Strümpfer,
    Klaus Schulten, Jasper Knoester, and Ulrich Kleinekathöfer. From atomistic modeling
    to excitation transfer and two-dimensional spectra of the fmo light-harvesting complex.
    The Journal of Physical Chemistry B, 115(26):8609–8621, 2011.
    [7] Guang-Yin Chen, Neill Lambert, Che-Ming Li, Yueh-Nan Chen, and Franco Nori.
    Rerouting excitation transfers in the fenna-matthews-olson complex. Physical Review
    E, 88(3):032120, 2013.
    [8] Martin B Plenio and Susana F Huelga. Dephasing-assisted transport: quantum networks
    and biomolecules. New Journal of Physics, 10(11):113019, 2008.
    [9] Julia Adolphs and Thomas Renger. How proteins trigger excitation energy transfer in
    the fmo complex of green sulfur bacteria. Biophysical Journal, 91(8):2778–2797, 2006.
    [10] Gregory S Engel, Tessa R Calhoun, Elizabeth L Read, Tae-Kyu Ahn, Tomáš Mančal,
    Yuan-Chung Cheng, Robert E Blankenship, and Graham R Fleming. Evidence for
    wavelike energy transfer through quantum coherence in photosynthetic systems. Nature,
    446(7137):782, 2007.
    [11] Alexandra Olaya-Castro, Chiu Fan Lee, Francesca Fassioli Olsen, and Neil F Johnson.
    Efficiency of energy transfer in a light-harvesting system under quantum coherence.
    Physical Review B, 78(8):085115, 2008.
    [12] Filippo Caruso, Animesh Datta, Susana F Huelga, Martin B Plenio, and Alex W Chin.
    Fundamental mechanisms of noise supported energy transfer in biological systems.
    Technical report, 2009.
    [13] Filippo Caruso, Alex W Chin, Animesh Datta, Susana F Huelga, and Martin B Plenio.
    Highly efficient energy excitation transfer in light-harvesting complexes: The
    fundamental role of noise-assisted transport. The Journal of Chemical Physics,
    131(10):09B612, 2009.
    [14] Patrick Rebentrost, Masoud Mohseni, Ivan Kassal, Seth Lloyd, and Alán Aspuru-
    Guzik. Environment-assisted quantum transport. New Journal of Physics,
    11(3):033003, 2009.
    [15] Hohjai Lee, Yuan-Chung Cheng, and Graham R Fleming. Quantum coherence accelerating
    photosynthetic energy transfer. In Ultrafast Phenomena XVI, pages 607–609.
    Springer, 2009.
    [16] Jianzhong Wen, Jiro Harada, Kenny Buyle, Kevin Yuan, Hitoshi Tamiaki, Hirozo Ohoka,
    Richard A Loomis, and Robert E Blankenship. Characterization of an fmo variant
    of chlorobaculum tepidum carrying bacteriochlorophyll a esterified by geranylgeraniol.
    Biochemistry, 49(26):5455–5463, 2010.
    [17] Jeremy Moix, Jianlan Wu, Pengfei Huo, David Coker, and Jianshu Cao. Efficient energy
    transfer in light-harvesting systems, iii: The influence of the eighth bacteriochlorophyll
    on the dynamics and efficiency in fmo. The Journal of Physical Chemistry Letters,
    2(24):3045–3052, 2011.
    [18] Avinash Kolli, Ahsan Nazir, and Alexandra Olaya-Castro. Electronic excitation dynamics
    in multichromophoric systems described via a polaron-representation master
    equation. The Journal of chemical physics, 135(15):154112, 2011.
    [19] Joel Yuen-Zhou, Jacob J Krich, Masoud Mohseni, and Alán Aspuru-Guzik. Quantum
    state and process tomography of energy transfer systems via ultrafast spectroscopy. Proceedings
    of the National Academy of Sciences, 108(43):17615–17620, 2011.
    [20] Patrick Rebentrost, Sangwoo Shim, Joel Yuen-Zhou, and Alan Aspuru-Guzik. Characterization
    and quantification of the role of coherence in ultrafast quantum biological
    experiments using quantum master equations, atomistic simulations, and quantum process
    tomography. Procedia Chemistry, 3(1):332–346, 2011.
    [21] A Thilagam. Natural light harvesting systems: unraveling the quantum puzzles. Journal
    of Mathematical Chemistry, 53(2):466–494, 2015.
    [22] Rafael Saer, Gregory S Orf, Xun Lu, Hao Zhang, Matthew J Cuneo, Dean AA Myles,
    and Robert E Blankenship. Perturbation of bacteriochlorophyll molecules in fenna–
    matthews–olson protein complexes through mutagenesis of cysteine residues. Biochimica
    et Biophysica Acta (BBA)-Bioenergetics, 1857(9):1455–1463, 2016.
    [23] Davinder Singh and Shubhrangshu Dasgupta. Influence of pigment-protein coupling
    on excitation energy transfer in fmo complex. arXiv preprint arXiv:1605.00920, 2016.
    [24] Guang-Yin Chen, Neill Lambert, Yen-An Shih, Meng-Han Liu, Yueh-Nan Chen, and
    Franco Nori. Plasmonic bio-sensing for the fenna-matthews-olson complex. Scientific
    reports, 7:39720, 2017.
    [25] Gregory D Scholes, Graham R Fleming, Lin X Chen, Alán Aspuru-Guzik, Andreas
    Buchleitner, David F Coker, Gregory S Engel, Rienk Van Grondelle, Akihito Ishizaki,
    David M Jonas, et al. Using coherence to enhance function in chemical and biophysical
    systems. Nature, 543(7647):647, 2017.
    [26] Rafael G Saer, Valentyn Stadnytskyi, Nikki C Magdaong, Carrie Goodson, Sergei
    Savikhin, and Robert E Blankenship. Probing the excitonic landscape of the chlorobaculum
    tepidum fenna-matthews-olson (fmo) complex: a mutagenesis approach. Biochimica
    et Biophysica Acta (BBA)-Bioenergetics, 1858(4):288–296, 2017.
    [27] SA Oh, DF Coker, and DAW Hutchinson. Optimization of energy transport in the fennamatthews-
    olson complex via site-varying pigment-protein interactions. The Journal of
    chemical physics, 150(8):085102, 2019.
    [28] Heinz-Peter Breuer, Francesco Petruccione, et al. The theory of open quantum systems.
    Oxford University Press on Demand, 2002.
    [29] Seogjoo Jang, Yuan-Chung Cheng, David R Reichman, and Joel D Eaves. Theory of
    coherent resonance energy transfer, 2008.
    [30] Akihito Ishizaki, Tessa R Calhoun, Gabriela S Schlau-Cohen, and Graham R Fleming.
    Quantum coherence and its interplay with protein environments in photosynthetic
    electronic energy transfer. Physical Chemistry Chemical Physics, 12(27):7319–7337,
    2010.
    [31] Filippo Caruso, Susana F Huelga, and Martin B Plenio. Noise-enhanced classical
    and quantum capacities in communication networks. Physical review letters,
    105(19):190501, 2010.
    [32] MC Wakeham and MR Jones. Rewiring photosynthesis: engineering wrong-way electron
    transfer in the purple bacterial reaction centre, 2005.
    [33] Dugan Hayes, Jianzhong Wen, Gitt Panitchayangkoon, Robert E Blankenship, and Gregory
    S Engel. Robustness of electronic coherence in the fenna–matthews–olson complex
    to vibronic and structural modifications. Faraday discussions, 150:459–469, 2011.
    [34] Chung-Cheng Kuo, Shih-Hsuan Chen, Wei-Ting Lee, Hung-Ming Chen, He Lu, and
    Che-Ming Li. Quantum process capability. arXiv preprint arXiv:1811.10307, 2018.
    [35] Helge Kragh. Quantum generations: A history of physics in the twentieth century.
    Princeton University Press, 2002.
    [36] Michael A Nielsen and Isaac Chuang. Quantum computation and quantum information,
    2002.
    [37] Jen-Hsiang Hsieh, Shih-Hsuan Chen, and Che-Ming Li. Quantifying quantummechanical
    processes. Scientific reports, 7(1):13588, 2017.
    [38] RH Tütüncü, KC Toh, and MJ Todd. Sdpt3—a matlab software package for
    semidefinite-quadratic-linear programming, version 3.0. Web page http://www. math.
    nus. edu. sg/mattohkc/sdpt3. html, 2001.
    [39] Johan Lofberg. Yalmip: A toolbox for modeling and optimization in matlab. In
    2004 IEEE international conference on robotics and automation (IEEE Cat. No.
    04CH37508), pages 284–289. IEEE, 2004.
    [40] Nicolas Gisin and Rob Thew. Quantum communication. Nature photonics, 1(3):165,
    2007.
    [41] Thaddeus D Ladd, Fedor Jelezko, Raymond Laflamme, Yasunobu Nakamura, Christopher
    Monroe, and Jeremy Lloyd O’Brien. Quantum computers. Nature, 464(7285):45,
    2010.
    [42] Gavin Brennen, Elisabeth Giacobino, and Christoph Simon. Focus on quantum memory.
    New Journal of Physics, 17(5):050201, 2015.
    [43] Tillmann Baumgratz, Marcus Cramer, and Martin B Plenio. Quantifying coherence.
    Physical review letters, 113(14):140401, 2014.
    [44] Thomas Theurer, Nathan Killoran, Dario Egloff, and Martin B Plenio. Resource theory
    of superposition. Physical review letters, 119(23):230401, 2017.
    [45] Asher Peres. Separability criterion for density matrices. Physical Review Letters,
    77(8):1413, 1996.
    [46] R Horodecki. Horodecki. m., horodecki p. separability of mixed states: Necessary and
    sufficient conditions. Phys. Lett., 223:333, 1996.
    [47] Gerhard Ritschel, Jan Roden, Walter T Strunz, Alán Aspuru-Guzik, and Alexander Eisfeld.
    Absence of quantum oscillations and dependence on site energies in electronic
    excitation transfer in the fenna–matthews–olson trimer. The Journal of Physical Chemistry
    Letters, 2(22):2912–2917, 2011.
    [48] Robert M Pearlstein. Theory of the optical spectra of the bacteriochlorophyll a antenna
    protein trimer from prosthecochloris aestuarii. Photosynthesis research, 31(3):213–226,
    1992.
    [49] RJW Louwe, J Vrieze, AJ Hoff, and TJ Aartsma. Toward an integral interpretation of the
    optical steady-state spectra of the fmo-complex of prosthecochloris aestuarii. 2. exciton
    simulations. The Journal of Physical Chemistry B, 101(51):11280–11287, 1997.
    [50] Thomas Renger, Mohamed El-Amine Madjet, Marcel Schmidt Am Busch, Julian
    Adolphs, and Frank Müh. Structure-based modeling of energy transfer in photosynthesis.
    Photosynthesis research, 116(2-3):367–388, 2013.
    [51] Brian Hall, Monroe W Strickberger, et al. Strickberger’s evolution. Jones & Bartlett
    Learning, 2008.
    [52] Mark M Wilde, James M McCracken, and Ari Mizel. Could light harvesting complexes
    exhibit non-classical effects at room temperature? Proceedings of the Royal Society A:
    Mathematical, Physical and Engineering Sciences, 466(2117):1347–1363, 2009.
    [53] Hong-Bin Chen, Jiun-Yi Lien, Chi-Chuan Hwang, and Yueh-Nan Chen. Long-lived
    quantum coherence and non-markovianity of photosynthetic complexes. Physical Review
    E, 89(4):042147, 2014.

    無法下載圖示 校內:2021-08-31公開
    校外:不公開
    電子論文尚未授權公開,紙本請查館藏目錄
    QR CODE