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  1. NTU Theses and Dissertations Repository
  2. 理學院
  3. 化學系
請用此 Handle URI 來引用此文件: http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/1263
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dc.contributor.advisor鄭原忠(Yuan-Chung Cheng)
dc.contributor.authorYu-Jen Wangen
dc.contributor.author王佑仁zh_TW
dc.date.accessioned2021-05-12T09:35:09Z-
dc.date.available2018-03-01
dc.date.available2021-05-12T09:35:09Z-
dc.date.copyright2018-03-01
dc.date.issued2018
dc.date.submitted2018-02-20
dc.identifier.citation(1) Nitzan, A. Chemical dynamics in condensed phases: relaxation, transfer and reactions in condensed molecular systems; New York: Oxford University Press: 2006.
(2) Weiss, U. Quantum dissipative systems; World Scientific: Singapore: 2012.
(3) Chandrasekhar, S. Rev. Mod. Phys. 1943, 15, 1.
(4) Mohseni, M.; Rebentrost, P.; Lloyd, S.; Aspuru-Guzik, A. J. Chem. Phys. 2008, 129, 174106.
(5) Renger, T. Photosynth. Res. 2009, 102, 471–485.
(6) Engel, G. S.; Calhoun, T. R.; Read, E. L.; Ahn, T.-K.; Mančal, T.; Cheng, Y.-C.; Blankenship, R. E.; Fleming, G. R. Nature 2007, 446, 782.
(7) Lee, H.; Cheng, Y.-C.; Fleming, G. R. Science 2007, 316, 1462–1465.
(8) Adolphs, J.; Müh, F.; Madjet, M. E.-A.; Schmidt am Busch, M.; Renger, T. J. Am. Chem. Soc. 2010, 132, 3331–3343.
(9) Curutchet, C.; Kongsted, J.; Muñoz-Losa, A.; Hossein-Nejad, H.; Scholes, G. D.; Mennucci, B. J. Am. Chem. Soc. 2011, 133, 3078–3084.
(10) Strümpfer, J.; Sener, M.; Schulten, K. J. Phys. Chem. Lett. 2012, 3, 536–542.
(11) Curutchet, C.; Mennucci, B. Chem. Rev. 2016, 117, 294–343.
(12) Sundström, V.; Pullerits, T.; van Grondelle, R. J. Phys. Chem. B 1999, 103, 2327– 2346.
(13) Renger, T.; May, V.; Kühn, O. Phys. Rep. 2001, 343, 137–254.
(14) Hu, X.; Ritz, T.; Damjanović, A.; Autenrieth, F.; Schulten, K. Q. Rev. Biophys. 2002, 35, 1–62.
(15) Blankenship, R. E. Molecular mechanisms of photosynthesis; John Wiley & Sons: 2014.
(16) Hu, X.; Ritz, T.; Damjanović, A.; Schulten, K. J. Phys. Chem. B 1997, 101, 3854– 3871.
(17) Ritz, T.; Park, S.; Schulten, K. J. Phys. Chem. B 2001, 105, 8259–8267.
(18) Novoderezhkin, V. I.; Palacios, M. A.; Van Amerongen, H.; Van Grondelle, R. J. Phys. Chem. B 2004, 108, 10363–10375.
(19) Cho, M.; Vaswani, H. M.; Brixner, T.; Stenger, J.; Fleming, G. R. J. Phys. Chem. B 2005, 21, 10542–10556.
(20) Marcus, R. A. Can. J. Chem. 1959, 37, 155–163.
(21) Marcus, R. J. Phys. Chem. 1963, 67, 853–857.
(22) Förster, T. Modern Quantum Chemistry, Istanbul Lectures; Sinanoglu, O., Ed.; Aca- demic Press: New York, 1965; Vol. 3, pp 93–137.
(23) Scholes, G. D. Annu. Rev. Phys. Chem. 2003, 54, 57–87.
(24) May, V.; Kühn, O. Charge and energy transfer dynamics in molecular systems; John Wiley & Sons: 2008.
(25) Nakajima, S. Prog. Theor. Phys. 1958, 20, 948–959.
(26) Zwanzig, R. J. Chem. Phys. 1960, 33, 1338–1341.
(27) Zwanzig, R. Lect. Theor. Phys. 1960, 3, 106–141.
(28) van Grondelle, R. Biochim. Biophys. Acta, Rev. Bioenerg. 1985, 811, 147–195.
(29) Redfield, A. G. IBM J. Res. Dev. 1957, 1, 19–31.
(30) Redfield, A. G. In Advances in Magnetic Resonance, Waugh, J. S., Ed.; Advances in Magnetic and Optical Resonance Supplement C, Vol. 1; Academic Press: 1965, pp 1–32.
(31) Ishizaki, A.; Fleming, G. R. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 17255–17260.
(32) Rebentrost, P.; Mohseni, M.; Kassal, I.; Lloyd, S.; Aspuru-Guzik, A. New J. Phys. 2009, 11, 033003.
(33) Huo, P.; Coker, D. F. J. Chem. Phys 2010, 133, 11B606.
(34) Tao, G.; Miller, W. H. J. Phys. Chem. Lett. 2010, 1, 891–894.
(35) Kelly, A.; Rhee, Y. M. J. Phys. Chem. Lett. 2011, 2, 808–812.
(36) Chen, X.; Silbey, R. J. J. Phys. Chem. B 2011, 115, 5499–5509.
(37) Renaud, N.; Ratner, M.; Mujica, V. J. Chem. Phys. 2011, 135, 08B617.
(38) Vernon, F. L. The theory of a general quantum system interacting with a linear dissipative system. Ph.D. Thesis, California Institute of Technology, 1959.
(39) Feynman, R. P.; Vernon, F. L. Ann. Phys. 1963, 24, 118–173.
(40) Ullersma, P. Phys. 1966, 32, 27–55.
(41) Fromme, P.; Allen, J. P. In Biophysical techniques in photosynthesis; Springer: 2008, pp 97–124.
(42) Cheng, Y.-C.; Fleming, G. R. Annu. Rev. Phys. Chem. 2009, 60.
(43) Grover, M.; Silbey, R. J. Chem. Phys. 1971, 54, 4843–4851.
(44) Rackovsky, S.; Silbey, R. Mol. Phys. 1973, 25, 61–72.
(45) Haken, H.; Strobl, G. Z. Phys. A 1973, 262, 135–148.
(46) Kenkre, V.; Knox, R. Phys. Rev. Lett. 1974, 33, 803.
(47) Kenkre, V. M.; Reineker, P. In Exciton dynamics in molecular crystals and aggregates; Springer: Berlin, 1982.
(48) Zhang, W. M.; Meier, T.; Chernyak, V.; Mukamel, S. J. Chem. Phys. 1998, 108, 7763–7774.
(49) Yang, M.; Fleming, G. R. Chem. Phys. 2002, 282, 163–180.
(50) Jang, S.; Newton, M. D.; Silbey, R. J. Phys. Rev. Lett. 2004, 92, 218301.
(51) Cheng, Y.; Silbey, R. J. Phys. Rev. Lett. 2006, 96, 028103.
(52) Jang, S.; Newton, M. D.; Silbey, R. J. J. Phys. Chem. B 2007, 111, 6807–6814.
(53) Gaab, K. M.; Bardeen, C. J. J. Chem. Phys. 2004, 121, 7813–7820.
(54) Saam, J.; Tajkhorshid, E.; Hayashi, S.; Schulten, K. Biophys. J. 2002, 83, 3097– 3112.
(55) Olbrich, C.; Jansen, T. L.; Liebers, J.; Aghtar, M.; Strümpfer, J.; Schulten, K.; Knoester, J.; Kleinekathöfer, U. J. Phys. Chem. B 2011, 115, 8609–8621.
(56) Kim, H. W.; Kelly, A.; Park, J. W.; Rhee, Y. M. J. Am. Chem. Soc. 2012, 134, 11640–11651.
(57) Shim, S.; Rebentrost, P.; Valleau, S.; Aspuru-Guzik, A. Biophys. J. 2012, 102, 649– 660.
(58) Ponder, J. W.; Case, D. A. Adv. Protein Chem. 2003, 66, 27–85.
(59) Brooks, B. R.; Brooks, C. L.; MacKerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S., et al. J. Comput. Chem. 2009, 30, 1545–1614.
(60) Ridley, J.; Zerner, M. Theor. Chem. Acc. 1973, 32, 111–134.
(61) Zerner, M. C. Rev. Comput. Chem. 1991, 2, 313–365.
(62) MacKerell Jr, A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S., et al. J. Phys. Chem. B 1998, 102, 3586–3616.
(63) MacKerell, A. D.; Feig, M.; Brooks, C. L. J. Comput. Chem. 2004, 25, 1400–1415.
(64) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J. Am. Chem. Soc. 1995, 117, 5179–5197.
(65) Ishizaki, A.; Fleming, G. R. J. Chem. Phys. 2009, 130, 234111.
(66) Ishizaki, A.; Fleming, G. R. J. Chem. Phys. 2009, 130, 234110.
(67) Jang, S.; Cheng, Y.-C.; Reichman, D. R.; Eaves, J. D. Theory of coherent resonance energy transfer., 2008.
(68) Tokmakoff, A. Time-Dependent Quantum Mechanics and Spectroscopy, [Online]; 2014. http://tdqms.uchicago.edu/.
(69) Mukamel, S. Principles of nonlinear optical spectroscopy; New York: Oxford Uni- versity Press: 1995; Chapter 7, 8.
(70) Wigner, E. Phys. Rev. 1932, 40, 749.
(71) Wigner, E. Trans. Faraday Soc. 1938, 34, 29–41.
(72) Bader, J. S.; Berne, B. J. Chem. Phys. 1994, 100, 8359–8366.
(73) Egorov, S.; Skinner, J. J. Chem. Phys. 1996, 105, 7047–7058.
(74) Egorov, S.; Berne, B. J. Chem. Phys. 1997, 107, 6050–6061.
(75) Egorov, S.; Skinner, J. Chem. Phys. Lett. 1998, 293, 469–476.
(76) Valleau, S.; Eisfeld, A.; Aspuru-Guzik, A. J. Chem. Phys. 2012, 137, 224103.
(77) Davies, R.; Davies, K. Ann. Phys. 1975, 89, 261–273.
(78) Weyl, H. Z. Phys. A 1927, 46, 1–46.
(79) von Neumann, J. ger Nachr. Ges. Wiss. Goettingen, Math.-Phys. Kl. 1927, 1927, 273–291.
(80) Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: 2009.
(81) Egorov, S.; Everitt, K.; Skinner, J. J. Phys. Chem. A 1999, 103, 9494–9499.
(82) Meier, C.; Tannor, D. J. J. Chem. Phys. 1999, 111, 3365–3376.
(83) Liu, H.; Zhu, L.; Bai, S.; Shi, Q. J. Chem. Phys. 2014, 140, 134106.
(84) Grabert, H.; Weiss, U.; Talkner, P. Z. Phys. B 1984, 55, 87–94.
(85) Callen, H. B.; Welton, T. A. Phys. Rev. 1951, 83, 34.
(86) Johansson, J.; Nation, P.; Nori, F. Comput. Phys. Commun. 2012, 183, 1760–1772.
(87) Johansson, J.; Nation, P.; Nori, F. Comput. Phys. Commun. 2013, 184, 1234–1240.
(88) Hillery, M.; O’Connell, R. F.; Scully, M. O.; Wigner, E. P. Phys. Rep. 1984, 106, 121–167.
(89) 孫維良 數學傳播 2013, 37, 52–67.
(90) 陳建燁 數學傳播 2016, 40, 57–62.
dc.identifier.urihttp://tdr.lib.ntu.edu.tw/handle/123456789/1263-
dc.description.abstract以含有古典力學之分子動力學結果計算量子動力學時,量子修正實 為必要。量子修正過去已廣泛應用在紅外線等光譜計算上,但應用於 激發能轉移動力學上的研究則較少。本研究之目的在於測試並比較前 人提出的標準法與簡諧法、我們提出的擬合法與 Prony 法等量子修正 方法在激發能轉移應用上的效果。希望能對量子修正在激發能轉移上 的應用提出有用之建議。為此,本論文利用線性地耦合了簡諧熱庫的 雙階系統以釐清量子修正在不同參數條件的表現。我們的計算結果說 明了以分子動力學研究激發能轉移時使用量子修正的必要性;並發現 在前述模型中,簡諧法表現最佳,擬合法與標準法表現接近、並都在 高溫時表現較佳、或在由相干性主導弛豫時表現較佳,且 Prony 法有 嚴重缺陷。zh_TW
dc.description.abstractQuantum correction is necessary when calculating dissipative quantum dynamics based on results from classical molecular dynamics simulation in which quantum effects are ignored. Quantum correction has been used in many fields to make use of classical trajectories in quantum simulations, such as calculation of infrared spectra. However, in the context of excitation energy transfer in molecular system, the need of applications of quantum corrections is less discussed. In this study, we examine four quantum correction methods, including the Harmonic method and the Standard method proposed by other groups previously, and the Fitting method and the Prony method proposed by us. We aim to elucidate the performance of the correction by the four correc- tion methods in order to properly apply them to simulating excitation energy transfer dynamics. We focus on a model that describes a two-level system linearly coupled to a harmonic bath to explore the applicability of quantum correction methods in various parameter conditions. Our results reveal the necessity of applying quantum correction when studying excitation energy transfer dynamics based on results of classical molecular dynamics simula- tion. Our calculations also conclude that the Harmonic method performs the best among the four approaches and that the Prony method has serious draw- backs. The Fitting method provides similar results as the Standard method, and both methods perform well at a higher temperature or in the condition where relaxation is driven by coherent evolution.en
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Previous issue date: 2018
en
dc.description.tableofcontents第一章 緒論....................................... 1
1.1 前言..................................... 1
1.2 分子動力學模擬.............................. 3
1.3 連結分子動力學模擬與開放量子動力學................. 3
1.4 以簡諧振子的位移解釋躍遷能之擾動 .................. 5
1.5 位移諧振子模型下分子動力學與開放式量子動力學的關係 . . . . . . 7
第二章 量子修正..................................... 9
2.1 量子修正的理論基礎 ........................... 9
2.2 四種量子修正方法............................. 9
2.2.1 簡諧法 ............................... 10
2.2.2 標準法 ............................... 11
2.2.3 擬合法 ............................... 12
2.2.4 Prony法 .............................. 13
第三章 頻域上的熱庫時間自相關函數........................ 15
3.1 光譜密度.................................. 16
3.2 溫度的效應................................. 17
3.3 Prony法................................... 17
3.4 擬合法 ................................... 18
3.5 比較各修正法 ............................... 20
第四章 激發能傳遞的動力學模擬........................... 29
4.1 雙階系統.................................. 29
4.2 Redfield理論................................ 29
4.3 結果與討論................................. 30
4.3.1 弱系統熱庫耦合下的分子間耦合強度對動力學的影響 . . . . 30
4.3.2 強系統熱庫耦合下的分子間耦合強度對動力學的影響 . . . . 31
4.3.3 在中等條件下比較不同溫度對動力學的影響.......... 31
4.3.4 在大的分子能階差下比較分子間耦合強度 ........... 32
4.3.5 在無分子能階差下比較分子間耦合強度 ............ 32
4.3.6 總結 ................................ 32
第五章 結論....................................... 39
第六章 附錄....................................... 41
6.1 簡諧振子的量子修正因子......................... 41
6.1.1 古典諧振子之位置自相關函數.................. 41
6.1.2 量子諧振子之位置自相關函數.................. 42
6.1.3 諧振子之量子修正因子...................... 44
6.2 標準修正式的推導............................. 45
6.2.1 TCF的對稱性 ........................... 45
6.2.2 TCF的實部與虛部的關係 .................... 46
6.3 時域上的標準修正............................. 47
6.4 Prony分析 ................................. 47
6.4.1 Prony分析之目的 ......................... 47
6.4.2 概要 ................................ 48
6.4.3 原理 ................................ 49
6.4.4 以矩陣實作 ............................ 50
6.5 Redfield理論之推導............................ 51
6.5.1 從薛丁格方程式到劉維爾-馮紐曼方程式 ............ 51
6.5.2 量子主方程式之推導 ....................... 52
6.6 曲線擬合之結果 .............................. 55
6.7 更多不同參數條件下的動力學過程的比較 ............... 56
參考文獻.......................................... 59
dc.language.isozh-TW
dc.title熱庫時間自相關函數的量子修正—於激發能轉移動力學上的應用zh_TW
dc.titleQuantum Correction on Bath Time-Correlation Functions: Applications on Excitation Energy Transfer Dynamicsen
dc.typeThesis
dc.date.schoolyear106-1
dc.description.degree碩士
dc.contributor.oralexamcommittee金必耀(Bih-Yaw Jin),陸駿逸(Chun-Yi David Lu)
dc.subject.keyword開放量子動力學,量子修正,分子動力學模擬,時間自相關函數,zh_TW
dc.subject.keywordopen quantum dynamics,quantum correction,molecular dynamics simulation,time-correlation function,en
dc.relation.page68
dc.identifier.doi10.6342/NTU201800569
dc.rights.note同意授權(全球公開)
dc.date.accepted2018-02-20
dc.contributor.author-college理學院zh_TW
dc.contributor.author-dept化學研究所zh_TW
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