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研究生: 何顯龍
HE, Xian-Long
論文名稱: 單肽分子電導之第一原理研究
First-principles Study of Conductance of Single-Peptide Molecules
指導教授: 關肇正
Kaun, Chao-Cheng
口試委員: 張景皓
Chang, Ching-Hao
徐斌睿
Hsu, Pin-Jui
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: 2019
畢業學年度: 107
語文別: 中文
論文頁數: 43
中文關鍵詞: 第一原理電導單肽
外文關鍵詞: first-principle, conductance, peptide
相關次數: 點閱:3下載:0
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  • 胜肽的種類很多,不同單分子胜肽有不一樣的結構與特性,但也因為分子細小與難以量測,各類相似的胜肽常常很難簡易地區分,因此我們利用第一原理計算分析不同胜肽通過金電極間隙時的電導,並比較其與量測到的電導的差異。
    我們計算了12種胜肽的電導,包括tryptophan(W)、tyrosine(Y)、Phenylaniline(F)、Histidine(H)、phosphopyrosine(py)、proline(P)、lysine(K)、cysteine(C)、Methionine(M)、glutamic acid(E)、aspartic acid(D)、isoleuine(I) 等分子。利用兩側的金電極,中間包含胜肽,算出Transmission spectra與conductance,以了解各類胜肽在金電極連接下電導的差異,進而能幫助胜肽的檢測。
    我們改變胜肽分子在y軸的位置,從-2Å至2Å,分五點,再加上轉動胜肽分子,分三種角度,來模擬單分子胜肽在金電極移動的情形,並將每個移動胜肽的數據作統計上分析,來觀察不同胜肽在transmission上的差異。我們觀察在不同的金極距離下,不同胜肽電導是否會發生改變,以及在Au[1 1 1]與Au[0 0 1]等電極方向下的影響。我們也探索將交換能從LDA轉換成GGA時,對12種胜肽電導的效應。我們希望了解何種結構的胜肽有較高的電導,以幫助實驗上的量測與分析,藉此提高生物檢測器的應用。
    我們發現proline(P)與Histidine(H),有較高的電導值。proline(P)高於其他胜肽,而Histidine(H)在金電極0.7nm至1.15nm時,其電導有逐漸高於其他胜肽的跡象。我們也觀察到,在金電極拉開長度越長時,包括lysine(K) Methionine(M)和Aspartic acid(D),其電導都有些微的上升,我們判斷可能是因為其沒有酚官能基,或是其他複雜分子構成,為長鏈型的分子。


    We calculated the conductance of 12 peptides, including tryptophan (W), tyrosine (Y), Phenylaniline (F), Histidine (H), phosphopyrosine (py), proline (P), lysine (K), cysteine (C). , Methionine (M), glutamic acid (E), aspartic acid (D), isoleine (I) and other molecules. Using the gold electrodes on both sides, the middle contains the peptide, and the transmission spectra and conductance are calculated to understand the difference in the conductance of the various peptides under the gold electrode connection.
    We changed the position of the peptide molecule on the y-axis, from -2Å to 2Å, divided into five points, plus the rotation of the peptide molecule, in three angles, to simulate the movement of the single-molecule peptide on the gold electrode. The data of the mobile peptide was statistically analyzed to observe the difference in transmission of different peptides. We observed whether the conductance of different peptides will change under different gold pole distances, and the influence of electrodes such as Au[1 1 1] and Au[0 0 1]. We also explored the effects of 12 peptides on the conductance of exchanges from LDA to GGA.
    We found that proline (P) and Histidine (H) have higher conductance values. Proline (P) is higher than other peptides, and Histidine (H) has a higher conductivity than other peptides at 0.7nm to 1.15nm. We also observed that the conductance is increased including the lysine(K) Methionine(M) and Aspartic acid(D).

    目錄 摘要…………………………………………………………………………………………i 誌謝………………………………………………………………………………………..iii 目錄………………………………………………………………………………………..iv 圖目錄………………………………………………………………………………………v 第一章 緒論……………………………………………………………………………….1 緣起………………………………………………………………………….1 緒論………………………………………………………………………….1 研究動機…………………………………………………………………….4 第二章 理論計算 2.1 第一原理簡介……………………………………………………………….5 2.2 量子力學發展與演進……………………………………………………….6 2.3多電子系統與各類型的近似方法……………………………………………7 2.4 密度泛函理論(DFT) ……………………………………………………….8 2.4.1密度泛函理論(DFT)緣起…………………………………………….8 2.4.2 Hohenberg-Kohn定理……………………………………………….9 2.4.3 Kohn-Sham方程 …………………………………………………..10 2.4.4 局部密度近似法(LDA) …………………………………………….10 2.4.5 廣義梯度近似法(GGA) …………………………………………….11 2.5自洽場的方法……………………………………………………………….12 2.6非平衡態下格林函數NEGF-DFT…………………………………………….12 第三章 模擬軟體的介紹………………………………………………………………….17 第四章 模擬結果與分析………………………………………………………………….18 4-1電極的選擇………………………………………………………………….18 4-2 胜肽於Au[0 0 1]電極間之結構最佳化…………………………………..19 4-3 胜肽tyrosine於金Au[0 0 1]於0.7nm之LDA下Transmission影響.20 4-4胜肽tyrosine於Au[0 0 1]之Conductance的影響……………………24 4-5 12種胜肽於Au[0 0 1]間的Conductance…………..………………….27 4-6 12種胜肽於Au[1 1 1]下的Conductanc……………..…………………32 4-7 12種胜肽於Au[0 0 1]之GGA下的Conductance……………………….36 第五章 結論………………………………………………………………………………..40 參考文獻…………………………………………………………………………………….41   圖目錄 圖 1-1: Post-translational modification of insulin. ………………………...2 圖1-2: Proline……………………………………………………………………………2 圖1-3 : Histidine……………………………………………………………………….3 圖1-4 Conductance histograms of amino acid and time histograms of amino acid and phosphotyrosine molecules using 0.7nm nanogap electrode[8] …….4 圖2-1 局部密度近似法示意圖……………………………………………………………11 圖2-2計算DFT自洽流程圖[ 17] ……………………………………………………….12 圖2-3開放性的量子傳輸系統…………………………………………………………….13 圖2-4計算NEGF-DFT自洽流程圖[ 17]………………………………………………….13 圖2-5 NEGF-DFT的系統結構[ 18] ……………………………………………………..14 圖2-6 NEGF-DFT的密度積分矩陣積分路線……………………………………………..15 圖4-1 12種胜肽結構……………………………………………………………………..18 圖4-2 金Au[0 0 1],上圖為左邊電極(Leftelectrode)下圖右邊電極(Rightectrode)右邊為方向的設定………………………………………………………………………….18 圖4-3 金Au[1 1 1],上圖為左邊電極(Leftelectrode)下圖右邊電極(Rightectrode)右邊為方向的設定………………………………………………………………………….19 圖4-4 金Au[0 0 1]兩側距離0.7nm 中間放置胜肽而進行測量。…………………….19 圖4-5 Histidine放置中間,在金兩側距離0.7nm 與1.0nm時,作siesta的結構最佳化。………………………………………………………………………………………….20 圖4-6為Au-tyrosine-Au為系統和分子轉動X、 X〖rot90〗^°和z〖rot90〗^°結構圖…………20 圖4-7 Au-tyrosine-Au 在0.2nm~-0.2nm的transmission spectra………………..21 圖4-8 Au-tyrosine-Au 在 X〖rot90〗^°下,0.2nm~-0.2nm的transmission spectra……………………………………………………………………………………..21 圖4-9 Au-tyrosine-Au 在 Z〖rot90〗^°下,0.2nm~-0.2nm的transmission spectra……………………………………………………………………………………..22 圖4-10 Au-tyrosine-Au的conductance………………………………………………..23 圖4-11Au-tyrosine-Au在不同距離與三種不同角度之conductance圖……………..23 圖4-12胜肽tyrosine於Au[0 0 1]相距0.55 nm下的conductance………….…….24 圖4-13胜肽tyrosine於金Au[0 0 1]之相距0.55nm下conductance……………….24 圖4-14胜肽tyrosine於金Au[0 0 1]之相距1.0nm下conductance圖……………..24 圖4-15胜肽tyrosine於金Au[0 0 1]之相距1.0nm下conductance………………..25 圖4-16胜肽tyrosine於金Au[0 0 1]之相距1.15nm 下conductance……………….25 圖4-17胜肽tyrosine於金Au[0 0 1]之相距1.15nm 下conductance圖……………25 圖4-18胜肽tyrosine於Au[0 0 1]相距0.55~1.15nm 下的平均conductance ……………………………………………………………………………………………….26 圖4-19 Conductance histograms of amino acid molecules using 0.55nm nanogap electrodes.[8] ………………………………………………………………………….27 圖4-20 12種胜肽於金Au[0 0 1]之相距0.55~1.15nm 下平均 conductance……………………………………………………………………………….28 圖4-21 12種胜肽於金Au[0 0 1]之相距0.55nm下平均 conductance圖………….28 圖4-22 12種胜肽於金Au[0 0 1]之相距0.7nm 下平均 conductance圖………….29 圖4-23 12種胜肽於金Au[0 0 1]之相距1.0nm 下平均 conductance圖………….29 圖4-24 12種胜肽於金Au[0 0 1]之相距1.15nm 下平均 conductance圖…………30 圖4-25 12種胜肽於LDA下於金[ 0 0 1 ]之相距0.55nm~0.7nm計算與實驗電導值比較圖…………………………………………………………………………………………30 圖4-26 12種胜肽於Au[0 0 1]相距0.7nm 下的Transmission譜………………….31 圖4-27 12種胜肽於金Au[1 1 1]之相距0.55~1.15nm 下平均 conductance……..32 圖4-28 12種胜肽於金Au[1 1 1]之相距0.55nm 下平均 conductance圖………..33 圖4-29 12種胜肽於金Au[1 1 1]之相距0.7nm 下平均 conductance圖………….33 圖4-30 12種胜肽於金Au[1 1 1]之相距1.0nm 下平均 conductance圖………….34 圖4-31 12種胜肽於金Au[1 1 1]之相距1.0nm 下平均 conductance圖………….34 圖4-32 12種胜肽於GGA下於金[ 0 0 1]之相距0.55nm~0.7nm計算與實驗電導值比較圖…………………………………………………………………………………………..35 圖4-33 12種胜肽於金Au[0 0 1]之相距0.55~1.15nm GGA下平均 conductance……………………………………………………………………………….36 圖4-34 12種胜肽於金Au[0 0 1]之相距0.55nm GGA下平均 conductance圖…….37 圖4-35 12種胜肽於金Au[0 0 1]之相距0.7nm GGA下平均 conductance圖………37 圖4-36 12種胜肽於Au[0 0 1]相距1.0 nm GGA下的平均conductance圖………..38 圖4-37 12種胜肽於金Au[0 0 1]之相距1.15nm GGA下平均 conductance圖…….38 圖4-38 12種胜肽於GGA下於Au[ 0 0 1]之計算與實驗電導值比較圖……………………………………………………………………………………......39

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