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題名 以作用粒子中介之高分子鏈凝聚過程的幾何分析
Geometric analysis of interacting-particle mediated aggregation in systems of polymer chains
作者 張喬雯
Chang, Chiao-Wen
貢獻者 馬文忠
Ma, Wen-Jong
張喬雯
Chang, Chiao-Wen
關鍵詞 分子動力模擬
徑向分布函數
蛋白質凝聚
高分子聚合物
molecular dynamics simulation
radial distribution function
protein aggregation
macromolecule polymer chain
日期 2020
上傳時間 2-九月-2020 12:17:12 (UTC+8)
摘要 本論文以分子動力模擬，研究聚合物分子鏈系統的凝聚過程與其受外加吸附粒子影響，對其中結構改變進行詳細的分析。此議題有助於了解以奈米顆粒加入蛋白質溶液中以影響蛋白質凝聚程序的實驗。在高韌度模型分子鏈系統中，次序性出現的過程是從鏈段間的部分對齊引導的短程排序開始，延伸到沿著主骨幹形成了遠程排序，最終形成柱狀結構。在外加吸附粒子出現的情況下，分子鏈由變形的骨架引導的有序對齊。短程排序如何被修改以及是否沿主骨幹進行更長程的排序，是我們有興趣的問題。在這項研究中，我們詳細分析各類徑向分佈、設計各種參數計算，以了解凝聚物近程結構變動的幾何特性。以此為基礎，進一步追蹤各系統隨時間演變之變化，幫助我們更進一步詳細理解其中凝聚過程與吸附過程交互影響的細節。
We study the aggregation process in systems of polymer chains and the effect of attached adduct particles. In this thesis, we carry out detailed
analysis on the structural changes in the processes. Our study is useful to understand the experiments of protein solutions with nano-particle adduct. In systems of stiff polymer chains, the ordering is initiated by
the segment-alignment between individual chains and followed by the extension of alignment along the backbones, eventually to form bundled stuctures. It is interesting to know how the deformation of the backbones
caused by the attached particles, would conduct the alignment and ordering. In our study, we investigate various kinds of radial distribution functions and define parameters to find the local geometric characters of aggregated clusters. Based on the analysis, we track on the time evolutions of the systems and understand the mutual interplays between the process of aggregation and that of particle attachment.
參考文獻 [1] 陳昱慈, 蛋白質的錯誤折疊、疾病與演化, https://investigator.tw/
8756/%E8%9B%8B%E7%99%BD%E8%B3%AA%E7%9A%84%E9%8C%AF%E8%
AA%A4%E6%8A%98%E7%96%8A%E3%80%81%E7%96%BE%E7%97%85%E8%
88%87%E6%BC%94%E5%8C%96/ 2019.
[2] R. Chetty and M. Singh, International Journal of Biological Macromolecules 156,
1022 (2020).
[3] K. Siposova et al., Effect of nanoceria on insulin amyloid aggregation: Experimental
and theoretical studies (poster), 11th international confernce structure and stability
of biomacromolecules 2019 (3 6
september 2019, košice, slovakia), 2019.09.
[4] W.J.
Ma and C.K.
Hu, Scientific Reports 7, 1 (2017).
[5] W.J.
Ma and C.K.
Hu, Journal of the Physical Society of Japan 79, 104002 (2010).
[6] G. Strobl, Rev. Mod. Phys. 81, 1287 (2009).
[7] Y. T. Shen, T. H. Kim, A. K. Gangopadhyay, and K. F. Kelton, Phys. Rev. Lett. 102,
057801 (2009).
[8] H. W. Sheng, W. K. Luo, F. M. Alamgir, J. M. Bai, and E. Ma, Nature 439, 419
(2006).
[9] M. P. Allen and D. J. Tildesley, Computer simulation of liquids, Oxford University
Press, 2nd ed. edition, 2017.
參考文獻
[10] R. K. Pathria, Statistical mechanics, ScienceDirect., Academic Press, Boston, 3rd
ed. / r.k. pathria, paul d. beale. edition, 2011.
[11] A. I. Grosberg, Statistical physics of macromolecules / Alexander Yu. Grosberg,
Alexei R. Khokhlov ; translated by Yuri A. Atanov., AIP series in polymers and
complex materials., AIP Press, New York, 1994.
描述 碩士
國立政治大學
應用物理研究所
107755001
資料來源 http://thesis.lib.nccu.edu.tw/record/#G0107755001
資料類型 thesis
dc.contributor.advisor 馬文忠zh_TW
dc.contributor.advisor Ma, Wen-Jongen_US
dc.contributor.author (作者) 張喬雯zh_TW
dc.contributor.author (作者) Chang, Chiao-Wenen_US
dc.creator (作者) 張喬雯zh_TW
dc.creator (作者) Chang, Chiao-Wenen_US
dc.date (日期) 2020en_US
dc.date.accessioned 2-九月-2020 12:17:12 (UTC+8)-
dc.date.available 2-九月-2020 12:17:12 (UTC+8)-
dc.date.issued (上傳時間) 2-九月-2020 12:17:12 (UTC+8)-
dc.identifier (其他 識別碼) G0107755001en_US
dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/131639-
dc.description (描述) 碩士zh_TW
dc.description (描述) 國立政治大學zh_TW
dc.description (描述) 應用物理研究所zh_TW
dc.description (描述) 107755001zh_TW
dc.description.abstract (摘要) 本論文以分子動力模擬，研究聚合物分子鏈系統的凝聚過程與其受外加吸附粒子影響，對其中結構改變進行詳細的分析。此議題有助於了解以奈米顆粒加入蛋白質溶液中以影響蛋白質凝聚程序的實驗。在高韌度模型分子鏈系統中，次序性出現的過程是從鏈段間的部分對齊引導的短程排序開始，延伸到沿著主骨幹形成了遠程排序，最終形成柱狀結構。在外加吸附粒子出現的情況下，分子鏈由變形的骨架引導的有序對齊。短程排序如何被修改以及是否沿主骨幹進行更長程的排序，是我們有興趣的問題。在這項研究中，我們詳細分析各類徑向分佈、設計各種參數計算，以了解凝聚物近程結構變動的幾何特性。以此為基礎，進一步追蹤各系統隨時間演變之變化，幫助我們更進一步詳細理解其中凝聚過程與吸附過程交互影響的細節。zh_TW
dc.description.abstract (摘要) We study the aggregation process in systems of polymer chains and the effect of attached adduct particles. In this thesis, we carry out detailed
analysis on the structural changes in the processes. Our study is useful to understand the experiments of protein solutions with nano-particle adduct. In systems of stiff polymer chains, the ordering is initiated by
the segment-alignment between individual chains and followed by the extension of alignment along the backbones, eventually to form bundled stuctures. It is interesting to know how the deformation of the backbones
caused by the attached particles, would conduct the alignment and ordering. In our study, we investigate various kinds of radial distribution functions and define parameters to find the local geometric characters of aggregated clusters. Based on the analysis, we track on the time evolutions of the systems and understand the mutual interplays between the process of aggregation and that of particle attachment.		en_US
dc.description.tableofcontents 致謝i
中文摘要iii
Abstract v
Contents vii
1 聚合物凝聚問題的背景介紹1
2 模型與分析方式9
2.1 分子鏈模型簡介. . . 9
2.2 徑向分布函數. . . .11
2.2.1 平行投影徑向方佈函數( parallel-projected radial distribution function ) . . .12
2.2.2 垂直投影徑向方佈函數( perpendicular-projected
radial distributionfunction ) . . . 12
2.3 持續長度( persistence length ) . . . 13
2.4 第k 階近程次序參數( kth-rank parameter for shortrange
ordering ) ：Gk . . . 14
3 分子鏈凝聚物之短程結構與外加粒子吸附之效應17
3.1 結構分析：無吸附效應的系統I-N與II-N. . . 17
3.2 結構分析：具吸附效應的系統I-A
系列與II-A. . . 22
3.3 系統隨時間演變之分析. . . 30
3.3.1 持續長度( persistence length ) . . . 30
3.3.2 橫向近程次序有效範圍參數( transverse effective range parameter for short-range ordering ) ：R∗ . . . 36
3.3.3 縱向近程次序有效範圍參數( tangential effective range parameter for short-range ordering ) ：H∗ . . . 38
3.3.4 第k 階近程次序參數( kth rank parameter for short-range ordering ) ：Gk . . . 41
4 結論45
A 模型相關參數49
參考文獻53		zh_TW
dc.format.extent 25839280 bytes-
dc.format.mimetype application/pdf-
dc.source.uri (資料來源) http://thesis.lib.nccu.edu.tw/record/#G0107755001en_US
dc.subject (關鍵詞) 分子動力模擬zh_TW
dc.subject (關鍵詞) 徑向分布函數zh_TW
dc.subject (關鍵詞) 蛋白質凝聚zh_TW
dc.subject (關鍵詞) 高分子聚合物zh_TW
dc.subject (關鍵詞) molecular dynamics simulationen_US
dc.subject (關鍵詞) radial distribution functionen_US
dc.subject (關鍵詞) protein aggregationen_US
dc.subject (關鍵詞) macromolecule polymer chainen_US
dc.title (題名) 以作用粒子中介之高分子鏈凝聚過程的幾何分析zh_TW
dc.title (題名) Geometric analysis of interacting-particle mediated aggregation in systems of polymer chainsen_US
dc.type (資料類型) thesisen_US
dc.relation.reference (參考文獻) [1] 陳昱慈, 蛋白質的錯誤折疊、疾病與演化, https://investigator.tw/
8756/%E8%9B%8B%E7%99%BD%E8%B3%AA%E7%9A%84%E9%8C%AF%E8%
AA%A4%E6%8A%98%E7%96%8A%E3%80%81%E7%96%BE%E7%97%85%E8%
88%87%E6%BC%94%E5%8C%96/ 2019.
[2] R. Chetty and M. Singh, International Journal of Biological Macromolecules 156,
1022 (2020).
[3] K. Siposova et al., Effect of nanoceria on insulin amyloid aggregation: Experimental
and theoretical studies (poster), 11th international confernce structure and stability
of biomacromolecules 2019 (3 6
september 2019, košice, slovakia), 2019.09.
[4] W.J.
Ma and C.K.
Hu, Scientific Reports 7, 1 (2017).
[5] W.J.
Ma and C.K.
Hu, Journal of the Physical Society of Japan 79, 104002 (2010).
[6] G. Strobl, Rev. Mod. Phys. 81, 1287 (2009).
[7] Y. T. Shen, T. H. Kim, A. K. Gangopadhyay, and K. F. Kelton, Phys. Rev. Lett. 102,
057801 (2009).
[8] H. W. Sheng, W. K. Luo, F. M. Alamgir, J. M. Bai, and E. Ma, Nature 439, 419
(2006).
[9] M. P. Allen and D. J. Tildesley, Computer simulation of liquids, Oxford University
Press, 2nd ed. edition, 2017.
參考文獻
[10] R. K. Pathria, Statistical mechanics, ScienceDirect., Academic Press, Boston, 3rd
ed. / r.k. pathria, paul d. beale. edition, 2011.
[11] A. I. Grosberg, Statistical physics of macromolecules / Alexander Yu. Grosberg,
Alexei R. Khokhlov ; translated by Yuri A. Atanov., AIP series in polymers and
complex materials., AIP Press, New York, 1994.		zh_TW
dc.identifier.doi (DOI) 10.6814/NCCU202001633en_US