請用此 Handle URI 來引用此文件：
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/98789完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 張書瑋 | zh_TW |
| dc.contributor.advisor | Shu-Wei Chang | en |
| dc.contributor.author | 林泓佑 | zh_TW |
| dc.contributor.author | Hong-You Lin | en |
| dc.date.accessioned | 2025-08-19T16:12:37Z | - |
| dc.date.available | 2025-08-20 | - |
| dc.date.copyright | 2025-08-19 | - |
| dc.date.issued | 2025 | - |
| dc.date.submitted | 2025-08-07 | - |
| dc.identifier.citation | [1]Maharana, J., Wang, C.-H., Tsai, L.-A., Liao, Y.-T., Yang, C.-H., Shen, M. C., Macale, L. S., Tran, T. N., Narsico, J., Perez, R. J., Tewary, S. K., Wu, J.-L., Lin, H.-Y., Chang, S.-W., Franklin, A., Moynihan, P. J., Jacobs-Sera, D., Freeman, K. G., Hatfull, G. F., Lowary, T. L., & Ho, M.-C. (2025). Cryo-EM and cryo-ET reveal the molecular architecture and host interactions of mycobacteriophage Douge. Cell Reports, 44(8), 116057. https://doi.org/10.1016/j.celrep.2025.116057
[2]Zeng, Y., Li, P., Liu, S. et al. Salmonella enteritidis acquires phage resistance through a point mutation in rfbD but loses some of its environmental adaptability. Vet Res 55, 85 (2024). https://doi.org/10.1186/s13567-024-01341-7 [3]Berryhill, B. A., Gil-Gil, T., Smith, A. P., & Levin, B. R. (2025). The future of phage therapy in the USA. Trends in Molecular Medicine. https://doi.org/10.1016/j.molmed.2025.03.013 [4]Cui, L., Kiga, K., Kondabagil, K. et al. Current and future directions in bacteriophage research for developing therapeutic innovations. Sci Rep 14, 24404 (2024). https://doi.org/10.1038/s41598-024-76427-5 [5]Ranveer, S.A., Dasriya, V., Ahmad, M.F. et al. Positive and negative aspects of bacteriophages and their immense role in the food chain. npj Sci Food 8, 1 (2024). https://doi.org/10.1038/s41538-023-00245-8 [6]Wójcicki, M., Sokołowska, B., Górski, A., & Jończyk-Matysiak, E. (2025). Dual Nature of Bacteriophages: Friends or Foes in Minimally Processed Food Products-A Comprehensive Review. Viruses, 17(6), 778. https://doi.org/10.3390/v17060778 [7]Cui, L., Watanabe, S., Miyanaga, K., Kiga, K., Sasahara, T., Aiba, Y., Tan, X. E., Veeranarayanan, S., Thitiananpakorn, K., Nguyen, H. M., & Wannigama, D. L. (2024). A Comprehensive Review on Phage Therapy and Phage-Based Drug Development. Antibiotics (Basel, Switzerland), 13(9), 870. https://doi.org/10.3390/antibiotics13090870 [8]Leprince, A., & Mahillon, J. (2023). Phage Adsorption to Gram-Positive Bacteria. Viruses, 15(1), 196. https://doi.org/10.3390/v15010196 [9]Costa, S. P., Cunha, A. P., Freitas, P. P., & Carvalho, C. M. (2022). A phage receptor-binding protein as a promising tool for the detection of Escherichia coli in human specimens. Frontiers in Microbiology, 13, 871855. https://doi.org/10.3389/fmicb.2022.871855 [10]Ding G, Liu H, Lan J, Qian T, Zhou Y, Zhu T, Zhang T.2024.Identification of receptor-binding protein and host receptor of non-lytic dsRNA phage phiNY. Microbiol Spectr12:e01467-24. https://doi.org/10.1128/spectrum.01467-24 [11]González-Huici, V., Salas, M. and Hermoso, J.M. (2004), The push–pull mechanism of bacteriophage Ø29 DNA injection. Molecular Microbiology, 52: 529-540. https://doi.org/10.1111/j.1365-2958.2004.03993.x [12]van den Berg, B., Silale, A., Baslé, A., Brandner, A. F., Mader, S. L., & Khalid, S. (2022). Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Proceedings of the National Academy of Sciences of the United States of America, 119(42), e2211672119. https://doi.org/10.1073/pnas.2211672119 [13]Abedon S. T. (2023). Bacteriophage Adsorption: Likelihood of Virion Encounter with Bacteria and Other Factors Affecting Rates. Antibiotics (Basel, Switzerland), 12(4), 723. https://doi.org/10.3390/antibiotics12040723 [14]J.D. Antani, T. Ward, T. Emonet, & P.E. Turner, Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells, Proc. Natl. Acad. Sci. U.S.A. 121 (52) e2410905121, https://doi.org/10.1073/pnas.2410905121 (2024). [15]Zampara, A., Sørensen, M. C. H., Grimon, D., Antenucci, F., Vitt, A. R., Bortolaia, V., Briers, Y., & Brøndsted, L. (2020). Exploiting phage receptor binding proteins to enable endolysins to kill Gram-negative bacteria. Scientific reports, 10(1), 12087. https://doi.org/10.1038/s41598-020-68983-3 [16]Taslem Mourosi, J., Awe, A., Guo, W., Batra, H., Ganesh, H., Wu, X., & Zhu, J. (2022). Understanding Bacteriophage Tail Fiber Interaction with Host Surface Receptor: The Key "Blueprint" for Reprogramming Phage Host Range. International journal of molecular sciences, 23(20), 12146. https://doi.org/10.3390/ijms232012146 [17]Zhu, Y., Shang, J., Peng, C., & Sun, Y. (2022). Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Frontiers in Microbiology, 13, 1032186. https://doi.org/10.3389/fmicb.2022.1032186 [18]Ongenae, V., Briegel, A., & Claessen, D. (2021). Cell wall deficiency as an escape mechanism from phage infection. Open biology, 11(9), 210199. https://doi.org/10.1098/rsob.210199 [19]Lopes, A., Tavares, P., Petit, MA. et al. Automated classification of tailed bacteriophages according to their neck organization. BMC Genomics 15, 1027 (2014). https://doi.org/10.1186/1471-2164-15-1027 [20]Valencia-Toxqui G, Ramsey J.2024.How to introduce a new bacteriophage on the block: a short guide to phage classification. J Virol98:e01821-23.https://doi.org/10.1128/jvi.01821-23 [21]D’Acapito, A., Decombe, A., Arnaud, C.-A., & Breyton, C. (2025). Comparative anatomy of siphophage tails before and after interaction with their receptor. Current Opinion in Structural Biology, 92, 103045. https://doi.org/10.1016/j.sbi.2025.103045 [22]Xiao, H., Tan, L., Tan, Z., Zhang, Y., Chen, W., Li, X., Song, J., Cheng, L., & Liu, H. (2023). Structure of the siphophage neck–tail complex suggests that conserved tail tip proteins facilitate receptor binding and tail assembly. PLOS Biology, 21(12), e3002441. https://doi.org/10.1371/journal.pbio.3002441 [23]Auzat, I., Ouldali, M., Jacquet, E. et al. Dual function of a highly conserved bacteriophage tail completion protein essential for bacteriophage infectivity. Commun Biol 7, 590 (2024). https://doi.org/10.1038/s42003-024-06221-6 [24]Ge, X., Wang, J. Structural mechanism of bacteriophage lambda tail’s interaction with the bacterial receptor. Nat Commun 15, 4185 (2024). https://doi.org/10.1038/s41467-024-48686-3 [25]Storms, Z. J., & Sauvageau, D. (2015). Modeling tailed bacteriophage adsorption: Insight into mechanisms. Virology, 485, 355–362. https://doi.org/10.1016/j.virol.2015.08.007 [26]Hatfull, G. F., SEA-PHAGES Program. (n.d.). Douge. PhagesDB. Retrieved July 2, 2025, from https://phagesdb.org/phages/Douge/ [27]Hagan, M. F., & Zandi, R. (2016). Recent advances in coarse-grained modeling of virus assembly. Current opinion in virology, 18, 36–43. https://doi.org/10.1016/j.coviro.2016.02.012 [28]Perlmutter, J. D., & Hagan, M. F. (2015). Mechanisms of virus assembly. Annual review of physical chemistry, 66, 217–239. https://doi.org/10.1146/annurev-physchem-040214-121637 [29]Yu, A., Pak, A. J., He, P., Monje-Galvan, V., Casalino, L., Gaieb, Z., Dommer, A. C., Amaro, R. E., & Voth, G. A. (2021). A multiscale coarse-grained model of the SARS-CoV-2 virion. Biophysical Journal, 120(6), 1097–1104. https://doi.org/10.1016/j.bpj.2020.10.048 [30]Leong, T., Voleti, C., & Zhangli, P. (2021). Coarse-grained modeling of coronavirus spike proteins and ACE2 receptors. Frontiers in Physics, 9. https://doi.org/10.3389/fphy.2021.680983 [31]Guo, W., Alarcon, E., Sanchez, J. E., Xiao, C., & Li, L. (2024). Modeling Viral Capsid Assembly: A Review of Computational Strategies and Applications. Cells, 13(24), 2088. https://doi.org/10.3390/cells13242088 [32]Arkhipov, A., Yin, Y., & Schulten, K. (2008). Four-scale description of membrane sculpting by BAR domains. Biophysical journal, 95(6), 2806–2821. https://doi.org/10.1529/biophysj.108.132563 [33]Ingólfsson, H.I., Lopez, C.A., Uusitalo, J.J., de Jong, D.H., Gopal, S.M., Periole, X. and Marrink, S.J. (2014), The power of coarse graining in biomolecular simulations. WIREs Comput Mol Sci, 4: 225-248. https://doi.org/10.1002/wcms.1169 [34]Arkhipov, A., Freddolino, P. L., & Schulten, K. (2006). Stability and dynamics of virus capsids described by coarse-grained modeling. Structure (London, England : 1993), 14(12), 1767–1777. https://doi.org/10.1016/j.str.2006.10.003 [35]Jones, J.E. (1924) On the Determination of Molecular Fields. II. From the Equation of State of a Gas. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 106, 463-477.http://dx.doi.org/10.1098/rspa.1924.0082 [36]Frenkel, D., & Smit, B. (2002). Understanding molecular simulation: From algorithms to applications (2nd ed.). Academic Press. [37]Nalbach, M., Chalupa-Gantner, F., Spoerl, F., de Bar, V., Baumgartner, B., Andriotis, O. G., Ito, S., Ovsianikov, A., Schitter, G., & Thurner, P. J. (2022). Instrument for tensile testing of individual collagen fibrils with facile sample coupling and uncoupling. The Review of scientific instruments, 93(5), 054103. https://doi.org/10.1063/5.0072123 [38]Doi, M., & Edwards, S. F. (1986). The theory of polymer dynamics. Oxford University Press. [39]Rahman, A. (1964). Correlations in the motion of atoms in liquid argon. Physical Review, 136(2A), A405. https://doi.org/10.1103/PhysRev.136.A405 [40]Wolf, Sharon & Shimoni, Eyal & Elbaum, Michael & Houben, Lothar. (2018). STEM Tomography in Biology. 10.1007/978-3-319-68997-5_2. [41]Valentová, L., Füzik, T., Nováček, J., Hlavenková, Z., Pospíšil, J., & Plevka, P. (2024). Structure and replication of Pseudomonas aeruginosa phage JBD30. The EMBO Journal, 43(19), 4384–4405. https://doi.org/10.1038/s44318-024-00195-1 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/98789 | - |
| dc.description.abstract | 本研究針對噬菌體感染初期的吸附階段，探討尾管彎矩剛性與宿主細胞表面曲率對其吸附行為與效率之影響，並嘗試補足實驗觀察於時間與空間解析度上的限制。研究以 Douge 噬菌體為藍本，建構具物理參考性的二維粗粒徑模型，並採用粗粒徑分子動力學模擬方法，設計多組模擬情境進行系統性比較分析。模擬內容包含單一噬菌體於細胞表面附近之吸附行為、柔性與剛硬尾管條件下的結構變化，以及多顆噬菌體於平坦與具曲率細胞表面中的擴散與群體吸附特性。所有模擬皆採用 NVT 系綜並引入熱擾動條件，以捕捉吸附前後的構型演化與動態特徵。
模擬結果顯示，柔韌性尾管相較於剛硬尾管可更有效率地完成吸附，不僅吸附成功率較高，且所需時間較短、所需旋轉與橫向位移較小，展現出較佳的動態適應性。此外，在柔韌性尾管的多組模擬中均可觀察到一特有吸附機制：噬菌體先以衣殼接近細胞表面，底板完成附著後再由尾管驅動整體結構站立，最終完成穩定吸附。 另一方面，細胞表面幾何形貌亦對吸附效率產生明顯影響，具曲率的表面能有效提升短距離吸附事件之完成速率，整體平均吸附時間低於平坦表面條件，顯示曲率對於完成吸附行為具有積極作用。 本研究所建構之模擬系統與分析結果，除可作為實驗觀察的輔助與延伸，亦為噬菌體結構設計、表面功能化與未來精準醫療應用提供理論依據與模擬參考基礎。 | zh_TW |
| dc.description.abstract | This study explores the adsorption behavior of bacteriophages during the early infection phase, focusing on the effects of tail tube bending stiffness and host cell surface curvature. A physically grounded two-dimensional coarse-grained model of the Douge phage was developed, and molecular dynamics simulations were conducted under various mechanical and geometric conditions. Simulation scenarios included single-phage adsorption, comparisons of flexible versus rigid tail tubes, and multi-phage interactions with flat and curved surfaces.
Results show that flexible tail tubes lead to higher adsorption success rates and faster attachment, requiring less rotation and displacement. A distinct multi-stage mechanism was observed: phages initially approach with the capsid, then attach via the baseplate, and finally stand upright driven by tail tube mechanics. Curved surfaces further improve adsorption efficiency by reducing completion time for short-range interactions. The findings provide theoretical insights into phage adsorption dynamics and offer guidance for future phage design and biomedical applications. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2025-08-19T16:12:37Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2025-08-19T16:12:37Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 誌謝 i
中文摘要 ii ABSTRACT iii 目次 iv 圖次 viii 表次 xii 第1章 諸論 1 1.1 研究背景與動機 1 1.2 研究目的 3 1.3 前提假設與研究範疇 3 1.4 論文架構說明 4 第2章 文獻回顧 5 2.1 噬菌體的應用與功能 5 2.2 噬菌體感染機制與吸附階段 6 2.3 噬菌體分類與尾部結構差異 8 2.4 長尾型噬菌體 10 2.5 Douge 噬菌體 11 2.6 粗粒徑分子動力學模擬應用於病毒研究 14 第3章 研究方法 15 3.1 粗粒徑分子動力學模擬原理與框架 15 3.1.1 粗粒化模擬 15 3.1.2 粒子間作用力模型與數學描述 16 3.1.3 系綜 19 3.1.4 週期性邊界條件 19 3.2 二維模型建構 20 3.2.1 尾部模型建構 20 3.2.2 衣殼模型建構與尾部連接設計 22 3.2.3 背景液體與宿主構件建構 24 3.2.4 多噬菌體系統設計 25 3.3 三維模型建構 25 3.3.1 尾部結構建構 26 3.3.2 衣殼建構與尾部連接設計 28 3.3.3 背景液體與宿主構件建構 30 3.4 模擬設計與參數配置 31 3.4.1 模擬流程 31 3.4.2 模擬時間步長設計與穩定性評估依據 32 3.4.3 吸附判定方式 33 3.5 二維模擬試驗內容 33 3.5.1 真空環境下之結構性能分析 33 3.5.2 溶液環境下之擴散與距離行為 36 3.5.3 噬菌體接近細胞表面行為 40 3.5.4 多噬菌體平坦與曲率細胞表面吸附行為測試 42 3.6 三維模擬試驗內容 45 3.6.1 真空環境下之結構性能分析 45 3.6.2 溶液環境下之擴散行為 47 第4章 模擬結果與討論 49 4.1 時間步長穩定性分析 49 4.2 模型與 cryo-EM 結構之靜態比對 50 4.3 二維模擬結果 52 4.3.1 尾管拉伸模擬結果 52 4.3.2 衣殼拉伸模擬結果 54 4.3.3 真空環境下尾管端到端距離變化 56 4.3.4 溶液粒子分析 59 4.3.5 溶液環境下衣殼MSD分析 61 4.3.6 溶液環境下尾管端到端距離變化 63 4.3.7 噬菌體近細胞表面行為分析 66 4.3.8 底板吸附成功率 68 4.3.9 多噬菌體平坦細胞表面吸附行為分析 70 4.3.10 多噬菌體曲率細胞表面吸附行為分析 79 4.4 三維模擬結果 98 4.4.1 尾管拉伸模擬結果 98 4.4.2 衣殼拉伸模擬結果 99 4.4.3 真空環境下尾管端到端距離變化 101 4.4.4 溶液粒子RDF分析 101 4.4.5 溶液環境下尾管端到端距離變化 103 第5章 結論與未來展望 104 5.1 結論 104 5.2 未來展望 104 參考文獻 106 附錄A 不同溫度、密度、ε配置下溶液粒子RDF曲線 112 附錄B 不同溫度下溶液粒子之平均MSD Contour 113 附錄C 不同溫度、ε配置下溶液粒子MSD曲線(密度=1.3061e-02Å-1) 114 附錄D 二維噬菌體模型參數列表 115 附錄E 三維噬菌體模型參數表 116 | - |
| dc.language.iso | zh_TW | - |
| dc.subject | 噬菌體 | zh_TW |
| dc.subject | 粗粒徑模擬 | zh_TW |
| dc.subject | 尾管柔韌性 | zh_TW |
| dc.subject | 彎矩剛性 | zh_TW |
| dc.subject | 吸附效率 | zh_TW |
| dc.subject | 細胞表面曲率 | zh_TW |
| dc.subject | 感染機制 | zh_TW |
| dc.subject | Coarse-grained simulation | en |
| dc.subject | Infection mechanism | en |
| dc.subject | Surface curvature | en |
| dc.subject | Adsorption efficiency | en |
| dc.subject | Bending stiffness | en |
| dc.subject | Tail tube flexibility | en |
| dc.subject | Phage | en |
| dc.title | 以粗粒徑分子動力學探討尾管彎矩剛性對噬菌體吸附行為之影響 | zh_TW |
| dc.title | Investigating the Influence of Tail Tube Bending Rigidity on Bacteriophage Adsorption Behavior Using Coarse-Grained Molecular Dynamics | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-2 | - |
| dc.description.degree | 碩士 | - |
| dc.contributor.oralexamcommittee | 何孟樵;洪子倫;周佳靚 | zh_TW |
| dc.contributor.oralexamcommittee | Meng-Chiao Ho;Tzyy-Leng Horng;Chia-Ching Chou | en |
| dc.subject.keyword | 噬菌體,粗粒徑模擬,尾管柔韌性,彎矩剛性,吸附效率,細胞表面曲率,感染機制, | zh_TW |
| dc.subject.keyword | Phage,Coarse-grained simulation,Tail tube flexibility,Bending stiffness,Adsorption efficiency,Surface curvature,Infection mechanism, | en |
| dc.relation.page | 116 | - |
| dc.identifier.doi | 10.6342/NTU202503620 | - |
| dc.rights.note | 同意授權(限校園內公開) | - |
| dc.date.accepted | 2025-08-12 | - |
| dc.contributor.author-college | 工學院 | - |
| dc.contributor.author-dept | 土木工程學系 | - |
| dc.date.embargo-lift | 2030-08-07 | - |
| 顯示於系所單位： | 土木工程學系 | |
文件中的檔案：
| 檔案 | 大小 | 格式 | |
|---|---|---|---|
| ntu-113-2.pdf 未授權公開取用 | 16.87 MB | Adobe PDF | 檢視/開啟 |
系統中的文件，除了特別指名其著作權條款之外，均受到著作權保護，並且保留所有的權利。