臺灣博碩士論文加值系統

隨著三維動畫技術和演算法設計的進步，將這些技術應用於藝術創作提供了無限可能。本創作除了聚焦於傳統的仿生學觀點，還有探索如何通過實驗性動畫技術，創造出反映絲狀微生物生長過程的視覺表現。受到演算法藝術家Andy Lomas在《Cellular Forms》中對細胞形態學藝術探索的啟發，本創作通過結合自然界的生長模式與數學演算法，以及利用三維動畫技術，來探索和呈現絲狀微生物的多樣化生長樣態及其生理機制。
本創作動畫專注於開發和應用實驗性演算法，模擬絲狀微生物的生長方式和形態變化，從而揭示其背後的隨機性和規律性。本創作的目的是透過創新的技術手段，提供一種新的視角來觀察和理解微觀生命的複雜性，同時為動畫技術創作、生物學研究及其他相關領域提供實驗性的探索工具。
本創作強調以圓點供給養分驅使微生物生長的實驗性動畫技術，探索自然界微觀生命形態中的應用，並探討這些技術如何幫助我們以另一種方式模擬微生物生長的方式，以及透過模擬基礎的生長方式而非預先設定模型的最終形態，讓動畫中的微生物自然演化至最終的自然形狀。本創作的方法揭示出生長過程中的不可預測性和多樣性。

With the advancement of three-dimensional animation technologies and algorithm design, applying these technologies in artistic creation has opened up limitless possibilities. This work focuses not only on the traditional perspective of bionics but also explores how experimental animation techniques can be used to create visual representations of the growth process of filamentous microorganisms. Inspired by the algorithmic art exploration of cellular morphology by Andy Lomas in "Cellular Forms," this creation combines natural growth patterns with mathematical algorithms and utilizes three-dimensional animation technology to explore and present the diverse growth forms and physiological mechanisms of filamentous microorganisms.
This animated creation focuses on developing and applying experimental algorithms to simulate the growth modes and morphological changes of filamentous microorganisms, thereby revealing the underlying randomness and regularity. The purpose of this work is to provide a new perspective for observing and understanding the complexity of microscopic life through innovative technical means, while offering experimental exploration tools for animation technology creation, biological research, and other related fields.
This work emphasizes the experimental animation technique of driving microbial growth through the supply of nutrients at focal points, exploring its application in the natural micro-life forms, and discussing how these techniques help us simulate microbial growth in another way. By simulating the fundamental modes of growth rather than pre-setting the final form of the model, the microorganisms in the animation naturally evolve into their final natural shapes. This approach reveals the unpredictability and diversity in the growth process.

目錄
摘要 i
Abstract ii
誌謝 iii
目錄 iv
圖目錄 vii
表目錄 x
第一章 緒論 1
第一節 創作背景 1
第二節 創作動機 4
第三節 創作目的 5
第二章 文獻探討 7
第一節 影響絲狀微生物之生長因素 7
2-1-1 水 9
2-1-2 氮源 9
2-1-3 溫度 10
2-1-4 pH 值 11
2-1-5 氧 12
2-1-6 碳源 13
第二節 三種不同生長樣態的絲狀微生物 15
2-2-1 團塊狀生長 15
2-2-2 散支狀生長 17
2-2-3 放射狀生長 19
小結 22
第三節 Andy Lomas的作品分析 26
2-3-1 Aggregation 作品探討 27
2-3-2 Cellular Form 作品探討 27
2-3-3 Morphogenetic Vase Forms 作品探討 29
2-3-4 Plantlike Forms 作品探討 32
第三章 創作方法 34
第一節 創作流程圖 34
第二節 創作概念 35
第三節 創作工具 36
3-3-1 Houdini 軟體 36
3-3-2 VEX 37
3-3-3 Arnold 39
第四章 創作論述 41
第一節 創作理念 41
第二節 故事腳本 42
第三節 絲狀微生物生長與限制之設定 44
4-3-1 Attribute Wrangle 45
4-3-2 Solver 46
4-3-3 VEX 代碼設定 47
4-3-4 三角形面積公式 52
4-3-5 計算角度的數學公式 55
第四節 最終作品呈現 59
4-4-1 場次S1&S4 - 團塊狀生長 59
4-4-2 場次S2&S5 -散支狀生長 61
4-4-3 場次S3&S6 -放射狀生長 62
第五章 結論 64
第一節 創作經驗與回饋 64
5-1-1 技術歸納 64
5-1-1-1 海倫公式歸納 64
5-1-1-2 餘弦定理歸納 65
5-1-2 延伸應用 66
5-1-3 變數轉換的創意價值與建議 68
第二節 結語 69

 
圖目錄
圖1-1 On Growth and Form 用數學解釋細胞分裂的角度 (D’Arcy Thompson, 1917) 2
圖1-2 圖靈模式（Turing pattern） 3
圖1-3 細胞自動機（Cellular Automata） 3
圖1-4 Andy Lomas的作品 Cellular Forms (Andy Lomas 2014) 5
圖2-1 尖鐮孢的菌絲尖端 8
圖2-2 ，2-3，2-4 在光學顯微鏡下的灰葡萄孢活菌絲 8
圖2-5 溫度對真菌生長的影響 10
圖2-6不同種的真菌在各種 pH 值環境下的生長速率 11
圖2-7 pH值對真菌生長的影響 11
圖2-8氧含量對於真菌生長的影響 (Nell, M., Mammerler, R., & Steinkellner, S., 2006) 13
圖2-9 粗糙脈孢菌跨碳源轉錄組的層次聚類和 WGCNA 14
圖2-10 NA-seq 差異表達分析的 log2 倍數變化與 DAP-seq 峰強度或峰頂到翻譯起始位點 (ATG) 的距離的關係 14
圖2-11 CRE-1四重鎖機制調節碳分解代謝物的抑制 15
圖2-12（A）銅綠假單胞菌在共焦雷射掃描顯微鏡下的影像（B）具有平坦邊界的生長生物膜的簡單模型 (Allen & Waclaw, 2019) 15
圖2-13（A,B）是綠膿桿菌宏觀下的型態，（C, D）是綠膿桿菌圍觀下的型態 16
圖2-14二分裂無性繁殖示意圖 17
圖 2-15 根黴 17
圖 2-16 毛黴菌絲行有性生殖 18
圖 2-17 黴菌菌絲行無性生殖的分生孢子 18
圖2-18多頭絨泡菌 19
圖2-19活性瘧原蟲多頭絨泡菌形成的智慧生長網 (Kay et al., 2022) 19
圖2-20絨泡菌網絡與東京鐵路網的比較 (Tero et al., 2010) 20
圖2-21多頭絨泡菌的生命周期 21
圖2-22 細菌生長曲線 23
圖2-23 電影恐懼大街第二部中的怪物 24
圖2-24異星智慧(Life)中的外星生物卡爾文(Calvin) 25
圖2-25 The Last of Us片頭動畫中仿生真菌的場景 26
圖2-26 Aggregation (Andy Lomas, 2005) 27
圖2-27 Cellular Form (Andy Lomas , 2020) 28
圖2-28 t-SNE 2D 降維技術 (Andy Lomas , 2020) 28
圖2-29 Vase form 初始配置、約束和影響 (Andy Lomas , 2019) 30
圖2-30 Species Explorer 使用者介面 (Andy Lomas , 2019) 31
圖2-31突變的 Vase Forms (Andy Lomas , 2019) 31
圖2-32 Vase Forms 變形序列 (Andy Lomas , 2019) 32
圖2-33倫敦 V&A 博物館舉辦的倫敦設計節 Vase forms 展覽 32
圖2-34 Plantlike Forms (Andy Lomas , 2014) 33
圖3-1 研究流程圖 35
圖3-2 Houdini 37
圖3-3 Arnold 40
圖4-1隨著營養物質分佈生長的綠膿桿菌 42
圖4-2 Attribute Wrangle 節點介紹 45
圖4-3 Solver 節點介紹 47
圖4-4 團塊狀生長的種子細胞 49
圖4-5 箭頭指向的紅色的點是發送養分的 49
圖4-6 箭頭指向的黃色的點是發送養分的 50
圖4-7 箭頭指向的黃色的點是發送養分的 51
圖4-8 底乘以高除以2－三角形面積計算公式示意圖 52
圖4-9 紅色的點為停止生長的細胞，黃色的點為發送養分的點 54
圖4-10 海倫公式檢測養分路徑是否被阻擋之示意圖 55
圖4-11餘弦定理示意圖 56
圖4-12本動畫繪製的控制絲狀微生物的生長範圍截圖 57
圖4-13 圖解檢測範圍內的點 58
圖4-14 團塊狀微生物生長樣態之演算法流程圖 60
圖4-15 團塊狀微生物最終呈現截圖 60
圖4-16 散支狀微生物生長樣態之演算法流程圖 61
圖4-17 散支狀微生物最終呈現截圖 62
圖4-18 放射狀微生物生長樣態之演算法流程圖 63
圖4-19 放射狀微生物最終呈現截圖 63
圖5-1 海倫計算公式應用至本創作的空間計算圖示 65
圖5-2 餘弦定理應用至本創作的計算圖示 66
圖5-3 Timothée Chalamet 躲在全息灌木叢中的場景 67
圖5-4 決戰異世界：未來復甦場景圖 67
圖5-5 電影猛毒 (Venom) 的場景 68
圖5-6 另一種Vertex Color 的呈現方式 69


 
表目錄
表2-1 絲狀微生物的生長方式小結 22
表4-1 使用到的VEX代碼（本研究繪製） 47
表4-2 將海倫公式和底乘以高除以2編寫成 VEX 代碼的結果 54
表4-3 將餘弦定理編寫成 VEX 代碼的結果 57

1.Abubakar, A.; Suberu, H.A.; Bello, I.M.; Abdulkadir, R.; Daudu, O.A. and Lateef, A.A. (2013). Effect of pH on mycelial growth and sporulation of Aspergillus parasiticus. Journal of Plant Sciences. 1(4), 64-67.
2.Adamatzky, A., & Jones, J. (2010). Road planning with slime mould: If Physarum built motorways it would route M6/M74 through Newcastle. International Journal of Bifurcation and Chaos, 20(10), 3065–3084.
3.Adamatzky, A., & Alonso-Sanz, R. (2011, July). Rebuilding Iberian motorways with slime mould. Biosystems, 5(1), 89–100.
4.Berger, H., Basheer, A., Böck, S., Reyes-Dominguez, Y., Dalik, T., Altmann, F., et al. (2008).Dissecting individual steps of nitrogen transcription factor cooperation in the Aspergillus nidulans nitrate cluster. Mol. Microbiol. 69, 1385-1398. doi: 10.1111/j.1365-2958.2008.06359.x.
5.Ben-Jacob, E., Cohen, I., & Levine, H. (2000). Cooperative self-organization of microorganisms. Advances in Physics, 49, 395–554.
6.Ben-Jacob, E., Cohen, I., & Gutnick, D. L. (1998). Cooperative organization of bacterial colonies: From genotype to morphotype. Annual Review of Microbiology, 52, 779–806.
7.Bleichrodt, R. J., Vinck, A., Read, N. D., & Wösten, H. A. B. (2015). Selective transport between heterogeneous hyphal compartments via the plasma membrane lining septal walls of Aspergillus niger. Fungal Genetics and Biology, 82, 193–200.
8.Broekaert, W. F., Terras, F. R. G., Cammue, B. P. A., & Vanderleyden, J. (1990). An automated assay for fungal growth inhibition. FEMS Microbiological Letters, 69, 55–60.
9.Carlos, A. and Josep, A. (2012). Effects of Temperature, pH and Water Potential on Mycelial Growth, Sporulation and Chlamydospore Production in Culture of Cylindrocarpon species Associated with Black Foot of Grape vines. Phytopathologia Mediterranea, 51(1), 37-50.
10.Carlile, M.J. (1995) In N.A.R. Gow and G.M. Gadd (Eds.), The Growing Fungus, Chapmanand Hall, London, pp. 3-19.
11.Cheung, Y.Y.; Lee, S.H.C.; Hui, M. and Luk, T.N.M. (2014). Effect of pH on fungal growth: problems with using vinegar (5% acetic acid) in treating superficial fungal infections. Hong Kong J. Dermatol. Venereol. 22, 57-64.
12.Chimileski, S., & Kolter, R. (2018). Life at the Edge of Sight. Harvard University Press.
13.Deshmukh, A.J.; Mehta, B.P.; Sabalpara, A.N. and Patil, V.A. (2012). In vitro effect of various nitrogen, carbon sources and pH regimes on the growth and sporulation of Colletotrichum gloeosporioides Penz. And Sacc causing anthracnose of Indian bean. Journal of Biopest. 5, 46-49.
14.Fraser, J. A., Davis, M. A., and Hynes, M. J. (2001). The formamidase gene of Aspergillus nidulans: regulation by nitrogen metabolite repression and transcriptional interference by an overlapping upstream gene. Genetics 157, 119–131.
15.
16.Howard, R.J and J.R.Aist (1979) J.Ultrastruct. Res. 66: 224-234.
17.Ishitsuka Y, Savage N, Li Y, Bergs A, Grün N, Kohler D, et al., (2015). Superresolu- tion microscopy reveals a dynamic picture of cell polarity maintenance during directional growth. Science Advances, 1, e1500947.
18.Kahm, M. and Hasenbrink, G. and Lichtenberg-Fraté, H. and Ludwig, J. and Kschischo, M. grofit: Fitting Biological Growth Curves with R. Journal of Statistical Software 33 (7). 2010: 1–21
19.Latty, Tanya; Beekman, Madeleine (2010). "Speed–accuracy trade-offs during foraging decisions in the acellular slime mould Physarum polycephalum". Proceedings of the Royal Society B: Biological Sciences. The Royal Society. 278(1705), 539–545.
20.Li, Y.; Wadso, L. and Larsson, L. (2009). Impact of temperature on growth and metabolic efficiency of Penicillium roqueforti – correlations between produced heat, ergosterol content and biomass. Journal of Applied Microbiology. 106, 1494 -1501.
21.Lomas, A. (2005). Aggregation: Complexity out of Simplicity.
22.Lomas, A. (2014). Cellular Forms: an Artistic Exploration of Morphogenesis. In SIGGRAPH 2014: Proceedings of the 41st Graphics and Interactive Techniques Conference, August 10-14, Vancouver, British Columbia, Canada. ACM.
23.Lomas, A. (2019). Morphogenetic vase forms. In The 2019 Conference on Artificial Life: A Hybrid of the European Conference on Artificial Life (ECAL) and the International Conference on the Synthesis and Simulation of Living Systems (ALIFE) (pp. 525-528).
24.Ludwig, A., & Boller, T. (1990). A method for the study of fungal growth inhibition by plant proteins. FEMS Microbiological Letters, 69, 61–66.
25.Maaten, L. v. d., & Hinton, G. (2008). Visualizing data using t-sne. Journal of Machine Learning Research, 9 (Nov), 2579–2605.
26.Magasanik, B., and Kaiser, C. A. (2002). Nitrogen regulation in Saccharomyces cerevisiae. Gene 290, 1–18. doi: 10.1016/S0378-1119(02)00558-9
27.Makhzani, A., Shlens, J., Jaitly, N., Goodfellow, I., Frey, B.: Adversarial autoen- coders. arXiv preprint arXiv:1511.05644 (2015)
28.Maor, E. (2002). Trigonometric delights. Princeton University Press.
29.Marzluf, G. A. (1997). Genetic regulation of nitrogen metabolism in the fungi. Micrbiol. Mol. Biol. Rev. 61,17-32.
30.McInnes, L., Healy, J., Melville, J.: UMAP: Uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:1802.03426 (2018)
31.MORGAN, MIKE PR Week, London ed.; London (2019), 90.
32.Muro-Pastor, M. I., Strauss, J., Ramón, A., and Scazzocchio, C. (2004). A paradoxical mutant GATA factor. Eukaryot. Cell 3, 393-405. doi: 10.1128/EC.3.2.393- 405.2004
33.McCormack, J., & Lomas, A. (2020). Understanding Aesthetic Evaluation using Deep Learning. In Proceedings of the evoMUSART Conference (pp. 3-5), 15-17 April, Seville, Spain.
34.Narendja, F., Goller, S. P., Wolschuk, M., and Strauss, J. (2002). Nitrate and the GATA factor AreA are necessary for in vivo binding of NirA, the pathway-specific transcriptional activator of Aspergillus nidulans. Mol. Microbiol. 44, 573-583. doi: 10.1046/j.1365-2958.2002.02911.x
35.Nakagaki, Toshiyuki; Yamada, Hiroyasu; Tóth, Ágota (2000). Intelligence: Maze-solving by an amoeboid organism. Nature. 407 (6803), 470.
36.Nielsen, K.F. (2001). Mould growth on building materials, secondary metabolites, mycotoxins and biomarkers. PhD thesis. Technical University of Denmark. Lyngby, Denmark.
37.Oiartzabal-Arano, E., Perez-de-Nanclares-Arregi, E., Espeso, E. A., & Etxebeste, O. (2016). Apical control of conidiation in Aspergillus nidulans. Current Genetics, 62, 371–377.
38.Pardo, E.; Marin, S.; Ramos, A.J. and Sanchis, V. (2006). Ecophysiology of ochratoxigenic Aspergillus ochraceus and Penicillium verrucosum isolates. Predictive models for fungal spoilage prevention - a review. 23(4), 398-410.
39.Remy, W., T.N. Taylor, H. Haas and H. Kerp (1994) Proc. Natl. Acad. Sci. USA 91: 11841-11843.
40.Rockefeller University - The Journal of Cell Biology 87, 55-64 (1980).
41.Sibounnavoung, P.; Kalaw, S.P.; Divina, C.C. and Soytong, K. (2009). Mycelial Growth and Sporulation of Emericella nidulans, A New Fungal Antagonist On Two Culture Media. Journal of Agricultural Technology, 5(2), 317-324.
42.Simon, L., J. Bousquet, R.C. Levesque and M. Lalonde (1993) Nature 363: 67-69.
43.Steinberg, G., Peñalva, M. A., Riquelme, M., Wösten, H. A., & Harris, S. D. (2017). Cell biology of hyphal growth. Microbiology Spectrum, 5, 1–34.
44.Takeshita, N., & Fischer, R. (2011). On the role of microtubules, cell end markers, and septal microtubule organizing centres on site selection for polar growth in Aspergillus nidulans. Fungal Biology, 115(5), 506–517.
45.Takeshita N, Mania D, Herrero S, Ishitsuka Y, Nienhaus GU, Podolski M,et al. ,(2013).The cell-end marker TeaA and the microtubule polymerase AlpA contribute to microtubule guidance at the hyphal tip cortex of Aspergil- lus nidulans to provide polarity maintenance. Journal of Cell Science, 126 (Pt 23):5400.
46.Tero, A., Takagi, S., Saigusa, T., Ito, K., Bebber, D. P., Fricker, M. D., Yumiki, K., Kobayashi, R., & Nakagaki, T. (2010). Rules for biologically inspired adaptive network design. Science, 327(5964), 439-442.
47.Tero, A., Takagi, S., Saigusa, T., Ito, K., Bebber, D. P., Fricker, M. D., Yumiki, K., Kobayashi, R., & Nakagaki, T. (2010). Rules for biologically inspired adaptive network design. Science, 327(5964), 439–442. https://doi.org/10.1126/science.1177894.
48.Thompson, D. W. (1917). On Growth and Form, pp.302.
49.Wadso, L.; Li, Y. and Bjurman, J. (2004). Measurements on two mold fungi with a calorespirometric method. Thermochimica Acta, 422, 63-68.
50.Weisstein, E. W. (Ed.). (2009, July 6). Heron's formula. MathWorld--A Wolfram Web Resource. Wolfram Research, Inc.
51.Weisstein, E. W. (n.d.). Heron's formula. MathWorld--A Wolfram Web Resource. Wolfram Research, Inc. Retrieved July 6, 2009.
52.Weber, R.W.S., G.E. Wakley and D.Pitt (1999) Histochem. J. 31(in press).
53.Wiame, J. M., Grenson, M., and Arst, H. N. Jr. (1985). Nitrogen catabolite repression in yeasts and filamentous fungi. Adv. Microb. Physiol. 26, 1–88.
54.Wiemann, P., and Tudzynski, B. (2013). “The nitrogen regulation network and its impact on secondary metabolism and pathogenicity,” in Fusarium: Genomics, Molecular and Cellular Biology, eds D. W. Brown and R. H. Proctor (Norwich: Caister Academic Press), 111–142.
55.Wong, K. H., Hynes, M. J., and Davis, M. A. (2008). Recent advances in nitrogen reg- ulation: a comparison between Saccharomyces cerevisiae and filamentous fungi. Eukaryot. Cell 7, 917–925. doi:10.1128/EC.00076-08
56.Wu, V. W., Thieme, N., Huberman, L. B., Dietschmann, A., Bleek, E., Kowbel, D. J., Lee, J., Calhoun, S., Singan, V., Lipzen, A., Xiong, Y., Monti, R., Blow, M. J., O'Malley, R. C., Grigoriev, I. V., Benz, J. P., & Glass, N. L. (2020). The regulatory and transcriptional landscape associated with carbon utilization in a filamentous fungus. PNAS, 117(11), 6003–6013.