第五章 結論與未來展望
5.2 科教用途
Nucleic Acid, DNA)結構的繞射圖樣「相片 51」(攝於 1952)[41][42],說明 DNA 雙股螺旋的發現以及X 光的發明、繞射等物理章節。但由這副圖像如何得知
另一種方法則是Amand A Lucas 等人使用電腦模擬,嘗試將多種DNA形貌 直接用惠更斯-菲涅耳原理算出繞射圖樣,並找出與「相片51」最相似的一種,
並模擬該DNA形貌的雷射繞射圖樣。[45-47]
圖5.4 選擇 12 種不同 DNA 形貌生成繞射 [47]
前者可以與課綱中雙狹縫章節合併進行,以實驗的方式讓學生對波動光學 的有實感的理解;後者則忠實的呈現DNA形貌與繞射圖的對應關係。本論文的 提議是結合這兩者的好處。Franklin使用X光照在寬度約為3.4 nm的B型DNA 上,仿照這個比例,以紅光雷射製造對應寬對的樣品,能在屏幕上呈現出放大 版的「相片51」給學生們觀察,觀察為隨即放進相位取回演算法去重建,能讓 同學在不用計算複雜數學的情形下,理解並相似的體驗繞射紋如何被取得,被 技術性的重建,並且解出真的來是雙股螺旋。
如第二章所述,繞射圖與樣品並非只是傅立葉轉換的關係,當中還丟失了 相位的資訊,普遍適用的相位取回方法是在1980年才發展出來,在那之前,不 同的繞射圖樣必須要藉由其他的先驗資訊(prior information),以DNA來說,就 是化學鹼基的排列、鍵結方式 [48],並且要等到「相片51」這張結構較簡單的 繞射圖,才能將雙股螺旋的結構解出來,因此才是那麼非凡難得的成就。真正 直接拍攝的DNA影像在2012年才問世。[49]
圖5.6 首張直接拍攝的 DNA 雙股螺旋照片 [49]
作者認為這項教案適合作為探究與實作課程的原因分為內容與取材方面,
此教案包含中學的既有內容:DNA雙股螺旋的發現以及X光的發明、狹縫干涉 繞射實驗,能連結並強化對這些章節的學習;又能藉由顯微鏡的演進史、光 源、解析度,使學生對於尺度(Scale)這個物理中的重要概念印象深刻;最終,
還能介紹這種越來越被廣泛應用的顯微術 — CDI。學生能藉由實驗的過程理 解,CDI顯微術所做的工作,正如Watson與Click在電子顯微鏡解析度還未到達 10 nm之前,就解出寬度為3.4 nm的週期性結構。而本篇HIO、PIE演算法,能夠 重建更多樣的樣品,是顯微技術上值得研究、發展的方向。
可見光作為光源的CDI除了方便操作以外,可視化使其更適合作為教學演 示之用,所使用的實驗用品甚至與既有的雙狹縫干涉高度重疊,僅需製作適當 比例的DNA樣品即可。若能選取較適當的樣品、並將數據處理的過程合併於一 個應用程式中,HIO相位取回演算法將很適合這樣的課程設計來使用。
參考文獻
1. E. Ruska, M. Knoll, “Die magnetische Sammelspule fuer schnelle Elektronenstrahlen”, Z. Techn. Physik. 12, 389 (1931).
2. von Ardenne, Manfred, “Das Elektronen-Rastermikroskop. Praktische Ausführung”, Zeitschrift für technische Physik 19, 407 (1938).
3. Wikimedia. (2008). Image illustrating the principle of various microscopes.
Retrieved from https://commons.wikimedia.org/w/index.php?curid=3938464 4. David A Muller. (2018). Smaller than the space between atoms: The technology
behind the highest-resolution microscope image. Retrieved from
https://devicematerialscommunity.nature.com/posts/36567-smaller-than-the- space-between-atoms-the-technology-behind-the-highest-resolution-microscope-image
5. J.C. Meyer et. al., “Accurate Measurement of Electron Beam Induced
Displacement Cross Sections for Single-Layer Graphene” , Phys. Rev. Lett. 108, 196102 (2012).
6. Trevor H. Moser, Tolou Shokuhfar, James E. Evans, “Considerations for imaging thick, low contrast, and beam sensitive samples with liquid cell transmission electron microscopy”, Micron Volume 117 (2019).
7. C.Y. Lin, “Low-kilovolt Coherent Electron Diffraction Imaging Based on a Single-Atom Electron Source” (Unpublished doctoral dissertation), National Taiwan University, Taipei (2016).
8. C.Y. Lin, W.T. Chang et. al., “Low-voltage coherent electron microscopy based on a highly coherent electron source built from a nanoemitter”, Journal of Vacuum Science & Technology B 36, 032901 (2018).
9. J.C.H. Spence, U. Weierstall, M. Howells, “Coherence and sampling
requirements for diffractive imaging”, Ultramicroscopy 101, 149 (2004).
10. J. Miao, J. Kriz, D. Sayre, “The oversampling phasing method”, Acta Crystallogr D Biol Crystallogr 56, 1312 (2000).
11. J. R. Fienup, “ Invariant error metrics for image reconstruction” , Appl. Opt. 36, 32, 10 (1997).
12. W. C. Huang, “Holographic Simulations and Reconstructions of Low energy Electron Point Projection Microscopy” (Unpublished master’s thesis), National Taiwan University, Taipei (2018).
13. G. J. Yu, “Ptychographical coherent diffraction microscopy for extend periodic structure” (Unpublished master’s thesis), National Chiao Tung University, Hsinchu (2014).
14. R.W. Gerchberg, W.O. Saxton, “A practical algorithm for the determination of the phase from image and diffraction plane pictures”, Optik 35 237 (1972).
15. J.R. Fienup, “Reconstruction of an object from the modulus of its Fourier transform”, Opt. Lett. 3, 27 (1978).
16. J.R. Fienup, “Phase retrieval algorithms: a comparison”, Appl. Opt. 21, 2758 (1982).
17. R. Hegerl, W. Hoppe, “Dynamische theorie der kristallstrukturanalyse durch elektronenbeugung im inhomogenen primärstrahlwellenfeld”, Berichte der Bunsengesellschaft für physikalische Chemie. 74, 11, 1148 (1970).
18. W. Hoppe, “ Diffraction in inhomogeneous primary wave fields. 1. Principle of phase determination from electron diffraction interference”, Acta Crystallogr. A
21. J. Rodenburg, H. Faulkner, “A phase retrieval algorithm for shifting Illumination”, Applied physics letters 85, 20, 4795 (2004).
22. J. Miao, P. Charalambous, J. Kriz, D. Sayre, “Extending the methodology of X-ray crystallography to allow imaging of micrometer-sized non-crystalline specimens“, Nature 400, 342 (1999).
23. U. Weierstall, Q. Chen, J.C.H. Spence, M.R. Howells, M. Isaacson, R.R.
Panepucci, “Image reconstruction from electron and X-ray diffraction patterns using iterative algorithms: experiment and simulation“, Ultramicroscopy 90, 171 (2002).
24. J.M. Zuo, I. Vartanyants, M. Gao, R. Zhang, L.A. Nagahara, “Atomic resolution imaging of a carbon nanotube from diffraction intensities“, Science 300, 1419 (2003).
25. S. Morishita, J. Yamasaki, K. Nakamura, T. Kato, N. Tanaka, “Diffractive imaging of the dumbbell structure in silicon by spherical-aberration corrected electron diffraction”, Appl. Phys. Lett. 93, 183103 (2008).
26. W.J. Huang, J.M. Zuo, B. Jiang, K.W. Kwon, M. Shim,
“sub-ångström-resolution diffractive imaging of single nanocrystals”, Nat. Phys. 5, 129 (2009).
27. L.D. Caro, E. Carlino, G. Caputo, P.D. Cozzoli, C. Giannin, “Electron diffractive imaging of oxygen atoms in nanocrystals at sub- sub-ångström resolution”, Nat.
Nanotechnol. 5, 360 (2010).
28. O. Kamimura, Y. Maehara, T. Dobashi, K. Kobayashi, R. Kitaura, H. Shinohara, H. Shioya, K. Gohara, “Low voltage electron diffractive imaging of atomic structure in single-wall carbon nanotubes”, Appl. Phys. Lett. 98 174103 (2011).
29. O. Kamimura, T. Dobashi, K. Kawahara, T. Abe, K. Gohar, “10-kV diffractive imaging using newly developed electron diffraction microscope”,
Ultramicroscopy 110 130 (2010).
30. M.J. Humphry, B. Kraus, A.C. Hurst, A.M. Maiden, J.M. Rodenburg,
“Ptychographic electron microscopy using high-angle dark-field scattering for sub-nanometre resolution imaging”, Nature Commu. 3 730 (2012).
31. L.N. Longchamp, T. Latychevskaia, C. Escher, H.W. Fink, “Graphene unit cell imaging by holographic coherent diffraction“, Phys. Rev. Lett.110 255501 (2013).
32. J. C. H. Spence, U. Weierstall, M. Howells,“Phase recovery and lensless imaging by iterative methods in optical, X-ray and electron diffraction”, Phil. Trans. R.
Soc. Lond. A 360, 875 (2002).
33. A. C. Hurst and J. M. Rodenburg, “ An optical demonstration of ptychographical imaging for focussed-probe illumination”, Journal of Physics: Conference Series 126, 012093 (2008).
34. Martin Dierolf et al., “Coherent laser scanning diffraction microscopy”, Journal of Physics: Conference Series 186, 012052 (2009).
35. Oliver Bunk et. al., “Influence of the overlap parameter on the convergence of the ptychographical iterative engine”, Ultramicroscopy 108, 481 (2008).
36. Rob Sumner, “Processing RAW Images in MATLAB”, Department of Electrical Engineering, UC Santa Cruz (2014).
37. 張國誌主編(2016):近代光學實驗課程,第一版。台南:國立成功大學物 理系。基礎光路架設。引用網址:
http://teachlab.phys.ncku.edu.tw/media/course_pdf/%E5%9F%BA%E7%A4%8
40. 邱美虹(2008):模型與建模能力之理論架構。科學教育月刊,306,2-9。
41. J.D. Watson, and F.H. Crick, “A structure for deoxyribose nucleic acid.”, Nature 171, 737 (1953).
42. R. Franklin and R. G. Gosling, “Molecular configuration in sodium thymonucleate,” Nature 171, 740 (1953).
43. Gregory Braun, Dennis Tierney, Heidrun Schmitzer, “How Rosalind Franklin Discovered the Helical Structure of DNA: Experiments in Diffraction.”, The Physics Teacher 49, 140 (2011).
44. J. Thompson et. al., “Rosalind Franklin's X-ray photo of DNA as an
undergraduate optical diffraction experiment.”, American Journal of Physics 86, 95 (2018).
45. A. A. Lucas et. al., “Revealing the Backbone Structure of B-DNA from Laser Optical Simulations of Its X-ray Diffraction Diagram.” J. Chem. Educ. 76, 3, 378 (1999).
46. Amand A Lucas and Philippe Lambin, “Diffraction by DNA, carbon nanotubes and other helical nanostructures.”, Rep. Prog. Phys. 68 1181 (2005).
47. Amand A. Lucas, “A-DNA and B-DNA: Comparing their Historical X-Ray Fibre Diffraction Images.”, J. Chem. Educ. 85, 5, 737 (2008).
48. F.H.Crick, J.D.Watson, “The Complementary Structure of Deoxyribonucleic Acid.” Proceedings of the Royal Society of London. Series A, Mathematical and Physical Sciences 223, 1152, 80 (1954).
49. Francesco Gentile et. al., “Direct Imaging of DNA Fibers: The Visage of Double Helix.”, American Chemical Society. Nano Lett. 12, 6453 (2012).
50. J. R. Fienup, T. R. Crimmins, and W. Holsztynski, “Reconstruction of the support of an object from the support of its autocorrelation” J. Opt. Soc.. 72, 5 (1982).