Final project – Fractal interpretation of DNA winding structure.

Yinrou Wang, A91424838

VIS 159/ICAN 150 Final, Winter 2015

TA: Stephanie Sherman

Mar. 17, 2015

Title: Fractal interpretation of DNA winding structure.

Artist: Yinrou Wang

Completion Date: March, 17, 2015

Place of Creation: Mesa apartment, desktop computer

Style: Fractal

Genre: 3D Computer Animation

Technique: Computer Process

Material: Digital Fractal Program, Incendia.

Link to documentation of piece: https://vimeo.com/122507098

 

Descriptive paragraph:

Continuing my previous project topic on DNA unwinding, I decided to tackle the multiple-scale supercoil arrangement structure of compacted DNA while invoking the use of digital fractal art. I was mostly inspired by Ron Eglash’s TED talk on how fractals are everywhere, as well as the 2008 David Borgo video called “Fractal world.” I was especially taken by the beauty of recursive iterations of self-similar features in nature. Since the way DNA strands need to be highly compacted in chromosomes, arranging in coils after coils across multiple scales, I was quite surprised that I haven’t seen a really good fractal representation of it. However, my own trek through the fractal learning curve would soon make me realize just how difficult it is.

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Figure 1 –  3D molecular representation of DNA and histone structures by Griffiths et al. (http://www.mun.ca/biology/scarr/Histone_Protein_Structure.html)

For generating fractals, I tried many popular open source fractal programs. During the last lecture of my VIS 159 course, a former student showed us just how easy it is to create fractals by “Apophysis” so I thought that everything should t so quick and smooth. However, despite generating many stunning random fractal flames after flames, I was not able to get through the rather unintuitive editing interface to create exactly what I wanted. Worse, I couldn’t find much tutorials for customizing your own fractals. The closest I got to something resembling DNA structure was based on parameters published by the user ObsidianFire on DeviantArt (http://0bsidianfire.deviantart.com/art/The-DNA-of-Chrome-417723420), but I wasn’t very satisfied with it because it wasn’t possible for me to add in the major structural protein complex – histones, to the fractal image. After days of trying, I gave up using that program anymore, and started to try UltraFractal.

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Figure 2 – DNA fractal based on changes to Obsidianfire’s rendition.

 

I came about UltraFractal through youtube videos on fractal tutorials. At first I thought it is very easy to use since the interface allows rather direct access to a lot of embellishments that you can see right away. However, upon generating an example output, I noticed watermarks displaying “Evaluation Copy” all over the image, so I had to abandon this platform as well.

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Figure 3 – UltraFractal output watermarks.

Finally, I remembered Alice Kelley that I introduced on my blog in week 8, and she mentioned how she created 3D fractals via Incendia, so I moved on to that next. To my pleasant surprise, there are a lot more documentation and tutorials available for Incendia, and the 3D and animation features built in were really top notch! After a weekend of exploration, I was able to create a supercoil representation complete with the relative positioning of histones with the DNA double strands. The final image/animation is actually still quite rough because I haven’t figured out a way to link the representative DNA strands together across the fractal repeats; however, I am quite happy with at least showing the viewers how DNA strands are coiled around histones (creating the nucleosome complex) and then the superstructure are then coiled around a set of such complex (to create the solenoid), and so on and on till it fill the whole chromosome. I hope you will enjoy my fractal image as well as the short animation clip!

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Figure 4 – Incendia rendition of DNA supercoil structure. DNA strands (blue/yellow strands) wrapping around histones (red).

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