3D engine implemented in DNA code

Yes, this is more like a thought experiment and it will require lots of efforts and money to realize it smoothly in a wet lab.

However, it is far more realizable than some other DNA implementations described in papers.

The idea to publish DNA code on GitHub with CI, tests, linters, badges etc. is obviously a form of joke, but the project itself was done like a serious applied maths research.

>OK, Get a microplate with 384 wells (== test tubes).

Why 384? You could get any amount you want, you'd just have to modify the coefficients for row and column accordingly (linear increase with decrease of number per axis).

Imagine if you'd skip every other row and column, the image would still be the same, just lower resolution.

> According to what table? There is no "table below".

CTRL-F environment variables. Click on that.

>A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?

???

The concentrations are determined by row and column, thus encode position.

Someone should price this out on transcript aka https://strateos.com/ cloud lab...

There was a lot of interest in this field in the late '90s over fears of Moore's Law eventually hitting a brick wall

https://en.wikipedia.org/wiki/DNA_computing

> A pipette is used to dispense fluid. How does a pipette "encode position"??

The illustration shows this relatively clearly: at row N column M, you put N drops of solution A and M drops of solution B.

> A pipette is used to dispense fluid. How does a pipette "encode position"?? Start what computation?

This is shown in the picture; you put X drops of one fluid and Y drops of a different fluid, where (X, Y) is the position of a given test tube.

1) The answer is both yes and no. Any particular digital circuit can be implemented, but not universal Turing machine, simply because there is no way to deal with arrays.

There is mind-blowing paper, that gives exhaustive anwser to this question: https://hal.inria.fr/hal-01519828/document

This paper is about chemical reaction networks, but in 2010 it was shown, that any chemical reaction network is realizable in DNA: https://www.pnas.org/content/pnas/107/12/5393.full.pdf

2) Yes, it was figured out in 2006, how to do logic gates in DNA: https://science.sciencemag.org/content/314/5805/1585

This is exactly the feeling I got when reading (Adelman's?) paper on finding Euler paths in graphs using DNA.

I still feel this way although after a lot of googling it's a little better, I wish I had a good book or other resource on it.

Reading a machine translated version of the Russian article linked from GitHub (that seems far more complete) the author mentions RNA can behave like NOR gates, so all other gates must be possible as well

yes, DNA is turing complete. all of the basic circuits can be implemented.Unfortunately, practically speaking it's hard to scale these up to be "useful" (competitive with modern CPUs or hard drives).

Yes, I've made CRN++ version as well (in this pull request: https://github.com/marko-vasic/crnPlusPlus/pull/1), but it required much more reactions and was less stable. So I decided to make it from scratch by using different approach.

That's not how this works. The computation is done in tubes via chemical reactions. The inputs (column and row) are specified by providing a variable concentration of two input solutions to the same base solution which encodes the ray marching algorithm. The scene is static, but you can theoretically sample it at arbitrary points and resolutions by varying the inputs.

Isn't this how fragment shaders work? These also run computation per pixel and here one pixel corresponds to one tube.

Each tube renders/computes a "pixel". The concentrations are not proportional to brightness, but instead linearly correspond to x / y position of the pipettes.