Molecular computers

Can you believe that such a complex, intricate sequence of hundreds of chemical reactions is possible, in the right order, in the presence of randomness and without any assistance from a human director? At a molecular level?

Yes, it is possible. Here is why.
What you see in this video is a virtual molecule, which enters in random chemical reactions in a soup of invisible enzymes. All chemical reactions consist in the enzymes interacting with a small number of atoms (color coded in the video), in a random order, and facilitating certain, well chosen reactions.
Everything is purely local, there is nothing else behind the scenes.
And still it works.
This is not real chemistry (but who knows? I believe it is, with the condition to identify real chemical reactions like those virtual ones).
The chemical reactions needed are listed at this page.
If you want to play with this (made-up) chemistry, called “chemlambda”, then go to the github repository

clone it and just type:
and then choose one of the molecules, encoded as .mol files, from the list.
There are a bunch of demos, which show animations for different molecules, made in d3.js, at the link
What is different in this video, which is a screen recording at 4X speed of an animation made with the script, is that it is now possible to see the virtual molecules as made of “atoms” (they may be smaller, well chosen molecules themselves).
This is possible because of a modification of the script called by the sh script, i.e. the awk script check_1_mov2_rand_metabo.awk .
The visualization of the “true” virtual atoms is realized by representing the chemlambda nodes and their ports according to a color scheme which uses the “all_nodes_atom” field of the nodes and ports.

UPDATE: here is d3.js demo page for that.


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