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.
http://chorasimilarity.github.io/chemlambda-gui/dynamic/moves.html
If you want to play with this (made-up) chemistry, called “chemlambda”, then go to the github repository

https://github.com/chorasimilarity/chemlambda-gui/tree/gh-pages/dynamic

clone it and just type:
bash moving_random_metabo.sh
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

http://chorasimilarity.github.io/chemlambda-gui/dynamic/demos.html
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. http://chorasimilarity.github.io/chemlambda-gui/dynamic/molecular_comp.html

_________________________________________________

Advertisements

One thought on “Molecular computers”

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s