Oritatami

Overview

Oritatami is a model of molecular folding based on co-transcriptional folding. It is intended to model the fact that in molecular folding, the folding process does not wait the end of the production to begin. Oritatami means folding, in Japanese. It is an extension of DNA origami, hence the name. Despite being algorithmically easy to predict (in polynomial time in the length of the sequence), it is surprisingly powerful: it can simulate Turing machines with only a polynomial overhead. To program Oritatami, you first need to choose a sequence of bead types, and an attraction rule between bead types. If you want, you can also add a seed, which is a set of beads initially present. Then, beads will get transcribed, one by one, and attach to the beads around them that maximize the number of bonds by the attraction rule.