Difference between revisions of "Oritatami"
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Oritatami, folding in Japanese, is a model of molecular folding based on co-transcriptional folding. It is an extension of DNA origami, hence the name. It is intended to model the fact that in molecular folding, the folding process does not wait until the end of the production to begin. 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, an attraction rule between bead types, and a delay factor $\delta$. If you want, you can also add a seed, which is a set of beads initially present. The beads will then get transcribed and attach to the beads around them that maximize the number of bonds by the attraction rule. The delay factor determines how many beads are made before making their final attachments. | Oritatami, folding in Japanese, is a model of molecular folding based on co-transcriptional folding. It is an extension of DNA origami, hence the name. It is intended to model the fact that in molecular folding, the folding process does not wait until the end of the production to begin. 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, an attraction rule between bead types, and a delay factor $\delta$. If you want, you can also add a seed, which is a set of beads initially present. The beads will then get transcribed and attach to the beads around them that maximize the number of bonds by the attraction rule. The delay factor determines how many beads are made before making their final attachments. | ||
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| + | == Software== | ||
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| + | [[OritatamiSim]] - an Oritatami simulator | ||
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| + | [[OritatamiShapeMaker]] - a program for generating Oritatami systems which self-assemble user-defined shapes | ||
[[Category:DNA manipulation techniques]] | [[Category:DNA manipulation techniques]] | ||
[[Category:Self-assembly]] | [[Category:Self-assembly]] | ||
Revision as of 11:17, 17 July 2017
Overview
Oritatami, folding in Japanese, is a model of molecular folding based on co-transcriptional folding. It is an extension of DNA origami, hence the name. It is intended to model the fact that in molecular folding, the folding process does not wait until the end of the production to begin. 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, an attraction rule between bead types, and a delay factor \(\delta\). If you want, you can also add a seed, which is a set of beads initially present. The beads will then get transcribed and attach to the beads around them that maximize the number of bonds by the attraction rule. The delay factor determines how many beads are made before making their final attachments.
Software
OritatamiSim - an Oritatami simulator
OritatamiShapeMaker - a program for generating Oritatami systems which self-assemble user-defined shapes
