Oritatami: A Computational Model for Molecular Co-Transcriptional Folding
AbstractWe introduce and study the computational power of Oritatami, a theoretical model that explores greedy molecular folding, whereby a molecular strand begins to fold before its production is complete. This model is inspired by our recent experimental work demonstrating the construction of shapes at the nanoscale from RNA, where strands of RNA fold into programmable shapes during their transcription from an engineered sequence of synthetic DNA. In the model of Oritatami, we explore the process of folding a single-strand bit by bit in such a way that the final fold emerges as a space-time diagram of computation. One major requirement in order to compute within this model is the ability to program a single sequence to fold into different shapes dependent on the state of the surrounding inputs. Another challenge is to embed all of the computing components within a contiguous strand, and in such a way that different fold patterns of the same strand perform different functions of computation. Here, we introduce general design techniques to solve these challenges in the Oritatami model. Our main result in this direction is the demonstration of a periodic Oritatami system that folds upon itself algorithmically into a prescribed set of shapes, depending on its current local environment, and whose final folding displays the sequence of binary integers from 0 to
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Geary, C.; Meunier, P.-É.; Schabanel, N.; Seki, S. Oritatami: A Computational Model for Molecular Co-Transcriptional Folding. Int. J. Mol. Sci. 2019, 20, 2259.
Geary C, Meunier P-É, Schabanel N, Seki S. Oritatami: A Computational Model for Molecular Co-Transcriptional Folding. International Journal of Molecular Sciences. 2019; 20(9):2259.Chicago/Turabian Style
Geary, Cody; Meunier, Pierre-Étienne; Schabanel, Nicolas; Seki, Shinnosuke. 2019. "Oritatami: A Computational Model for Molecular Co-Transcriptional Folding." Int. J. Mol. Sci. 20, no. 9: 2259.
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