Abstract
RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene. The oritatami system (OS) is a computation model of this phenomenon, which lets its sequence of beads (abstract molecules) fold cotranscriptionally by the interactions between beads according to its ruleset. We study the problem of reducing the ruleset size while maintaining the terminal conformations geometrically same. We first prove the hardness of finding the smallest ruleset, and suggest two approaches that reduce the ruleset size efficiently.
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In the original paper, the seed was defined by a single term \(\sigma \).
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Han, YS., Kim, H. (2017). Ruleset Optimization on Isomorphic Oritatami Systems. In: Brijder, R., Qian, L. (eds) DNA Computing and Molecular Programming. DNA 2017. Lecture Notes in Computer Science(), vol 10467. Springer, Cham. https://doi.org/10.1007/978-3-319-66799-7_3
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DOI: https://doi.org/10.1007/978-3-319-66799-7_3
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