Rule set design problems for oritatami systems

DOI10.1016/J.TCS.2016.09.010MaRDI QIDQ529023zbMATH OpenOpenAlexFDO

Authors Makoto Ota, Shinnosuke Seki

Publication date 18 May 2017

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2016.09.010

zbMATH Keywords

algorithmic self-assemblytime complexityco-transcriptional foldinglinear-time 2SAT solveroritatami system

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Analysis of algorithms and problem complexity (68Q25) Modes of computation (nondeterministic, parallel, interactive, probabilistic, etc.) (68Q10) Computer graphics; computational geometry (digital and algorithmic aspects) (68U05)

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Cites work

• scientific article; zbMATH DE number 3639144 (Why is no real title available?)
• scientific article; zbMATH DE number 941396 (Why is no real title available?)
• A linear-time algorithm for testing the truth of certain quantified Boolean formulas
• Control of Boolean networks: hardness results and algorithms for tree structured networks
• Graph theory
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence
• P-completeness of Cellular Automaton Rule 110
• Programming biomolecules that fold greedily during transcription
• The complexity of satisfiability problems

Cited in

(17)

• Proving the Turing universality of oritatami co-transcriptional folding
• Nondeterministic seedless oritatami systems and hardness of testing their equivalence
• Design principles for single-stranded RNA origami structures
• Know when to fold 'em: self-assembly of shapes by folding in oritatami
• Transcript design problem of oritatami systems
• Ruleset optimization on isomorphic oritatami systems
• Programming biomolecules that fold greedily during transcription
• Self-attraction removal from oritatami systems
• Algorithmic design of cotranscriptionally folding 2D RNA origami structures
• Ruleset optimization on isomorphic oritatami systems
• Impossibility of strict assembly of infinite fractals by oritatami
• Self-attraction removal from oritatami systems
• Counting infinitely by oritatami co-transcriptional folding
• Counting infinitely by oritatami co-transcriptional folding
• Towards composable computations by RNA co-transcriptional folding: a proof-of-concept demonstration of nested loops in oritatami
• Transcript design problem of oritatami systems
• Programmable single-stranded architectures for computing

Describes a project that uses

Uses Software

• ViennaRNA

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