Ruleset optimization on isomorphic oritatami systems

Yo-Sub Han, Hwee Kim

Research output: Contribution to journalArticle

Abstract

We study an optimization problem of a computational folding model, proving its hardness and proposing heuristic algorithms. RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene. An oritatami model (OM) is a computational model of this phenomenon that 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 keeping the terminal conformations geometrically the same. We first prove the hardness of finding the smallest ruleset, and then suggest two approaches that reduce the ruleset size efficiently.

Original languageEnglish
JournalTheoretical Computer Science
DOIs
Publication statusPublished - 2019 Jan 1

Fingerprint

Folding
Hardness
Fold
Isomorphic
RNA
Optimization
Conformation
Heuristic algorithm
Computational Model
Molecules
Heuristic algorithms
Optimization Problem
Gene
Conformations
Genes
Interaction
Model

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

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Ruleset optimization on isomorphic oritatami systems. / Han, Yo-Sub; Kim, Hwee.

In: Theoretical Computer Science, 01.01.2019.

Research output: Contribution to journalArticle

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