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 language | English |
|---|---|
| Pages (from-to) | 128-139 |
| Number of pages | 12 |
| Journal | Theoretical Computer Science |
| Volume | 785 |
| DOIs | |
| Publication status | Published - 2019 Sep 20 |
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All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)
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Ruleset optimization on isomorphic oritatami systems. / Han, Yo Sub; Kim, Hwee.
In: Theoretical Computer Science, Vol. 785, 20.09.2019, p. 128-139.Research output: Contribution to journal › Article
TY - JOUR
T1 - Ruleset optimization on isomorphic oritatami systems
AU - Han, Yo Sub
AU - Kim, Hwee
PY - 2019/9/20
Y1 - 2019/9/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85063721248&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85063721248&partnerID=8YFLogxK
U2 - 10.1016/j.tcs.2019.03.020
DO - 10.1016/j.tcs.2019.03.020
M3 - Article
AN - SCOPUS:85063721248
VL - 785
SP - 128
EP - 139
JO - Theoretical Computer Science
JF - Theoretical Computer Science
SN - 0304-3975
ER -