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 |
Bibliographical note
Funding Information:Han was supported by the International Cooperation Program (NRF-2017K2A9A2A08000270) and the Basic Science Research Program (NRF-2018R1D1A1A09084107). Kim was supported in part by the NIH grant R01 GM109459 and NSF grant DMS-1800443.☆ Han was supported by the International Cooperation Program ( NRF-2017K2A9A2A08000270) and the Basic Science Research Program ( NRF-2018R1D1A1A09084107). Kim was supported in part by the NIH grant R01 GM109459 and NSF grant DMS-1800443.
Funding Information:
Han was supported by the International Cooperation Program (NRF-2017K2A9A2A08000270) and the Basic Science Research Program (NRF-2018R1D1A1A09084107). Kim was supported in part by the NIH grant R01 GM109459 and NSF grant DMS-1800443.
Publisher Copyright:
© 2019 Elsevier B.V.
All Science Journal Classification (ASJC) codes
- Theoretical Computer Science
- Computer Science(all)