Affiliations: [a] Department of Computer Science and Computer Engineering, University of Arkansas, USA. tar003@uark.edu | [b] Department of Computer and Network Engineering, The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 1828585, Japan. s.seki@uec.ac.jp
Correspondence:
[†]
Address for correspondence: Department of Computer Science and Computer Engineering, University of Arkansas, USA
Note: [*] This author’s research was supported by the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE-1450079, and National Science Foundation grants CAREER-1553166 and CCF-1422152.
Note: [‡] His work is supported in part by JST Program to Disseminate Tenure Tracking System, MEXT, Japan, No. 6F36 and by JSPS Grant-in-Aid for Young Scientists (A) No. 16H05854.
Abstract: RNA sequences start folding immediately as they are synthesized by RNA polymerase (cotranscriptional folding). The oritatami system (OS) is a novel mathematical model to study computational aspects of cotranscriptional folding. In this paper, we first provide a survey throughout existing research topics and results on oritatami systems and offer research directions of significance. Simulation of an oritatami system in a different ratio (delay) of transcription speed to the speed of folding is one of them. We will introduce a simple notion of simulation, and prove that there is an OS of delay δ that cannot be simulated by any oritatami system at larger delay.
