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Self-attraction Removal from Oritatami Systems

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Descriptional Complexity of Formal Systems (DCFS 2017)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10316))

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Abstract

RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized (transcribed). Oritatami is a computational model of this phenomenon, which lets its transcript, a sequence of beads (abstract molecules) fold cotranscriptionally via interactions between beads according to its ruleset. In this paper, we study the problem of removing self-attractions, which lets a bead interact with another bead of the same kind, from a given oritatami system without changing its behavior. We provide an algorithm for that with overhead linear in the delay parameter, which should be considerably smaller than the length of its transcript. We also show that this overhead is tight.

Y.-S. Han—Supported by International Cooperation Program (2017K2A9A2A08000270) and Basic Science Research Program (2015R1D1A1A01060097) by NRF of Korea.

Kim was supported by NRF (National Research Foundation of Korea) Grant funded by the Korean Government (NRF-2013-Global Ph.D. Fellowship Program).

T.A. Rogers—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.

S. Seki—In part supported by JST Program to Disseminate Tenure Tracking System No. 6F36 and JSPS KAKENHI Grant-in-Aid for Young Scientists (A) No. 16H05854.

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Author information

Authors and Affiliations

  1. Department of Computer Science, Yonsei University, 50 Yonsei-Ro, Seodaemun-Gu, Seoul, 03722, Republic of Korea

    Yo-Sub Han & Hwee Kim

  2. Department of Computer Sceince and Computer Engineering, University of Arkansas, Fayetteville, AR, 72701, USA

    Trent A. Rogers

  3. Department of Computer and Network Engineering, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, 1828585, Japan

    Shinnosuke Seki

Authors
  1. Yo-Sub Han
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  2. Hwee Kim
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  3. Trent A. Rogers
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  4. Shinnosuke Seki
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Correspondence to Shinnosuke Seki .

Editor information

Editors and Affiliations

  1. Università degli Studi di Milano, Milan, Italy

    Giovanni Pighizzini

  2. University of Prince Edward Island, Charlottetown, Prince Edward Island, Canada

    Cezar Câmpeanu

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Han, YS., Kim, H., Rogers, T.A., Seki, S. (2017). Self-attraction Removal from Oritatami Systems. In: Pighizzini, G., Câmpeanu, C. (eds) Descriptional Complexity of Formal Systems. DCFS 2017. Lecture Notes in Computer Science(), vol 10316. Springer, Cham. https://doi.org/10.1007/978-3-319-60252-3_13

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  • DOI: https://doi.org/10.1007/978-3-319-60252-3_13

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-319-60252-3

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