Know When to Fold ’Em: Self-assembly of Shapes by Folding in Oritatami
| Autor: | Hadley Thomas, Shinnosuke Seki, Matthew J. Patitz, Jacob Hendricks, Erik D. Demaine, Meagan Olsen, Trent A. Rogers, Nicolas Schabanel |
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| Přispěvatelé: | Computer Science and Artificial Intelligence Laboratory [Cambridge] (CSAIL), Massachusetts Institute of Technology (MIT), University of Wisconsin Whitewater, Computer Science and Computer Engineering [Fayetteville] (CSCE), University of Arkansas [Fayetteville], Department of Computer Science and Engineering [Texas A&M University] (CSE), Texas A&M University [College Station], University of Central Arkansas (UCA), Modèles de calcul, Complexité, Combinatoire (MC2), Laboratoire de l'Informatique du Parallélisme (LIP), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS), Institut Rhône-Alpin des systèmes complexes (IXXI), École normale supérieure de Lyon (ENS de Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), University of Electro-Communications [Tokyo] (UEC), Colorado School of Mines, École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), École normale supérieure - Lyon (ENS Lyon)-Université Lumière - Lyon 2 (UL2)-Université Jean Moulin - Lyon 3 (UJML) |
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
FOS: Computer and information sciences
0301 basic medicine Physics Transcription rate 0102 computer and information sciences Fold (geology) 01 natural sciences 03 medical and health sciences Crystallography 030104 developmental biology 010201 computation theory & mathematics Computer Science - Data Structures and Algorithms Data Structures and Algorithms (cs.DS) [INFO]Computer Science [cs] Self-assembly [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] |
| Zdroj: | DNA 2018 DNA 2018, Oct 2018, Jinan, China. pp.19-36 arXiv Lecture Notes in Computer Science ISBN: 9783030000295 DNA |
| Popis: | An oritatami system (OS) is a theoretical model of self-assembly via co-transcriptional folding. It consists of a growing chain of beads which can form bonds with each other as they are transcribed. During the transcription process, the $\delta$ most recently produced beads dynamically fold so as to maximize the number of bonds formed, self-assemblying into a shape incrementally. The parameter $\delta$ is called the delay and is related to the transcription rate in nature. This article initiates the study of shape self-assembly using oritatami. A shape is a connected set of points in the triangular lattice. We first show that oritatami systems differ fundamentally from tile-assembly systems by exhibiting a family of infinite shapes that can be tile-assembled but cannot be folded by any OS. As it is NP-hard in general to determine whether there is an OS that folds into (self-assembles) a given finite shape, we explore the folding of upscaled versions of finite shapes. We show that any shape can be folded from a constant size seed, at any scale n >= 3, by an OS with delay 1. We also show that any shape can be folded at the smaller scale 2 by an OS with unbounded delay. This leads us to investigate the influence of delay and to prove that, for all {\delta} > 2, there are shapes that can be folded (at scale 1) with delay {\delta} but not with delay {\delta}' |
| Databáze: | OpenAIRE |
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