{"title":"有向非合作瓦片组装系统有限终端组装规模的线性约束","authors":"Sergiu Ivanov, Damien Regnault","doi":"arxiv-2405.18630","DOIUrl":null,"url":null,"abstract":"The abstract tile assembly model (aTam) is a model of DNA self-assembly. Most\nof the studies focus on cooperative aTam where a form of synchronization\nbetween the tiles is possible. Simulating Turing machines is achievable in this\ncontext. Few results and constructions are known for the non-cooperative case\n(a variant of Wang tilings where assemblies do not need to cover the whole\nplane and some mismatches may occur). Introduced by P.E. Meunier and D. Regnault, efficient paths are a non-trivial\nconstruction for non-cooperative aTam. These paths of width nlog(n) are\ndesigned with n different tile types. Assembling them relies heavily on a form\nof ``non-determinism''. Indeed, the set of tiles may produced different finite\nterminal assemblies but they all contain the same efficient path. Directed\nnon-cooperative aTam does not allow this non-determinism as only one assembly\nmay be produced by a tile assembly system. This variant of aTam is the only one\nwho was shown to be decidable. In this paper, we show that if the terminal assembly of a directed\nnon-cooperative tile assembly system is finite then its width and length are of\nlinear size according to the size of the tile assembly system. This result\nimplies that the construction of efficient paths cannot be generalized to the\ndirected case and that some computation must rely on a competition between\ndifferent paths. It also implies that the construction of a square of width n\nusing 2n-1 tiles types is asymptotically optimal. Moreover, we hope that the\ntechniques introduced here will lead to a better comprehension of the\nnon-directed case.","PeriodicalId":501024,"journal":{"name":"arXiv - CS - Computational Complexity","volume":"53 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A linear bound for the size of the finite terminal assembly of a directed non-cooperative tile assembly system\",\"authors\":\"Sergiu Ivanov, Damien Regnault\",\"doi\":\"arxiv-2405.18630\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The abstract tile assembly model (aTam) is a model of DNA self-assembly. Most\\nof the studies focus on cooperative aTam where a form of synchronization\\nbetween the tiles is possible. Simulating Turing machines is achievable in this\\ncontext. 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引用次数: 0
摘要
抽象瓦片组装模型(aTam)是一种 DNA 自组装模型。大多数研究都集中在合作型 aTam 上,在这种模型中,瓦片之间可能存在某种形式的同步。在这种情况下,模拟图灵机是可以实现的。对于非合作的情况(Wang tilings 的一种变体,在这种情况下,组装不需要覆盖整个平面,也可能出现一些错配),已知的结果和构造很少。由 P.E. Meunier 和 D. Regnault 提出的高效路径是非合作平面的一种非难构造。这些宽度为 nlog(n) 的路径由 n 种不同的瓦片类型设计而成。组装它们在很大程度上依赖于一种 "非确定性"。事实上,瓦片集合可能产生不同的有限确定性组合,但它们都包含相同的有效路径。有向非合作 aTam 不允许这种非确定性,因为瓦片装配系统只能产生一个装配体。这种 aTam 变体是唯一被证明是可解的。在本文中,我们证明了如果有向非合作瓦片装配系统的终端装配是有限的,那么它的宽度和长度与瓦片装配系统的大小成线性关系。这一结果表明,高效路径的构造不能推广到有向情况,某些计算必须依赖于不同路径之间的竞争。这也意味着,用 2n-1 种瓦片构建宽度为 n 的正方形是渐进最优的。此外,我们希望这里介绍的技术能让我们更好地理解非定向情况。
A linear bound for the size of the finite terminal assembly of a directed non-cooperative tile assembly system
The abstract tile assembly model (aTam) is a model of DNA self-assembly. Most
of the studies focus on cooperative aTam where a form of synchronization
between the tiles is possible. Simulating Turing machines is achievable in this
context. Few results and constructions are known for the non-cooperative case
(a variant of Wang tilings where assemblies do not need to cover the whole
plane and some mismatches may occur). Introduced by P.E. Meunier and D. Regnault, efficient paths are a non-trivial
construction for non-cooperative aTam. These paths of width nlog(n) are
designed with n different tile types. Assembling them relies heavily on a form
of ``non-determinism''. Indeed, the set of tiles may produced different finite
terminal assemblies but they all contain the same efficient path. Directed
non-cooperative aTam does not allow this non-determinism as only one assembly
may be produced by a tile assembly system. This variant of aTam is the only one
who was shown to be decidable. In this paper, we show that if the terminal assembly of a directed
non-cooperative tile assembly system is finite then its width and length are of
linear size according to the size of the tile assembly system. This result
implies that the construction of efficient paths cannot be generalized to the
directed case and that some computation must rely on a competition between
different paths. It also implies that the construction of a square of width n
using 2n-1 tiles types is asymptotically optimal. Moreover, we hope that the
techniques introduced here will lead to a better comprehension of the
non-directed case.