通过二维和勉强三维自组装之间的折叠,证明温度为 1 时新的定向瓦片复杂性下限

IF 1.7 4区 计算机科学 Q3 COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE
David Furcy, Scott M. Summers, Hailey Vadnais
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引用次数: 0

摘要

我们研究的问题是,在 Winfree 的抽象瓦片组装模型(aTAM)中,如何确定能唯一自组装成给定目标形状的最小瓦片集的大小,这是一个优雅的 DNA 瓦片自组装理论模型。这个问题也被称为 "定向瓦片复杂性 "问题。在最小结合强度阈值(温度)设为 1 的 aTAM 变体中,我们证明了与定向瓦片复杂性问题相关的两个主要结果。对于我们的第一个结果,自组装发生在一个 "勉强三维 "的环境中,在这个环境中,自组装单元立方体被允许放置在 \(z=0\) 和 \(z=1\) 平面上。弗西、萨默斯和威瑟斯(DNA 2021)最近也是在这种情况下证明了在温度为1的情况下,有向瓦片复杂度的下限和上限,分别是(Omega \left( N^{\frac{1}{k}}right) \)和(O/left( N^{\frac{1}{k-1}}+\log N\right) \)、分别成立,而后者在(k=2)时并不成立。我们的第一个结果通过证明在温度为1的情况下,一个几乎是三维的(2乘以N)矩形的有向瓦片复杂度的渐近紧约束((\Theta (N)\)),缩小了(k=2)的这一差距。我们的证明使用了一个新颖的过程,通过这个过程,一个刚体三维装配序列被 "展开 "为一个等价的二维装配序列。对于我们的第二个结果,我们使用了 Furcy、Summers 和 Withers 的上述下限,以及一个与我们的三维到二维展开过程在精神上互补的新过程、通过这个过程,我们把一个二维瓦片组合 "折叠 "成一个等价的勉强算得上三维的组合,从而证明了一个温度为1的二维(k乘以N)矩形的有向瓦片复杂度的新下界(\Omega \left( \frac{N^{\frac{2}{k + (k bmod 2)}}}{k} )。\right) \)。对于固定的 k,我们的新边界比 \(k < 的一般偶数值有近乎二次方的改进,并且相匹配;\在温度为1的情况下,Furcy、Summers和Wendlandt(DNA 2019)提出的有向瓦片复杂度下限为(Omega \left( N^{\frac{1}{k}}\right) \)。虽然我们的这两个结果都代表了对之前相应技术水平结果的改进,但通过新颖的例子,我们可以推理出瓷砖自组装发生在二维(just-barely 3D ),就好像它发生在just-barely 3D (2D)。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Proving new directed tile complexity lower bounds at temperature 1 by folding between 2D and just-barely 3D self-assembly

Proving new directed tile complexity lower bounds at temperature 1 by folding between 2D and just-barely 3D self-assembly

We study the problem of determining the size of the smallest tile set that uniquely self-assembles into a given target shape in Winfree’s abstract Tile Assembly Model (aTAM), an elegant theoretical model of DNA tile self-assembly. This problem is also known as the “directed tile complexity” problem. We prove two main results related to the directed tile complexity problem within a variant of the aTAM in which the minimum binding strength threshold (temperature) is set to 1. For our first result, self-assembly happens in a “just-barely 3D” setting, where self-assembling unit cubes are allowed to be placed in the \(z=0\) and \(z=1\) planes. This is the same setting in which Furcy, Summers and Withers (DNA 2021) recently proved lower and upper bounds on the directed tile complexity of a just-barely 3D \(k \times N\) rectangle at temperature 1 of \(\Omega \left( N^{\frac{1}{k}}\right) \) and \(O\left( N^{\frac{1}{k-1}}+\log N\right) \), respectively, the latter of which does not hold for \(k=2\). Our first result closes this gap for \(k=2\) by proving an asymptotically tight bound of \(\Theta (N)\) on the directed tile complexity of a just-barely 3D \(2 \times N\) rectangle at temperature 1. Our proof uses a novel process by which a just-barely 3D assembly sequence is “unfolded” to an equivalent 2D assembly sequence. For our second result, we use the aforementioned lower bound by Furcy, Summers and Withers and a novel process that is complementary-in-spirit to our 3D-to-2D unfolding process, by which we “fold” a 2D tile assembly to an equivalent just-barely 3D assembly to prove a new lower bound on the directed tile complexity of a 2D \(k \times N\) rectangle at temperature 1 of \(\Omega \left( \frac{N^{\frac{2}{k + (k \bmod 2)}}}{k} \right) \). For fixed k, our new bound gives a nearly quadratic improvement over, and matches for general even values of \(k < \frac{\log N}{\log \log N - \log \log \log N}\) the state of the art lower bound on the directed tile complexity of a \(k \times N\) rectangle at temperature 1 by Furcy, Summers and Wendlandt (DNA 2019) of \(\Omega \left( N^{\frac{1}{k}}\right) \). While both of our results represent improvements over previous corresponding state of the art results, the proofs thereof are facilitated by novel examples of reasoning about tile self-assembly happening in 2D (just-barely 3D) as though it is happening in just-barely 3D (2D).

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来源期刊
Natural Computing
Natural Computing Computer Science-Computer Science Applications
CiteScore
4.40
自引率
4.80%
发文量
49
审稿时长
3 months
期刊介绍: The journal is soliciting papers on all aspects of natural computing. Because of the interdisciplinary character of the journal a special effort will be made to solicit survey, review, and tutorial papers which would make research trends in a given subarea more accessible to the broad audience of the journal.
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