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arXiv 1607.08078cs.CCcs.ETq-bio.BM
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以指数级速度计算:使用DNA实现非确定性通用图灵机

Computing exponentially faster: Implementing a nondeterministic universal Turing machine using DNA

Andrew Currin, Konstantin Korovin, Maria Ababi, Katherine Roper, Douglas B. Kell, Philip J. Day, Ross D. King

摘要:

计算机科学的理论是基于通用图灵机(UTM):能够执行所有可能算法的抽象机器。现代数字计算机是UTM的物理体现。非确定性多项式(NP)时间复杂性问题是计算机科学中最重要的一类问题,解决这类问题的有效方法(即多项式P)具有深远的经济和社会意义。根据定义,非确定性UTM(NUTM)在P时间内解决NP完全问题。然而,NUTM以前被认为是物理上不可能构建的。这些字符串重写系统在计算上等价于UTM,并且自然是不确定的。在这里,我们描述了一个NUTM,实现了一个通用的Thue系统的物理设计。该设计利用DNA的复制能力,在P时间内执行指数数量的计算路径。每个Thue重写步骤都体现在使用聚合酶链式反应和定点诱变的新组合实施的DNA编辑中。我们证明,这种设计的作品使用计算建模和体外分子生物学实验。目前的设计有局限性,如有限的纠错。然而,它开辟了工程NUTM为基础的计算机能够在重要的实际问题上优于所有标准的计算机的前景。

英文摘要:

The theory of computer science is based around Universal Turing Machines (UTMs): abstract machines able to execute all possible algorithms. Modern digital computers are physical embodiments of UTMs. The nondeterministic polynomial (NP) time complexity class of problems is the most significant in computer science, and an efficient (i.e. polynomial P) way to solve such problems would be of profound economic and social importance. By definition nondeterministic UTMs (NUTMs) solve NP complete problems in P time. However, NUTMs have previously been believed to be physically impossible to construct. Thue string rewriting systems are computationally equivalent to UTMs, and are naturally nondeterministic. Here we describe the physical design for a NUTM that implements a universal Thue system. The design exploits the ability of DNA to replicate to execute an exponential number of computational paths in P time. Each Thue rewriting step is embodied in a DNA edit implemented using a novel combination of polymerase chain reactions and site-directed mutagenesis. We demonstrate that this design works using both computational modelling and in vitro molecular biology experimentation. The current design has limitations, such as restricted error-correction. However, it opens up the prospect of engineering NUTM based computers able to outperform all standard computers on important practical problems.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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