DNA walker circuits: computational potential, design, and verification
DNA walker circuits: computational potential, design, and verification
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DOI：
10.1007/s11047-014-9426-9
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发表时间：
2015-06-01
影响因子：
2.1
通讯作者：
Turberfield, Andrew J.
中科院分区：
文献类型：
--
作者：
Dannenberg, Frits;Kwiatkowska, Marta;Turberfield, Andrew J.
与传统的硅计算机不同，DNA计算机与化学和生物系统都有天然的接口。这些可以用于许多应用，包括纳米级物质的精确排列和智能生物传感器的创建。像硅电路一样，DNA链置换系统（DSD）可以评估非平凡的功能。然而，这些系统可能很慢并且容易出错。有人建议，局部杂交反应可以克服这些挑战中的一些。局部反应发生在DNA“步行者”系统中，该系统最近被证明能够导航拴在折纸瓦片上的可编程轨道。我们调查这些系统的计算潜力，用于评估布尔函数和形成组合电路。我们发现，系统的多个步行者有严重限制的潜力，并行电路评估。与DSD一样，DNA步行者也容易出错。我们开发了一个离散的随机模型的DNA步行者“电路”的实验数据的基础上，并证明了使用概率模型检测技术来分析其可靠性，性能和正确性的优点。这种分析有助于设计可靠和有效的DNA步行者电路。
Unlike their traditional, silicon counterparts, DNA computers have natural interfaces with both chemical and biological systems. These can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, DNA strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in DNA 'walker' systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions and forming composable circuits. We find that systems of multiple walkers have severely limited potential for parallel circuit evaluation. DNA walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of DNA walker 'circuits' based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness. This analysis aids in the design of reliable and efficient DNA walker circuits.