Song Tianqi, Garg Sudhanshu, Mokhtar Reem, Bui Hieu, Reif John
Department of Computer Science, Duke University , Durham, North Carolina 27708, United States.
ACS Synth Biol. 2016 Aug 19;5(8):898-912. doi: 10.1021/acssynbio.6b00144. Epub 2016 Jul 22.
DNA circuits have been widely used to develop biological computing devices because of their high programmability and versatility. Here, we propose an architecture for the systematic construction of DNA circuits for analog computation based on DNA strand displacement. The elementary gates in our architecture include addition, subtraction, and multiplication gates. The input and output of these gates are analog, which means that they are directly represented by the concentrations of the input and output DNA strands, respectively, without requiring a threshold for converting to Boolean signals. We provide detailed domain designs and kinetic simulations of the gates to demonstrate their expected performance. On the basis of these gates, we describe how DNA circuits to compute polynomial functions of inputs can be built. Using Taylor Series and Newton Iteration methods, functions beyond the scope of polynomials can also be computed by DNA circuits built upon our architecture.
由于其高度的可编程性和通用性，DNA电路已被广泛用于开发生物计算设备。在此，我们提出了一种基于DNA链置换的用于模拟计算的DNA电路系统构建架构。我们架构中的基本门包括加法门、减法门和乘法门。这些门的输入和输出都是模拟的，这意味着它们分别直接由输入和输出DNA链的浓度表示，无需转换为布尔信号的阈值。我们提供了门的详细结构设计和动力学模拟，以证明其预期性能。基于这些门，我们描述了如何构建用于计算输入多项式函数的DNA电路。使用泰勒级数和牛顿迭代方法，超出多项式范围的函数也可以通过基于我们架构构建的DNA电路来计算。
