SHF: Small: DNA Circuits for Analog Computations

模拟电路比布尔电路有潜在的优势，特别是在执行数值计算时，模拟电路通常更紧凑，需要更少的资源。这些进步在资源稀缺和紧凑设计至关重要的分子尺度上得到加强。PI提出将DNA计算从布尔计算扩展到模拟计算。模拟DNA电路可用于控制各种分子器件。该项目的中心目标是：(i)开发（设计、模拟和实验测试）模拟DNA电路的两种架构，（ii）开发基于DNA的数字到模拟和模数转换方法，以允许混合模拟-数字DNA电路，以及（iii）提供模拟DNA电路的应用演示。这项工作将涉及各个层次的学生：研究生、本科生和高中生。尤其是女性和少数民族学生。参与该项目的学生将在杜克大学接受计算机科学、化学和基于dna的纳米科学方面的培训。此外，还有本科生和高中生暑期实习的机会。模拟DNA电路有许多重要的潜在应用，如模拟控制设备，其中真实值被感知和模拟计算提供控制输出。先前用于控制化学反应系统的装置，提供分子物种传感和响应，仅限于有限状态控制；模拟DNA电路将允许更复杂的模拟处理和控制。基于DNA的分子机器人技术已经允许设备自主操作（例如，在纳米结构上行走），但仅限于有限状态控制，模拟DNA电路将允许分子机器人技术包括实时模拟控制电路，以提供更复杂的控制，例如控制分子机器人的铰接关节。肢体。许多动态学习的系统（如神经网络和概率推理）需要模拟计算，模拟DNA电路可以用于神经网络的反向传播计算和概率推理系统的贝叶斯推理计算。该项目介绍了两种用于分子尺度模拟计算的体系结构。在这两种方法中，模拟门的输入和输出分别由输入和输出链的相对浓度直接编码，不需要阈值来转换为布尔信号。第一种架构有3个门：加法、减法和乘法。由这些门构成的模拟电路可以计算多项式，也可以计算近似逆和除法。第二个提出的架构提供了一种新的基于dna的方法来计算分析函数，如sqrt(x), ln(x)和exp(x)，使用多个基于dna的自催化反应系统协同工作。该项目还引入了DNA模数（A/D）和数模（D/A）转换器，使模拟和数字DNA电路之间的通信成为可能。该项目包括两种架构的全尺寸设计、模拟和实验演示，模拟-数字混合DNA电路的演示，以及模拟DNA电路用于控制化学反应系统的应用的小规模演示：感应分子输入浓度和控制分子浓度输出。

Analog devices have potential advantages over Boolean circuits, particularly for performing numerical computations, and analog circuits are often much more compact and require less resources. These advances are enhanced at molecular scales, where resources are scarce and compact designs are crucial. PI proposes extension of DNA computation from Boolean to analog computation. The analog DNA circuits can be used to control a wide variety of molecular devices. The central goals of this project are (i) to develop (design, simulate, and experimentally test) two architectures for analog DNA circuits, (ii) develop DNA-based methods for digital-to-analog and analog-to-digital conversions to allow hybrid analog-digital DNA circuits, and (iii) to provide demonstrations of applications of analog DNA circuits.The work will involve students at all levels: the graduates students, undergraduates, and high school students. Females and minority students will especially be recruited. Students working on this project will receive training at Duke Univ. in computer science, chemistry, and DNA-based nanoscience. In addition, there are also opportunities for summer internships for undergraduates and high school students. Analog DNA circuits have many important potential applications such as analog control devices, where real values are sensed and analog computations provide controlling output. Prior devices for control of chemical reactions systems that provide for molecular species sensing and response have been limited to finite-state control; analog DNA circuits will allow much more sophisticated analog processing and control. DNA-based molecular robotics have allowed devices to operate autonomously (e.g., to walk on a nanostructure) but have been limited to finite-state control, and analog DNA circuits will allow molecular robotics to include real-time analog control circuits to provide much more sophisticated control, e.g. for control articulated joints of a molecular robot?s limb. Many systems that dynamically learn (e.g., neural networks and probabilistic inference) require analog computation, and analog DNA circuits can be used for back-propagation computation of neural nets and Bayesian inference computation of probabilistic inference systems.The project introduces two architectures for molecular-scale analog computation. In both, the input and outputs of analog gates are directly encoded by relative concentrations of input and output strands respectively, without requiring thresholds for converting to Boolean signals. The 1st architecture has 3 gates: addition, subtraction, and multiplication. Analog circuits constructed from these gates can compute polynomials as well as approximate inverse, and division. The 2nd proposed architecture provides a novel DNA-based method to compute analytic functions such as sqrt(x), ln(x), and exp(x) using multiple DNA-based autocatalytic reaction systems working together. The project also introduces DNA analog-to-digital (A/D) and digital-to-analog (D/A) converters that enable the communication between analog and digital DNA circuits. The project includes full-scale designs, simulations, and experimental demonstrations of the two architectures, demonstrations of hybrid analog-digital DNA circuits, and a small-scale demonstration of an application of analog DNA circuits for control of a chemical reaction system: sensing input concentrations of molecules and controlling output of concentrations of molecules.