SHF: Small: DNA Circuits for Analog Computations

与布尔电路相比，模拟器件具有潜在的优势，特别是在执行数值计算方面，而且模拟电路通常更紧凑，需要的资源更少。这些进展在分子水平上得到了加强，那里的资源稀缺，紧凑的设计至关重要。PI建议将DNA计算从布尔扩展到模拟计算。模拟DNA电路可用于控制各种分子设备。这个项目的中心目标是(I)开发(设计、模拟和实验测试)两种模拟DNA电路的体系结构，(Ii)开发基于DNA的数模和模数转换方法，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。这项工作将涉及所有层次的学生：研究生、本科生和高中生。将特别招收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培训。在计算机科学、化学和基于DNA的纳米科学中。此外，本科生和高中生也有暑期实习机会。模拟DNA电路有许多重要的潜在应用，例如模拟控制设备，在这些设备中，实际值被感测，模拟计算提供控制输出。以前用于控制化学反应系统的设备，提供分子物种传感和响应，已被限制在有限状态控制；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包括实时模拟控制电路，以提供更复杂的控制，例如用于控制分子机器人的关节-S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，而模拟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。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，而不需要转换为布尔信号的阈值。第一个体系结构有3个门：加法、减法和乘法。用这些门构成的模拟电路可以计算多项式、近似求逆和除法。提出的第二种体系结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电路之间能够进行通信。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电路在化学反应系统控制中的应用的小规模演示：传感分子的输入浓度和控制分子浓度的输出。

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.