SHF: Small: DNA Circuits for Analog Computations

SHF：小型：用于模拟计算的 DNA 电路

• 批准号: 1617791
• 负责人: John Reif
• 金额: $ 30.8万
• 依托单位: Duke University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2019-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1617791&HistoricalAwards=false
• 关键词: SHF; Small; DNA; Circuits; Analog

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.

模拟设备比布尔电路具有潜在的优势，尤其是用于执行数值计算，并且模拟电路通常更紧凑，需要更少的资源。这些进步在分子尺度上得到了增强，其中资源很少，紧凑的设计至关重要。 PI提出将DNA计算从布尔值扩展到模拟计算。模拟DNA电路可用于控制各种分子设备。该项目的核心目标是（i）开发（设计，模拟和实验测试）两个用于模拟DNA电路的架构，（ii）开发用于数字到数字到分析和类似物数字转换的基于DNA的方法，以允许混合模糊DNA DNA电路，以及（III），以及（iii），以提供类似于DNA的应用程序：涉及类似于DNA的学生。本科生和高中生。女性和少数族裔学生将特别招募。从事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的纳米科学领域。此外，还为大学生​​和高中生提供暑期实习机会。模拟DNA电路具有许多重要的潜在应用，例如模拟控制设备，其中感知实际值，模拟计算提供了控制输出。用于控制化学反应系统的先前设备可以提供分子种类感应和反应的设备，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的分子机器人技术使设备可以自主操作（例如，在纳米结构上行走），但已限于有限状态控制，并且模拟DNA电路将使分子机器人能够包括实时模拟控制电路，以提供更复杂的控制控制，例如。用于控制分子机器人肢体的铰接关节。许多动态学习的系统（例如，神经网络和概率推断）需要模拟计算，并且可以将模拟DNA电路用于对神经网络的后传播计算和贝叶斯概率推理系统的贝叶斯推理计算。在这两者中，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，而无需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。这些门构建的模拟电路可以计算多项式以及近似逆和分裂。第二个提出的体系结构提供了一种基于DNA的新方法，以使用基于多个基于DNA的自催化反应系统一起工作，以计算SQRT（X），LN（X）和EXP（X）等分析功能。该项目还引入了DNA类似物对数字（A/D）和数字到Analog（D/A）转换器，以实现模拟和数字DNA电路之间的通信。该项目包括两种体系结构的全尺度设计，模拟和实验演示，混合模拟数字DNA电路的演示，以及用于控制化学反应系统的模拟DNA电路的应用：传感输入分子浓度和分子浓度输出的感应输入。