SHF: Small: Advanced Digital Signal Processing with DNA

SHF：小型：采用 DNA 的先进数字信号处理

• 批准号: 1423407
• 负责人: Keshab Parhi
• 金额: $ 40万
• 依托单位: University of Minnesota-Twin Cities
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2017-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1423407&HistoricalAwards=false
• 关键词: SHF; Small; Advanced; Digital; Signal

This project will develop techniques for implementing computation in general, and advanced digital signal processing operations in particular, using molecular reactions in general, and DNA-based reactions in particular. Just as electronic systems implement computation in terms of voltage (energy per unit charge), one can conceive of molecular systems that compute in terms of chemical concentrations (molecules per unit volume). This proposal will explore techniques for implementing a variety of computational constructs such as logic, memory, arithmetic, and signal processing. A technique called DNA strand displacement is the target experimental chassis. The impetus for this research is not computation per se. Molecular computation will never compete with conventional computers made of silicon integrated circuits for tasks such as number crunching. Chemical systems are inherently slow and messy, taking minutes or even hours to finish, and producing fragmented results. Rather, the goal is to create "embedded controllers" - viruses and bacteria that are engineered to perform useful molecular computation in situ where it is needed, for instance in drug delivery and biochemical sensing applications.The digital circuit design community has unique expertise that can be brought to bear on the challenging design problems encountered in synthetic biology. Applications in biology, in turn, offer a wealth of interesting problems in algorithmic development. With its cross-disciplinary emphasis, this project will bring new perspectives to both fields. If successful, the proposed research will transform disciplines such as genetic engineering of drug-delivery systems. Currently, a costly and ineffective ad-hoc approach prevails. With robust techniques for implementing operations such as digital signal processing, much more effective systems will be developed. An important goal of the project is to communicate the impetus for interdisciplinary research to a wide audience. Building upon current research efforts that include female students, underrepresented students will be recruited into the project.This proposal will build on the success of prior work, exploring the implementation of complex signal processing functions for both discrete-time and digital signal processing applications with DNA. The project will develop synthesis techniques for molecular implementations of signal processing functions such as finite-impulse response (FIR) and infinite impulse response (IIR) digital filters, fast Fourier transforms (FFT), and power spectral density (PSD) computations. A major component of this project is to study how to implement analog-to-digital (A/D) and digital-to-analog (D/A) conversion with molecular reactions. A distinction will be made between discrete-time signal processing and digital signal processing. While signals are sampled periodically in both systems, the signal is represented as an analog value in the former while the signal is quantized to a digital value in the latter. Each has its advantages. Discrete-time signal processing systems are similar to sampled data systems and require lower molecular concentrations; however, the resolution cannot be precisely controlled. Digital systems are more precise, but require higher molecular concentrations.Specific research thrusts are as follows. Firstly, a complete digital signal processing system will be demonstrated. Such a system will contain A/D and D/A converters and will implement a full repertoire of complex operations. Secondly, the project will develop faster implementations of both discrete-time and digital signal processing systems. The main bottleneck in prior discrete-time signal processing implementations has been speed. In contrast to electronic systems, where the speed is limited by changes in electric charge, the speed in molecular systems is limited by changes in molecular concentrations, which are inherently slow. The project will develop new scheduling approaches where multiple computations are mapped to different phases of transfer. The computation will be synchronous, with molecular transfers synchronized by a "clock", implemented through sustained chemical oscillations. The new scheduling approaches will allow computation of parallel outputs without increasing the number of delay transfer reactions. Reducing currently achievable sample periods from 40-80 hours to 4-8 hours will enable experimental demonstration of some example signal processing functions using DNA. Finally, the project will investigate tradeoffs in discrete-time and digital implementations of signal processing functions with respect to speed, accuracy, and robustness. Detailed studies of the system properties and behaviors will be performed, e.g., how the resolution correlates with changing molecular concentrations and how robust the designs are to parametric variations.

该项目将开发用于实现一般计算、特别是高级数字信号处理操作的技术，一般使用分子反应，特别是基于 DNA 的反应。 正如电子系统根据电压（每单位电荷的能量）进行计算一样，我们可以设想根据化学浓度（每单位体积的分子）进行计算的分子系统。该提案将探索实现各种计算结构的技术，例如逻辑、内存、算术和信号处理。一种称为 DNA 链置换的技术是目标实验底盘。这项研究的动力并不是计算本身。在数字运算等任务上，分子计算永远无法与由硅集成电路制成的传统计算机竞争。化学系统本质上是缓慢且混乱的，需要几分钟甚至几小时才能完成，并产生支离破碎的结果。相反，我们的目标是创建“嵌入式控制器”——病毒和细菌，它们被设计为在需要的地方进行有用的分子计算，例如在药物输送和生化传感应用中。数字电路设计社区拥有独特的专业知识，可以用来解决合成生物学中遇到的具有挑战性的设计问题。反过来，生物学中的应用为算法开发提供了大量有趣的问题。由于其跨学科的重点，该项目将为这两个领域带来新的视角。 如果成功，拟议的研究将改变药物输送系统基因工程等学科。目前，普遍采用成本高昂且低效的临时方法。借助用于实现数字信号处理等操作的强大技术，将开发出更有效的系统。该项目的一个重要目标是向广大受众传达跨学科研究的动力。在当前包括女学生在内的研究工作的基础上，该项目将招募代表性不足的学生。该提案将建立在先前工作的成功基础上，探索利用 DNA 实现离散时间和数字信号处理应用的复杂信号处理功能。 该项目将开发用于分子实现信号处理功能的合成技术，例如有限脉冲响应（FIR）和无限脉冲响应（IIR）数字滤波器、快速傅立叶变换（FFT）和功率谱密度（PSD）计算。 该项目的一个主要组成部分是研究如何通过分子反应实现模数（A/D）和数模（D/A）转换。离散时间信号处理和数字信号处理之间存在区别。虽然在两个系统中都会定期对信号进行采样，但在前者中信号被表示为模拟值，而在后者中信号被量化为数字值。每个都有其优点。离散时间信号处理系统与采样数据系统类似，需要较低的分子浓度；然而，分辨率无法精确控制。数字系统更精确，但需要更高的分子浓度。具体研究重点如下。首先，将演示一个完整的数字信号处理系统。这样的系统将包含 A/D 和 D/A 转换器，并将执行完整的复杂操作。其次，该项目将开发更快的离散时间和数字信号处理系统的实现。先前离散时间信号处理实现的主要瓶颈是速度。电子系统的速度受到电荷变化的限制，而分子系统的速度则受到分子浓度变化的限制，分子浓度的变化本身就很慢。该项目将开发新的调度方法，将多个计算映射到传输的不同阶段。计算将是同步的，分子转移由“时钟”同步，通过持续的化学振荡实现。新的调度方法将允许计算并行输出，而无需增加延迟传输反应的数量。将目前可实现的采样周期从 40-80 小时减少到 4-8 小时，将使使用 DNA 的一些示例信号处理功能的实验演示成为可能。最后，该项目将研究信号处理功能的离散时间和数字实现在速度、准确性和鲁棒性方面的权衡。将对系统特性和行为进行详细研究，例如，分辨率如何与分子浓度变化相关，以及设计对参数变化的鲁棒性如何。