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.

该项目将开发用于通常使用分子反应，尤其是基于DNA的反应的技术，尤其是用于实施计算的技术。 正如电子系统以电压（每单位电荷能量）来实施计算一样，可以构想根据化学浓度（单位体积分子）计算的分子系统。该建议将探讨用于实施各种计算构建的技术，例如逻辑，内存，算术和信号处理。一种称为DNA链位移的技术是目标实验底盘。这项研究的动力本身不是计算。分子计算将永远不会与由硅集成电路制成的传统计算机竞争，例如数字处理等任务。化学系统本质上是缓慢而凌乱的，需要数分钟甚至数小时才能完成，并产生零散的结果。相反，目的是创建“嵌入式控制器”的病毒和细菌，这些病毒和细菌旨在在需要的情况下进行有用的分子计算，例如在药物输送和生化传感应用中进行。数字电路设计社区具有独特的专业知识，可以在合成生物学中遇到的挑战性设计问题带来。反过来，生物学中的应用在算法开发中提供了许多有趣的问题。凭借其跨学科的重点，该项目将为这两个领域带来新的观点。 如果成功，拟议的研究将改变学科，例如药物传递系统的基因工程。目前，一种昂贵且无效的临时方法占了上风。借助用于实施数字信号处理之类的操作的强大技术，将开发更有效的系统。该项目的一个重要目标是将跨学科研究的动力传达给广泛的受众。基于包括女学生在内的当前研究工作，将招募代表性不足的学生。该提案将基于先前工作的成功，探讨使用DNA的离散时间和数字信号处理应用程序的复杂信号处理功能的实施。 该项目将开发用于信号处理函数的分子实现的合成技术，例如有限型响应（FIR）和无限脉冲响应（IIR）数字过滤器，快速傅立叶变换（FFT）以及功率频谱密度（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施类似物到数字（A/D）和数字到Analog（D/A）转换。离散时间信号处理和数字信号处理将有区别。虽然在两个系统中定期对信号进行采样，但信号表示为前者的模拟值，而信号则在后者中量化为数字值。每个都有其优势。离散的信号处理系统类似于采样的数据系统，需要较低的分子浓度。但是，该分辨率不能得到精确控制。数字系统更精确，但需要更高的分子浓度。特定的研究推力如下。首先，将展示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，并将实施复杂操作的完整曲目。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。先前的离散时间信号处理实现中的主要瓶颈是速度。与电子系统相比，速度受到电荷变化的限制，分子系统的速度受到分子浓度的变化的限制，分子浓度固有缓慢。该项目将开发新的调度方法，其中将多个计算映射到不同的转移阶段。该计算将是同步的，通过通过持续化学振荡实现的“时钟”分子传输同步。新的调度方法将允许计算并行输出，而不会增加延迟传输反应的数量。将当前可实现的样品周期从40-80小时减少到4-8小时，将实现使用DNA的一些示例信号处理函数的实验证明。最后，该项目将在信号处理功能的离散时间和数字实施方面调查速度，准确性和鲁棒性的权衡。将对系统属性和行为进行详细研究，例如，分辨率与分子浓度的变化以及设计与参数变化的鲁棒程度相关。