SHF: Small :Digital Signal Processing with Biomolecular Reactions

SHF：小型：生物分子反应的数字信号处理

• 批准号: 1117168
• 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: 2011
• 资助国家: 美国
• 起止时间: 2011-08-01 至 2014-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1117168&HistoricalAwards=false
• 关键词: SHF; Small; Digital; Signal; Processing

Digital signal processing has been a cornerstone of the modern communications and electronics revolution, transforming application areas such as wired and wireless communications, storage, and biomedical signal processing. This project will study digital signal processing in an entirely new domain: molecular systems. In contrast to electronic systems, where signals are represented by time-varying voltage values, in molecular systems signals are represented by time-varying concentrations of different molecular types, such as proteins, RNA and DNA. This project will develop, implement, and evaluate molecular-level designs for a variety of digital signal processing operations such as filtering, equalization, and noise cancellation. These operations will be synchronized by clock signals, created through sustained chemical oscillations. Memory will be created by transferring signals between different molecular types in alternating phases of the clock. The key idea underpinning this research is that the computation should be essentially rate-independent: it should only depend on coarse categories for the rates of the chemical reactions (e.g., ?fast? vs. ?slow?). It should not matter how fast any ?fast? reaction is ? only that ?fast? reactions are fast relative to ?slow? reactions. Designs with this property can be mapped to different chemical substrates. They compute accurately in spite of variations in environmental conditions such as temperature. The impetus for this work is not computation per se; chemical systems will never be useful for number crunching. Rather the field of molecular computing aims for the design of custom, embedded biological ?sensors? and ?controllers? ? viruses and bacteria that are engineered to perform useful tasks in situ, such as cancer detection and drug therapy. As an experimental chassis, this project will map designs for digital signal processing operations to chemical reactions involving DNA strands. These designs will be evaluated with computer simulations of the chemical kinetics.Techniques for analyzing the dynamics of biological systems are well established. However, synthesizing computation with such mechanisms requires new techniques ? and an entirely new mindset. 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, ineffective ad-hoc approach prevails. With robust and rate-independent 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. A new course will be developed, titled "Circuits, Computation, and Biology" offered jointly through the Electrical Engineering Department and the Biomedical Informatics and Computational Biology Program at the University of Minnesota. Building upon current recruitment efforts that have brought in female students, students from underrepresented groups will be recruited into the project.

数字信号处理是现代通信和电子革命的基石，改变了有线和无线通信、存储和生物医学信号处理等应用领域。该项目将研究一个全新领域的数字信号处理：分子系统。与其中信号由时变电压值表示的电子系统相反，在分子系统中，信号由不同分子类型（诸如蛋白质、RNA和DNA）的时变浓度表示。 该项目将开发、实施和评估用于各种数字信号处理操作（如滤波、均衡和噪声消除）的分子级设计。这些操作将通过持续的化学振荡产生的时钟信号来同步。存储器将通过在时钟的交替相位中在不同分子类型之间传输信号来创建。 支撑这项研究的关键思想是，计算应该基本上是与速率无关的：它应该只依赖于化学反应速率的粗略类别（例如，?快吗vs.？慢？）。它应该没有任何问题有多快？快吗反应是？只有这个吗快吗反应相对于？慢？反应.具有此属性的设计可以映射到不同的化学底物。尽管环境条件（如温度）发生变化，它们仍能准确计算。这项工作的动力不是计算本身;化学系统永远不会对数字运算有用。相反，分子计算领域的目标是设计定制的，嵌入式生物？传感器？然后呢？控制器？?病毒和细菌被改造成在原位执行有用的任务，如癌症检测和药物治疗。作为一个实验性的底盘，该项目将映射数字信号处理操作的设计，涉及DNA链的化学反应。这些设计将通过化学动力学的计算机模拟来评估。生物系统动力学分析的技术已经很成熟。然而，合成计算与这种机制需要新的技术？和全新的思维方式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，生物学中的应用在算法开发中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，拟议的研究将改变学科，如药物输送系统的基因工程。目前，普遍采用的是一种代价高昂、效率低下的临时办法。随着用于实现诸如数字信号处理之类的操作的鲁棒的和速率无关的技术，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。一个新的课程将开发，题为“电路，计算和生物学”通过电气工程系和生物医学信息学和计算生物学计划在明尼苏达大学联合提供。在目前招收女学生的努力基础上，将招收代表性不足群体的学生参加该项目。