CAREER: Pioneering Nucleic Acid Based Computing: New Approachs and Experiments

项目概述本研究的广泛目标是探索分子生物学、计算机科学和进化之间的相互作用，重点是模拟分子进化作为构建基于核酸的计算机的载体。这种跨学科的方法结合了来自不同领域的理论和实验来探索分子水平的计算。DNA计算为执行和查看计算提供了一种新的范式，从而激起了巨大的兴奋：它是生物数学，同时也是数学生物学。DNA串的数据编码与分子生物学的力量相结合，使得在实验室中对单链DNA进行计算操作成为可能。由于一小滴溶液可以容纳数万亿个DNA分子，DNA计算机比传统计算机消耗更少的能量和空间。因此，它们提供了有朝一日超越电子计算机的诱人潜力。DNA计算也是大规模并行的，数十亿甚至数万亿的分子同时进行化学反应，几乎是自发地进行计算。作为计算机科学与分子生物学截然不同的结合的产物，DNA计算机这一新兴领域始于1994年，当时Adleman使用DNA分子、蛋白质酶和化学物质解决了一个有向哈密顿路径问题的实例，令科学界感到惊讶。本研究建议将基于DNA的计算机领域扩展到RNA，具体而言：(1)开发一组用于计算的基于RNA的工具(2)使用这些工具库来解决广泛的数学搜索问题。(3)解决实验设计各方面可扩展性的限制；(4)仔细检查分子计算中RNA与DNA的差异；(5)解决一系列更大的计算问题。虽然这将是第一个利用RNA计算潜力的项目，但它也将是第一个使用生物分子来解决超出先前原理验证实验范围的问题的项目之一。教育计划：计划一系列以DNA计算为中心的跨学科课程、研讨会和会议。将为进入工程、数学、生物和物理科学以及人文学科领域的新生开设一门关于DNA计算的研讨会课程。本课程将向下一代科学家介绍一个新的研究领域，同时向非科学专业的学生介绍分子计算机的前沿领域。其他教育计划包括指导本科生和研究生，在分子进化的夏季研讨会上教授DNA计算，以及参加高中教师的科学推广计划。

PROJECT SUMMARYThe wide-ranging goal of this research is to explore the interplay between molecular biology, computer science, and evolution, with emphasis on simulated molecular evolution as a vehicle for constructing nucleic acid based computers. This interdisciplinary approach combines theory and experiments from verv different fields to explore computation at the molecular level.DNA computing has fueled a tremendous amount of excitement by offering a fresh paradigm for performing and viewing computations: it is biological mathematics, while also mathematical biology. Encoding of data in DNA strings coupled with the power of molecular biology allows the execution of computational operations on single strands of DNA in the laboratory. As a small drop of solution can house several quadrillion DNA molecules, DNA computers use much less energy and space than traditional computers. Consequently, they offer the tantalizing potential of one day outperforming electronic computers. Computing with DNA is also massively parallel, with billions and trillions of molecules undergoing simultaneous chemical reactions and performing computations almost spontaneously. The product of a radically different marriage of computer science to molecular biology, the fledgling field of DNA computers began in 1994, when Adleman surprised the scientific community by using DNA molecules, protein enzymes, and chemicals to solve an instance of the Directed Hamiltonian Path Problem.This research proposes to expand the field of DNA based computers to RNA, specificaly:(1) To develop a panel of RNA based tools for use in computation(2) To use this repertoire of tools to tackle a wide class of mathematical search problems. (3) To address the limits of scalability of each aspect of the design of experiments,(4) To carefully examine the differences between RNA versus DNA for molecular computing(5) To address a series of larger computational problems. While this will be the first project to exploit RNA for its computing potential, it will also be one of the first projects to use biological molecules to solve problems beyond the scope of previous proof-of-principle experiments.Education Plan: A series of interdisciplinary courses, seminars, and conferences centered around DNA computing are planned. A seminar course will be developed on DNA computing for freshmen entering the fields of engineering, mathematics, the biological and physical sciences, as well as humanities. This course will introduce a new area of research to the next generation of scientists while at the same time educating non-science majors about the cutting edge field of molecular computers. Other educational plans include mentoring undergraduate and graduate students, teaching DNA Computing at a summer Workshop on Molecular Evolution, and participating in a science outreach program for high school teachers.