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

项目总结这项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计算通过提供一种执行和查看计算的新范式而激起了巨大的兴奋：它是生物数学，同时也是数学生物学。对DNA字符串中的数据进行编码，再加上分子生物学的力量，可以在实验室对DNA单链进行计算操作。由于一小滴溶液可以容纳几千万亿个DNA分子，DNA计算机比传统计算机消耗的能量和空间要少得多。因此，它们提供了诱人的潜力，有一天会超过电子计算机。用DNA进行计算也是大规模并行的，数十亿和数万亿个分子同时进行化学反应，几乎是自发地进行计算。DNA计算机是计算机科学与分子生物学完全不同结合的产物，羽翼未丰的DNA计算机领域始于1994年，当时Adleman使用DNA分子、蛋白质酶和化学物质来解决有向哈密尔顿路径问题的一个实例，令科学界感到惊讶。这项研究建议将基于DNA的计算机领域扩展到RNA，具体地说：(1)开发一组用于计算的基于RNA的工具(2)使用这一工具库来解决广泛的数学搜索问题。(3)解决实验设计每个方面的可伸缩性限制，(4)仔细检查用于分子计算的RNA和DNA之间的差异(5)解决一系列更大的计算问题。虽然这将是第一个利用RNA的计算潜力的项目，但它也将是第一个使用生物分子解决以前原理验证实验范围之外的问题的项目。教育计划：计划以DNA计算为中心的一系列跨学科课程、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发一门关于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，同时教育非理科专业的学生有关分子计算机的尖端领域。其他教育计划包括指导本科生和研究生，在分子进化暑期研讨会上教授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.