Collaborative Research: Molecular Programming Architectures, Abstractions, Algorithms, and Applications

合作研究：分子编程架构、抽象、算法和应用

• 批准号: 1317640
• 负责人: Shawn Douglas
• 金额: $ 100万
• 依托单位: University of California-San Francisco
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-10-01 至 2018-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1317640&HistoricalAwards=false
• 关键词: Collaborative; Research; Molecular; Programming; Architectures

The computing revolution began over two thousand years ago with the advent of mechanical devices for calculating the motions of celestial bodies. Sophisticated clockwork automata were developed centuries later to control the machinery that drove the industrial revolution, culminating in Babbage's remarkable design for a programmable mechanical computer. With the electronic revolution of the last century, the speed and complexity of computers increased dramatically. Using embedded computers we now program the behavior of a vast array of electro-mechanical devices, from cell phones and satellites to industrial manufacturing robots and self-driving cars. The history of computing has taught researchers two things: first, that the principles of computing can be embodied in a wide variety of physical substrates from gears to transistors, and second, that the mastery of a new physical substrate for computing has the potential to transform technology. Another revolution is just beginning, one whose inspiration is the incredible chemistry and molecular machinery of life, one whose physical computing substrate consists of synthetic biomolecules and designed chemical reactions. Like the previous revolutions, this "molecular programming revolution" will have the principles of computer science at its core. By systematically programming the behaviors of a wide array of complex information-based molecular systems, from decision-making circuitry and molecular-scale manufacturing to biomedical diagnosis and smart therapeutics, it has the potential to radically transform material, chemical, biological, and medical industries. With molecular programming, chemistry will become a major new information technology of the 21st century.This Expeditions-in-Computing project aims to establish solid foundations for molecular programming. Building on advances in DNA nanotechnology, DNA computing, and synthetic biology, the project will develop methods for programmable self-assembly of DNA strands to create sophisticated 2D and 3D structures, dynamic biochemical circuitry based on programmable interactions between DNA, RNA, and proteins, and integrated behaviors within spatially organized molecular systems and living cells. These architectures will provide systematic building blocks for creating programmable molecular systems able to sense molecular input, compute decisions about those inputs, and act on their environment. To manage system complexity and to provide modularity, the project will establish abstraction hierarchies with associated high-level languages for programming structure and behavior, compilers that turn high-level code into lists of synthesizable DNA sequences, and analysis software that can predict the performance of the sequences. This will allow molecular programmers to specify, design, and verify the correctness of their systems before they are ever synthesized in the laboratory. In addition to these software tools, the project will study the theory of molecular algorithms in order to understand the potential and limitations of information-based molecular systems, what makes them efficient at the tasks they can perform, and how they can be effectively designed and analyzed. Putting the products of this fundamental research to the test, the project will pursue real-world applications such as molecular instruments for probing biological systems and programmable fabrication of nanoscale devices.This project will expand the network of scientists and engineers working in molecular programming by building a diverse community of students, teachers, researchers, scientists, and engineers. This community will be fostered through the creation of publicly accessible software tools, courses, textbooks, workshops, tutorials, undergraduate research competitions, and popular science videos to teach the principles and methods of molecular programming and to engage young researchers and the public in this exciting new field. Industrial partnerships with relevant biotechnology and other high-tech companies will ensure fast transfer of knowledge generated into real-world products. Perhaps most importantly, as molecular programming becomes a widespread technology, it has the potential to transform industry with new complex nanostructured materials, to transform chemistry with integrated and autonomous control of reactions, to transform biology with advanced molecular instruments, and to transform health care with more sophisticated diagnostics and therapeutics.

计算革命始于两千多年前的机械设备来计算天体的运动。几个世纪后开发了复杂的发条自动机，以控制驱动工业革命的机械，最终在Babbage为可编程机械计算机设计出色的设计中。随着上世纪的电子革命，计算机的速度和复杂性急剧增加。使用嵌入式计算机，我们现在对从手机和卫星到工业制造机器人和自动驾驶汽车的各种电力机械设备的行为进行编程。计算的历史教会了研究人员两件事：首先，计算原理可以体现在从齿轮到晶体管的各种物理基板中，其次，对新的物理基板进行计算的掌握具有转换技术的潜力。 另一场革命才刚刚开始，它的灵感是令人难以置信的化学和分子机制，其物理计算底物由合成生物分子和设计化学反应组成。 像以前的革命一样，这种“分子编程革命”将具有计算机科学原理。 通过系统地编程，从决策电路和分子规模的制造到生物医学诊断和智能治疗剂的广泛基于信息的分子系统的行为，它有可能从根本上改变材料，化学，生物学和医疗工业。 借助分子编程，化学将成为21世纪的主要新信息技术。这项计算项目旨在为分子编程建立坚实的基础。 Building on advances in DNA nanotechnology, DNA computing, and synthetic biology, the project will develop methods for programmable self-assembly of DNA strands to create sophisticated 2D and 3D structures, dynamic biochemical circuitry based on programmable interactions between DNA, RNA, and proteins, and integrated behaviors within spatially organized molecular systems and living cells.这些体系结构将为创建能够感知分子输入，计算这些输入的决策并在其环境上采取的决策的系统构建块，以创建可编程的分子系统。为了管理系统的复杂性并提供模块化，该项目将建立具有用于编程结构和行为的相关高级语言的抽象层次结构，将高级代码转换为可综合DNA序列列表的编译器，以及可以预测序列性能的分析软件。 这将使分子程序员在实验室合成之前指定，设计和验证其系统的正确性。除这些软件工具外，该项目还将研究分子算法的理论，以了解基于信息的分子系统的潜在和局限性，使它们在可以执行的任务以及如何有效设计和分析的任务上有效的是什么。该项目将这项基本研究的产物置于测试中，将追求现实世界中的应用，例如用于探测生物系统的分子仪器和纳米级设备的可编程制造。本项目将扩大通过建立学生，教师，研究人员，研究人员，科学家和工程师以及建立多样化的学生社区，教师，研究人员，研究人员，研究员，以及工程师的分子计划网络。将通过创建公开访问的软件工具，课程，教科书，讲习班，教程，本科研究竞赛和流行的科学视频来教授分子编程的原理和方法，并在这个令人兴奋的新领域中吸引年轻研究人员和公众，从而促进该社区。与相关生物技术和其他高科技公司与相关生物技术的工业合作伙伴关系将确保快速转移到现实世界中的知识。 也许最重要的是，随着分子编程成为一种广泛的技术，它具有通过新的复杂纳米结构材料来转变行业的潜力，可以通过反应的综合和自主控制来转变化学，从而用先进的分子仪器转化生物学，并使用更复杂的诊断和治疗疗法来转变医疗保健。