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: 1317694
• 负责人: Erik Winfree
• 金额: $ 500万
• 依托单位: California Institute of Technology
• 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 2019-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1317694&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.

随着计算天体运动的机械设备的出现，计算革命开始于两千多年前。几个世纪后，复杂的发条自动机被开发出来，用于控制推动工业革命的机械，最终导致巴贝奇对可编程机械计算机的卓越设计。随着上世纪的电子革命，计算机的速度和复杂性急剧增加。现在，我们使用嵌入式计算机对大量机电设备的行为进行编程，从手机和卫星到工业制造机器人和自动驾驶汽车。计算的历史教会了研究人员两件事：第一，计算原理可以体现在从齿轮到晶体管的各种物理基底中；第二，掌握新的计算物理基底有可能改变技术。 另一场革命才刚刚开始，这场革命的灵感来自生命中令人难以置信的化学和分子机械，其物理计算基础由合成生物分子和设计的化学反应组成。 与之前的革命一样，这场“分子编程革命”将以计算机科学原理为核心。 通过系统地编程各种复杂的基于信息的分子系统的行为，从决策电路和分子规模制造到生物医学诊断和智能治疗，它有可能从根本上改变材料、化学、生物和医疗行业。 借助分子编程，化学将成为21世纪重大的新型信息技术。此次计算探索项目旨在为分子编程奠定坚实的基础。 该项目以 DNA 纳米技术、DNA 计算和合成生物学的进步为基础，将开发 DNA 链可编程自组装方法，以创建复杂的 2D 和 3D 结构，以及基于 DNA、RNA 和蛋白质之间可编程相互作用的动态生化电路，以及空间组织的分子系统和活细胞内的整合行为。这些架构将为创建可编程分子系统提供系统构建块，该系统能够感知分子输入、计算有关这些输入的决策并对其环境采取行动。为了管理系统复杂性并提供模块化，该项目将建立抽象层次结构，其中包括用于编程结构和行为的相关高级语言、将高级代码转换为可合成 DNA 序列列表的编译器以及可以预测 DNA 序列性能的分析软件。序列。 这将使分子程序员能够在实验室合成系统之前指定、设计和验证系统的正确性。除了这些软件工具之外，该项目还将研究分子算法理论，以了解基于信息的分子系统的潜力和局限性，是什么使它们能够高效地执行任务，以及如何有效地设计和使用它们。分析了。该项目将对该基础研究的产品进行测试，以追求现实世界的应用，例如用于探测生物系统的分子仪器和纳米级器件的可编程制造。该项目将通过建立由学生、教师、研究人员、科学家和工程师组成的多元化社区。该社区将通过创建可公开访问的软件工具、课程、教科书、研讨会、教程、本科生研究竞赛和科普视频来培育，以教授分子编程的原理和方法，并让年轻研究人员和公众参与到这一令人兴奋的活动中。新领域。与相关生物技术和其他高科技公司的工业合作伙伴关系将确保将产生的知识快速转移到现实世界的产品中。 也许最重要的是，随着分子编程成为一种广泛应用的技术，它有可能通过新型复杂纳米结构材料改变工业，通过反应的集成和自主控制改变化学，通过先进的分子仪器改变生物学，并通过先进的分子仪器改变医疗保健。更复杂的诊断和治疗。

项目成果

Effective design principles for leakless strand displacement systems

• DOI: 10.1073/pnas.1806859115
• 发表时间: 2018-12-26
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Wang, Boya;Thachuk, Chris;Soloveichik, David
• 通讯作者: Soloveichik, David

Automated sequence-level analysis of kinetics and thermodynamics for domain-level DNA strand-displacement systems

• DOI: 10.1098/rsif.2018.0107
• 发表时间: 2018-12-01
• 期刊: JOURNAL OF THE ROYAL SOCIETY INTERFACE
• 影响因子: 3.9
• 作者: Berleant, Joseph;Berlind, Christopher;Winfree, Erik
• 通讯作者: Winfree, Erik

Towards space- and energy-efficient computations

迈向空间和能源高效的计算

• 发表时间: 2019
• 期刊: The Energetics of Computing in Life and Machines
• 作者: Condon, Anne;Thachuk, Chris
• 通讯作者: Thachuk, Chris

Verifying chemical reaction network implementations: A pathway decomposition approach

验证化学反应网络的实现：路径分解方法

• DOI: 10.1016/j.tcs.2017.10.011
• 发表时间: 2017
• 期刊: Theoretical Computer Science
• 影响因子: 1.1
• 作者: Shin, Seung Woo;Thachuk, Chris;Winfree, Erik
• 通讯作者: Winfree, Erik

A cargo-sorting DNA robot

• DOI: 10.1126/science.aan6558
• 发表时间: 2017-09-15
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Thubagere, Anupama J.;Li, Wei;Qian, Lulu
• 通讯作者: Qian, Lulu