SHF: Small: A reconfigurable architecture for digital circuit computation by fast, robust, and leakless DNA strand displacement cascades

SHF：小型：通过快速、稳健且无泄漏的 DNA 链位移级联进行数字电路计算的可重构架构

基本信息

批准号：
1718938
负责人：
Erik Winfree
金额：
$ 46.5万
依托单位：
California Institute of Technology
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2017
资助国家：
美国
起止时间：
2017-07-01 至 2020-12-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1718938&HistoricalAwards=false
关键词：
SHF Small reconfigurable architecture digital

项目摘要

The promise of molecular programming lies in its ability to not only process information autonomously, but to do so in a biochemical context in order to sense and actuate matter. For its simplicity and its programmability, one attractive option for chemical information processing is built upon the DNA strand displacement (DSD) primitive, where a soup of rationally designed nucleotide sequences interact, react, and recombine over time in order to carry out sophisticated computation. The focus of this proposal is the creation of a reconfigurable DSD architecture akin to a molecular breadboard. Its purpose is to "scale-up" what is possible with this technology and to "scale-out" its adoption to new contexts and new areas of study. A small number of fast, robust and well-understood molecular components will be developed that compose seamlessly. The necessary tools to facilitate rapid circuit design and characterization will also be developed. The reconfigurable architecture will be designed to meet the challenges required in real-world applications ranging from point-of-care diagnostics to sensing and actuation within molecular systems. Due to its ease of use, we envision that this molecular breadboard will be an ideal vehicle to teach molecular programming and to facilitate wider adoption of DSD systems.Building on a new leak reduction paradigm for DNA strand displacement systems, a new design for robust molecular computing gates will be developed, experimentally tested, and refined. By perfecting a set of molecular components suitable for use in modular and reconfigurable circuits, this will result in a fixed set of dozens of high quality gates that can be arbitrarily wired-up in order to create bespoke molecular circuits. A compiler will be developed that takes as input a circuit or logic function and provides as output the optimized set of biochemical "wires" necessary to activate the desired logic behavior. If successful, it will be possible to create and execute fast, leakless and robust molecular circuits, for circuits 2×-10× larger than have been previously demonstrated and with completion times 10×-100× faster. This increase in complexity creates an even greater need for design verification that will be addressed by the development of more efficient kinetic simulation software. The breadboard promises to be robust enough for immediate use in applications, such as diagnostics and molecular imaging, and in new contexts such as paper-based devices.

分子编程的前景在于它不仅能够自主处理信息，而且能够在生化环境中感知和驱动物质，因为它的简单性和可编程性，化学信息处理的一个有吸引力的选择是建立在分子编程的基础上的。 DNA 链置换 (DSD) 原语，其中合理设计的核苷酸序列随着时间的推移相互作用、反应和重组，以执行复杂的计算。该提案的重点是创建类似于分子的可重新配置的 DSD 架构。其目的是“扩大”该技术的可能性，并将其应用到新的环境和新的研究领域。还将开发促进快速电路设计和表征的必要工具，以满足从现场诊断到分子内传感和驱动等实际应用中所需的挑战。由于其系统。易于使用，我们设想这种分子面包板将成为教授分子编程和促进 DSD 系统更广泛采用的理想工具。基于 DNA 链置换系统的新泄漏减少范例，稳健的分子计算门的新设计将通过完善一组适用于模块化和可重构电路的分子组件，这将产生一组固定的数十个高质量门，这些门可以任意连接以创建定制的。分子将开发一种编译器，将电路或逻辑函数作为输入，并提供激活所需逻辑行为所需的优化生化“线路”集。如果成功，将可以快速、无泄漏地创建和执行。和强大的分子电路，电路比之前演示的大 2×-10×，完成时间快 10×-100×。这种复杂性的增加对设计验证提出了更大的需求，这将通过开发更多的电路来解决。高效的动力学模拟该面包板有望足够强大，可以立即用于诊断和分子成像等应用以及纸质设备等新环境中。

项目成果

期刊论文数量（11）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

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：
2017-10
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

Effective design principles for leakless strand displacement systems

无泄漏线位移系统的有效设计原则

DOI：
10.1073/pnas.1806859115
发表时间：
2018-12
期刊：
Proceedings of the National Academy of Sciences
影响因子：
0
作者：
Wang, Boya;Thachuk, Chris;Ellington, Andrew D.;Winfree, Erik;Soloveichik, David
通讯作者：
Soloveichik, David

A cargo-sorting DNA robot

货物分拣 DNA 机器人

DOI：
10.1126/science.aan6558
发表时间：
2017-09
期刊：
Science
影响因子：
56.9
作者：
Thubagere, Anupama J.;Li, Wei;Johnson, Robert F.;Chen, Zibo;Doroudi, Shayan;Lee, Yae Lim;Izatt, Gregory;Wittman, Sarah;Srinivas, Niranjan;Woods, Damien;et al
通讯作者：
et al

A general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities

具有形式验证、优化和模拟功能的通用 CRN 到 DSD 编译器

DOI：
10.1007/978-3-319-66799-7_15
发表时间：
2017-01
期刊：
DNA Computing and Molecular Programming
影响因子：
0
作者：
Badelt, Stefan;Shin, Seung Woo;Johnson, Robert F;Dong, Qing;Thachuk, Chris;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