FET: Medium: Collaborative Research: Engineerable Molecular Computing: Flying like an Airplane, not like a Bird

FET：媒介：协作研究：工程分子计算：像飞机一样飞行，而不是像鸟一样

• 批准号: 1900931
• 负责人: David Doty
• 金额: $ 40万
• 依托单位: University of California-Davis
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-15 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1900931&HistoricalAwards=false
• 关键词: FET; Medium; Collaborative; Research; Engineerable

Computation via chemical reactions is prevalent in biology as every cell performs sophisticated information processing on internal and external chemical signals. Engineering synthetic biochemical pathways that are likewise capable of decision-making will impact a range of applications in manufacturing, chemical sensing, and medicine. Work funded by this project constructs smart molecular systems using two novel paradigms that, although inspired by biology, are very different from evolved biological systems (analogously to how airplanes do not fly by flapping their wings). The success of this project will lead to a new understanding of how chemical reactions can perform information processing, and to a new generation of functional molecular devices. The educational and outreach activities funded by this project, in collaboration with the Association for Women in Mathematics, also address the serious problem of the low percentage of women in computer science research.Direct analysis and manipulation of molecular information (e.g., the information encoded in the concentrations of various molecules) is where molecular computing outcompetes its electronic counterparts. The project advances the computer science theory and experimental capability to engineer chemical information processing with nucleic acids (DNA) by two new paradigms: (1) molecular computation programmed by the stoichiometry of reactions (independent of reaction rates); (2) molecular computation programmed by a simple combinatorial model of thermodynamics. The new paradigms result in greater robustness and easier programmability than existing approaches. Also, in contrast to existing methods, this proposal will yield reusable molecular computation, whereby switching the input results in dynamically updating output.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

通过化学反应进行计算在生物学中很普遍，因为每个细胞都会对内部和外部化学信号进行复杂的信息处理。同样具有决策能力的工程合成生化途径将影响制造、化学传感和医学领域的一系列应用。该项目资助的工作使用两种新颖的范式构建智能分子系统，尽管受到生物学的启发，但与进化的生物系统有很大不同（类似于飞机不是通过拍打翅膀来飞行的）。该项目的成功将带来对化学反应如何进行信息处理的新理解，以及新一代功能性分子设备。该项目与女性数学协会合作资助的教育和推广活动也解决了计​​算机科学研究中女性比例低下的严重问题。分子信息的直接分析和操作（例如，编码在计算机中的信息）各种分子的浓度）是分子计算胜过电子计算的地方。该项目通过两种新范式推进计算机科学理论和实验能力，以利用核酸（DNA）进行化学信息处理：（1）通过反应化学计量编程的分子计算（与反应速率无关）； (2)通过简单的热力学组合模型编程的分子计算。与现有方法相比，新范例具有更高的鲁棒性和更容易的可编程性。此外，与现有方法相比，该提案将产生可重复使用的分子计算，从而在动态更新输出中切换输入结果。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查进行评估，被认为值得支持标准。

项目成果

Rate-independent Computation in Continuous Chemical Reaction Networks

连续化学反应网络中的速率无关计算

• DOI: 10.1145/3590776
• 发表时间: 2023-06
• 期刊: Journal of the ACM
• 影响因子: 2.5
• 作者: Chen, Ho;Doty, David;Reeves, Wyatt;Soloveichik, David
• 通讯作者: Soloveichik, David

A time and space optimal stable population protocol solving exact majority

解决绝对多数问题的时间和空间最优稳定群体协议

• DOI: 10.1109/focs52979.2021.00104
• 发表时间: 2022-02
• 期刊: 62nd Annual IEEE Symposium on Foundations of Computer Science
• 作者: Doty, David;Eftekhari, Mahsa;Gasieniec, Leszek;Severson, Eric;Uznanski, Przemyslaw;Stachowiak, Grzegorz
• 通讯作者: Stachowiak, Grzegorz

Brief Announcement: A Time and Space Optimal Stable Population Protocol Solving Exact Majority

简短公告：解决绝对多数的时空最优稳定种群协议

• DOI: 10.1145/3465084.3467942
• 发表时间: 2021-07
• 期刊: Proceedings of the 40th ACM Symposium on Principles of Distributed Computing
• 作者: Doty, David;Eftekhari, Mahsa;Gąsieniec, Leszek;Severson, Eric;Stachowiak, Grzegorz;Uznański, Przemyslaw
• 通讯作者: Uznański, Przemyslaw

Simulating 3-symbol Turing machines with SIMD||DNA

使用 SIMD ||DNA 模拟 3 符号图灵机

• 发表时间: 2023-01
• 期刊: SAND 2022: 1st Symposium on Algorithmic Foundations of Dynamic Networks
• 作者: David Doty and Aaron Ong

ppsim: A software package for efficiently simulating and visualizing population protocols

ppsim：用于有效模拟和可视化群体协议的软件包

• DOI: 10.1007/978-3-030-85633-5_16
• 发表时间: 2021-09
• 期刊: CMSB 2021: Proceedings of the 19th International Conference on Computational Methods in Systems Biology
• 作者: Doty, David;Severson, Eric
• 通讯作者: Severson, Eric