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，因为每个细胞都对内部和外部化学信号进行复杂的信息处理。设计同样能够决策的合成生化途径将影响制造，化学传感和医学中的一系列应用。由该项目资助的工作使用两种新的范式构建智能分子系统，虽然受到生物学的启发，但与进化的生物系统非常不同（类似于飞机如何通过拍打翅膀飞行）。该项目的成功将导致对化学反应如何进行信息处理的新理解，以及新一代功能分子器件。该项目与数学界妇女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妇女比例低的严重问题。在各种分子的浓度中编码的信息）是分子计算胜过其电子对应物的地方。该项目通过两种新的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）通过反应的化学计量（独立于反应速率）编程的分子计算;（2）通过热力学的简单组合模型编程的分子计算。新的范例比现有的方法具有更强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，从而切换输入导致动态更新输出。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评估被认为值得支持影响审查标准。

项目成果

A time and space optimal stable population protocol solving exact majority

• DOI: 10.1109/focs52979.2021.00104
• 发表时间: 2022-02
• 期刊: 2021 IEEE 62nd Annual Symposium on Foundations of Computer Science (FOCS)
• 作者: David Doty;Mahsa Eftekhari;L. Gąsieniec;Eric E. Severson;P. Uznański;Grzegorz Stachowiak

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
• 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

A survey of size counting in population protocols

人口方案中规模计数的调查

• DOI: 10.1016/j.tcs.2021.08.038
• 发表时间: 2021
• 期刊: Theoretical Computer Science
• 影响因子: 1.1
• 作者: Doty, David;Eftekhari, Mahsa
• 通讯作者: Eftekhari, Mahsa

Computing Properties of Thermodynamic Binding Networks: An Integer Programming Approach

• DOI: 10.4230/lipics.dna.27.2
• 发表时间: 2020-11
• 作者: David Haley;David Doty

Programming Substrate-Independent Kinetic Barriers With Thermodynamic Binding Networks

• DOI: 10.1109/tcbb.2019.2959310
• 发表时间: 2021-01-01
• 期刊: IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
• 影响因子: 4.5
• 作者: Breik, Keenan;Chalk, Cameron;Soloveichik, David
• 通讯作者: Soloveichik, David