Collaborative Research: Evolvable Living Computing - Understanding and Quantifying Synthetic Biological Systems' Applicability, Performance, and Limits
协作研究:进化生命计算 - 理解和量化合成生物系统的适用性、性能和局限性
基本信息
- 批准号:1522074
- 负责人:
- 金额:$ 400万
- 依托单位:
- 依托单位国家:美国
- 项目类别:Continuing Grant
- 财政年份:2015
- 资助国家:美国
- 起止时间:2015-12-15 至 2021-11-30
- 项目状态:已结题
- 来源:
- 关键词:
项目摘要
Successful computing systems leverage their underlying technologies to solve problems humans simply cannot. Electronic systems harness the power of radio waves and electrons. Mechanical systems use physical force and physical interactions. Biological systems represent a computing paradigm that can harness evolution, adaptation, replication, self-repair, chemistry, and living organisms. Engineered, living biological systems which make decisions, process "data", record events, adapt to their environment, and communicate to one another will deliver exciting new solutions in bio-therapeutics, bio-materials, bio-energy, and bio-remediation. This project will create a quantitative set of freely available design principles, computational tools, mathematical models, physical biological artifacts, educational resources, and outreach activities. Once available, these resources will allow for novel, living biological solutions to be built more quickly, perform better, be more reliable to manufacture, and cost less to produce. This project is unique in that these resources will be explicitly developed to validate key computational concepts to understand how well these concepts can be applied rigorously and repeatedly to biology. This project decomposes these concepts into three areas: Computing Paradigm (digital, analog, memory, and communication), Computing Activity (specification, design, and verification), and Computing Metric (time, space, quality, and complexity). Once complete, this project will provide the most comprehensive, freely available, and computationally relevant set of building blocks to engineer biological systems to date. By developing the tools, techniques, and materials outlined in this project, this research will fundamentally change the way biological systems are specified, designed, assembled, and tested. Advanced bio-energy, bio-sensing, bio-therapeutics, and bio-materials all will become increasingly viable commercial technologies that can be made better, cheaper, faster, and more safely as a result of this project. The education of an entire new generation of engineers will occur through workshops, coursework, and community engagement activities. This new generation will have access to these approaches which will influence how biological computation is done and how that process is communicated to the community. This project will bring computational questions and methods to the forefront of biotechnology via an interdisciplinary research team focused not on one-off solutions but on foundational computing principles. Explicitly five unanswered questions will be addressed in this project: (1) What computational models are available to biology, what are their limits, and how do they perform? (2) What communication mechanisms are available to biology, what are their limits, and how do they perform? (3) What are the theoretical and empirical measures of quality, scale, time, and space in biological computing systems? (4) How generalizable are the concepts and "design rules" which can be learned from studying biological systems? (5) How can the results (data and learnings) from biological specification, design, and verification be authoritatively disseminated to the community as design principles and grand challenges? This project addresses these questions with an interdisciplinary team with expertise in theoretical computer science, electronic design automation, bio-physics/chemistry, control theory, and molecular cell biology. For more information visit www.programmingbiology.org.
成功的计算系统利用它们的底层技术来解决人类根本无法解决的问题。电子系统利用无线电波和电子的能量。机械系统使用物理力和物理相互作用。生物系统代表了一种计算范例,它可以利用进化、适应、复制、自我修复、化学和活的有机体。经过改造的生物系统能够做出决策、处理“数据”、记录事件、适应环境,并相互交流,将在生物疗法、生物材料、生物能源和生物修复方面提供令人兴奋的新解决方案。该项目将创建一套可免费获得的量化设计原则、计算工具、数学模型、物理生物制品、教育资源和推广活动。一旦可用,这些资源将允许更快地建立新的、活的生物解决方案,性能更好,制造更可靠,生产成本更低。这个项目的独特之处在于,这些资源将被明确开发来验证关键的计算概念,以了解这些概念如何能够严格和重复地应用于生物学。本项目将这些概念分解为三个领域:计算范式(数字、模拟、存储和通信)、计算活动(规范、设计和验证)和计算度量(时间、空间、质量和复杂性)。一旦完成,这个项目将提供迄今为止最全面、最免费和计算上最相关的一套构建块来设计生物系统。通过开发该项目中概述的工具、技术和材料,这项研究将从根本上改变指定、设计、组装和测试生物系统的方式。先进的生物能源、生物传感、生物疗法和生物材料都将成为越来越可行的商业技术,这些技术可以因为这个项目而变得更好、更便宜、更快、更安全。整个新一代工程师的教育将通过研讨会、课程作业和社区参与活动来进行。新一代将能够接触到这些方法,这些方法将影响生物计算的进行方式以及如何将这一过程传达给社区。该项目将通过一个跨学科研究小组将计算问题和方法带到生物技术的前沿,该小组不是专注于一次性解决方案,而是专注于基本计算原则。本项目将明确提出五个悬而未决的问题:(1)生物学可用的计算模型是什么,它们的局限性是什么,它们是如何执行的?(2)生物学可用的通信机制是什么,它们的局限性是什么,它们是如何执行的?(3)生物计算系统中质量、规模、时间和空间的理论和经验度量是什么?(4)从研究生物系统中可以学到的概念和“设计规则”有多普遍?(5)从生物学规范、设计、并将验证作为设计原则和重大挑战权威地传播给社会?这个项目与一个跨学科的团队一起解决这些问题,他们拥有理论计算机科学、电子设计自动化、生物物理/化学、控制理论和分子细胞生物学方面的专业知识。欲了解更多信息,请访问www.Programmingbiology.org。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Douglas Densmore其他文献
Component library creation and pixel array generation with micromilled droplet microfluidics
使用微铣削液滴微流控技术创建组件库和生成像素阵列
- DOI:
10.1038/s41378-024-00839-6 - 发表时间:
2025-01-14 - 期刊:
- 影响因子:9.900
- 作者:
David McIntyre;Diana Arguijo;Kaede Kawata;Douglas Densmore - 通讯作者:
Douglas Densmore
Improving engineered biological systems with electronics and microfluidics
用电子学和微流体技术改进工程化生物系统
- DOI:
10.1038/s41587-025-02709-6 - 发表时间:
2025-06-27 - 期刊:
- 影响因子:41.700
- 作者:
Rabia Tugce Yazicigil;Akshaya Bali;Dilara Caygara;Douglas Densmore - 通讯作者:
Douglas Densmore
Douglas Densmore的其他文献
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{{ truncateString('Douglas Densmore', 18)}}的其他基金
Travel: NSF Student Travel Grant for the 2022 International Workshop on Bio-Design Automation (IWBDA)
旅行:2022 年国际生物设计自动化研讨会 (IWBDA) 的 NSF 学生旅行补助金
- 批准号:
2302269 - 财政年份:2022
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
Collaborative Research: Model-guided design of bacterial interspecies interactions and trans-organismic communication in living intercellular circuits
合作研究:活体细胞间回路中细菌种间相互作用和跨有机体通讯的模型引导设计
- 批准号:
2211040 - 财政年份:2022
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
SemiSynBio-II: Hybrid Bio-Electronic Microfluidic Memory Arrays for Large Scale Testing and Remote Deployment
SemiSynBio-II:用于大规模测试和远程部署的混合生物电子微流控存储器阵列
- 批准号:
2027045 - 财政年份:2020
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
NSF Convergence Accelerator: Workshop for the Development of Infrastructure for Distributed Bio-Manufacturing and Bio-Readiness
NSF 融合加速器:分布式生物制造和生物就绪基础设施开发研讨会
- 批准号:
2035346 - 财政年份:2020
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
NSF Student Travel Grant for the 2019 International Workshop on Bio-Design Automation (IWBDA)
NSF 学生旅费资助 2019 年国际生物设计自动化研讨会 (IWBDA)
- 批准号:
1934263 - 财政年份:2019
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
NSF Student Travel Grant for the 2018 International Workshop on Bio-Design Automation (IWBDA)
NSF 学生旅费资助 2018 年国际生物设计自动化研讨会 (IWBDA)
- 批准号:
1836716 - 财政年份:2018
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
International Workshop on Bio-Design Automation (IWBDA)
国际生物设计自动化研讨会(IWBDA)
- 批准号:
1741851 - 财政年份:2017
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
International Workshop on Bio-Design Automation (IWBDA)
国际生物设计自动化研讨会(IWBDA)
- 批准号:
1633969 - 财政年份:2016
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
International Workshop on Bio-Design Automation (IWBDA)
国际生物设计自动化研讨会(IWBDA)
- 批准号:
1540970 - 财政年份:2015
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
International Workshop on BioDesign Automation (IWBDA)
国际生物设计自动化研讨会(IWBDA)
- 批准号:
1440574 - 财政年份:2014
- 资助金额:
$ 400万 - 项目类别:
Standard Grant
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