SHF: Medium: Microbiology on a Programmable Biochip: An Integrated Hardware/Software Digital Microfluidics Platform

SHF：媒介：可编程生物芯片上的微生物学：集成硬件/软件数字微流体平台

• 批准号: 1702596
• 负责人: Krishnendu Chakrabarty
• 金额: $ 90万
• 依托单位: Duke University
• 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: 2017-07-15 至 2022-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1702596&HistoricalAwards=false
• 关键词: SHF; Medium; Microbiology; Programmable; Biochip

The goal of this research is to develop miniaturized, low-cost, and smart microfluidic biochips that can perform "epigenetics in a drop". Such a platform will revolutionize data acquisition for molecular biology studies. The knowledge gained from applying molecular biology protocols to microfluidic biochips will facilitate the understanding of diseases such as cancer, and knowledge about epigenetic modifications in cells from inheritance will broaden the understanding of disease development. The results from this research will also be applicable to quantitative analysis protocols such as gene expression analysis. This project will foster multi-disciplinary education for engineering students and it has the potential to pave the way for new high-tech companies. This research has been structured as an interdisciplinary collaboration between investigators with complementary expertise in design automation and system architecture for microfluidics, digital microfluidics technology, and molecular biology. It will lead to an integrated 5-layer system architecture for the seamless on-chip execution of complex biochemical protocols. Breakthroughs in design automation will enable real-time decision-making based on prescribed decision criteria; such a design will allow a diverse collection of protocol paths to be traversed. Research objectives include system design and optimization methods to support quantitative analysis protocols, demonstration of biomolecular protocols on microfluidic biochips, and evaluation of design automation solutions using test cases extracted from benchtop implementation of biomolecular protocols.

这项研究的目标是开发小型化、低成本、智能的微流控生物芯片，可以进行“一滴水表观遗传学”。这样的平台将彻底改变分子生物学研究的数据采集。将分子生物学方案应用于微流控生物芯片所获得的知识将有助于理解癌症等疾病，而有关细胞遗传修饰的知识将拓宽对疾病发展的理解。这项研究的结果也将适用于基因表达分析等定量分析方案。该项目将促进工程专业学生的多学科教育，并有可能为新型高科技公司铺平道路。这项研究是研究人员之间的跨学科合作，他们在微流控设计自动化和系统架构、数字微流控技术和分子生物学方面具有互补的专业知识。它将形成一个集成的 5 层系统架构，用于复杂生化协议的无缝片上执行。设计自动化的突破将能够根据规定的决策标准进行实时决策；这种设计将允许遍历多种协议路径。研究目标包括支持定量分析协议的系统设计和优化方法、微流控生物芯片上生物分子协议的演示以及使用从生物分子协议的台式实施中提取的测试用例评估设计自动化解决方案。

项目成果

IJTAG-based Fault Recovery and Robust Microelectrode-Cell Design for MEDA Biochips

适用于 MEDA 生物芯片的基于 IJTAG 的故障恢复和鲁棒微电极单元设计

• DOI: 10.1109/tcad.2020.2986741
• 发表时间: 2020
• 期刊: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
• 影响因子: 2.9
• 作者: Zhong, Zhanwei;Chakrabarty, Krishnendu
• 通讯作者: Chakrabarty, Krishnendu

BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips ∗

BioScan：使用 MEDA 生物芯片对合成生物电路进行参数空间探索 —

• DOI: 10.23919/date.2019.8715282
• 发表时间: 2019
• 期刊: Automation & Test in Europe Conference & Exhibition (DATE
• 作者: Ibrahim, Mohamed;Bhattacharya, Bhargab B.;Chakrabarty, Krishnendu
• 通讯作者: Chakrabarty, Krishnendu

Parallel Droplet Control in MEDA Biochips using Multi-Agent Reinforcement Learning

• 发表时间: 2021
• 作者: Tung-Che Liang;Jin Zhou;Yun-Sheng Chan;Tsung-Yi Ho;K. Chakrabarty;Cy Lee

Enhancing the Reliability of MEDA Biochips Using IJTAG and Wear Leveling

使用 IJTAG 和磨损均衡增强 MEDA 生物芯片的可靠性

• DOI: 10.1109/tcad.2020.3032629
• 发表时间: 2020
• 期刊: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
• 影响因子: 2.9
• 作者: Zhong, Zhanwei;Liang, Tung-Che;Chakrabarty, Krishnendu
• 通讯作者: Chakrabarty, Krishnendu

Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA Biochips

使用 MEDA 生物芯片上的液滴等分操作有效调节合成生物电路

• DOI: 10.1109/tcad.2021.3108909
• 发表时间: 2022
• 期刊: IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems
• 影响因子: 2.9
• 作者: Ibrahim, Mohamed;Zhong, Zhanwei;Bhattacharya, Bhargab B.;Chakrabarty, Krishnendu
• 通讯作者: Chakrabarty, Krishnendu