Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization Concepts

生化计算：纠错和数字化概念的实验和理论发展

• 批准号: 0726698
• 负责人: Evgeny Katz
• 金额: $ 24万
• 依托单位: Clarkson University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-15 至 2010-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0726698&HistoricalAwards=false
• 关键词: Biochemical; Computing; Experimental; Theoretical; Development

NSF 0726698 ? Biochemical Computing: Experimental and Theoretical Development of Error Correction and Digitalization ConceptsPI: Evgeny Katz, co-PI: Vladimir Privman AbstractThis research is directed towards the developments of new concepts in biochemical computing. Biocomputing shows promise of providing the mechanisms to better couple ordinary electronics with the signaling of biological organisms. On the conceptual level, it will further understanding of how living organisms manage to control extremely complex and coupled biochemical reactions, i.e., interpret metabolic pathways in the language of information theory. Biocomputing systems of even moderate complexity will allow effective interfacing between complex physiological processes and implantable biomedical devices and will be able to operate in nanobiorobotic and sensing systems. Great advances have been made in biocomputing research in recent years. However, to be practical, as well as compatible with ordinary electronics, biocomputing should be researched for ways to minimize/correct errors and develop "digitalization" concepts. This challenge is taken up in the present research program. Experimental exploration as well as theoretical modeling and optimization are performed for new systems based on encoded DNA sequences, enzymes and DNAzymes that show promise for digital biochemical computing, including the first attempt for an experimental realization of error correction. The experimental approach includes information processing using encoded DNA sequences, DNAzyme-biocatalyzed reactions and the use of DNA-functionalized magnetic nanoparticles. The error-free DNA sequences are purified using the hybridization procedure with the DNA-functionalized magnetic nanoparticles, amplified by a PCR technique and used as input signals for DNAzyme-based logic gates. Digital XOR and NAND logic gates, copying (fanout), error correction by utilizing redundancy, and signal rectification, are demonstrated. Electronic and optoelectronic probes of the encoded DNA sequences are used to read out the results.

国家科学基金0726698？生化计算：纠错和数字化概念的实验和理论发展PI：叶夫根尼·卡茨，共同PI：弗拉基米尔·普里夫曼摘要这项研究是针对生化计算中新概念的发展。生物计算显示了提供更好地将普通电子学与生物有机体信号相结合的机制的希望。在概念层面上，它将进一步理解生物体如何控制极其复杂和耦合的生化反应，即用信息论的语言解释代谢途径。即使是中等复杂性的生物计算系统也将允许复杂的生理过程和可植入的生物医学设备之间的有效接口，并将能够在纳米生物机器人和传感系统中运行。近年来，生物计算的研究取得了很大的进展。然而，为了实用，并与普通电子学兼容，生物计算应该研究如何最大限度地减少/纠正错误和发展“数字化”概念。这一挑战在目前的研究计划中得到了解决。对基于编码的DNA序列、酶和DNAzyme的新系统进行了实验探索以及理论建模和优化，显示了数字生化计算的前景，包括首次尝试通过实验实现纠错。实验方法包括使用编码的DNA序列进行信息处理、DNAzyme生物催化反应和使用DNA功能化的磁性纳米颗粒。利用DNA功能化磁性纳米颗粒的杂交程序纯化无错误的DNA序列，通过PCR技术进行扩增，并将其用作基于DNAzyme的逻辑门的输入信号。演示了数字XOR和NAND逻辑门、复制(扇出)、利用冗余进行纠错和信号整流。使用编码的DNA序列的电子和光电探针来读出结果。