ITR: Solution Phase Computation with Enzymatic Networks

【摘要】itr：基于酶网络的溶液相计算基于磷酸二酯酶和连接酶酶促反应的寡核苷酸级逻辑门与纳米粒子珠之间的通信正在被研究，以实现可扩展和鲁棒的分子计算，可应用于自主分子器件的控制。特别是，中等规模的前馈（级联）和反馈电路以及可编程阵列正在实验室中设计和评估。正在开发的电路包括振荡器、时钟、触发器存储器和带有内部纠错的计数器。这些电路在细胞工程特性方面的应用正在研究中。流式细胞术正被用于开发能够分析单个计算元素的大规模并行网络的方法学。通过这项跨学科的工作，包括电路设计、数学建模和实验室工作，正在开发用于体外计算的大规模分子电路和用于细胞内和体内应用的小型电路合成所需的工程原理。为这些电路在分子自主设备中的应用奠定了基础，这些设备可以分析环境并以预编程的方式响应环境变化。该计算策略将在数字逻辑电路的复杂网络中实现，将在各种合成细胞系统的设计中得到应用。计算机科学和生物化学的新一代学生正在接受训练，以理解和欣赏这两个学科的问题和方法。此外，通过参与该项目，高中生们还将了解先进的科学概念。

AbstractAugust 7, 2003ITR: Solution Phase Computation with Enzymatic NetworksDarko StefanovicColumbia University03248845Communication between oligonucleotide-scale logic gates based on phosphodiesterase and ligase enzymatic reactions as well as nanoparticle beads is being investigated in order to achieve scalable and robust molecular computation that can be applied to contol of autonomous molecular devices. In particular, medium-scale feedforward (cascaded) and feedback circuits and programmable arrays are being designed and evaluated in the laboratory. The circuits being developed include oscillators, clocks, flip-flop memories, and counters with internal error correction. Applications of these circuits for engineering properties of cells are being investigated. Flow-cytometry is being used to develop methodology that will be able to analyze massively parallel networks of individual computation elements.Through this work, which is interdisciplinary, and involves circuit design, mathematical modeling, and laboratory work, the engineering principles needed to synthesize large-scale molecular circuits for in vitro computations and small circuits for intracellular and in vivo applications are being developed. Foundations are being laid for applications of these circuits in molecular autonomous devices which can analyze the environment and respond in preprogrammed fashion to changes in environment. The computational strategy which will be implemented in complex networks of digital logic circuits-will find application in the design of various sorts of synthetic cellular systems.A new generation of students from computer science and biochemistry is being trained to understand and appreciate the problems and approaches of both disciplines. Also, high-school students are being introduced through participation in this project to advanced scientific concepts.