ITR: Solution Phase Computation with Enzymatic Networks

摘要2003年8月7日ITR：酶网络的溶液相计算Darko Stefanovic哥伦比亚大学03248845基于磷酸二酯酶和连接酶酶反应以及纳米颗粒珠的磷脂规模逻辑门之间的通信正在研究中，以实现可扩展的和鲁棒的分子计算，可以应用于控制自主分子设备。 特别是，中等规模的前馈（级联）和反馈电路和可编程阵列正在设计和评估在实验室中。 正在开发的电路包括振荡器、时钟、触发器存储器和具有内部纠错功能的计数器。这些电路的工程性能的细胞的应用正在调查中。流式细胞术被用于开发能够分析单个计算元件的大规模并行网络的方法。通过这项跨学科的工作，涉及电路设计，数学建模和实验室工作，正在开发合成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电路所需的工程原理。 这些电路在分子自主装置中的应用正在奠定基础，这些分子自主装置可以分析环境并以预先编程的方式对环境变化做出反应。 将在数字逻辑电路的复杂网络中实现的计算策略将在各种合成细胞系统的设计中得到应用。来自计算机科学和生物化学的新一代学生正在接受培训，以理解和欣赏这两个学科的问题和方法。 此外，通过参加该项目，向高中生介绍了先进的科学概念。

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.