基于布尔运算元的DNA自组装网络的建模及动力学分析

DNA self-assembly is a process in which the fundamental assemble units spontaneously form the ordered structures by non-covalent DNA-DNA interactions. The current DNA self-assembly methods are mostly static self-assemblies, the research on dynamic self-assemblies with energy and material exchanges are only in its infancy, and how to build the complex functional assembly systems is still a difficult problem. The modeling and kinetics behavior of DNA self-assemblied networks based on Boolean operators as the basic structural units of network will be studied in this project. The main research topics of this project are as follows: The kinetics database of DNA self-assembly will be constructed by developing the accurate and efficient data processing methods to integrate the high-throughput experimental data of DNA self-assembly. Based on the experimental data, the system model which describes the interior level and the hiberarchy relationships of the networks will be constructed by developing the efficient and integrative algorithms. The computable model which describes the behavior features of DNA self-assembly will also be constructed by utilizing the theories of complex networks and dynamical system, as well as combining with the demonstrations of DNA self-assembly. The driving nodes of networks will be explored and the quantitative control methods for the growth of DNA self-assemblied networks will also be studied by utilizing the theories of complex networks and engineering controls. This project will provide not only the new methods of modeling and analysis for systems biology, but also new ideas and theoretical supports for DNA self-assembly applications.

DNA自组装是DNA组装基元通过分子间相互作用自发形成有序结构的过程。当前的DNA自组装方法多为静态自组装，具有能量和物质交换的动态自组装尚处于初级研究阶段，构建复杂的功能组装体系仍是一个难题。本项目拟以布尔运算元为网络的基本结构单元开展DNA自组装网络的建模与动力学行为研究。主要研究内容包括：发展高效精确的数据处理方法，通过整合DNA自组装的高通量实验数据，构建DNA自组装的动力学数据库；以DNA自组装的动力学数据为驱动，发展高效综合算法，建立描述DNA自组装网络层次内部及层次间关系的系统模型；利用复杂网络和系统动力学，结合DNA自组装网络实证，构建反映DNA自组装行为特征的可计算模型；基于工程控制论和系统动力学，寻找网络的驱动节点，实现对DNA自组装网络组装生长的定量控制。本项目的研究将为系统生物学的建模和分析提供新方法，同时也为DNA自组装相关应用领域提供新思路和理论支撑。

利用高效精确的数据处理方法，获取DNA自组装和链置换的高通量数据；基于DNA自组装和DNA链置换反应，获取较复杂DNA逻辑运算元数据，实现DNA自组装网络层次内部及层次间关系的系统建模；结合DNA自组装网络实证，构建反映DNA自组装行为的可计算模型；运用非线性系统理论进行动力学分析，采用DNA链置换技术实现对DNA自组装网络组装生长的定量控制；以核酸分子作为信息载体，探讨信息安全等方面应用。本项目的研究为动态DNA自组装的建模和分析提供新方法，也为DNA自组装相关应用领域提供新思路和理论支撑。